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 PTENP1 0 broad.mit.edu 37 9 33675379 33675379 + RNA SNP C C A TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr9:33675379C>A ENST00000532280.1 - 0 2118 NR_023917.1 AAAAAGGTCCCTTTTCAGTTT 0.318000 3 33 0.115264 0.115264 1 1 0 CWF19L1 55280 broad.mit.edu 37 10 101993060 101993060 + Missense_Mutation SNP C C T TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr10:101993060C>T ENST00000354105.4 - 14 1627 c.1541G>A c.(1540-1542)aGc>aAc p.S514N CWF19L1_ENST00000478047.1_5'UTR|CWF19L1_ENST00000370379.1_Missense_Mutation_p.S229N|RP11-316M21.6_ENST00000444359.1_RNA NM_018294.4 NP_060764.3 Q69YN2 C19L1_HUMAN CWF19-like 1, cell cycle control (S. pombe) 514 catalytic activity cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|stomach(2) 17 Colorectal(252;0.117) Epithelial(162;3.78e-10)|all cancers(201;3.1e-08) GTCTTCCTTGCTGATCTGACA 0.473000 10 61 0 0 1 0 0 APOBEC3B 9582 broad.mit.edu 37 22 39382336 39382336 + Missense_Mutation SNP A A G TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr22:39382336A>G ENST00000402182.3 + 4 543 c.488A>G c.(487-489)aAt>aGt p.N163S APOBEC3B_ENST00000407298.3_Missense_Mutation_p.N163S|APOBEC3B_ENST00000333467.3_Missense_Mutation_p.N163S Q9UH17 ABC3B_HUMAN apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B 163 negative regulation of transposition hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines|RNA binding|zinc ion binding cervix(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1) 13 Melanoma(58;0.04) TTTGTGTACAATGAAGGTCAG 0.512000 35 131 0 0 1 0 0 MYO3A 53904 broad.mit.edu 37 10 26446395 26446395 + Nonsense_Mutation SNP C C T TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr10:26446395C>T ENST00000265944.5 + 26 3116 c.2950C>T c.(2950-2952)Cga>Tga p.R984* MYO3A_ENST00000543632.1_Intron NM_017433.4 NP_059129.3 Q8NEV4 MYO3A_HUMAN myosin IIIA 984 Myosin head-like. protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception cytoplasm|filamentous actin|filopodium|myosin complex actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity p.R984*(3) NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2) 146 AGCAAGAATTCGAAGACTAGG 0.363000 20 73 0 0 1 0 0 PPP2CA 5515 broad.mit.edu 37 5 133541656 133541656 + Missense_Mutation SNP C C T TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr5:133541656C>T ENST00000481195.1 - 2 549 c.269G>A c.(268-270)gGa>gAa p.G90E CDKL3_ENST00000518409.1_5'UTR|PPP2CA_ENST00000231504.5_5'UTR NM_002715.2 NP_002706.1 protein phosphatase 2, catalytic subunit, alpha isozyme endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|skin(1) 12 KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) TGAATAATATCCTCTGTCAAC 0.368000 10 34 0 0 1 0 0 ADAMTS1 9510 broad.mit.edu 37 21 28212235 28212235 + Missense_Mutation SNP C C T TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr21:28212235C>T ENST00000284984.2 - 6 2265 c.1811G>A c.(1810-1812)cGc>cAc p.R604H NM_006988.3 NP_008919.3 Q9UHI8 ATS1_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 1 604 TSP type-1 1. integrin-mediated signaling pathway|negative regulation of cell proliferation|proteolysis heparin binding|zinc ion binding central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(20)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1) 42 Breast(209;0.000962) Lung(58;0.215) GGATCTGTAGCGCACTCGTTT 0.473000 5 112 0 0 1 0 0 F2R 2149 broad.mit.edu 37 5 76028613 76028613 + Missense_Mutation SNP C C T TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr5:76028613C>T ENST00000319211.4 + 2 828 c.563C>T c.(562-564)gCc>gTc p.A188V NM_001992.3 NP_001983.2 P25116 PAR1_HUMAN coagulation factor II (thrombin) receptor 188 activation of caspase activity|anatomical structure morphogenesis|connective tissue replacement involved in inflammatory response wound healing|negative regulation of cell proliferation|platelet activation|positive regulation of blood coagulation|positive regulation of cell migration|positive regulation of collagen biosynthetic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of JAK-STAT cascade|positive regulation of MAPKKK cascade|positive regulation of release of sequestered calcium ion into cytosol|positive regulation of transcription, DNA-dependent|STAT protein import into nucleus|tyrosine phosphorylation of STAT protein caveola|extracellular region|Golgi apparatus|integral to plasma membrane|platelet dense tubular network receptor binding|thrombin receptor activity NS(1)|breast(1)|endometrium(3)|kidney(1)|lung(7)|ovary(3) 16 all_lung(232;0.000414)|Lung NSC(167;0.0011)|Prostate(461;0.00955)|Ovarian(174;0.0129) all cancers(79;4.43e-43) Streptokinase(DB00086) AACATGTACGCCTCTATCTTG 0.493000 11 129 0 0 1 0 0 NTRK1 4914 broad.mit.edu 37 1 156849884 156849884 + Missense_Mutation SNP G G A TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr1:156849884G>A ENST00000368196.3 + 15 2242 c.2122G>A c.(2122-2124)Ggc>Agc p.G708S NTRK1_ENST00000524377.1_Missense_Mutation_p.G714S|NTRK1_ENST00000531606.1_3'UTR|NTRK1_ENST00000358660.3_Missense_Mutation_p.G711S|NTRK1_ENST00000392302.2_Missense_Mutation_p.G678S NM_001012331.1 NP_001012331.1 P04629 NTRK1_HUMAN neurotrophic tyrosine kinase, receptor, type 1 714 Protein kinase. activation of adenylate cyclase activity|activation of MAPKK activity|activation of phospholipase C activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development|phosphatidylinositol-mediated signaling|Ras protein signal transduction endosome|integral to plasma membrane ATP binding|neurotrophin receptor activity|transmembrane receptor protein serine/threonine kinase activity|transmembrane receptor protein tyrosine kinase activity breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3) 74 all_hematologic(923;0.0839)|Hepatocellular(266;0.158) Imatinib(DB00619) GTGGAGCTTCGGCGTGGTGCT 0.647000 T """TPM3, TPR, TFG""" papillary thyroid TSP Lung(10;0.080) 3 71 0 0 1 0 0 RBM48 84060 broad.mit.edu 37 7 92164118 92164118 + Missense_Mutation SNP G G A TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr7:92164118G>A ENST00000481551.1 + 4 892 c.851G>A c.(850-852)cGc>cAc p.R284H RBM48_ENST00000265732.5_Missense_Mutation_p.R284H Q5RL73 CG064_HUMAN RNA binding motif protein 48 284 nucleotide binding p.R284H(1) CTGCAGGAGCGCAAAAGAAGA 0.428000 3 41 0 0 1 0 0 PTPRH 5794 broad.mit.edu 37 19 55713580 55713580 + Missense_Mutation SNP C C T TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr19:55713580C>T ENST00000376350.3 - 6 1019 c.997G>A c.(997-999)Gag>Aag p.E333K PTPRH_ENST00000263434.5_Missense_Mutation_p.E155K|PTPRH_ENST00000588559.1_5'UTR NM_002842.3 NP_002833.3 Q9HD43 PTPRH_HUMAN protein tyrosine phosphatase, receptor type, H 333 Fibronectin type-III 4. apoptosis cytoplasm|integral to plasma membrane protein binding|transmembrane receptor protein tyrosine phosphatase activity breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2) 67 Renal(1328;0.245) BRCA - Breast invasive adenocarcinoma(297;0.209) GBM - Glioblastoma multiforme(193;0.0479) CCAGTGTACTCAACCCCGTAG 0.567000 4 73 0 0 1 0 0 FGL2 10875 broad.mit.edu 37 7 76828504 76828504 + Missense_Mutation SNP G G T TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr7:76828504G>T ENST00000248598.5 - 1 639 c.607C>A c.(607-609)Cgt>Agt p.R203S CCDC146_ENST00000285871.4_Intron|CCDC146_ENST00000431197.1_Intron NM_006682.2 NP_006673.1 Q14314 FGL2_HUMAN fibrinogen-like 2 203 signal transduction fibrinogen complex receptor binding p.R203S(1) breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(2) 13 ATACCTGGACGTGACTGTATT 0.323000 5 87 0.000602214 0.000655745 1 1 0 SSX7 280658 broad.mit.edu 37 X 52681974 52681974 + Nonsense_Mutation SNP C C A TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chrX:52681974C>A ENST00000298181.5 - 3 288 c.130G>T c.(130-132)Gag>Tag p.E44* NM_173358.2 NP_775494.1 Q7RTT5 SSX7_HUMAN synovial sarcoma, X breakpoint 7 44 KRAB-related. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus nucleic acid binding endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|skin(1) 16 Ovarian(276;0.236) CTGATTTTCTCCAAGGATTTC 0.383000 27 56 8.88839e-20 1.08883e-19 1 1 0 PSG8 0 broad.mit.edu 37 19 43268205 43268205 + Missense_Mutation SNP C C T rs142736244 by1000genomes TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr19:43268205C>T ENST00000404209.4 - 2 389 c.293G>A c.(292-294)cGa>cAa p.R98Q PSG8_ENST00000406636.3_Intron|PSG8_ENST00000401467.2_Missense_Mutation_p.R98Q|PSG8_ENST00000306511.4_Missense_Mutation_p.R98Q NM_001130167.1 NP_001123639.1 Q9UQ74 PSG8_HUMAN pregnancy specific beta-1-glycoprotein 8 98 Ig-like V-type. extracellular region breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(19)|prostate(1)|skin(3)|upper_aerodigestive_tract(1) 40 Prostate(69;0.00899) TATTGTTTCTCGTCCACTGTA 0.423000 7 308 0 0 1 0 0 NET1 10276 broad.mit.edu 37 10 5493864 5493864 + Missense_Mutation SNP A A C TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr10:5493864A>C ENST00000355029.4 + 4 469 c.327A>C c.(325-327)agA>agC p.R109S NET1_ENST00000380359.3_Missense_Mutation_p.R55S|NET1_ENST00000542715.1_5'UTR NM_001047160.1 NP_001040625.1 Q7Z628 ARHG8_HUMAN neuroepithelial cell transforming 1 109 apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell growth|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|nucleus Rho guanyl-nucleotide exchange factor activity breast(4)|kidney(2)|large_intestine(9)|lung(5)|prostate(2)|skin(1) 23 CTCCTGTAAGAAATGGAGCTG 0.403000 15 103 0 0 1 0 0 CWF19L1 55280 broad.mit.edu 37 10 101993058 101993058 + Nonsense_Mutation SNP T T A TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr10:101993058T>A ENST00000354105.4 - 14 1629 c.1543A>T c.(1543-1545)Aag>Tag p.K515* CWF19L1_ENST00000478047.1_5'UTR|CWF19L1_ENST00000370379.1_Nonsense_Mutation_p.K230*|RP11-316M21.6_ENST00000444359.1_RNA NM_018294.4 NP_060764.3 Q69YN2 C19L1_HUMAN CWF19-like 1, cell cycle control (S. pombe) 515 catalytic activity cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|stomach(2) 17 Colorectal(252;0.117) Epithelial(162;3.78e-10)|all cancers(201;3.1e-08) TCGTCTTCCTTGCTGATCTGA 0.473000 10 60 0 0 1 0 0 FSHR 0 broad.mit.edu 37 2 49190290 49190290 + Missense_Mutation SNP C C T rs150235567 TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr2:49190290C>T ENST00000406846.2 - 10 1789 c.1670G>A c.(1669-1671)cGg>cAg p.R557Q FSHR_ENST00000346173.3_Missense_Mutation_p.R495Q|FSHR_ENST00000541117.1_Missense_Mutation_p.R293Q|FSHR_ENST00000304421.4_Missense_Mutation_p.R531Q NM_000145.3 NP_000136.2 P23945 FSHR_HUMAN follicle stimulating hormone receptor 557 female gamete generation|male gonad development|spermatogenesis integral to membrane|plasma membrane follicle-stimulating hormone receptor activity|protein binding NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|liver(1)|lung(45)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2) 73 all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094) GTTGGGGTTCCGCACTGTGAG 0.527000 Gonadal Dysgenesis, 46 XX 4 28 0 0 1 0 0 IFT74 80173 broad.mit.edu 37 9 27062709 27062709 + Missense_Mutation SNP C C A TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr9:27062709C>A ENST00000443698.1 + 20 1949 c.1778C>A c.(1777-1779)gCt>gAt p.A593D IFT74_ENST00000380062.5_Missense_Mutation_p.A593D|IFT74_ENST00000433700.1_Missense_Mutation_p.A593D NM_001099222.1 NP_001092692.1 Q96LB3 IFT74_HUMAN intraflagellar transport 74 homolog (Chlamydomonas) 593 cytoplasmic membrane-bounded vesicle|intraflagellar transport particle B|microtubule-based flagellum endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1) 6 all_neural(11;2.36e-10) Lung(218;1.4e-05)|LUSC - Lung squamous cell carcinoma(38;0.000114) ATCGTGGATGCTTTACATAGC 0.388000 3 62 6.4e-05 7.29302e-05 1 1 0 SNX16 64089 broad.mit.edu 37 8 82727590 82727590 + Silent SNP C C A TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr8:82727590C>A ENST00000396330.2 - 6 1157 c.651G>T c.(649-651)ccG>ccT p.P217P SNX16_ENST00000353788.4_Silent_p.P188P|SNX16_ENST00000345957.4_Silent_p.P217P|RP13-923O23.6_ENST00000524337.1_RNA NM_022133.3 NP_071416.2 P57768 SNX16_HUMAN sorting nexin 16 217 PX. cell communication|early endosome to late endosome transport|endosome to lysosome transport|protein targeting to lysosome early endosome membrane|extrinsic to endosome membrane|late endosome membrane|lysosome identical protein binding|phosphatidylinositol binding large_intestine(1)|ovary(1)|pancreas(1)|skin(2) 5 CAAATGGACCCGGTGGATCAT 0.338000 6 36 1.06961e-07 1.27832e-07 1 1 0 LRRIQ1 84125 broad.mit.edu 37 12 85518199 85518199 + Silent SNP G G A TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr12:85518199G>A ENST00000393217.2 + 17 3970 c.3909G>A c.(3907-3909)aaG>aaA p.K1303K NM_001079910.1 NP_001073379.1 Q96JM4 LRIQ1_HUMAN leucine-rich repeats and IQ motif containing 1 1303 breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2) 83 GBM - Glioblastoma multiforme(134;0.212) AAGACAGCAAGGCAAGCAGTA 0.398000 12 159 0 0 1 0 0 HRG 3273 broad.mit.edu 37 3 186386777 186386777 + Silent SNP G G A rs143118011 by1000genomes TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr3:186386777G>A ENST00000232003.4 + 2 317 c.237G>A c.(235-237)tcG>tcA p.S79S NM_000412.2 NP_000403.1 P04196 HRG_HUMAN histidine-rich glycoprotein 79 Cystatin 1.|Interaction with ATP5A1. S -> L (in dbSNP:rs4516605). fibrinolysis|platelet activation|platelet degranulation extracellular region|plasma membrane|platelet alpha granule lumen cysteine-type endopeptidase inhibitor activity|heparin binding breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 37 all_cancers(143;6.64e-12)|Ovarian(172;0.0339) OV - Ovarian serous cystadenocarcinoma(80;5.73e-20) GBM - Glioblastoma multiforme(93;0.0683) CGGACTGTTCGGTCCTATCCA 0.428000 4 70 0 0 1 0 0 EVI2A 2123 broad.mit.edu 37 17 29645857 29645857 + Missense_Mutation SNP T T G TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr17:29645857T>G ENST00000247270.3 - 3 580 c.244A>C c.(244-246)Att>Ctt p.I82L NF1_ENST00000581113.2_Intron|NF1_ENST00000358273.4_Intron|NF1_ENST00000356175.3_Intron|EVI2A_ENST00000462804.2_Missense_Mutation_p.I59L|EVI2A_ENST00000461237.1_Missense_Mutation_p.I59L NM_001003927.2 NP_001003927.1 P22794 EVI2A_HUMAN ecotropic viral integration site 2A 59 integral to membrane transmembrane receptor activity p.0?(8)|p.?(3) breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1) 14 all_cancers(10;6.97e-11)|all_epithelial(10;0.0051)|all_hematologic(16;0.0149)|Breast(31;0.0155)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|all_lung(9;0.0468)|Lung NSC(157;0.094) UCEC - Uterine corpus endometrioid carcinoma (4;6.64e-05)|all cancers(4;5.94e-13)|Epithelial(4;7.98e-12)|OV - Ovarian serous cystadenocarcinoma(4;9.4e-12)|GBM - Glioblastoma multiforme(4;0.18) TTTGTGTTAATGTTTTCATTT 0.368000 5 108 0 0 1 0 0 ASTN1 460 broad.mit.edu 37 1 176852023 176852023 + Nonsense_Mutation SNP G G A TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr1:176852023G>A ENST00000367654.2 - 20 3371 c.3358C>T c.(3358-3360)Cga>Tga p.R1120* ASTN1_ENST00000424564.2_Nonsense_Mutation_p.R1112*|ASTN1_ENST00000361833.2_Nonsense_Mutation_p.R1112*|ASTN1_ENST00000367657.3_Nonsense_Mutation_p.R1112* O14525 ASTN1_HUMAN astrotactin 1 1120 Fibronectin type-III 1. cell migration|neuron cell-cell adhesion integral to membrane NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3) 153 TCCAGGCATCGTATGATCAGA 0.502000 8 38 0 0 1 0 0 NCOA6 23054 broad.mit.edu 37 20 33345744 33345744 + Silent SNP C C T TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr20:33345744C>T ENST00000374796.2 - 8 3377 c.807G>A c.(805-807)caG>caA p.Q269Q NCOA6_ENST00000359003.2_Silent_p.Q269Q Q14686 NCOA6_HUMAN nuclear receptor coactivator 6 269 CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region. brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter transcription factor complex chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding p.Q269Q(15) NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1) 107 gctgctgctgctgttgttgtt 0.537000 3 33 0 0 1 0 0 EMR2 30817 broad.mit.edu 37 19 14883284 14883284 + Silent SNP C C T rs146183015 byFrequency TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr19:14883284C>T ENST00000315576.3 - 5 676 c.225G>A c.(223-225)tcG>tcA p.S75S EMR2_ENST00000594294.1_Silent_p.S75S|EMR2_ENST00000346057.1_Silent_p.S75S|EMR2_ENST00000595839.1_Silent_p.S75S|EMR2_ENST00000596991.2_Silent_p.S75S|EMR2_ENST00000599423.1_5'UTR|EMR2_ENST00000594076.1_Silent_p.S75S|EMR2_ENST00000353876.1_Silent_p.S75S|EMR2_ENST00000392965.3_Silent_p.S75S|EMR2_ENST00000392967.2_Silent_p.S75S|EMR2_ENST00000353005.1_Silent_p.S75S|EMR2_ENST00000601345.1_Silent_p.S75S NM_013447.2 NP_038475.2 Q9UHX3 EMR2_HUMAN egf-like module containing, mucin-like, hormone receptor-like 2 75 EGF-like 2; calcium-binding. cell adhesion|neuropeptide signaling pathway integral to membrane|plasma membrane calcium ion binding|G-protein coupled receptor activity breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1) 48 ATGACACTTTCGACAGTGTTG 0.537000 8 47 0 0 1 0 0 ULBP1 80329 broad.mit.edu 37 6 150289967 150289967 + Nonsense_Mutation SNP C C T TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr6:150289967C>T ENST00000229708.2 + 2 353 c.310C>T c.(310-312)Caa>Taa p.Q104* ULBP1_ENST00000367345.1_Nonsense_Mutation_p.Q104* NM_025218.2 NP_079494.1 Q9BZM6 N2DL1_HUMAN UL16 binding protein 1 104 MHC class I alpha-1 like. antigen processing and presentation|immune response|natural killer cell activation|regulation of immune response anchored to membrane|endoplasmic reticulum|MHC class I protein complex MHC class I receptor activity large_intestine(3)|lung(5)|pancreas(1)|skin(1) 10 Ovarian(120;0.0907) BRCA - Breast invasive adenocarcinoma(37;0.193) OV - Ovarian serous cystadenocarcinoma(155;2.14e-11) CCTTAAAGGGCAACTGCTTGA 0.413000 16 64 0 0 1 0 0 TENM2 57451 broad.mit.edu 37 5 167545362 167545362 + Missense_Mutation SNP G G A TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr5:167545362G>A ENST00000519204.1 + 9 1634 c.1516G>A c.(1516-1518)Ggc>Agc p.G506S TENM2_ENST00000403607.2_Missense_Mutation_p.G460S|CTB-178M22.1_ENST00000517408.1_RNA|TENM2_ENST00000518659.1_Missense_Mutation_p.G627S|TENM2_ENST00000520394.1_Missense_Mutation_p.G395S|TENM2_ENST00000545108.1_Missense_Mutation_p.G627S teneurin transmembrane protein 2 GTGCTACAGCGGCTGGAAAGG 0.567000 33 95 0 0 1 0 0 KDM2B 84678 broad.mit.edu 37 12 121880305 121880305 + Missense_Mutation SNP T T G TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr12:121880305T>G ENST00000377069.4 - 18 3138 c.2732A>C c.(2731-2733)gAg>gCg p.E911A KDM2B_ENST00000542973.1_Missense_Mutation_p.E348A|KDM2B_ENST00000536437.1_Intron|KDM2B_ENST00000377071.4_Missense_Mutation_p.E980A NM_001005366.1 NP_001005366.1 Q8NHM5 KDM2B_HUMAN lysine (K)-specific demethylase 2B 980 embryonic camera-type eye morphogenesis|fourth ventricle development|histone H2A monoubiquitination|initiation of neural tube closure|lateral ventricle development|midbrain development|midbrain-hindbrain boundary morphogenesis|negative regulation of neural precursor cell proliferation|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|spermatogenesis|third ventricle development|transcription, DNA-dependent nucleolus DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1) 19 CTCCTCGCCCTCGCTCTCAGG 0.682000 12 21 0 0 1 0 0 RP11-481J13.1 0 broad.mit.edu 37 2 56216130 56216130 + RNA SNP C C A TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr2:56216130C>A ENST00000606639.1 + 0 82 AC011306.2_ENST00000446139.1_lincRNA|MIR216A_ENST00000385063.1_RNA TCCCAGAGACCACTGTGAGGG 0.433000 4 140 0.014758 0.015386 1 1 0 INSRR 3645 broad.mit.edu 37 1 156821758 156821758 + Missense_Mutation SNP C C G TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr1:156821758C>G ENST00000368195.3 - 3 1259 c.863G>C c.(862-864)gGc>gCc p.G288A NTRK1_ENST00000392302.2_Intron NM_014215.2 NP_055030.1 P14616 INSRR_HUMAN insulin receptor-related receptor 288 protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|insulin receptor substrate binding|metal ion binding|phosphatidylinositol 3-kinase binding|transmembrane receptor protein tyrosine kinase activity breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2) 42 all_hematologic(923;0.0839)|Hepatocellular(266;0.158) GGAGGCACGGCCGGGCACAGA 0.662000 7 23 0 0 1 0 0 KRI1 65095 broad.mit.edu 37 19 10668457 10668457 + Missense_Mutation SNP C C T TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr19:10668457C>T ENST00000312962.6 - 15 1511 c.1492G>A c.(1492-1494)Gtg>Atg p.V498M KRI1_ENST00000361821.5_Missense_Mutation_p.V494M NM_023008.3 NP_075384.3 Q8N9T8 KRI1_HUMAN KRI1 homolog (S. cerevisiae) 498 NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1) 26 Epithelial(33;9.2e-06)|all cancers(31;3.9e-05) GGTTCAAACACGGGCTTCTCC 0.701000 4 36 0 0 1 0 0 DCAF12L1 139170 broad.mit.edu 37 X 125685748 125685748 + Silent SNP A A G TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chrX:125685748A>G ENST00000371126.1 - 1 1086 c.844T>C c.(844-846)Ttg>Ctg p.L282L NM_178470.4 NP_848565.2 Q5VU92 DC121_HUMAN DDB1 and CUL4 associated factor 12-like 1 282 breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(39)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2) 68 TAGCCGTCCAAGGACACCGCT 0.627000 14 17 0 0 1 0 0 BCLAF1 9774 broad.mit.edu 37 6 136599145 136599145 + Missense_Mutation SNP T T C TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr6:136599145T>C ENST00000531224.1 - 4 1126 c.874A>G c.(874-876)Att>Gtt p.I292V BCLAF1_ENST00000527759.1_Missense_Mutation_p.I290V|BCLAF1_ENST00000527536.1_Missense_Mutation_p.I292V|BCLAF1_ENST00000392348.2_Missense_Mutation_p.I290V|BCLAF1_ENST00000530767.1_Missense_Mutation_p.I292V|BCLAF1_ENST00000353331.4_Missense_Mutation_p.I290V NM_001077441.1|NM_014739.2 NP_001070909.1|NP_055554.1 Q9NYF8 BCLF1_HUMAN BCL2-associated transcription factor 1 292 induction of apoptosis|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleolus DNA binding|protein binding haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1) 9 Colorectal(23;0.24) GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331) ATGTGATGAATTGGACTATTC 0.463000 5 73 0 0 1 0 0 ZBTB49 166793 broad.mit.edu 37 4 4317416 4317416 + Missense_Mutation SNP A A G TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr4:4317416A>G ENST00000337872.4 + 6 1551 c.1430A>G c.(1429-1431)aAa>aGa p.K477R ZBTB49_ENST00000355834.3_Intron|ZBTB49_ENST00000538529.1_5'UTR NM_145291.3 NP_660334.3 Q6ZSB9 ZBT49_HUMAN zinc finger and BTB domain containing 49 477 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1) 28 TCAGGAGAAAAACCACACTTG 0.398000 7 37 0 0 1 0 0 DMRT1 1761 broad.mit.edu 37 9 916850 916850 + Missense_Mutation SNP G G A rs141672484 TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr9:916850G>A ENST00000382276.3 + 4 1059 c.910G>A c.(910-912)Gtg>Atg p.V304M DMRT1_ENST00000569227.1_Missense_Mutation_p.V146M NM_021951.2 NP_068770.2 Q9Y5R6 DMRT1_HUMAN doublesex and mab-3 related transcription factor 1 304 cell differentiation|male gonad development|sex determination nucleus DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity large_intestine(2)|lung(10)|ovary(1) 13 all_lung(10;2.66e-10)|Lung NSC(10;2.82e-10)|Breast(48;0.232) Lung(218;0.037) GGGCCAGAGCGTGCCCCAGTT 0.542000 9 30 0 0 1 0 0 G2E3 55632 broad.mit.edu 37 14 31066655 31066655 + Silent SNP C C T TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr14:31066655C>T ENST00000206595.6 + 7 712 c.558C>T c.(556-558)ttC>ttT p.F186F G2E3_ENST00000553504.1_Silent_p.F216F|G2E3_ENST00000438909.2_Silent_p.F140F|G2E3_ENST00000544007.1_3'UTR NM_017769.3 NP_060239.2 Q7L622 G2E3_HUMAN G2/M-phase specific E3 ubiquitin protein ligase 186 apoptosis|multicellular organismal development|protein modification process Golgi apparatus|nucleolus acid-amino acid ligase activity|protein binding|zinc ion binding endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1) 23 GAGTGTTTTTCTTTAGGTGTA 0.313000 17 112 0 0 1 0 0 COBLL1 22837 broad.mit.edu 37 2 165551251 165551251 + Missense_Mutation SNP G G A TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr2:165551251G>A ENST00000375458.2 - 11 2872 c.2651C>T c.(2650-2652)gCt>gTt p.A884V COBLL1_ENST00000342193.4_Missense_Mutation_p.A922V|COBLL1_ENST00000392717.2_Missense_Mutation_p.A960V|COBLL1_ENST00000194871.6_Missense_Mutation_p.A989V|COBLL1_ENST00000409184.3_Missense_Mutation_p.A922V NM_001278460.1|NM_001278461.1 NP_001265389.1|NP_001265390.1 Q53SF7 COBL1_HUMAN cordon-bleu WH2 repeat protein-like 1 960 central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2) 47 ACTCTTGGCAGCTGCAGATGT 0.468000 3 40 0 0 1 0 0 GAREM 64762 broad.mit.edu 37 18 29867774 29867774 + Silent SNP G G A TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr18:29867774G>A ENST00000399218.4 - 4 841 c.786C>T c.(784-786)ctC>ctT p.L262L RP11-344B2.2_ENST00000579580.1_RNA|GAREM_ENST00000269209.6_Silent_p.L262L NM_001242409.1|NM_022751.2 NP_001229338.1|NP_073588.1 GRB2 associated, regulator of MAPK1 GGATGAAGTGGAGGTCGTATG 0.542000 5 52 0 0 1 0 0 RFPL4B 442247 broad.mit.edu 37 6 112671564 112671564 + Silent SNP C C A TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr6:112671564C>A ENST00000441065.2 + 3 966 c.654C>A c.(652-654)atC>atA p.I218I NM_001013734.2 NP_001013756.2 Q6ZWI9 RFPLB_HUMAN ret finger protein-like 4B 218 B30.2/SPRY. zinc ion binding breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|skin(1) 14 all_cancers(87;9.44e-05)|all_hematologic(75;0.000114)|all_epithelial(87;0.00265)|Colorectal(196;0.0209) all cancers(137;0.0202)|OV - Ovarian serous cystadenocarcinoma(136;0.0477)|Epithelial(106;0.0646)|GBM - Glioblastoma multiforme(226;0.0866)|BRCA - Breast invasive adenocarcinoma(108;0.244) TAGAAGAAATCCAGTTTTTTG 0.458000 7 46 3.09899e-07 3.61548e-07 1 1 0 SPAG17 200162 broad.mit.edu 37 1 118526457 118526457 + Missense_Mutation SNP T T C TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr1:118526457T>C ENST00000336338.5 - 42 5914 c.5849A>G c.(5848-5850)cAa>cGa p.Q1950R SPAG17_ENST00000492438.1_5'UTR NM_206996.2 NP_996879.1 Q6Q759 SPG17_HUMAN sperm associated antigen 17 1950 cilium|flagellar axoneme|microtubule NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1) 123 Esophageal squamous(2;0.0106) all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01) Lung(183;0.0858) AGATGTATCTTGAACAGCTGT 0.333000 3 30 0 0 1 0 0 LRRK2 120892 broad.mit.edu 37 12 40761496 40761496 + Missense_Mutation SNP C C A TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr12:40761496C>A ENST00000298910.7 + 51 7571 c.7513C>A c.(7513-7515)Caa>Aaa p.Q2505K NM_198578.3 NP_940980.3 Q5S007 LRRK2_HUMAN leucine-rich repeat kinase 2 2505 activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb external side of mitochondrial outer membrane ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2) 181 all_cancers(12;0.00108)|Breast(8;0.218) Lung NSC(34;0.0942)|all_lung(34;0.11) ACATGAAGTGCAAAATTTAGA 0.323000 7 66 0.00448238 0.00477471 1 1 0 LIPC 3990 broad.mit.edu 37 15 58830668 58830668 + Silent SNP C C T rs146362585 by1000genomes TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr15:58830668C>T ENST00000414170.3 + 3 512 c.225C>T c.(223-225)tgC>tgT p.C75C LIPC_ENST00000433326.2_Silent_p.C75C|LIPC_ENST00000356113.6_Silent_p.C75C|LIPC_ENST00000299022.5_Silent_p.C75C P11150 LIPC_HUMAN lipase, hepatic 75 cholesterol homeostasis|chylomicron remnant clearance|fatty acid biosynthetic process|high-density lipoprotein particle remodeling|intermediate-density lipoprotein particle remodeling|low-density lipoprotein particle remodeling|phosphatidylcholine catabolic process|triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle remodeling high-density lipoprotein particle apolipoprotein binding|heparin binding|low-density lipoprotein particle binding|phospholipase activity|triglyceride lipase activity p.C75C(1) breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 31 Colorectal(260;0.215) GBM - Glioblastoma multiforme(80;0.00213)|all cancers(107;0.00548) TACAGGAGTGCGGCTTCAACT 0.473000 4 139 0 0 1 0 0 AC079776.3 0 broad.mit.edu 37 2 130697404 130697404 + RNA DEL T T - TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr2:130697404delT ENST00000450840.1 + 0 346 ATACAAAATATTCCAGATAAA 0.358 2 4 --- --- --- --- LRIG1 26018 broad.mit.edu 37 3 66433531 66433531 + Frame_Shift_Del DEL T T - TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr3:66433531delT ENST00000383703.3 - 16 2900 c.2297delA c.(2296-2298)gtfs p.D766fs LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000273261.3_Frame_Shift_Del_p.D789fs|SLC25A26_ENST00000536651.1_Intron Q96JA1 LRIG1_HUMAN leucine-rich repeats and immunoglobulin-like domains 1 789 Ig-like C2-type 3. integral to membrane NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1) 42 Lung NSC(201;0.0101) BRCA - Breast invasive adenocarcinoma(55;0.00047) CGTGGTCCCATCCTTCCTGCA 0.597 36 99 --- --- --- --- OTOP1 133060 broad.mit.edu 37 4 4228274 4228282 + In_Frame_Del DEL CCACAGCAG CCACAGCAG - rs111245977 TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr4:4228274_4228282delCCACAGCAG ENST00000296358.4 - 1 334_342 c.310_318delCTGCTGTGG c.(310-318)del p.LLW104del NM_177998.1 NP_819056.1 Q7RTM1 OTOP1_HUMAN otopetrin 1 104 biomineral tissue development extracellular space|integral to membrane p.L104_W106delLLW(1) NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1) 34 UCEC - Uterine corpus endometrioid carcinoma (64;0.168) ACCACAGCATCCACAGCAGCTGCAGCAGC 0.727 6 7 --- --- --- --- TREML2 79865 broad.mit.edu 37 6 41166145 41166163 + Frame_Shift_Del DEL GTATACACTGTCAGCAGAG GTATACACTGTCAGCAGAG - rs77704965 byFrequency TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr6:41166145_41166163delGTATACACTGTCAGCAGAG ENST00000483722.1 - 2 245_263 c.60_78delCTCTGCTGACAGTGTATAC c.(58-78)ccfs p.PSADSVY20fs NM_024807.2 NP_079083.2 Q5T2D2 TRML2_HUMAN triggering receptor expressed on myeloid cells-like 2 20 Ig-like V-type. T cell activation cell surface|integral to membrane|plasma membrane protein binding|receptor activity breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1) 18 Ovarian(28;0.0418)|Colorectal(47;0.196) TCACTTTTGTGTATACACTGTCAGCAGAGGGGCCTGTGG 0.470 9 117 --- --- --- --- FAM66D 0 broad.mit.edu 37 8 11994579 11994580 + RNA DEL TG TG - TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr8:11994579_11994580delTG ENST00000434078.2 + 0 608 NR_027425.1 TGTTCgtgtttgtgtgtgtgtg 0.505 2 4 --- --- --- --- PTEN 5728 broad.mit.edu 37 10 89720803 89720804 + Frame_Shift_Del DEL TA TA - rs146650273 TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr10:89720803_89720804delTA ENST00000371953.3 + 8 2311_2312 c.954_955delTA c.(952-957)ctctfs p.LT320fs PTEN_ENST00000472832.1_3'UTR NM_000314.4 NP_000305.3 P60484 PTEN_HUMAN phosphatase and tensin homolog 320 C2 tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.0?(37)|p.L318fs*2(27)|p.T319fs*1(24)|p.T319fs*6(6)|p.R55fs*1(5)|p.V317fs*3(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.T319del(2)|p.V317fs*6(2)|p.T319_K332del(1)|p.G165_*404del(1)|p.L318fs*3(1)|p.L316fs*1(1)|p.T319fs*4(1)|p.W274_F341del(1)|p.V317_K322del(1)|p.T318fs*2(1) NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17) 2771 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) ATCTAGTACTTACTTTAACAAA 0.327 31 """D, Mis, N, F, S""" """glioma, prostate, endometrial""" """harmartoma, glioma, prostate, endometrial""" Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18) 14 91 --- --- --- --- CTCFL 140690 broad.mit.edu 37 20 56099187 56099187 + Frame_Shift_Del DEL T T - TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr20:56099187delT ENST00000426658.2 - 1 736 c.75delA c.(73-75)aafs p.K25fs CTCFL_ENST00000432255.2_Frame_Shift_Del_p.K25fs|CTCFL_ENST00000422869.2_Frame_Shift_Del_p.K25fs|CTCFL_ENST00000423479.2_Frame_Shift_Del_p.K25fs|CTCFL_ENST00000422109.2_Frame_Shift_Del_p.K25fs|CTCFL_ENST00000429804.2_Frame_Shift_Del_p.K25fs|CTCFL_ENST00000433949.2_Frame_Shift_Del_p.K25fs|CTCFL_ENST00000539382.1_Intron|CTCFL_ENST00000243914.3_Frame_Shift_Del_p.K25fs|CTCFL_ENST00000371196.2_Frame_Shift_Del_p.K25fs|CTCFL_ENST00000502686.2_Intron Q8NI51 CTCFL_HUMAN CCCTC-binding factor (zinc finger protein)-like 25 cell cycle|DNA methylation involved in gamete generation|histone methylation|positive regulation of transcription, DNA-dependent|regulation of gene expression by genetic imprinting|regulation of histone H3-K4 methylation|transcription, DNA-dependent cytoplasm|nucleus histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 58 Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242) BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07) CCTTCAGGCCTTTTTCCGGCA 0.502 10 321 --- --- --- --- MN1 4330 broad.mit.edu 37 22 28194933 28194934 + In_Frame_Ins INS - - TGC rs34890218 TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chr22:28194933_28194934insTGC ENST00000302326.4 - 1 2552_2553 c.1598_1599insGCA c.(1597-1599)cca>cGCAca p.533_533P>RT NM_002430.2 NP_002421.3 Q10571 MN1_HUMAN meningioma (disrupted in balanced translocation) 1 533 Poly-Gln. binding NS(1)|breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(1) 45 gctgctgctgttgctgctgctg 0.653 T ETV6 """AML, meningioma""" 5 5 --- --- --- --- DGKK 139189 broad.mit.edu 37 X 50165595 50165596 + RNA INS - - AC rs59226442 TCGA-4L-AA1F-01A-11D-A41K-08 TCGA-4L-AA1F-10A-01D-A41N-08 Untested Somatic Phase_I WXS none Illumina GAIIx c0222802-6dcc-4ec8-a7de-cb26d52f09ee e3a32f56-a8b5-40ca-a15b-7714da6f0ac7 g.chrX:50165595_50165596insAC ENST00000376025.2 - 0 816 Q5KSL6 DGKK_HUMAN diacylglycerol kinase, kappa activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|diacylglycerol metabolic process|intracellular signal transduction|platelet activation|response to oxidative stress cytoplasm|plasma membrane ATP binding|diacylglycerol kinase activity|metal ion binding central_nervous_system(1)|endometrium(12)|kidney(4)|large_intestine(5)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 45 Ovarian(276;0.236) TTAAAAGGTAAacacacacaca 0.411 3 5 --- --- --- ---