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 TEC 7006 broad.mit.edu 37 4 48158749 48158749 + Nonsense_Mutation SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr4:48158749C>T ENST00000381501.3 - 9 897 c.740G>A c.(739-741)tGg>tAg p.W247* NM_003215.2 NP_003206.2 P42680 TEC_HUMAN tec protein tyrosine kinase 247 SH2. intracellular protein kinase cascade cytosol ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1) 31 TCTGCAATACCATCTGAACAG 0.323000 26 37 0 0 1 0 0 MIIP 60672 broad.mit.edu 37 1 12082367 12082367 + Missense_Mutation SNP A A T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr1:12082367A>T ENST00000235332.4 + 3 499 c.330A>T c.(328-330)agA>agT p.R110S MIIP_ENST00000436478.2_Missense_Mutation_p.R110S|MIIP_ENST00000466860.1_3'UTR NM_021933.3 NP_068752.2 Q5JXC2 MIIP_HUMAN migration and invasion inhibitory protein 110 autonomic_ganglia(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(1) 15 GCCGACCGAGACCCCACTCAG 0.677000 15 20 0 0 1 0 0 TTN 7273 broad.mit.edu 37 2 179426877 179426877 + Silent SNP C C A TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr2:179426877C>A ENST00000589042.1 - 326 84206 c.83982G>T c.(83980-83982)gtG>gtT p.V27994V TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342992.6_Silent_p.V25426V|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Silent_p.V19054V|TTN_ENST00000460472.2_Silent_p.V18929V|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Silent_p.V19121V|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000591111.1_Silent_p.V26353V NM_001267550.1 NP_001254479.1 Q8WZ42 TITIN_HUMAN titin 26353 Fibronectin type-III 104. ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26) 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TTCTCCAGTTCACAGTAGCTT 0.378000 12 14 3.07112e-06 3.19908e-06 1 1 0 ELF3 1999 broad.mit.edu 37 1 201984390 201984390 + Missense_Mutation SNP A A G TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr1:201984390A>G ENST00000359651.3 + 8 4247 c.1055A>G c.(1054-1056)tAc>tGc p.Y352C ELF3_ENST00000367284.5_Missense_Mutation_p.Y352C|RP11-510N19.5_ENST00000504773.1_RNA|ELF3_ENST00000367283.3_Missense_Mutation_p.Y352C P78545 ELF3_HUMAN E74-like factor 3 (ets domain transcription factor, epithelial-specific ) 352 epidermis development|epithelial cell differentiation|inflammatory response|mammary gland involution|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter Golgi apparatus|nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1) 20 CGACTCGTCTACAAGTTTGGC 0.547000 43 26 0 0 1 0 0 BTN2A3P 54718 broad.mit.edu 37 6 26422353 26422353 + RNA SNP C C T rs141013110 TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr6:26422353C>T ENST00000466808.2 + 0 7 p.P3S(2) GCTCATGGAACCAGCTGCTGC 0.622000 4 68 0 0 1 0 0 KMT2D 8085 broad.mit.edu 37 12 49437650 49437650 + Splice_Site SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr12:49437650C>T ENST00000301067.7 - 22 5319 c.e22+1 NM_003482.3 NP_003473.3 lysine (K)-specific methyltransferase 2D CTGAGACCCACCTGCAAGTAA 0.557000 OREG0021780 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 30 44 0 0 1 0 0 ADAMTS12 81792 broad.mit.edu 37 5 33535053 33535053 + Silent SNP T T C rs138703073 TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr5:33535053T>C ENST00000504830.1 - 23 4826 c.4491A>G c.(4489-4491)caA>caG p.Q1497Q ADAMTS12_ENST00000352040.3_Silent_p.Q1412Q NM_030955.2 NP_112217.2 P58397 ATS12_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 12 1497 TSP type-1 8. proteolysis proteinaceous extracellular matrix metalloendopeptidase activity|zinc ion binding NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5) 216 AGGGCACACATTGGACAGTCC 0.488000 HNSCC(64;0.19) 23 42 0 0 1 0 0 LRGUK 136332 broad.mit.edu 37 7 133848156 133848156 + Missense_Mutation SNP A A G TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr7:133848156A>G ENST00000285928.2 + 7 872 c.803A>G c.(802-804)aAc>aGc p.N268S NM_144648.1 NP_653249.1 Q96M69 LRGUK_HUMAN leucine-rich repeats and guanylate kinase domain containing 268 ATP binding|kinase activity breast(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 49 TAGAGCAATAACCAGATTGAG 0.398000 3 62 0 0 1 0 0 HIP1R 9026 broad.mit.edu 37 12 123345049 123345049 + Missense_Mutation SNP G G A TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr12:123345049G>A ENST00000253083.4 + 27 2764 c.2639G>A c.(2638-2640)gGc>gAc p.G880D NM_003959.1 NP_003950.1 O75146 HIP1R_HUMAN huntingtin interacting protein 1 related 880 I/LWEQ.|Important for actin binding. receptor-mediated endocytosis clathrin coated vesicle membrane|coated pit|perinuclear region of cytoplasm actin binding|phosphatidylinositol binding breast(1)|endometrium(5)|kidney(6)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3) 26 all_neural(191;0.0837)|Medulloblastoma(191;0.163) OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2) AAGGCTGTGGGCTGGGGAGCC 0.652000 OREG0022225 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 25 44 0 0 1 0 0 MYO18A 399687 broad.mit.edu 37 17 27425437 27425437 + Silent SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr17:27425437C>T ENST00000527372.1 - 24 3987 c.3807G>A c.(3805-3807)aaG>aaA p.K1269K MYO18A_ENST00000533112.1_Silent_p.K1269K|MYO18A_ENST00000354329.4_Silent_p.K1269K|MYO18A_ENST00000531253.1_Silent_p.K1269K NM_078471.3 NP_510880.2 Q92614 MY18A_HUMAN myosin XVIIIA 1269 anti-apoptosis|DNA metabolic process ER-Golgi intermediate compartment|myosin complex ATP binding|DNA binding|DNA-dependent ATPase activity|identical protein binding|motor activity NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2) 36 Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031) CCTTCTCGAGCTTGCTCCGCA 0.637000 13 30 0 0 1 0 0 CMTR2 55783 broad.mit.edu 37 16 71318890 71318890 + Missense_Mutation SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr16:71318890C>T ENST00000338099.5 - 3 1270 c.934G>A c.(934-936)Gaa>Aaa p.E312K CMTR2_ENST00000434935.2_Missense_Mutation_p.E312K cap methyltransferase 2 312 ACATAGACTTCGGAGTTTCCT 0.413000 29 54 0 0 1 0 0 THNSL1 79896 broad.mit.edu 37 10 25312642 25312642 + Missense_Mutation SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr10:25312642C>T ENST00000524413.1 + 3 837 c.490C>T c.(490-492)Cgt>Tgt p.R164C THNSL1_ENST00000376356.4_Missense_Mutation_p.R164C Q8IYQ7 THNS1_HUMAN threonine synthase-like 1 (S. cerevisiae) 164 threonine biosynthetic process ATP binding|pyridoxal phosphate binding|shikimate kinase activity|threonine synthase activity NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(5)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3) 28 L-Threonine(DB00156)|Pyridoxal Phosphate(DB00114) TCTAATTTGTCGTCTAAAATT 0.348000 22 32 0 0 1 0 0 CLIP4 79745 broad.mit.edu 37 2 29368223 29368223 + Silent SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr2:29368223C>T ENST00000320081.5 + 8 1266 c.1011C>T c.(1009-1011)gcC>gcT p.A337A CLIP4_ENST00000401617.2_Silent_p.A230A|CLIP4_ENST00000404424.1_Silent_p.A337A|CLIP4_ENST00000401605.1_Silent_p.A337A NM_024692.4 NP_078968.3 Q8N3C7 CLIP4_HUMAN CAP-GLY domain containing linker protein family, member 4 337 CAP-Gly 1. endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1) 26 Acute lymphoblastic leukemia(172;0.155) TTAAATGTGCCCCCAAGTATG 0.343000 18 29 0 0 1 0 0 XIRP1 165904 broad.mit.edu 37 3 39226128 39226128 + Silent SNP G G A TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr3:39226128G>A ENST00000340369.3 - 2 5037 c.4809C>T c.(4807-4809)gtC>gtT p.V1603V XIRP1_ENST00000421646.1_Silent_p.V286V|XIRP1_ENST00000396251.1_3'UTR NM_194293.2 NP_919269.2 Q702N8 XIRP1_HUMAN xin actin-binding repeat containing 1 1603 actin binding breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6) 71 KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065) TTTGACCTCCGACCTCCTGGC 0.557000 60 100 0 0 1 0 0 MALAT1 378938 broad.mit.edu 37 11 65267867 65267867 + RNA SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr11:65267867C>T ENST00000534336.1 + 0 2635 NR_002819.2 ACAGCTGACCCAGGTGCTACA 0.408000 11 21 0 0 1 0 0 PDILT 204474 broad.mit.edu 37 16 20387497 20387497 + Missense_Mutation SNP C C T rs143170020 TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr16:20387497C>T ENST00000302451.4 - 4 684 c.436G>A c.(436-438)Gtt>Att p.V146I NM_174924.1 NP_777584.1 Q8N807 PDILT_HUMAN protein disulfide isomerase-like, testis expressed 146 cell differentiation|cell redox homeostasis|multicellular organismal development|spermatogenesis endoplasmic reticulum isomerase activity breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(33)|prostate(3)|skin(1)|urinary_tract(1) 61 CTCAACCAAACGACTAAGGCA 0.458000 14 21 0 0 1 0 0 EXTL3 2137 broad.mit.edu 37 8 28574319 28574319 + Missense_Mutation SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr8:28574319C>T ENST00000220562.4 + 3 1645 c.743C>T c.(742-744)cCg>cTg p.P248L EXTL3_ENST00000523149.1_Intron|EXTL3_ENST00000519886.1_Intron NM_001440.2 NP_001431.1 O43909 EXTL3_HUMAN exostosin-like glycosyltransferase 3 248 integral to membrane|intrinsic to endoplasmic reticulum membrane glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|metal ion binding|protein binding biliary_tract(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(8)|ovary(1)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(1) 36 Ovarian(32;0.069) KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228) ATGCAGGAGCCGGTGGTGCTG 0.527000 20 28 0 0 1 0 0 ACTR5 79913 broad.mit.edu 37 20 37378814 37378814 + Silent SNP G G T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr20:37378814G>T ENST00000243903.4 + 2 574 c.537G>T c.(535-537)tcG>tcT p.S179S NM_024855.3 NP_079131.3 Q9H9F9 ARP5_HUMAN ARP5 actin-related protein 5 homolog (yeast) 179 DNA recombination|double-strand break repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent|UV-damage excision repair cytoplasm|Ino80 complex ATP binding|protein binding kidney(2)|large_intestine(2)|liver(1)|lung(5)|skin(2) 12 Myeloproliferative disorder(115;0.00878) CAAAGAACTCGATGTGCAGTG 0.448000 25 39 2.41591e-17 2.83115e-17 1 1 0 NETO2 81831 broad.mit.edu 37 16 47117214 47117214 + Missense_Mutation SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr16:47117214C>T ENST00000562435.1 - 9 1880 c.1496G>A c.(1495-1497)cGa>cAa p.R499Q NETO2_ENST00000303155.5_Missense_Mutation_p.R492Q NM_018092.4 NP_060562.3 Q8NC67 NETO2_HUMAN neuropilin (NRP) and tolloid (TLL)-like 2 499 integral to membrane receptor activity p.R499Q(1) breast(1)|cervix(1)|endometrium(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(4) 29 all_cancers(37;0.00114)|all_lung(18;0.00432)|Lung NSC(13;0.0384)|Breast(268;0.174) CTCCATTACTCGGTCTTCCAG 0.443000 HNSCC(25;0.065) 36 65 0 0 1 0 0 SEMA3B 7869 broad.mit.edu 37 3 50314099 50314099 + RNA SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr3:50314099C>T ENST00000418948.1 + 0 2446 Q13214 SEM3B_HUMAN sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B axon guidance|cell-cell signaling endoplasmic reticulum|extracellular region|membrane receptor activity central_nervous_system(2)|kidney(1)|lung(2)|skin(1) 6 BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605) CCCTGAGCCTCGCGCTGAGCG 0.697000 9 7 0 0 1 0 0 PPOX 5498 broad.mit.edu 37 1 161138879 161138879 + Missense_Mutation SNP A A C TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr1:161138879A>C ENST00000367999.4 + 7 979 c.713A>C c.(712-714)cAg>cCg p.Q238P PPOX_ENST00000495483.1_3'UTR|PPOX_ENST00000535223.1_Intron|PPOX_ENST00000352210.5_Missense_Mutation_p.Q238P|PPOX_ENST00000432542.2_Intron|PPOX_ENST00000544598.1_Intron NM_001122764.1 NP_001116236.1 P50336 PPOX_HUMAN protoporphyrinogen oxidase 238 heme biosynthetic process intrinsic to mitochondrial inner membrane|mitochondrial intermembrane space flavin adenine dinucleotide binding|oxygen-dependent protoporphyrinogen oxidase activity breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(3) 15 all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.00275) ATGTTGCCTCAGGCCCTTGAA 0.632000 26 77 0 0 1 0 0 EFEMP1 2202 broad.mit.edu 37 2 56145174 56145174 + Missense_Mutation SNP C C A TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr2:56145174C>A ENST00000394555.2 - 4 578 c.143G>T c.(142-144)tGt>tTt p.C48F EFEMP1_ENST00000424836.2_5'UTR|EFEMP1_ENST00000355426.3_Missense_Mutation_p.C48F|EFEMP1_ENST00000394554.1_Missense_Mutation_p.C48F NM_001039348.2|NM_001039349.2 NP_001034437.1|NP_001034438.1 Q12805 FBLN3_HUMAN EGF containing fibulin-like extracellular matrix protein 1 48 EGF-like 1; atypical. negative regulation of chondrocyte differentiation|peptidyl-tyrosine phosphorylation|regulation of transcription, DNA-dependent|visual perception extracellular space|proteinaceous extracellular matrix calcium ion binding|epidermal growth factor receptor activity|epidermal growth factor receptor binding|growth factor activity NS(1)|breast(2)|endometrium(4)|large_intestine(6)|lung(5)|ovary(5)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1) 28 LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132) GACAATGTCACATTCATCAAT 0.373000 29 37 7.38237e-10 8.26384e-10 1 1 0 GRIA1 2890 broad.mit.edu 37 5 153026645 153026645 + Silent SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr5:153026645C>T ENST00000285900.5 + 3 721 c.378C>T c.(376-378)cgC>cgT p.R126R GRIA1_ENST00000518142.1_Intron|GRIA1_ENST00000521843.2_Silent_p.R57R|GRIA1_ENST00000518783.1_Silent_p.R136R|GRIA1_ENST00000340592.5_Silent_p.R126R|GRIA1_ENST00000518862.1_3'UTR|GRIA1_ENST00000448073.4_Silent_p.R136R NM_000827.3|NM_001258019.1 NP_000818.2|NP_001244948.1 P42261 GRIA1_HUMAN glutamate receptor, ionotropic, AMPA 1 126 synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding NS(1)|breast(4)|endometrium(7)|kidney(3)|large_intestine(24)|liver(2)|lung(23)|ovary(4)|pancreas(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2) 81 Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21) Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785) Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236) TTCAGCTGCGCCCTGAACTGC 0.512000 33 54 0 0 1 0 0 CPSF3 51692 broad.mit.edu 37 2 9582014 9582014 + Missense_Mutation SNP G G C TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr2:9582014G>C ENST00000460593.1 + 9 2031 c.893G>C c.(892-894)gGc>gCc p.G298A CPSF3_ENST00000238112.3_Missense_Mutation_p.G335A Q9UKF6 CPSF3_HUMAN cleavage and polyadenylation specific factor 3, 73kDa 335 histone mRNA 3'-end processing|mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription mRNA cleavage and polyadenylation specificity factor complex|ribonucleoprotein complex 5'-3' exonuclease activity|endoribonuclease activity|metal ion binding|protein binding|RNA binding NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 24 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) all_cancers(51;2.39e-25)|all_epithelial(98;8.75e-19)|Lung NSC(108;2.38e-06)|Ovarian(717;0.0308) all cancers(51;2.2e-40)|Epithelial(75;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(76;4.35e-21)|STAD - Stomach adenocarcinoma(1183;0.00644) ATGCAAAGTGGCTTATCCAGA 0.428000 21 57 0 0 1 0 0 PHLDB2 90102 broad.mit.edu 37 3 111637979 111637979 + Missense_Mutation SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr3:111637979C>T ENST00000431670.2 + 4 2191 c.1780C>T c.(1780-1782)Cgg>Tgg p.R594W PHLDB2_ENST00000481953.1_Missense_Mutation_p.R594W|PHLDB2_ENST00000393925.3_Missense_Mutation_p.R594W|PHLDB2_ENST00000412622.1_Missense_Mutation_p.R594W|PHLDB2_ENST00000393923.3_Missense_Mutation_p.R621W|PHLDB2_ENST00000495180.1_Missense_Mutation_p.R180W NM_001134438.1 NP_001127910.1 Q86SQ0 PHLB2_HUMAN pleckstrin homology-like domain, family B, member 2 594 cytoplasm|intermediate filament cytoskeleton|plasma membrane p.R594R(2)|p.R621R(1) breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(8)|lung(23)|ovary(6)|skin(7)|stomach(1) 55 GGAAGAAACCCGGATAGTCAT 0.408000 39 74 0 0 1 0 0 NRG1 3084 broad.mit.edu 37 8 32599593 32599593 + Splice_Site SNP A A C TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr8:32599593A>C ENST00000341377.5 + 7 1217 c.700A>C c.(700-702)Agt>Cgt p.S234R NRG1_ENST00000521670.1_Splice_Site_p.K234Q|NRG1_ENST00000287845.5_Intron|NRG1_ENST00000520502.2_Intron|NRG1_ENST00000519301.1_Intron|NRG1_ENST00000405005.3_Splice_Site_p.K234Q|NRG1_ENST00000523079.1_Intron|NRG1_ENST00000539990.1_Intron|NRG1_ENST00000338921.4_Splice_Site_p.K234Q|NRG1_ENST00000520407.1_Intron|NRG1_ENST00000356819.4_Intron|NRG1_ENST00000287842.3_Intron NM_013964.3 NP_039258.1 Q02297 NRG1_HUMAN neuregulin 1 234 activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane cytokine activity|ErbB-3 class receptor binding|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1) 39 Breast(100;0.203) KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943) AAACCAAGAAAGTATGTCAAA 0.398000 6 40 0 0 1 0 0 IGDCC3 9543 broad.mit.edu 37 15 65621420 65621420 + Missense_Mutation SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr15:65621420C>T ENST00000327987.4 - 14 2523 c.2272G>A c.(2272-2274)Ggc>Agc p.G758S NM_004884.3 NP_004875.2 Q8IVU1 IGDC3_HUMAN immunoglobulin superfamily, DCC subclass, member 3 758 breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(9)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 30 TCCATCAGGCCGCACCCCTGA 0.697000 3 10 0 0 1 0 0 DAXX 1616 broad.mit.edu 37 6 33286835 33286835 + Missense_Mutation SNP G G A TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr6:33286835G>A ENST00000374542.5 - 7 2306 c.2102C>T c.(2101-2103)cCt>cTt p.P701L DAXX_ENST00000414083.2_Missense_Mutation_p.P626L|DAXX_ENST00000266000.6_Missense_Mutation_p.P701L 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 701 Interaction with SPOP. 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 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 GGCTGGAGAAGGGATGCAGAG 0.607000 """Mis, F, N""" Pancreatic neuroendocrine tumors. Paediatric GBM 32 53 0 0 1 0 0 KLF8 11279 broad.mit.edu 37 X 56291623 56291623 + Missense_Mutation SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chrX:56291623C>T ENST00000374928.3 + 4 578 c.92C>T c.(91-93)tCt>tTt p.S31F KLF8_ENST00000468660.1_Missense_Mutation_p.S31F NM_001159296.1 NP_001152768.1 O95600 KLF8_HUMAN Kruppel-like factor 8 31 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding kidney(4)|large_intestine(6)|lung(5)|ovary(1) 16 GTCACTGCTTCTGTTCGGAAC 0.398000 18 3 0 0 1 0 0 CEP41 95681 broad.mit.edu 37 7 130067796 130067796 + Splice_Site SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr7:130067796C>T ENST00000223208.5 - 2 367 c.97G>A c.(97-99)Ggt>Agt p.G33S CEP41_ENST00000541543.1_Splice_Site_p.D33N|CEP41_ENST00000489512.1_Splice_Site_p.G33S|CEP41_ENST00000343969.5_Splice_Site_p.G33S|CEP41_ENST00000495702.1_5'UTR NM_001257158.1|NM_018718.2 NP_001244087.1|NP_061188.1 Q9BYV8 CEP41_HUMAN centrosomal protein 41kDa G2/M transition of mitotic cell cycle centrosome|cytosol CTTTACTCACCAGTGTCCAGT 0.303000 8 27 0 0 1 0 0 RYR2 6262 broad.mit.edu 37 1 237619919 237619919 + Missense_Mutation SNP T T C TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr1:237619919T>C ENST00000366574.2 + 16 1813 c.1496T>C c.(1495-1497)cTt>cCt p.L499P RYR2_ENST00000542537.1_Missense_Mutation_p.L483P|RYR2_ENST00000360064.6_Missense_Mutation_p.L497P NM_001035.2 NP_001026.2 Q92736 RYR2_HUMAN ryanodine receptor 2 (cardiac) 499 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 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) AACCTCGTGCTTGAGTGCATA 0.418000 30 76 0 0 1 0 0 FAM189B 10712 broad.mit.edu 37 1 155217728 155217728 + Missense_Mutation SNP C C A TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr1:155217728C>A ENST00000361361.2 - 12 2361 c.1852G>T c.(1852-1854)Ggc>Tgc p.G618C FAM189B_ENST00000368368.3_Missense_Mutation_p.G600C|FAM189B_ENST00000350210.2_Missense_Mutation_p.G522C NM_006589.2 NP_006580.2 P81408 F189B_HUMAN family with sequence similarity 189, member B 618 integral to membrane WW domain binding breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2) 23 CCAGGCCGGCCCCACAGGCTC 0.622000 8 15 0.00448238 0.00454295 1 1 0 THNSL2 55258 broad.mit.edu 37 2 88474290 88474290 + Missense_Mutation SNP G G T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr2:88474290G>T ENST00000324166.5 + 2 2047 c.356G>T c.(355-357)tGc>tTc p.C119F THNSL2_ENST00000343544.4_Missense_Mutation_p.C119F|THNSL2_ENST00000449349.1_Missense_Mutation_p.C87F|THNSL2_ENST00000402102.1_Missense_Mutation_p.C119F|THNSL2_ENST00000377254.3_Missense_Mutation_p.C119F|THNSL2_ENST00000358591.2_Missense_Mutation_p.C119F NM_018271.4 NP_060741.3 Q86YJ6 THNS2_HUMAN threonine synthase-like 2 (S. cerevisiae) 119 threonine biosynthetic process threonine synthase activity breast(4)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2) 27 TCCCTGTCCTGCACAACACAG 0.522000 40 48 4.14481e-20 4.9343e-20 1 1 0 GSTT2 2953 broad.mit.edu 37 22 24323194 24323194 + Silent SNP G G T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr22:24323194G>T ENST00000215780.5 + 2 218 c.168G>T c.(166-168)acG>acT p.T56T GSTT2_ENST00000402588.3_Silent_p.T56T NM_000854.3 NP_000845.1 P0CG30 GSTT2_HUMAN glutathione S-transferase theta 2 56 GST N-terminal. cytoplasm glutathione transferase activity p.T56T(1) lung(1) 1 AACTGCCGACGCTCAAGGATG 0.557000 15 93 2.4624e-09 2.71588e-09 1 1 0 BPIFB4 149954 broad.mit.edu 37 20 31682938 31682938 + Silent SNP A A T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr20:31682938A>T ENST00000375483.3 + 10 1377 c.1377A>T c.(1375-1377)acA>acT p.T459T NM_182519.2 NP_872325.2 P59827 LPLC4_HUMAN BPI fold containing family B, member 4 459 cytoplasm|extracellular region lipid binding CCACAGCCACACTGGGAGCCC 0.498000 5 97 0 0 1 0 0 NRXN3 9369 broad.mit.edu 37 14 79175615 79175615 + Missense_Mutation SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr14:79175615C>T ENST00000554719.1 + 4 649 c.158C>T c.(157-159)gCg>gTg p.A53V NRXN3_ENST00000335750.5_Missense_Mutation_p.A53V|RP11-232C2.2_ENST00000555680.1_RNA NM_004796.4 NP_004787.2 Q9HDB5 NRX3B_HUMAN neurexin 3 0 angiogenesis|cell adhesion integral to membrane NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(23)|lung(40)|ovary(3)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(9)|urinary_tract(1) 104 Renal(4;0.00876) BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223) GCCCGGATTGCGGACACCAAG 0.463000 26 34 0 0 1 0 0 JPH1 56704 broad.mit.edu 37 8 75227740 75227740 + Silent SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr8:75227740C>T ENST00000342232.4 - 2 535 c.495G>A c.(493-495)tcG>tcA p.S165S NM_020647.2 NP_065698.1 Q9HDC5 JPH1_HUMAN junctophilin 1 165 calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity integral to membrane|junctional membrane complex|junctional sarcoplasmic reticulum membrane|plasma membrane endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|skin(1)|upper_aerodigestive_tract(2) 24 Breast(64;0.00576) BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176) CGCTGCGCAGCGAGGCCAGCG 0.721000 14 6 0 0 1 0 0 CREB3L1 90993 broad.mit.edu 37 11 46329488 46329488 + Silent SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr11:46329488C>T ENST00000529193.1 + 3 904 c.453C>T c.(451-453)gcC>gcT p.A151A CREB3L1_ENST00000288400.3_Silent_p.A151A Q96BA8 CR3L1_HUMAN cAMP responsive element binding protein 3-like 1 151 Poly-Ala. response to unfolded protein endoplasmic reticulum membrane|integral to membrane|nucleus protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity FUS/CREB3L1(6) NS(2)|breast(1)|large_intestine(4)|lung(2)|ovary(3) 12 GBM - Glioblastoma multiforme(35;0.0285) CTGCCGCGGCCGCCATGGCCA 0.692000 T FUS myxofibrosarcoma 3 3 0 0 1 0 0 CEBPA 1050 broad.mit.edu 37 19 33792337 33792337 + Silent SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr19:33792337C>T ENST00000498907.2 - 1 1133 c.984G>A c.(982-984)gtG>gtA p.V328V CTD-2540B15.7_ENST00000587312.1_RNA NM_004364.3 NP_004355.2 P49715 CEBPA_HUMAN CCAAT/enhancer binding protein (C/EBP), alpha 328 Leucine-zipper. cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding p.D322_V328del(1)|p.H200_K352>Q(1)|p.?(1) cervix(1)|haematopoietic_and_lymphoid_tissue(912)|lung(5)|prostate(1)|stomach(1) 920 Esophageal squamous(110;0.137) TCAGCTGTTCCACCCGCTTGC 0.662000 """Mis, N, F""" """AML, MDS""" Acute Myeloid Leukemia, Familial, associated with CEBPA germline mutation 15 21 0 0 1 0 0 PPP3CA 5530 broad.mit.edu 37 4 101953424 101953424 + Splice_Site SNP C C G TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr4:101953424C>G ENST00000394854.3 - 12 2022 c.1339G>C c.(1339-1341)Gct>Cct p.A447P PPP3CA_ENST00000507176.1_Splice_Site_p.A349P|PPP3CA_ENST00000323055.6_Splice_Site_p.A405P|PPP3CA_ENST00000512215.1_Splice_Site_p.A215P|PPP3CA_ENST00000394853.4_Splice_Site_p.A447P|PPP3CA_ENST00000523694.2_Splice_Site_p.A380P NM_000944.4 NP_000935.1 Q08209 PP2BA_HUMAN protein phosphatase 3, catalytic subunit, alpha isozyme 447 protein dephosphorylation calcineurin complex|cytosol|nucleus calcium ion binding|calmodulin binding breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|urinary_tract(1) 20 OV - Ovarian serous cystadenocarcinoma(123;6.79e-08) GCCTGCTTACCGCTTTGCAGG 0.517000 6 6 0 0 1 0 0 CDIPT 10423 broad.mit.edu 37 16 29872617 29872617 + Missense_Mutation SNP G G T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr16:29872617G>T ENST00000561555.1 - 1 398 c.214C>A c.(214-216)Ctg>Atg p.L72M CDIPT_ENST00000219789.6_Intron|CDIPT_ENST00000563415.1_Intron|CDIPT_ENST00000569956.1_Intron|CDIPT_ENST00000570016.1_Intron|CDIPT_ENST00000566113.1_Intron O14735 CDIPT_HUMAN CDP-diacylglycerol--inositol 3-phosphatidyltransferase 144 endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane CDP-diacylglycerol-inositol 3-phosphatidyltransferase activity|phosphatidylinositol transporter activity endometrium(1)|lung(3) 4 TTATGGCACAGTGGATGCAGG 0.572000 8 10 0.0381472 0.0381472 1 1 0 HNRNPH1 3187 broad.mit.edu 37 5 179048027 179048027 + Missense_Mutation SNP G G A TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr5:179048027G>A ENST00000356731.5 - 3 1798 c.263C>T c.(262-264)tCa>tTa p.S88L HNRNPH1_ENST00000329433.6_Missense_Mutation_p.S88L|HNRNPH1_ENST00000393432.4_Missense_Mutation_p.S88L|HNRNPH1_ENST00000442819.2_Missense_Mutation_p.S88L|HNRNPH1_ENST00000524180.1_5'UTR|HNRNPH1_ENST00000510411.1_Missense_Mutation_p.S88L P31943 HNRH1_HUMAN heterogeneous nuclear ribonucleoprotein H1 (H) 88 RRM 1. regulation of RNA splicing actin cytoskeleton|catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm nucleotide binding|poly(U) RNA binding|protein binding breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|skin(1) 14 AACGTTGTTTGACTTGAATAC 0.418000 8 70 0 0 1 0 0 PCNT 5116 broad.mit.edu 37 21 47852001 47852001 + Missense_Mutation SNP T T A TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr21:47852001T>A ENST00000359568.5 + 38 8730 c.8623T>A c.(8623-8625)Tta>Ata p.L2875I PCNT_ENST00000480896.1_Intron NM_006031.5 NP_006022.3 O95613 PCNT_HUMAN pericentrin 2875 cilium assembly|G2/M transition of mitotic cell cycle cytosol|microtubule calmodulin binding NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2) 104 Breast(49;0.112) GCAGGCAGAATTAGAGCAGTC 0.602000 5 70 0 0 1 0 0 FAM179B 23116 broad.mit.edu 37 14 45432146 45432146 + Silent SNP G G A TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr14:45432146G>A ENST00000361462.2 + 1 705 c.522G>A c.(520-522)gaG>gaA p.E174E FAM179B_ENST00000361577.3_Silent_p.E174E|FAM179B_ENST00000382233.2_Silent_p.E174E Q9Y4F4 F179B_HUMAN family with sequence similarity 179, member B 174 binding endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2) 45 AGCTTGAAGAGGCCTTTAGCT 0.542000 30 49 0 0 1 0 0 PPP1R3A 5506 broad.mit.edu 37 7 113519937 113519937 + Missense_Mutation SNP G G T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr7:113519937G>T ENST00000284601.3 - 4 1278 c.1210C>A c.(1210-1212)Cct>Act p.P404T NM_002711.3 NP_002702.2 Q16821 PPR3A_HUMAN protein phosphatase 1, regulatory subunit 3A 404 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 TCCTCTGAAGGTTGATGTGTA 0.403000 57 76 7.41606e-26 8.97103e-26 1 1 0 PAN2 9924 broad.mit.edu 37 12 56712105 56712105 + Missense_Mutation SNP G G T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr12:56712105G>T ENST00000425394.2 - 25 3866 c.3490C>A c.(3490-3492)Cac>Aac p.H1164N PAN2_ENST00000548043.1_Missense_Mutation_p.H1164N|PAN2_ENST00000440411.3_Missense_Mutation_p.H1160N|PAN2_ENST00000257931.5_Missense_Mutation_p.H1163N|PAN2_ENST00000549090.1_5'UTR NM_001127460.2 NP_001120932 Q504Q3 PAN2_HUMAN PAN2 poly(A) specific ribonuclease subunit homolog (S. cerevisiae) 1164 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|ubiquitin-dependent protein catabolic process cytosol|nucleus nucleic acid binding|poly(A)-specific ribonuclease activity|ubiquitin thiolesterase activity NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 41 AGCACCTTGTGGAAAGACTCA 0.522000 4 97 2.56e-06 2.70423e-06 1 1 0 TYK2 7297 broad.mit.edu 37 19 10473002 10473002 + Missense_Mutation SNP C C A TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr19:10473002C>A ENST00000525621.1 - 11 2088 c.1607G>T c.(1606-1608)tGc>tTc p.C536F TYK2_ENST00000529370.1_Missense_Mutation_p.C536F|TYK2_ENST00000264818.6_Missense_Mutation_p.C536F|TYK2_ENST00000524462.1_Missense_Mutation_p.C351F NM_003331.4 NP_003322.3 P29597 TYK2_HUMAN tyrosine kinase 2 536 intracellular protein kinase cascade|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway cytoskeleton|cytosol|membrane|nucleus ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity breast(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(11)|kidney(6)|large_intestine(3)|lung(19)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 64 OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06) CCTCAGCAAGCAGCCCTGCAA 0.647000 8 26 2.17888e-05 2.23857e-05 1 1 0 INPP5F 22876 broad.mit.edu 37 10 121567541 121567541 + Missense_Mutation SNP G G T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr10:121567541G>T ENST00000361976.2 + 13 1704 c.1538G>T c.(1537-1539)aGc>aTc p.S513I NM_014937.3 NP_055752.1 Q9Y2H2 SAC2_HUMAN inositol polyphosphate-5-phosphatase F 513 SAC. phosphoric ester hydrolase activity breast(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(9)|lung(5)|ovary(5)|pancreas(1)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3) 42 Lung NSC(174;0.109)|all_lung(145;0.142) all cancers(201;0.00205)|BRCA - Breast invasive adenocarcinoma(275;0.158) GACTCCATTAGCAGACAGTAT 0.443000 30 58 2.36697e-06 2.53604e-06 1 1 0 HMCN1 83872 broad.mit.edu 37 1 186043957 186043957 + Nonsense_Mutation SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr1:186043957C>T ENST00000271588.4 + 53 8453 c.8224C>T c.(8224-8226)Cga>Tga p.R2742* HMCN1_ENST00000367492.2_Nonsense_Mutation_p.R2742* NM_031935.2 NP_114141.2 Q96RW7 HMCN1_HUMAN hemicentin 1 2742 Ig-like C2-type 25. response to stimulus|visual perception basement membrane calcium ion binding NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18) 308 AGACACCGGACGATATACTTG 0.343000 37 48 0 0 1 0 0 ATRX 546 broad.mit.edu 37 X 76939543 76939543 + Missense_Mutation SNP A A G TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chrX:76939543A>G ENST00000373344.5 - 9 1419 c.1205T>C c.(1204-1206)aTt>aCt p.I402T ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Missense_Mutation_p.I364T NM_000489.3 NP_000480.3 P46100 ATRX_HUMAN alpha thalassemia/mental retardation syndrome X-linked 402 DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding p.?(1) bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2) 145 Phosphatidylserine(DB00144) AGCCTTCTTAATATCAGCCAA 0.348000 """Mis, F, N""" """Pancreatic neuroendocrine tumors, paediatric GBM""" ATR-X (alpha thalassemia/mental retardation) syndrome 202 40 0 0 1 0 0 HSD17B7P2 158160 broad.mit.edu 37 10 38654432 38654432 + RNA SNP A A G rs2257765 TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr10:38654432A>G ENST00000494540.1 + 0 599 NR_003086.1 TCATCTCGCAATGCAAGGAAA 0.453000 4 46 0 0 1 0 0 ZNF770 54989 broad.mit.edu 37 15 35274551 35274551 + Missense_Mutation SNP T T G TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr15:35274551T>G ENST00000356321.4 - 3 1429 c.1085A>C c.(1084-1086)aAa>aCa p.K362T NM_014106.3 NP_054825.2 Q6IQ21 ZN770_HUMAN zinc finger protein 770 362 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(11)|ovary(1) 29 Lung NSC(122;4.59e-10)|all_lung(180;8.78e-09) all cancers(64;1.97e-18)|GBM - Glioblastoma multiforme(113;2.11e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0643) GAAACTCTTTTTAAATACTTT 0.338000 12 21 0 0 1 0 0 PER1 5187 broad.mit.edu 37 17 8052950 8052950 + Missense_Mutation SNP G G A TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr17:8052950G>A ENST00000317276.4 - 6 920 c.683C>T c.(682-684)aCg>aTg p.T228M PER1_ENST00000581082.1_Intron|PER1_ENST00000354903.5_Missense_Mutation_p.T212M NM_002616.2 NP_002607.2 O15534 PER1_HUMAN period circadian clock 1 228 PAS 1. circadian rhythm|entrainment of circadian clock|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus signal transducer activity breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 47 GATTCGGCCCGTCAGGAAGGA 0.617000 T ETV6 """AML, CMML""" Other conserved DNA damage response genes 7 80 0 0 1 0 0 CDON 50937 broad.mit.edu 37 11 125831779 125831779 + Silent SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr11:125831779C>T ENST00000392693.3 - 19 3598 c.3471G>A c.(3469-3471)gtG>gtA p.V1157V CDON_ENST00000263577.7_Silent_p.V1157V|CDON_ENST00000531738.1_Silent_p.V534V NM_001243597.1|NM_016952.4 NP_001230526.1|NP_058648.4 Q4KMG0 CDON_HUMAN cell adhesion associated, oncogene regulated 1157 cell adhesion|muscle cell differentiation|positive regulation of muscle cell differentiation integral to membrane|plasma membrane protein binding breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1) 61 all_hematologic(175;0.177) Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604) GGCATACAGGCACCTTCACGT 0.567000 12 21 0 0 1 0 0 PREX2 80243 broad.mit.edu 37 8 69005874 69005874 + Missense_Mutation SNP A A G TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr8:69005874A>G ENST00000288368.4 + 21 2562 c.2285A>G c.(2284-2286)gAg>gGg p.E762G PREX2_ENST00000529398.1_3'UTR|RP11-403D15.2_ENST00000526901.1_RNA NM_024870.2|NM_025170.4 NP_079146.2|NP_079446.3 Q70Z35 PREX2_HUMAN phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2 762 G-protein coupled receptor protein signaling pathway|intracellular signal transduction intracellular protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2) 178 AATAGCATTGAGAGTGCTCAA 0.418000 14 94 0 0 1 0 0 TNC 3371 broad.mit.edu 37 9 117797570 117797570 + Silent SNP C C T rs150811111 TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr9:117797570C>T ENST00000350763.4 - 22 6111 c.5700G>A c.(5698-5700)tcG>tcA p.S1900S TNC_ENST00000341037.4_Silent_p.S1718S|TNC_ENST00000542877.1_Silent_p.S1537S|TNC_ENST00000340094.3_Silent_p.S1536S|TNC_ENST00000346706.3_Silent_p.S1354S|TNC_ENST00000345230.3_Silent_p.S1263S|TNC_ENST00000535648.1_Silent_p.S1445S|TNC_ENST00000537320.1_Silent_p.S1263S|TNC_ENST00000423613.2_Silent_p.S1627S NM_002160.3 NP_002151.2 P24821 TENA_HUMAN tenascin C 1900 Fibronectin type-III 15. cell adhesion|response to wounding|signal transduction extracellular space receptor binding|syndecan binding NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2) 120 GGGCAGTTTCCGACTGAACCT 0.483000 30 13 0 0 1 0 0 OPRK1 4986 broad.mit.edu 37 8 54141918 54141918 + Missense_Mutation SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr8:54141918C>T ENST00000265572.3 - 4 1379 c.1082G>A c.(1081-1083)cGa>cAa p.R361Q RP11-162D9.3_ENST00000524425.1_RNA|OPRK1_ENST00000520287.1_Missense_Mutation_p.R361Q|OPRK1_ENST00000524278.1_Missense_Mutation_p.R272Q NM_000912.3 NP_000903.2 P41145 OPRK_HUMAN opioid receptor, kappa 1 361 behavior|immune response|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception|synaptic transmission|viral genome replication integral to plasma membrane kappa-opioid receptor activity|protein binding p.R361Q(1) NS(2)|breast(3)|endometrium(3)|kidney(12)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1) 43 all_epithelial(80;0.066)|Lung NSC(129;0.0804)|all_lung(136;0.136) Buprenorphine(DB00921)|Butorphanol(DB00611)|Cocaine(DB00907)|Codeine(DB00318)|Dezocine(DB01209)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Meperidine(DB00454)|Mirtazapine(DB00370)|Morphine(DB00295)|Nalbuphine(DB00844)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pentazocine(DB00652)|Propoxyphene(DB00647)|Tramadol(DB00193) AACTGTATTTCGGACTCTGCT 0.478000 28 35 0 0 1 0 0 DNAJC13 23317 broad.mit.edu 37 3 132181319 132181319 + Silent SNP C C A TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr3:132181319C>A ENST00000260818.6 + 16 1970 c.1722C>A c.(1720-1722)tcC>tcA p.S574S DNAJC13_ENST00000486798.1_3'UTR NM_015268.3 NP_056083.3 O75165 DJC13_HUMAN DnaJ (Hsp40) homolog, subfamily C, member 13 574 heat shock protein binding breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1) 34 AGCATCCTTCCATGGCAATAA 0.318000 54 73 1.16596e-39 1.43355e-39 1 1 0 KMT2D 8085 broad.mit.edu 37 12 49440047 49440047 + Nonsense_Mutation SNP C C A TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr12:49440047C>A ENST00000301067.7 - 16 4578 c.4579G>T c.(4579-4581)Gaa>Taa p.E1527* NM_003482.3 NP_003473.3 lysine (K)-specific methyltransferase 2D TCTCACCGTTCACAGTGGCGG 0.542000 15 21 4.93089e-13 5.68949e-13 1 1 0 DCLK1 9201 broad.mit.edu 37 13 36700195 36700195 + Missense_Mutation SNP A A C TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr13:36700195A>C ENST00000255448.4 - 2 291 c.80T>G c.(79-81)gTg>gGg p.V27G DCLK1_ENST00000379892.4_Missense_Mutation_p.V27G|DCLK1_ENST00000360631.3_Missense_Mutation_p.V27G NM_004734.4 NP_004725.1 O15075 DCLK1_HUMAN doublecortin-like kinase 1 27 cell differentiation|central nervous system development|endosome transport|intracellular signal transduction|response to virus integral to plasma membrane ATP binding|protein serine/threonine kinase activity|receptor signaling protein activity breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1) 64 Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122) KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169) all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638) CAGGCCGTTCACCCGCGACCC 0.617000 34 67 0 0 1 0 0 POM121L12 285877 broad.mit.edu 37 7 53103647 53103647 + Missense_Mutation SNP G G C TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr7:53103647G>C ENST00000408890.4 + 1 299 c.283G>C c.(283-285)Gag>Cag p.E95Q NM_182595.3 NP_872401.3 Q8N7R1 P1L12_HUMAN POM121 transmembrane nucleoporin-like 12 95 endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2) 61 GGTGGTCTCCGAGGGCTGGAG 0.701000 10 11 0 0 1 0 0 FUT9 10690 broad.mit.edu 37 6 96651577 96651577 + Silent SNP G G A TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr6:96651577G>A ENST00000302103.5 + 3 872 c.546G>A c.(544-546)gtG>gtA p.V182V NM_006581.3 NP_006572.2 Q9Y231 FUT9_HUMAN fucosyltransferase 9 (alpha (1,3) fucosyltransferase) 182 L-fucose catabolic process|protein glycosylation Golgi cisterna membrane|integral to membrane alpha(1,3)-fucosyltransferase activity NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|liver(2)|lung(10)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2) 34 all_cancers(76;4.77e-07)|Acute lymphoblastic leukemia(125;4.01e-09)|all_hematologic(75;1.25e-06)|all_epithelial(107;0.00279)|Colorectal(196;0.0356) BRCA - Breast invasive adenocarcinoma(108;0.08) TGTTTGAAGTGCCAAGCAAAG 0.448000 26 32 0 0 1 0 0 LTBP4 8425 broad.mit.edu 37 19 41120272 41120272 + Missense_Mutation SNP G G A TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr19:41120272G>A ENST00000308370.7 + 22 2933 c.2933G>A c.(2932-2934)tGt>tAt p.C978Y LTBP4_ENST00000396819.3_Missense_Mutation_p.C911Y|LTBP4_ENST00000204005.9_Missense_Mutation_p.C941Y|LTBP4_ENST00000243562.9_Missense_Mutation_p.C76Y|LTBP4_ENST00000545697.1_Missense_Mutation_p.C431Y|LTBP4_ENST00000602240.1_3'UTR NM_001042544.1 NP_001036009.1 Q8N2S1 LTBP4_HUMAN latent transforming growth factor beta binding protein 4 978 Cys-rich. growth hormone secretion|multicellular organismal development|protein folding|regulation of cell differentiation|regulation of cell growth|regulation of proteolysis|regulation of transforming growth factor beta receptor signaling pathway extracellular space|proteinaceous extracellular matrix calcium ion binding|glycosaminoglycan binding|integrin binding|transforming growth factor beta binding|transforming growth factor beta receptor activity central_nervous_system(1) 1 Lung(22;0.000158)|LUSC - Lung squamous cell carcinoma(20;0.000384) TCGCAGCGCTGTGAGAACTCT 0.687000 18 28 0 0 1 0 0 RIOK3 8780 broad.mit.edu 37 18 21044061 21044061 + Missense_Mutation SNP A A G TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr18:21044061A>G ENST00000339486.3 + 3 927 c.310A>G c.(310-312)Aat>Gat p.N104D RIOK3_ENST00000581585.1_Missense_Mutation_p.N88D|RIOK3_ENST00000577501.1_Missense_Mutation_p.N104D NM_003831.3 NP_003822.2 O14730 RIOK3_HUMAN RIO kinase 3 104 chromosome segregation ATP binding|protein binding|protein serine/threonine kinase activity central_nervous_system(1)|kidney(3)|large_intestine(1)|lung(3)|ovary(2) 10 all_cancers(21;0.000106)|all_epithelial(16;6.74e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0202)|Ovarian(20;0.127) AAAAAAATTCAATGGAGATAG 0.358000 25 39 0 0 1 0 0 PHLDB3 653583 broad.mit.edu 37 19 44002018 44002018 + Missense_Mutation SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr19:44002018C>T ENST00000292140.5 - 5 905 c.545G>A c.(544-546)cGg>cAg p.R182Q PHLDB3_ENST00000599242.1_Missense_Mutation_p.R182Q NM_198850.3 NP_942147.3 Q6NSJ2 PHLB3_HUMAN pleckstrin homology-like domain, family B, member 3 182 breast(1)|central_nervous_system(1)|lung(5) 7 Prostate(69;0.0153) CTGGCTCAGCCGCCTCTGTTC 0.607000 3 5 0 0 1 0 0 PAM 5066 broad.mit.edu 37 5 102364618 102364618 + Missense_Mutation SNP G G A TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr5:102364618G>A ENST00000438793.3 + 25 3241 c.2771G>A c.(2770-2772)gGt>gAt p.G924D PAM_ENST00000348126.2_Missense_Mutation_p.G817D|PAM_ENST00000304400.7_Missense_Mutation_p.G925D|PAM_ENST00000346918.2_Missense_Mutation_p.G838D|PAM_ENST00000455264.2_Missense_Mutation_p.G856D|PAM_ENST00000379787.4_Missense_Mutation_p.G286D|PAM_ENST00000274392.9_Missense_Mutation_p.G826D NM_000919.3|NM_001177306.1|NM_138766.2 NP_000910.2|NP_001170777.1|NP_620121.1 P19021 AMD_HUMAN peptidylglycine alpha-amidating monooxygenase 924 peptide metabolic process|protein modification process extracellular region|integral to membrane|stored secretory granule L-ascorbic acid binding|peptidylamidoglycolate lyase activity|peptidylglycine monooxygenase activity|protein binding endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1) 25 all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284) Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127) Vitamin C(DB00126) TTAAACCTTGGTAATTTCTTT 0.413000 21 31 0 0 1 0 0 BEND3 57673 broad.mit.edu 37 6 107390668 107390668 + Missense_Mutation SNP C C T TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr6:107390668C>T ENST00000429433.2 - 5 2376 c.1727G>A c.(1726-1728)cGc>cAc p.R576H BEND3_ENST00000369042.1_Missense_Mutation_p.R576H NM_001080450.2 NP_001073919.1 Q5T5X7 BEND3_HUMAN BEN domain containing 3 576 BEN 3. central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(7)|lung(10)|ovary(4)|prostate(3) 30 CACCAGCAGGCGCGAGGCGAA 0.642000 25 54 0 0 1 0 0 FOXP2 93986 broad.mit.edu 37 7 114270000 114270000 + Silent SNP G G A TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr7:114270000G>A ENST00000393500.3 + 11 1132 c.312G>A c.(310-312)caG>caA p.Q104Q FOXP2_ENST00000393498.2_Silent_p.Q159Q|FOXP2_ENST00000393489.3_Silent_p.Q87Q|FOXP2_ENST00000378237.3_Silent_p.Q179Q|FOXP2_ENST00000350908.4_Silent_p.Q179Q|FOXP2_ENST00000390668.3_Silent_p.Q203Q|FOXP2_ENST00000403559.4_Silent_p.Q196Q|FOXP2_ENST00000360232.4_Silent_p.Q179Q|FOXP2_ENST00000408937.3_Silent_p.Q204Q|FOXP2_ENST00000393491.3_Silent_p.Q87Q|AC020606.1_ENST00000580664.1_RNA|FOXP2_ENST00000393494.2_Silent_p.Q179Q O15409 FOXP2_HUMAN forkhead box P2 179 Gln-rich. camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning cytoplasm|transcription factor complex chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding p.Q204Q(1) breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 52 agcaacaacagcagcagcagc 0.498000 4 52 0 0 1 0 0 RP5-884C9.2 0 broad.mit.edu 37 1 38562824 38562825 + RNA DEL AG AG - TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr1:38562824_38562825delAG ENST00000432922.1 + 0 301 ccacagaaacagagagagagag 0.500 3 5 --- --- --- --- PCSK9 255738 broad.mit.edu 37 1 55505553 55505555 + In_Frame_Del DEL CTG CTG - rs67610340 TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr1:55505553_55505555delCTG ENST00000302118.5 + 1 333_335 c.43_45delCTG c.(43-45)ctgdel p.L23del PCSK9_ENST00000452118.2_In_Frame_Del_p.L23del NM_174936.3 NP_777596.2 Q8NBP7 PCSK9_HUMAN proprotein convertase subtilisin/kexin type 9 23 L -> LL (this polymoprhism seems to have a modifier effect on LDLR mutation and familial hypercholesterolemia). cellular response to insulin stimulus|cellular response to starvation|cholesterol homeostasis|cholesterol metabolic process|kidney development|liver development|low-density lipoprotein particle receptor catabolic process|lysosomal transport|negative regulation of catalytic activity|negative regulation of low-density lipoprotein particle clearance|negative regulation of receptor recycling|neuron differentiation|positive regulation of neuron apoptosis|positive regulation of receptor internalization|protein autoprocessing|regulation of receptor activity extracellular space|late endosome|lysosome|perinuclear region of cytoplasm apolipoprotein receptor binding|identical protein binding|low-density lipoprotein particle receptor binding|serine-type endopeptidase activity|very-low-density lipoprotein particle receptor binding p.P14_L15insL(2) NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1) 32 gccgctgccactgctgctgctgc 0.709 3 3 --- --- --- --- NBPF9 400818 broad.mit.edu 37 1 144828607 144828613 + Frame_Shift_Del DEL TTCTACT TTCTACT - rs12026633 by1000genomes TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr1:144828607_144828613delTTCTACT ENST00000338347.4 + 14 1653_1659 c.1653_1659delTTCTACT c.(1651-1659)tattctactfs p.YST551fs NBPF9_ENST00000468645.1_3'UTR|NBPF9_ENST00000281815.8_Frame_Shift_Del_p.YST149fs|NBPF9_ENST00000440491.2_3'UTR neuroblastoma breakpoint family, member 9 p.S552S(1) NS(2)|prostate(1) 3 ATGGATGTTATTCTACTCCGTCAATGT 0.469 21 69 --- --- --- --- B3GALT2 8707 broad.mit.edu 37 1 193150465 193150467 + In_Frame_Del DEL GTG GTG - TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr1:193150465_193150467delGTG ENST00000367434.4 - 2 981_983 c.226_228delCAC c.(226-228)cacdel p.H76del CDC73_ENST00000367435.3_Intron NM_003783.3 NP_003774.1 O43825 B3GT2_HUMAN UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2 76 protein glycosylation Golgi membrane|integral to membrane UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|ovary(2) 16 GAAGGGAGCTGTGGTTTGTCTCA 0.453 94 68 --- --- --- --- PXK 54899 broad.mit.edu 37 3 58395317 58395318 + Frame_Shift_Ins INS - - A TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr3:58395317_58395318insA ENST00000463280.1 + 13 1359_1360 c.1268_1269insA c.(1267-1272)agaaaafs p.RK423fs PXK_ENST00000356151.2_Frame_Shift_Ins_p.RK456fs|PXK_ENST00000302779.5_Frame_Shift_Ins_p.RK439fs|PXK_ENST00000479241.1_Frame_Shift_Ins_p.RK439fs|PXK_ENST00000484288.1_Frame_Shift_Ins_p.RK456fs|PXK_ENST00000383716.3_Frame_Shift_Ins_p.RK423fs|PXK_ENST00000536660.1_Frame_Shift_Ins_p.RK319fs|PXK_ENST00000383715.4_Frame_Shift_Ins_p.RK439fs Q7Z7A4 PXK_HUMAN PX domain containing serine/threonine kinase 456 Protein kinase. cell communication|inflammatory response|negative regulation of ATPase activity|negative regulation of ion transport|regulation of synaptic transmission centrosome|cytoplasm|nucleus|plasma membrane actin binding|ATP binding|phosphatidylinositol binding|protein C-terminus binding|protein kinase activity cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|urinary_tract(1) 19 BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22) GAGGAGGAAAGAAAAAAAAGAA 0.416 14 29 --- --- --- --- VEZF1P1 647319 broad.mit.edu 37 3 192873948 192873949 + RNA DEL TG TG - TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr3:192873948_192873949delTG ENST00000414895.1 - 0 425 TGGCGCACCATGTGTGTCCGCA 0.495 26 47 --- --- --- --- CASP8AP2 9994 broad.mit.edu 37 6 90556398 90556398 + RNA DEL T T - TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr6:90556398delT ENST00000551025.1 + 0 1492 Q9UKL3 C8AP2_HUMAN caspase 8 associated protein 2 cell cycle|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent cytoplasm|nucleus caspase activator activity|death receptor binding|transcription corepressor activity NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2) 51 all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238) BRCA - Breast invasive adenocarcinoma(108;0.0953) TCTAAtttccttttttttttt 0.418 3 3 --- --- --- --- KMT2C 58508 broad.mit.edu 37 7 151835931 151835932 + Frame_Shift_Del DEL CT CT - TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr7:151835931_151835932delCT ENST00000355193.2 - 59 14981_14982 c.14763_14764delAG c.(14761-14766)agaggafs p.G4922fs KMT2C_ENST00000485655.2_Frame_Shift_Del_p.G70fs|KMT2C_ENST00000262189.6_Frame_Shift_Del_p.G4865fs lysine (K)-specific methyltransferase 2C ATTTTGTGTCCTCTCTCAAAAG 0.446 56 118 --- --- --- --- CPEB3 22849 broad.mit.edu 37 10 93999434 93999434 + Frame_Shift_Del DEL G G - TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr10:93999434delG ENST00000412050.4 - 2 762 c.674delC c.(673-675)gcgfs p.A225fs CPEB3_ENST00000265997.4_Frame_Shift_Del_p.A225fs NM_001178137.1 NP_001171608.1 Q8NE35 CPEB3_HUMAN cytoplasmic polyadenylation element binding protein 3 225 Ala-rich. nucleotide binding|RNA binding breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(2) 18 Colorectal(252;0.0869) GGCTGCAACCGCCGAAGACGA 0.716 2 4 --- --- --- --- BTRC 8945 broad.mit.edu 37 10 103298108 103298109 + Frame_Shift_Del DEL CT CT - TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr10:103298108_103298109delCT ENST00000370187.3 + 13 1754_1755 c.1636_1637delCT c.(1636-1638)ctcfs p.L546fs BTRC_ENST00000408038.2_Frame_Shift_Del_p.L510fs|BTRC_ENST00000393441.4_Frame_Shift_Del_p.L505fs|BTRC_ENST00000493877.1_3'UTR NM_033637.3 NP_378663.1 Q9Y297 FBW1A_HUMAN beta-transducin repeat containing E3 ubiquitin protein ligase 546 anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|positive regulation of proteolysis|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein destabilization|viral reproduction|Wnt receptor signaling pathway cytosol|nucleus|SCF ubiquitin ligase complex endometrium(4)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1) 27 Colorectal(252;0.234) Epithelial(162;1.05e-08)|all cancers(201;6.59e-07) TGCAGGGACACTCTGTCTACGG 0.446 52 78 --- --- --- --- ERGIC2 51290 broad.mit.edu 37 12 29509323 29509323 + Frame_Shift_Del DEL T T - TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr12:29509323delT ENST00000360150.4 - 8 639 c.564delA c.(562-564)acafs p.T188fs NM_016570.2 NP_057654.2 Q96RQ1 ERGI2_HUMAN ERGIC and golgi 2 188 vesicle-mediated transport endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi apparatus|integral to membrane|nucleus endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(2)|urinary_tract(1) 10 Lung NSC(12;2.02e-08)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)|Lung SC(9;0.184) Arsenic trioxide(DB01169) ACTTGCCCACTGTTATGTGAA 0.383 32 70 --- --- --- --- LINC00621 100996930 broad.mit.edu 37 13 23489755 23489755 + RNA DEL G G - rs113790872 by1000genomes TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr13:23489755delG ENST00000577004.1 - 0 652 GGGAGTGGGCGGGAGGGAGAG 0.697 2 4 --- --- --- --- IGHV1OR15-1 388077 broad.mit.edu 37 15 22448683 22448683 + RNA DEL G G - TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr15:22448683delG ENST00000604066.1 - 0 51 lung(4) 4 ACCTGGGAGTGGGCACCTGTG 0.572 58 223 --- --- --- --- IQGAP1 8826 broad.mit.edu 37 15 91020003 91020004 + Frame_Shift_Del DEL AA AA - TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr15:91020003_91020004delAA ENST00000268182.5 + 24 3017_3018 c.2893_2894delAA c.(2893-2895)aagfs p.K965fs IQGAP1_ENST00000560738.1_Frame_Shift_Del_p.K393fs NM_003870.3 NP_003861.1 P46940 IQGA1_HUMAN IQ motif containing GTPase activating protein 1 965 C1. energy reserve metabolic process|regulation of insulin secretion|small GTPase mediated signal transduction actin filament|cytoplasm|midbody|nucleus|plasma membrane calmodulin binding|GTPase inhibitor activity|protein phosphatase binding|Ras GTPase activator activity breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 59 Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488) BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194) GAGCAAGGAGAAGAGAGAGAAG 0.351 51 92 --- --- --- --- CREBBP 1387 broad.mit.edu 37 16 3828757 3828778 + Frame_Shift_Del DEL GGTTTTCCATGCGGCGATCCTT GGTTTTCCATGCGGCGATCCTT - TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr16:3828757_3828778delGGTTTTCCATGCGGCGATCCTT ENST00000262367.5 - 9 2673_2694 c.1864_1885delAAGGATCGCCGCATGGAAAACC c.(1864-1887)aaggatcgccgcatggaaaacctgfs p.KDRRMENL622fs CREBBP_ENST00000382070.3_Frame_Shift_Del_p.KDRRMENL584fs NM_004380.2 NP_004371.2 Q92793 CBP_HUMAN CREB binding protein 622 KIX. cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia cytoplasm|nuclear body histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21) 295 Ovarian(90;0.0266) OV - Ovarian serous cystadenocarcinoma(1;3.54e-05) TAGGCTACCAGGTTTTCCATGCGGCGATCCTTTAGAGCTGCG 0.459 """T, N, F, Mis, O""" """MLL, MORF, RUNXBP2""" """ALL, AML, DLBCL, B-NHL """ Rubinstein-Taybi syndrome 18 94 --- --- --- --- CMTR2 55783 broad.mit.edu 37 16 71319087 71319104 + In_Frame_Del DEL TCACCTGGGTTTCCTTGG TCACCTGGGTTTCCTTGG - TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr16:71319087_71319104delTCACCTGGGTTTCCTTGG ENST00000338099.5 - 3 1056_1073 c.720_737delCCAAGGAAACCCAGGTGA c.(718-738)tgccaaggaaacccaggtgaa>tga p.240_246CQGNPGE>* CMTR2_ENST00000434935.2_In_Frame_Del_p.240_246CQGNPGE>* cap methyltransferase 2 240 AGCTTCTTGTTCACCTGGGTTTCCTTGGCAATCAAAAC 0.422 16 44 --- --- --- --- CD79A 973 broad.mit.edu 37 19 42383354 42383375 + Splice_Site DEL TGCGCCGTGAGTGGCCCAGCCC TGCGCCGTGAGTGGCCCAGCCC - TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr19:42383354_42383375delTGCGCCGTGAGTGGCCCAGCCC ENST00000221972.3 + 2 559_564 c.374_379delTGCGCCGTGAGTGGCCCAGCCC c.(373-381)gtgcgccgt>ggt p.VRR125fs CD79A_ENST00000444740.2_Intron NM_001783.3|NM_021601.3 NP_001774.1|NP_067612.1 P11912 CD79A_HUMAN CD79a molecule, immunoglobulin-associated alpha 125 B cell differentiation|B cell proliferation|B cell receptor signaling pathway B cell receptor complex|external side of plasma membrane|integral to membrane|membrane raft|multivesicular body transmembrane receptor activity large_intestine(3)|lung(3)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1) 11 TACCTCCGCGTGCGCCGTGAGTGGCCCAGCCCTGGCCCCTAC 0.590 """O, S""" DLBCL 5 10 --- --- --- --- RSPH1 89765 broad.mit.edu 37 21 43905780 43905780 + Splice_Site DEL T T - TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr21:43905780delT ENST00000291536.3 - 5 667 c.500delA c.(499-501)aat>at p.N167fs RSPH1_ENST00000398352.3_Splice_Site_p.N129fs NM_080860.2 NP_543136.1 Q8WYR4 RSPH1_HUMAN radial spoke head 1 homolog (Chlamydomonas) 167 meiosis cytosol|nucleus large_intestine(7)|lung(2)|ovary(1)|prostate(1)|stomach(1) 12 TGGACTTACATTTTTGTTCAA 0.493 23 88 --- --- --- --- MAPK11 5600 broad.mit.edu 37 22 50708667 50708667 + Frame_Shift_Del DEL C C - TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chr22:50708667delC ENST00000330651.6 - 1 155 c.55delG c.(55-57)gagfs p.E19fs MAPK11_ENST00000495277.1_Intron|MAPK11_ENST00000449719.2_5'UTR NM_002751.5 NP_002742.3 Q15759 MK11_HUMAN mitogen-activated protein kinase 11 19 activation of MAPK activity|innate immune response|mRNA metabolic process|muscle cell differentiation|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|Ras protein signal transduction|regulation of sequence-specific DNA binding transcription factor activity|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 cytosol|nucleoplasm ATP binding|MAP kinase activity|protein binding breast(1)|central_nervous_system(1)|lung(4) 6 all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113) BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247) TGCGGCACCTCCCACACGGTC 0.781 2 4 --- --- --- --- GPC3 2719 broad.mit.edu 37 X 133119384 133119386 + In_Frame_Del DEL CGG CGG - TCGA-CF-A9FL-01A-11D-A38G-08 TCGA-CF-A9FL-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx db6babbd-b14c-405b-8c1f-9908ea26b574 0f99d9d0-87af-4846-9a43-7a9209fbdd35 g.chrX:133119384_133119386delCGG ENST00000370818.3 - 1 536_538 c.91_93delCCG c.(91-93)ccgdel p.P31del GPC3_ENST00000394299.2_In_Frame_Del_p.P31del|GPC3_ENST00000543339.1_In_Frame_Del_p.P31del NM_001164618.1|NM_004484.3 NP_001158090.1|NP_004475.1 P51654 GPC3_HUMAN glypican 3 31 extracellular space|integral to plasma membrane|proteinaceous extracellular matrix heparan sulfate proteoglycan binding|peptidyl-dipeptidase inhibitor activity breast(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|prostate(1)|skin(2) 36 Acute lymphoblastic leukemia(192;0.000127) AGGTGGCGTCCGGCGGCGGCGGC 0.690 """T, D, Mis, N, F, S""" Wilms tumour Simpson-Golabi-Behmel syndrome 2 4 --- --- --- ---