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 USP24 23358 genome.wustl.edu 37 1 55564204 55564204 + Missense_Mutation SNP T T A novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 T T Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_015306.2 -1 validated p.N1640Y 1.000 43 0% 25 16% 0 - probably_damaging(0.983) deleterious(0.01) deleterious(0.835) HMMPfam_UCH,superfamily_Cysteine proteinases ARNT 405 genome.wustl.edu 37 1 150814904 150814904 + Missense_Mutation SNP C C T novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_001668.2 -1 reviewed p.A90T 1.000 266 0% 246 44.7% 0 - probably_damaging(0.992) deleterious(0.04) deleterious(0.796) HMMPfam_HLH,superfamily_HLH helix-loop-helix DNA-binding domain DDR2 4921 genome.wustl.edu 37 1 162740317 162740317 + Missense_Mutation SNP G G A novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b ENST00000458105 +1 known p.V117M 0.000 43 0% 94 66% 0 - possibly_damaging(0.819) deleterious(0.01) deleterious(0.715) NULL PROX1 5629 genome.wustl.edu 37 1 214171027 214171027 + Silent SNP C C T novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_002763.3 +1 provisional p.F383 1.000 393 0% 271 42.8% 1 0% - - - HMMPfam_Prox1 CYP27C1 339761 genome.wustl.edu 37 2 127957069 127957069 + Missense_Mutation SNP C C T novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_001001665.3 -1 reviewed p.M145I 0.884 44 0% 26 30.8% 0 - benign(0.001) tolerated(0.06) neutral(0.323) HMMPfam_p450,superfamily_Cytochrome P450 CPB1 1360 genome.wustl.edu 37 3 148575316 148575316 + Missense_Mutation SNP G G T novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_001871.2 +1 reviewed p.A352S 1.000 122 0% 69 42% 0 - benign(0.044) tolerated(0.58) neutral(0.007) HMMPfam_Peptidase_M14,HMMSmart_SM00631,superfamily_Zn-dependent exopeptidases PIK3CA 5290 genome.wustl.edu 37 3 178916854 178916854 + Missense_Mutation SNP G G A novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_006218.2 +1 reviewed p.E81K 1.000 255 0% 164 53% 2 0% probably_damaging(0.998) deleterious(0) deleterious(0.919) HMMPfam_PI3K_p85B,HMMSmart_PI3K_p85B ARAP3 64411 genome.wustl.edu 37 5 141041613 141041613 + Missense_Mutation SNP C C A novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_022481.5 -1 reviewed p.A1004S 1.000 268 0% 126 34.1% 4 25% possibly_damaging(0.832) tolerated(0.2) neutral(0.366) HMMPfam_RhoGAP,HMMSmart_RhoGAP,superfamily_Rho_GAP COL14A1 7373 genome.wustl.edu 37 8 121228617 121228617 + Missense_Mutation SNP G G C novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_021110.1 +1 validated p.R542T 1.000 252 0% 209 32.5% 3 0% possibly_damaging(0.712) tolerated(0.22) neutral(0.299) HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III PSIP1 11168 genome.wustl.edu 37 9 15486823 15486900 + Splice_Site DEL GTTTAAAATGTTAGGAGAAATAGAACATACCTCATTGCTGGCTTTTTCTTCATGGTCGGTATCTTCCTTTGAAACACT GTTTAAAATGTTAGGAGAAATAGAACATACCTCATTGCTGGCTTTTTCTTCATGGTCGGTATCTTCCTTTGAAACACT - novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 GTTTAAAATGTTAGGAGAAATAGAACATACCTCATTGCTGGCTTTTTCTTCATGGTCGGTATCTTCCTTTGAAACACT GTTTAAAATGTTAGGAGAAATAGAACATACCTCATTGCTGGCTTTTTCTTCATGGTCGGTATCTTCCTTTGAAACACT Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_001128217.1 -1 validated e5-1 0.997:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:0.989:0.288:0.306:0.481:0.989:1.000:1.000:1.000:1.000:1.000:1.000:1.000:0.999:0.994:0.993:0.984:0.997:0.997:0.983:0.993:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:0.995:0.984:0.937 - - - - - - - - - - NUP214 8021 genome.wustl.edu 37 9 134073775 134073775 + Missense_Mutation SNP G G A novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_005085.2 +1 reviewed p.A1632T 0.033 194 0% 125 43.2% 27 37% benign(0) tolerated(1) - NULL MS4A4A 51338 genome.wustl.edu 37 11 60059853 60059853 + Missense_Mutation SNP T T C novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 T T Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_148975.1 +1 reviewed p.L66P 0.478 121 0% 141 39% 1 0% probably_damaging(1) deleterious(0) deleterious(0.945) NULL SOCS4 122809 genome.wustl.edu 37 14 55511039 55511039 + Missense_Mutation SNP A A G novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 A A Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_080867.2 +1 reviewed p.K427R 1.000 115 0% 77 42.9% 4 75% probably_damaging(0.983) tolerated(0.51) neutral(0.438) NULL TMED8 283578 genome.wustl.edu 37 14 77812811 77812811 + Missense_Mutation SNP C C A novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_213601.1 -1 provisional p.V70L 0.996 279 0% 169 27.8% 1 0% possibly_damaging(0.643) deleterious(0) deleterious(0.670) NULL GABRB3 2562 genome.wustl.edu 37 15 26866466 26866466 + Silent SNP C C A novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_000814.4 -1 reviewed p.G152 0.948 269 0% 91 47.3% 0 - - - - HMMPfam_Neur_chan_LBD,superfamily_Nicotinic receptor ligand binding domain-like CHRM5 1133 genome.wustl.edu 37 15 34355985 34355985 + Missense_Mutation SNP A A G novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 A A Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_012125.3 +1 validated p.Y356C 0.952 212 0% 98 56.1% 0 - possibly_damaging(0.884) tolerated(0.17) neutral(0.404) HMMPfam_7tm_1,superfamily_SSF81321 BMF 90427 genome.wustl.edu 37 15 40398215 40398215 + Nonsense_Mutation SNP G G A novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_001003940.1 -1 reviewed p.Q25* 1.000 67 0% 24 25% 1 0% - - - NULL FBXL19 54620 genome.wustl.edu 37 16 30958263 30958263 + Missense_Mutation SNP C C G novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_001099784.2 +1 provisional p.L634V 1.000 20 0% 25 40% 81 6.1% probably_damaging(0.973) deleterious(0) deleterious(0.859) superfamily_RNI-like ZNF267 10308 genome.wustl.edu 37 16 31926099 31926099 + Missense_Mutation SNP C C G novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_003414.4 +1 validated p.Q177E 0.021 156 0% 272 24.3% 1 0% benign(0.017) tolerated(0.57) neutral(0.007) NULL ANKRD11 29123 genome.wustl.edu 37 16 89351187 89351187 + Nonsense_Mutation SNP G G T novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_013275.4 -1 validated p.S588* 1.000 54 0% 18 72.2% 5 100% - - - superfamily_Ankyrin repeat OR3A2 4995 genome.wustl.edu 37 17 3181503 3181503 + Nonsense_Mutation SNP G G A novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_002551.3 -1 validated p.R243* 0.931 141 0% 117 64.1% 0 - - - - HMMPfam_7tm_1,superfamily_SSF81321 TP53 7157 genome.wustl.edu 37 17 7577120 7577120 + Missense_Mutation SNP C C T novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_000546.4 -1 reviewed p.R273H 0.864 166 0% 56 83.9% 27 88.8% possibly_damaging(0.936) deleterious(0.01) deleterious(0.787) superfamily_p53-like transcription factors,HMMPfam_P53 AOC3 8639 genome.wustl.edu 37 17 41003742 41003742 + Missense_Mutation SNP G G A novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_003734.2 +1 reviewed p.V128I 0.986 68 0% 28 75% 0 - benign(0.007) tolerated(1) - HMMPfam_Cu_amine_oxidN2,superfamily_Cu_amine_oxidase_N-reg DCC 1630 genome.wustl.edu 37 18 50683801 50683801 + Missense_Mutation SNP G G A novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_005215.3 +1 reviewed p.R446H 1.000 368 0% 255 41.6% 0 - probably_damaging(0.995) tolerated(0.12) deleterious(0.718) HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III SALL3 27164 genome.wustl.edu 37 18 76757209 76757209 + Missense_Mutation SNP C C T novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_171999.2 +1 validated p.R1264C 0.994 87 0% 52 44.2% 0 - probably_damaging(0.997) deleterious(0.02) deleterious(0.849) NULL ZNF560 147741 genome.wustl.edu 37 19 9578900 9578900 + Silent SNP C C T novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_152476.2 -1 validated p.T241 0.001 174 0% 139 43.9% 0 - - - - NULL ZNF829 374899 genome.wustl.edu 37 19 37405898 37405929 + Splice_Site DEL ATTCTTTCCTCCTCTTCTGGGTGACACCTGGA ATTCTTTCCTCCTCTTCTGGGTGACACCTGGA - novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 ATTCTTTCCTCCTCTTCTGGGTGACACCTGGA ATTCTTTCCTCCTCTTCTGGGTGACACCTGGA Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_001037232.3 -1 validated e2-1 0.973:0.975:0.954:0.937:0.735:0.707:0.359:0.040:0.031:0.031:0.033:0.049:0.049:0.050:0.060:0.059:0.048:0.064:0.057:0.002:0.002:0.000:0.000:0.000:0.002:0.001:0.002:0.000:0.000 - - - - - - - - - - ZNF135 7694 genome.wustl.edu 37 19 58578553 58578553 + Missense_Mutation SNP G G A novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_003436.3 +1 validated p.R234Q 0.003 333 0% 112 75.9% 0 - probably_damaging(0.994) tolerated(0.06) deleterious(0.774) HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers ENSG00000211459 0 genome.wustl.edu 37 MT 1105 1105 + RNA SNP C C T novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b ENST00000389680 +1 known NULL NULL 62 0% 28 46.4% 1425 43.7% - - - - SYAP1 94056 genome.wustl.edu 37 X 16754330 16754330 + Silent SNP T T G novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 T T Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_032796.3 +1 validated p.V112 0.991 125 0% 61 34.4% 78 34.6% - - - NULL MSN 4478 genome.wustl.edu 37 X 64956747 64956747 + Missense_Mutation SNP G G T rs182327269 by1000genomes TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_002444.2 +1 reviewed p.R350S 0.969 136 0% 89 33.7% 50 0% benign(0.265) deleterious(0) deleterious(0.472) HMMPfam_ERM ACSL4 2182 genome.wustl.edu 37 X 108911504 108911504 + Splice_Site SNP T T G novel TCGA-AP-A052-01A-11W-A027-09 TCGA-AP-A052-10A-01W-A027-09 T T Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx f0db6f06-8dab-4387-a39f-19eb40b1b8d2 861be91b-a756-4ff0-bdda-edee07afad7b NM_022977.2 -1 reviewed e9-2 0.996 233 0.4% 217 35.9% 0 - - - - -