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 transcript_name strand transcript_status amino_acid_change ucsc_cons normal_depth normal_vaf tumor_depth tumor_vaf rna_depth rna_vaf polyphen sift condel domain ARID1A 8289 genome.wustl.edu 37 1 27100195 27100195 + Nonsense_Mutation SNP C C T novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_006015.4 +1 reviewed p.Q1331* 1.000 122 0.8% 105 47.6% 4 50% - - - NULL IGSF3 3321 genome.wustl.edu 37 1 117122291 117122292 + In_Frame_Ins INS - - TCC novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 - - Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_001542.2 -1 validated p.1040in_frame_insE 0.000:0.001 - - - - - - - - - HMMSmart_IG,HMMPfam_ig,superfamily_SSF48726 SLC9A11 284525 genome.wustl.edu 37 1 173569254 173569254 + Splice_Site SNP A A G novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 A A Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_178527.3 -1 validated e2+2 0.987 157 0% 203 38.4% 0 - - - - - QSOX1 5768 genome.wustl.edu 37 1 180159578 180159578 + Missense_Mutation SNP T T C novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 T T Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_002826.4 +1 reviewed p.L384P 0.003 168 0% 181 37% 22 45.4% possibly_damaging(0.945) deleterious(0) deleterious(0.834) NULL TMEM131 23505 genome.wustl.edu 37 2 98431767 98431767 + Missense_Mutation SNP G G C novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_015348.1 -1 validated p.S396W 1.000 253 0% 272 37.9% 0 - benign(0) deleterious(0.02) neutral(0.383) NULL LRRFIP2 9209 genome.wustl.edu 37 3 37107760 37107760 + Silent SNP G G A novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 ENST00000440742 -1 known p.Q89* 1.000 406 0% 496 39.3% 1 0% - - - HMMPfam_DUF2051 CTNNB1 1499 genome.wustl.edu 37 3 41266113 41266113 + Missense_Mutation SNP C C T rs121913403 byCluster TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_001098209.1 +1 reviewed p.S37F 1.000 121 0% 148 44.6% 19 26.3% probably_damaging(1) deleterious(0) deleterious(0.945) NULL ATR 545 ucsc.edu 37 3 142274739 142274740 + Frame_Shift_Ins INS - T T novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 - - Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_001184.3 -1 reviewed p.I774fs 0.000:0.000 - - - - - - - - - superfamily_ARM repeat IGSF10 285313 genome.wustl.edu 37 3 151165992 151165992 + Missense_Mutation SNP G G C novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_178822.4 -1 validated p.L593V 0.927 231 0% 267 42.3% 0 - probably_damaging(0.991) tolerated(0.09) deleterious(0.740) HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set,superfamily_Immunoglobulin DDIT4L 115265 genome.wustl.edu 37 4 101111093 101111093 + Silent SNP T T A novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 T T Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_145244.2 -1 provisional p.S16 0.723 105 0% 106 53.8% 3 33.3% - - - NULL FAT4 79633 genome.wustl.edu 37 4 126239981 126239981 + Silent SNP C C T novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_024582.4 +1 validated p.N805 0.962 270 0% 289 40.8% 0 - - - - HMMPfam_Cadherin,superfamily_Cadherin-like PIK3R1 5295 genome.wustl.edu 37 5 67589572 67589589 + In_Frame_Del DEL AGGGAAAAAATTACATGA AGGGAAAAAATTACATGA - novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 AGGGAAAAAATTACATGA AGGGAAAAAATTACATGA Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_181523.1 +1 reviewed p.GKKLHE446in_frame_del 0.996:1.000:1.000:0.998:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000 - - - - - - - - - NULL HHLA1 10086 genome.wustl.edu 37 8 133099921 133099921 + Missense_Mutation SNP T T A novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 T T Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_001145095.1 -1 provisional p.S219C 1.000 301 0% 350 36.6% 0 - probably_damaging(0.989) deleterious(0) deleterious(0.884) NULL PARD3 56288 genome.wustl.edu 37 10 34671762 34671762 + Missense_Mutation SNP G G C novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_019619.3 -1 validated p.L369V 0.987 313 0% 299 39.1% 0 - possibly_damaging(0.929) tolerated(0.34) neutral(0.399) superfamily_PDZ domain-like PTEN 5728 genome.wustl.edu 37 10 89692904 89692904 + Missense_Mutation SNP C C G rs121909224 byCluster TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 ENST00000371953 +1 known p.R130G 1.000 395 0% 450 38.4% 5 0% probably_damaging(1) deleterious(0) deleterious(0.945) HMMPfam_DSPc,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II PTEN 5728 genome.wustl.edu 37 10 89692980 89692980 + Missense_Mutation SNP A A G novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 A A Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 ENST00000371953 +1 known p.Y155C 1.000 211 0% 216 41.2% 0 - probably_damaging(1) deleterious(0) deleterious(0.945) HMMSmart_SM00404,superfamily_(Phosphotyrosine protein) phosphatases II MYOF 26509 genome.wustl.edu 37 10 95162075 95162075 + Missense_Mutation SNP G G C novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_013451.3 -1 reviewed p.L302V 1.000 188 0% 221 43.9% 0 - probably_damaging(1) deleterious(0) deleterious(0.945) superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMPfam_FerI ENSG00000189332 0 genome.wustl.edu 37 11 18231374 18231374 + Missense_Mutation SNP G G A novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 ENST00000340135 +1 known p.A54T 0.828 100 0% 101 44.6% 0 - benign(0.005) tolerated(0.39) neutral(0.016) superfamily_Mitochondrial carrier OR5AS1 219447 genome.wustl.edu 37 11 55798258 55798258 + Missense_Mutation SNP C C T novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_001001921.1 +1 provisional p.R122C 1.000 325 0% 322 38.5% 0 - probably_damaging(1) deleterious(0.02) deleterious(0.883) HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321 CD4 920 genome.wustl.edu 37 12 6925366 6925366 + Missense_Mutation SNP G G T novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_000616.3 +1 validated p.W251L 0.542 117 0% 129 39.5% 2 0% probably_damaging(1) tolerated(0.28) deleterious(0.531) HMMSmart_SM00409,HMMPfam_CD4-extracel,superfamily_Immunoglobulin OR10P1 121130 genome.wustl.edu 37 12 56030803 56030803 + Missense_Mutation SNP C C A novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_206899.1 +1 provisional p.S43Y 0.000 156 0% 158 39.2% 0 - possibly_damaging(0.644) tolerated(1) neutral(0.226) HMMPfam_7tm_1,superfamily_SSF81321 C14orf162 56936 genome.wustl.edu 37 14 70037868 70037868 + RNA SNP C C T novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NR_024630.1 -1 validated NULL 0.001 41 0% 46 56.5% 0 - - - - - FLVCR2 55640 genome.wustl.edu 37 14 76091024 76091024 + Missense_Mutation SNP A A G novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 A A Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_017791.2 +1 validated p.D294G 0.413 351 0.3% 350 40.6% 0 - possibly_damaging(0.452) tolerated(0.23) neutral(0.190) HMMPfam_MFS_1,superfamily_MFS_gen_substrate_transporter BEGAIN 57596 genome.wustl.edu 37 14 101011384 101011384 + Missense_Mutation SNP C C T novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_020836.3 -1 validated p.A66T 1.000 126 0% 125 36% 0 - possibly_damaging(0.645) tolerated(0.38) neutral(0.243) NULL CTCF 10664 genome.wustl.edu 37 16 67655479 67655479 + Nonsense_Mutation SNP C C T novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_006565.2 +1 reviewed p.R448* 1.000 240 0% 222 39.2% 5 0% - - - HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers MYO15A 51168 genome.wustl.edu 37 17 18035775 18035775 + Silent SNP C C T novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_016239.3 +1 reviewed p.N1405 0.885 61 0% 40 37.5% 0 - - - - HMMPfam_Myosin_head,HMMSmart_SM00242,superfamily_P-loop containing nucleoside triphosphate hydrolases ADAM11 4185 genome.wustl.edu 37 17 42851730 42851734 + Frame_Shift_Del DEL GGCGG GGCGG - novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 GGCGG GGCGG Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_002390.4 +1 reviewed p.G355fs 1.000:0.998:0.119:1.000:1.000 - - - - - - - - - "HMMPfam_Reprolysin,superfamily_Metalloproteases (""zincins"") catalytic domain" PPP4R1 9989 genome.wustl.edu 37 18 9550056 9550057 + Frame_Shift_Ins INS - - AC novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 - - Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_001042388.1 -1 validated p.C848fs 0.999:1.000 - - - - - - - - - superfamily_ARM repeat FARSA 2193 genome.wustl.edu 37 19 13039242 13039242 + Missense_Mutation SNP A A G novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 A A Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_004461.2 -1 validated p.I252T 0.999 171 0% 134 37.3% 41 43.9% possibly_damaging(0.879) deleterious(0) deleterious(0.787) HMMPfam_tRNA-synt_2d,superfamily_Class II aaRS and biotin synthetases NFIX 4784 genome.wustl.edu 37 19 13192667 13192667 + Nonsense_Mutation SNP C C T novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_002501.2 +1 validated p.Q418* 1.000 61 0% 58 46.6% 7 0% - - - HMMPfam_CTF_NFI FOXA2 3170 genome.wustl.edu 37 20 22563374 22563374 + Missense_Mutation SNP G G A novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_021784.4 -1 reviewed p.S169L 1.000 120 0% 116 37.9% 89 46% probably_damaging(0.999) deleterious(0) deleterious(0.935) HMMPfam_Fork_head,HMMSmart_FH,PatternScan_FORK_HEAD_1,superfamily_SSF46785 SOGA1 140710 genome.wustl.edu 37 20 35444182 35444182 + Missense_Mutation SNP C C T novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_199181.2 -1 validated p.V317M 0.971 24 0% 28 28.6% 0 - probably_damaging(0.991) tolerated(0.19) deleterious(0.493) NULL GAL3ST1 9514 genome.wustl.edu 37 22 30951447 30951447 + Silent SNP G G A novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_004861.1 -1 reviewed p.F255 1.000 31 0% 34 35.3% 15 66.6% - - - HMMPfam_Gal-3-0_sulfotr MORC4 79710 genome.wustl.edu 37 X 106199721 106199721 + Nonsense_Mutation SNP C C A novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_024657.4 -1 reviewed p.E500* 0.738 308 0% 390 37.7% 0 - - - - NULL UBE2NL 389898 genome.wustl.edu 37 X 142967347 142967347 + Missense_Mutation SNP G G A novel TCGA-D1-A16Q-01A-12D-A12J-09 TCGA-D1-A16Q-10A-01D-A12J-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 65ea2de5-a412-43f4-9bd5-6f94ea4078c3 6e680543-e5c4-4024-9fc5-1348aceca495 NM_001012989.1 +1 reviewed p.E49K 1.000 203 0% 174 43.7% 0 - benign(0.049) deleterious(0.01) neutral(0.409) HMMPfam_UQ_con,HMMSmart_UBCc,superfamily_UBQ-conjugat/RWD-like