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
SLC25A33	84275	broad.mit.edu	37	1	9642417	9642417	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9642417C>T	uc001apw.2	+	7	1047	c.824C>T	c.(823-825)GCG>GTG	p.A275V	SLC25A33_uc001apx.2_Missense_Mutation_p.A208V	NM_032315	NP_115691	Q9BSK2	S2533_HUMAN	mitochondrial carrier protein MGC4399	275	Solcar 3.				transport	integral to membrane|mitochondrial inner membrane					0	all_lung(157;0.246)	all_epithelial(116;1.16e-18)|all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Breast(348;0.00191)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.01e-08)|COAD - Colon adenocarcinoma(227;1.44e-05)|Kidney(185;0.000262)|KIRC - Kidney renal clear cell carcinoma(229;0.000957)|BRCA - Breast invasive adenocarcinoma(304;0.0019)|STAD - Stomach adenocarcinoma(132;0.00355)|READ - Rectum adenocarcinoma(331;0.0419)		GTCCAGACGGCGCGCCTGGTG	0.498													44	24	---	---	---	---	PASS
MST1P9	11223	broad.mit.edu	37	1	17085189	17085189	+	Intron	SNP	A	G	G			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17085189A>G	uc010ock.1	-						CROCC_uc009voy.1_Intron|MST1P9_uc001azp.3_Silent_p.H32H	NR_002729				SubName: Full=Hepatocyte growth factor-like protein homolog;												0						TCCAGGATTGATGGCGGCTGG	0.572													3	23	---	---	---	---	PASS
PHACTR4	65979	broad.mit.edu	37	1	28802704	28802704	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28802704C>T	uc001bpw.2	+	8	1789	c.1507C>T	c.(1507-1509)CCA>TCA	p.P503S	PHACTR4_uc001bpv.1_RNA|PHACTR4_uc001bpx.2_Missense_Mutation_p.P487S|PHACTR4_uc001bpy.2_Missense_Mutation_p.P513S	NM_001048183	NP_001041648	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4 isoform 1	503							actin binding|protein phosphatase inhibitor activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		TCCTAAATTACCACAGTGTCT	0.433													5	46	---	---	---	---	PASS
ZCCHC11	23318	broad.mit.edu	37	1	52911672	52911672	+	Silent	SNP	A	G	G			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52911672A>G	uc001ctx.2	-	23	3930	c.3696T>C	c.(3694-3696)CCT>CCC	p.P1232P	ZCCHC11_uc001cty.2_Silent_p.P1232P|ZCCHC11_uc001ctz.2_Silent_p.P1232P|ZCCHC11_uc009vze.1_Silent_p.P1232P|ZCCHC11_uc001cua.1_Silent_p.P149P	NM_015269	NP_056084	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11 isoform	1232	PAP-associated 2.				miRNA catabolic process|pre-miRNA processing|RNA 3'-end processing|stem cell maintenance	cytoplasm|nucleolus	nucleic acid binding|protein binding|protein binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)|skin(1)	3						TCAAGTCAAAAGGGTCTACAA	0.303													3	138	---	---	---	---	PASS
VCAM1	7412	broad.mit.edu	37	1	101200121	101200121	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101200121T>G	uc001dti.2	+	8	1976	c.1856T>G	c.(1855-1857)GTC>GGC	p.V619G	VCAM1_uc001dtj.2_Missense_Mutation_p.V527G|VCAM1_uc010ouj.1_Missense_Mutation_p.V557G	NM_001078	NP_001069	P19320	VCAM1_HUMAN	vascular cell adhesion molecule 1 isoform a	619	Ig-like C2-type 7.|Extracellular (Potential).				heterophilic cell-cell adhesion|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|leukocyte tethering or rolling|membrane to membrane docking|positive regulation of T cell proliferation|regulation of immune response	alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex|apical part of cell|external side of plasma membrane|extracellular space|filopodium|integral to membrane|microvillus|podosome	cell adhesion molecule binding|integrin binding			central_nervous_system(1)	1		all_epithelial(167;3.83e-06)|all_lung(203;0.000485)|Lung NSC(277;0.0011)		Epithelial(280;0.0227)|all cancers(265;0.0276)|COAD - Colon adenocarcinoma(174;0.149)|Colorectal(144;0.169)|Lung(183;0.196)	Carvedilol(DB01136)	GGAGACACTGTCATCATCTCT	0.388													59	27	---	---	---	---	PASS
INSRR	3645	broad.mit.edu	37	1	156821255	156821255	+	Intron	SNP	G	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156821255G>T	uc010pht.1	-						NTRK1_uc001fqf.1_Intron|NTRK1_uc009wsi.1_Intron|INSRR_uc009wsj.1_Missense_Mutation_p.L423I	NM_014215	NP_055030	P14616	INSRR_HUMAN	insulin receptor-related receptor precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|insulin receptor substrate binding|metal ion binding|phosphatidylinositol 3-kinase binding|transmembrane receptor protein tyrosine kinase activity			lung(11)|ovary(5)|skin(2)|kidney(1)|central_nervous_system(1)	20	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GGCTGGAGTAGGAGCAAGGAA	0.592													3	63	---	---	---	---	PASS
ZNF281	23528	broad.mit.edu	37	1	200378037	200378037	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200378037C>A	uc001gve.2	-	2	904	c.797G>T	c.(796-798)TGT>TTT	p.C266F	uc010ppi.1_5'Flank|ZNF281_uc001gvf.1_Missense_Mutation_p.C266F|ZNF281_uc001gvg.1_Missense_Mutation_p.C230F	NM_012482	NP_036614	Q9Y2X9	ZN281_HUMAN	zinc finger protein 281	266	C2H2-type 1.				negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|breast(1)	2						AGCAGCACTACAGTGATCACA	0.488													4	112	---	---	---	---	PASS
CR1	1378	broad.mit.edu	37	1	207700214	207700214	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207700214G>C	uc001hfy.2	+	6	1143	c.1003G>C	c.(1003-1005)GCT>CCT	p.A335P	CR1_uc009xcl.1_Intron|CR1_uc001hfx.2_Missense_Mutation_p.A335P|CR1_uc009xcj.1_Intron|CR1_uc009xck.1_Missense_Mutation_p.A335P|CR1_uc010psh.1_5'Flank	NM_000573	NP_000564	P17927	CR1_HUMAN	complement receptor 1 isoform F precursor	335	Sushi 5.|Extracellular (Potential).				complement activation, classical pathway|innate immune response	integral to plasma membrane	complement receptor activity			ovary(3)	3						CCTCAGAGGGGCTGCGTCTAT	0.557													62	41	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141110542	141110542	+	Missense_Mutation	SNP	T	C	C	rs144480841		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141110542T>C	uc002tvj.1	-	76	12602	c.11630A>G	c.(11629-11631)AAT>AGT	p.N3877S		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	3877	Extracellular (Potential).|EGF-like 9.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GCAGGTGTTATTTCTTTCTTG	0.308										TSP Lung(27;0.18)			5	283	---	---	---	---	PASS
PABPC1P2	728773	broad.mit.edu	37	2	147346720	147346720	+	3'UTR	SNP	C	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147346720C>A	uc002twf.3	+	1						NR_026904				RecName: Full=Putative protein PABPC1-like; AltName: Full=Polyadenylate-binding protein pseudogene 2;												0						GCACCCTACTCTTGCTGGTAA	0.428													4	19	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152529113	152529113	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152529113G>T	uc010fnx.2	-	37	4260	c.4069C>A	c.(4069-4071)CAC>AAC	p.H1357N		NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	1357	Nebulin 34.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		TTCATATAGTGGACCAGCTTG	0.458													108	112	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10183725	10183725	+	Nonsense_Mutation	SNP	C	A	A	rs5030826		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10183725C>A	uc003bvc.2	+	1	407	c.194C>A	c.(193-195)TCG>TAG	p.S65*	VHL_uc003bvd.2_Nonsense_Mutation_p.S65*	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	65			S -> L (in VHLD; type I).|S -> A (in pheochromocytoma).|S -> W (in VHLD; type I).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.S65*(8)|p.S65L(8)|p.S65S(2)|p.S65W(2)|p.S65fs*2(2)|p.S65P(1)|p.E52_S65del(1)|p.S65fs*92(1)|p.R60fs*35(1)|p.S65>Q(1)|p.S65_N67del(1)|p.P61fs*61(1)|p.R64fs*63(1)|p.V62fs*1(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GTGCTGCGCTCGGTGAACTCG	0.721		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				8	3	---	---	---	---	PASS
SLITRK3	22865	broad.mit.edu	37	3	164905805	164905805	+	Silent	SNP	C	G	G	rs145516007	byFrequency	TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164905805C>G	uc003fej.3	-	2	3258	c.2814G>C	c.(2812-2814)TCG>TCC	p.S938S	SLITRK3_uc003fek.2_Silent_p.S938S	NM_014926	NP_055741	O94933	SLIK3_HUMAN	slit and trk like 3 protein precursor	938	Cytoplasmic (Potential).					integral to membrane				ovary(6)|skin(3)|pancreas(1)	10						CCTTTCCAGCCGAGAAGAGAA	0.502										HNSCC(40;0.11)			170	276	---	---	---	---	PASS
SERPINI1	5274	broad.mit.edu	37	3	167508254	167508254	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167508254A>C	uc003ffa.3	+	3	543	c.345A>C	c.(343-345)CAA>CAC	p.Q115H	SERPINI1_uc003ffb.3_Missense_Mutation_p.Q115H	NM_001122752	NP_001116224	Q99574	NEUS_HUMAN	neuroserpin precursor	115					central nervous system development|peripheral nervous system development|regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			skin(1)	1						TGTTTGTGCAAAATGGATTTC	0.348													60	130	---	---	---	---	PASS
LIPH	200879	broad.mit.edu	37	3	185252677	185252677	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185252677A>C	uc003fpm.2	-	2	403	c.293T>G	c.(292-294)GTT>GGT	p.V98G	LIPH_uc010hyh.2_Missense_Mutation_p.V98G	NM_139248	NP_640341	Q8WWY8	LIPH_HUMAN	lipase, member H precursor	98					lipid catabolic process	extracellular space|plasma membrane	heparin binding|phospholipase activity			ovary(1)|pancreas(1)	2	all_cancers(143;8.87e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			CATGTCTTCAACAGAGAGCAA	0.433													12	215	---	---	---	---	PASS
LPHN3	23284	broad.mit.edu	37	4	62363009	62363009	+	5'UTR	SNP	G	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62363009G>A	uc010ihh.2	+	1					LPHN3_uc003hcq.3_5'UTR|LPHN3_uc010ihg.1_5'UTR	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18						TGAGTAGACAGCCATGTGGCC	0.353													3	70	---	---	---	---	PASS
UGT2B7	7364	broad.mit.edu	37	4	69964299	69964299	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69964299G>A	uc003heg.3	+	2	809	c.763G>A	c.(763-765)GTA>ATA	p.V255I	UGT2B7_uc010ihq.2_Missense_Mutation_p.V255I	NM_001074	NP_001065	P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2B7 precursor	255					lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			ovary(1)|skin(1)	2						GAAAGCTGACGTATGGCTTAT	0.393													5	290	---	---	---	---	PASS
FBXW7	55294	broad.mit.edu	37	4	153332528	153332528	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153332528A>T	uc003ims.2	-	2	577	c.428T>A	c.(427-429)GTC>GAC	p.V143D	FBXW7_uc011cii.1_Missense_Mutation_p.V143D|FBXW7_uc003imt.2_Missense_Mutation_p.V143D|FBXW7_uc003imu.2_Missense_Mutation_p.V143D	NM_033632	NP_361014	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7 isoform	143					interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development	nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex	protein binding|protein binding			haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1)	308	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				GGAGTTCGTGACACTGTTAGT	0.353			Mis|N|D|F		colorectal|endometrial|T-ALL								33	66	---	---	---	---	PASS
FSTL5	56884	broad.mit.edu	37	4	162680647	162680647	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:162680647C>T	uc003iqh.2	-	6	1079	c.643G>A	c.(643-645)GAT>AAT	p.D215N	FSTL5_uc003iqi.2_Missense_Mutation_p.D214N|FSTL5_uc010iqv.2_Missense_Mutation_p.D214N	NM_020116	NP_064501	Q8N475	FSTL5_HUMAN	follistatin-like 5 isoform a	215	EF-hand 2.					extracellular region	calcium ion binding			ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|skin(1)	8	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		AAAGTACAATCAAAGAGATCC	0.294													4	143	---	---	---	---	PASS
C4orf41	60684	broad.mit.edu	37	4	184585186	184585186	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184585186C>T	uc003ivx.2	+	2	342	c.166C>T	c.(166-168)CTC>TTC	p.L56F	C4orf41_uc003ivw.2_Missense_Mutation_p.L56F|C4orf41_uc010isc.2_Intron	NM_021942	NP_068761	Q7Z392	CD041_HUMAN	hypothetical protein LOC60684 isoform a	56											0		all_lung(41;4.4e-14)|Lung NSC(41;1.03e-13)|Colorectal(36;0.00139)|all_hematologic(60;0.00756)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.202)		all cancers(43;1.39e-26)|Epithelial(43;2.42e-22)|OV - Ovarian serous cystadenocarcinoma(60;6.85e-10)|GBM - Glioblastoma multiforme(59;6.71e-06)|Colorectal(24;9.67e-06)|STAD - Stomach adenocarcinoma(60;2.36e-05)|COAD - Colon adenocarcinoma(29;7.07e-05)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.171)		TTTCAAGGTGCTCCCAGGTGA	0.478													115	132	---	---	---	---	PASS
ALDH7A1	501	broad.mit.edu	37	5	125891622	125891622	+	Splice_Site	SNP	C	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125891622C>T	uc003ktx.2	-	12	1285	c.1093_splice	c.e12+1	p.P365_splice	ALDH7A1_uc003ktv.2_Splice_Site|ALDH7A1_uc003kty.2_Splice_Site|ALDH7A1_uc011cxa.1_Intron	NM_001182	NP_001173	P49419	AL7A1_HUMAN	aldehyde dehydrogenase 7 family, member A1						cellular aldehyde metabolic process|lysine catabolic process|sensory perception of sound	cytosol|mitochondrial matrix|nucleus	aldehyde dehydrogenase (NAD) activity|betaine-aldehyde dehydrogenase activity|L-aminoadipate-semialdehyde dehydrogenase activity			kidney(2)|ovary(1)	3		all_cancers(142;0.24)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0417)|OV - Ovarian serous cystadenocarcinoma(64;0.068)|all cancers(49;0.109)	NADH(DB00157)|Pyridoxine(DB00165)	GAGATACTCACGGTCCCATGG	0.413													52	65	---	---	---	---	PASS
PCDHA5	56143	broad.mit.edu	37	5	140202183	140202183	+	Nonsense_Mutation	SNP	G	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140202183G>T	uc003lhl.2	+	1	823	c.823G>T	c.(823-825)GAA>TAA	p.E275*	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_Nonsense_Mutation_p.E275*|PCDHA5_uc003lhj.1_Nonsense_Mutation_p.E275*	NM_018908	NP_061731	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5 isoform 1 precursor	275	Extracellular (Potential).|Cadherin 3.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(1)|breast(1)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CATCAATAAGGAAATAGTGTA	0.328													60	150	---	---	---	---	PASS
PCDHAC2	56134	broad.mit.edu	37	5	140347848	140347848	+	Silent	SNP	G	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140347848G>A	uc003lii.2	+	1	1737	c.1497G>A	c.(1495-1497)AAG>AAA	p.K499K	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_uc003lih.2_Intron|PCDHAC2_uc011dag.1_Silent_p.K499K	NM_018899	NP_061722	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2 isoform 1	499	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|skin(2)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGATGAAAAGGAGAATGCAG	0.507													26	229	---	---	---	---	PASS
PCDHB10	56126	broad.mit.edu	37	5	140573503	140573503	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140573503G>T	uc003lix.2	+	1	1552	c.1378G>T	c.(1378-1380)GTC>TTC	p.V460F		NM_018930	NP_061753	Q9UN67	PCDBA_HUMAN	protocadherin beta 10 precursor	460	Cadherin 5.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CACCCTGTTCGTCCGCGAGAA	0.637													39	113	---	---	---	---	PASS
PCDHB10	56126	broad.mit.edu	37	5	140573506	140573506	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140573506C>T	uc003lix.2	+	1	1555	c.1381C>T	c.(1381-1383)CGC>TGC	p.R461C		NM_018930	NP_061753	Q9UN67	PCDBA_HUMAN	protocadherin beta 10 precursor	461	Cadherin 5.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCTGTTCGTCCGCGAGAACAA	0.632													36	115	---	---	---	---	PASS
SFXN1	94081	broad.mit.edu	37	5	174949468	174949468	+	Intron	SNP	C	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174949468C>T	uc003mda.2	+						SFXN1_uc003mdb.1_3'UTR	NM_022754	NP_073591	Q9H9B4	SFXN1_HUMAN	sideroflexin 1						iron ion homeostasis	integral to membrane	cation transmembrane transporter activity|protein binding			ovary(1)	1	all_cancers(89;0.00922)|Renal(175;0.000269)|Lung NSC(126;0.00515)|all_lung(126;0.00873)	Medulloblastoma(196;0.0399)|all_neural(177;0.0663)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			AGTAttaatcctaaaaaccaa	0.174													92	235	---	---	---	---	PASS
HDGFL1	154150	broad.mit.edu	37	6	22569747	22569747	+	5'UTR	SNP	C	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22569747C>T	uc003nds.2	+	1						NM_138574	NP_612641	Q5TGJ6	HDGL1_HUMAN	hepatoma derived growth factor-like 1												0	Ovarian(93;0.163)					TTACTGCGCGCGCGCAGACTT	0.682													15	20	---	---	---	---	PASS
ZBTB12	221527	broad.mit.edu	37	6	31867889	31867889	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31867889C>A	uc003nyd.1	-	2	1370	c.1194G>T	c.(1192-1194)CAG>CAT	p.Q398H	EHMT2_uc011don.1_5'Flank|EHMT2_uc003nxz.1_5'Flank|EHMT2_uc003nya.1_5'Flank|EHMT2_uc003nyb.1_5'Flank|C2_uc003nyc.2_Intron|C2_uc011doo.1_Intron|C2_uc011dop.1_5'Flank	NM_181842	NP_862825	Q9Y330	ZBT12_HUMAN	zinc finger and BTB domain containing 12	398	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GGGTGGACTTCTGTGTGAAGC	0.607													24	22	---	---	---	---	PASS
CAPN11	11131	broad.mit.edu	37	6	44141055	44141055	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44141055C>A	uc003owt.1	+	7	801	c.763C>A	c.(763-765)CCT>ACT	p.P255T		NM_007058	NP_008989	Q9UMQ6	CAN11_HUMAN	calpain 11	255	Calpain catalytic.				proteolysis	acrosomal vesicle	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			ovary(1)|breast(1)	2	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CCAGAGGCCCCCTCAGAACCT	0.473											OREG0017466	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	28	30	---	---	---	---	PASS
SENP6	26054	broad.mit.edu	37	6	76421100	76421100	+	Silent	SNP	A	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76421100A>T	uc003pid.3	+	21	3496	c.2877A>T	c.(2875-2877)GGA>GGT	p.G959G	SENP6_uc003pie.3_Silent_p.G952G|SENP6_uc010kbf.2_RNA	NM_015571	NP_056386	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6 isoform 1	959	Protease.				proteolysis	cytoplasm|nucleus	cysteine-type peptidase activity			breast(2)|urinary_tract(1)|ovary(1)|lung(1)|skin(1)	6		all_hematologic(105;0.189)				CAGAAATAGGACAGTGGCATT	0.338													20	42	---	---	---	---	PASS
INTS1	26173	broad.mit.edu	37	7	1522154	1522154	+	Intron	SNP	C	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1522154C>T	uc003skn.2	-						INTS1_uc003skp.1_3'UTR	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1						snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		AGTCAGCAGCCCCTGCCCAAG	0.692													15	28	---	---	---	---	PASS
ACTB	60	broad.mit.edu	37	7	5568380	5568380	+	Intron	SNP	T	G	G			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5568380T>G	uc003sos.3	-						ACTB_uc003sor.3_5'UTR|ACTB_uc003sot.3_Intron|ACTB_uc003soq.3_Intron|ACTB_uc010ksy.2_Intron	NM_001101	NP_001092	P60709	ACTB_HUMAN	beta actin						'de novo' posttranslational protein folding|adherens junction organization|axon guidance|blood coagulation|cell junction assembly|cellular component movement	cytoskeleton|cytosol|MLL5-L complex|NuA4 histone acetyltransferase complex|ribonucleoprotein complex	ATP binding|kinesin binding|nitric-oxide synthase binding|structural constituent of cytoskeleton				0		Ovarian(82;0.0606)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)|OV - Ovarian serous cystadenocarcinoma(56;4.24e-37)		CATGTCACACTGGGGAAGCCA	0.552													5	40	---	---	---	---	PASS
LOC643955	643955	broad.mit.edu	37	7	62752706	62752706	+	3'UTR	SNP	G	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62752706G>A	uc011kdj.1	-	3						NR_003952				Homo sapiens cDNA clone IMAGE:30377995, containing frame-shift errors.												0						TAAGGTTTGCGGACCAGCTAA	0.418													19	113	---	---	---	---	PASS
C7orf64	84060	broad.mit.edu	37	7	92164269	92164269	+	Silent	SNP	G	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92164269G>A	uc003ulz.2	+	4	1043	c.1002G>A	c.(1000-1002)CGG>CGA	p.R334R	C7orf64_uc003uma.2_Silent_p.R334R	NM_032120	NP_115496	Q5RL73	CG064_HUMAN	hypothetical protein LOC84060	334							nucleotide binding			ovary(2)	2						ATTTAATTCGGCATAAACTTA	0.343													4	114	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100674890	100674890	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100674890G>A	uc003uxp.1	+	3	246	c.193G>A	c.(193-195)GCA>ACA	p.A65T	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	65	Extracellular (Potential).			A -> T (in Ref. 1; CAE54435/CAE54436).		extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					AGGTTCTGCGGCAAACACCGC	0.418													4	109	---	---	---	---	PASS
CPA2	1358	broad.mit.edu	37	7	129916502	129916502	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129916502C>T	uc003vpq.2	+	7	639	c.620C>T	c.(619-621)ACT>ATT	p.T207I	CPA2_uc011kpc.1_Missense_Mutation_p.T207I	NM_001869	NP_001860	P48052	CBPA2_HUMAN	carboxypeptidase A2 (pancreatic) precursor	207					proteolysis|vacuolar protein catabolic process	extracellular region|vacuole	metallocarboxypeptidase activity|zinc ion binding			ovary(1)	1	Melanoma(18;0.0435)					CCATCCATCACTTCCATTCTG	0.453													120	214	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	142144058	142144058	+	Intron	SNP	C	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142144058C>T	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron|uc003vys.1_RNA					SubName: Full=V_segment translation product; Flags: Fragment;																		GAGAAAAGGCCACACAGCACA	0.602													9	173	---	---	---	---	PASS
CLU	1191	broad.mit.edu	37	8	27466547	27466547	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27466547C>T	uc003xfw.1	-	2	212	c.154G>A	c.(154-156)GGG>AGG	p.G52R	CLU_uc010lux.1_Intron|CLU_uc003xfx.1_Missense_Mutation_p.G52R|CLU_uc003xfy.1_Missense_Mutation_p.G63R|CLU_uc003xfz.1_Missense_Mutation_p.G104R	NM_203339	NP_976084	P10909	CLUS_HUMAN	clusterin isoform 2	52				G -> Q (in Ref. 10; AA sequence).	chaperone-mediated protein folding|complement activation, classical pathway|innate immune response|lipid metabolic process|negative regulation of apoptosis|negative regulation of protein homooligomerization|platelet activation|platelet degranulation|positive regulation of NF-kappaB transcription factor activity|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|response to misfolded protein|response to virus|reverse cholesterol transport	chromaffin granule|cytosol|endoplasmic reticulum|microsome|mitochondrial membrane|nucleus|perinuclear region of cytoplasm|platelet alpha granule lumen|spherical high-density lipoprotein particle	misfolded protein binding|ubiquitin protein ligase binding			ovary(2)	2		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|Colorectal(74;0.132)		TGTTTCACCCCGTTGACAGCA	0.443													52	55	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77776353	77776353	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77776353C>T	uc003yav.2	+	11	10655	c.10268C>T	c.(10267-10269)TCA>TTA	p.S3423L		NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	3419	C2H2-type 20.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			CACCTCCAGTCAAGCTTGCAC	0.453										HNSCC(33;0.089)			19	47	---	---	---	---	PASS
CDH17	1015	broad.mit.edu	37	8	95183159	95183159	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95183159G>T	uc003ygh.2	-	8	963	c.838C>A	c.(838-840)CCA>ACA	p.P280T	CDH17_uc011lgo.1_Intron|CDH17_uc011lgp.1_Missense_Mutation_p.P280T	NM_004063	NP_004054	Q12864	CAD17_HUMAN	cadherin 17 precursor	280	Extracellular (Potential).|Cadherin 3.					integral to membrane	calcium ion binding			ovary(5)|skin(1)	6	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			GGGAATCTTGGCAGCTTCTCT	0.453													41	122	---	---	---	---	PASS
CA9	768	broad.mit.edu	37	9	35676103	35676103	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35676103C>G	uc003zxo.3	+	4	689	c.647C>G	c.(646-648)CCC>CGC	p.P216R	C9orf100_uc003zxl.2_5'Flank|CA9_uc003zxp.3_Missense_Mutation_p.P216R	NM_001216	NP_001207	Q16790	CAH9_HUMAN	carbonic anhydrase IX precursor	216	Extracellular.|Catalytic.				one-carbon metabolic process	integral to membrane|microvillus membrane|nucleolus	carbonate dehydratase activity|zinc ion binding			ovary(4)|skin(1)	5	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GCTCTGGGTCCCGGGCGGGAG	0.701													9	6	---	---	---	---	PASS
COL15A1	1306	broad.mit.edu	37	9	101777786	101777786	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101777786G>A	uc004azb.1	+	10	1647	c.1441G>A	c.(1441-1443)GTC>ATC	p.V481I		NM_001855	NP_001846	P39059	COFA1_HUMAN	alpha 1 type XV collagen precursor	481	3.|Nonhelical region 1 (NC1).|4 X tandem repeats.				angiogenesis|cell differentiation|signal transduction	collagen type XV|extracellular space|integral to membrane	binding			ovary(6)	6		Acute lymphoblastic leukemia(62;0.0562)				AGCCAGTGGGGTCCCCACAGA	0.547													5	25	---	---	---	---	PASS
OR1J2	26740	broad.mit.edu	37	9	125273604	125273604	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125273604C>T	uc004bmj.1	+	4	1379	c.524C>T	c.(523-525)CCC>CTC	p.P175L	OR1J2_uc011lyv.1_Missense_Mutation_p.P175L	NM_054107	NP_473448	Q8NGS2	OR1J2_HUMAN	olfactory receptor, family 1, subfamily J,	175	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)|pancreas(1)|breast(1)	5						AACACCATCCCCCATGTCTTC	0.532													39	203	---	---	---	---	PASS
LCN9	392399	broad.mit.edu	37	9	138555246	138555246	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138555246A>C	uc004cgk.1	+	1	79	c.79A>C	c.(79-81)AAC>CAC	p.N27H		NM_001001676	NP_001001676	Q8WX39	LCN9_HUMAN	lipocalin 9	27						extracellular region	pheromone binding|transporter activity			large_intestine(2)	2		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;3.43e-07)|Epithelial(140;1.97e-06)|all cancers(34;6.1e-05)		TATGCAGAGGAACTACAACGT	0.627													12	15	---	---	---	---	PASS
OR52K1	390036	broad.mit.edu	37	11	4510760	4510760	+	Silent	SNP	G	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4510760G>A	uc001lza.1	+	1	630	c.630G>A	c.(628-630)GTG>GTA	p.V210V		NM_001005171	NP_001005171	Q8NGK4	O52K1_HUMAN	olfactory receptor, family 52, subfamily K,	210	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;1.76e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0836)|LUSC - Lung squamous cell carcinoma(625;0.192)		TTATTGTGGTGTTGGACCTGC	0.502													81	323	---	---	---	---	PASS
OR51V1	283111	broad.mit.edu	37	11	5221093	5221093	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5221093C>T	uc010qyz.1	-	1	838	c.838G>A	c.(838-840)GTG>ATG	p.V280M		NM_001004760	NP_001004760	Q9H2C8	O51V1_HUMAN	olfactory receptor, family 51, subfamily V,	280	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.83e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACGTGGGCCACGGGGGAAAGG	0.473													44	48	---	---	---	---	PASS
ATP2A2	488	broad.mit.edu	37	12	110720427	110720427	+	Splice_Site	SNP	G	C	C			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110720427G>C	uc001tqk.3	+	2	699	c.136_splice	c.e2+1	p.G46_splice	ATP2A2_uc001tql.3_Splice_Site_p.G46_splice|ATP2A2_uc010sxy.1_Splice_Site_p.G46_splice	NM_170665	NP_733765	P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, slow twitch 2 isoform						ATP biosynthetic process|cell adhesion|epidermis development|platelet activation|sarcoplasmic reticulum calcium ion transport	integral to plasma membrane|microsome|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	ATP binding|calcium-transporting ATPase activity|protein C-terminus binding|S100 alpha binding			ovary(3)|skin(1)	4						GCTGAAGAAGGTAATCTTAAC	0.363													165	227	---	---	---	---	PASS
PCDH9	5101	broad.mit.edu	37	13	67800364	67800364	+	Silent	SNP	G	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67800364G>A	uc001vik.2	-	2	2901	c.2209C>T	c.(2209-2211)CTG>TTG	p.L737L	PCDH9_uc001vil.2_Silent_p.L737L|PCDH9_uc010thl.1_Silent_p.L737L|PCDH9_uc001vin.3_Silent_p.L737L	NM_203487	NP_982354	Q9HC56	PCDH9_HUMAN	protocadherin 9 isoform 1 precursor	737	Extracellular (Potential).|Cadherin 7.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)|skin(1)	6		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		TTTTCTTCCAGAGTAATGTTA	0.433													67	202	---	---	---	---	PASS
NIN	51199	broad.mit.edu	37	14	51224783	51224783	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51224783C>T	uc001wym.2	-	18	3156	c.2965G>A	c.(2965-2967)GCC>ACC	p.A989T	NIN_uc001wyi.2_Missense_Mutation_p.A989T|NIN_uc001wyj.2_Intron|NIN_uc001wyk.2_Intron|NIN_uc010tqp.1_Missense_Mutation_p.A995T|NIN_uc001wyo.2_Missense_Mutation_p.A989T	NM_182946	NP_891991	Q8N4C6	NIN_HUMAN	ninein isoform 5	989	Potential.				centrosome localization	centrosome|microtubule	calcium ion binding|GTP binding|protein binding			skin(3)|ovary(1)|kidney(1)|central_nervous_system(1)	6	all_epithelial(31;0.00244)|Breast(41;0.127)					TTCTCCATGGCTAGAAGCTTG	0.502			T	PDGFRB	MPD								124	148	---	---	---	---	PASS
SPTB	6710	broad.mit.edu	37	14	65289684	65289684	+	Silent	SNP	G	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65289684G>A	uc001xht.2	-	1	183	c.129C>T	c.(127-129)TCC>TCT	p.S43S	SPTB_uc001xhr.2_Silent_p.S43S|SPTB_uc001xhs.2_Silent_p.S43S|SPTB_uc001xhu.2_Silent_p.S43S	NM_000347	NP_000338	P11277	SPTB1_HUMAN	spectrin beta isoform b	43	Actin-binding.				actin filament capping|axon guidance	cell surface|cytosol|intrinsic to internal side of plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	actin filament binding|structural constituent of cytoskeleton			ovary(7)|skin(2)|lung(1)|central_nervous_system(1)	11		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		CCTTTATCCGGGACCTCTCAA	0.577											OREG0022736	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	30	89	---	---	---	---	PASS
MLH3	27030	broad.mit.edu	37	14	75513873	75513873	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75513873T>G	uc001xrd.1	-	2	2702	c.2486A>C	c.(2485-2487)AAG>ACG	p.K829T	MLH3_uc001xre.1_Missense_Mutation_p.K829T|MLH3_uc010tuy.1_RNA	NM_001040108	NP_001035197	Q9UHC1	MLH3_HUMAN	mutL homolog 3 isoform 1	829					mismatch repair|reciprocal meiotic recombination	chiasma|MutLbeta complex|synaptonemal complex	ATP binding|ATPase activity|mismatched DNA binding|protein binding|satellite DNA binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.00688)		GAATGGAAACTTCTCTGAGTT	0.383								MMR					17	126	---	---	---	---	PASS
DUOX2	50506	broad.mit.edu	37	15	45398798	45398798	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45398798G>A	uc010bea.2	-	16	2076	c.1873C>T	c.(1873-1875)CGA>TGA	p.R625*	DUOX2_uc001zun.2_Nonsense_Mutation_p.R625*	NM_014080	NP_054799	Q9NRD8	DUOX2_HUMAN	dual oxidase 2 precursor	625	Cytoplasmic (Potential).				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|response to virus	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|peroxidase activity			ovary(2)|skin(2)|pancreas(1)	5		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		TTGTGTTCTCGGCCCCGGAAA	0.557													41	146	---	---	---	---	PASS
SPESP1	246777	broad.mit.edu	37	15	69238414	69238414	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69238414G>C	uc002arn.1	+	2	669	c.541G>C	c.(541-543)GTC>CTC	p.V181L	NOX5_uc002arp.1_Intron|NOX5_uc002arq.1_Intron|NOX5_uc010bid.1_Intron|NOX5_uc002aro.2_Intron	NM_145658	NP_663633	Q6UW49	SPESP_HUMAN	sperm equatorial segment protein 1 precursor	181					multicellular organismal development	acrosomal vesicle					0						CAAGTCACCTGTCACCACTTT	0.448													63	182	---	---	---	---	PASS
MESP2	145873	broad.mit.edu	37	15	90321551	90321551	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90321551G>A	uc002bon.2	+	2	1180	c.1180G>A	c.(1180-1182)GGC>AGC	p.G394S	MESP2_uc010uqa.1_Missense_Mutation_p.G96S	NM_001039958	NP_001035047	Q0VG99	MESP2_HUMAN	mesoderm posterior 2 homolog	394					Notch signaling pathway	nucleus	DNA binding				0	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)			GGCCCGCCTGGGCATCTTCTA	0.547													3	34	---	---	---	---	PASS
TELO2	9894	broad.mit.edu	37	16	1557029	1557029	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1557029A>G	uc002cly.2	+	18	2494	c.2203A>G	c.(2203-2205)ATG>GTG	p.M735V		NM_016111	NP_057195	Q9Y4R8	TELO2_HUMAN	TEL2, telomere maintenance 2, homolog	735						chromosome, telomeric region|cytoplasm|membrane|nucleus	protein binding				0		Hepatocellular(780;0.219)				AGGGGCCCTGATGTGCCTGGC	0.647													12	20	---	---	---	---	PASS
KIAA0430	9665	broad.mit.edu	37	16	15706525	15706525	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15706525G>C	uc002ddr.2	-	17	3556	c.3363C>G	c.(3361-3363)ATC>ATG	p.I1121M	KIAA0430_uc002ddq.2_Missense_Mutation_p.I955M|KIAA0430_uc010uzv.1_Missense_Mutation_p.I1117M|KIAA0430_uc010uzw.1_Missense_Mutation_p.I1120M	NM_014647	NP_055462	Q9Y4F3	LKAP_HUMAN	limkain b1	1120						peroxisome	nucleotide binding|RNA binding				0						TGAAATGACTGATGGGTATGA	0.468													175	286	---	---	---	---	PASS
HYDIN	54768	broad.mit.edu	37	16	70884503	70884503	+	Silent	SNP	A	G	G			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70884503A>G	uc002ezr.2	-	74	12624	c.12496T>C	c.(12496-12498)TTG>CTG	p.L4166L	HYDIN_uc010cfy.2_RNA	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	4167										ovary(1)|skin(1)	2		Ovarian(137;0.0654)				TTGCAGATCAAATTAAAGTTC	0.443													38	73	---	---	---	---	PASS
PIK3R5	23533	broad.mit.edu	37	17	8793400	8793400	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8793400G>A	uc002glt.2	-	8	768	c.701C>T	c.(700-702)GCA>GTA	p.A234V	PIK3R5_uc010vuz.1_Missense_Mutation_p.A234V|PIK3R5_uc002glu.3_5'UTR|PIK3R5_uc010coa.1_Intron|PIK3R5_uc010cob.1_5'UTR	NM_014308	NP_055123	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5	234				AKTLAELEDIFTETAEAQELASGIGDAAEARRWLRTKLQAV GEKAGFPGVLDTAKPGKLHTIPIPVARCYTYSWSQDS -> TLQNQGSSIPSPSLSPGATPTAGARTALTSCRKSCSRNRSC SSQGSWEMMKRRKRRRRRWRRTWKLMGTVPREIPCSP (in Ref. 6; AAW63122).	platelet activation	cytosol|membrane|nucleus				breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5						CTGTGCCTCTGCGGTCTCCGT	0.627													25	34	---	---	---	---	PASS
NPC1	4864	broad.mit.edu	37	18	21112249	21112249	+	Intron	SNP	C	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21112249C>A	uc002kum.3	-						NPC1_uc010dlu.1_Intron|NPC1_uc010xaz.1_Intron	NM_000271	NP_000262	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1 precursor						autophagy|bile acid metabolic process|cholesterol efflux|cholesterol homeostasis|lysosomal transport	endoplasmic reticulum|integral to plasma membrane|late endosome membrane|lysosomal membrane|nuclear envelope|perinuclear region of cytoplasm	hedgehog receptor activity|protein binding|sterol transporter activity			ovary(2)	2	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					ACTGATGGCCCTATGAGAGAG	0.348													4	159	---	---	---	---	PASS
GNG7	2788	broad.mit.edu	37	19	2514986	2514986	+	3'UTR	SNP	G	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2514986G>A	uc002lwd.2	-	5					GNG7_uc010dte.1_Intron	NM_052847	NP_443079	O60262	GBG7_HUMAN	guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	signal transducer activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		gagagagaaagagagagagag	0.308													3	40	---	---	---	---	PASS
ELSPBP1	64100	broad.mit.edu	37	19	48517560	48517560	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48517560G>T	uc002pht.2	+	3	358	c.203G>T	c.(202-204)AGT>ATT	p.S68I		NM_022142	NP_071425	Q96BH3	ESPB1_HUMAN	epididymal sperm binding protein 1 precursor	68	Fibronectin type-II 1.				single fertilization	extracellular region					0		all_cancers(25;8.7e-09)|all_lung(116;1.15e-06)|all_epithelial(76;1.17e-06)|Lung NSC(112;2.56e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000253)|all cancers(93;0.00129)|Epithelial(262;0.0314)|GBM - Glioblastoma multiforme(486;0.0606)		TACTGCCAGAGTGAAGGTGAG	0.473													42	67	---	---	---	---	PASS
DMD	1756	broad.mit.edu	37	X	31462683	31462683	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31462683C>A	uc004dda.1	-	60	9243	c.8999G>T	c.(8998-9000)CGC>CTC	p.R3000L	DMD_uc004dcq.1_Missense_Mutation_p.R271L|DMD_uc004dcr.1_Missense_Mutation_p.R540L|DMD_uc004dcs.1_Missense_Mutation_p.R540L|DMD_uc004dct.1_Missense_Mutation_p.R540L|DMD_uc004dcu.1_Missense_Mutation_p.R540L|DMD_uc004dcv.1_Missense_Mutation_p.R540L|DMD_uc004dcw.2_Missense_Mutation_p.R1656L|DMD_uc004dcx.2_Missense_Mutation_p.R1659L|DMD_uc004dcz.2_Missense_Mutation_p.R2877L|DMD_uc004dcy.1_Missense_Mutation_p.R2996L|DMD_uc004ddb.1_Missense_Mutation_p.R2992L	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform	3000	Spectrin 22.				muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				GGTAAGCTGGCGAGCAAGGTC	0.478													4	165	---	---	---	---	PASS
CACNA1F	778	broad.mit.edu	37	X	49071691	49071691	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49071691T>G	uc004dnb.2	-	29	3547	c.3485A>C	c.(3484-3486)GAA>GCA	p.E1162A	CACNA1F_uc010nip.2_Missense_Mutation_p.E1151A	NM_005183	NP_005174	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type,	1162	Cytoplasmic (Potential).				axon guidance|detection of light stimulus involved in visual perception	voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			breast(3)|ovary(1)|kidney(1)|skin(1)	6					Verapamil(DB00661)	GAGGGCATATTCCACACATTG	0.587													11	21	---	---	---	---	PASS
ATRX	546	broad.mit.edu	37	X	76813066	76813066	+	Silent	SNP	C	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76813066C>T	uc004ecp.3	-	30	6787	c.6555G>A	c.(6553-6555)CTG>CTA	p.L2185L	ATRX_uc004ecq.3_Silent_p.L2147L|ATRX_uc004eco.3_Silent_p.L1970L	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	2185	Helicase C-terminal.				DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	CTCGAAAAGACAGTGACTGCT	0.348			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						114	209	---	---	---	---	PASS
GABRQ	55879	broad.mit.edu	37	X	151821523	151821523	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151821523C>A	uc004ffp.1	+	9	1698	c.1678C>A	c.(1678-1680)CTT>ATT	p.L560I		NM_018558	NP_061028	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) receptor, theta	560						cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|neurotransmitter transporter activity			ovary(2)|pancreas(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)					TACCTGGGGCCTTAATGATGA	0.517													58	68	---	---	---	---	PASS
TRIM45	80263	broad.mit.edu	37	1	117659023	117659023	+	Intron	DEL	T	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117659023delT	uc001egz.2	-						TRIM45_uc009whe.2_Intron|TRIM45_uc001eha.2_Intron	NM_025188	NP_079464	Q9H8W5	TRI45_HUMAN	tripartite motif-containing 45 isoform 1							cytoplasm|nucleus	zinc ion binding			central_nervous_system(1)	1	Lung SC(450;0.225)	all_cancers(81;0.000979)|all_lung(203;7.65e-05)|all_epithelial(167;0.000134)|Lung NSC(69;0.000389)		Lung(183;0.0537)|Colorectal(144;0.172)|LUSC - Lung squamous cell carcinoma(189;0.187)		tcccggctaattttttttttt	0.000													4	2	---	---	---	---	
NDUFS2	4720	broad.mit.edu	37	1	161181961	161181961	+	Intron	DEL	A	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161181961delA	uc001fyv.2	+						NDUFS2_uc001fyw.2_Intron|NDUFS2_uc010pkj.1_Intron|NDUFS2_uc001fyx.2_Intron	NM_004550	NP_004541	O75306	NDUS2_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 2						mitochondrial electron transport, NADH to ubiquinone|response to oxidative stress|transport	mitochondrial respiratory chain complex I	4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NAD binding|NADH dehydrogenase (ubiquinone) activity|protein binding|quinone binding			skin(1)	1	all_cancers(52;1.16e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		NADH(DB00157)	CCTGTTTCAGAAAAAAAAAAA	0.244													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	219785369	219785370	+	IGR	INS	-	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219785369_219785370insA								LYPLAL1 (399163 upstream) : SLC30A10 (73399 downstream)																							ATGTAGAATAGAAAAAAAAATA	0.446													4	2	---	---	---	---	
HEATR1	55127	broad.mit.edu	37	1	236751520	236751520	+	Intron	DEL	A	-	-	rs34200005		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236751520delA	uc001hyd.1	-							NM_018072	NP_060542	Q9H583	HEAT1_HUMAN	protein BAP28						rRNA processing	nucleolus|ribonucleoprotein complex	protein binding			ovary(2)|skin(1)	3	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			GGGCCTTTTGAGATTAATAAT	0.343													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	10356283	10356284	+	IGR	INS	-	GGAA	GGAA			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10356283_10356284insGGAA								C2orf48 (4427 upstream) : HPCAL1 (86756 downstream)																							gaaaaggaaagggaaggaagga	0.139													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	30445955	30445956	+	IGR	INS	-	GGAAGGAA	GGAAGGAA			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30445955_30445956insGGAAGGAA								YPEL5 (62557 upstream) : LBH (8441 downstream)																							CTCTGTCCCTTggaaggaagga	0.282													8	4	---	---	---	---	
C2orf86	51057	broad.mit.edu	37	2	63364354	63364356	+	Intron	DEL	TGT	-	-	rs76203086		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63364354_63364356delTGT	uc002sch.2	-						C2orf86_uc002sce.2_Intron|C2orf86_uc002scf.2_Intron|C2orf86_uc010ypu.1_Intron|C2orf86_uc002scg.2_Intron	NM_015910	NP_056994	O95876	FRITZ_HUMAN	hypothetical protein LOC51057 isoform 2						cilium morphogenesis|regulation of embryonic cell shape|regulation of protein localization|septin cytoskeleton organization	cilium axoneme|cytoplasm|cytoskeleton|plasma membrane					0						tgccatcatctgttgttgttgtt	0.000													4	2	---	---	---	---	
RGPD1	400966	broad.mit.edu	37	2	87204958	87204958	+	Intron	DEL	T	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87204958delT	uc010fgv.2	+						RMND5A_uc002srs.3_Intron|RGPD1_uc002ssb.2_Intron|RGPD1_uc002ssc.2_Intron	NM_001024457	NP_001019628	Q68DN6	RGPD1_HUMAN	RANBP2-like and GRIP domain containing 1						intracellular transport		binding				0						Gttatttttattttttttttt	0.318													4	2	---	---	---	---	
RAPH1	65059	broad.mit.edu	37	2	204355784	204355784	+	Intron	DEL	G	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204355784delG	uc002vad.2	-						RAPH1_uc002vae.2_Intron|RAPH1_uc002vaf.2_Intron	NM_213589	NP_998754	Q70E73	RAPH1_HUMAN	Ras association and pleckstrin homology domains						cell-matrix adhesion|signal transduction	cytoplasm|cytoskeleton|filopodium|lamellipodium|nucleus|plasma membrane				ovary(3)|breast(3)|central_nervous_system(2)|lung(1)|skin(1)	10						aaaaaaaaaagaaaaaagaaa	0.134													6	3	---	---	---	---	
PSMD1	5707	broad.mit.edu	37	2	232029736	232029745	+	Intron	DEL	ATTTATATAT	-	-	rs36227127		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232029736_232029745delATTTATATAT	uc002vrn.1	+						PSMD1_uc002vrm.1_Intron|PSMD1_uc010fxu.1_Intron	NM_002807	NP_002798	Q99460	PSMD1_HUMAN	proteasome 26S non-ATPase subunit 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of protein catabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	enzyme regulator activity|protein binding			ovary(1)|skin(1)	2		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)	TTATTCTTTGATTtatatatatttatatat	0.224													8	4	---	---	---	---	
EPHA3	2042	broad.mit.edu	37	3	89448278	89448278	+	Intron	DEL	A	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89448278delA	uc003dqy.2	+						EPHA3_uc003dqx.1_Intron|EPHA3_uc010hon.1_Intron	NM_005233	NP_005224	P29320	EPHA3_HUMAN	ephrin receptor EphA3 isoform a precursor							extracellular region|integral to plasma membrane	ATP binding			lung(17)|ovary(7)|large_intestine(4)|central_nervous_system(2)|stomach(1)|skin(1)|pancreas(1)	33	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		gactttgtctaaaaaaaaaaa	0.109										TSP Lung(6;0.00050)			3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	98907966	98907967	+	IGR	INS	-	AAGGAAGGAAGGAAAGAAGG	AAGGAAGGAAGGAAAGAAGG	rs147407384	by1000genomes	TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98907966_98907967insAAGGAAGGAAGGAAAGAAGG								DCBLD2 (287433 upstream) : COL8A1 (449487 downstream)																							aggaaggaagaaaggaaggaag	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	104324402	104324403	+	IGR	INS	-	AG	AG	rs149610512	by1000genomes	TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104324402_104324403insAG								None (None upstream) : ALCAM (761310 downstream)																							aaaaaaaaaaaggaaggaagga	0.010													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	111197863	111197868	+	IGR	DEL	CACACA	-	-	rs7650195		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111197863_111197868delCACACA								PVRL3 (285490 upstream) : CD96 (63058 downstream)																							CGAACAGCCTcacacacacacacaca	0.442													5	3	---	---	---	---	
ARHGAP31	57514	broad.mit.edu	37	3	119128224	119128230	+	Intron	DEL	TGAGGGA	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119128224_119128230delTGAGGGA	uc003ecj.3	+							NM_020754	NP_065805	Q2M1Z3	RHG31_HUMAN	Cdc42 GTPase-activating protein						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion|lamellipodium	GTPase activator activity			ovary(2)	2						GGCGGTGAGCTGAGGGAATTCCCTCCA	0.386													8	5	---	---	---	---	
PPM1L	151742	broad.mit.edu	37	3	160672749	160672749	+	Intron	DEL	T	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160672749delT	uc003fdr.2	+						PPM1L_uc003fds.2_Intron|PPM1L_uc003fdt.2_Intron|PPM1L_uc010hwf.2_Intron	NM_139245	NP_640338	Q5SGD2	PPM1L_HUMAN	protein phosphatase 1 (formerly 2C)-like						protein dephosphorylation|sphingolipid metabolic process	endoplasmic reticulum membrane|integral to membrane|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			breast(1)	1			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			ccttccttcctttcctttcct	0.020													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	25042989	25042989	+	IGR	DEL	T	-	-	rs35642561		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25042989delT								LGI2 (10575 upstream) : SEPSECS (78639 downstream)																							tctttcttgcttttttttttt	0.000													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	34373434	34373435	+	IGR	DEL	TG	-	-	rs34289687		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:34373434_34373435delTG								None (None upstream) : None (None downstream)																							GAtgtgtttttgtgtgtgtgtg	0.431													2	5	---	---	---	---	
CCDC109B	55013	broad.mit.edu	37	4	110581324	110581325	+	Intron	INS	-	T	T	rs139082600	by1000genomes	TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110581324_110581325insT	uc011cfs.1	+						CCDC109B_uc010imf.2_Intron	NM_017918	NP_060388	Q9NWR8	C109B_HUMAN	coiled-coil domain containing 109B							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(123;6.65e-06)		AAATTTACTCATTTTTTTTTCT	0.282													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	116724334	116724335	+	IGR	INS	-	GC	GC	rs2389091	by1000genomes	TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:116724334_116724335insGC								NDST4 (689302 upstream) : MIR1973 (496546 downstream)																							tgtgtgtgtgtgCGCGCGCATG	0.272													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	145477185	145477186	+	IGR	DEL	GT	-	-	rs71832426		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145477185_145477186delGT								GYPA (415281 upstream) : HHIP (89987 downstream)																							GCGCACGAGCgtgtgtgtgtgt	0.371													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	7207157	7207157	+	IGR	DEL	T	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7207157delT								PAPD7 (449996 upstream) : ADCY2 (189186 downstream)																							cctcccttccttttcttcctt	0.090													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	17339524	17339527	+	IGR	DEL	CTTC	-	-	rs59681041	by1000genomes	TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17339524_17339527delCTTC								BASP1 (62589 upstream) : None (None downstream)																							ttctttctttcttccttccttcct	0.049													4	3	---	---	---	---	
PDE4D	5144	broad.mit.edu	37	5	59768934	59768935	+	Intron	INS	-	AG	AG	rs146131896	by1000genomes	TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59768934_59768935insAG	uc003jsb.2	-						PDE4D_uc010iwj.1_Intron	NM_006203	NP_006194	Q08499	PDE4D_HUMAN	phosphodiesterase 4D isoform 2						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)	gaaagaaagaaagagagagaga	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	77965253	77965256	+	IGR	DEL	AAGG	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77965253_77965256delAAGG								LHFPL2 (20605 upstream) : ARSB (107783 downstream)																							gacAGACagaaaggaaggaaggaa	0.010													7	4	---	---	---	---	
LOC441089	441089	broad.mit.edu	37	5	79646840	79646840	+	RNA	DEL	T	-	-	rs34240292		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79646840delT	uc010jaj.1	-	1		c.946delA				NR_003665				Homo sapiens CRSP8 pseudogene (LOC441089), non-coding RNA.												0						GCGTGGGGGCTTACTGCCGGC	0.632													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	122554046	122554047	+	IGR	DEL	GT	-	-	rs112928698		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122554046_122554047delGT								PRDM6 (30302 upstream) : CEP120 (126533 downstream)																							tgtgtgtgtggtgtgtgtgtgt	0.337													4	2	---	---	---	---	
PPP2R2B	5521	broad.mit.edu	37	5	146295011	146295012	+	Intron	DEL	AC	-	-	rs72407231		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146295011_146295012delAC	uc011dbv.1	-						PPP2R2B_uc003loi.3_Intron|PPP2R2B_uc003loh.3_Intron|PPP2R2B_uc003loj.3_Intron|PPP2R2B_uc003lok.3_Intron|PPP2R2B_uc011dbu.1_Intron	NM_181675	NP_858061	Q00005	2ABB_HUMAN	beta isoform of regulatory subunit B55, protein						apoptosis|signal transduction	cytoskeleton|mitochondrial outer membrane|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)|prostate(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTACCTATGTacacacacacac	0.178													4	3	---	---	---	---	
CYFIP2	26999	broad.mit.edu	37	5	156750834	156750835	+	Intron	INS	-	A	A	rs111716109		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156750834_156750835insA	uc003lwq.2	+						CYFIP2_uc011ddn.1_Intron|CYFIP2_uc011ddo.1_Intron|CYFIP2_uc003lwr.2_Intron|CYFIP2_uc003lws.2_Intron|CYFIP2_uc003lwt.2_Intron|CYFIP2_uc011ddp.1_Intron	NM_001037333	NP_001032410	Q96F07	CYFP2_HUMAN	cytoplasmic FMR1 interacting protein 2						apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GACATCTGCAGAAAAAAAAAAA	0.416													4	2	---	---	---	---	
NOP16	51491	broad.mit.edu	37	5	175814066	175814069	+	Intron	DEL	TCTC	-	-	rs145796794		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175814066_175814069delTCTC	uc011dfl.1	-						NOP16_uc003med.2_Intron|NOP16_uc003mee.2_Intron|NOP16_uc011dfm.1_Intron|HIGD2A_uc003meg.2_5'Flank	NM_016391	NP_057475	Q9Y3C1	NOP16_HUMAN	NOP16 nucleolar protein homolog							nucleolus				ovary(1)|central_nervous_system(1)	2						GGAGGCTTTTTCTCTCTCtctctc	0.245													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	179513203	179513203	+	IGR	DEL	T	-	-	rs146020552		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179513203delT								RNF130 (14094 upstream) : RASGEF1C (14593 downstream)																							AAGAGATTAGttttttttttt	0.209													4	3	---	---	---	---	
HLA-DRB5	3127	broad.mit.edu	37	6	32547001	32547001	+	Intron	DEL	C	-	-	rs67419769		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32547001delC	uc003obk.3	-						HLA-DRB1_uc011dqa.1_Intron|HLA-DRB6_uc003obo.1_Intron|uc010jub.1_5'Flank|HLA-DRB1_uc003obp.3_Intron|HLA-DRB1_uc011dqb.1_Intron	NM_002125	NP_002116	Q30154	DRB5_HUMAN	major histocompatibility complex, class II, DR						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0						TCCTGAGTCTCCCCTGAGCCA	0.448													4	2	---	---	---	---	
HLA-DRB5	3127	broad.mit.edu	37	6	32557290	32557291	+	Intron	INS	-	T	T	rs145132878	by1000genomes	TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32557290_32557291insT	uc003obk.3	-						HLA-DRB1_uc003obp.3_Intron	NM_002125	NP_002116	Q30154	DRB5_HUMAN	major histocompatibility complex, class II, DR						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0						TTTGGGATCCAATGATAAAGAT	0.416													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	101557311	101557330	+	IGR	DEL	CTTCCTTCCTTCCTTCCTTT	-	-	rs71028063	by1000genomes	TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101557311_101557330delCTTCCTTCCTTCCTTCCTTT								ASCC3 (228087 upstream) : GRIK2 (289575 downstream)																							tccttccttccttccttccttccttcctttctttctttct	0.000													11	5	---	---	---	---	
L3MBTL3	84456	broad.mit.edu	37	6	130387432	130387433	+	Intron	DEL	TA	-	-	rs66543366		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130387432_130387433delTA	uc003qbt.2	+						L3MBTL3_uc003qbu.2_Intron	NM_032438	NP_115814	Q96JM7	LMBL3_HUMAN	l(3)mbt-like 3 isoform a						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)		tatttttgtgtatatatatata	0.257													6	5	---	---	---	---	
RAPGEF5	9771	broad.mit.edu	37	7	22194363	22194364	+	Intron	INS	-	T	T	rs150777301	by1000genomes	TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22194363_22194364insT	uc003svg.2	-						RAPGEF5_uc011jyl.1_Intron	NM_012294	NP_036426	Q92565	RPGF5_HUMAN	Rap guanine nucleotide exchange factor (GEF) 5						nervous system development|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	nucleus	GTP-dependent protein binding|Rap guanyl-nucleotide exchange factor activity			ovary(1)	1						ACAGAGTTAGATTTTTTATATA	0.386													4	7	---	---	---	---	
TRA2A	29896	broad.mit.edu	37	7	23545204	23545205	+	Intron	INS	-	A	A	rs34037907		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23545204_23545205insA	uc003swi.2	-						TRA2A_uc011jzb.1_Intron|TRA2A_uc011jzc.1_Intron|TRA2A_uc011jzd.1_Intron	NM_013293	NP_037425	Q13595	TRA2A_HUMAN	transformer-2 alpha						nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|RNA binding			ovary(1)	1						agagaaaaagcaaaaaaaaaaa	0.223													5	3	---	---	---	---	
SEPT14	346288	broad.mit.edu	37	7	55910601	55910601	+	Intron	DEL	A	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55910601delA	uc003tqz.2	-							NM_207366	NP_997249	Q6ZU15	SEP14_HUMAN	septin 14						cell cycle|cell division	septin complex	GTP binding|protein binding				0	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			actccgtctcaaaaaaaaaaa	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	56357562	56357563	+	IGR	INS	-	AAA	AAA			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56357562_56357563insAAA								PSPH (173472 upstream) : DKFZp434L192 (206353 downstream)																							gactccatctcaaaaaaaaaaa	0.158													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57929464	57929464	+	IGR	DEL	G	-	-	rs76511107		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57929464delG								ZNF716 (396199 upstream) : None (None downstream)																							AGGACCTTTCGAAATAAAATG	0.423													4	2	---	---	---	---	
C7orf61	402573	broad.mit.edu	37	7	100054638	100054638	+	Intron	DEL	T	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100054638delT	uc003uuz.1	-							NM_001004323	NP_001004323	Q8IZ16	CG061_HUMAN	hypothetical protein LOC402573												0						TGTGCATGCGTAAATAGCTGG	0.507													3	7	---	---	---	---	
CUX1	1523	broad.mit.edu	37	7	101903042	101903043	+	Intron	INS	-	A	A	rs149960983		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101903042_101903043insA	uc003uyt.2	+						CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_001913	NP_001904	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform b						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8						aaaaaagaaagaaaagagaaag	0.124													4	2	---	---	---	---	
ATXN7L1	222255	broad.mit.edu	37	7	105459892	105459892	+	Intron	DEL	A	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105459892delA	uc003vde.2	-						ATXN7L1_uc003vdi.2_Intron	NM_020725	NP_065776	Q9ULK2	AT7L1_HUMAN	ataxin 7-like 1 isoform 1												0						TTTGGGatttaaaaaaaaaaa	0.398													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	122611130	122611133	+	IGR	DEL	TTCC	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122611130_122611133delTTCC								CADPS2 (84576 upstream) : TAS2R16 (23626 downstream)																							CGACTATATAttccttccttcctt	0.225													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	33465290	33465293	+	IGR	DEL	TTCC	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33465290_33465293delTTCC								DUSP26 (7851 upstream) : None (None downstream)																							cttcccttctttccttccttcctt	0.000													4	2	---	---	---	---	
SLC30A8	169026	broad.mit.edu	37	8	118184908	118184909	+	Frame_Shift_Del	DEL	CC	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118184908_118184909delCC	uc003yoh.2	+	8	1328_1329	c.1098_1099delCC	c.(1096-1101)GACCCCfs	p.D366fs	SLC30A8_uc010mcz.2_Frame_Shift_Del_p.D317fs|SLC30A8_uc011lia.1_Frame_Shift_Del_p.D317fs|SLC30A8_uc003yog.2_Frame_Shift_Del_p.D317fs	NM_173851	NP_776250	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 member 8	366_367	Cytoplasmic (Potential).				insulin secretion|positive regulation of insulin secretion|regulation of sequestering of zinc ion|regulation of vesicle-mediated transport|response to glucose stimulus|sequestering of zinc ion	integral to membrane|plasma membrane|secretory granule membrane|transport vesicle membrane	protein homodimerization activity|zinc ion transmembrane transporter activity			ovary(2)|skin(2)	4	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			TCTGTGAAGACCCCTGTGACTA	0.460													137	87	---	---	---	---	
GLIS3	169792	broad.mit.edu	37	9	4266596	4266599	+	Intron	DEL	ACAC	-	-	rs112670602		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4266596_4266599delACAC	uc003zhx.1	-						GLIS3_uc003zic.1_Intron|GLIS3_uc003zie.1_Intron|GLIS3_uc010mhh.1_Intron|GLIS3_uc003zid.1_Intron|GLIS3_uc010mhi.1_Intron|GLIS3_uc003zif.1_Intron|GLIS3_uc003zig.1_Intron|GLIS3_uc003zih.1_Intron	NM_001042413	NP_001035878	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3 isoform a						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		ATGCGCGTGTacacacacacacac	0.358													3	3	---	---	---	---	
KIAA1432	57589	broad.mit.edu	37	9	5720540	5720540	+	Intron	DEL	T	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5720540delT	uc003zji.2	+						KIAA1432_uc003zjh.2_Intron|KIAA1432_uc003zjl.3_Intron|KIAA1432_uc003zjj.1_Intron	NM_020829	NP_065880	Q4ADV7	RIC1_HUMAN	connexin 43-interacting protein 150 isoform a							integral to membrane					0		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)		AACTTACAGGTTTTTCTGGCA	0.348													48	40	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	29533507	29533508	+	IGR	INS	-	TGTG	TGTG	rs141409947	by1000genomes	TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:29533507_29533508insTGTG								MIR873 (644554 upstream) : None (None downstream)																							actgtcctaaatgtgtgtgtgt	0.000													3	3	---	---	---	---	
NSUN6	221078	broad.mit.edu	37	10	18874728	18874729	+	Intron	INS	-	ACAAG	ACAAG	rs144035042	by1000genomes	TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18874728_18874729insACAAG	uc010qcp.1	-							NM_182543	NP_872349	Q8TEA1	NSUN6_HUMAN	NOL1/NOP2/Sun domain family, member 6								methyltransferase activity|RNA binding			ovary(2)	2						ttcaaattaccacaaggataag	0.000													3	3	---	---	---	---	
WDR11	55717	broad.mit.edu	37	10	122624869	122624870	+	Intron	INS	-	T	T	rs138501915	by1000genomes	TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122624869_122624870insT	uc010qtf.1	+						WDR11_uc010qte.1_Intron|WDR11_uc001lfd.1_Intron	NM_018117	NP_060587	Q9BZH6	WDR11_HUMAN	bromodomain and WD repeat domain containing 2							integral to membrane					0						ATTTTAGATTGTTTTTTTTGTC	0.307													4	2	---	---	---	---	
ZNF143	7702	broad.mit.edu	37	11	9501000	9501001	+	Intron	INS	-	T	T			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9501000_9501001insT	uc001mhr.2	+						ZNF143_uc009yfu.2_Intron|ZNF143_uc010rby.1_Intron	NM_003442	NP_003433	P52747	ZN143_HUMAN	zinc finger protein 143						regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase III promoter|transcription from RNA polymerase II promoter|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding|zinc ion binding				0				all cancers(16;4.12e-09)|Epithelial(150;2.29e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0212)		CATTTTAAAGCTTTATTTTATT	0.327													93	66	---	---	---	---	
PIK3C2A	5286	broad.mit.edu	37	11	17143576	17143576	+	Intron	DEL	A	-	-	rs77774534		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17143576delA	uc001mmq.3	-						PIK3C2A_uc009ygu.1_Intron|PIK3C2A_uc010rcw.1_Intron|PIK3C2A_uc001mmr.3_Intron	NM_002645	NP_002636	O00443	P3C2A_HUMAN	phosphoinositide-3-kinase, class 2 alpha						cell communication|phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling	clathrin-coated vesicle|Golgi apparatus|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(4)|central_nervous_system(4)|stomach(1)|ovary(1)	10					Phosphatidylserine(DB00144)	GTAGATTATTAAAAAAAAAAA	0.239													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	67558602	67558614	+	IGR	DEL	CTCTCAGGCTCCC	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67558602_67558614delCTCTCAGGCTCCC								ALDH3B2 (109917 upstream) : LOC645332 (626 downstream)																							CTCCAGGCAGCTCTCAGGCTCCCTTGGTTCTCT	0.573													13	7	---	---	---	---	
RAB30	27314	broad.mit.edu	37	11	82703778	82703779	+	Intron	INS	-	ACAC	ACAC	rs141714457	by1000genomes	TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82703778_82703779insACAC	uc001ozu.2	-						RAB30_uc009yve.2_Intron|RAB30_uc010rst.1_Intron|RAB30_uc001ozv.2_Intron|RAB30_uc009yvg.1_Intron	NM_014488	NP_055303	Q15771	RAB30_HUMAN	RAB30, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	Golgi stack|plasma membrane	GTP binding|GTPase activity				0						ctctGTCACCAacacacacaca	0.198													4	2	---	---	---	---	
CCDC77	84318	broad.mit.edu	37	12	518377	518377	+	Intron	DEL	A	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:518377delA	uc001qig.2	+						CCDC77_uc009zdk.2_Intron|CCDC77_uc010sdp.1_Intron|CCDC77_uc010sdq.1_Intron	NM_032358	NP_115734	Q9BR77	CCD77_HUMAN	coiled-coil domain containing 77 isoform a							centrosome				ovary(1)	1	all_cancers(10;0.0149)|all_epithelial(11;0.035)|all_lung(10;0.111)|Ovarian(42;0.142)|Lung NSC(10;0.156)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.033)			acactgtctcaaaaaaaaaaa	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	39928563	39928570	+	IGR	DEL	AGAAAGAA	-	-	rs35441126		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39928563_39928570delAGAAAGAA								KIF21A (91645 upstream) : ABCD2 (16452 downstream)																							agaaagaaagagaaagaaagaaagaaag	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	65527520	65527523	+	IGR	DEL	GGAA	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65527520_65527523delGGAA								WIF1 (12404 upstream) : LEMD3 (35848 downstream)																							ATAGAGCTGTggaaggaaggaagg	0.181													9	4	---	---	---	---	
CHFR	55743	broad.mit.edu	37	12	133454390	133454391	+	Intron	INS	-	T	T	rs146711897	by1000genomes	TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133454390_133454391insT	uc001ulf.2	-						CHFR_uc001ulc.1_5'Flank|CHFR_uc001ule.2_Intron|CHFR_uc010tbs.1_Intron|CHFR_uc001uld.2_Intron|CHFR_uc010tbt.1_Intron	NM_001161344	NP_001154816	Q96EP1	CHFR_HUMAN	checkpoint with forkhead and ring finger domains						cell division|mitosis|mitotic cell cycle checkpoint|modification-dependent protein catabolic process|protein polyubiquitination	PML body	nucleotide binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			skin(1)	1	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00552)|all_epithelial(31;0.226)		OV - Ovarian serous cystadenocarcinoma(86;2.59e-08)|Epithelial(86;6.38e-07)|all cancers(50;1.56e-05)		ACATAAAGAAAttttttttttt	0.173													4	2	---	---	---	---	
TPTE2	93492	broad.mit.edu	37	13	20067207	20067207	+	Intron	DEL	C	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20067207delC	uc001umd.2	-						TPTE2_uc009zzk.2_Intron|TPTE2_uc009zzl.2_Intron|TPTE2_uc001ume.2_Intron|TPTE2_uc009zzm.2_Intron|TPTE2_uc010tcm.1_Intron	NM_199254	NP_954863	Q6XPS3	TPTE2_HUMAN	TPTE and PTEN homologous inositol lipid							endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		GGCAATTACACTAACAGGAAG	0.363													4	3	---	---	---	---	
BRCA2	675	broad.mit.edu	37	13	32950672	32950673	+	Intron	DEL	AG	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32950672_32950673delAG	uc001uub.1	+							NM_000059	NP_000050	P51587	BRCA2_HUMAN	breast cancer 2, early onset						cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding			ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1)	64		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		aaaaaaaaaaagaaaaaaCTTT	0.139			D|Mis|N|F|S		breast|ovarian|pancreatic	breast|ovarian|pancreatic|leukemia  (FANCB|FANCD1)		Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome	TCGA Ovarian(8;0.087)			7	4	---	---	---	---	
THSD1P1	374500	broad.mit.edu	37	13	52803642	52803642	+	Intron	DEL	T	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52803642delT	uc001vgm.1	-						uc001vgn.2_Intron					Homo sapiens cDNA FLJ14630 fis, clone NT2RP2000459.												0						CAGTTTTCCCTTTTTTTTTTT	0.328													4	4	---	---	---	---	
TDRD3	81550	broad.mit.edu	37	13	61141478	61141479	+	Intron	INS	-	TTTTC	TTTTC	rs141427579	by1000genomes	TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61141478_61141479insTTTTC	uc001via.2	+						TDRD3_uc001vhz.3_Intron|TDRD3_uc010aeg.2_Intron|TDRD3_uc001vib.3_Intron	NM_030794	NP_110421	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3 isoform 2						chromatin modification	cytoplasm|nucleus	chromatin binding|methylated histone residue binding|nucleic acid binding|transcription coactivator activity			upper_aerodigestive_tract(1)|skin(1)	2		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		TATCCCTGCCTttttcttttct	0.287													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	23295975	23295976	+	IGR	INS	-	TGTG	TGTG	rs142382788		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23295975_23295976insTGTG								SLC7A7 (6961 upstream) : MRPL52 (3116 downstream)																							CTCATCTTTTCtgtgtgtgtgt	0.050													4	2	---	---	---	---	
SDCCAG1	9147	broad.mit.edu	37	14	50269012	50269013	+	Intron	INS	-	A	A			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50269012_50269013insA	uc001wxc.2	-						SDCCAG1_uc010anj.1_Intron|SDCCAG1_uc001wwz.2_5'Flank|SDCCAG1_uc001wxa.2_5'Flank|SDCCAG1_uc010tqi.1_Intron|SDCCAG1_uc001wxe.2_Intron|SDCCAG1_uc001wxd.1_Intron	NM_004713	NP_004704	O60524	NEMF_HUMAN	serologically defined colon cancer antigen 1							cytoplasm|nucleus					0	all_epithelial(31;0.000822)|Breast(41;0.0117)	all_lung(585;1.02e-05)		OV - Ovarian serous cystadenocarcinoma(311;5.99e-34)		TTAGCATTTCCAAAAAAAAAAA	0.203													6	5	---	---	---	---	
DYNC1H1	1778	broad.mit.edu	37	14	102450010	102450010	+	Intron	DEL	T	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102450010delT	uc001yks.2	+							NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1						cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10						ttgtttggtgttttttttttg	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	7825301	7825301	+	IGR	DEL	A	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7825301delA								A2BP1 (61961 upstream) : TMEM114 (794202 downstream)																							ggagggaaggaaagaaggaag	0.000													4	4	---	---	---	---	
OTOA	146183	broad.mit.edu	37	16	21725621	21725622	+	Intron	INS	-	CTTC	CTTC	rs34598445		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21725621_21725622insCTTC	uc002djh.2	+						uc002diq.3_Intron|OTOA_uc010vbj.1_Intron|OTOA_uc002dji.2_Intron|OTOA_uc010vbk.1_Intron	NM_144672	NP_653273	Q7RTW8	OTOAN_HUMAN	otoancorin isoform 1						sensory perception of sound	anchored to membrane|apical plasma membrane|proteinaceous extracellular matrix				ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(48;0.0414)		tcttttcctttcttccttcctt	0.000													8	6	---	---	---	---	
CDH3	1001	broad.mit.edu	37	16	68713597	68713598	+	Intron	INS	-	AA	AA	rs71382055		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68713597_68713598insAA	uc002ewf.2	+						CDH3_uc010vli.1_Intron	NM_001793	NP_001784	P22223	CADH3_HUMAN	cadherin 3, type 1 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion|response to stimulus|visual perception	integral to membrane	calcium ion binding	p.?(1)		ovary(3)|breast(1)|skin(1)	5		Ovarian(137;0.0564)		OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384)		gacttcatctcaaaaaaaaaaa	0.158													15	8	---	---	---	---	
TUBB3	10381	broad.mit.edu	37	16	89996502	89996505	+	Intron	DEL	TTCC	-	-	rs113176575		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89996502_89996505delTTCC	uc002fph.1	+						TUBB3_uc002fpf.2_Intron|TUBB3_uc010ciz.1_Intron|TUBB3_uc010cja.1_Intron|TUBB3_uc002fpg.1_Intron|TUBB3_uc002fpi.1_Intron|TUBB3_uc002fpj.1_5'Flank|TUBB3_uc010cjb.1_5'Flank	NM_006086	NP_006077	Q13509	TBB3_HUMAN	tubulin, beta, 4						'de novo' posttranslational protein folding|axon guidance|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity			ovary(2)|pancreas(1)	3		all_cancers(9;1.69e-11)|Lung NSC(15;8.94e-06)|all_lung(18;1.39e-05)|all_neural(9;0.00581)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0273)		tcttccttcattccttccttcctt	0.044													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	20978234	20978237	+	IGR	DEL	CCTC	-	-	rs75278704		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20978234_20978237delCCTC								USP22 (31161 upstream) : DHRS7B (52021 downstream)																							ttccttctttcctccctccctccc	0.015													5	4	---	---	---	---	
MYO18A	399687	broad.mit.edu	37	17	27401310	27401311	+	3'UTR	DEL	AA	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27401310_27401311delAA	uc002hdt.1	-	42					MYO18A_uc010wbc.1_3'UTR|MYO18A_uc002hds.2_3'UTR|MYO18A_uc010csa.1_3'UTR|MYO18A_uc002hdu.1_3'UTR|TIAF1_uc002hdv.1_5'UTR	NM_078471	NP_510880	Q92614	MY18A_HUMAN	myosin 18A isoform a						anti-apoptosis|DNA metabolic process	ER-Golgi intermediate compartment|myosin complex	ATP binding|DNA binding|DNA-dependent ATPase activity|identical protein binding|motor activity				0			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			TATTTAAATTAAAAAGTAGAAA	0.559													6	3	---	---	---	---	
AATF	26574	broad.mit.edu	37	17	35358754	35358754	+	Intron	DEL	A	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35358754delA	uc002hni.2	+						AATF_uc002hnj.2_Intron	NM_012138	NP_036270	Q9NY61	AATF_HUMAN	apoptosis antagonizing transcription factor						anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|negative regulation of superoxide anion generation|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to DNA damage stimulus	centrosome|focal adhesion|nucleolus	leucine zipper domain binding|sequence-specific DNA binding transcription factor activity				0		Breast(25;0.00607)				aggaaggaagaaaAAAAAAAA	0.015													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	67358091	67358098	+	IGR	DEL	CCTTCCTT	-	-	rs34045164		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67358091_67358098delCCTTCCTT								ABCA5 (34768 upstream) : MAP2K6 (52740 downstream)																							tttcctttcCccttccttccttccttcc	0.053													3	4	---	---	---	---	
TRIM47	91107	broad.mit.edu	37	17	73872910	73872911	+	Intron	INS	-	C	C			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73872910_73872911insC	uc002jpw.2	-						TRIM47_uc002jpv.2_Intron	NM_033452	NP_258411	Q96LD4	TRI47_HUMAN	tripartite motif-containing 47							cytoplasm|nucleus	zinc ion binding			ovary(2)|prostate(1)|lung(1)|breast(1)	5			Epithelial(20;4.23e-06)|all cancers(21;5.24e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			GACAACACCCTCCATGAGTGTG	0.629													16	9	---	---	---	---	
SMAD4	4089	broad.mit.edu	37	18	48573269	48573269	+	Intron	DEL	T	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48573269delT	uc010xdp.1	+						SMAD4_uc010xdo.1_Intron	NM_005359	NP_005350	Q13485	SMAD4_HUMAN	mothers against decapentaplegic homolog 4						BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway	activin responsive factor complex|centrosome|cytosol	I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity			pancreas(170)|large_intestine(108)|thyroid(19)|lung(11)|small_intestine(9)|upper_aerodigestive_tract(8)|biliary_tract(8)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1)	369		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GATGTGTGTCTTTTTTTTTTT	0.318									Juvenile_Polyposis|Hereditary_Hemorrhagic_Telangiectasia				5	3	---	---	---	---	
ZFP112	7771	broad.mit.edu	37	19	44841031	44841031	+	Intron	DEL	T	-	-	rs113034578		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44841031delT	uc010ejj.2	-						ZFP112_uc002ozc.3_Intron|ZFP112_uc010xwy.1_Intron|ZFP112_uc010xwz.1_Intron	NM_001083335	NP_001076804	Q9UJU3	ZF112_HUMAN	zinc finger protein 228 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)	5						CATGAttttcttttttttttt	0.040													4	2	---	---	---	---	
C20orf26	26074	broad.mit.edu	37	20	20243445	20243446	+	Intron	DEL	TG	-	-	rs79559760	by1000genomes	TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20243445_20243446delTG	uc002wru.2	+						C20orf26_uc010zse.1_Intron|C20orf26_uc002wrw.2_Intron|C20orf26_uc002wrv.2_Intron	NM_015585	NP_056400	Q8NHU2	CT026_HUMAN	hypothetical protein LOC26074											ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)		CACCTGTTTTTGTGTTTTTTTT	0.223													6	3	---	---	---	---	
C20orf185	359710	broad.mit.edu	37	20	31653329	31653330	+	Intron	INS	-	GAAG	GAAG			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31653329_31653330insGAAG	uc002wym.1	+							NM_182658	NP_872599	P59826	LPLC3_HUMAN	antimicrobial peptide RYA3 precursor						innate immune response	cytoplasm|extracellular region	lipid binding|protein binding			ovary(4)	4						aaaaagagaaagaaggaaggaa	0.000													6	3	---	---	---	---	
HUNK	30811	broad.mit.edu	37	21	33295887	33295890	+	Intron	DEL	GAGG	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33295887_33295890delGAGG	uc002yph.2	+							NM_014586	NP_055401	P57058	HUNK_HUMAN	hormonally upregulated Neu-associated kinase						multicellular organismal development|signal transduction		ATP binding|protein serine/threonine kinase activity			stomach(1)|skin(1)	2						ggaaggaagcgagggagggaggga	0.167													4	2	---	---	---	---	
DSCAM	1826	broad.mit.edu	37	21	41384834	41384835	+	3'UTR	INS	-	T	T	rs11451228		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41384834_41384835insT	uc002yyq.1	-	33					DSCAM_uc002yyr.1_RNA	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				AGTATTTTCTCttttttttttt	0.317													4	3	---	---	---	---	
CBS	875	broad.mit.edu	37	21	44476000	44476001	+	Intron	INS	-	T	T	rs79861734		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44476000_44476001insT	uc002zcu.2	-						CBS_uc002zcs.1_Intron|CBS_uc002zct.2_Intron|CBS_uc002zcw.3_Intron|CBS_uc002zcv.2_Intron|CBS_uc002zcx.2_3'UTR	NM_000071	NP_000062	P35520	CBS_HUMAN	cystathionine-beta-synthase						cysteine biosynthetic process from serine|cysteine biosynthetic process via cystathionine|homocysteine catabolic process|hydrogen sulfide biosynthetic process|L-cysteine catabolic process|L-serine catabolic process	cytosol|nucleolus	cystathionine beta-synthase activity|heme binding|protein homodimerization activity|pyridoxal phosphate binding|ubiquitin protein ligase binding				0					L-Cysteine(DB00151)|L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|S-Adenosylmethionine(DB00118)	gaatttgcatctttttttTTTT	0.238													6	3	---	---	---	---	
CYTSA	23384	broad.mit.edu	37	22	24761815	24761815	+	Intron	DEL	T	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24761815delT	uc002zzw.2	+						CYTSA_uc002zzv.3_Intron|CYTSA_uc011ajq.1_Intron	NM_015330	NP_056145	Q69YQ0	CYTSA_HUMAN	cytospin A						cell cycle|cell division						0						CAGCTGTATCTTTTTTTTTTT	0.343													4	3	---	---	---	---	
INPP5J	27124	broad.mit.edu	37	22	31509421	31509421	+	Intron	DEL	A	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31509421delA	uc010gwf.2	+						SELM_uc011alj.1_Intron			Q15735	PI5PA_HUMAN	RecName: Full=Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A;          EC=3.1.3.56; AltName: Full=Inositol polyphosphate 5-phosphatase J;							cytoplasm|ruffle	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|SH3 domain binding			skin(1)	1						GCCTACaattaaaaaaaaaaa	0.378													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	48474076	48474077	+	IGR	DEL	TG	-	-	rs34757203		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48474076_48474077delTG								TBC1D22A (904354 upstream) : FAM19A5 (411211 downstream)																							tgtgtgcgcatgtgtgtgtgtg	0.000													4	3	---	---	---	---	
PLXNB2	23654	broad.mit.edu	37	22	50715729	50715730	+	Intron	INS	-	A	A	rs34557850		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50715729_50715730insA	uc003bkv.3	-						PLXNB2_uc003bkt.1_Intron|PLXNB2_uc003bku.1_Intron	NM_012401	NP_036533	O15031	PLXB2_HUMAN	plexin B2 precursor						regulation of small GTPase mediated signal transduction	integral to membrane|intracellular	GTPase activator activity|protein binding|receptor activity			ovary(4)|central_nervous_system(1)|skin(1)	6		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		gactccatctcaaaaaaaaaaa	0.193													4	3	---	---	---	---	
PDHA1	5160	broad.mit.edu	37	X	19363864	19363864	+	Intron	DEL	C	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19363864delC	uc004czg.3	+						PDHA1_uc004czh.3_Intron|PDHA1_uc011mjc.1_Intron|PDHA1_uc011mjd.1_Intron|PDHA1_uc010nfk.2_Intron	NM_000284	NP_000275	P08559	ODPA_HUMAN	pyruvate dehydrogenase E1 alpha 1 precursor						glycolysis|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	protein binding|pyruvate dehydrogenase (acetyl-transferring) activity			ovary(1)	1	Hepatocellular(33;0.183)				NADH(DB00157)	TTTGCAGGGTCCCCCCCCCCC	0.468													13	6	---	---	---	---	
ATP7A	538	broad.mit.edu	37	X	77299156	77299156	+	Intron	DEL	T	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77299156delT	uc004ecx.3	+							NM_000052	NP_000043	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide						ATP biosynthetic process|blood vessel development|blood vessel remodeling|cartilage development|cellular copper ion homeostasis|cerebellar Purkinje cell differentiation|collagen fibril organization|copper ion import|detoxification of copper ion|dopamine metabolic process|elastic fiber assembly|elastin biosynthetic process|epinephrine metabolic process|hair follicle morphogenesis|locomotory behavior|lung alveolus development|negative regulation of metalloenzyme activity|neuroprotection|peptidyl-lysine modification|pigmentation|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|pyramidal neuron development|regulation of oxidative phosphorylation|removal of superoxide radicals|serotonin metabolic process|skin development|T-helper cell differentiation|tryptophan metabolic process	basolateral plasma membrane|cytosol|endoplasmic reticulum|endoplasmic reticulum|integral to membrane|late endosome|neuron projection|neuronal cell body|perinuclear region of cytoplasm|trans-Golgi network|trans-Golgi network transport vesicle	ATP binding|copper-dependent protein binding|copper-exporting ATPase activity|superoxide dismutase copper chaperone activity				0						TCCCTCCAACttttttttttt	0.129													5	3	---	---	---	---	
SLC6A14	11254	broad.mit.edu	37	X	115572488	115572490	+	Intron	DEL	AAA	-	-			TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115572488_115572490delAAA	uc004eqi.2	+						SLC6A14_uc011mtm.1_Intron	NM_007231	NP_009162	Q9UN76	S6A14_HUMAN	solute carrier family 6 (amino acid						cellular amino acid metabolic process|response to toxin	integral to membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity			ovary(2)|pancreas(1)	3					L-Proline(DB00172)	TGGGCTGCAGAAATGGGAAGGAT	0.350													3	4	---	---	---	---	
THOC2	57187	broad.mit.edu	37	X	122772579	122772580	+	Intron	DEL	AC	-	-	rs35181346		TCGA-B0-5102-01A-01D-1421-08	TCGA-B0-5102-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122772579_122772580delAC	uc004etu.2	-						THOC2_uc011muh.1_Intron	NM_001081550	NP_001075019	Q8NI27	THOC2_HUMAN	THO complex 2						intronless viral mRNA export from host nucleus|mRNA processing|RNA splicing	THO complex part of transcription export complex	protein binding|RNA binding			ovary(3)	3						acacacacgtacacacacacac	0.139													5	3	---	---	---	---	
