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	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_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
SAMD11	148398	broad.mit.edu	37	1	871255	871255	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:871255G>A	uc001abw.1	+	5	489	c.409G>A	c.(409-411)GAG>AAG	p.E137K	SAMD11_uc001abv.1_Missense_Mutation_p.E137K|SAMD11_uc001abx.1_Missense_Mutation_p.E16K	NM_152486	NP_689699	Q96NU1	SAM11_HUMAN	sterile alpha motif domain containing 11	137						nucleus					0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.74e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000472)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		AGGCAGCCTGGAGATTGGCCT	0.677													32	33	---	---	---	---	PASS
TNFRSF4	7293	broad.mit.edu	37	1	1148065	1148065	+	Silent	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1148065T>C	uc001ade.2	-	4	395	c.390A>G	c.(388-390)CCA>CCG	p.P130P	TNFRSF4_uc001adf.2_Silent_p.P134P	NM_003327	NP_003318	P43489	TNR4_HUMAN	tumor necrosis factor receptor superfamily,	130	TNFR-Cys 4.|Extracellular (Potential).				immune response|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|positive regulation of B cell proliferation|positive regulation of immunoglobulin secretion|T cell proliferation	integral to plasma membrane	tumor necrosis factor receptor activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		AGAAGTGCCCTGGAGGGCAGG	0.557													8	9	---	---	---	---	PASS
TNFRSF9	3604	broad.mit.edu	37	1	7993258	7993258	+	Missense_Mutation	SNP	G	A	A	rs143524950		TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7993258G>A	uc001aot.2	-	7	771	c.643C>T	c.(643-645)CGG>TGG	p.R215W		NM_001561	NP_001552	Q07011	TNR9_HUMAN	tumor necrosis factor receptor superfamily,	215	Cytoplasmic (Potential).|Interaction with LRR-1.				induction of apoptosis|negative regulation of cell proliferation	integral to plasma membrane	binding|receptor activity			large_intestine(1)|lung(1)|ovary(1)|skin(1)	4	Ovarian(185;0.0634)|all_lung(157;0.151)	all_epithelial(116;9.63e-21)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.000625)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.93e-71)|GBM - Glioblastoma multiforme(8;3.72e-37)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;7.71e-06)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000419)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00103)|READ - Rectum adenocarcinoma(331;0.0649)		TTTCTGCCCCGTTTAACAACA	0.428													34	43	---	---	---	---	PASS
RERE	473	broad.mit.edu	37	1	8601355	8601355	+	Missense_Mutation	SNP	A	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8601355A>C	uc001ape.2	-	8	1558	c.748T>G	c.(748-750)TTT>GTT	p.F250V	RERE_uc001apf.2_Missense_Mutation_p.F250V|RERE_uc001aph.1_Missense_Mutation_p.F250V	NM_012102	NP_036234	Q9P2R6	RERE_HUMAN	atrophin-1 like protein isoform a	250	BAH.				multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		ATGTCAGAAAAATGGGAGATG	0.398													60	64	---	---	---	---	PASS
CAPZB	832	broad.mit.edu	37	1	19670914	19670914	+	Silent	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19670914T>C	uc010ocz.1	-	8	1184	c.756A>G	c.(754-756)AAA>AAG	p.K252K	CAPZB_uc001bce.2_Silent_p.K223K|CAPZB_uc009vpk.2_Intron|CAPZB_uc001bcd.2_Silent_p.K211K	NM_004930	NP_004921	P47756	CAPZB_HUMAN	F-actin capping protein beta subunit	223					actin cytoskeleton organization|actin filament capping|blood coagulation|cellular component movement	cytosol|F-actin capping protein complex|WASH complex	actin binding				0		Colorectal(325;3.93e-05)|Renal(390;0.000147)|all_lung(284;0.000169)|Lung NSC(340;0.000202)|Breast(348;0.000496)|Ovarian(437;0.00428)|Myeloproliferative disorder(586;0.0262)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Kidney(64;8.63e-06)|BRCA - Breast invasive adenocarcinoma(304;4.06e-05)|KIRC - Kidney renal clear cell carcinoma(64;0.000175)|GBM - Glioblastoma multiforme(114;0.000525)|STAD - Stomach adenocarcinoma(196;0.00779)|READ - Rectum adenocarcinoma(331;0.103)|Lung(427;0.173)		TACTTCTGATTTTATTTTCCA	0.438											OREG0013171	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	31	112	---	---	---	---	PASS
BMP8B	656	broad.mit.edu	37	1	40228856	40228856	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40228856G>A	uc001cdz.1	-	6	1343	c.967C>T	c.(967-969)CAA>TAA	p.Q323*	PPIE_uc001cdv.2_Intron|PPIE_uc001cdw.2_Intron	NM_001720	NP_001711	P34820	BMP8B_HUMAN	bone morphogenetic protein 8B preproprotein	323					cartilage development|cell differentiation|growth|ossification	extracellular space	cytokine activity|growth factor activity				0	all_cancers(7;5.56e-14)|all_lung(5;3.88e-17)|all_epithelial(6;3.78e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;1.92e-17)|all cancers(16;4.03e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			GAGTAGCCTTGGGGAGCGATG	0.622													39	142	---	---	---	---	PASS
BCL10	8915	broad.mit.edu	37	1	85741980	85741980	+	Missense_Mutation	SNP	T	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85741980T>A	uc001dkz.2	-	2	761	c.56A>T	c.(55-57)GAC>GTC	p.D19V	uc001dla.1_5'Flank	NM_003921	NP_003912	O95999	BCL10_HUMAN	B-cell CLL/lymphoma 10	19	CARD.				apoptosis|cellular response to mechanical stimulus|innate immune response|interleukin-6 biosynthetic process|lymphotoxin A biosynthetic process|negative regulation of mature B cell apoptosis|neural tube closure|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 biosynthetic process|positive regulation of mast cell cytokine production|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of protein ubiquitination|positive regulation of transcription, DNA-dependent|protein homooligomerization|response to molecule of bacterial origin|T cell receptor signaling pathway	CBM complex|cytosol|lysosome|membrane raft|nucleus|perinuclear region of cytoplasm	NF-kappaB binding|protease binding|protein C-terminus binding|protein kinase B binding|protein self-association|transcription coactivator activity|ubiquitin binding|ubiquitin protein ligase binding			lung(2)	2				all cancers(265;0.0114)|Epithelial(280;0.0311)		GTTACTCACGTCCTTCTTCAC	0.682			T	IGH@	MALT 								28	99	---	---	---	---	PASS
DPYD	1806	broad.mit.edu	37	1	97544505	97544505	+	3'UTR	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97544505T>C	uc001drv.2	-	23						NM_000110	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase isoform 1						'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)	GACATGAAAGTTCACAGCAAC	0.348													34	114	---	---	---	---	PASS
CD2	914	broad.mit.edu	37	1	117311413	117311413	+	3'UTR	SNP	A	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117311413A>G	uc001egu.3	+	5						NM_001767	NP_001758	P06729	CD2_HUMAN	CD2 molecule precursor						blood coagulation|cell surface receptor linked signaling pathway|cell-cell adhesion|induction of apoptosis|leukocyte migration|membrane raft polarization|natural killer cell activation|positive regulation of myeloid dendritic cell activation|regulation of T cell differentiation|T cell activation	integral to plasma membrane	receptor activity			breast(1)	1	Lung SC(450;0.225)	all_cancers(81;3.15e-06)|Acute lymphoblastic leukemia(138;1.7e-08)|all_epithelial(167;8.38e-07)|all_lung(203;3.37e-06)|Lung NSC(69;2.31e-05)		Epithelial(280;6.71e-26)|OV - Ovarian serous cystadenocarcinoma(397;4.74e-24)|all cancers(265;1.93e-22)|Lung(183;0.0543)|Kidney(133;0.0813)|Colorectal(144;0.174)|KIRC - Kidney renal clear cell carcinoma(1967;0.176)|LUSC - Lung squamous cell carcinoma(189;0.189)|BRCA - Breast invasive adenocarcinoma(282;0.201)	Alefacept(DB00092)	TAAAAAAGATAGAAACTGTCT	0.473													34	146	---	---	---	---	PASS
NES	10763	broad.mit.edu	37	1	156639511	156639511	+	Missense_Mutation	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156639511T>C	uc001fpq.2	-	4	4602	c.4469A>G	c.(4468-4470)CAG>CGG	p.Q1490R		NM_006617	NP_006608	P48681	NEST_HUMAN	nestin	1490	Tail.				brain development|embryonic camera-type eye development|G2/M transition of mitotic cell cycle|negative regulation of apoptosis|positive regulation of intermediate filament depolymerization|positive regulation of neural precursor cell proliferation|stem cell proliferation	cytoplasm|intermediate filament	intermediate filament binding|structural molecule activity			ovary(6)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					AGCACTGTCCTGGGACTCCGT	0.587													20	81	---	---	---	---	PASS
SELP	6403	broad.mit.edu	37	1	169578782	169578782	+	Silent	SNP	A	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169578782A>G	uc001ggi.3	-	8	1358	c.1293T>C	c.(1291-1293)GAT>GAC	p.D431D	SELP_uc001ggh.2_Silent_p.D266D|SELP_uc009wvr.2_Silent_p.D431D	NM_003005	NP_002996	P16109	LYAM3_HUMAN	selectin P precursor	431	Sushi 4.|Extracellular (Potential).				platelet activation|platelet degranulation|positive regulation of platelet activation	external side of plasma membrane|extracellular space|integral to plasma membrane|membrane fraction|platelet alpha granule membrane|platelet dense granule membrane|soluble fraction	fucose binding|glycosphingolipid binding|heparin binding|lipopolysaccharide binding|oligosaccharide binding|sialic acid binding			ovary(2)|skin(2)	4	all_hematologic(923;0.208)				Clopidogrel(DB00758)|Heparin(DB01109)|Tirofiban(DB00775)	GTCCCAAGTTATCACACCGAA	0.488													42	32	---	---	---	---	PASS
DNM3	26052	broad.mit.edu	37	1	172007570	172007570	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172007570G>A	uc001gie.2	+	7	1137	c.961G>A	c.(961-963)GAC>AAC	p.D321N	DNM3_uc001gid.3_Missense_Mutation_p.D321N|DNM3_uc009wwb.2_Missense_Mutation_p.D321N|DNM3_uc001gif.2_Missense_Mutation_p.D321N	NM_015569	NP_056384	Q9UQ16	DYN3_HUMAN	dynamin 3 isoform a	321					endocytosis|filopodium assembly|synapse assembly	dendritic spine|microtubule|perinuclear region of cytoplasm|postsynaptic density	GTP binding|GTPase activity|protein binding			breast(1)	1						CAAACCAGAAGACCCAACAAG	0.418													90	78	---	---	---	---	PASS
XPR1	9213	broad.mit.edu	37	1	180843064	180843064	+	Silent	SNP	A	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180843064A>G	uc001goi.2	+	13	1986	c.1794A>G	c.(1792-1794)CCA>CCG	p.P598P	XPR1_uc009wxn.2_Silent_p.P533P	NM_004736	NP_004727	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor	598	EXS.|Cytoplasmic (Potential).					integral to plasma membrane	G-protein coupled receptor activity				0						TCTTTGCCCCACTTGAGGTTT	0.363													40	37	---	---	---	---	PASS
FAM179A	165186	broad.mit.edu	37	2	29258360	29258360	+	Silent	SNP	G	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29258360G>T	uc010ezl.2	+	17	2607	c.2256G>T	c.(2254-2256)GGG>GGT	p.G752G	FAM179A_uc010ymm.1_Silent_p.G697G|FAM179A_uc002rmr.3_Silent_p.G279G|FAM179A_uc002rms.1_Silent_p.G50G	NM_199280	NP_954974	Q6ZUX3	F179A_HUMAN	hypothetical protein LOC165186	752							binding			ovary(3)|skin(1)	4						GGCTGGTGGGGCTGCGCTCCA	0.667													6	9	---	---	---	---	PASS
PNPT1	87178	broad.mit.edu	37	2	55895071	55895071	+	Silent	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55895071T>C	uc002rzf.2	-	12	1052	c.999A>G	c.(997-999)CCA>CCG	p.P333P	PNPT1_uc002rzg.2_RNA	NM_033109	NP_149100	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	333					mRNA catabolic process|RNA processing	plasma membrane	3'-5'-exoribonuclease activity|polyribonucleotide nucleotidyltransferase activity|RNA binding				0			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			TTATTTCATATGGATCGGCTT	0.274													22	61	---	---	---	---	PASS
DYSF	8291	broad.mit.edu	37	2	71795448	71795448	+	Missense_Mutation	SNP	G	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71795448G>T	uc002sie.2	+	26	3166	c.2790G>T	c.(2788-2790)TGG>TGT	p.W930C	DYSF_uc010feg.2_Missense_Mutation_p.W961C|DYSF_uc010feh.2_Missense_Mutation_p.W916C|DYSF_uc002sig.3_Missense_Mutation_p.W916C|DYSF_uc010yqx.1_RNA|DYSF_uc010fee.2_Missense_Mutation_p.W930C|DYSF_uc010fef.2_Missense_Mutation_p.W947C|DYSF_uc010fei.2_Missense_Mutation_p.W947C|DYSF_uc010fek.2_Missense_Mutation_p.W948C|DYSF_uc010fej.2_Missense_Mutation_p.W917C|DYSF_uc010fel.2_Missense_Mutation_p.W917C|DYSF_uc010feo.2_Missense_Mutation_p.W962C|DYSF_uc010fem.2_Missense_Mutation_p.W931C|DYSF_uc010fen.2_Missense_Mutation_p.W948C|DYSF_uc002sif.2_Missense_Mutation_p.W931C	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8	930	Cytoplasmic (Potential).		W -> C (in LGMD2B; uncetain pathogenicity).			cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7						CTGGAGATTGGTTCGTGTGTC	0.647													222	460	---	---	---	---	PASS
REG1B	5968	broad.mit.edu	37	2	79313656	79313656	+	Intron	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79313656C>T	uc002sny.2	-						REG1B_uc010ffv.1_Intron|REG1B_uc010ffw.2_3'UTR	NM_006507	NP_006498	P48304	REG1B_HUMAN	regenerating islet-derived 1 beta precursor						cell proliferation	extracellular region	sugar binding			central_nervous_system(1)|skin(1)	2						ATGGAGCACTCAGTGGAGAAG	0.507													51	125	---	---	---	---	PASS
SLC5A7	60482	broad.mit.edu	37	2	108604766	108604766	+	Missense_Mutation	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108604766T>C	uc002tdv.2	+	2	431	c.155T>C	c.(154-156)TTG>TCG	p.L52S	SLC5A7_uc010ywm.1_5'UTR|SLC5A7_uc010fjj.2_Missense_Mutation_p.L52S|SLC5A7_uc010ywn.1_Intron	NM_021815	NP_068587	Q9GZV3	SC5A7_HUMAN	solute carrier family 5 (choline transporter),	52	Helical; (Potential).				acetylcholine biosynthetic process|neurotransmitter secretion	integral to membrane|plasma membrane	choline:sodium symporter activity			ovary(2)|central_nervous_system(1)|skin(1)	4					Choline(DB00122)	ATTGGTTTATTGGTTGGTGGA	0.542													30	76	---	---	---	---	PASS
PKP4	8502	broad.mit.edu	37	2	159519804	159519804	+	Silent	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159519804C>T	uc002tzv.2	+	15	2684	c.2424C>T	c.(2422-2424)ATC>ATT	p.I808I	PKP4_uc002tzu.2_Silent_p.I808I|PKP4_uc002tzw.2_Silent_p.I808I|PKP4_uc002tzx.2_Silent_p.I465I|PKP4_uc002uaa.2_Silent_p.I660I|uc002uab.1_Intron|PKP4_uc002uac.2_5'UTR	NM_003628	NP_003619	Q99569	PKP4_HUMAN	plakophilin 4 isoform a	808					cell adhesion	desmosome	protein binding			ovary(5)|skin(2)	7						TTGGTCCTATCCCAGGACTGT	0.483										HNSCC(62;0.18)			21	54	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	168104737	168104737	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168104737G>A	uc002udx.2	+	8	6853	c.6835G>A	c.(6835-6837)GAG>AAG	p.E2279K	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.E2104K|XIRP2_uc010fpq.2_Missense_Mutation_p.E2057K|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_Intron	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	2104					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						CTTTAACCCTGAGAATAATGT	0.413													36	88	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179616127	179616127	+	Missense_Mutation	SNP	T	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179616127T>G	uc002unb.2	-	46	11224	c.11000A>C	c.(10999-11001)AAA>ACA	p.K3667T	TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron	NM_133379	NP_596870	Q8WZ42	TITIN_HUMAN	titin isoform novex-3	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTAATCTGTTTTCTTGGCAGA	0.363													50	106	---	---	---	---	PASS
SUMF1	285362	broad.mit.edu	37	3	4508955	4508955	+	Splice_Site	SNP	G	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4508955G>C	uc003bpz.1	-	1	1	c.-24_splice	c.e1-1		SUMF1_uc003bps.1_Splice_Site|SUMF1_uc011ass.1_Splice_Site|SUMF1_uc010hby.1_Splice_Site|SUMF1_uc011ast.1_Splice_Site	NM_182760	NP_877437	Q8NBK3	SUMF1_HUMAN	sulfatase modifying factor 1 isoform 1							endoplasmic reticulum lumen	metal ion binding|oxidoreductase activity			upper_aerodigestive_tract(1)	1		Melanoma(143;0.068)|Colorectal(144;0.233)		Epithelial(13;0.0147)|OV - Ovarian serous cystadenocarcinoma(96;0.0444)|all cancers(10;0.0549)		ATGTGACCCGGTTGGTCACGT	0.577													5	16	---	---	---	---	PASS
BAP1	8314	broad.mit.edu	37	3	52440379	52440379	+	Missense_Mutation	SNP	C	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52440379C>G	uc003ddx.2	-	9	788	c.673G>C	c.(673-675)GAC>CAC	p.D225H	BAP1_uc003ddw.2_5'Flank|BAP1_uc010hmg.2_5'Flank|BAP1_uc010hmh.2_5'Flank	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	225					monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		AAGCGGATGTCGTGGTAGGGC	0.632			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								25	21	---	---	---	---	PASS
COL6A6	131873	broad.mit.edu	37	3	130292969	130292969	+	Missense_Mutation	SNP	C	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130292969C>A	uc010htl.2	+	7	3178	c.3147C>A	c.(3145-3147)CAC>CAA	p.H1049Q		NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	1049	Nonhelical region.|VWFA 6.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8						ATACCTATCACCCGGAGTTTC	0.433													24	56	---	---	---	---	PASS
DNAJC13	23317	broad.mit.edu	37	3	132247081	132247081	+	Missense_Mutation	SNP	A	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132247081A>G	uc003eor.2	+	54	6495	c.6430A>G	c.(6430-6432)ATT>GTT	p.I2144V		NM_015268	NP_056083	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	2144							heat shock protein binding			ovary(1)|breast(1)	2						ACTCGAAGGCATTGGCCTTGA	0.418													33	78	---	---	---	---	PASS
SLC33A1	9197	broad.mit.edu	37	3	155547717	155547717	+	Intron	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155547717T>C	uc003fan.3	-						SLC33A1_uc003fao.1_Intron|SLC33A1_uc003fap.1_RNA	NM_004733	NP_004724	O00400	ACATN_HUMAN	acetyl-coenzyme A transporter						cell death|transmembrane transport	endoplasmic reticulum membrane|Golgi membrane|integral to plasma membrane|membrane fraction	acetyl-CoA transporter activity			ovary(2)|large_intestine(1)|pancreas(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			AAAACATCTTTAGTATGATTA	0.289													13	30	---	---	---	---	PASS
PGM2	55276	broad.mit.edu	37	4	37850207	37850207	+	Silent	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37850207G>A	uc011byb.1	+	11	1420	c.1347G>A	c.(1345-1347)GAG>GAA	p.E449E	PGM2_uc011byc.1_Silent_p.E289E	NM_018290	NP_060760	Q96G03	PGM2_HUMAN	phosphoglucomutase 2	449					glucose 1-phosphate metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol	magnesium ion binding|phosphoglucomutase activity|phosphopentomutase activity			ovary(1)	1						TAAGTGCAGAGTTGGCTAGCT	0.408													58	85	---	---	---	---	PASS
UGT2B7	7364	broad.mit.edu	37	4	69962362	69962362	+	Missense_Mutation	SNP	A	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69962362A>G	uc003heg.3	+	1	170	c.124A>G	c.(124-126)ATC>GTC	p.I42V	UGT2B7_uc010ihq.2_Missense_Mutation_p.I42V	NM_001074	NP_001065	P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2B7 precursor	42					lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			ovary(1)|skin(1)	2						TATAAAGACAATCCTGGATGA	0.418													64	141	---	---	---	---	PASS
HNRPDL	9987	broad.mit.edu	37	4	83347685	83347685	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83347685C>T	uc003hmr.2	-	6	1658	c.1123G>A	c.(1123-1125)GGC>AGC	p.G375S	HNRPDL_uc003hmq.2_RNA|HNRPDL_uc003hms.2_RNA|HNRPDL_uc003hmt.2_Intron	NM_031372	NP_112740	O14979	HNRDL_HUMAN	heterogeneous nuclear ribonucleoprotein D-like	375	Tyr-rich.|Necessary for interaction with TNPO1.|Gly-rich.				regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	cytoplasm|heterogeneous nuclear ribonucleoprotein complex	double-stranded DNA binding|nucleotide binding|poly(A) RNA binding|protein binding|single-stranded DNA binding			skin(1)	1		Hepatocellular(203;0.114)				TCATATCCGCCATAGCCACTA	0.353													26	75	---	---	---	---	PASS
MYOZ2	51778	broad.mit.edu	37	4	120107259	120107259	+	Silent	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120107259T>C	uc003icp.3	+	6	912	c.699T>C	c.(697-699)AAT>AAC	p.N233N		NM_016599	NP_057683	Q9NPC6	MYOZ2_HUMAN	myozenin 2	233							protein phosphatase 2B binding				0						GGTCCTTTAATAGGACTCCTA	0.393													22	72	---	---	---	---	PASS
MYOZ2	51778	broad.mit.edu	37	4	120107338	120107338	+	Missense_Mutation	SNP	G	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120107338G>C	uc003icp.3	+	6	991	c.778G>C	c.(778-780)GAA>CAA	p.E260Q		NM_016599	NP_057683	Q9NPC6	MYOZ2_HUMAN	myozenin 2	260							protein phosphatase 2B binding				0						CACTGTACCAGAATCAGAAGA	0.383													14	48	---	---	---	---	PASS
WWC2	80014	broad.mit.edu	37	4	184114848	184114848	+	Missense_Mutation	SNP	C	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184114848C>G	uc010irx.2	+	2	410	c.228C>G	c.(226-228)ATC>ATG	p.I76M	WWC2_uc003ivk.3_Translation_Start_Site	NM_024949	NP_079225	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	76	WW 2.									ovary(2)|lung(1)	3		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		TCTACTACATCGATCACATCA	0.423													16	38	---	---	---	---	PASS
C5orf42	65250	broad.mit.edu	37	5	37183002	37183002	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37183002C>T	uc011cpa.1	-	26	5512	c.5281G>A	c.(5281-5283)GAT>AAT	p.D1761N	C5orf42_uc011coy.1_Missense_Mutation_p.D262N|C5orf42_uc003jks.2_RNA|C5orf42_uc011coz.1_Missense_Mutation_p.D836N|C5orf42_uc011cpb.1_Missense_Mutation_p.D642N	NM_023073	NP_075561	E9PH94	E9PH94_HUMAN	hypothetical protein LOC65250	1761										ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			ATACCAGAATCACAGAGTAGC	0.413													44	74	---	---	---	---	PASS
NUP155	9631	broad.mit.edu	37	5	37293028	37293028	+	Silent	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37293028T>C	uc003jku.1	-	34	4108	c.3990A>G	c.(3988-3990)TTA>TTG	p.L1330L	NUP155_uc003jkt.1_Silent_p.L1271L|NUP155_uc010iuz.1_Silent_p.L1266L	NM_153485	NP_705618	O75694	NU155_HUMAN	nucleoporin 155kDa isoform 1	1330					carbohydrate metabolic process|glucose transport|mRNA transport|nucleocytoplasmic transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore	protein binding|structural constituent of nuclear pore|transporter activity			ovary(1)	1	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ATCTTATCAATAATACATGTA	0.313													69	137	---	---	---	---	PASS
FAM169A	26049	broad.mit.edu	37	5	74077398	74077398	+	Missense_Mutation	SNP	C	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74077398C>A	uc003kdm.2	-	13	1943	c.1900G>T	c.(1900-1902)GAT>TAT	p.D634Y	FAM169A_uc010izm.2_Missense_Mutation_p.D574Y|FAM169A_uc003kdl.2_Missense_Mutation_p.D452Y	NM_015566	NP_056381	Q9Y6X4	F169A_HUMAN	hypothetical protein LOC26049	634											0						GAGCTGCTATCCACAGCTTTT	0.458													59	204	---	---	---	---	PASS
CXCL14	9547	broad.mit.edu	37	5	134907360	134907360	+	3'UTR	SNP	A	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134907360A>G	uc003lay.2	-	4						NM_004887	NP_004878	O95715	CXL14_HUMAN	small inducible cytokine B14 precursor						cell-cell signaling|chemotaxis|immune response|signal transduction	extracellular space|Golgi apparatus	chemokine activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ATAAAATGTAAAAACTGACCG	0.348													4	9	---	---	---	---	PASS
TMCO6	55374	broad.mit.edu	37	5	140024591	140024591	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140024591C>T	uc003lgl.2	+	12	1491	c.1390C>T	c.(1390-1392)CAG>TAG	p.Q464*	TMCO6_uc003lgm.2_Nonsense_Mutation_p.Q470*|TMCO6_uc010jft.2_Nonsense_Mutation_p.Q224*|TMCO6_uc003lgn.2_Nonsense_Mutation_p.Q355*|TMCO6_uc003lgo.2_Nonsense_Mutation_p.Q224*|IK_uc011czk.1_5'Flank|IK_uc003lgq.2_5'Flank	NM_018502	NP_060972	Q96DC7	TMCO6_HUMAN	transmembrane and coiled-coil domains 6	464					protein import into nucleus	cytoplasm|nuclear pore	binding|protein transporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTCCTGCAGCAGTCAGGGCT	0.542													97	144	---	---	---	---	PASS
PCDHAC1	56135	broad.mit.edu	37	5	140308488	140308488	+	Missense_Mutation	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140308488T>C	uc003lih.2	+	1	2187	c.2011T>C	c.(2011-2013)TGG>CGG	p.W671R	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Intron|PCDHA13_uc003lif.2_Intron|PCDHAC1_uc003lig.1_Missense_Mutation_p.W671R	NM_018898	NP_061721	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1 isoform 1	671	Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			skin(3)|ovary(2)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGAAGATGTCTGGGAACCAGG	0.483													58	241	---	---	---	---	PASS
CSF1R	1436	broad.mit.edu	37	5	149460456	149460456	+	Missense_Mutation	SNP	A	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149460456A>G	uc003lrl.2	-	2	376	c.181T>C	c.(181-183)TAC>CAC	p.Y61H	CSF1R_uc011dcd.1_5'UTR|CSF1R_uc010jhc.2_RNA|CSF1R_uc003lrm.2_Missense_Mutation_p.Y61H|CSF1R_uc011dce.1_Missense_Mutation_p.Y61H|CSF1R_uc011dcf.1_Missense_Mutation_p.Y61H	NM_005211	NP_005202	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor precursor	61	Ig-like C2-type 1.|Extracellular (Potential).				cell proliferation|multicellular organismal development|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane|receptor complex	ATP binding|cytokine binding|macrophage colony-stimulating factor receptor activity|protein homodimerization activity	p.Y61Y(2)		haematopoietic_and_lymphoid_tissue(38)|lung(6)|central_nervous_system(3)|liver(3)|breast(2)|endometrium(1)|ovary(1)	54			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	CCATCAGAGTACAGGGTCCAG	0.612													15	51	---	---	---	---	PASS
SLC36A1	206358	broad.mit.edu	37	5	150844717	150844717	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150844717G>A	uc003luc.2	+	5	623	c.406G>A	c.(406-408)GCA>ACA	p.A136T	GM2A_uc011dcs.1_Intron|SLC36A1_uc003lub.1_Missense_Mutation_p.A136T|SLC36A1_uc010jhw.1_Missense_Mutation_p.A136T	NM_078483	NP_510968	Q7Z2H8	S36A1_HUMAN	solute carrier family 36 member 1	136	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process|ion transport	endoplasmic reticulum|integral to membrane|lysosomal membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			skin(1)	1		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)|all_neural(839;0.138)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Glycine(DB00145)|L-Alanine(DB00160)	CCGGAACCACGCACACTGGGG	0.493													31	84	---	---	---	---	PASS
NSD1	64324	broad.mit.edu	37	5	176562709	176562709	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176562709G>A	uc003mfr.3	+	2	743	c.605G>A	c.(604-606)GGT>GAT	p.G202D	NSD1_uc003mft.3_Intron|NSD1_uc003mfs.1_Missense_Mutation_p.G202D|NSD1_uc011dfx.1_Intron|NSD1_uc003mfp.2_Missense_Mutation_p.G202D|NSD1_uc003mfq.2_Missense_Mutation_p.G202D	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	202					negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		TCAGAGAATGGTGTAAAAGTG	0.468			T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			58	100	---	---	---	---	PASS
OR2V2	285659	broad.mit.edu	37	5	180581946	180581946	+	Missense_Mutation	SNP	G	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180581946G>C	uc011dhj.1	+	1	4	c.4G>C	c.(4-6)GAG>CAG	p.E2Q		NM_206880	NP_996763	Q96R30	OR2V2_HUMAN	olfactory receptor, family 2, subfamily V,	2	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)	2	all_cancers(89;8.26e-06)|all_epithelial(37;1.02e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.0103)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.0652)|all_lung(500;0.149)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCGAGCCATGGAGACGTGGGT	0.493													72	109	---	---	---	---	PASS
ZBTB22	9278	broad.mit.edu	37	6	33284382	33284382	+	Silent	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33284382G>A	uc003oeb.2	-	2	464	c.312C>T	c.(310-312)GCC>GCT	p.A104A	TAPBP_uc003odx.1_5'Flank|TAPBP_uc010jus.1_5'Flank|TAPBP_uc003ody.2_5'Flank|TAPBP_uc003odz.2_5'Flank|TAPBP_uc010jut.1_5'Flank|TAPBP_uc011drc.1_5'Flank|ZBTB22_uc010juu.2_Silent_p.A104A	NM_005453	NP_005444	O15209	ZBT22_HUMAN	zinc finger and BTB domain containing 22	104	BTB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						CAGTCTCAAAGGCGCCTGGGT	0.577													52	210	---	---	---	---	PASS
SLC17A5	26503	broad.mit.edu	37	6	74331540	74331540	+	Missense_Mutation	SNP	A	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74331540A>G	uc003phn.3	-	7	1093	c.965T>C	c.(964-966)TTC>TCC	p.F322S	SLC17A5_uc010kax.2_Intron|SLC17A5_uc010kay.2_RNA|SLC17A5_uc011dyo.1_Missense_Mutation_p.F191S	NM_012434	NP_036566	Q9NRA2	S17A5_HUMAN	sialin	322					anion transport	integral to plasma membrane|lysosomal membrane|membrane fraction	sialic acid:hydrogen symporter activity			skin(5)|central_nervous_system(1)	6						TTGAACATTGAACCTTAGGAT	0.313													12	36	---	---	---	---	PASS
SIM1	6492	broad.mit.edu	37	6	100868687	100868687	+	Silent	SNP	G	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100868687G>T	uc003pqj.3	-	9	1353	c.1146C>A	c.(1144-1146)TCC>TCA	p.S382S	SIM1_uc010kcu.2_Silent_p.S382S	NM_005068	NP_005059	P81133	SIM1_HUMAN	single-minded homolog 1	382	Single-minded C-terminal.|Nuclear localization signal (By similarity).				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(4)	4		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		GGGAAGTCCTGGATTTTGACT	0.468													47	84	---	---	---	---	PASS
SIM1	6492	broad.mit.edu	37	6	100868688	100868688	+	Missense_Mutation	SNP	G	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100868688G>C	uc003pqj.3	-	9	1352	c.1145C>G	c.(1144-1146)TCC>TGC	p.S382C	SIM1_uc010kcu.2_Missense_Mutation_p.S382C	NM_005068	NP_005059	P81133	SIM1_HUMAN	single-minded homolog 1	382	Single-minded C-terminal.|Nuclear localization signal (By similarity).				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(4)	4		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		GGAAGTCCTGGATTTTGACTT	0.473													47	82	---	---	---	---	PASS
C6orf58	352999	broad.mit.edu	37	6	127912784	127912784	+	3'UTR	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127912784C>T	uc003qbh.2	+	6						NM_001010905	NP_001010905	Q6P5S2	CF058_HUMAN	hypothetical protein LOC352999 precursor							extracellular region					0				GBM - Glioblastoma multiforme(226;0.0405)|all cancers(137;0.156)		TAACTTCAAACTTCAGGAAAT	0.279													19	43	---	---	---	---	PASS
RAET1G	353091	broad.mit.edu	37	6	150240778	150240778	+	Missense_Mutation	SNP	C	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150240778C>A	uc010kii.1	-	2	328	c.260G>T	c.(259-261)TGG>TTG	p.W87L	RAET1G_uc003qnm.2_RNA	NM_001001788	NP_001001788	Q6H3X3	RET1G_HUMAN	retinoic acid early transcript 1G precursor	87	MHC class I alpha-1 like.|Extracellular (Potential).				antigen processing and presentation|immune response	integral to membrane|MHC class I protein complex	protein binding				0		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.73e-12)		CTGTGCTTTCCAGGCCGTTGT	0.488													125	181	---	---	---	---	PASS
FAM126A	84668	broad.mit.edu	37	7	22985595	22985595	+	Silent	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22985595T>C	uc003svm.3	-	11	1434	c.1179A>G	c.(1177-1179)GAA>GAG	p.E393E	FAM126A_uc003svn.3_3'UTR	NM_032581	NP_115970	Q9BYI3	HYCCI_HUMAN	family with sequence similarity 126, member A	393						cytoplasm|membrane	signal transducer activity			central_nervous_system(1)	1						TAGTTTCTTTTTCTTTTCCTC	0.418													113	195	---	---	---	---	PASS
GLI3	2737	broad.mit.edu	37	7	42004980	42004980	+	Missense_Mutation	SNP	G	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42004980G>T	uc011kbh.1	-	15	3782	c.3691C>A	c.(3691-3693)CTC>ATC	p.L1231I	GLI3_uc011kbg.1_Missense_Mutation_p.L1172I	NM_000168	NP_000159	P10071	GLI3_HUMAN	GLI-Kruppel family member GLI3	1231					negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1)	19						CTGTTGTGGAGCATCAAGTGC	0.632									Greig_Cephalopolysyndactyly|Pallister-Hall_syndrome				41	94	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	142131871	142131871	+	Intron	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142131871G>A	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron|uc010lnz.1_Missense_Mutation_p.P3S					SubName: Full=V_segment translation product; Flags: Fragment;																		AGGAGCCCGGGGCCCATGGCA	0.607													48	70	---	---	---	---	PASS
MYST3	7994	broad.mit.edu	37	8	41794882	41794882	+	Missense_Mutation	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41794882T>C	uc010lxb.2	-	17	3788	c.3244A>G	c.(3244-3246)AGA>GGA	p.R1082G	MYST3_uc010lxc.2_Missense_Mutation_p.R1082G|MYST3_uc003xon.3_Missense_Mutation_p.R1082G	NM_001099412	NP_001092882	Q92794	MYST3_HUMAN	MYST histone acetyltransferase (monocytic	1082					histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7	all_epithelial(6;1.12e-27)|all_lung(13;3.94e-12)|Lung NSC(13;6.54e-11)|Ovarian(28;0.00744)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000294)|Lung NSC(58;0.00105)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	Epithelial(1;2.82e-19)|all cancers(1;1.15e-16)|BRCA - Breast invasive adenocarcinoma(8;9.17e-11)|OV - Ovarian serous cystadenocarcinoma(14;9.4e-05)|Colorectal(10;0.000728)|Lung(22;0.00153)|LUSC - Lung squamous cell carcinoma(45;0.00741)|COAD - Colon adenocarcinoma(11;0.0171)			AAGTATTCTCTAGGGAAAAGT	0.428													43	59	---	---	---	---	PASS
ATP6V1H	51606	broad.mit.edu	37	8	54745612	54745612	+	Missense_Mutation	SNP	T	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54745612T>A	uc003xrl.2	-	3	300	c.148A>T	c.(148-150)ATT>TTT	p.I50F	ATP6V1H_uc003xrk.2_Missense_Mutation_p.I10F|ATP6V1H_uc003xrm.2_Missense_Mutation_p.I50F|ATP6V1H_uc003xrn.2_Missense_Mutation_p.I50F|ATP6V1H_uc011ldv.1_Intron|ATP6V1H_uc010lyd.2_Intron|ATP6V1H_uc003xro.1_Missense_Mutation_p.I47F	NM_213620	NP_998785	Q9UI12	VATH_HUMAN	ATPase, H+ transporting, lysosomal 50/57kDa, V1	50					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|endocytosis|insulin receptor signaling pathway|interspecies interaction between organisms|regulation of defense response to virus by virus|transferrin transport|vacuolar acidification|viral reproduction	cytosol|plasma membrane|vacuolar proton-transporting V-type ATPase, V1 domain	enzyme regulator activity|protein binding|proton-transporting ATPase activity, rotational mechanism				0		all_epithelial(80;0.0487)|Lung NSC(129;0.109)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;2.79e-06)|Epithelial(17;0.000629)|all cancers(17;0.00359)			AACCTCTGAATAAACTCACAA	0.368													79	77	---	---	---	---	PASS
MOS	4342	broad.mit.edu	37	8	57026488	57026488	+	Silent	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57026488C>T	uc011leb.1	-	1	54	c.54G>A	c.(52-54)TCG>TCA	p.S18S		NM_005372	NP_005363	P00540	MOS_HUMAN	v-mos Moloney murine sarcoma viral oncogene	18							ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)|ovary(1)|central_nervous_system(1)	4			Epithelial(17;0.00117)|all cancers(17;0.00879)			GCGCGTCCACCGATGGGGAAA	0.697													12	35	---	---	---	---	PASS
COL22A1	169044	broad.mit.edu	37	8	139620181	139620181	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139620181G>A	uc003yvd.2	-	57	4477	c.4030C>T	c.(4030-4032)CCT>TCT	p.P1344S	COL22A1_uc011ljo.1_Missense_Mutation_p.P624S	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1344	Pro-rich.|Gly-rich.|Collagen-like 13.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GAACTCACAGGGGTTCCTGAA	0.512										HNSCC(7;0.00092)			27	68	---	---	---	---	PASS
KIAA0020	9933	broad.mit.edu	37	9	2804299	2804299	+	3'UTR	SNP	A	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2804299A>T	uc003zhp.1	-	18					KIAA0020_uc010mhc.1_3'UTR|KIAA0020_uc003zhq.1_3'UTR	NM_014878	NP_055693	Q15397	K0020_HUMAN	KIAA0020 protein							endoplasmic reticulum|nucleolus	RNA binding			ovary(1)	1				GBM - Glioblastoma multiforme(50;0.0319)		GAACAGAAAAAATCATTCCAT	0.383													35	65	---	---	---	---	PASS
TPD52L3	89882	broad.mit.edu	37	9	6330127	6330127	+	3'UTR	SNP	A	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6330127A>C	uc003zjw.2	+	1					TPD52L3_uc003zjv.2_Intron|TPD52L3_uc003zjx.1_Intron	NM_033516	NP_277051	Q96J77	TPD55_HUMAN	protein kinase NYD-SP25 isoform 1								protein binding				0		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0198)|Lung(218;0.1)		TATGCCTTTGAATGGACCTAA	0.413													42	73	---	---	---	---	PASS
DENND4C	55667	broad.mit.edu	37	9	19296129	19296129	+	Missense_Mutation	SNP	A	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19296129A>G	uc003znq.2	+	2	250	c.217A>G	c.(217-219)ACA>GCA	p.T73A	DENND4C_uc011lnc.1_Translation_Start_Site	NM_017925	NP_060395	Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	73	DENN.					integral to membrane				ovary(1)|skin(1)	2						ATCCATCAATACAAACAAATG	0.393													87	169	---	---	---	---	PASS
GNA14	9630	broad.mit.edu	37	9	80262686	80262686	+	Silent	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80262686G>A	uc004aku.2	-	1	547	c.24C>T	c.(22-24)TCC>TCT	p.S8S		NM_004297	NP_004288	O95837	GNA14_HUMAN	G alpha 14	8					activation of phospholipase C activity by dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(2)	2						TCTCCTCCGCGGACAGGCAGC	0.711													9	14	---	---	---	---	PASS
AGTPBP1	23287	broad.mit.edu	37	9	88257814	88257814	+	Silent	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88257814T>C	uc011ltd.1	-	12	1263	c.1230A>G	c.(1228-1230)CAA>CAG	p.Q410Q	AGTPBP1_uc004aod.3_Silent_p.Q36Q|AGTPBP1_uc011ltc.1_Silent_p.Q308Q|AGTPBP1_uc010mqc.2_Silent_p.Q370Q|AGTPBP1_uc011lte.1_Silent_p.Q422Q	NM_015239	NP_056054	Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	410					C-terminal protein deglutamylation|cerebellar Purkinje cell differentiation|eye photoreceptor cell differentiation|mitochondrion organization|neuromuscular process|olfactory bulb development|protein side chain deglutamylation|proteolysis	cytosol|mitochondrion|nucleus	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(4)|large_intestine(2)|skin(1)	7						GTCCCGGTTCTTGCTGGGGTT	0.294													19	78	---	---	---	---	PASS
CUBN	8029	broad.mit.edu	37	10	16911660	16911660	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16911660C>T	uc001ioo.2	-	59	9481	c.9429G>A	c.(9427-9429)TGG>TGA	p.W3143*	CUBN_uc009xjq.1_RNA|CUBN_uc009xjr.1_Nonsense_Mutation_p.W499*	NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	3143	CUB 23.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AAGACATCTTCCAGCCTTTTG	0.448													149	201	---	---	---	---	PASS
CUBN	8029	broad.mit.edu	37	10	16911845	16911845	+	Missense_Mutation	SNP	C	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16911845C>G	uc001ioo.2	-	59	9296	c.9244G>C	c.(9244-9246)GAT>CAT	p.D3082H	CUBN_uc009xjq.1_RNA|CUBN_uc009xjr.1_Missense_Mutation_p.D438H	NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	3082	CUB 23.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ACATCAAAATCACTGAACCTG	0.413													38	57	---	---	---	---	PASS
ARMC3	219681	broad.mit.edu	37	10	23290965	23290965	+	Missense_Mutation	SNP	A	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23290965A>G	uc001irm.3	+	12	1626	c.1543A>G	c.(1543-1545)AAT>GAT	p.N515D	ARMC3_uc010qcv.1_Missense_Mutation_p.N515D|ARMC3_uc010qcw.1_Missense_Mutation_p.N252D	NM_173081	NP_775104	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3	515							binding				0						GCTGACGGCCAATGAATTATG	0.532													13	23	---	---	---	---	PASS
POLR3A	11128	broad.mit.edu	37	10	79769683	79769683	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79769683G>A	uc001jzn.2	-	13	1803	c.1709C>T	c.(1708-1710)TCA>TTA	p.S570L		NM_007055	NP_008986	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide	570					innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	DNA-directed RNA polymerase III complex	DNA binding|DNA-directed RNA polymerase activity|ribonucleoside binding|zinc ion binding				0	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			AACCAGTATTGAAGCAATGAT	0.453													21	50	---	---	---	---	PASS
ATRNL1	26033	broad.mit.edu	37	10	117607452	117607452	+	Missense_Mutation	SNP	T	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117607452T>G	uc001lcg.2	+	28	4354	c.3968T>G	c.(3967-3969)TTT>TGT	p.F1323C	ATRNL1_uc010qsm.1_Missense_Mutation_p.F452C|ATRNL1_uc010qsn.1_RNA	NM_207303	NP_997186	Q5VV63	ATRN1_HUMAN	attractin-like 1 precursor	1323	Cytoplasmic (Potential).					integral to membrane	sugar binding			ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		CTGACTGTGTTTCTTTGTCTA	0.473													30	59	---	---	---	---	PASS
INPP5A	3632	broad.mit.edu	37	10	134579295	134579295	+	Missense_Mutation	SNP	G	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134579295G>C	uc001llp.2	+	12	1170	c.922G>C	c.(922-924)GAG>CAG	p.E308Q	INPP5A_uc001llo.1_Missense_Mutation_p.E308Q|INPP5A_uc001llq.2_Missense_Mutation_p.E203Q	NM_005539	NP_005530	Q14642	I5P1_HUMAN	inositol polyphosphate-5-phosphatase A	308					cell communication	membrane	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|PH domain binding			skin(1)	1		all_cancers(35;8.59e-13)|all_epithelial(44;5.49e-09)|Lung NSC(174;0.000854)|all_lung(145;0.00146)|all_neural(114;0.0299)|Colorectal(31;0.0599)|Breast(234;0.0849)|Melanoma(40;0.124)|all_hematologic(284;0.196)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;0.000102)|Epithelial(32;0.00023)|all cancers(32;0.000326)		GTTTGACAAGGAGTTGTCTGT	0.502													25	84	---	---	---	---	PASS
SYCE1	93426	broad.mit.edu	37	10	135369108	135369108	+	Silent	SNP	G	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135369108G>T	uc001lno.2	-	11	928	c.823C>A	c.(823-825)CGG>AGG	p.R275R	CYP2E1_uc001lnl.1_3'UTR|SYCE1_uc001lnm.2_Silent_p.R147R|SYCE1_uc009ybn.2_Silent_p.R275R|SYCE1_uc001lnn.2_Silent_p.R239R	NM_001143764	NP_001137236	Q8N0S2	SYCE1_HUMAN	synaptonemal complex central element protein 1	275	Gln-rich.|Potential.				cell division	central element				ovary(1)	1		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		CACCTctgccgcttctgctgc	0.373													9	22	---	---	---	---	PASS
OR51A2	401667	broad.mit.edu	37	11	4976305	4976305	+	Silent	SNP	A	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4976305A>G	uc010qyt.1	-	1	639	c.639T>C	c.(637-639)ATT>ATC	p.I213I		NM_001004748	NP_001004748	Q8NGJ7	O51A2_HUMAN	olfactory receptor, family 51, subfamily A,	213	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		CAGCAATGAGAATAAAGTCTA	0.433													14	16	---	---	---	---	PASS
NLRP14	338323	broad.mit.edu	37	11	7079645	7079645	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7079645C>T	uc001mfb.1	+	8	2920	c.2597C>T	c.(2596-2598)GCC>GTC	p.A866V		NM_176822	NP_789792	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	866					cell differentiation|multicellular organismal development|spermatogenesis		ATP binding			ovary(3)|breast(2)|pancreas(1)|lung(1)|skin(1)	8				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		ATGAGTGATGCCCTGCAACAT	0.363													49	58	---	---	---	---	PASS
COPB1	1315	broad.mit.edu	37	11	14490389	14490389	+	Missense_Mutation	SNP	C	A	A	rs139561241	byFrequency	TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14490389C>A	uc001mli.2	-	16	2290	c.1983G>T	c.(1981-1983)AGG>AGT	p.R661S	COPB1_uc001mlg.2_Missense_Mutation_p.R661S|COPB1_uc001mlh.2_Missense_Mutation_p.R661S	NM_016451	NP_057535	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1	661					COPI coating of Golgi vesicle|interspecies interaction between organisms|intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol|ER-Golgi intermediate compartment|plasma membrane	protein binding|structural molecule activity			ovary(1)|central_nervous_system(1)	2						CTGTCACATTCCTCTTTTCAG	0.378													47	181	---	---	---	---	PASS
INSC	387755	broad.mit.edu	37	11	15212291	15212291	+	Silent	SNP	A	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15212291A>G	uc001mly.2	+	6	811	c.765A>G	c.(763-765)ACA>ACG	p.T255T	INSC_uc001mlz.2_Silent_p.T208T|INSC_uc001mma.2_Silent_p.T208T|INSC_uc010rcs.1_Silent_p.T243T|INSC_uc001mmb.2_Silent_p.T208T|INSC_uc001mmc.2_Silent_p.T208T	NM_001031853	NP_001027024	Q1MX18	INSC_HUMAN	inscuteable isoform a	255					cell differentiation|nervous system development	cytoplasm	binding			upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1)	5						TCTACACCACAGAGTCCACCA	0.507													107	150	---	---	---	---	PASS
KCNA4	3739	broad.mit.edu	37	11	30033503	30033503	+	Silent	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30033503C>T	uc001msk.2	-	2	1875	c.723G>A	c.(721-723)CTG>CTA	p.L241L		NM_002233	NP_002224	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related	241						voltage-gated potassium channel complex	potassium ion binding|protein binding|voltage-gated potassium channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4						CTGGCCTCTTCAGGCGGCCTC	0.498													61	99	---	---	---	---	PASS
SNX32	254122	broad.mit.edu	37	11	65617193	65617193	+	Intron	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65617193G>A	uc001ofr.2	+						SNX32_uc009yqt.2_Missense_Mutation_p.S94N|SNX32_uc010rop.1_Intron	NM_152760	NP_689973	Q86XE0	SNX32_HUMAN	sorting nexin 6B						cell communication|protein transport		phosphatidylinositol binding				0				READ - Rectum adenocarcinoma(159;0.171)		CTCCTGGAAAGTGAGCCTCTT	0.582													8	6	---	---	---	---	PASS
ATM	472	broad.mit.edu	37	11	108218083	108218083	+	Missense_Mutation	SNP	A	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108218083A>T	uc001pkb.1	+	59	9047	c.8662A>T	c.(8662-8664)ATA>TTA	p.I2888L	ATM_uc009yxr.1_Missense_Mutation_p.I2888L|C11orf65_uc010rvx.1_Intron|C11orf65_uc009yxu.1_Intron|ATM_uc001pke.1_Missense_Mutation_p.I1540L	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	2888	PI3K/PI4K.				cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding	p.I2888T(1)		haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		ACTTGTACATATAGATCTAGG	0.303			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			53	89	---	---	---	---	PASS
CBL	867	broad.mit.edu	37	11	119170369	119170369	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119170369C>T	uc001pwe.2	+	16	2737	c.2599C>T	c.(2599-2601)CAG>TAG	p.Q867*		NM_005188	NP_005179	P22681	CBL_HUMAN	Cas-Br-M (murine) ecotropic retroviral	867	Interaction with CD2AP.|UBA.				epidermal growth factor receptor signaling pathway|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of receptor-mediated endocytosis	cytosol|nucleus	calcium ion binding|sequence-specific DNA binding transcription factor activity|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(135)|lung(10)|central_nervous_system(2)|ovary(1)|breast(1)	149		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		CCTCATGAGTCAGGGGTACTC	0.532									CBL_gene-associated_Juvenile_Myelomonocytic_Leukemia_and_Developmental_Anomalies|Noonan_syndrome				267	202	---	---	---	---	PASS
FOXRED1	55572	broad.mit.edu	37	11	126139231	126139231	+	Intron	SNP	C	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126139231C>G	uc001qdi.2	+						SRPR_uc001qdh.2_5'Flank|SRPR_uc010sbm.1_5'Flank|FOXRED1_uc010sbn.1_Intron|FOXRED1_uc010sbo.1_Intron|FOXRED1_uc010sbp.1_Intron|FOXRED1_uc010sbq.1_Intron|FOXRED1_uc001qdj.2_Intron|FOXRED1_uc010sbr.1_5'UTR|FOXRED1_uc001qdk.2_5'Flank	NM_017547	NP_060017	Q96CU9	FXRD1_HUMAN	FAD-dependent oxidoreductase domain containing							integral to membrane|mitochondrion	oxidoreductase activity|protein binding				0	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0729)		TGGGTTGTCCCCAACCTCCGA	0.612													30	22	---	---	---	---	PASS
CD27	939	broad.mit.edu	37	12	6554303	6554303	+	Silent	SNP	C	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6554303C>A	uc001qod.2	+	1	253	c.42C>A	c.(40-42)ACC>ACA	p.T14T	LOC678655_uc001qob.2_Intron|LOC678655_uc001qoc.2_Intron|LOC678655_uc009zel.1_Intron|CD27_uc001qoe.2_5'Flank	NM_001242	NP_001233	P26842	CD27_HUMAN	tumor necrosis factor receptor superfamily,	14					anti-apoptosis|apoptosis|cell surface receptor linked signaling pathway|immunoglobulin mediated immune response|induction of apoptosis|positive regulation of B cell differentiation|positive regulation of JNK cascade|release of cytoplasmic sequestered NF-kappaB	extracellular region|integral to plasma membrane	caspase inhibitor activity|protein binding|transmembrane receptor activity				0						TTCTGGGGACCCTGGTGGGGC	0.627													10	23	---	---	---	---	PASS
CD27	939	broad.mit.edu	37	12	6554304	6554304	+	Missense_Mutation	SNP	C	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6554304C>G	uc001qod.2	+	1	254	c.43C>G	c.(43-45)CTG>GTG	p.L15V	LOC678655_uc001qob.2_Intron|LOC678655_uc001qoc.2_Intron|LOC678655_uc009zel.1_Intron|CD27_uc001qoe.2_5'Flank	NM_001242	NP_001233	P26842	CD27_HUMAN	tumor necrosis factor receptor superfamily,	15					anti-apoptosis|apoptosis|cell surface receptor linked signaling pathway|immunoglobulin mediated immune response|induction of apoptosis|positive regulation of B cell differentiation|positive regulation of JNK cascade|release of cytoplasmic sequestered NF-kappaB	extracellular region|integral to plasma membrane	caspase inhibitor activity|protein binding|transmembrane receptor activity				0						TCTGGGGACCCTGGTGGGGCT	0.632													10	22	---	---	---	---	PASS
SLCO1B3	28234	broad.mit.edu	37	12	21242857	21242857	+	Silent	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21242857C>T	uc010sil.1	+	16	2129	c.2064C>T	c.(2062-2064)GGC>GGT	p.G688G	LST-3TM12_uc010sim.1_Silent_p.G627G|LST-3TM12_uc010sin.1_Silent_p.G580G			Q9NPD5	SO1B3_HUMAN	SubName: Full=Liver-specific organic anion transporter 3TM13; SubName: Full=Organic anion transporter LST-3c;	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)					CCTTCTTCGGCTTGAAGGTAG	0.299													15	48	---	---	---	---	PASS
SLC4A8	9498	broad.mit.edu	37	12	51856143	51856143	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51856143C>T	uc001rys.1	+	10	1329	c.1151C>T	c.(1150-1152)GCG>GTG	p.A384V	SLC4A8_uc010sni.1_Missense_Mutation_p.A331V|SLC4A8_uc001rym.2_Missense_Mutation_p.A331V|SLC4A8_uc001ryn.2_Missense_Mutation_p.A331V|SLC4A8_uc001ryo.2_Missense_Mutation_p.A331V|SLC4A8_uc001ryp.1_3'UTR|SLC4A8_uc010snj.1_Missense_Mutation_p.A411V|SLC4A8_uc001ryq.3_Missense_Mutation_p.A384V|SLC4A8_uc001ryr.2_Missense_Mutation_p.A384V|SLC4A8_uc010snk.1_Missense_Mutation_p.A331V	NM_001039960	NP_001035049	Q2Y0W8	S4A8_HUMAN	solute carrier family 4, sodium bicarbonate	384	Extracellular (Potential).				bicarbonate transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity			ovary(3)|pancreas(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.15)		GATCTCCTGGCGGGGATTGAT	0.458													33	142	---	---	---	---	PASS
PAN2	9924	broad.mit.edu	37	12	56720613	56720613	+	Silent	SNP	A	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56720613A>G	uc001skx.2	-	7	1423	c.1050T>C	c.(1048-1050)TCT>TCC	p.S350S	PAN2_uc001skw.2_5'Flank|PAN2_uc001skz.2_Silent_p.S350S|PAN2_uc001sky.2_Silent_p.S350S	NM_001127460	NP_001120932	Q504Q3	PAN2_HUMAN	PAN2 polyA specific ribonuclease subunit homolog	350					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			ovary(2)|skin(2)|large_intestine(1)|breast(1)	6						CACAGCCCTCAGAATCCCCAA	0.557													165	205	---	---	---	---	PASS
LRIG3	121227	broad.mit.edu	37	12	59271541	59271541	+	Missense_Mutation	SNP	G	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:59271541G>C	uc001sqr.2	-	15	2423	c.2177C>G	c.(2176-2178)CCT>CGT	p.P726R	LRIG3_uc009zqh.2_Missense_Mutation_p.P666R|LRIG3_uc010ssh.1_RNA	NM_153377	NP_700356	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like	726	Ig-like C2-type 3.					integral to membrane				skin(3)|ovary(1)	4			GBM - Glioblastoma multiforme(1;1.17e-18)			GTTCAGTTTAGGGGGAGGGCT	0.488													33	119	---	---	---	---	PASS
XPOT	11260	broad.mit.edu	37	12	64815090	64815090	+	Missense_Mutation	SNP	A	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64815090A>G	uc001ssb.2	+	9	1345	c.919A>G	c.(919-921)AGT>GGT	p.S307G	XPOT_uc009zqm.1_Missense_Mutation_p.S217G	NM_007235	NP_009166	O43592	XPOT_HUMAN	tRNA exportin	307	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport|tRNA export from nucleus	cytoplasm|nucleoplasm	protein transporter activity|tRNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(28;0.0404)		AGTTAGTTGGAGTAAATTAAT	0.373													47	166	---	---	---	---	PASS
CNOT2	4848	broad.mit.edu	37	12	70672040	70672040	+	Nonsense_Mutation	SNP	A	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70672040A>T	uc001svv.2	+	2	613	c.34A>T	c.(34-36)AAA>TAA	p.K12*	CNOT2_uc009zro.2_Nonsense_Mutation_p.K12*|CNOT2_uc009zrp.2_5'UTR|CNOT2_uc009zrq.2_Nonsense_Mutation_p.K12*	NM_014515	NP_055330	Q9NZN8	CNOT2_HUMAN	CCR4-NOT transcription complex, subunit 2	12					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	protein binding|RNA polymerase II transcription cofactor activity				0	Renal(347;0.236)		GBM - Glioblastoma multiforme(1;4.77e-09)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)			ATTATCTGAGAAAAGAAACTA	0.398													38	105	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	12	95702317	95702317	+	RNA	SNP	G	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95702317G>C	uc001teb.2	+	1		c.27G>C								full-length cDNA clone CS0DF007YJ21 of Fetal brain of Homo sapiens (human).																		CATCAAGAGTGTGAAGACTGA	0.458													8	23	---	---	---	---	PASS
SLC5A8	160728	broad.mit.edu	37	12	101595946	101595946	+	Missense_Mutation	SNP	A	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101595946A>T	uc001thz.3	-	3	855	c.465T>A	c.(463-465)AAT>AAA	p.N155K		NM_145913	NP_666018	Q8N695	SC5A8_HUMAN	solute carrier family 5 (iodide transporter),	155	Extracellular (Potential).				apoptosis|sodium ion transport	apical plasma membrane|integral to membrane	monocarboxylic acid transmembrane transporter activity|passive transmembrane transporter activity|symporter activity				0						ATGTACCTTGATTCAAAGCCA	0.388													29	47	---	---	---	---	PASS
NAA25	80018	broad.mit.edu	37	12	112499125	112499125	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112499125G>A	uc001ttm.2	-	12	1237	c.1217C>T	c.(1216-1218)GCT>GTT	p.A406V	NAA25_uc001ttn.3_RNA|NAA25_uc009zvz.1_Missense_Mutation_p.A378V|NAA25_uc009zwa.1_Missense_Mutation_p.A406V	NM_024953	NP_079229	Q14CX7	NAA25_HUMAN	mitochondrial distribution and morphology 20	406						cytoplasm	protein binding			ovary(1)|breast(1)|pancreas(1)	3						TCTGATGTCAGCAGGCAGTGC	0.458													33	36	---	---	---	---	PASS
GPR133	283383	broad.mit.edu	37	12	131487771	131487771	+	Silent	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131487771C>T	uc001uit.3	+	10	1627	c.1068C>T	c.(1066-1068)ACC>ACT	p.T356T	GPR133_uc010tbm.1_Silent_p.T388T	NM_198827	NP_942122	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133 precursor	356	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)|skin(2)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		CTATTGACACCGTCATGGGCC	0.602													52	167	---	---	---	---	PASS
ANKLE2	23141	broad.mit.edu	37	12	133327289	133327289	+	Missense_Mutation	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133327289T>C	uc001ukx.2	-	3	854	c.787A>G	c.(787-789)ACG>GCG	p.T263A	ANKLE2_uc001uky.3_Missense_Mutation_p.T201A	NM_015114	NP_055929	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	263						cytoplasm|integral to membrane|nuclear envelope					0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		GGTAAGGACGTTTTGCTTGGA	0.423													46	40	---	---	---	---	PASS
TRPC4	7223	broad.mit.edu	37	13	38320157	38320157	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38320157G>A	uc001uws.2	-	3	1049	c.814C>T	c.(814-816)CGA>TGA	p.R272*	TRPC4_uc010abv.2_5'UTR|TRPC4_uc001uwt.2_Nonsense_Mutation_p.R272*|TRPC4_uc010tey.1_Nonsense_Mutation_p.R272*|TRPC4_uc010abw.2_Intron|TRPC4_uc010abx.2_Nonsense_Mutation_p.R272*|TRPC4_uc010aby.2_Nonsense_Mutation_p.R272*	NM_016179	NP_057263	Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel,	272	Cytoplasmic (Potential).|Multimerization domain (By similarity).				axon guidance|calcium ion import	basolateral plasma membrane|calcium channel complex|cell surface|cortical cytoskeleton	beta-catenin binding|cadherin binding|store-operated calcium channel activity			ovary(3)|skin(2)|breast(1)	6				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		TTGTCATCTCGGTAATTAAGA	0.418													109	281	---	---	---	---	PASS
SCEL	8796	broad.mit.edu	37	13	78178541	78178541	+	Missense_Mutation	SNP	A	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78178541A>G	uc001vki.2	+	19	1318	c.1148A>G	c.(1147-1149)AAT>AGT	p.N383S	SCEL_uc001vkj.2_Missense_Mutation_p.N363S|SCEL_uc010thx.1_Intron	NM_144777	NP_659001	O95171	SCEL_HUMAN	sciellin isoform 1	383	16 X approximate tandem repeats.|7.				embryo development|keratinocyte differentiation	cornified envelope|cytoplasm|membrane	protein binding|zinc ion binding			ovary(4)|breast(1)	5		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)		ACAAATAAAAATATTACGAGG	0.333													83	182	---	---	---	---	PASS
LRP10	26020	broad.mit.edu	37	14	23344694	23344694	+	Silent	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23344694C>T	uc001whd.2	+	5	1090	c.537C>T	c.(535-537)TTC>TTT	p.F179F	LRP10_uc001whe.2_Silent_p.F55F	NM_014045	NP_054764	Q7Z4F1	LRP10_HUMAN	low density lipoprotein receptor-related protein	179	Extracellular (Potential).				endocytosis	coated pit|integral to membrane				central_nervous_system(1)	1	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.00549)		CAGACCCCTTCCCTGGCCTGA	0.582													71	191	---	---	---	---	PASS
TINF2	26277	broad.mit.edu	37	14	24710327	24710327	+	Intron	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24710327G>A	uc001woa.3	-						TINF2_uc010alm.2_5'UTR|TINF2_uc001wob.3_Intron|TINF2_uc010tof.1_Intron|TINF2_uc001woc.3_Intron	NM_001099274	NP_001092744	Q9BSI4	TINF2_HUMAN	TERF1 (TRF1)-interacting nuclear factor 2						negative regulation of epithelial cell proliferation|negative regulation of protein ADP-ribosylation|negative regulation of telomere maintenance via telomerase|positive regulation of telomere maintenance|protein localization to chromosome, telomeric region|telomere assembly|telomere maintenance via telomere lengthening	nuclear telomere cap complex|nucleoplasm|perinucleolar chromocenter	protein binding|protein binding|telomeric DNA binding				0				GBM - Glioblastoma multiforme(265;0.0185)		CTGAAGCTGTGGGCAGGGACA	0.547									Ataxia_Pancytopenia_syndrome|Congenital_Dyskeratosis				118	280	---	---	---	---	PASS
MIPOL1	145282	broad.mit.edu	37	14	37838794	37838794	+	Missense_Mutation	SNP	C	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37838794C>G	uc001wuc.2	+	11	1404	c.901C>G	c.(901-903)CTG>GTG	p.L301V	MIPOL1_uc010amr.2_Intron|MIPOL1_uc001wub.3_Missense_Mutation_p.L270V|MIPOL1_uc001wud.2_Missense_Mutation_p.L301V|MIPOL1_uc010ams.2_Missense_Mutation_p.L301V|MIPOL1_uc001wue.2_Missense_Mutation_p.L270V|MIPOL1_uc010amt.2_Missense_Mutation_p.L120V	NM_138731	NP_620059	Q8TD10	MIPO1_HUMAN	mirror-image polydactyly 1	301	Potential.									ovary(1)|central_nervous_system(1)	2	Breast(36;0.119)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;6.03e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.047)|all cancers(34;0.0953)|LUSC - Lung squamous cell carcinoma(13;0.0975)|BRCA - Breast invasive adenocarcinoma(188;0.196)	GBM - Glioblastoma multiforme(112;0.0358)		CATGAGACATCTGACTGCTGA	0.463													27	52	---	---	---	---	PASS
MIPOL1	145282	broad.mit.edu	37	14	37838795	37838795	+	Missense_Mutation	SNP	T	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37838795T>A	uc001wuc.2	+	11	1405	c.902T>A	c.(901-903)CTG>CAG	p.L301Q	MIPOL1_uc010amr.2_Intron|MIPOL1_uc001wub.3_Missense_Mutation_p.L270Q|MIPOL1_uc001wud.2_Missense_Mutation_p.L301Q|MIPOL1_uc010ams.2_Missense_Mutation_p.L301Q|MIPOL1_uc001wue.2_Missense_Mutation_p.L270Q|MIPOL1_uc010amt.2_Missense_Mutation_p.L120Q	NM_138731	NP_620059	Q8TD10	MIPO1_HUMAN	mirror-image polydactyly 1	301	Potential.									ovary(1)|central_nervous_system(1)	2	Breast(36;0.119)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;6.03e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.047)|all cancers(34;0.0953)|LUSC - Lung squamous cell carcinoma(13;0.0975)|BRCA - Breast invasive adenocarcinoma(188;0.196)	GBM - Glioblastoma multiforme(112;0.0358)		ATGAGACATCTGACTGCTGAA	0.463													28	50	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106110214	106110214	+	RNA	SNP	G	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106110214G>T	uc010tyt.1	-	3642		c.61037C>A			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_RNA					Parts of antibodies, mostly variable regions.												0						GACCTCAGGGGTCCGGGAGAT	0.602													58	60	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106641519	106641519	+	RNA	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106641519T>C	uc010tyt.1	-	1022		c.24449A>G								Parts of antibodies, mostly variable regions.												0						GCCTCCTCCCTGGGGTTTCTG	0.473													69	217	---	---	---	---	PASS
NDNL2	56160	broad.mit.edu	37	15	29560949	29560949	+	3'UTR	SNP	T	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29560949T>G	uc001zco.2	-	1					FAM189A1_uc010azk.1_Intron	NM_138704	NP_619649	Q96MG7	MAGG1_HUMAN	necdin-like 2						regulation of growth	cytoplasm|nucleus					0		all_lung(180;4.69e-11)|Breast(32;0.0013)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00736)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		AAACTGTGCCTTTGGGTCTCA	0.522													13	32	---	---	---	---	PASS
FSIP1	161835	broad.mit.edu	37	15	39910371	39910371	+	Missense_Mutation	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39910371T>C	uc001zki.2	-	11	1482	c.1264A>G	c.(1264-1266)ATC>GTC	p.I422V		NM_152597	NP_689810	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	422										ovary(2)|skin(1)	3		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		AGTTTAATGATGGATTTTTGT	0.368													53	65	---	---	---	---	PASS
NME4	4833	broad.mit.edu	37	16	449378	449378	+	Splice_Site	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:449378G>A	uc002cgz.2	+	3	257	c.226_splice	c.e3-1	p.A76_splice	NME4_uc002cgy.2_Splice_Site_p.A6_splice|NME4_uc002cha.2_Splice_Site|DECR2_uc002chb.2_5'Flank|DECR2_uc002chc.2_5'Flank|DECR2_uc010bqv.2_5'Flank|DECR2_uc002chd.2_5'Flank	NM_005009	NP_005000	O00746	NDKM_HUMAN	nucleoside diphosphate kinase 4 precursor						CTP biosynthetic process|GTP biosynthetic process|nucleobase, nucleoside and nucleotide interconversion|UTP biosynthetic process	mitochondrial inner membrane|mitochondrial intermembrane space	ATP binding|metal ion binding|nucleoside diphosphate kinase activity				0		Hepatocellular(16;0.00015)				ATGCCACCCAGGCACCAGAGA	0.607													130	282	---	---	---	---	PASS
NAGPA	51172	broad.mit.edu	37	16	5075418	5075418	+	3'UTR	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5075418C>T	uc002cyg.2	-	10					NAGPA_uc010buc.2_3'UTR|NAGPA_uc002cyf.2_3'UTR|NAGPA_uc002cyh.2_RNA|NAGPA_uc002cyi.2_3'UTR	NM_016256	NP_057340	Q9UK23	NAGPA_HUMAN	N-acetylglucosamine-1-phosphodiester						carbohydrate metabolic process|lysosome organization|protein modification process|protein targeting to lysosome	Golgi cisterna membrane|integral to membrane	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase activity				0					N-Acetyl-D-glucosamine(DB00141)	ATTTCCCCTGCAGAAGCCAGA	0.632													105	101	---	---	---	---	PASS
PDXDC1	23042	broad.mit.edu	37	16	15224610	15224610	+	Intron	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15224610C>T	uc002ddc.2	+						uc010uzs.1_RNA|uc002ddh.2_Missense_Mutation_p.V91I|uc002ddi.2_5'UTR|uc010uzt.1_Missense_Mutation_p.V91I	NM_015027	NP_055842	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)	TGCAGGTAGACTGCCAGGTAG	0.677													21	48	---	---	---	---	PASS
C16orf54	283897	broad.mit.edu	37	16	29756070	29756070	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29756070C>T	uc002dtp.2	-	2	312	c.203G>A	c.(202-204)CGT>CAT	p.R68H	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|uc002dtq.1_5'Flank	NM_175900	NP_787096	Q6UWD8	CP054_HUMAN	hypothetical protein LOC283897	68						integral to membrane					0						GGTGGGTGCACGGTGGCTGGG	0.677													4	3	---	---	---	---	PASS
CENPT	80152	broad.mit.edu	37	16	67863976	67863976	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67863976G>A	uc002eun.3	-	12	1427	c.878C>T	c.(877-879)GCC>GTC	p.A293V	CENPT_uc002eum.3_Missense_Mutation_p.A293V|CENPT_uc010vkc.1_Missense_Mutation_p.A51V|CENPT_uc010vkd.1_Missense_Mutation_p.A46V|CENPT_uc010vke.1_3'UTR	NM_025082	NP_079358	Q96BT3	CENPT_HUMAN	centromere protein T	293					mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleus	DNA binding				0		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00429)|Epithelial(162;0.019)|all cancers(182;0.124)		CAGAAACTGGGCTGGTTTCCC	0.567													32	36	---	---	---	---	PASS
FTSJD1	55783	broad.mit.edu	37	16	71319027	71319027	+	Missense_Mutation	SNP	A	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71319027A>C	uc010cga.2	-	3	1203	c.797T>G	c.(796-798)CTT>CGT	p.L266R	FTSJD1_uc002ezy.3_Missense_Mutation_p.L266R|FTSJD1_uc002ezz.3_Missense_Mutation_p.L266R	NM_001099642	NP_001093112	Q8IYT2	FTSJ1_HUMAN	FtsJ methyltransferase domain containing 1	266						integral to membrane	methyltransferase activity|nucleic acid binding			skin(1)	1						ACCGTTTCCAAGAGTGGTCAG	0.398													29	60	---	---	---	---	PASS
ZZEF1	23140	broad.mit.edu	37	17	3920781	3920781	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3920781C>T	uc002fxe.2	-	48	7949	c.7885G>A	c.(7885-7887)GAG>AAG	p.E2629K	ZZEF1_uc002fxg.1_5'UTR	NM_015113	NP_055928	O43149	ZZEF1_HUMAN	zinc finger, ZZ type with EF hand domain 1	2629							calcium ion binding|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4						CTAGGCCACTCGGCGAGCAGG	0.577													21	44	---	---	---	---	PASS
GP1BA	2811	broad.mit.edu	37	17	4836215	4836215	+	Missense_Mutation	SNP	C	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4836215C>A	uc010vsq.1	+	2	391	c.316C>A	c.(316-318)CAA>AAA	p.Q106K	uc002fzn.1_RNA	NM_000173	NP_000164	P07359	GP1BA_HUMAN	platelet glycoprotein Ib alpha polypeptide	106											0						CAATCAGCTGCAAAGCCTGCC	0.612													57	103	---	---	---	---	PASS
PER1	5187	broad.mit.edu	37	17	8046123	8046123	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8046123C>T	uc002gkd.2	-	20	3341	c.3103G>A	c.(3103-3105)GCA>ACA	p.A1035T	PER1_uc010cns.2_5'Flank|PER1_uc010vuq.1_RNA	NM_002616	NP_002607	O15534	PER1_HUMAN	period 1	1035	Ser-rich.				circadian rhythm|entrainment of circadian clock|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	signal transducer activity			lung(2)|breast(2)|skin(2)|large_intestine(1)|ovary(1)|kidney(1)	9						CCGGAAAGTGCGTCCTGATTG	0.647			T	ETV6	AML|CMML			Other_conserved_DNA_damage_response_genes					8	26	---	---	---	---	PASS
TOP3A	7156	broad.mit.edu	37	17	18196135	18196135	+	Missense_Mutation	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18196135T>C	uc002gsx.1	-	11	1334	c.1105A>G	c.(1105-1107)ATT>GTT	p.I369V	TOP3A_uc010cpz.1_5'Flank|TOP3A_uc010vxr.1_Intron|TOP3A_uc002gsw.1_Intron|TOP3A_uc010vxs.1_Missense_Mutation_p.I267V	NM_004618	NP_004609	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	369					DNA topological change|meiosis	chromosome|PML body	ATP binding|DNA topoisomerase type I activity|protein binding|zinc ion binding			skin(3)	3						CTGGGAAAAATGTTTGTTTCT	0.483													48	86	---	---	---	---	PASS
EFCAB5	374786	broad.mit.edu	37	17	28405458	28405458	+	Missense_Mutation	SNP	C	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28405458C>G	uc002het.2	+	15	3155	c.2963C>G	c.(2962-2964)GCT>GGT	p.A988G	EFCAB5_uc010cse.2_Missense_Mutation_p.A743G|EFCAB5_uc010csf.2_Intron	NM_198529	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5 isoform a	988							calcium ion binding			ovary(1)|skin(1)	2						ATCCAATGTGCTGCAGAGACA	0.473													22	54	---	---	---	---	PASS
EVI2B	2124	broad.mit.edu	37	17	29631980	29631980	+	Missense_Mutation	SNP	C	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29631980C>G	uc002hgk.2	-	2	803	c.648G>C	c.(646-648)TTG>TTC	p.L216F	NF1_uc002hgg.2_Intron|NF1_uc002hgh.2_Intron|NF1_uc002hgi.1_Intron|NF1_uc010cso.2_Intron|EVI2B_uc010csq.2_Missense_Mutation_p.L231F	NM_006495	NP_006486	P34910	EVI2B_HUMAN	ecotropic viral integration site 2B precursor	216	Helical; (Potential).					cytoplasm|integral to plasma membrane				ovary(2)	2		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;6.88e-13)|Epithelial(4;8.95e-12)|OV - Ovarian serous cystadenocarcinoma(4;1.01e-11)|GBM - Glioblastoma multiforme(4;0.184)		TTATAGCTACCAACATAGAAG	0.343													53	161	---	---	---	---	PASS
KPNB1	3837	broad.mit.edu	37	17	45750422	45750422	+	Missense_Mutation	SNP	A	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45750422A>G	uc002ilt.1	+	13	1922	c.1586A>G	c.(1585-1587)TAT>TGT	p.Y529C	KPNB1_uc010wkw.1_Missense_Mutation_p.Y384C|KPNB1_uc010wkx.1_Missense_Mutation_p.Y313C	NM_002265	NP_002256	Q14974	IMB1_HUMAN	karyopherin beta 1	529					DNA fragmentation involved in apoptotic nuclear change|NLS-bearing substrate import into nucleus|protein import into nucleus, translocation|ribosomal protein import into nucleus|viral genome transport in host cell|viral infectious cycle	cytosol|nuclear pore|nucleoplasm	nuclear localization sequence binding|protein domain specific binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3						AGTTCTGCATATGAATCTCTG	0.423													39	67	---	---	---	---	PASS
HOXB4	3214	broad.mit.edu	37	17	46654171	46654171	+	Missense_Mutation	SNP	C	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46654171C>A	uc002inp.2	-	2	731	c.669G>T	c.(667-669)TTG>TTT	p.L223F	HOXB3_uc010wlm.1_Intron|HOXB3_uc010dbf.2_Intron|HOXB3_uc010dbg.2_Intron|HOXB3_uc002ino.2_5'Flank|HOXB3_uc010wlk.1_5'Flank|HOXB3_uc010wll.1_Intron	NM_024015	NP_076920	P17483	HXB4_HUMAN	homeobox B4	223						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						TGGTGTTGGGCAACTTGTGGT	0.677													66	121	---	---	---	---	PASS
HEATR6	63897	broad.mit.edu	37	17	58145064	58145064	+	Silent	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58145064T>C	uc002iyk.1	-	8	986	c.969A>G	c.(967-969)CCA>CCG	p.P323P	HEATR6_uc010ddk.1_5'Flank|HEATR6_uc010wos.1_Silent_p.P155P	NM_022070	NP_071353	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6	323	Poly-Lys.						binding			ovary(1)|skin(1)	2	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)			GGATTTTCTTTGGTTTTACTT	0.413													43	99	---	---	---	---	PASS
CDC42EP4	23580	broad.mit.edu	37	17	71281971	71281971	+	Silent	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71281971G>A	uc002jjn.2	-	2	816	c.669C>T	c.(667-669)AGC>AGT	p.S223S	CDC42EP4_uc002jjo.2_Silent_p.S223S|CDC42EP4_uc002jjp.1_Silent_p.S153S	NM_012121	NP_036253	Q9H3Q1	BORG4_HUMAN	Cdc42 effector protein 4	223					positive regulation of pseudopodium assembly|regulation of cell shape	actin cytoskeleton|cytoplasm|endomembrane system|membrane|microtubule cytoskeleton	GTP-Rho binding				0			LUSC - Lung squamous cell carcinoma(166;0.0352)|Lung(188;0.0711)			TGTCCATGATGCTGAGGACGT	0.657													70	103	---	---	---	---	PASS
LAMA3	3909	broad.mit.edu	37	18	21437915	21437915	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21437915G>A	uc002kuq.2	+	33	4330	c.4244G>A	c.(4243-4245)GGA>GAA	p.G1415E	LAMA3_uc002kur.2_Missense_Mutation_p.G1415E	NM_198129	NP_937762	Q16787	LAMA3_HUMAN	laminin alpha 3 subunit isoform 1	1415	Laminin EGF-like 12.|Domain III B.				cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|skin(2)|central_nervous_system(1)	11	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	ACTGAGCCAGGAGTGTGTGAC	0.562													57	71	---	---	---	---	PASS
ZNF317	57693	broad.mit.edu	37	19	9271246	9271246	+	Missense_Mutation	SNP	G	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9271246G>T	uc002mku.2	+	7	1200	c.925G>T	c.(925-927)GAT>TAT	p.D309Y	ZNF317_uc002mkv.2_Missense_Mutation_p.D168Y|ZNF317_uc002mkw.2_Missense_Mutation_p.D277Y|ZNF317_uc002mkx.2_Missense_Mutation_p.D224Y|ZNF317_uc002mky.2_Missense_Mutation_p.D192Y	NM_020933	NP_065984	Q96PQ6	ZN317_HUMAN	zinc finger protein 317	309	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TTACAAGTGTGATCAGTGCGG	0.577													38	77	---	---	---	---	PASS
ZNF317	57693	broad.mit.edu	37	19	9271247	9271247	+	Missense_Mutation	SNP	A	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9271247A>T	uc002mku.2	+	7	1201	c.926A>T	c.(925-927)GAT>GTT	p.D309V	ZNF317_uc002mkv.2_Missense_Mutation_p.D168V|ZNF317_uc002mkw.2_Missense_Mutation_p.D277V|ZNF317_uc002mkx.2_Missense_Mutation_p.D224V|ZNF317_uc002mky.2_Missense_Mutation_p.D192V	NM_020933	NP_065984	Q96PQ6	ZN317_HUMAN	zinc finger protein 317	309	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TACAAGTGTGATCAGTGCGGG	0.572													39	78	---	---	---	---	PASS
TYK2	7297	broad.mit.edu	37	19	10475635	10475635	+	Silent	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10475635G>A	uc002moc.3	-	8	1479	c.1101C>T	c.(1099-1101)GAC>GAT	p.D367D	TYK2_uc010dxe.2_Silent_p.D182D|TYK2_uc002mod.2_Silent_p.D367D	NM_003331	NP_003322	P29597	TYK2_HUMAN	tyrosine kinase 2	367	FERM.				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			lung(5)|large_intestine(2)|ovary(1)|breast(1)	9			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			CCCGCGGCCTGTCTGCCGGCT	0.617													21	50	---	---	---	---	PASS
KEAP1	9817	broad.mit.edu	37	19	10597496	10597496	+	Intron	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10597496T>C	uc002moq.1	-						KEAP1_uc002mop.1_Intron|KEAP1_uc002mor.1_Intron	NM_012289	NP_036421	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|midbody|nucleus	protein binding			lung(12)|breast(3)|ovary(1)|pancreas(1)	17			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)			CATAGCCTCCTGCGGGAAGAA	0.537													34	40	---	---	---	---	PASS
COMP	1311	broad.mit.edu	37	19	18896789	18896789	+	Missense_Mutation	SNP	T	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18896789T>A	uc002nke.2	-	13	1511	c.1475A>T	c.(1474-1476)CAG>CTG	p.Q492L	COMP_uc002nkd.2_Missense_Mutation_p.Q459L|COMP_uc010xqj.1_Missense_Mutation_p.Q439L	NM_000095	NP_000086	P49747	COMP_HUMAN	cartilage oligomeric matrix protein precursor	492	TSP type-3 7.				anti-apoptosis|apoptosis|cell adhesion|limb development	extracellular space|proteinaceous extracellular matrix	calcium ion binding|collagen binding|extracellular matrix structural constituent|heparan sulfate proteoglycan binding|heparin binding				0						CGCGTCCTCCTGGCCGGGGTT	0.711													17	14	---	---	---	---	PASS
ZNF585A	199704	broad.mit.edu	37	19	37642436	37642436	+	3'UTR	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37642436G>A	uc002ofo.1	-	5					ZNF585A_uc002ofm.1_3'UTR|ZNF585A_uc002ofn.1_3'UTR	NM_199126	NP_954577	Q6P3V2	Z585A_HUMAN	zinc finger protein 585A						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CTGCATGCGTGCAACAGTGTA	0.473													15	25	---	---	---	---	PASS
PLEKHG2	64857	broad.mit.edu	37	19	39909602	39909602	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39909602C>T	uc010xuz.1	+	11	1547	c.1222C>T	c.(1222-1224)CGC>TGC	p.R408C	PLEKHG2_uc010xuy.1_Missense_Mutation_p.R349C|PLEKHG2_uc002olj.2_Missense_Mutation_p.R408C|PLEKHG2_uc010xva.1_Missense_Mutation_p.R215C	NM_022835	NP_073746	Q9H7P9	PKHG2_HUMAN	common-site lymphoma/leukemia guanine nucleotide	408	PH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			skin(2)|pancreas(1)|breast(1)	4	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CTGTCTCCAGCGCCTCTTCTT	0.612													86	180	---	---	---	---	PASS
C19orf54	284325	broad.mit.edu	37	19	41248527	41248527	+	Silent	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41248527G>A	uc002oou.1	-	6	987	c.867C>T	c.(865-867)TCC>TCT	p.S289S	C19orf54_uc002oow.1_Silent_p.S117S|C19orf54_uc002oox.1_RNA|C19orf54_uc002ooy.1_Intron|C19orf54_uc010xvs.1_RNA	NM_198476	NP_940878	Q5BKX5	CS054_HUMAN	hypothetical protein LOC284325	289											0			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			TGCCCTGCTTGGACAGCAGGT	0.657													10	34	---	---	---	---	PASS
CEACAM6	4680	broad.mit.edu	37	19	42260767	42260767	+	Silent	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42260767G>A	uc002orm.2	+	2	473	c.324G>A	c.(322-324)CTG>CTA	p.L108L		NM_002483	NP_002474	P40199	CEAM6_HUMAN	carcinoembryonic antigen-related cell adhesion	108	Ig-like V-type.				cell-cell signaling|signal transduction	anchored to membrane|integral to plasma membrane				ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(3;0.00575)|all cancers(3;0.0352)|Epithelial(262;0.0797)		CATCCCTGCTGATCCAGAACG	0.458													166	382	---	---	---	---	PASS
ERCC2	2068	broad.mit.edu	37	19	45856352	45856352	+	Missense_Mutation	SNP	C	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45856352C>G	uc002pbj.2	-	19	1867	c.1820G>C	c.(1819-1821)GGA>GCA	p.G607A	ERCC2_uc002pbh.2_Missense_Mutation_p.G170A|ERCC2_uc002pbi.2_Missense_Mutation_p.G300A|ERCC2_uc010ejz.2_Missense_Mutation_p.G529A|ERCC2_uc002pbk.2_Missense_Mutation_p.G583A	NM_000400	NP_000391	P18074	ERCC2_HUMAN	excision repair cross-complementing rodent	607	Mediates interaction with MMS19.				cell cycle checkpoint|chromosome segregation|hair cell differentiation|induction of apoptosis|interspecies interaction between organisms|mRNA capping|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein phosphorylation|response to oxidative stress|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|UV protection|viral reproduction	cytoplasm|holo TFIIH complex|MMXD complex	5'-3' DNA helicase activity|ATP binding|ATP-dependent DNA helicase activity|DNA binding|iron-sulfur cluster binding|metal ion binding|protein C-terminus binding|protein N-terminus binding			lung(2)|pancreas(1)	3		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		AAAGTCGATTCCCTCGGACAC	0.642			Mis|N|F|S			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				43	109	---	---	---	---	PASS
GIPR	2696	broad.mit.edu	37	19	46172841	46172841	+	Silent	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46172841G>A	uc002pcu.1	+	2	162	c.63G>A	c.(61-63)CAG>CAA	p.Q21Q	GIPR_uc002pct.1_Silent_p.Q21Q|GIPR_uc010xxp.1_Silent_p.Q21Q|GIPR_uc010xxq.1_RNA	NM_000164	NP_000155	P48546	GIPR_HUMAN	gastric inhibitory polypeptide receptor	21					generation of precursor metabolites and energy|response to nutrient	integral to membrane|plasma membrane				skin(1)	1		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0056)|GBM - Glioblastoma multiforme(486;0.0832)|Epithelial(262;0.199)		TGCTGCTCCAGAGGGCGGAGG	0.597													6	12	---	---	---	---	PASS
SLC6A16	28968	broad.mit.edu	37	19	49797169	49797169	+	Silent	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49797169G>A	uc002pmz.2	-	9	1767	c.1533C>T	c.(1531-1533)AGC>AGT	p.S511S	SLC6A16_uc002pna.2_Silent_p.S511S	NM_014037	NP_054756	Q9GZN6	S6A16_HUMAN	solute carrier family 6, member 16	511	Helical; Name=8; (Potential).					integral to membrane|intracellular	neurotransmitter:sodium symporter activity			skin(2)|ovary(1)|kidney(1)	4		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00099)|GBM - Glioblastoma multiforme(486;0.0336)		CTATTGCGCTGCTCAGCCCCA	0.483													86	176	---	---	---	---	PASS
VRK3	51231	broad.mit.edu	37	19	50492998	50492998	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50492998G>A	uc002prg.2	-	11	1092	c.994C>T	c.(994-996)CGC>TGC	p.R332C	VRK3_uc002prh.1_Missense_Mutation_p.R332C|VRK3_uc002pri.1_Missense_Mutation_p.R282C|VRK3_uc010ens.2_Missense_Mutation_p.R332C|VRK3_uc010ybl.1_Missense_Mutation_p.R282C|VRK3_uc010ybm.1_Missense_Mutation_p.R101C|VRK3_uc002prj.1_Missense_Mutation_p.R282C|VRK3_uc002prk.1_Missense_Mutation_p.R332C|VRK3_uc010ent.1_Missense_Mutation_p.R88C|VRK3_uc002prl.2_Missense_Mutation_p.R332C|VRK3_uc010ybn.1_3'UTR	NM_016440	NP_057524	Q8IV63	VRK3_HUMAN	vaccinia related kinase 3 isoform 1	332	Protein kinase.					nucleus	ATP binding|protein kinase activity			stomach(1)|skin(1)	2		all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00166)|OV - Ovarian serous cystadenocarcinoma(262;0.00652)		GGGCAATAGCGGAAGGCGAAG	0.552													20	28	---	---	---	---	PASS
CTU1	90353	broad.mit.edu	37	19	51607330	51607330	+	Missense_Mutation	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51607330T>C	uc010eop.2	-	2	562	c.497A>G	c.(496-498)CAC>CGC	p.H166R		NM_145232	NP_660275	Q7Z7A3	CTU1_HUMAN	ATP binding domain 3	166					tRNA thio-modification|tRNA wobble uridine modification	cytosol	ATP binding|protein binding|transferase activity|tRNA binding				0						TGTCACGATGTGCGTGGCTCC	0.706													10	12	---	---	---	---	PASS
LENG8	114823	broad.mit.edu	37	19	54971986	54971986	+	3'UTR	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54971986C>T	uc002qfv.1	+	14					LENG8_uc002qfw.2_Silent_p.L761L			Q96PV6	LENG8_HUMAN	RecName: Full=Leukocyte receptor cluster member 8;								protein binding			central_nervous_system(1)|pancreas(1)	2	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		GCAGGCCGAGCTGGCCTTCGA	0.711													7	7	---	---	---	---	PASS
ZNF133	7692	broad.mit.edu	37	20	18295856	18295856	+	Missense_Mutation	SNP	G	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18295856G>T	uc010gcq.2	+	5	666	c.361G>T	c.(361-363)GAT>TAT	p.D121Y	ZNF133_uc010zrv.1_Missense_Mutation_p.D124Y|ZNF133_uc010zrw.1_Missense_Mutation_p.D58Y|ZNF133_uc010gcr.2_Missense_Mutation_p.D121Y|ZNF133_uc010zrx.1_Missense_Mutation_p.D26Y|ZNF133_uc002wql.3_Missense_Mutation_p.D120Y|ZNF133_uc010gcs.2_Missense_Mutation_p.D120Y|ZNF133_uc010zry.1_Missense_Mutation_p.D26Y|ZNF133_uc002wqm.2_Missense_Mutation_p.D121Y	NM_003434	NP_003425	P52736	ZN133_HUMAN	zinc finger protein 133	121						nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|pancreas(1)	2						CCAGCCTGGGGATCCGGGCCC	0.562													79	185	---	---	---	---	PASS
POFUT1	23509	broad.mit.edu	37	20	30803206	30803206	+	Silent	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30803206T>C	uc002wxp.2	+	3	430	c.381T>C	c.(379-381)TTT>TTC	p.F127F	POFUT1_uc002wxo.2_Silent_p.F127F|POFUT1_uc010ztt.1_Silent_p.F19F|POFUT1_uc010ztu.1_Intron	NM_015352	NP_056167	Q9H488	OFUT1_HUMAN	protein O-fucosyltransferase 1 isoform 1	127					fucose metabolic process|Notch signaling pathway|O-glycan processing|regulation of transcription, DNA-dependent	endoplasmic reticulum|membrane	peptide-O-fucosyltransferase activity			breast(1)	1			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			CATACTGCTTTGAGGTGGCAG	0.602													85	180	---	---	---	---	PASS
CPNE1	8904	broad.mit.edu	37	20	34214192	34214192	+	Missense_Mutation	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34214192T>C	uc002xdf.2	-	18	1948	c.1585A>G	c.(1585-1587)AAG>GAG	p.K529E	CPNE1_uc002xdc.2_Missense_Mutation_p.K191E|CPNE1_uc010zvj.1_Missense_Mutation_p.K534E|CPNE1_uc002xde.2_Missense_Mutation_p.K505E|CPNE1_uc002xdg.2_Missense_Mutation_p.K473E|CPNE1_uc010gfi.2_RNA|CPNE1_uc010gfj.2_RNA|CPNE1_uc002xdh.2_Missense_Mutation_p.K529E|CPNE1_uc002xdi.2_Missense_Mutation_p.K529E|CPNE1_uc002xdj.2_Missense_Mutation_p.K529E|CPNE1_uc002xdk.2_Missense_Mutation_p.K529E|CPNE1_uc002xdl.2_Missense_Mutation_p.K529E|CPNE1_uc002xdm.2_Missense_Mutation_p.K529E	NM_152931	NP_690908	Q99829	CPNE1_HUMAN	copine I isoform a	529					lipid metabolic process|vesicle-mediated transport		calcium-dependent phospholipid binding|phosphatidylserine binding|transporter activity			upper_aerodigestive_tract(1)	1	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			GCAGGATCCTTGGCTGAGGGT	0.627													88	207	---	---	---	---	PASS
ICOSLG	23308	broad.mit.edu	37	21	45651249	45651249	+	Missense_Mutation	SNP	A	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45651249A>C	uc002zee.2	-	5	910	c.776T>G	c.(775-777)ATC>AGC	p.I259S	ICOSLG_uc011afc.1_Missense_Mutation_p.I169S|ICOSLG_uc002zef.2_Missense_Mutation_p.I142S|ICOSLG_uc010gpp.1_Missense_Mutation_p.I259S	NM_015259	NP_056074	O75144	ICOSL_HUMAN	inducible T-cell co-stimulator ligand precursor	259	Helical; (Potential).				B cell activation|defense response|hyperosmotic response|positive regulation of activated T cell proliferation|signal transduction|T cell activation|T cell costimulation		receptor binding				0				Colorectal(79;0.0163)|READ - Rectum adenocarcinoma(84;0.0772)		GACAGCCAGGATGCTCCACGT	0.562													25	45	---	---	---	---	PASS
EP300	2033	broad.mit.edu	37	22	41489057	41489057	+	Missense_Mutation	SNP	A	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41489057A>G	uc003azl.3	+	1	444	c.49A>G	c.(49-51)AAA>GAA	p.K17E		NM_001429	NP_001420	Q09472	EP300_HUMAN	E1A binding protein p300	17	Interaction with ALX1.|Nuclear localization signal (Potential).				apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia	centrosome|histone acetyltransferase complex	androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1)	64						CAAGCGGCCTAAACTCTCATC	0.552			T| N|F|Mis|O	MLL|RUNXBP2	colorectal|breast|pancreatic|AML|ALL|DLBCL				Rubinstein-Taybi_syndrome				75	132	---	---	---	---	PASS
BMX	660	broad.mit.edu	37	X	15574250	15574250	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15574250C>T	uc004cww.2	+	19	2196	c.2008C>T	c.(2008-2010)CGG>TGG	p.R670W	BMX_uc004cwx.3_Missense_Mutation_p.R670W|BMX_uc004cwy.3_Missense_Mutation_p.R670W	NM_203281	NP_975010	P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase	670	Protein kinase.		R -> W (in a lung large cell carcinoma sample; somatic mutation).		cellular component disassembly involved in apoptosis|intracellular signal transduction|mesoderm development	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding|signal transducer activity	p.R670W(2)		lung(3)|ovary(2)	5	Hepatocellular(33;0.183)					TGAACCACTTCGGGAAAAAGA	0.383													56	127	---	---	---	---	PASS
ACE2	59272	broad.mit.edu	37	X	15599440	15599440	+	Missense_Mutation	SNP	T	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15599440T>G	uc004cxa.1	-	8	1142	c.974A>C	c.(973-975)CAA>CCA	p.Q325P	ACE2_uc004cxb.2_Missense_Mutation_p.Q325P	NM_021804	NP_068576	Q9BYF1	ACE2_HUMAN	angiotensin I converting enzyme 2 precursor	325	Extracellular (Potential).				angiotensin-mediated drinking behavior|proteolysis|receptor biosynthetic process|regulation of cell proliferation|virion attachment, binding of host cell surface receptor	cell surface|extracellular space|integral to membrane|membrane raft|plasma membrane	carboxypeptidase activity|glycoprotein binding|metallopeptidase activity|peptidyl-dipeptidase activity|viral receptor activity|zinc ion binding			ovary(3)	3	Hepatocellular(33;0.183)				Moexipril(DB00691)	CCAGAATCCTTGAGTCATATT	0.478													115	81	---	---	---	---	PASS
NKRF	55922	broad.mit.edu	37	X	118723319	118723319	+	Missense_Mutation	SNP	T	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118723319T>C	uc004erq.2	-	2	2722	c.2069A>G	c.(2068-2070)AAT>AGT	p.N690S	NKRF_uc004err.2_Missense_Mutation_p.N690S	NM_017544	NP_060014	O15226	NKRF_HUMAN	transcription factor NRF	690					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|double-stranded RNA binding			ovary(1)|central_nervous_system(1)	2						AAGATCTCAATTTGCTTGAGG	0.383													48	25	---	---	---	---	PASS
TKTL1	8277	broad.mit.edu	37	X	153558141	153558141	+	3'UTR	SNP	A	G	G			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153558141A>G	uc004fkg.2	+	13					TKTL1_uc011mzl.1_3'UTR|TKTL1_uc011mzm.1_3'UTR|TKTL1_uc004fkh.2_3'UTR	NM_012253	NP_036385	P51854	TKTL1_HUMAN	transketolase-like 1 isoform a						glucose catabolic process|thiamine metabolic process	cytoplasm|nucleus	metal ion binding|transketolase activity			ovary(3)|skin(1)	4	all_cancers(53;5.05e-16)|all_epithelial(53;1.82e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TCTTAAAAGCAAAGCCAGCTA	0.373													19	4	---	---	---	---	PASS
EXOSC10	5394	broad.mit.edu	37	1	11141199	11141200	+	Frame_Shift_Ins	INS	-	C	C			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11141199_11141200insC	uc001asa.2	-	11	1426_1427	c.1376_1377insG	c.(1375-1377)GGCfs	p.G459fs	EXOSC10_uc001asb.2_Frame_Shift_Ins_p.G459fs|EXOSC10_uc009vmy.1_Frame_Shift_Ins_p.G459fs	NM_001001998	NP_001001998	Q01780	EXOSX_HUMAN	exosome component 10 isoform 1	459					CUT catabolic process|histone mRNA catabolic process|maturation of 5.8S rRNA|nuclear polyadenylation-dependent rRNA catabolic process|nuclear retention of unspliced pre-mRNA at the site of transcription|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasm|nuclear exosome (RNase complex)|nucleolus|transcriptionally active chromatin	3'-5' exonuclease activity|exoribonuclease activity|identical protein binding|nucleotide binding|protein serine/threonine kinase activity|RNA binding			upper_aerodigestive_tract(1)	1	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.18e-07)|COAD - Colon adenocarcinoma(227;8.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000315)|Kidney(185;0.000832)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|READ - Rectum adenocarcinoma(331;0.0526)|STAD - Stomach adenocarcinoma(313;0.202)		GCTGCCCGTTGCCGCGCTCCCA	0.604													102	20	---	---	---	---	
FAM40A	85369	broad.mit.edu	37	1	110580466	110580484	+	Intron	DEL	TAAATAGAATGATCCTTTT	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110580466_110580484delTAAATAGAATGATCCTTTT	uc001dza.1	+						FAM40A_uc001dyz.1_Intron|FAM40A_uc009wfp.1_Intron	NM_033088	NP_149079	Q5VSL9	FA40A_HUMAN	hypothetical protein LOC85369							nucleus	protein binding			ovary(3)|large_intestine(1)	4		all_cancers(81;8.51e-05)|all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0154)|all cancers(265;0.0732)|Epithelial(280;0.0781)|Colorectal(144;0.115)|LUSC - Lung squamous cell carcinoma(189;0.137)		GTTTCTTTGATAAATAGAATGATCCTTTTTCCTAAAGCT	0.420													48	16	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145109975	145109976	+	Intron	INS	-	C	C	rs11458983		TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145109975_145109976insC	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|SEC22B_uc001eml.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						CAGGAACTTTGCTAAAGATCTA	0.386													3	5	---	---	---	---	
SH2D1B	117157	broad.mit.edu	37	1	162372496	162372498	+	Intron	DEL	TGT	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162372496_162372498delTGT	uc001gbz.1	-						SH2D1B_uc001gca.1_Intron	NM_053282	NP_444512	O14796	SH21B_HUMAN	SH2 domain containing 1B											pancreas(1)	1	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			CCAACTTTTGTGTTGTTGTTGTT	0.414													195	7	---	---	---	---	
XPR1	9213	broad.mit.edu	37	1	180843056	180843056	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180843056delT	uc001goi.2	+	13	1978	c.1786delT	c.(1786-1788)TTTfs	p.F596fs	XPR1_uc009wxn.2_Frame_Shift_Del_p.F531fs	NM_004736	NP_004727	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor	596	EXS.|Cytoplasmic (Potential).					integral to plasma membrane	G-protein coupled receptor activity				0						TGCTACTGTCTTTGCCCCACT	0.368													51	39	---	---	---	---	
C1orf21	81563	broad.mit.edu	37	1	184528723	184528724	+	Intron	INS	-	CCTT	CCTT	rs141160537	by1000genomes	TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184528723_184528724insCCTT	uc001gqv.1	+							NM_030806	NP_110433	Q9H246	CA021_HUMAN	chromosome 1 open reading frame 21												0		Breast(1374;0.00262)		Colorectal(1306;4.8e-08)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)		ctctcttcctcccttccttcct	0.010													4	2	---	---	---	---	
ELF3	1999	broad.mit.edu	37	1	201982385	201982389	+	Frame_Shift_Del	DEL	AAGAG	-	-	rs137861501		TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201982385_201982389delAAGAG	uc001gxg.3	+	6	3956_3960	c.764_768delAAGAG	c.(763-768)AAAGAGfs	p.K255fs	ELF3_uc001gxi.3_Frame_Shift_Del_p.K255fs|ELF3_uc001gxh.3_Frame_Shift_Del_p.K255fs	NM_004433	NP_004424	P78545	ELF3_HUMAN	E74-like factor 3 (ets domain transcription	255_256					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				0						AAGCTGAGCAAAGAGTACTGGGACT	0.644													71	66	---	---	---	---	
C1orf57	84284	broad.mit.edu	37	1	233091276	233091277	+	Intron	INS	-	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233091276_233091277insT	uc001hvj.1	+						C1orf57_uc001hvi.2_Intron|C1orf57_uc009xft.1_Intron	NM_032324	NP_115700	Q9BSD7	NTPCR_HUMAN	nucleoside-triphosphatase C1orf57								ATP binding|nucleoside-triphosphatase activity|nucleotide phosphatase activity|transferase activity				0		all_cancers(173;0.0818)|Prostate(94;0.137)				GGCttttcttcttttttttttt	0.366													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	34041837	34041838	+	IGR	INS	-	CCTCC	CCTCC	rs141683394	by1000genomes	TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34041837_34041838insCCTCC								MYADML (88553 upstream) : None (None downstream)																							tcttctcttctcctcccctccc	0.000													4	2	---	---	---	---	
DYNC2LI1	51626	broad.mit.edu	37	2	44032037	44032038	+	Intron	INS	-	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44032037_44032038insA	uc002rtk.2	+						DYNC2LI1_uc002rtj.2_Intron|DYNC2LI1_uc002rtl.2_Intron|DYNC2LI1_uc010ynz.1_Intron	NM_016008	NP_057092	Q8TCX1	DC2L1_HUMAN	dynein 2 light intermediate chain isoform 1							apical part of cell|axonemal dynein complex|cilium axoneme|cytoplasm|microtubule|motile primary cilium	motor activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				CTGTGGGGGTTAAAAAAAAAAA	0.361													4	2	---	---	---	---	
PNPT1	87178	broad.mit.edu	37	2	55895089	55895089	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55895089delT	uc002rzf.2	-	12	1034	c.981delA	c.(979-981)AAAfs	p.K327fs	PNPT1_uc002rzg.2_RNA	NM_033109	NP_149100	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	327					mRNA catabolic process|RNA processing	plasma membrane	3'-5'-exoribonuclease activity|polyribonucleotide nucleotidyltransferase activity|RNA binding				0			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			CTTCTGGAAATTTTTCTATAG	0.284													65	19	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	60173938	60173939	+	IGR	INS	-	TG	TG	rs138732608	by1000genomes	TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60173938_60173939insTG								None (None upstream) : BCL11A (504364 downstream)																							TTGTGTTTGATtgtgtgtgtgt	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	73583885	73583886	+	IGR	INS	-	AAGGAAGGAAGG	AAGGAAGGAAGG	rs147210009	by1000genomes	TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73583885_73583886insAAGGAAGGAAGG								EGR4 (63056 upstream) : ALMS1 (29000 downstream)																							aaaaagaaagaaaggaaggaag	0.000													4	3	---	---	---	---	
CKAP2L	150468	broad.mit.edu	37	2	113503944	113503948	+	Intron	DEL	AACTC	-	-	rs111479646		TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113503944_113503948delAACTC	uc002tie.2	-						CKAP2L_uc002tif.2_Intron|CKAP2L_uc010yxp.1_Intron	NM_152515	NP_689728	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like							centrosome					0						AACAACAGAGAACTCACATGAAAGA	0.332													222	27	---	---	---	---	
PPARG	5468	broad.mit.edu	37	3	12434280	12434293	+	Intron	DEL	TATTATTCTCATTA	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12434280_12434293delTATTATTCTCATTA	uc003bwx.2	+						PPARG_uc003bwr.2_Intron|PPARG_uc003bws.2_Intron|PPARG_uc003bwu.2_Intron|PPARG_uc003bwv.2_Intron|PPARG_uc010hea.1_Intron|PPARG_uc003bwq.1_Intron|PPARG_uc003bwt.1_Intron|PPARG_uc003bww.1_Intron	NM_015869	NP_056953	P37231	PPARG_HUMAN	peroxisome proliferative activated receptor						activation of caspase activity|cell fate commitment|cell maturation|cellular response to insulin stimulus|epithelial cell differentiation|glucose homeostasis|induction of apoptosis|innate immune response|lipid homeostasis|lipoprotein transport|long-chain fatty acid transport|low-density lipoprotein particle receptor biosynthetic process|monocyte differentiation|negative regulation of cholesterol storage|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|placenta development|positive regulation of fat cell differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to lipid|response to low-density lipoprotein particle stimulus|white fat cell differentiation	cytosol|nucleoplasm	activating transcription factor binding|arachidonic acid binding|drug binding|enzyme binding|prostaglandin receptor activity|retinoid X receptor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|kidney(1)	2					Atorvastatin(DB01076)|Icosapent(DB00159)|Pioglitazone(DB01132)|Rosiglitazone(DB00412)|Troglitazone(DB00197)	CCATATACTTTATTATTCTCATTATAGCTGCCAG	0.360			T	PAX8	follicular thyroid		Insulin resistance ; lipodystrophy|familial partial L;diabetes mellitus|insulin-resistantI|with acanthosis nigricans and hypertension						318	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	99015537	99015538	+	IGR	INS	-	ACAC	ACAC	rs150126551	by1000genomes	TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99015537_99015538insACAC								DCBLD2 (395004 upstream) : COL8A1 (341916 downstream)																							cagacacacagacacacacaca	0.272													4	2	---	---	---	---	
TBC1D14	57533	broad.mit.edu	37	4	6998263	6998263	+	Intron	DEL	A	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6998263delA	uc011bwg.1	+						TBC1D14_uc003gjs.3_Intron|TBC1D14_uc010idh.2_Intron|TBC1D14_uc011bwh.1_5'Flank	NM_001113361	NP_001106832	Q9P2M4	TBC14_HUMAN	TBC1 domain family, member 14 isoform a							intracellular	Rab GTPase activator activity			ovary(1)|pancreas(1)	2						GTCTTCCAGTAAAAAAAAAAA	0.224													3	4	---	---	---	---	
STIM2	57620	broad.mit.edu	37	4	27009063	27009063	+	Intron	DEL	T	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27009063delT	uc003gsh.3	+						STIM2_uc003gsg.3_Intron|STIM2_uc010iex.2_Intron|STIM2_uc010iey.2_Intron	NM_020860	NP_065911	Q9P246	STIM2_HUMAN	stromal interaction molecule 2						activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)				TTAAAATAGCTTTTTTTTTTT	0.169													4	2	---	---	---	---	
WDR19	57728	broad.mit.edu	37	4	39216394	39216394	+	Intron	DEL	T	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39216394delT	uc003gtv.2	+						WDR19_uc010ifl.1_Intron|WDR19_uc003gtu.1_Intron|WDR19_uc011byi.1_Intron|WDR19_uc003gtw.1_5'Flank	NM_025132	NP_079408	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19						cell projection organization	microtubule basal body|motile cilium|photoreceptor connecting cilium	binding			large_intestine(1)	1						GGAGGAATAAttttttttttt	0.169													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	61289208	61289208	+	IGR	DEL	A	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:61289208delA								None (None upstream) : LPHN3 (777766 downstream)																							cactgcaaggaaggaagggag	0.000													4	2	---	---	---	---	
NSUN2	54888	broad.mit.edu	37	5	6623158	6623158	+	Intron	DEL	A	-	-	rs111573762		TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6623158delA	uc003jdu.2	-						NSUN2_uc003jdt.2_5'Flank|NSUN2_uc011cmk.1_Intron|NSUN2_uc003jdv.2_Intron	NM_017755	NP_060225	Q08J23	NSUN2_HUMAN	NOL1/NOP2/Sun domain family, member 2							cytoplasm|nucleolus	tRNA (cytosine-5-)-methyltransferase activity|tRNA binding			ovary(1)	1						GACaaaaaagaaaaaaaaaaa	0.259													4	3	---	---	---	---	
TNPO1	3842	broad.mit.edu	37	5	72195791	72195816	+	Intron	DEL	GTTGGCGTTTGGTGGTGTATAACCGT	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72195791_72195816delGTTGGCGTTTGGTGGTGTATAACCGT	uc003kck.3	+						TNPO1_uc011csj.1_Intron|TNPO1_uc003kch.2_Intron|TNPO1_uc003kci.3_Intron|TNPO1_uc003kcg.3_Intron	NM_002270	NP_002261	Q92973	TNPO1_HUMAN	transportin 1 isoform 1						interspecies interaction between organisms|mRNA metabolic process|protein import into nucleus, translocation	cytosol|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			skin(3)|urinary_tract(1)|ovary(1)|kidney(1)|central_nervous_system(1)	7		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		TCATGTCTTGGTTGGCGTTTGGTGGTGTATAACCGTGATTGCGTTA	0.398													105	18	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	139686076	139686077	+	IGR	INS	-	AAGG	AAGG			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139686076_139686077insAAGG								PFDN1 (3387 upstream) : HBEGF (26352 downstream)																							agaaagggagaaaggaaggaag	0.000													4	3	---	---	---	---	
ITPR3	3710	broad.mit.edu	37	6	33655955	33655971	+	Intron	DEL	GGGCAGCAGGGGCGGGC	-	-	rs147230646	by1000genomes	TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33655955_33655971delGGGCAGCAGGGGCGGGC	uc011drk.1	+						ITPR3_uc003oey.2_Intron	NM_002224	NP_002215	Q14573	ITPR3_HUMAN	inositol 1,4,5-triphosphate receptor, type 3						activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding			ovary(6)|lung(5)|central_nervous_system(5)|breast(2)|kidney(1)	19						GTGGGCCTGTGGGCAGCAGGGGCGGGCGTGGGAGCCT	0.645													94	12	---	---	---	---	
CENPQ	55166	broad.mit.edu	37	6	49459995	49459995	+	3'UTR	DEL	T	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49459995delT	uc003ozh.1	+	9						NM_018132	NP_060602	Q7L2Z9	CENPQ_HUMAN	centromere protein Q						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	chromosome, centromeric region|cytosol|nucleoplasm				ovary(2)	2	Lung NSC(77;0.0128)					TTAAAGAGTGTTTTTTTTTTA	0.318													58	7	---	---	---	---	
DST	667	broad.mit.edu	37	6	56373242	56373243	+	Intron	INS	-	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56373242_56373243insT	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TGTTAACAGAGTAACTCCTAAC	0.332													20	7	---	---	---	---	
ORC3L	23595	broad.mit.edu	37	6	88299926	88299927	+	Intron	INS	-	GCGC	GCGC			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88299926_88299927insGCGC	uc003pmh.2	+						ORC3L_uc011dzl.1_Intron|ORC3L_uc011dzm.1_Intron|ORC3L_uc011dzn.1_Intron|ORC3L_uc003pmg.2_Intron|ORC3L_uc003pmi.2_Intron|ORC3L_uc011dzo.1_Intron|ORC3L_uc011dzp.1_Intron|RARS2_uc003pmb.2_5'Flank|RARS2_uc003pmc.2_5'Flank|RARS2_uc003pmd.2_5'Flank|RARS2_uc003pme.2_5'Flank|RARS2_uc003pmf.2_5'Flank	NM_012381	NP_036513	Q9UBD5	ORC3_HUMAN	origin recognition complex, subunit 3 isoform 2						cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA replication origin binding|protein binding				0		all_cancers(76;9.05e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;5.29e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.0469)		TGGTGGCCGATGCGCACTGTGG	0.599													115	17	---	---	---	---	
TPD52L1	7164	broad.mit.edu	37	6	125493266	125493267	+	Intron	INS	-	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125493266_125493267insT	uc003pzu.1	+						TPD52L1_uc003pzv.1_Intron|TPD52L1_uc003pzw.1_Intron|TPD52L1_uc003pzx.1_Intron|TPD52L1_uc003pzy.1_Intron	NM_003287	NP_003278	Q16890	TPD53_HUMAN	tumor protein D52-like 1 isoform 1						DNA fragmentation involved in apoptotic nuclear change|G2/M transition of mitotic cell cycle|induction of apoptosis|positive regulation of JNK cascade|positive regulation of MAP kinase activity	perinuclear region of cytoplasm	caspase activator activity|protein heterodimerization activity|protein homodimerization activity				0			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0265)		ttctttctttctttctttcttt	0.035													4	2	---	---	---	---	
LAMA2	3908	broad.mit.edu	37	6	129498972	129498972	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129498972delC	uc003qbn.2	+	10	1533	c.1428delC	c.(1426-1428)AGCfs	p.S476fs	LAMA2_uc003qbo.2_Frame_Shift_Del_p.S476fs	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	476	Laminin EGF-like 4.				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GGTTAGGGAGCAAAAATGAGG	0.478													83	37	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	1343348	1343352	+	IGR	DEL	AGAGG	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1343348_1343352delAGAGG								UNCX (66736 upstream) : MICALL2 (130644 downstream)																							aggaaaggaaagaggagaggagagg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	2433788	2433788	+	IGR	DEL	T	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2433788delT								EIF3B (13413 upstream) : CHST12 (9435 downstream)																							tttcttcttcttttttttttt	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	22813177	22813178	+	IGR	INS	-	C	C	rs145036723	by1000genomes	TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22813177_22813178insC								IL6 (41558 upstream) : TOMM7 (39076 downstream)																							TCCTAGATAAGCCCCTACACTC	0.337													5	3	---	---	---	---	
PMS2L4	5382	broad.mit.edu	37	7	66762433	66762433	+	Intron	DEL	A	-	-	rs68053451		TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66762433delA	uc003tvo.2	-						PMS2L4_uc003tvq.2_Intron|PMS2L4_uc003tvr.3_Intron|PMS2L4_uc003tvs.3_Intron					Homo sapiens cDNA clone IMAGE:4081618.												0						tctcaaaaagaaaaaaaaaaa	0.124													4	2	---	---	---	---	
CPA2	1358	broad.mit.edu	37	7	129919306	129919318	+	Frame_Shift_Del	DEL	CTGGAGCCAGCAG	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129919306_129919318delCTGGAGCCAGCAG	uc003vpq.2	+	9	810_822	c.791_803delCTGGAGCCAGCAG	c.(790-804)CCTGGAGCCAGCAGCfs	p.P264fs		NM_001869	NP_001860	P48052	CBPA2_HUMAN	carboxypeptidase A2 (pancreatic) precursor	264_268					proteolysis|vacuolar protein catabolic process	extracellular region|vacuole	metallocarboxypeptidase activity|zinc ion binding			ovary(1)	1	Melanoma(18;0.0435)					TCCCCAGGACCTGGAGCCAGCAGCAACCCTTGC	0.502													84	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	144703242	144703243	+	IGR	INS	-	A	A			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144703242_144703243insA								TPK1 (170096 upstream) : None (None downstream)																							TACTGCCATGCAAAGGGCATGG	0.554													95	29	---	---	---	---	
XKR6	286046	broad.mit.edu	37	8	11058892	11058892	+	5'Flank	DEL	C	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11058892delC	uc003wtk.1	-							NM_173683	NP_775954	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related							integral to membrane				ovary(1)|skin(1)	2				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)		ggagggacggcgggggggggg	0.249													4	2	---	---	---	---	
IMPAD1	54928	broad.mit.edu	37	8	57905985	57906000	+	Frame_Shift_Del	DEL	CCGCGGGCCCCGCCGC	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57905985_57906000delCCGCGGGCCCCGCCGC	uc003xte.3	-	1	428_443	c.145_160delGCGGCGGGGCCCGCGG	c.(145-162)GCGGCGGGGCCCGCGGCCfs	p.A49fs		NM_017813	NP_060283	Q9NX62	IMPA3_HUMAN	inositol monophosphatase domain containing 1	49_54	Poly-Ala.					Golgi apparatus|integral to membrane	inositol-1(or 4)-monophosphatase activity|metal ion binding			ovary(1)	1		all_cancers(86;0.175)|all_lung(136;0.0321)|Lung NSC(129;0.0417)|all_epithelial(80;0.0448)				TcggccgcggccgcgggccccgccgcgccgccgccA	0.588													9	5	---	---	---	---	
MRPL13	28998	broad.mit.edu	37	8	121411176	121411177	+	Intron	DEL	AC	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121411176_121411177delAC	uc003ypa.2	-						MRPL13_uc010mdf.2_Intron	NM_014078	NP_054797	Q9BYD1	RM13_HUMAN	mitochondrial ribosomal protein L13						translation	mitochondrial large ribosomal subunit	protein binding|structural constituent of ribosome			central_nervous_system(1)	1	Lung NSC(37;1.69e-07)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			acacacacaaacacacacacac	0.000													4	2	---	---	---	---	
FER1L6	654463	broad.mit.edu	37	8	125034095	125034096	+	Intron	INS	-	T	T	rs138450142	by1000genomes	TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125034095_125034096insT	uc003yqw.2	+						uc003yqx.1_Intron	NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6							integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			AGCTTTATTCATTTTTTTTTCA	0.386													7	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	127178246	127178277	+	IGR	DEL	CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTC	-	-	rs143003783	by1000genomes	TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127178246_127178277delCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTC								TRIB1 (727604 upstream) : FAM84B (386410 downstream)																							ttccttccttccttccttccttccttccttccttccttcctcccttccttcc	0.004													9	11	---	---	---	---	
KIF27	55582	broad.mit.edu	37	9	86523674	86523674	+	Intron	DEL	T	-	-	rs34030009		TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86523674delT	uc004ana.2	-						KIF27_uc010mpw.2_Intron|KIF27_uc010mpx.2_Intron	NM_017576	NP_060046	Q86VH2	KIF27_HUMAN	kinesin family member 27						cilium assembly|microtubule-based movement	cilium|cytoplasm|microtubule	ATP binding|microtubule motor activity			lung(4)|skin(1)	5						ATATTATAACttttttttttt	0.119													5	4	---	---	---	---	
RALGDS	5900	broad.mit.edu	37	9	135977871	135977872	+	Frame_Shift_Ins	INS	-	CGCT	CGCT			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135977871_135977872insCGCT	uc004cco.2	-	14	2020_2021	c.2000_2001insAGCG	c.(1999-2001)CGCfs	p.R667fs	RALGDS_uc004cct.1_5'Flank|RALGDS_uc004ccn.2_5'Flank|RALGDS_uc004ccp.2_RNA|RALGDS_uc004ccq.2_Frame_Shift_Ins_p.R655fs|RALGDS_uc004ccr.2_Frame_Shift_Ins_p.R666fs|RALGDS_uc011mcv.1_Frame_Shift_Ins_p.R638fs|RALGDS_uc004ccs.2_Frame_Shift_Ins_p.R612fs|RALGDS_uc011mcw.1_Frame_Shift_Ins_p.R738fs|RALGDS_uc004ccv.1_Frame_Shift_Ins_p.R436fs|RALGDS_uc004ccu.1_Frame_Shift_Ins_p.R436fs	NM_006266	NP_006257	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	667					nerve growth factor receptor signaling pathway|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol	Ral guanyl-nucleotide exchange factor activity			large_intestine(1)|lung(1)|ovary(1)	3				OV - Ovarian serous cystadenocarcinoma(145;3.66e-06)|Epithelial(140;2.77e-05)		ACTCGCTCCAGCGCTTGACAAT	0.515			T	CIITA	PMBL|Hodgkin Lymphona|								155	19	---	---	---	---	
AKR1C2	1646	broad.mit.edu	37	10	5041594	5041595	+	Intron	INS	-	C	C	rs11818926	by1000genomes	TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5041594_5041595insC	uc010qan.1	-						AKR1E2_uc001ihl.1_Intron|AKR1C3_uc001ihr.2_Intron|AKR1C2_uc009xhy.2_Intron|AKR1C2_uc001ihs.2_Intron|AKR1C2_uc001iht.2_Intron	NM_205845	NP_995317	P52895	AK1C2_HUMAN	aldo-keto reductase family 1, member C2						digestion|prostaglandin metabolic process|steroid metabolic process	cytoplasm	androsterone dehydrogenase (A-specific) activity|bile acid binding|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity				0					NADH(DB00157)|Ursodeoxycholic acid(DB01586)	CCAGAGAGTGGTATGTACAAAG	0.401													10	7	---	---	---	---	
AKR1CL1	340811	broad.mit.edu	37	10	5202044	5202044	+	Intron	DEL	A	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5202044delA	uc009xhz.2	-							NR_027916				Homo sapiens cDNA FLJ16347 fis, clone TESTI2036288, moderately similar to PROSTAGLANDIN-F SYNTHASE 1 (EC 1.1.1.188).												0						TGTGAACAGCAAAAAGTCAGA	0.348													4	2	---	---	---	---	
PLA2G16	11145	broad.mit.edu	37	11	63381431	63381437	+	Intron	DEL	GGCTCCC	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63381431_63381437delGGCTCCC	uc001nxh.2	-						PLA2G16_uc001nxi.2_Intron|PLA2G16_uc009you.1_Intron	NM_007069	NP_009000	P53816	PAG16_HUMAN	HRAS-like suppressor 3						lipid catabolic process	integral to membrane|perinuclear region of cytoplasm	hydrolase activity|protein binding			ovary(1)	1						ACTAACAGGGGGCTcccagccccgccc	0.517													107	23	---	---	---	---	
ARHGEF17	9828	broad.mit.edu	37	11	73057719	73057719	+	Intron	DEL	G	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73057719delG	uc001otu.2	+							NM_014786	NP_055601	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity				0						GGTGTAAGTCGGGGGCAGGGG	0.652													4	2	---	---	---	---	
CASP5	838	broad.mit.edu	37	11	104869775	104869776	+	Intron	INS	-	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104869775_104869776insT	uc010rva.1	-						CASP5_uc010ruz.1_Intron|CASP5_uc010rvb.1_Intron|CASP5_uc010rvc.1_Intron|CASP5_uc009yxh.2_Intron|CASP5_uc010rvd.1_Intron	NM_004347	NP_004338	P51878	CASP5_HUMAN	caspase 5 isoform a precursor						apoptosis|cellular response to mechanical stimulus|proteolysis|regulation of apoptosis	intracellular	cysteine-type endopeptidase activity|protein binding			ovary(2)|lung(1)	3		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000943)|Epithelial(105;0.0104)|all cancers(92;0.042)		CATCAACTttctttttttttta	0.238													54	7	---	---	---	---	
PPHLN1	51535	broad.mit.edu	37	12	42692995	42692996	+	Intron	INS	-	A	A	rs5797787		TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42692995_42692996insA	uc001rmy.2	+							NM_201439	NP_958847	Q8NEY8	PPHLN_HUMAN	periphilin 1 isoform 3						keratinization	cytoplasm|nucleus				ovary(1)|breast(1)	2	all_cancers(12;0.00049)|Breast(8;0.165)	Lung NSC(34;0.123)		GBM - Glioblastoma multiforme(48;0.0875)		aagactctgtcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
MDM2	4193	broad.mit.edu	37	12	69210560	69210577	+	Intron	DEL	TTTAATGCTCAGAAATCA	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69210560_69210577delTTTAATGCTCAGAAATCA	uc001sui.2	+						MDM2_uc009zri.2_Intron|MDM2_uc009zqx.2_Intron|MDM2_uc009zqw.2_Intron|MDM2_uc001suk.2_Intron|MDM2_uc009zqy.1_Intron|MDM2_uc001sun.3_Intron|MDM2_uc009zqz.2_Intron|MDM2_uc009zra.2_Intron|MDM2_uc009zrb.1_Intron|MDM2_uc001sum.1_Intron|MDM2_uc009zrd.2_Intron|MDM2_uc009zrc.2_Intron|MDM2_uc009zre.2_Intron|MDM2_uc009zrf.2_Intron|MDM2_uc001suo.2_Intron|MDM2_uc009zrg.2_Intron|MDM2_uc009zrh.2_Intron	NM_002392	NP_002383	Q00987	MDM2_HUMAN	mouse double minute 2 homolog isoform MDM2						cellular response to hypoxia|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|establishment of protein localization|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell cycle arrest|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of cell proliferation|positive regulation of mitotic cell cycle|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein complex assembly|protein destabilization|protein localization to nucleus|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to antibiotic|synaptic transmission	cytosol|endocytic vesicle membrane|insoluble fraction|nucleolus|nucleoplasm|plasma membrane|protein complex	enzyme binding|identical protein binding|p53 binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)|central_nervous_system(1)	3	all_cancers(1;8.46e-121)|all_epithelial(5;3.21e-36)|Lung NSC(4;2.16e-33)|all_lung(4;3.03e-31)|Glioma(1;1.9e-09)|Breast(13;1.59e-06)|all_neural(1;1.03e-05)|Melanoma(1;0.0171)|Renal(347;0.0684)		all cancers(2;8.67e-65)|GBM - Glioblastoma multiforme(2;8.89e-62)|BRCA - Breast invasive adenocarcinoma(5;2.43e-08)|Lung(24;1.5e-05)|LUAD - Lung adenocarcinoma(15;8.5e-05)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			TTTAGTTTTCTTTAATGCTCAGAAATCATATTTGTATT	0.284			A		sarcoma|glioma|colorectal|other								44	11	---	---	---	---	
BBS10	79738	broad.mit.edu	37	12	76742124	76742126	+	In_Frame_Del	DEL	CAT	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76742124_76742126delCAT	uc001syd.1	-	1	97_99	c.13_15delATG	c.(13-15)ATGdel	p.M5del		NM_024685	NP_078961	Q8TAM1	BBS10_HUMAN	Bardet-Biedl syndrome 10	5					cellular protein metabolic process|nonmotile primary cilium assembly|photoreceptor cell maintenance|response to stimulus|retina homeostasis	cilium	ATP binding			ovary(1)|skin(1)	2						CTGCAGCGGCCATAGAACTTAAC	0.611									Bardet-Biedl_syndrome		OREG0022001	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	18	10	---	---	---	---	
PLEKHG7	440107	broad.mit.edu	37	12	93155419	93155419	+	Intron	DEL	A	-	-	rs145042614	by1000genomes	TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93155419delA	uc001tcj.2	+							NM_001004330	NP_001004330	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1						agaaagaaagaaagaaagaaa	0.090													4	3	---	---	---	---	
KSR2	283455	broad.mit.edu	37	12	117965154	117965157	+	Intron	DEL	ACAC	-	-	rs7309204		TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117965154_117965157delACAC	uc001two.2	-							NM_173598	NP_775869	Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2						intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					acacacacagacacacacacacac	0.230													4	2	---	---	---	---	
SRRM4	84530	broad.mit.edu	37	12	119560098	119560105	+	Intron	DEL	AGGAAGGA	-	-	rs146974381	by1000genomes	TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119560098_119560105delAGGAAGGA	uc001txa.1	+							NM_194286	NP_919262	A7MD48	SRRM4_HUMAN	KIAA1853 protein						cell differentiation|mRNA processing|nervous system development|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding			ovary(2)	2						gcaggaaggcaggaaggaaggaaggaag	0.197													5	3	---	---	---	---	
PRKAB1	5564	broad.mit.edu	37	12	120110460	120110461	+	Intron	DEL	AG	-	-	rs150497180		TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120110460_120110461delAG	uc009zwu.2	+						PRKAB1_uc001txg.2_Intron	NM_006253	NP_006244	Q9Y478	AAKB1_HUMAN	AMP-activated protein kinase beta 1						cell cycle arrest|fatty acid biosynthetic process|insulin receptor signaling pathway|regulation of fatty acid oxidation	cytosol					0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.166)	Adenosine monophosphate(DB00131)|Metformin(DB00331)	TACAGAAGAAAGAGAATATTTC	0.342													3	6	---	---	---	---	
LOC374491	374491	broad.mit.edu	37	13	25169014	25169015	+	Intron	INS	-	TAG	TAG			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25169014_25169015insTAG	uc001upm.2	+						LOC374491_uc001upn.2_Intron|LOC374491_uc001upo.2_Intron					Homo sapiens mRNA; cDNA DKFZp434J0717 (from clone DKFZp434J0717).												0						actgactggaaagagagttagg	0.000													13	11	---	---	---	---	
CDADC1	81602	broad.mit.edu	37	13	49833659	49833660	+	Splice_Site	INS	-	GTAA	GTAA			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49833659_49833660insGTAA	uc001vcu.2	+	4	506	c.430_splice	c.e4+1	p.A144_splice	CDADC1_uc001vcs.1_Splice_Site|CDADC1_uc001vct.1_Splice_Site_p.A26_splice|CDADC1_uc010tgk.1_Intron|CDADC1_uc001vcv.2_Splice_Site	NM_030911	NP_112173	Q9BWV3	CDAC1_HUMAN	cytidine and dCMP deaminase domain containing 1								hydrolase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		Lung NSC(96;0.000705)|Breast(56;0.0011)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;1.06e-08)|COAD - Colon adenocarcinoma(199;0.216)		GATTGTAAATGGTAAGTGCAGA	0.272													156	16	---	---	---	---	
ABCC4	10257	broad.mit.edu	37	13	95714740	95714741	+	Intron	INS	-	CACACACA	CACACACA	rs141058174	by1000genomes	TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95714740_95714741insCACACACA	uc001vmd.3	-						ABCC4_uc010afj.2_Intron|ABCC4_uc010afk.2_Intron	NM_005845	NP_005836	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)	TTATTAAATATcacacacacac	0.287													4	2	---	---	---	---	
ZC3H14	79882	broad.mit.edu	37	14	89029871	89029881	+	Intron	DEL	CCCAGCCCCCG	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89029871_89029881delCCCAGCCCCCG	uc001xww.2	+						ZC3H14_uc010twd.1_Intron|ZC3H14_uc010twe.1_Intron|ZC3H14_uc001xwx.2_Intron|ZC3H14_uc010twf.1_Intron|ZC3H14_uc001xwy.2_Intron	NM_024824	NP_079100	Q6PJT7	ZC3HE_HUMAN	zinc finger CCCH-type containing 14 isoform 1							cytoplasm|cytoplasm|nuclear speck	protein binding|RNA binding|zinc ion binding			ovary(2)|skin(1)	3						CGAGGCTCCTCCCAGCCCCCGCCCGGGGGAT	0.711													12	10	---	---	---	---	
MT1A	4489	broad.mit.edu	37	16	56672500	56672519	+	5'Flank	DEL	GCGCAGGCGCAGGGCGGGTC	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56672500_56672519delGCGCAGGCGCAGGGCGGGTC	uc002ejq.2	+						MT1A_uc002eji.2_Intron	NM_005946	NP_005937	P04731	MT1A_HUMAN	metallothionein 1A							cytoplasm	cadmium ion binding|copper ion binding|zinc ion binding				0						AGCGGGGCGGGCGCAGGCGCAGGGCGGGTCCTTTGCGTCC	0.664													7	9	---	---	---	---	
PHLPP2	23035	broad.mit.edu	37	16	71690658	71690658	+	Intron	DEL	T	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71690658delT	uc002fax.2	-						PHLPP2_uc002fav.2_Intron|PHLPP2_uc010cgf.2_Intron	NM_015020	NP_055835	Q6ZVD8	PHLP2_HUMAN	PH domain and leucine rich repeat protein							cytoplasm|membrane|nucleus	metal ion binding|phosphoprotein phosphatase activity			ovary(1)|central_nervous_system(1)	2						AATAGTAttcttttttttttt	0.164													46	7	---	---	---	---	
PMFBP1	83449	broad.mit.edu	37	16	72205093	72205101	+	Splice_Site	DEL	TACCTCATC	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72205093_72205101delTACCTCATC	uc002fcc.3	-	2	184	c.12_splice	c.e2+1	p.E4_splice	PMFBP1_uc002fcd.2_Splice_Site_p.E4_splice|PMFBP1_uc002fce.2_Splice_Site|PMFBP1_uc002fcf.2_Splice_Site	NM_031293	NP_112583	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1											ovary(2)	2		Ovarian(137;0.179)				TTAGGAGCCTTACCTCATCTTTCATTTCC	0.330													179	14	---	---	---	---	
RCVRN	5957	broad.mit.edu	37	17	9801300	9801301	+	3'UTR	DEL	TG	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9801300_9801301delTG	uc002gme.1	-	3						NM_002903	NP_002894	P35243	RECO_HUMAN	recoverin						visual perception		calcium ion binding|calcium sensitive guanylate cyclase activator activity				0						CTGGGGTGGAtgtgtgtgtgtg	0.446													22	7	---	---	---	---	
ALDH3A2	224	broad.mit.edu	37	17	19576700	19576700	+	Intron	DEL	T	-	-	rs66737570		TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19576700delT	uc002gwb.1	+						ALDH3A2_uc002gwa.1_Intron|ALDH3A2_uc010cqr.1_Intron|ALDH3A2_uc002gwc.1_Intron|ALDH3A2_uc002gwd.1_Intron	NM_000382	NP_000373	P51648	AL3A2_HUMAN	aldehyde dehydrogenase 3A2 isoform 2						cellular aldehyde metabolic process|central nervous system development|epidermis development|lipid metabolic process|peripheral nervous system development	endoplasmic reticulum membrane|integral to membrane	3-chloroallyl aldehyde dehydrogenase activity|aldehyde dehydrogenase (NAD) activity|aldehyde dehydrogenase			ovary(2)	2	all_cancers(12;1.39e-05)|all_epithelial(12;0.00158)|Breast(13;0.245)				NADH(DB00157)	tttatttttgttttttttttg	0.184													11	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21518762	21518763	+	IGR	DEL	AT	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21518762_21518763delAT								C17orf51 (41031 upstream) : FAM27L (306607 downstream)																							TCTCTGTCACATATTTTTTTCT	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	22066949	22066949	+	IGR	DEL	T	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:22066949delT								FLJ36000 (153879 upstream) : None (None downstream)																							CCAGAAAAAATATGTGAGAGA	0.323													8	4	---	---	---	---	
EFCAB5	374786	broad.mit.edu	37	17	28419180	28419181	+	Intron	INS	-	T	T			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28419180_28419181insT	uc002het.2	+						EFCAB5_uc010cse.2_Intron|EFCAB5_uc010csf.2_Intron	NM_198529	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5 isoform a								calcium ion binding			ovary(1)|skin(1)	2						AAATTTGTAAGTTTTTTTTTAA	0.248													52	8	---	---	---	---	
UBTF	7343	broad.mit.edu	37	17	42285461	42285472	+	Intron	DEL	TTTTTTTTTTTT	-	-	rs10542928		TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42285461_42285472delTTTTTTTTTTTT	uc002igb.2	-						UBTF_uc002igc.2_Intron|UBTF_uc010czs.2_Intron|UBTF_uc002igd.2_Intron|UBTF_uc010czt.2_Intron	NM_014233	NP_055048	P17480	UBF1_HUMAN	upstream binding transcription factor, RNA						positive regulation of transcription from RNA polymerase I promoter|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleolus|nucleoplasm	DNA binding|protein binding				0		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		ACAGCTCTAAtttttttttttttttttttttt	0.151													4	2	---	---	---	---	
CYTH1	9267	broad.mit.edu	37	17	76696603	76696603	+	Intron	DEL	T	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76696603delT	uc002jvw.2	-						CYTH1_uc010wtw.1_Intron|CYTH1_uc010wtx.1_Intron	NM_017456	NP_059430	Q15438	CYH1_HUMAN	cytohesin 1 isoform 2						regulation of ARF protein signal transduction|regulation of cell adhesion|vesicle-mediated transport	cytoplasm|plasma membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1						CTGCCAATGAttttttttttc	0.229													4	2	---	---	---	---	
LAMA3	3909	broad.mit.edu	37	18	21437864	21437877	+	Frame_Shift_Del	DEL	GCTTTCCTGAGTGT	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21437864_21437877delGCTTTCCTGAGTGT	uc002kuq.2	+	33	4279_4292	c.4193_4206delGCTTTCCTGAGTGT	c.(4192-4206)CGCTTTCCTGAGTGTfs	p.R1398fs	LAMA3_uc002kur.2_Frame_Shift_Del_p.R1398fs	NM_198129	NP_937762	Q16787	LAMA3_HUMAN	laminin alpha 3 subunit isoform 1	1398_1402	Domain III B.|Laminin EGF-like 11.				cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|skin(2)|central_nervous_system(1)	11	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	GGGTTTTACCGCTTTCCTGAGTGTGTTCCCTGCA	0.519													105	53	---	---	---	---	
ME2	4200	broad.mit.edu	37	18	48450474	48450480	+	Frame_Shift_Del	DEL	AAAGCAA	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48450474_48450480delAAAGCAA	uc002ley.2	+	11	1319_1325	c.1063_1069delAAAGCAA	c.(1063-1071)AAAGCAAAAfs	p.K355fs	ME2_uc010dpd.2_Frame_Shift_Del_p.K355fs	NM_002396	NP_002387	P23368	MAOM_HUMAN	malic enzyme 2, NAD(+)-dependent, mitochondrial	355_357					malate metabolic process	mitochondrial matrix	electron carrier activity|malate dehydrogenase (decarboxylating) activity|malate dehydrogenase (oxaloacetate-decarboxylating) activity|metal ion binding|NAD binding				0		Colorectal(6;0.0273)|all_epithelial(6;0.118)		Colorectal(21;0.0313)|READ - Rectum adenocarcinoma(32;0.105)|STAD - Stomach adenocarcinoma(97;0.184)	NADH(DB00157)	TTAGGGACGGAAAGCAAAAATAGATAG	0.314													60	38	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	3131446	3131446	+	IGR	DEL	C	-	-	rs66993077		TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3131446delC								GNA11 (9994 upstream) : GNA15 (4745 downstream)																							aaaaaaaaaacaaaaaaaaaa	0.348													3	4	---	---	---	---	
FSD1	79187	broad.mit.edu	37	19	4311683	4311683	+	Intron	DEL	A	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4311683delA	uc002lzy.2	+						FSD1_uc002lzz.2_Intron|FSD1_uc002maa.2_5'UTR	NM_024333	NP_077309	Q9BTV5	FSD1_HUMAN	fibronectin type III and SPRY domain containing						cell division|mitosis	cleavage furrow|microtubule|microtubule organizing center|nucleus				skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.034)|STAD - Stomach adenocarcinoma(1328;0.18)		ctctgtctctaaaaaaaaaaa	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	4778409	4778412	+	IGR	DEL	CTTC	-	-	rs111648876	by1000genomes	TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4778409_4778412delCTTC								C19orf30 (5842 upstream) : FEM1A (13316 downstream)																							ttctttctttcttccttccttcct	0.000													5	3	---	---	---	---	
FBXW9	84261	broad.mit.edu	37	19	12800714	12800728	+	Intron	DEL	AGCTCAGGCCGGGCT	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12800714_12800728delAGCTCAGGCCGGGCT	uc010xmp.1	-						uc002mul.1_3'UTR|FBXW9_uc002mum.1_Intron|FBXW9_uc002mun.1_Intron|FBXW9_uc010dyx.2_Intron			Q5XUX1	FBXW9_HUMAN	Homo sapiens cDNA FLJ41042 fis, clone NT2RI2005166, highly similar to F-box/WD repeat protein 9.								protein binding			ovary(1)	1						GGGACGGGACAGCTCAGGCCGGGCTGGGCCTGCAA	0.674													60	26	---	---	---	---	
NUCB1	4924	broad.mit.edu	37	19	49414663	49414663	+	Intron	DEL	T	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49414663delT	uc002plb.3	+						NUCB1_uc002pla.2_Intron|NUCB1_uc002plc.2_Intron	NM_006184	NP_006175	Q02818	NUCB1_HUMAN	nucleobindin 1 precursor							ER-Golgi intermediate compartment|extracellular space|Golgi apparatus|membrane|microtubule cytoskeleton	calcium ion binding|DNA binding				0		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000171)|all cancers(93;0.000333)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0244)		ttttcttttcttttttttttt	0.254													4	2	---	---	---	---	
PRRG2	5639	broad.mit.edu	37	19	50093096	50093113	+	Intron	DEL	TCCTCCCTAGTCTAGGTA	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50093096_50093113delTCCTCCCTAGTCTAGGTA	uc002pon.3	+						PRRG2_uc010yaz.1_Intron|PRR12_uc002poo.3_5'Flank	NM_000951	NP_000942	O14669	TMG2_HUMAN	proline rich Gla (G-carboxyglutamic acid) 2							extracellular region|integral to plasma membrane	calcium ion binding			skin(1)	1		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00295)|GBM - Glioblastoma multiforme(134;0.0121)		TCCCCTCTCTTCCTCCCTAGTCTAGGTATCCTGTAAGT	0.518													183	7	---	---	---	---	
ZNF765	91661	broad.mit.edu	37	19	53916793	53916793	+	Intron	DEL	A	-	-	rs143686963	by1000genomes	TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53916793delA	uc002qbn.2	+									Q7L2R6	ZN765_HUMAN	Homo sapiens cDNA FLJ50389 complete cds, moderately similar to Zinc finger protein 611.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00379)		CTTTTCATTTAAAAAAAAAGT	0.289													4	2	---	---	---	---	
CHRNA4	1137	broad.mit.edu	37	20	61991219	61991220	+	Intron	DEL	CT	-	-	rs67528285		TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61991219_61991220delCT	uc002yes.2	-						CHRNA4_uc002yet.1_Intron|CHRNA4_uc011aaw.1_Intron|CHRNA4_uc010gke.1_5'Flank|CHRNA4_uc002yev.1_Intron|CHRNA4_uc010gkf.1_Intron	NM_000744	NP_000735	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 subunit						B cell activation|behavioral response to nicotine|calcium ion transport|cognition|DNA repair|membrane depolarization|regulation of action potential|regulation of dopamine secretion|regulation of inhibitory postsynaptic membrane potential|response to hypoxia|response to oxidative stress|sensory perception of pain|synaptic transmission, cholinergic	cell junction|dendrite|external side of plasma membrane|membrane fraction|neuronal cell body|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			central_nervous_system(1)|skin(1)	2	all_cancers(38;1.71e-10)				Nicotine(DB00184)|Varenicline(DB01273)	CGGGCGTGCGCTCtgtgtgtgt	0.490													2	5	---	---	---	---	
KCNQ2	3785	broad.mit.edu	37	20	62074539	62074541	+	Intron	DEL	CAC	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62074539_62074541delCAC	uc002yey.1	-						KCNQ2_uc002yez.1_Intron|KCNQ2_uc002yfa.1_Intron|KCNQ2_uc002yfb.1_Intron|KCNQ2_uc011aax.1_Intron|KCNQ2_uc002yfc.1_Intron	NM_172107	NP_742105	O43526	KCNQ2_HUMAN	potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)	ccatcaccatcaccaccaccacc	0.000													4	3	---	---	---	---	
ZNF512B	57473	broad.mit.edu	37	20	62602059	62602062	+	5'Flank	DEL	CCTT	-	-	rs113164162	by1000genomes	TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62602059_62602062delCCTT	uc002yhl.1	-							NM_020713	NP_065764	Q96KM6	Z512B_HUMAN	zinc finger protein 512B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					tgcctgcctgccttccttccttcc	0.230													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11114453	11114455	+	IGR	DEL	TAA	-	-	rs55649022		TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11114453_11114455delTAA								BAGE (15516 upstream) : None (None downstream)																							AATTTTTTTTTAAAAAGCAAGTT	0.305													5	3	---	---	---	---	
SLC37A1	54020	broad.mit.edu	37	21	43995178	43995179	+	Intron	INS	-	TC	TC	rs143404028	by1000genomes	TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43995178_43995179insTC	uc002zbi.2	+						SLC37A1_uc002zbj.2_Intron	NM_018964	NP_061837	P57057	GLPT_HUMAN	solute carrier family 37 member 1						carbohydrate transport|transmembrane transport	integral to membrane					0						CTAAAGCTCCTTCTCTCTCTGA	0.386											OREG0026239	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	20151841	20151842	+	IGR	INS	-	CAC	CAC	rs10627070		TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20151841_20151842insCAC								ZDHHC8 (16312 upstream) : LOC150197 (42013 downstream)																							accaccaccatcaccaccacca	0.025													6	5	---	---	---	---	
SEC14L2	23541	broad.mit.edu	37	22	30818522	30818522	+	3'UTR	DEL	T	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30818522delT	uc003ahr.2	+	12					SEC14L2_uc011akx.1_3'UTR|SEC14L2_uc003ahs.2_3'UTR|SEC14L2_uc011aky.1_3'UTR|SEC14L2_uc003aht.2_RNA|SEC14L2_uc003ahu.3_Intron|SEC14L2_uc010gvv.2_RNA|SEC14L2_uc010gvw.1_Intron|MTP18_uc010gvx.1_Intron|MTP18_uc003ahv.1_Intron|MTP18_uc010gvy.1_Intron	NM_012429	NP_036561	O76054	S14L2_HUMAN	SEC14-like 2 isoform 1						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane|nucleus	phospholipid binding|transporter activity|vitamin E binding				0					Vitamin E(DB00163)	CCTCAGGAGCTTTCATTTCAG	0.527													16	11	---	---	---	---	
TAB1	10454	broad.mit.edu	37	22	39815792	39815792	+	Intron	DEL	A	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39815792delA	uc003axt.2	+						TAB1_uc003axr.2_Intron|TAB1_uc011aok.1_Intron|TAB1_uc003axu.1_Intron	NM_006116	NP_006107	Q15750	TAB1_HUMAN	mitogen-activated protein kinase kinase kinase 7						activation of MAPK activity|activation of MAPKKK activity|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB 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|endosome membrane	catalytic activity|protein binding			breast(1)	1						accctgtctcaaaaaaaaaaa	0.249													4	2	---	---	---	---	
PDZD4	57595	broad.mit.edu	37	X	153068717	153068718	+	3'UTR	DEL	CA	-	-			TCGA-CU-A0YR-01	TCGA-CU-A0YR-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153068717_153068718delCA	uc004fiz.1	-	8					PDZD4_uc004fiy.1_3'UTR|PDZD4_uc004fix.2_3'UTR|PDZD4_uc004fja.1_3'UTR|PDZD4_uc011mze.1_3'UTR	NM_032512	NP_115901	Q76G19	PDZD4_HUMAN	PDZ domain containing 4							cell cortex				breast(1)	1	all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					cgcgcgcgcgcacacacacaca	0.510													5	3	---	---	---	---	
