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 C1orf9 51430 genome.wustl.edu 37 1 172501827 172501827 + Missense_Mutation SNP C C G novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 ENST00000367723 +1 known p.S72C 0.000 44 0% 38 18.4% - - benign(0.223) - - NULL CNTNAP5 129684 genome.wustl.edu 37 2 125555704 125555704 + Silent SNP G G A novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_130773.2 +1 reviewed p.S1007 0.007 71 0% 73 35.6% - - - - - superfamily_ConA_like_lec_gl KCNH7 90134 genome.wustl.edu 37 2 163228550 163228550 + Nonsense_Mutation SNP G G C novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_033272.2 -1 reviewed p.S1127* 1.000 38 0% 58 19% - - - - - NULL DZIP1L 199221 genome.wustl.edu 37 3 137787104 137787104 + Missense_Mutation SNP C C T novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_173543.2 -1 validated p.R574H 0.000 36 0% 33 15.2% - - benign(0) tolerated(0.15) neutral(0.241) NULL PIK3CA 5290 genome.wustl.edu 37 3 178916930 178916930 + Missense_Mutation SNP G G T novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_006218.2 +1 reviewed p.G106V 1.000 27 0% 34 35.3% - - probably_damaging(1) deleterious(0.02) deleterious(0.883) HMMPfam_PI3K_p85B,HMMSmart_PI3K_p85B,superfamily_SSF54236 DGKG 1608 genome.wustl.edu 37 3 185986619 185986619 + Missense_Mutation SNP C C T novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_001346.2 -1 reviewed p.A363T 1.000 41 0% 44 11.4% - - benign(0.327) deleterious(0.01) deleterious(0.508) HMMPfam_C1_1,HMMSmart_SM00109,PatternScan_ZF_DAG_PE_1,superfamily_Cysteine-rich domain DCHS2 54798 genome.wustl.edu 37 4 155241761 155241761 + Missense_Mutation SNP G G A novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_017639.3 -1 validated p.T1142I 1.000 99 0% 99 23.2% - - probably_damaging(0.99) tolerated(0.08) deleterious(0.742) HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like NPY5R 4889 genome.wustl.edu 37 4 164272619 164272619 + Silent SNP T T C novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 T T Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_006174.2 +1 provisional p.I398 1.000 104 0% 74 16.2% - - - - - HMMPfam_7tm_1,superfamily_SSF81321 RIPK1 8737 genome.wustl.edu 37 6 3078126 3078126 + Missense_Mutation SNP A A T novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 A A Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_003804.3 +1 validated p.E93V 1.000 21 0% 35 34.3% - - probably_damaging(1) deleterious(0.01) deleterious(0.905) HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase FAM65B 9750 genome.wustl.edu 37 6 24843369 24843369 + Silent SNP C C T novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_014722.2 -1 validated p.E547 1.000 55 0% 64 45.3% - - - - - NULL NOTCH4 4855 genome.wustl.edu 37 6 32191659 32191661 + In_Frame_Del DEL AGC AGC - rs72110219 TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 AGC AGC Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_004557.3 -1 reviewed p.L16in_frame_del 0.003:0.005:0.005 - - - - - - - - - NULL ZNF777 27153 genome.wustl.edu 37 7 149152882 149152882 + Missense_Mutation SNP C C T novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_015694.2 -1 validated p.G78R 1.000 33 0% 19 42.1% - - probably_damaging(0.991) deleterious(0) deleterious(0.889) NULL CDK5RAP2 55755 genome.wustl.edu 37 9 123202195 123202195 + Missense_Mutation SNP A A C novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 A A Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_018249.4 -1 reviewed p.N1068K 0.000 27 0% 21 28.6% - - possibly_damaging(0.893) deleterious(0) deleterious(0.796) NULL FUT11 170384 genome.wustl.edu 37 10 75535310 75535310 + Missense_Mutation SNP T T G novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 T T Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_173540.2 +1 validated p.M449R 1.000 48 0% 57 47.4% - - probably_damaging(0.983) deleterious(0.03) deleterious(0.793) NULL SFTPD 6441 genome.wustl.edu 37 10 81700532 81700533 + Frame_Shift_Del DEL AG AG - novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 AG AG Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_003019.4 -1 validated p.L227fs 1.000:1.000 - - - - - - - - - HMMPfam_Surfac_D-trimer CYP26A1 1592 genome.wustl.edu 37 10 94836837 94836837 + Missense_Mutation SNP C C T novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_000783.3 +1 reviewed p.P424S 0.160 19 0% 35 17.1% - - possibly_damaging(0.538) tolerated(0.89) neutral(0.182) HMMPfam_p450,superfamily_Cytochrome_P450 LOXL4 84171 genome.wustl.edu 37 10 100013439 100013439 + Missense_Mutation SNP G G T novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_032211.6 -1 reviewed p.A569E 0.995 44 0% 35 54.3% - - probably_damaging(1) tolerated(0.07) deleterious(0.819) HMMPfam_Lysyl_oxidase KAZALD1 81621 genome.wustl.edu 37 10 102827757 102827758 + Frame_Shift_Ins INS - - T rs75759946 byCluster;by1000genomes TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 - - Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 ENST00000313664 +1 known p.G237fs 0.000:0.000 - - - - - - - - - NULL PHRF1 57661 genome.wustl.edu 37 11 608503 608514 + In_Frame_Del DEL GGACGCGCTCTG GGACGCGCTCTG - rs144630030 by1000genomes TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 GGACGCGCTCTG GGACGCGCTCTG Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_020901.2 +1 validated p.GTRS1019in_frame_del 0.000:0.000:0.000:0.003:0.000:0.010:0.008:0.000:0.404:0.408:0.000:0.000 - - - - - - - - - NULL MARK2 2011 genome.wustl.edu 37 11 63670587 63670587 + Missense_Mutation SNP C C T novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_001039469.2 +1 reviewed p.R458W 1.000 30 0% 52 36.5% - - probably_damaging(1) deleterious(0) deleterious(0.945) NULL B3GNT6 192134 genome.wustl.edu 37 11 76751619 76751620 + Frame_Shift_Ins INS - - GGCCACGAGGGCATCCGGCCCTTCGGCGTGCAGCTGCCTGGCGCACAGC novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 - - Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 ENST00000354301 +1 known p.Q341fs 0.000:0.000 - - - - - - - - - NULL LRP1 4035 genome.wustl.edu 37 12 57605984 57605984 + Silent SNP C C T novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_002332.2 +1 reviewed p.G4478 0.845 23 0% 30 26.7% - - - - - NULL NOS1 4842 genome.wustl.edu 37 12 117698325 117698325 + Missense_Mutation SNP G G A rs150227193 TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_000620.2 -1 reviewed p.S771L 1.000 37 0% 53 17% - - possibly_damaging(0.794) deleterious(0) deleterious(0.742) HMMPfam_Flavodoxin_1,superfamily_Flavoproteins POLE 5426 genome.wustl.edu 37 12 133250238 133250238 + Missense_Mutation SNP C C T novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_006231.2 -1 validated p.A428T 1.000 13 0% 23 30.4% - - benign(0.005) tolerated(0.71) neutral(0.002) HMMSmart_POLBc,superfamily_RNaseH_fold CHD2 1106 genome.wustl.edu 37 15 93540599 93540599 + Missense_Mutation SNP T T G novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 T T Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_001271.3 +1 reviewed p.I1284S 1.000 76 0% 100 26% - - probably_damaging(0.988) deleterious(0) deleterious(0.882) superfamily_Homeodomain-like,superfamily_P-loop containing nucleoside triphosphate hydrolases ITPRIPL2 162073 genome.wustl.edu 37 16 19126044 19126046 + In_Frame_Del DEL CTC CTC - novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 CTC CTC Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_001034841.3 +1 validated p.S89in_frame_del 0.005:0.005:0.005 - - - - - - - - - NULL TP53 7157 genome.wustl.edu 37 17 7578406 7578406 + Missense_Mutation SNP C C T novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_000546.4 -1 reviewed p.R175H 1.000 29 0% 20 70% - - probably_damaging(1) deleterious(0) deleterious(0.945) superfamily_p53-like transcription factors,HMMPfam_P53 KRT15 3866 genome.wustl.edu 37 17 39673185 39673185 + Missense_Mutation SNP C C T novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_002275.3 -1 reviewed p.V205I 1.000 97 0% 58 41.4% - - probably_damaging(0.999) deleterious(0) deleterious(0.935) HMMPfam_Filament CCDC130 81576 genome.wustl.edu 37 19 13869786 13869786 + Missense_Mutation SNP G G A novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_030818.2 +1 provisional p.R121H 1.000 8 0.000 15 0.533 - - probably_damaging(0.968) tolerated(0.1) deleterious(0.696) HMMPfam_DUF572 PPP2R1A 5518 genome.wustl.edu 37 19 52715971 52715971 + Missense_Mutation SNP C C G novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_014225.5 +1 reviewed p.P179R 1.000 22 0% 19 26.3% - - probably_damaging(1) deleterious(0) deleterious(0.945) HMMPfam_HEAT,superfamily_ARM repeat PHACTR3 116154 genome.wustl.edu 37 20 58420298 58420298 + Missense_Mutation SNP G G T novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_080672.3 +1 reviewed p.A548S 1.000 46 0% 66 40.9% - - benign(0.393) tolerated(0.18) neutral(0.182) NULL GMEB2 26205 genome.wustl.edu 37 20 62229210 62229210 + Missense_Mutation SNP C C T novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_012384.3 -1 reviewed p.D121N 0.977 36 0% 30 36.7% - - benign(0) tolerated(1) - HMMPfam_SAND,HMMSmart_SAND,superfamily_SAND_like PLXNB2 23654 genome.wustl.edu 37 22 50720611 50720624 + Frame_Shift_Del DEL GGACTGACCGTCAT GGACTGACCGTCAT - novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 GGACTGACCGTCAT GGACTGACCGTCAT Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_012401.2 -1 validated p.M1038fs 0.995:0.989:0.541:0.046:0.024:0.007:0.000:0.000 - - - - - - - - - HMMPfam_TIG,HMMSmart_IPT,superfamily_Ig_E-set ZC4H2 55906 genome.wustl.edu 37 X 64139015 64139015 + Silent SNP G G A novel TCGA-AP-A1DQ-01A-11D-A135-09 TCGA-AP-A1DQ-10A-01D-A135-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 76f5098b-0e2b-4fb7-b065-d2ed4ffa20fc 135c9478-60ff-4573-9946-5f709dc92cd9 NM_018684.2 -1 validated p.A156 0.436 33 0% 30 13.3% - - - - - HMMPfam_zf-C4H2