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 XPA 7507 broad.mit.edu 37 9 100459557 100459557 + Silent SNP C C T TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr9:100459557C>T ENST00000375128.4 - 1 82 c.18G>A c.(16-18)ggG>ggA p.G6G NM_000380.3 NP_000371.1 P23025 XPA_HUMAN xeroderma pigmentosum, complementation group A 6 Interaction with CEP164 and required for UV resistance. nucleotide-excision repair, DNA damage removal nucleoplasm damaged DNA binding|metal ion binding|nucleotide binding|protein domain specific binding|protein homodimerization activity breast(1)|endometrium(4)|large_intestine(1)|lung(4)|prostate(1) 11 Acute lymphoblastic leukemia(62;0.158) CCGGCAAAGCCCCGTCGGCCG 0.731000 """Mis, N, F, S""" """skin basal cell, skin squamous cell, melanoma""" Nucleotide excision repair (NER) Xeroderma Pigmentosum 6 22 0 0 1 0 0 LCE2B 26239 broad.mit.edu 37 1 152659435 152659435 + Missense_Mutation SNP C C T TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr1:152659435C>T ENST00000368780.3 + 2 170 c.116C>T c.(115-117)cCa>cTa p.P39L LCE2B_ENST00000417924.2_Missense_Mutation_p.P39L NM_014357.4 NP_055172.1 O14633 LCE2B_HUMAN late cornified envelope 2B 39 Cys-rich.|Pro-rich. keratinization endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1) 11 Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242) LUSC - Lung squamous cell carcinoma(543;0.206) TGCCCAGCTCCATGTTCCCCT 0.622000 8 175 0 0 1 0 0 ZFHX3 463 broad.mit.edu 37 16 72831385 72831385 + Silent SNP T T C rs76691369 byFrequency TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr16:72831385T>C ENST00000268489.5 - 9 5868 c.5196A>G c.(5194-5196)caA>caG p.Q1732Q ZFHX3_ENST00000397992.5_Silent_p.Q818Q NM_006885.3 NP_008816.3 Q15911 ZFHX3_HUMAN zinc finger homeobox 3 1732 Poly-Gln. muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation transcription factor complex enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11) 153 Ovarian(137;0.13) gttgttgttgttgctgttgct 0.537000 3 13 0 0 1 0 0 KRT75 9119 broad.mit.edu 37 12 52822482 52822482 + Nonsense_Mutation SNP G G A rs151328629 TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr12:52822482G>A ENST00000252245.5 - 6 1301 c.1081C>T c.(1081-1083)Cga>Tga p.R361* NM_004693.2 NP_004684.2 O95678 K2C75_HUMAN keratin 75 361 Coil 2.|Rod. keratin filament structural molecule activity central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1) 28 BRCA - Breast invasive adenocarcinoma(357;0.192) TTGGTGTTTCGAAGGTCATCC 0.532000 7 43 0 0 1 0 0 CIC 23152 broad.mit.edu 37 19 42791393 42791393 + Splice_Site SNP G G A TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr19:42791393G>A ENST00000572681.2 + 4 3247 c.e4+1 CIC_ENST00000575354.2_Splice_Site|CIC_ENST00000160740.3_Splice_Site Q96RK0 CIC_HUMAN capicua transcriptional repressor regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|protein binding autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2) 82 Prostate(69;0.00682) ATGATGATGCGTGAGTTCCCT 0.647000 """Mis, F, S""" oligodendroglioma 11 7 0 0 1 0 0 POLK 51426 broad.mit.edu 37 5 74892057 74892057 + Missense_Mutation SNP A A G TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr5:74892057A>G ENST00000241436.4 + 13 1711 c.1539A>G c.(1537-1539)atA>atG p.I513M POLK_ENST00000506928.1_3'UTR|POLK_ENST00000504026.1_Intron|POLK_ENST00000380481.3_Missense_Mutation_p.I423M|POLK_ENST00000352007.5_Missense_Mutation_p.I315M|POLK_ENST00000508526.1_Missense_Mutation_p.I315M NM_016218.2 NP_057302.1 Q9UBT6 POLK_HUMAN polymerase (DNA directed) kappa 513 DNA replication|nucleotide-excision repair, DNA gap filling nucleus damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding endometrium(1)|kidney(4)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1) 27 all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184) OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42) GTGTTCGGATATCTAGTTTTC 0.378000 DNA polymerases (catalytic subunits) 7 28 0 0 1 0 0 ACSM2B 348158 broad.mit.edu 37 16 20556560 20556560 + Missense_Mutation SNP G G C TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr16:20556560G>C ENST00000329697.6 - 10 1368 c.1200C>G c.(1198-1200)aaC>aaG p.N400K ACSM2B_ENST00000567288.1_5'UTR|ACSM2B_ENST00000565232.1_Missense_Mutation_p.N400K|ACSM2B_ENST00000567001.1_Missense_Mutation_p.N400K|ACSM2B_ENST00000565322.1_Missense_Mutation_p.N321K NM_001105069.1 NP_001098539.1 Q68CK6 ACS2B_HUMAN acyl-CoA synthetase medium-chain family member 2B 400 fatty acid metabolic process|xenobiotic metabolic process mitochondrial matrix ATP binding|butyrate-CoA ligase activity|CoA-ligase activity|metal ion binding breast(4)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(33)|ovary(1)|prostate(1)|skin(5) 57 GGGGCAGGACGTTGCCCTTAT 0.507000 23 26 0 0 1 0 0 RP11-798G7.5 0 broad.mit.edu 37 17 43587576 43587576 + RNA SNP A A G rs145439557 by1000genomes TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr17:43587576A>G ENST00000253803.2 + 0 267 LRRC37A4P_ENST00000579913.1_RNA tctgaaaagaaaagaaaaaaa 0.428000 4 29 0 0 1 0 0 PRMT1 0 broad.mit.edu 37 19 50185264 50185264 + Missense_Mutation SNP C C T TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr19:50185264C>T ENST00000532489.1 + 4 658 c.152C>T c.(151-153)tCg>tTg p.S51L PRMT1_ENST00000454376.2_Missense_Mutation_p.S97L|PRMT1_ENST00000391851.4_Missense_Mutation_p.S79L Q8WUW5 Q8WUW5_HUMAN protein arginine methyltransferase 1 78 cytoplasm protein methyltransferase activity cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(2) 12 all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728) OV - Ovarian serous cystadenocarcinoma(262;0.00103)|GBM - Glioblastoma multiforme(134;0.012) GACGTCGGCTCGGGCACCGGC 0.637000 3 24 0 0 1 0 0 SNHG14 0 broad.mit.edu 37 15 25488832 25488832 + RNA SNP C C T TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr15:25488832C>T ENST00000453082.2 + 0 2332 SNORD115-40_ENST00000606510.1_RNA NR_003343.1 AATAGGATTACGCTGAGGCCC 0.498000 4 295 0 0 1 0 0 PRDM8 56978 broad.mit.edu 37 4 81122620 81122620 + Missense_Mutation SNP A A T TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr4:81122620A>T ENST00000339711.4 + 9 1627 c.396A>T c.(394-396)aaA>aaT p.K132N PRDM8_ENST00000415738.2_Missense_Mutation_p.K132N|PRDM8_ENST00000504452.1_Missense_Mutation_p.K132N NM_020226.3 NP_064611.3 Q9NQV8 PRDM8_HUMAN PR domain containing 8 132 SET. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(2) 10 GGTACGGGAAAGAACTGACTG 0.517000 OREG0016246 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 12 40 0 0 1 0 0 IGHV3-48 0 broad.mit.edu 37 14 106994047 106994047 + RNA SNP A A G TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr14:106994047A>G ENST00000390624.2 - 0 196 GCTGCACAGGAGAGTCTCAGG 0.562000 61 91 0 0 1 0 0 PHLPP2 23035 broad.mit.edu 37 16 71689222 71689222 + Missense_Mutation SNP C C T TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr16:71689222C>T ENST00000393524.2 - 15 3038 c.2305G>A c.(2305-2307)Gca>Aca p.A769T PHLPP2_ENST00000568954.1_Missense_Mutation_p.A836T|RP11-432I5.6_ENST00000567077.1_RNA|PHLPP2_ENST00000540628.1_Missense_Mutation_p.A46T|PHLPP2_ENST00000360429.3_Missense_Mutation_p.A836T|PHLPP2_ENST00000567016.1_Missense_Mutation_p.A871T|PHLPP2_ENST00000356272.3_Missense_Mutation_p.A836T Q6ZVD8 PHLP2_HUMAN PH domain and leucine rich repeat protein phosphatase 2 836 cytoplasm|membrane|nucleus metal ion binding|phosphoprotein phosphatase activity central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|skin(1)|stomach(1) 37 AGCACATCTGCCATCGTACAC 0.488000 7 119 0 0 1 0 0 UBR3 130507 broad.mit.edu 37 2 170937133 170937133 + Missense_Mutation SNP C C T TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr2:170937133C>T ENST00000272793.5 + 38 5538 c.5488C>T c.(5488-5490)Cgc>Tgc p.R1830C UBR3_ENST00000418381.1_Missense_Mutation_p.R1830C|UBR3_ENST00000392631.1_Missense_Mutation_p.R651C Q6ZT12 UBR3_HUMAN ubiquitin protein ligase E3 component n-recognin 3 (putative) 1830 sensory perception of smell|suckling behavior|ubiquitin-dependent protein catabolic process integral to membrane ubiquitin-protein ligase activity|zinc ion binding breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1) 33 TCGAGGTCACCGCTTCTGCCT 0.398000 22 22 0 0 1 0 0 ZNF407 55628 broad.mit.edu 37 18 72343568 72343568 + Missense_Mutation SNP G G T TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr18:72343568G>T ENST00000299687.5 + 1 593 c.593G>T c.(592-594)tGc>tTc p.C198F ZNF407_ENST00000577538.1_Missense_Mutation_p.C198F|ZNF407_ENST00000309902.6_Missense_Mutation_p.C198F|ZNF407_ENST00000582337.1_Missense_Mutation_p.C198F NM_017757.2 NP_060227.2 Q9C0G0 ZN407_HUMAN zinc finger protein 407 198 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2) 67 Esophageal squamous(42;0.131)|Prostate(75;0.173) BRCA - Breast invasive adenocarcinoma(31;0.184) TTTTCTTCTTGCTCTGACTTG 0.448000 10 140 0.00621372 0.00640201 1 1 0 AP005901.1 0 broad.mit.edu 37 18 15323276 15323276 + RNA SNP A A T TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr18:15323276A>T ENST00000455308.2 - 0 572 NR_027417.1 ATCAACTGCAATTGCATTTGC 0.308000 3 13 0 0 1 0 0 PKP1 5317 broad.mit.edu 37 1 201291189 201291189 + Silent SNP G G A TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr1:201291189G>A ENST00000263946.3 + 9 1745 c.1494G>A c.(1492-1494)gaG>gaA p.E498E PKP1_ENST00000367324.3_Silent_p.E477E|PKP1_ENST00000352845.3_Silent_p.E498E NM_000299.3 NP_000290.2 Q13835 PKP1_HUMAN plakophilin 1 (ectodermal dysplasia/skin fragility syndrome) 498 cell adhesion|cellular component disassembly involved in apoptosis|multicellular organismal development desmosome|intermediate filament|nucleus intermediate filament binding|signal transducer activity|structural constituent of epidermis NS(2)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(5)|prostate(1) 22 GCCAGCTGGAGTATAACGCCC 0.607000 6 19 0 0 1 0 0 DHX29 54505 broad.mit.edu 37 5 54577289 54577289 + Missense_Mutation SNP T T C TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr5:54577289T>C ENST00000251636.5 - 12 2168 c.2020A>G c.(2020-2022)Agg>Ggg p.R674G RP11-506H20.1_ENST00000506435.1_RNA NM_019030.2 NP_061903.2 Q7Z478 DHX29_HUMAN DEAH (Asp-Glu-Ala-His) box polypeptide 29 674 Helicase ATP-binding. ATP binding|ATP-dependent helicase activity|translation initiation factor activity breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|lung(6)|ovary(4)|prostate(1)|skin(3)|urinary_tract(2) 46 Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183) TAGAGTAACCTGGTAGATTCA 0.388000 11 33 0 0 1 0 0 LMNA 4000 broad.mit.edu 37 1 156105907 156105907 + Silent SNP G G A TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr1:156105907G>A ENST00000368300.4 + 6 1364 c.1152G>A c.(1150-1152)gaG>gaA p.E384E LMNA_ENST00000496738.1_3'UTR|LMNA_ENST00000368297.1_Silent_p.E303E|LMNA_ENST00000473598.2_Silent_p.E285E|LMNA_ENST00000448611.2_Silent_p.E272E|LMNA_ENST00000392353.3_Silent_p.E303E|LMNA_ENST00000368299.3_Silent_p.E384E|LMNA_ENST00000368301.2_Silent_p.E384E|LMNA_ENST00000361308.4_Silent_p.E384E|LMNA_ENST00000347559.2_Silent_p.E384E NM_170707.3 NP_733821.1 P02545 LMNA_HUMAN lamin A/C 384 Tail. cellular component disassembly involved in apoptosis|cellular response to hypoxia|establishment or maintenance of microtubule cytoskeleton polarity|muscle organ development|positive regulation of cell aging|regulation of apoptosis|regulation of cell migration cytoplasm|lamin filament|nuclear envelope|perinuclear region of cytoplasm protein binding|structural molecule activity NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4) 10 Hepatocellular(266;0.158) AGGGCGAGGAGGAGAGGTGGG 0.642000 Werner syndrome;Hutchinson-Gilford Progeria Syndrome 8 21 0 0 1 0 0 APOB 338 broad.mit.edu 37 2 21245798 21245798 + Silent SNP G G A rs72653068 TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr2:21245798G>A ENST00000233242.1 - 18 2848 c.2721C>T c.(2719-2721)caC>caT p.H907H NM_000384.2 NP_000375.2 P04114 APOB_HUMAN apolipoprotein B 907 Heparin-binding. cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6) 305 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) Atorvastatin(DB01076) GACCCGACTCGTGGAAGAAGT 0.507000 8 15 0 0 1 0 0 IRAK2 3656 broad.mit.edu 37 3 10255186 10255186 + Nonsense_Mutation SNP G G T TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr3:10255186G>T ENST00000256458.4 + 6 832 c.742G>T c.(742-744)Gga>Tga p.G248* NM_001570.3 NP_001561.3 O43187 IRAK2_HUMAN interleukin-1 receptor-associated kinase 2 248 Protein kinase. activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|interleukin-1-mediated signaling pathway|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of NF-kappaB transcription factor activity|positive regulation of NF-kappaB transcription factor activity|regulation of cytokine-mediated signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cell surface|cytosol|endosome membrane|plasma membrane ATP binding|NF-kappaB-inducing kinase activity|protein heterodimerization activity|protein homodimerization activity breast(4)|large_intestine(8)|lung(11)|prostate(1)|stomach(1) 25 TTCAAGTCCAGGATCAATCGA 0.463000 7 55 8.12818e-05 8.91478e-05 1 1 0 WDR90 197335 broad.mit.edu 37 16 705148 705148 + Splice_Site SNP G G A TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr16:705148G>A ENST00000549091.1 + 14 1648 c.e14+1 WDR90_ENST00000293879.4_Splice_Site|LA16c-349E10.1_ENST00000573609.1_RNA NM_145294.4 NP_660337.3 Q96KV7 WDR90_HUMAN WD repeat domain 90 endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2) 37 Hepatocellular(780;0.0218) ATGAAACCAGGTGATGCAGCC 0.657000 7 48 0 0 1 0 0 SI 6476 broad.mit.edu 37 3 164781241 164781241 + Missense_Mutation SNP C C T TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr3:164781241C>T ENST00000264382.3 - 8 958 c.896G>A c.(895-897)aGc>aAc p.S299N NM_001041.3 NP_001032.2 P14410 SUIS_HUMAN sucrase-isomaltase (alpha-glucosidase) 299 Isomaltase. carbohydrate metabolic process|polysaccharide digestion apical plasma membrane|brush border|Golgi apparatus|integral to membrane carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1) 218 Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199) Acarbose(DB00284) CATTGCATTGCTATTCATTAA 0.264000 HNSCC(35;0.089) 17 56 0 0 1 0 0 IDH1 3417 broad.mit.edu 37 2 209113112 209113112 + Missense_Mutation SNP C C T rs121913500 TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr2:209113112C>T ENST00000415913.1 - 4 776 c.395G>A c.(394-396)cGt>cAt p.R132H IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H O75874 IDHC_HUMAN isocitrate dehydrogenase 1 (NADP+), soluble 132 R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). 2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle cytosol|peroxisomal matrix isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1) NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1) 4887 Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136) ATAAGCATGACGACCTATGAT 0.393000 Mis gliobastoma 25 37 0 0 1 0 0 MPV17L 255027 broad.mit.edu 37 16 15501855 15501855 + Missense_Mutation SNP C C G TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr16:15501855C>G ENST00000287594.6 + 3 550 c.406C>G c.(406-408)Ctg>Gtg p.L136V RP11-1021N1.1_ENST00000568222.1_Intron|MPV17L_ENST00000396385.3_Silent_p.L159L NM_173803.3 NP_776164.2 Q2QL34 MP17L_HUMAN MPV17 mitochondrial membrane protein-like 0 integral to membrane|peroxisomal membrane kidney(2)|large_intestine(1)|skin(1) 4 GTGGTTTTCTCTGGGCCACCT 0.502000 3 60 0 0 1 0 0 ACTG1 71 broad.mit.edu 37 17 79478121 79478121 + Silent SNP G G A TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr17:79478121G>A ENST00000575842.1 - 4 1242 c.816C>T c.(814-816)tgC>tgT p.C272C ACTG1_ENST00000575087.1_Silent_p.C272C|AC139149.1_ENST00000584254.1_RNA|ACTG1_ENST00000331925.2_Silent_p.C272C|ACTG1_ENST00000573283.1_Silent_p.C272C P63261 ACTG_HUMAN actin, gamma 1 272 adherens junction organization|axon guidance|blood coagulation|cell junction assembly|cellular component movement cytoskeleton|cytosol ATP binding|identical protein binding breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|lung(8)|ovary(2)|prostate(5)|urinary_tract(1) 29 all_neural(118;0.0878)|Melanoma(429;0.242) BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0547) CGTGGATGCCGCAAGATTCCA 0.542000 4 79 0 0 1 0 0 RP11-798G7.5 0 broad.mit.edu 37 17 43587569 43587569 + RNA SNP G G C rs149697015 by1000genomes TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr17:43587569G>C ENST00000253803.2 + 0 267 LRRC37A4P_ENST00000579913.1_RNA aactccgtctgaaaagaaaag 0.443000 3 24 0 0 1 0 0 FUBP1 8880 broad.mit.edu 37 1 78444659 78444659 + Frame_Shift_Del DEL G G - TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr1:78444659delG ENST00000370767.1 - 1 117 c.30delC c.(28-30)ccfs p.P10fs FUBP1_ENST00000436586.2_Frame_Shift_Del_p.P10fs|FUBP1_ENST00000370768.2_Frame_Shift_Del_p.P10fs Q96AE4 FUBP1_HUMAN far upstream element (FUSE) binding protein 1 10 transcription from RNA polymerase II promoter nucleus protein binding|RNA binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3) 17 AGCCAGAAGAGGGGGGAGGCA 0.557 """F, N""" oligodendroglioma 9 12 --- --- --- --- NOTCH2 4853 broad.mit.edu 37 1 120612003 120612004 + Frame_Shift_Del DEL GG GG - TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr1:120612003_120612004delGG ENST00000256646.2 - 1 236_237 c.17_18delCC c.(16-18)cfs p.P6fs NM_024408.3 NP_077719.2 Q04721 NOTC2_HUMAN notch 2 6 anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity p.P6fs*27(2) breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1) 158 all_neural(166;0.153) all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809) Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133) ACAGCAGAGCGGGGCGCAGGGC 0.762 """N, F, Mis""" """marginal zone lymphoma, DLBCL""" Alagille Syndrome 4 5 --- --- --- --- SKIDA1 387640 broad.mit.edu 37 10 21805466 21805467 + In_Frame_Ins INS - - CCTCCT rs138084841 by1000genomes TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr10:21805466_21805467insCCTCCT ENST00000449193.2 - 4 3537_3538 c.1285_1286insAGGAGG c.(1285-1287)ggg>AGGAGGggg p.428_429insRR SKIDA1_ENST00000444772.3_In_Frame_Ins_p.349_350insRR NM_207371.3 NP_997254.3 SKI/DACH domain containing 1 p.E428_G429insEE(2) CCCGCTGCccccctcctcctcc 0.619 2 4 --- --- --- --- NELFCD 51497 broad.mit.edu 37 20 57556343 57556343 + Frame_Shift_Del DEL G G - TCGA-QH-A86X-01A-11D-A36O-08 TCGA-QH-A86X-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx d987213e-8137-4aff-9332-890b683cea2f 54b51d95-2a98-444a-9c72-6196b1788ec4 g.chr20:57556343delG ENST00000602795.1 + 1 81 c.33delG c.(31-33)gcfs p.A11fs NELFCD_ENST00000344018.3_Frame_Shift_Del_p.A2fs negative elongation factor complex member C/D AGGGCATGGCGGGGGCCGTGC 0.821 2 4 --- --- --- ---