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 Genome_Change Annotation_Transcript Transcript_Strand Transcript_Exon Transcript_Position cDNA_Change Codon_Change Protein_Change Other_Transcripts Refseq_mRNA_Id Refseq_prot_Id SwissProt_acc_Id SwissProt_entry_Id Description UniProt_AApos UniProt_Region UniProt_Site UniProt_Natural_Variations UniProt_Experimental_Info GO_Biological_Process GO_Cellular_Component GO_Molecular_Function COSMIC_overlapping_mutations COSMIC_fusion_genes COSMIC_tissue_types_affected COSMIC_total_alterations_in_gene Tumorscape_Amplification_Peaks Tumorscape_Deletion_Peaks TCGAscape_Amplification_Peaks TCGAscape_Deletion_Peaks DrugBank ref_context gc_content CCLE_ONCOMAP_overlapping_mutations CCLE_ONCOMAP_total_mutations_in_gene CGC_Mutation_Type CGC_Translocation_Partner CGC_Tumor_Types_Somatic CGC_Tumor_Types_Germline CGC_Other_Diseases DNARepairGenes_Role FamilialCancerDatabase_Syndromes MUTSIG_Published_Results OREGANNO_ID OREGANNO_Values t_alt_count t_ref_count validation_alt_allele validation_method validation_status validation_tumor_sample pox qox pox_cutoff isArtifactMode oxoGCut SPATA31C1 0 broad.mit.edu 37 9 90535283 90535283 + RNA SNP T T C rs118048695 by1000genomes TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr9:90535283T>C ENST00000602681.1 + 0 1187 CATGAGCCTATGGAAGATGCT 0.582000 5 298 0 0 1 0 0 KIAA0754 643314 broad.mit.edu 37 1 39879328 39879328 + Missense_Mutation SNP G G A TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr1:39879328G>A ENST00000530275.1 + 1 3178 c.2983G>A c.(2983-2985)Gcc>Acc p.A995T MACF1_ENST00000564288.1_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000317713.7_Intron NM_015038.1 NP_055853.1 O94854 K0754_HUMAN KIAA0754 995 Ala-rich. central_nervous_system(1)|large_intestine(6)|skin(1) 8 Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074) Myeloproliferative disorder(586;0.0393) OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204) AGAGGAGCCCGCCTCCCCAGC 0.711000 3 15 0 0 1 0 0 IL10RA 3587 broad.mit.edu 37 11 117864125 117864125 + Splice_Site SNP G G A TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr11:117864125G>A ENST00000227752.3 + 4 657 c.537_splice c.e4+1 p.T179_splice IL10RA_ENST00000545409.1_Splice_Site_p.T30_splice|IL10RA_ENST00000533700.1_3'UTR|IL10RA_ENST00000541785.1_Splice_Site_p.T159_splice NM_001558.3 NP_001549.2 Q13651 I10R1_HUMAN interleukin 10 receptor, alpha 179 integral to membrane|plasma membrane interleukin-10 receptor activity p.T179T(1) NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1) 19 all_hematologic(175;0.0487) Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234) BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108) GAAACTTCACGGTATGGGGTT 0.562000 3 83 0 0 1 0 0 NLRC4 58484 broad.mit.edu 37 2 32475161 32475161 + Missense_Mutation SNP A A T TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr2:32475161A>T ENST00000404025.2 - 5 2260 c.1772T>A c.(1771-1773)aTc>aAc p.I591N NLRC4_ENST00000402280.1_Missense_Mutation_p.I591N|NLRC4_ENST00000360906.5_Missense_Mutation_p.I591N|NLRC4_ENST00000342905.6_Intron Q9NPP4 NLRC4_HUMAN NLR family, CARD domain containing 4 591 activation of caspase activity|defense response to bacterium|detection of bacterium|interleukin-1 beta secretion|positive regulation of apoptosis cytoplasm ATP binding|magnesium ion binding|protein homodimerization activity p.I591N(1) breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2) 16 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208) GTAATCGGGGATGTTCCCTGA 0.408000 6 245 0 0 1 0 0 RAE1 8480 broad.mit.edu 37 20 55948583 55948583 + Missense_Mutation SNP C C T TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr20:55948583C>T ENST00000395841.2 + 9 1115 c.695C>T c.(694-696)gCc>gTc p.A232V RAE1_ENST00000395840.2_Missense_Mutation_p.A232V|RAE1_ENST00000371242.2_Missense_Mutation_p.A232V|RAE1_ENST00000527947.1_Missense_Mutation_p.A232V NM_003610.3 NP_003601.1 P78406 RAE1L_HUMAN ribonucleic acid export 1 232 carbohydrate metabolic process|glucose transport|mRNA export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction cytoplasm|cytoskeleton|nuclear outer membrane|nuclear pore microtubule binding|RNA binding p.A232V(1) breast(1)|endometrium(5)|large_intestine(4)|lung(6)|prostate(3)|skin(2) 21 Lung NSC(12;0.00263)|all_lung(29;0.00828)|Melanoma(10;0.242) BRCA - Breast invasive adenocarcinoma(4;3.7e-14)|Epithelial(14;1.07e-09)|all cancers(14;1.11e-08) ACTGGTTTTGCCCTGGGAAGT 0.398000 4 137 0 0 1 0 0 SPATA31C1 0 broad.mit.edu 37 9 90535290 90535290 + RNA SNP T T C rs55701842 by1000genomes TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr9:90535290T>C ENST00000602681.1 + 0 1194 CTATGGAAGATGCTGCTCCCA 0.592000 5 302 0 0 1 0 0 PCDH15 65217 broad.mit.edu 37 10 56287578 56287578 + Silent SNP G G T TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr10:56287578G>T ENST00000373965.2 - 3 545 c.151C>A c.(151-153)Cgg>Agg p.R51R RP11-257I14.1_ENST00000422842.1_RNA|PCDH15_ENST00000414778.1_Silent_p.R56R|PCDH15_ENST00000395442.1_Silent_p.R51R|PCDH15_ENST00000395433.1_Intron|PCDH15_ENST00000395445.1_Silent_p.R51R|PCDH15_ENST00000320301.6_Silent_p.R51R|PCDH15_ENST00000395446.1_Silent_p.R51R|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000437009.1_Silent_p.R51R|PCDH15_ENST00000361849.3_Silent_p.R51R|PCDH15_ENST00000395430.1_Silent_p.R51R|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395432.2_Silent_p.R51R|PCDH15_ENST00000395440.1_Silent_p.R51R|PCDH15_ENST00000395438.1_Silent_p.R51R|PCDH15_ENST00000373955.1_Silent_p.R51R NM_001142771.1|NM_001142772.1 NP_001136243.1|NP_001136244.1 Q96QU1 PCD15_HUMAN protocadherin-related 15 51 Cadherin 1. equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse calcium ion binding p.R51R(3)|p.R56R(2) NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1) 237 Melanoma(3;0.117)|Lung SC(717;0.238) TTACCATTCCGACTTTCTTCA 0.343000 HNSCC(58;0.16) 6 123 4.096e-09 4.9152e-09 1 1 0 XIST 0 broad.mit.edu 37 X 73066367 73066367 + RNA SNP T T C TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chrX:73066367T>C ENST00000429829.1 - 0 6221 NR_001564.2 AGTAGGACCTTATTCACATGG 0.448000 6 127 0 0 1 0 0 SH3BP5L 80851 broad.mit.edu 37 1 249107303 249107303 + Missense_Mutation SNP C C A TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr1:249107303C>A ENST00000366472.5 - 6 1825 c.596G>T c.(595-597)cGg>cTg p.R199L SH3BP5L_ENST00000411742.2_Missense_Mutation_p.R167L|SH3BP5L_ENST00000475978.1_5'UTR NM_030645.1 NP_085148.1 Q7L8J4 3BP5L_HUMAN SH3-binding domain protein 5-like 199 p.R199L(1) endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1) 23 all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199) all_cancers(173;0.19) OV - Ovarian serous cystadenocarcinoma(106;0.00805) TTGGCACAGCCGAGTCACTCG 0.637000 2 5 0.0784 0.0866526 1 1 0 CHMP7 91782 broad.mit.edu 37 8 23114023 23114023 + Silent SNP C C T TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr8:23114023C>T ENST00000397677.1 + 5 1356 c.708C>T c.(706-708)gaC>gaT p.D236D CHMP7_ENST00000313219.7_Silent_p.D236D NM_152272.3 NP_689485.1 Q8WUX9 CHMP7_HUMAN charged multivesicular body protein 7 236 cellular membrane organization|late endosome to vacuole transport cytosol|ESCRT III complex protein transporter activity p.D236D(1) breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1) 11 Prostate(55;0.0513) Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632) CAGTCAATGACGTAGATGTTG 0.502000 5 299 0 0 1 0 0 CPSF2 53981 broad.mit.edu 37 14 92608697 92608697 + Splice_Site SNP T T C TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr14:92608697T>C ENST00000298875.4 + 8 1134 c.e8+2 NM_017437.2 NP_059133.1 Q9P2I0 CPSF2_HUMAN cleavage and polyadenylation specific factor 2, 100kDa histone mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription mRNA cleavage and polyadenylation specificity factor complex hydrolase activity|protein binding|RNA binding p.?(1) breast(2)|cervix(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(3) 24 all_cancers(154;0.0766) COAD - Colon adenocarcinoma(157;0.222) AAGTCCCAGGTTTGTTCTCAT 0.383000 5 286 0 0 1 0 0 LTBP1 4052 broad.mit.edu 37 2 33172887 33172887 + Splice_Site SNP T T C TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr2:33172887T>C ENST00000404816.2 + 1 847 c.e1+2 LTBP1_ENST00000354476.3_Splice_Site Q14766 LTBP1_HUMAN latent transforming growth factor beta binding protein 1 negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta proteinaceous extracellular matrix calcium ion binding|growth factor binding|transforming growth factor beta receptor activity p.?(2) breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3) 108 all_hematologic(175;0.115) Medulloblastoma(90;0.215) GCTGCAGGGGTAAgcccacac 0.726000 2 9 0 0 1 0 0 NSFL1C 55968 broad.mit.edu 37 20 1433675 1433675 + Splice_Site SNP C C T TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr20:1433675C>T ENST00000216879.4 - 6 1515 c.e6+1 NSFL1C_ENST00000350991.4_Splice_Site|NSFL1C_ENST00000476071.1_Splice_Site|NSFL1C_ENST00000353088.2_Splice_Site|NSFL1C_ENST00000381658.4_Splice_Site|NSFL1C_ENST00000461211.1_Splice_Site NM_016143.4 NP_057227.2 Q9UNZ2 NSF1C_HUMAN NSFL1 (p97) cofactor (p47) chromosome|Golgi stack|nucleus lipid binding|protein binding p.?(1) breast(1)|large_intestine(5)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1) 16 TTTTCACTCACCCTCTGCGGA 0.453000 7 354 0 0 1 0 0 RYR2 6262 broad.mit.edu 37 1 237801684 237801684 + Silent SNP C C T TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr1:237801684C>T ENST00000366574.2 + 45 7137 c.6820C>T c.(6820-6822)Ctg>Ttg p.L2274L RYR2_ENST00000360064.6_Silent_p.L2272L|RYR2_ENST00000542537.1_Silent_p.L2258L NM_001035.2 NP_001026.2 Q92736 RYR2_HUMAN ryanodine receptor 2 (cardiac) 2274 4 X approximate repeats. cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding p.L2274L(1)|p.L2272L(1) NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4) 586 Ovarian(103;0.103) all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225) OV - Ovarian serous cystadenocarcinoma(106;0.00606) TGGTTGTGGACTGCAAAGTTG 0.413000 8 248 0 0 1 0 0 GABRR2 2570 broad.mit.edu 37 6 89974189 89974189 + Missense_Mutation SNP G G A rs149245573 by1000genomes TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr6:89974189G>A ENST00000402938.3 - 8 1161 c.1028C>T c.(1027-1029)gCg>gTg p.A343V GABRR2_ENST00000602399.1_Missense_Mutation_p.A368V P28476 GBRR2_HUMAN gamma-aminobutyric acid (GABA) A receptor, rho 2 368 synaptic transmission cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity p.A343V(3) central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(10)|prostate(2)|urinary_tract(1) 21 all_cancers(76;1.67e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.77e-07)|all_epithelial(107;2.51e-05)|Lung NSC(302;0.238) BRCA - Breast invasive adenocarcinoma(108;0.0158) GTTGACAGCCGCATACTCCAG 0.597000 3 53 0 0 1 0 0 ETV5 2119 broad.mit.edu 37 3 185797681 185797681 + Missense_Mutation SNP G G A rs141531791 TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr3:185797681G>A ENST00000306376.5 - 7 821 c.575C>T c.(574-576)gCg>gTg p.A192V ETV5_ENST00000434744.1_Missense_Mutation_p.A192V|ETV5_ENST00000537818.1_Missense_Mutation_p.A234V|ETV5-AS1_ENST00000453370.1_RNA NM_004454.2 NP_004445.1 P41161 ETV5_HUMAN ets variant 5 192 cellular response to oxidative stress nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding p.A192V(2) breast(2)|cervix(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2) 28 all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247) OV - Ovarian serous cystadenocarcinoma(80;1.62e-24) TCGGGGGACCGCAAATGTTTG 0.607000 T """TMPRSS2, SCL45A3""" Prostate 4 123 0 0 1 0 0 MFSD4 148808 broad.mit.edu 37 1 205549915 205549915 + Missense_Mutation SNP C C A TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr1:205549915C>A ENST00000367147.4 + 3 649 c.556C>A c.(556-558)Cat>Aat p.H186N MFSD4_ENST00000539267.1_Missense_Mutation_p.H186N|MFSD4_ENST00000536357.1_Intron NM_181644.4 NP_857595.3 Q8N468 MFSD4_HUMAN major facilitator superfamily domain containing 4 186 transmembrane transport integral to membrane p.H186N(1) central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 16 Breast(84;0.07) BRCA - Breast invasive adenocarcinoma(75;0.0908) CCACCTGTTCCATGTCTCCAG 0.617000 4 92 1 1 1 1 0 DAXX 1616 broad.mit.edu 37 6 33287900 33287900 + Silent SNP C C T TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr6:33287900C>T ENST00000374542.5 - 5 1557 c.1353G>A c.(1351-1353)gaG>gaA p.E451E DAXX_ENST00000414083.2_Silent_p.E376E|DAXX_ENST00000266000.6_Silent_p.E451E|DAXX_ENST00000477162.1_5'UTR NM_001141969.1|NM_001141970.1|NM_001350.4 NP_001135441.1|NP_001135442.1|NP_001341.1 Q9UER7 DAXX_HUMAN death-domain associated protein 451 Asp/Glu-rich (acidic).|Necessary for interaction with USP7. activation of JUN kinase activity|androgen receptor signaling pathway|apoptosis|induction of apoptosis via death domain receptors|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|regulation of protein ubiquitination|transcription, DNA-dependent chromosome, centromeric region|cytosol|nucleolus|PML body androgen receptor binding|heat shock protein binding|p53 binding|protein homodimerization activity|protein N-terminus binding|receptor signaling protein activity|transcription factor binding|ubiquitin protein ligase binding p.E451E(2) breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1) 55 cttcttcttcctcctcctcct 0.557000 """Mis, F, N""" Pancreatic neuroendocrine tumors. Paediatric GBM 3 91 0 0 1 0 0 PBX4 80714 broad.mit.edu 37 19 19675795 19675795 + Missense_Mutation SNP G G A rs139542458 TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr19:19675795G>A ENST00000251203.8 - 6 1158 c.872C>T c.(871-873)aCg>aTg p.T291M NM_025245.2 NP_079521.1 Q9BYU1 PBX4_HUMAN pre-B-cell leukemia homeobox 4 291 sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity p.T291M(1) large_intestine(1)|lung(4)|ovary(1)|prostate(3) 9 CCCAACTTCCGTGGTATCCAC 0.527000 9 377 0 0 1 0 0 MUC16 94025 broad.mit.edu 37 19 9075833 9075833 + Silent SNP C C T TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr19:9075833C>T ENST00000397910.4 - 3 11816 c.11613G>A c.(11611-11613)gaG>gaA p.E3871E NM_024690.2 NP_078966.2 Q8WXI7 MUC16_HUMAN mucin 16, cell surface associated 3872 Thr-rich. cell adhesion extracellular space|extrinsic to membrane|integral to membrane|plasma membrane protein binding p.E3871E(2) NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7) 590 ATTTTTCTTTCTCATTCCAGG 0.448000 8 100 0 0 1 0 0 SLC4A11 83959 broad.mit.edu 37 20 3209652 3209652 + Missense_Mutation SNP A A C TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr20:3209652A>C ENST00000380059.3 - 17 2254 c.2153T>G c.(2152-2154)gTg>gGg p.V718G SLC4A11_ENST00000380056.3_Missense_Mutation_p.V691G|SLC4A11_ENST00000474451.1_5'UTR|SLC4A11_ENST00000539553.1_Missense_Mutation_p.V675G NM_001174090.1 NP_001167561.1 Q8NBS3 S4A11_HUMAN solute carrier family 4, sodium borate transporter, member 11 691 Membrane (bicarbonate transporter). cellular cation homeostasis|fluid transport|phosphoenolpyruvate-dependent sugar phosphotransferase system basolateral plasma membrane|integral to membrane bicarbonate transmembrane transporter activity|borate transmembrane transporter activity|hydrogen ion channel activity|inorganic anion exchanger activity|sodium channel activity|sugar:hydrogen symporter activity p.V718G(1)|p.V691G(1) breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(4)|soft_tissue(1)|urinary_tract(1) 40 AGTGCCCTTCACCAGCCTGCA 0.667000 8 25 0 0 1 0 0 HSD17B7P2 0 broad.mit.edu 37 10 38654432 38654432 + RNA SNP A A G rs2257765 TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr10:38654432A>G ENST00000494540.1 + 0 599 NR_003086.1 TCATCTCGCAATGCAAGGAAA 0.453000 5 95 0 0 1 0 0 PEX1 5189 broad.mit.edu 37 7 92147136 92147136 + Silent SNP G G A TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr7:92147136G>A ENST00000248633.4 - 5 788 c.693C>T c.(691-693)aaC>aaT p.N231N PEX1_ENST00000428214.1_Silent_p.N231N|PEX1_ENST00000438045.1_Intron NM_000466.2 NP_000457.1 O43933 PEX1_HUMAN peroxisomal biogenesis factor 1 231 microtubule-based peroxisome localization|protein import into peroxisome matrix cytosol|nucleus|peroxisomal membrane ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding p.N231N(1) breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1) 41 all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592) Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123) GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23) TCTCTGACTCGTTTTCATTAG 0.363000 6 147 0 0 1 0 0 AE000661.37 0 broad.mit.edu 37 14 22932283 22932283 + RNA SNP G G T TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr14:22932283G>T ENST00000514473.2 - 0 225 AE000661.37_ENST00000556777.1_RNA|TRDC_ENST00000390477.2_RNA ATGTAACTGTGGACAAATCAT 0.443000 3 58 1 1 1 1 0 XRCC6 2547 broad.mit.edu 37 22 42057337 42057337 + Missense_Mutation SNP C C T TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr22:42057337C>T ENST00000359308.4 + 11 2180 c.1525C>T c.(1525-1527)Ccc>Tcc p.P509S XRCC6_ENST00000402580.3_Missense_Mutation_p.P468S|XRCC6_ENST00000405506.1_Missense_Mutation_p.P459S|XRCC6_ENST00000405878.1_Missense_Mutation_p.P509S|XRCC6_ENST00000428575.2_Missense_Mutation_p.P376S|XRCC6_ENST00000360079.3_Missense_Mutation_p.P509S P12956 XRCC6_HUMAN X-ray repair complementing defective repair in Chinese hamster cells 6 509 DNA ligation|double-strand break repair via nonhomologous end joining|initiation of viral infection|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|provirus integration|telomere maintenance|transcription, DNA-dependent DNA-dependent protein kinase-DNA ligase 4 complex|Ku70:Ku80 complex|membrane fraction|nuclear telomere cap complex|transcription factor complex 5'-deoxyribose-5-phosphate lyase activity|ATP binding|ATP-dependent DNA helicase activity|double-stranded DNA binding|protein C-terminus binding|transcription regulatory region DNA binding p.P509S(2) central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1) 31 TTTTCTAGTGCCCAAGGTTGA 0.473000 Non-homologous end-joining 7 250 0 0 1 0 0 ADCY1 107 broad.mit.edu 37 7 45744119 45744119 + Silent SNP C C A TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr7:45744119C>A ENST00000297323.7 + 17 2743 c.2721C>A c.(2719-2721)ctC>ctA p.L907L NM_021116.2 NP_066939.1 Q08828 ADCY1_HUMAN adenylate cyclase 1 (brain) 907 activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport integral to membrane|plasma membrane ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|calmodulin binding|metal ion binding p.L907L(1) breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1) 71 Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Adenosine(DB00640) AAACAAAGCTCATGGAAAAAG 0.498000 6 134 5.9392e-07 6.74179e-07 1 1 0 FAM207A 85395 broad.mit.edu 37 21 46387079 46387079 + Missense_Mutation SNP C C A TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr21:46387079C>A ENST00000291634.6 + 4 531 c.483C>A c.(481-483)agC>agA p.S161R FAM207A_ENST00000479127.1_3'UTR|FAM207A_ENST00000397826.3_Missense_Mutation_p.S146R NM_058190.2 NP_478070.1 Q9NSI2 CU070_HUMAN family with sequence similarity 207, member A 161 p.S161R(1) AGGCTGGCAGCCGGCGCCAAG 0.716000 3 22 0.115264 0.12413 1 1 0 CP 1356 broad.mit.edu 37 3 148905905 148905905 + Missense_Mutation SNP A A C TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr3:148905905A>C ENST00000264613.6 - 10 2060 c.1798T>G c.(1798-1800)Ttt>Gtt p.F600V CP_ENST00000462336.1_5'UTR NM_000096.3 NP_000087.1 P00450 CERU_HUMAN ceruloplasmin (ferroxidase) 600 F5/8 type A 2.|Plastocyanin-like 4. cellular iron ion homeostasis|copper ion transport|transmembrane transport extracellular space chaperone binding|ferroxidase activity p.F600V(1) breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 44 Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152) LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607) Drotrecogin alfa(DB00055) GCAGTTGTAAACATTCTAATA 0.343000 6 261 0 0 1 0 0 THNSL2 55258 broad.mit.edu 37 2 88478453 88478453 + Silent SNP G G A TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr2:88478453G>A ENST00000324166.5 + 4 2414 c.723G>A c.(721-723)caG>caA p.Q241Q THNSL2_ENST00000358591.2_Silent_p.Q241Q|THNSL2_ENST00000449349.1_Silent_p.Q209Q|THNSL2_ENST00000496844.1_3'UTR|THNSL2_ENST00000402102.1_Silent_p.Q241Q|THNSL2_ENST00000343544.4_Silent_p.Q241Q|THNSL2_ENST00000377254.3_Silent_p.Q241Q NM_018271.4 NP_060741.3 Q86YJ6 THNS2_HUMAN threonine synthase-like 2 (S. cerevisiae) 241 threonine biosynthetic process threonine synthase activity p.Q241Q(1) breast(4)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2) 27 CTTACTTCCAGTGTACGCCAT 0.552000 10 447 0 0 1 0 0 CDAN1 146059 broad.mit.edu 37 15 43022880 43022880 + Missense_Mutation SNP A A C TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr15:43022880A>C ENST00000356231.3 - 14 2113 c.2090T>G c.(2089-2091)gTg>gGg p.V697G NM_138477.2 NP_612486.2 Q8IWY9 CDAN1_HUMAN codanin 1 697 integral to membrane protein binding p.V697G(1) endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3) 24 all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215) GBM - Glioblastoma multiforme(94;2.49e-07) GAGAAACTCCACCAGCCAGGG 0.637000 6 41 0 0 1 0 0 POTEC 388468 broad.mit.edu 37 18 14513675 14513675 + Missense_Mutation SNP T T C TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr18:14513675T>C ENST00000358970.5 - 10 1518 c.1519A>G c.(1519-1521)Aaa>Gaa p.K507E NM_001137671.1 NP_001131143.1 B2RU33 POTEC_HUMAN POTE ankyrin domain family, member C 507 p.K507E(2) NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3) 52 GAATTCATTTTCTTTTCAGCC 0.284000 4 138 0 0 1 0 0 CSPG4 1464 broad.mit.edu 37 15 75980335 75980335 + Missense_Mutation SNP C C A TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr15:75980335C>A ENST00000308508.5 - 3 3163 c.3071G>T c.(3070-3072)aGc>aTc p.S1024I NM_001897.4 NP_001888.2 Q6UVK1 CSPG4_HUMAN chondroitin sulfate proteoglycan 4 1024 Gly/Ser-rich (glycosaminoglycan attachment domain).|Interaction with COL5A1 (By similarity).|Interaction with COL6A2 (By similarity). angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane protein kinase binding|signal transducer activity p.S1024I(1) breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4) 48 GAAGATCCGGCTGATGGTCTG 0.657000 4 118 1 1 1 1 0 AC096559.1 0 broad.mit.edu 37 2 12293381 12293382 + RNA INS - - TCCC TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr2:12293381_12293382insTCCC ENST00000412294.1 + 0 197 ccttccctccttccttccttcc 0.396 2 4 --- --- --- --- AC009499.1 0 broad.mit.edu 37 2 34041837 34041838 + RNA INS - - CCTCC rs140516377 by1000genomes TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr2:34041837_34041838insCCTCC ENST00000366209.2 + 0 68 tcttctcttctcctcccctccc 0.480 3 3 --- --- --- --- ALMS1P 0 broad.mit.edu 37 2 73900214 73900214 + RNA DEL A A - TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr2:73900214delA ENST00000450720.1 + 0 737 NR_003683.2 CCCTACATGTAGGGAGAAGAA 0.557 2 4 --- --- --- --- PPP1R3A 5506 broad.mit.edu 37 7 113519968 113519968 + Frame_Shift_Del DEL T T - TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr7:113519968delT ENST00000284601.3 - 4 1247 c.1179delA c.(1177-1179)aafs p.K393fs NM_002711.3 NP_002702.2 Q16821 PPR3A_HUMAN protein phosphatase 1, regulatory subunit 3A 393 glycogen metabolic process integral to membrane NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2) 121 CTGAGGAATATTTTTCATTGC 0.393 8 413 --- --- --- --- TBC1D3P1-DHX40P1 0 broad.mit.edu 37 17 58090680 58090681 + RNA INS - - T TCGA-CH-5789-01A-11D-1576-08 TCGA-CH-5789-10A-01D-1576-08 Untested Somatic Phase_I WXS none Illumina GAIIx b68c5ec2-0875-4d77-b4b7-738d2b2f313c ce3a5af9-17c9-4195-8da2-1bee4bac3cac g.chr17:58090680_58090681insT ENST00000407042.3 - 0 609 ACTCTGAATGATTTTTTTTTTT 0.455 2 4 --- --- --- ---