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 RAB39B 116442 broad.mit.edu 37 X 154493536 154493536 + Missense_Mutation SNP A A C TCGA-W2-A7HE-01A-11D-A35I-08 TCGA-W2-A7HE-10C-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1874e215-23e2-4990-97af-ab2ce3d029b9 3e485cf9-75ec-4d2c-90bc-1bbfed18c316 g.chrX:154493536A>C ENST00000369454.3 - 1 338 c.38T>G c.(37-39)gTc>gGc p.V13G NM_171998.2 NP_741995.1 Q96DA2 RB39B_HUMAN RAB39B, member RAS oncogene family 13 protein transport|small GTPase mediated signal transduction|synapse organization|vesicle-mediated transport Golgi apparatus|plasma membrane GTP binding p.V13D(1) breast(1)|central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(12) 19 all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) ATCCCCGATGACAATGAGCCG 0.667000 3 32 0 0 1 0 0 MALAT1 378938 broad.mit.edu 37 11 65273581 65273581 + RNA SNP A A G TCGA-W2-A7HE-01A-11D-A35I-08 TCGA-W2-A7HE-10C-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1874e215-23e2-4990-97af-ab2ce3d029b9 3e485cf9-75ec-4d2c-90bc-1bbfed18c316 g.chr11:65273581A>G ENST00000534336.1 + 0 8349 NR_002819.2 AAAAAAAAAAAGCAAAAGATG 0.413000 3 20 0 0 1 0 0 NCOA6 23054 broad.mit.edu 37 20 33345744 33345744 + Silent SNP C C T TCGA-W2-A7HE-01A-11D-A35I-08 TCGA-W2-A7HE-10C-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1874e215-23e2-4990-97af-ab2ce3d029b9 3e485cf9-75ec-4d2c-90bc-1bbfed18c316 g.chr20:33345744C>T ENST00000374796.2 - 8 3377 c.807G>A c.(805-807)caG>caA p.Q269Q NCOA6_ENST00000359003.2_Silent_p.Q269Q Q14686 NCOA6_HUMAN nuclear receptor coactivator 6 269 CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region. brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter transcription factor complex chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding p.Q269Q(15) NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1) 107 gctgctgctgctgttgttgtt 0.537000 3 32 0 0 1 0 0 RUNX2 860 broad.mit.edu 37 6 45390445 45390445 + Silent SNP A A G TCGA-W2-A7HE-01A-11D-A35I-08 TCGA-W2-A7HE-10C-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1874e215-23e2-4990-97af-ab2ce3d029b9 3e485cf9-75ec-4d2c-90bc-1bbfed18c316 g.chr6:45390445A>G ENST00000371438.1 + 2 532 c.174A>G c.(172-174)caA>caG p.Q58Q RUNX2_ENST00000352853.5_Silent_p.Q126Q|RUNX2_ENST00000465038.2_Silent_p.Q58Q|RUNX2_ENST00000371432.3_Silent_p.Q44Q|RUNX2_ENST00000576263.1_Silent_p.Q58Q|RUNX2_ENST00000371436.6_Silent_p.Q58Q|RUNX2_ENST00000359524.5_Silent_p.Q44Q|RUNX2_ENST00000541979.1_Silent_p.Q126Q NM_001024630.3 NP_001019801.3 Q13950 RUNX2_HUMAN runt-related transcription factor 2 58 Poly-Gln. negative regulation of transcription, DNA-dependent|osteoblast differentiation|positive regulation of transcription, DNA-dependent nucleus ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 34 agcagcagcaacagcagcagc 0.731000 3 18 0 0 1 0 0 LOC220729 220729 broad.mit.edu 37 3 197348674 197348674 + RNA SNP A A G rs144273946 by1000genomes TCGA-W2-A7HE-01A-11D-A35I-08 TCGA-W2-A7HE-10C-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1874e215-23e2-4990-97af-ab2ce3d029b9 3e485cf9-75ec-4d2c-90bc-1bbfed18c316 g.chr3:197348674A>G ENST00000418868.1 - 0 585 NR_003266.2 GGCTCTGTCCACCAAATGCAC 0.478000 3 63 0 0 1 0 0 HPS3 84343 broad.mit.edu 37 3 148884979 148884979 + Silent SNP G G A TCGA-W2-A7HE-01A-11D-A35I-08 TCGA-W2-A7HE-10C-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1874e215-23e2-4990-97af-ab2ce3d029b9 3e485cf9-75ec-4d2c-90bc-1bbfed18c316 g.chr3:148884979G>A ENST00000296051.2 + 15 2888 c.2748G>A c.(2746-2748)ccG>ccA p.P916P HPS3_ENST00000460120.1_Silent_p.P751P NM_032383.3 NP_115759.2 Q969F9 HPS3_HUMAN Hermansky-Pudlak syndrome 3 916 cytoplasm breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3) 34 LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607) AGAGATGCCCGGAGGCAGTCA 0.423000 Hermansky-Pudlak syndrome 3 41 0 0 1 0 0 PCDHA10 56139 broad.mit.edu 37 5 140236812 140236812 + Silent SNP G G A rs148283153 TCGA-W2-A7HE-01A-11D-A35I-08 TCGA-W2-A7HE-10C-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1874e215-23e2-4990-97af-ab2ce3d029b9 3e485cf9-75ec-4d2c-90bc-1bbfed18c316 g.chr5:140236812G>A ENST00000307360.5 + 1 1179 c.1179G>A c.(1177-1179)ccG>ccA p.P393P PCDHA7_ENST00000525929.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Silent_p.P393P|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron NM_018901.2|NM_031859.1 NP_061724.1|NP_114065.1 NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2) 79 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) CTCACGTTCCGTTCAAGCTGG 0.567000 8 47 0 0 1 0 0 LOC645752 645752 broad.mit.edu 37 15 78211548 78211548 + RNA SNP T T C TCGA-W2-A7HE-01A-11D-A35I-08 TCGA-W2-A7HE-10C-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1874e215-23e2-4990-97af-ab2ce3d029b9 3e485cf9-75ec-4d2c-90bc-1bbfed18c316 g.chr15:78211548T>C ENST00000565869.1 + 0 111 RP11-114H24.2_ENST00000567226.1_RNA CCACCTGGGATTGGAGCTTTC 0.562000 4 89 0 0 1 0 0 RNF213 57674 broad.mit.edu 37 17 78333905 78333905 + Missense_Mutation SNP A A T TCGA-W2-A7HE-01A-11D-A35I-08 TCGA-W2-A7HE-10C-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1874e215-23e2-4990-97af-ab2ce3d029b9 3e485cf9-75ec-4d2c-90bc-1bbfed18c316 g.chr17:78333905A>T ENST00000582970.1 + 38 11242 c.11099A>T c.(11098-11100)aAc>aTc p.N3700I RNF213_ENST00000508628.2_Missense_Mutation_p.N3749I|CTD-2047H16.4_ENST00000575034.1_RNA|CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.N1773I NM_001256071.1 NP_001243000.1 Q9HCF4 ALO17_HUMAN ring finger protein 213 0 NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3) 130 all_neural(118;0.0538) BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057) AACCACATGAACCTTTCCGAG 0.488000 5 14 0 0 1 0 0 LRRC28 123355 broad.mit.edu 37 15 99903465 99903465 + Missense_Mutation SNP C C A rs147857587 TCGA-W2-A7HE-01A-11D-A35I-08 TCGA-W2-A7HE-10C-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1874e215-23e2-4990-97af-ab2ce3d029b9 3e485cf9-75ec-4d2c-90bc-1bbfed18c316 g.chr15:99903465C>A ENST00000301981.3 + 9 1266 c.1026C>A c.(1024-1026)caC>caA p.H342Q LRRC28_ENST00000422500.2_Missense_Mutation_p.H273Q|LRRC28_ENST00000447360.2_Intron|LRRC28_ENST00000331450.5_Intron|LRRC28_ENST00000558879.1_Intron NM_144598.2 NP_653199.2 Q86X40 LRC28_HUMAN leucine rich repeat containing 28 342 endometrium(2)|large_intestine(3)|lung(6)|prostate(1) 12 Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163) OV - Ovarian serous cystadenocarcinoma(32;0.00106) CAGGGCTGCACCAGTGGTAAT 0.567000 4 42 1.23904e-05 1.23904e-05 1 1 0 PRG4 10216 broad.mit.edu 37 1 186276981 186276981 + Silent SNP A A G TCGA-W2-A7HE-01A-11D-A35I-08 TCGA-W2-A7HE-10C-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1874e215-23e2-4990-97af-ab2ce3d029b9 3e485cf9-75ec-4d2c-90bc-1bbfed18c316 g.chr1:186276981A>G ENST00000445192.2 + 7 2175 c.2130A>G c.(2128-2130)aaA>aaG p.K710K PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367485.4_Silent_p.K617K|PRG4_ENST00000367486.3_Silent_p.K667K|PRG4_ENST00000367483.4_Silent_p.K669K NM_005807.3 NP_005798.2 Q92954 PRG4_HUMAN proteoglycan 4 710 59 X 8 AA repeats of K-X-P-X-P-T-T-X. cell proliferation|immune response extracellular region polysaccharide binding|protein binding|scavenger receptor activity NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1) 102 CTACCCCTAAAGGGACTGCTC 0.582000 3 65 0 0 1 0 0 MST1L 11223 broad.mit.edu 37 1 17085189 17085189 + RNA SNP A A G TCGA-W2-A7HE-01A-11D-A35I-08 TCGA-W2-A7HE-10C-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1874e215-23e2-4990-97af-ab2ce3d029b9 3e485cf9-75ec-4d2c-90bc-1bbfed18c316 g.chr1:17085189A>G ENST00000455405.2 - 0 87 p.S428P(1) TCCAGGATTGATGGCGGCTGG 0.572000 3 22 0 0 1 0 0 OR2A2 442361 broad.mit.edu 37 7 143807113 143807113 + Silent SNP G G A rs141248378 by1000genomes TCGA-W2-A7HE-01A-11D-A35I-08 TCGA-W2-A7HE-10C-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1874e215-23e2-4990-97af-ab2ce3d029b9 3e485cf9-75ec-4d2c-90bc-1bbfed18c316 g.chr7:143807113G>A ENST00000408979.2 + 1 507 c.438G>A c.(436-438)acG>acA p.T146T NM_001005480.2 NP_001005480.2 Q6IF42 OR2A2_HUMAN olfactory receptor, family 2, subfamily A, member 2 146 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity p.T146T(1) endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|prostate(1)|skin(4) 22 Melanoma(164;0.0783) TGGTTCTCACGTCCTGGTCAT 0.517000 22 55 0 0 1 0 0 IP6K2 51447 broad.mit.edu 37 3 48732374 48732374 + Frame_Shift_Del DEL G G - TCGA-W2-A7HE-01A-11D-A35I-08 TCGA-W2-A7HE-10C-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1874e215-23e2-4990-97af-ab2ce3d029b9 3e485cf9-75ec-4d2c-90bc-1bbfed18c316 g.chr3:48732374delG ENST00000431721.2 - 3 753 c.516delC c.(514-516)ccfs p.P172fs IP6K2_ENST00000453202.1_Frame_Shift_Del_p.P117fs|IP6K2_ENST00000450045.1_Intron|IP6K2_ENST00000432678.2_Intron|IP6K2_ENST00000417896.1_Frame_Shift_Del_p.P117fs|IP6K2_ENST00000449610.1_Frame_Shift_Del_p.P117fs|IP6K2_ENST00000328631.5_Intron|IP6K2_ENST00000443964.1_Frame_Shift_Del_p.P176fs|IP6K2_ENST00000446860.1_Frame_Shift_Del_p.P175fs|IP6K2_ENST00000436134.1_Intron|IP6K2_ENST00000413298.1_Intron|IP6K2_ENST00000340879.4_Intron NM_001190316.1 NP_001177245.1 Q9UHH9 IP6K2_HUMAN inositol hexakisphosphate kinase 2 0 negative regulation of cell growth|phosphatidylinositol phosphorylation|positive regulation of apoptosis|type I interferon-mediated signaling pathway intermediate filament cytoskeleton|nucleus ATP binding|inositol hexakisphosphate 5-kinase activity|inositol trisphosphate 3-kinase activity biliary_tract(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1) 15 GCTGGGCTGAGGGCCaggagg 0.532 2 4 --- --- --- --- SOX4 6659 broad.mit.edu 37 6 21595266 21595267 + In_Frame_Ins INS - - GGC TCGA-W2-A7HE-01A-11D-A35I-08 TCGA-W2-A7HE-10C-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1874e215-23e2-4990-97af-ab2ce3d029b9 3e485cf9-75ec-4d2c-90bc-1bbfed18c316 g.chr6:21595266_21595267insGGC ENST00000244745.1 + 1 1295_1296 c.501_502insGGC c.(499-504)gggcgg>ggGGCgcgg p.167_168GR>GAR SOX4_ENST00000543472.1_In_Frame_Ins_p.167_168GR>GAR NM_003107.2 NP_003098.1 Q06945 SOX4_HUMAN SRY (sex determining region Y)-box 4 167 canonical Wnt receptor signaling pathway|cardiac ventricle formation|cellular response to glucose stimulus|DNA damage response, detection of DNA damage|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|glial cell development|glial cell proliferation|limb bud formation|negative regulation of apoptosis|negative regulation of cell proliferation|negative regulation of protein export from nucleus|negative regulation of protein ubiquitination|neural tube formation|neuroepithelial cell differentiation|noradrenergic neuron differentiation|positive regulation of apoptosis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell proliferation|positive regulation of insulin secretion|positive regulation of N-terminal peptidyl-lysine acetylation|positive regulation of translation|pro-B cell differentiation|protein stabilization|skeletal system development|spinal cord motor neuron differentiation|sympathetic nervous system development|T cell differentiation mitochondrion|nucleus core promoter sequence-specific DNA binding|protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|RNA polymerase II transcription coactivator activity kidney(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1) 6 Ovarian(93;0.163) all cancers(50;0.0751)|Epithelial(50;0.155) gcggccatgggggcggcggcgg 0.738 4 7 --- --- --- --- NUDT5 11164 broad.mit.edu 37 10 12226494 12226495 + Splice_Site INS - - A TCGA-W2-A7HE-01A-11D-A35I-08 TCGA-W2-A7HE-10C-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1874e215-23e2-4990-97af-ab2ce3d029b9 3e485cf9-75ec-4d2c-90bc-1bbfed18c316 g.chr10:12226494_12226495insA ENST00000378937.3 - 4 261_262 c.170_splice c.e4+1 p.LN56_splice NUDT5_ENST00000378940.3_Intron|NUDT5_ENST00000378952.3_Intron|NUDT5_ENST00000491614.1_Intron|NUDT5_ENST00000378927.3_Intron|NUDT5_ENST00000537776.1_Intron Q9UKK9 NUDT5_HUMAN nudix (nucleoside diphosphate linked moiety X)-type motif 5 44 D-ribose catabolic process|ribonucleoside diphosphate catabolic process intracellular ADP-ribose diphosphatase activity|magnesium ion binding breast(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1) 8 Renal(717;0.228) GGCACGTACCTCAAAATTAGCA 0.317 2 4 --- --- --- --- SLC6A5 9152 broad.mit.edu 37 11 20622825 20622825 + Frame_Shift_Del DEL C C - TCGA-W2-A7HE-01A-11D-A35I-08 TCGA-W2-A7HE-10C-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1874e215-23e2-4990-97af-ab2ce3d029b9 3e485cf9-75ec-4d2c-90bc-1bbfed18c316 g.chr11:20622825delC ENST00000525748.1 + 2 427 c.154delC c.(154-156)ccfs p.P52fs NM_004211.3 NP_004202.2 Q9Y345 SC6A5_HUMAN solute carrier family 6 (neurotransmitter transporter), member 5 52 synaptic transmission integral to membrane|plasma membrane glycine:sodium symporter activity|neurotransmitter:sodium symporter activity breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(34)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1) 63 Glycine(DB00145) GCCACGTGTGCCCAGGTCCGC 0.741 2 4 --- --- --- --- LINC00621 100996930 broad.mit.edu 37 13 23490121 23490121 + RNA DEL C C - TCGA-W2-A7HE-01A-11D-A35I-08 TCGA-W2-A7HE-10C-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1874e215-23e2-4990-97af-ab2ce3d029b9 3e485cf9-75ec-4d2c-90bc-1bbfed18c316 g.chr13:23490121delC ENST00000577004.1 - 0 387 GGAGCAGGAACCCAGCTTCTC 0.602 2 4 --- --- --- ---