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
CLCNKA	1187	broad.mit.edu	37	1	16360190	16360190	+	3'UTR	SNP	A	C	C	rs28418375	by1000genomes	TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16360190A>C	uc001axu.2	+	20					CLCNKA_uc001axt.2_RNA|CLCNKA_uc001axv.2_3'UTR|CLCNKA_uc010obw.1_3'UTR|CLCNKB_uc001axw.3_Intron	NM_004070	NP_004061	P51800	CLCKA_HUMAN	chloride channel Ka isoform 1						excretion	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			ovary(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	ACCCCAGCTGACCTGGTACTG	0.552													7	22	---	---	---	---	PASS
PLA2G2A	5320	broad.mit.edu	37	1	20304968	20304968	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20304968C>G	uc001bcu.2	-	3	308	c.90G>C	c.(88-90)AAG>AAC	p.K30N	PLA2G2A_uc001bcv.2_Missense_Mutation_p.K30N|PLA2G2A_uc010oda.1_Missense_Mutation_p.K30N|PLA2G2A_uc010odb.1_Missense_Mutation_p.K30N	NM_001161729	NP_001155201	P14555	PA2GA_HUMAN	phospholipase A2, group IIA precursor	30					defense response to Gram-positive bacterium|lipid catabolic process|low-density lipoprotein particle remodeling|phosphatidic acid metabolic process|positive regulation of inflammatory response|positive regulation of macrophage derived foam cell differentiation	endoplasmic reticulum|extracellular space|membrane	calcium ion binding|calcium-dependent phospholipase A2 activity|phospholipid binding				0		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00459)|Lung NSC(340;0.00475)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000138)|Kidney(64;0.000171)|GBM - Glioblastoma multiforme(114;0.00032)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CTGTCGTCAACTTGATCATTC	0.557													12	61	---	---	---	---	PASS
SPATA6	54558	broad.mit.edu	37	1	48865161	48865161	+	Silent	SNP	T	C	C			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48865161T>C	uc001crr.1	-	7	807	c.642A>G	c.(640-642)AAA>AAG	p.K214K	SPATA6_uc001crs.1_Silent_p.K214K|SPATA6_uc010omv.1_Silent_p.K200K|SPATA6_uc001crt.2_Silent_p.K106K	NM_019073	NP_061946	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6 precursor	214					cell differentiation|multicellular organismal development|spermatogenesis	extracellular region				ovary(1)	1						GAGAGTGTGATTTTGAAGAAA	0.413													9	505	---	---	---	---	PASS
ABCA4	24	broad.mit.edu	37	1	94508397	94508397	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94508397A>G	uc001dqh.2	-	22	3352	c.3248T>C	c.(3247-3249)GTG>GCG	p.V1083A		NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	1083	Cytoplasmic.|ABC transporter 1.				phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		GTCCAGAATCACCACCTTGGC	0.567													9	144	---	---	---	---	PASS
HIPK1	204851	broad.mit.edu	37	1	114510461	114510461	+	Silent	SNP	T	C	C			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114510461T>C	uc001eem.2	+	12	2616	c.2455T>C	c.(2455-2457)TTG>CTG	p.L819L	HIPK1_uc001eel.2_Silent_p.L819L|HIPK1_uc001een.2_Silent_p.L819L|HIPK1_uc001eeo.2_Silent_p.L445L|HIPK1_uc001eep.2_Silent_p.L425L|HIPK1_uc001eeq.2_Silent_p.L111L	NM_198268	NP_938009	Q86Z02	HIPK1_HUMAN	homeodomain-interacting protein kinase 1 isoform	819					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(4)	4	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CCATGTGACATTGGCCACTGC	0.488													7	210	---	---	---	---	PASS
FCRL4	83417	broad.mit.edu	37	1	157558993	157558993	+	Splice_Site	SNP	C	G	G			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157558993C>G	uc001fqw.2	-	3	443	c.307_splice	c.e3+1	p.D103_splice	FCRL4_uc010phy.1_Splice_Site	NM_031282	NP_112572	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4 precursor							integral to membrane|plasma membrane	receptor activity			ovary(2)|kidney(1)|skin(1)	4	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)				TTCTTTCTCACCTGAAGAAAA	0.493													18	146	---	---	---	---	PASS
OR6Y1	391112	broad.mit.edu	37	1	158517511	158517511	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158517511C>A	uc010pil.1	-	1	385	c.385G>T	c.(385-387)GTA>TTA	p.V129L		NM_001005189	NP_001005189	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y,	129	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_hematologic(112;0.0378)					CAAATGGCTACATAGCGGTCA	0.473													7	88	---	---	---	---	PASS
KIF21B	23046	broad.mit.edu	37	1	200978472	200978472	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200978472C>A	uc001gvs.1	-	2	503	c.186G>T	c.(184-186)CAG>CAT	p.Q62H	KIF21B_uc001gvr.1_Missense_Mutation_p.Q62H|KIF21B_uc009wzl.1_Missense_Mutation_p.Q62H|KIF21B_uc010ppn.1_Missense_Mutation_p.Q62H	NM_017596	NP_060066	O75037	KI21B_HUMAN	kinesin family member 21B	62	Kinesin-motor.				microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(3)	6						TGGAATAGATCTGTTCTTGCC	0.572													11	99	---	---	---	---	PASS
MAL	4118	broad.mit.edu	37	2	95713710	95713710	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95713710G>A	uc002stx.1	+	2	159	c.100G>A	c.(100-102)GGG>AGG	p.G34R	MAL_uc002sty.1_Intron|MAL_uc002stz.1_Missense_Mutation_p.G34R|MAL_uc002sua.1_Intron	NM_002371	NP_002362	P21145	MAL_HUMAN	T-lymphocyte maturation-associated protein	34	Helical; (Potential).|MARVEL.				apical protein localization|cell differentiation|central nervous system development|induction of apoptosis|membrane raft polarization|myelination	apical plasma membrane|endoplasmic reticulum|endosome|integral to plasma membrane|membrane raft	apoptotic protease activator activity|channel activity|lipid binding|structural constituent of myelin sheath				0				STAD - Stomach adenocarcinoma(1183;0.18)		GCAGATCTTCGGGGGCCTGGT	0.667													26	60	---	---	---	---	PASS
UXS1	80146	broad.mit.edu	37	2	106710437	106710437	+	3'UTR	SNP	C	G	G			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106710437C>G	uc002tdm.2	-	15					UXS1_uc002tdk.2_3'UTR|UXS1_uc002tdl.2_3'UTR|UXS1_uc002tdn.2_3'UTR|UXS1_uc002tdo.2_3'UTR	NM_025076	NP_079352	Q8NBZ7	UXS1_HUMAN	UDP-glucuronate decarboxylase 1						cellular metabolic process	Golgi cisterna membrane|integral to membrane	coenzyme binding|UDP-glucuronate decarboxylase activity			ovary(2)	2						AAAATACATCCCATCAAGTGT	0.393													6	105	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	139045874	139045874	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139045874G>A	uc010zbk.1	-	1	567	c.424C>T	c.(424-426)CCA>TCA	p.P142S						SubName: Full=cDNA, FLJ79100, highly similar to 14-3-3 protein epsilon (14-3-3E);																		TGCGCTGGTGGAAGTTCTGTC	0.448													10	302	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	168099282	168099282	+	Silent	SNP	T	G	G			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168099282T>G	uc002udx.2	+	8	1398	c.1380T>G	c.(1378-1380)CTT>CTG	p.L460L	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Silent_p.L285L|XIRP2_uc010fpq.2_Silent_p.L238L|XIRP2_uc010fpr.2_Intron	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	285					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						CTGACGTACTTCAAACTTCAG	0.448													24	188	---	---	---	---	PASS
TRIP12	9320	broad.mit.edu	37	2	230657838	230657838	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230657838T>C	uc002vpw.1	-	26	3876	c.3767A>G	c.(3766-3768)CAG>CGG	p.Q1256R	TRIP12_uc002vpx.1_Missense_Mutation_p.Q1304R|TRIP12_uc002vpy.1_Missense_Mutation_p.Q986R	NM_004238	NP_004229	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1256					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	proteasome complex	thyroid hormone receptor binding|ubiquitin-protein ligase activity			ovary(4)|lung(2)|breast(1)|central_nervous_system(1)|skin(1)	9		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		TTTTAAAGCCTGTGATCCTCT	0.328													16	119	---	---	---	---	PASS
SCLY	51540	broad.mit.edu	37	2	239000066	239000066	+	Intron	SNP	A	G	G			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239000066A>G	uc010fyv.2	+						SCLY_uc002vxm.3_Intron|SCLY_uc002vxn.2_3'UTR|SCLY_uc010znq.1_Intron|SCLY_uc010znr.1_Intron	NM_016510	NP_057594	Q96I15	SCLY_HUMAN	selenocysteine lyase						cellular amino acid metabolic process	cytosol	pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity			ovary(2)	2		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)		GTACTTTTTCAGATCTGTGGA	0.413													3	18	---	---	---	---	PASS
OXSM	54995	broad.mit.edu	37	3	25833004	25833004	+	Silent	SNP	T	C	C			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25833004T>C	uc003cdn.2	+	2	600	c.493T>C	c.(493-495)TTG>CTG	p.L165L	NGLY1_uc011awo.1_5'Flank|OXSM_uc011awp.1_Intron|OXSM_uc010hfh.2_Silent_p.L165L	NM_017897	NP_060367	Q9NWU1	OXSM_HUMAN	3-oxoacyl-ACP synthase, mitochondrial isoform 1	165					acyl-CoA metabolic process|medium-chain fatty acid biosynthetic process|short-chain fatty acid biosynthetic process	mitochondrion	3-oxoacyl-[acyl-carrier-protein] synthase activity			ovary(1)|breast(1)	2						TGAAACTGCTTTGAATTTTCA	0.423													29	268	---	---	---	---	PASS
LRRFIP2	9209	broad.mit.edu	37	3	37125219	37125219	+	Silent	SNP	A	G	G			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37125219A>G	uc003cgp.2	-	20	1609	c.1186T>C	c.(1186-1188)TTG>CTG	p.L396L	LRRFIP2_uc011ayf.1_Silent_p.L212L|LRRFIP2_uc003cgr.2_Silent_p.L164L|LRRFIP2_uc003cgs.3_Silent_p.L164L|LRRFIP2_uc003cgt.3_Silent_p.L140L	NM_006309	NP_006300	Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting	396	Potential.				Wnt receptor signaling pathway		LRR domain binding			ovary(1)	1						TGGTAGATCAAATTGTTCTTC	0.353													58	207	---	---	---	---	PASS
CCDC13	152206	broad.mit.edu	37	3	42784452	42784452	+	Missense_Mutation	SNP	G	A	A	rs143310118	by1000genomes	TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42784452G>A	uc003cly.3	-	8	1007	c.923C>T	c.(922-924)TCG>TTG	p.S308L		NM_144719	NP_653320	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	308	Potential.									ovary(1)	1						CTCCTGTGCCGACAGCTTCCT	0.572													10	276	---	---	---	---	PASS
MORC1	27136	broad.mit.edu	37	3	108724127	108724127	+	Silent	SNP	G	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108724127G>A	uc003dxl.2	-	19	1890	c.1803C>T	c.(1801-1803)GGC>GGT	p.G601G	MORC1_uc011bhn.1_Silent_p.G580G	NM_014429	NP_055244	Q86VD1	MORC1_HUMAN	MORC family CW-type zinc finger 1	601					cell differentiation|multicellular organismal development|spermatogenesis	nucleus	ATP binding|zinc ion binding			ovary(3)|skin(3)|breast(2)	8						TCAAGTCATCGCCCAAAAGCC	0.353													7	153	---	---	---	---	PASS
IFT80	57560	broad.mit.edu	37	3	160037613	160037613	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160037613C>T	uc011boy.1	-	9	1325	c.892G>A	c.(892-894)GTG>ATG	p.V298M	IFT80_uc003fda.2_RNA|IFT80_uc003fdb.1_Missense_Mutation_p.V161M|IFT80_uc003fdd.1_Translation_Start_Site|IFT80_uc003fde.1_Missense_Mutation_p.V161M	NM_020800	NP_065851	Q9P2H3	IFT80_HUMAN	WD repeat domain 56	298	WD 6.					cilium axoneme|microtubule basal body				ovary(1)	1			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			TGTTCCACCACATGTGCAAAA	0.398													8	219	---	---	---	---	PASS
AHSG	197	broad.mit.edu	37	3	186331026	186331026	+	Silent	SNP	C	T	T			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186331026C>T	uc003fqk.3	+	1	177	c.96C>T	c.(94-96)TGC>TGT	p.C32C	AHSG_uc003fqj.2_Silent_p.C32C|AHSG_uc003fql.3_Silent_p.C32C|AHSG_uc003fqm.3_Silent_p.C32C|AHSG_uc010hyp.2_Silent_p.C32C	NM_001622	NP_001613	P02765	FETUA_HUMAN	alpha-2-HS-glycoprotein	32	Cystatin fetuin-A-type 1.				acute-phase response|negative regulation of bone mineralization|negative regulation of insulin receptor signaling pathway|pinocytosis|positive regulation of phagocytosis|regulation of inflammatory response|skeletal system development	extracellular space	cysteine-type endopeptidase inhibitor activity|protein binding				0	all_cancers(143;3.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.27e-20)	GBM - Glioblastoma multiforme(93;0.0463)		AACCGAACTGCGATGATCCAG	0.512													5	108	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195505836	195505836	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195505836G>C	uc011bto.1	-	3	12691	c.12231C>G	c.(12229-12231)CAC>CAG	p.H4077Q	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGGCGTGACCTGTGG	0.597													4	6	---	---	---	---	PASS
CRIPAK	285464	broad.mit.edu	37	4	1388829	1388829	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1388829C>T	uc003gdf.2	+	1	3490	c.530C>T	c.(529-531)CCC>CTC	p.P177L		NM_175918	NP_787114	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	177	4.				ER-nucleus signaling pathway|negative regulation of protein kinase activity|regulation of cytoskeleton organization|response to estrogen stimulus	endoplasmic reticulum|nucleus|plasma membrane	protein binding				0			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			TGTGGAGTGCCCGCCTGCTCA	0.682													7	164	---	---	---	---	PASS
ARAP2	116984	broad.mit.edu	37	4	36130284	36130284	+	Silent	SNP	T	G	G			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36130284T>G	uc003gsq.1	-	21	3849	c.3511A>C	c.(3511-3513)AGA>CGA	p.R1171R		NM_015230	NP_056045	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH	1171	Rho-GAP.				regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytosol	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3						TTAAAGCTTCTTGCATCCTTT	0.358													11	175	---	---	---	---	PASS
KDR	3791	broad.mit.edu	37	4	55956221	55956221	+	Nonsense_Mutation	SNP	G	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55956221G>A	uc003has.2	-	23	3396	c.3094C>T	c.(3094-3096)CGA>TGA	p.R1032*	KDR_uc003hat.1_Nonsense_Mutation_p.R1032*	NM_002253	NP_002244	P35968	VGFR2_HUMAN	kinase insert domain receptor precursor	1032	Protein kinase.|Cytoplasmic (Potential).				angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(16)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|stomach(2)|skin(2)|ovary(2)|kidney(1)	33	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Sorafenib(DB00398)|Sunitinib(DB01268)	AGGATATTTCGTGCCGCCAGG	0.448			Mis		NSCLC|angiosarcoma				Familial_Infantile_Hemangioma	TSP Lung(20;0.16)			7	210	---	---	---	---	PASS
UGT2B10	7365	broad.mit.edu	37	4	69870669	69870669	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69870669C>A	uc011cao.1	-	9	1517	c.1381G>T	c.(1381-1383)GCT>TCT	p.A461S	UGT2B10_uc011can.1_Missense_Mutation_p.A377S			P36537	UDB10_HUMAN	RecName: Full=UDP-glucuronosyltransferase 2B28;          Short=UDPGT 2B28;          EC=2.4.1.17; Flags: Precursor;	498	Helical; (Potential).				lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(3)|ovary(2)	5						GCCACACAGGCCAGCAGGAAC	0.448													18	259	---	---	---	---	PASS
MRPL1	65008	broad.mit.edu	37	4	78784032	78784032	+	Missense_Mutation	SNP	A	C	C			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78784032A>C	uc003hku.2	+	1	228	c.30A>C	c.(28-30)AGA>AGC	p.R10S		NM_020236	NP_064621	Q9BYD6	RM01_HUMAN	mitochondrial ribosomal protein L1 precursor	10							RNA binding				0						GCATGGGTAGAGGTAAGGCGA	0.537													6	169	---	---	---	---	PASS
ADRB2	154	broad.mit.edu	37	5	148207351	148207351	+	Silent	SNP	T	G	G			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148207351T>G	uc003lpr.1	+	1	1196	c.957T>G	c.(955-957)TCT>TCG	p.S319S	SH3TC2_uc003lpp.1_Intron	NM_000024	NP_000015	P07550	ADRB2_HUMAN	adrenergic, beta-2-, receptor, surface	319	Helical; Name=7.				activation of transmembrane receptor protein tyrosine kinase activity|desensitization of G-protein coupled receptor protein signaling pathway by arrestin|endosome to lysosome transport|positive regulation of MAPKKK cascade|receptor-mediated endocytosis	endosome|integral to plasma membrane|lysosome|receptor complex	beta2-adrenergic receptor activity|norepinephrine binding|potassium channel regulator activity|protein homodimerization activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Alprenolol(DB00866)|Arformoterol(DB01274)|Bambuterol(DB01408)|Bisoprolol(DB00612)|Bitolterol(DB00901)|Bretylium(DB01158)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Epinephrine(DB00668)|Fenoterol(DB01288)|Formoterol(DB00983)|Isoproterenol(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Metipranolol(DB01214)|Nadolol(DB01203)|Norepinephrine(DB00368)|Orciprenaline(DB00816)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Pindolol(DB00960)|Pirbuterol(DB01291)|Procaterol(DB01366)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Ritodrine(DB00867)|Salbutamol(DB01001)|Salmeterol(DB00938)|Terbutaline(DB00871)|Timolol(DB00373)	ATGTCAATTCTGGTTTCAATC	0.478													15	142	---	---	---	---	PASS
HAVCR1	26762	broad.mit.edu	37	5	156479438	156479438	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156479438G>A	uc010jij.1	-	4	792	c.607C>T	c.(607-609)CCA>TCA	p.P203S	HAVCR1_uc011ddl.1_Missense_Mutation_p.P34S|HAVCR1_uc003lwi.2_Missense_Mutation_p.P203S|HAVCR1_uc011ddm.1_Missense_Mutation_p.P203S	NM_001099414	NP_001092884	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	198	Extracellular (Potential).|11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|11.|Thr-rich.				interspecies interaction between organisms	integral to membrane	receptor activity			ovary(1)|skin(1)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GTTGTCACTGGAACACTTGTT	0.468													67	448	---	---	---	---	PASS
SH3PXD2B	285590	broad.mit.edu	37	5	171821588	171821588	+	Silent	SNP	T	G	G			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171821588T>G	uc003mbr.2	-	4	459	c.288A>C	c.(286-288)ATA>ATC	p.I96I	SH3PXD2B_uc003mbs.1_Silent_p.I96I	NM_001017995	NP_001017995	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B	96	PX.				adipose tissue development|bone development|cell communication|cell differentiation|eye development|heart development|podosome assembly	cell junction|cell projection|cytoplasm|podosome	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-5-phosphate binding|SH2 domain binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CATCAATTGGTATCAGGCGTT	0.418													9	67	---	---	---	---	PASS
TRIM31	11074	broad.mit.edu	37	6	30080405	30080405	+	Missense_Mutation	SNP	C	T	T	rs143020056	byFrequency	TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30080405C>T	uc003npg.1	-	2	288	c.178G>A	c.(178-180)GTA>ATA	p.V60I	TRIM31_uc003npi.3_RNA	NM_007028	NP_008959	Q9BZY9	TRI31_HUMAN	tripartite motif protein 31	60						mitochondrion	ligase activity|zinc ion binding			lung(1)	1						TTCTTCCTTACGGAAGTTTTG	0.473													13	228	---	---	---	---	PASS
RXRB	6257	broad.mit.edu	37	6	33163498	33163498	+	Intron	SNP	G	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33163498G>A	uc003odb.2	-						RXRB_uc003odc.2_Intron|RXRB_uc003odd.2_Intron|RXRB_uc011dqr.1_Intron|RXRB_uc011dqs.1_3'UTR	NM_021976	NP_068811	P28702	RXRB_HUMAN	retinoid X receptor, beta						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	ligand-regulated transcription factor activity|retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			ovary(3)	3					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Etretinate(DB00926)|Tazarotene(DB00799)|Tretinoin(DB00755)	GGCAGCAAGGGTCAGGAGCCA	0.542													4	42	---	---	---	---	PASS
SLC22A7	10864	broad.mit.edu	37	6	43270068	43270068	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43270068C>T	uc003out.2	+	8	1291	c.1192C>T	c.(1192-1194)CGC>TGC	p.R398C	SLC22A7_uc010jyl.1_Missense_Mutation_p.R399C|SLC22A7_uc003ous.2_Missense_Mutation_p.R396C	NM_153320	NP_696961	Q9Y694	S22A7_HUMAN	solute carrier family 22 member 7 isoform b	398						basolateral plasma membrane|integral to plasma membrane|membrane fraction	anion:anion antiporter activity|sodium-independent organic anion transmembrane transporter activity				0			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)			CTTGTCGGTGCGCTACGCAGG	0.637													14	35	---	---	---	---	PASS
NSUN5P2	260294	broad.mit.edu	37	7	72419464	72419464	+	Missense_Mutation	SNP	T	G	G	rs138398938	byFrequency	TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72419464T>G	uc003twn.2	-	9	1272	c.560A>C	c.(559-561)CAA>CCA	p.Q187P	POM121_uc010lam.1_3'UTR|NSUN5P2_uc003twl.2_RNA|NSUN5P2_uc003twm.2_Missense_Mutation_p.Q163P|NSUN5P2_uc003two.2_Missense_Mutation_p.Q187P|NSUN5P2_uc003twq.2_Missense_Mutation_p.K190Q|NSUN5P2_uc010lan.1_Missense_Mutation_p.Q59P|NSUN5P2_uc003twp.2_Missense_Mutation_p.Q187P	NM_032158	NP_115534			NOL1/NOP2/Sun domain family, member 5C isoform												0						CAGCGCATCTTGTACCATGTC	0.632													3	58	---	---	---	---	PASS
GRM3	2913	broad.mit.edu	37	7	86468360	86468360	+	Silent	SNP	C	T	T			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86468360C>T	uc003uid.2	+	4	2629	c.1530C>T	c.(1528-1530)AGC>AGT	p.S510S	GRM3_uc010lef.2_Intron|GRM3_uc010leg.2_Silent_p.S382S|GRM3_uc010leh.2_Silent_p.S102S	NM_000840	NP_000831	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3 precursor	510	Extracellular (Potential).				synaptic transmission	integral to plasma membrane				lung(4)|ovary(3)|central_nervous_system(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)	13	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)				Acamprosate(DB00659)|Nicotine(DB00184)	CCCAGTGCAGCGACCCCTGTG	0.512													35	134	---	---	---	---	PASS
GNG11	2791	broad.mit.edu	37	7	93551428	93551428	+	5'UTR	SNP	C	T	T	rs4262	by1000genomes	TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93551428C>T	uc003und.2	+	1						NM_004126	NP_004117	P61952	GBG11_HUMAN	guanine nucleotide binding protein gamma 11						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway	heterotrimeric G-protein complex	GTPase activity|signal transducer activity			kidney(1)	1	all_cancers(62;2.39e-10)|all_epithelial(64;1.54e-09)|Lung NSC(181;0.218)		STAD - Stomach adenocarcinoma(171;0.000967)			AGAGCTAGCCCGAGCCCGGTT	0.602													11	5	---	---	---	---	PASS
PILRB	29990	broad.mit.edu	37	7	99943558	99943558	+	5'UTR	SNP	T	C	C	rs2405445	by1000genomes	TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99943558T>C	uc003uuk.2	+	4					PILRB_uc003uul.2_5'UTR	NM_013440	NP_038468	Q9UKJ0	PILRB_HUMAN	paired immunoglobulin-like type 2 receptor beta						activation of transmembrane receptor protein tyrosine kinase activity	integral to plasma membrane	protein binding|receptor activity				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AGGGATTTTTTTTTTTCAGAT	0.423													2	9	---	---	---	---	PASS
CFTR	1080	broad.mit.edu	37	7	117188739	117188739	+	Silent	SNP	T	C	C	rs62469440	by1000genomes	TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117188739T>C	uc003vjd.2	+	10	1386	c.1254T>C	c.(1252-1254)AAT>AAC	p.N418N	CFTR_uc011knq.1_5'UTR	NM_000492	NP_000483	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance	418	Cytoplasmic (Potential).				respiratory gaseous exchange	apical plasma membrane|basolateral plasma membrane|chloride channel complex|early endosome membrane	ATP binding|ATP-binding and phosphorylation-dependent chloride channel activity|channel-conductance-controlling ATPase activity|chloride channel regulator activity|enzyme binding|PDZ domain binding			central_nervous_system(2)|skin(2)|ovary(1)	5	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Glibenclamide(DB01016)	ACAATAACAATAGAAAAACTT	0.279									Cystic_Fibrosis				4	43	---	---	---	---	PASS
LRGUK	136332	broad.mit.edu	37	7	133859312	133859312	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133859312C>T	uc003vrm.1	+	8	960	c.944C>T	c.(943-945)GCT>GTT	p.A315V		NM_144648	NP_653249	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain	315	LRR 9.						ATP binding|kinase activity			lung(2)|skin(2)|kidney(1)	5						GAACAGATTGCTGAGCTGAGA	0.313													6	185	---	---	---	---	PASS
ADAMTS13	11093	broad.mit.edu	37	9	136313725	136313725	+	Missense_Mutation	SNP	A	C	C			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136313725A>C	uc004cdv.3	+	22	3181	c.2737A>C	c.(2737-2739)ATG>CTG	p.M913L	ADAMTS13_uc004cdp.3_Missense_Mutation_p.M140L|ADAMTS13_uc004cdt.1_Missense_Mutation_p.M913L|ADAMTS13_uc004cdu.1_Missense_Mutation_p.M882L|ADAMTS13_uc004cdw.3_Missense_Mutation_p.M913L|ADAMTS13_uc004cdx.3_Missense_Mutation_p.M882L|ADAMTS13_uc004cdy.1_RNA|ADAMTS13_uc004cdz.3_Missense_Mutation_p.M583L	NM_139025	NP_620594	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1	913	TSP type-1 5.				cell-matrix adhesion|glycoprotein metabolic process|integrin-mediated signaling pathway|peptide catabolic process|platelet activation|protein processing|proteolysis	cell surface|proteinaceous extracellular matrix	calcium ion binding|integrin binding|metalloendopeptidase activity|zinc ion binding			central_nervous_system(2)|skin(2)|ovary(1)|kidney(1)	6				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		CGCAGGTCTGATGGAGCTGCG	0.602													8	345	---	---	---	---	PASS
SLC2A6	11182	broad.mit.edu	37	9	136340607	136340607	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136340607G>T	uc004cee.2	-	5	784	c.689C>A	c.(688-690)GCC>GAC	p.A230D	SLC2A6_uc004cef.2_Missense_Mutation_p.A230D|SLC2A6_uc004ceg.2_Missense_Mutation_p.A207D|SLC2A6_uc011mdj.1_3'UTR	NM_017585	NP_060055	Q9UGQ3	GTR6_HUMAN	solute carrier family 2 (facilitated glucose	230	Cytoplasmic (Potential).					integral to membrane|plasma membrane	D-glucose transmembrane transporter activity				0				OV - Ovarian serous cystadenocarcinoma(145;8.47e-08)|Epithelial(140;9.37e-07)|all cancers(34;1.03e-05)		CGCCCGCAGGGCCTCTTCGTC	0.667													4	38	---	---	---	---	PASS
RPL13AP6	644511	broad.mit.edu	37	10	112696659	112696659	+	Silent	SNP	A	G	G			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112696659A>G	uc010qrh.1	-	1	355	c.333T>C	c.(331-333)CCT>CCC	p.P111P	SHOC2_uc001kzl.3_Intron|SHOC2_uc009xxx.2_Intron|SHOC2_uc010qrg.1_Intron	NR_026715				SubName: Full=cDNA FLJ51256, highly similar to 60S ribosomal protein L13a;												0						TCTTGTCGTAAGGCGGTGGGA	0.577													3	24	---	---	---	---	PASS
GRIK4	2900	broad.mit.edu	37	11	120833172	120833172	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120833172G>A	uc001pxn.2	+	18	2335	c.2048G>A	c.(2047-2049)CGC>CAC	p.R683H	GRIK4_uc009zav.1_Missense_Mutation_p.R683H|GRIK4_uc009zaw.1_Missense_Mutation_p.R683H|GRIK4_uc009zax.1_Missense_Mutation_p.R683H	NM_014619	NP_055434	Q16099	GRIK4_HUMAN	glutamate receptor KA1 precursor	683	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)	CAGAATTCCCGCTACCAGACC	0.483													5	42	---	---	---	---	PASS
GALNT8	26290	broad.mit.edu	37	12	4874640	4874640	+	Silent	SNP	G	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4874640G>A	uc001qne.1	+	10	1781	c.1689G>A	c.(1687-1689)GCG>GCA	p.A563A		NM_017417	NP_059113	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	563	Ricin B-type lectin.|Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(1)|skin(1)	4						CTGGCAAGGCGGAGAAGCCCA	0.463													5	98	---	---	---	---	PASS
MYL6	4637	broad.mit.edu	37	12	56554394	56554394	+	Intron	SNP	C	G	G			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56554394C>G	uc001sjw.1	+						MYL6_uc001sjv.2_3'UTR|MYL6_uc001sjx.1_Intron|MYL6_uc010sqd.1_3'UTR|MYL6_uc001sjz.2_3'UTR|MYL6_uc010sqe.1_Intron	NM_021019	NP_066299	P60660	MYL6_HUMAN	myosin, light chain 6, alkali, smooth muscle and						axon guidance|muscle filament sliding|skeletal muscle tissue development	cytosol|unconventional myosin complex	actin-dependent ATPase activity|calcium ion binding|motor activity|structural constituent of muscle			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(18;0.0979)			CCATGAATGTCTCTTCCTTCC	0.552													12	361	---	---	---	---	PASS
MYL6	4637	broad.mit.edu	37	12	56554423	56554423	+	Missense_Mutation	SNP	T	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56554423T>A	uc001sjw.1	+	6	527	c.441T>A	c.(439-441)CAT>CAA	p.H147Q	MYL6_uc001sjv.2_3'UTR|MYL6_uc001sjx.1_Intron|MYL6_uc010sqd.1_3'UTR|MYL6_uc001sjz.2_3'UTR|MYL6_uc010sqe.1_Missense_Mutation_p.H112Q	NM_021019	NP_066299	P60660	MYL6_HUMAN	myosin, light chain 6, alkali, smooth muscle and	147	EF-hand 3.				axon guidance|muscle filament sliding|skeletal muscle tissue development	cytosol|unconventional myosin complex	actin-dependent ATPase activity|calcium ion binding|motor activity|structural constituent of muscle			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(18;0.0979)			TTGTGAGGCATATCCTGTCGG	0.547													14	351	---	---	---	---	PASS
MYL6	4637	broad.mit.edu	37	12	56554425	56554425	+	Missense_Mutation	SNP	T	G	G			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56554425T>G	uc001sjw.1	+	6	529	c.443T>G	c.(442-444)ATC>AGC	p.I148S	MYL6_uc001sjv.2_3'UTR|MYL6_uc001sjx.1_Intron|MYL6_uc010sqd.1_3'UTR|MYL6_uc001sjz.2_3'UTR|MYL6_uc010sqe.1_Missense_Mutation_p.I113S	NM_021019	NP_066299	P60660	MYL6_HUMAN	myosin, light chain 6, alkali, smooth muscle and	148	EF-hand 3.				axon guidance|muscle filament sliding|skeletal muscle tissue development	cytosol|unconventional myosin complex	actin-dependent ATPase activity|calcium ion binding|motor activity|structural constituent of muscle			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(18;0.0979)			GTGAGGCATATCCTGTCGGGG	0.547													14	342	---	---	---	---	PASS
DPY19L2	283417	broad.mit.edu	37	12	63976243	63976243	+	Silent	SNP	T	C	C			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63976243T>C	uc001srp.1	-	18	1849	c.1668A>G	c.(1666-1668)CTA>CTG	p.L556L	DPY19L2_uc010sso.1_Silent_p.L3L	NM_173812	NP_776173	Q6NUT2	D19L2_HUMAN	dpy-19-like 2	556					multicellular organismal development|spermatid development	integral to membrane				central_nervous_system(1)|skin(1)	2			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		AAAACATCTTTAGCCTCATAA	0.343													23	82	---	---	---	---	PASS
SLC6A15	55117	broad.mit.edu	37	12	85270374	85270374	+	Missense_Mutation	SNP	T	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85270374T>A	uc001szv.2	-	6	1262	c.769A>T	c.(769-771)AGT>TGT	p.S257C	SLC6A15_uc010sul.1_Missense_Mutation_p.S150C	NM_182767	NP_877499	Q9H2J7	S6A15_HUMAN	solute carrier family 6, member 15 isoform 1	257	Helical; Name=5; (Potential).				cellular nitrogen compound metabolic process|leucine transport|proline transport	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity			pancreas(2)|ovary(1)	3						AACAGAGAACTAAAATATATG	0.303													5	141	---	---	---	---	PASS
MIPEP	4285	broad.mit.edu	37	13	24455845	24455845	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24455845C>A	uc001uox.3	-	3	545	c.445G>T	c.(445-447)GTA>TTA	p.V149L		NM_005932	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase precursor	149					protein processing involved in protein targeting to mitochondrion|proteolysis	mitochondrial matrix	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)		TACTTCTCTACCATGGTGCCA	0.502													11	115	---	---	---	---	PASS
SPG20	23111	broad.mit.edu	37	13	36886567	36886567	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36886567G>A	uc001uvn.2	-	8	1801	c.1531C>T	c.(1531-1533)CCA>TCA	p.P511S	SPG20_uc010ten.1_Missense_Mutation_p.P501S|SPG20_uc001uvm.2_Missense_Mutation_p.P511S|SPG20_uc001uvo.2_Missense_Mutation_p.P511S|SPG20_uc001uvq.2_Missense_Mutation_p.P511S	NM_001142296	NP_001135768	Q8N0X7	SPG20_HUMAN	spartin	511					cell death	cytoplasm	ubiquitin protein ligase binding				0		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;2.42e-08)|Epithelial(112;1.58e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00128)|BRCA - Breast invasive adenocarcinoma(63;0.0125)|GBM - Glioblastoma multiforme(144;0.026)		TTGACATGTGGAGCTAGTTCT	0.368													42	283	---	---	---	---	PASS
TRIM9	114088	broad.mit.edu	37	14	51446111	51446111	+	Silent	SNP	G	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51446111G>A	uc001wyx.3	-	9	2829	c.2064C>T	c.(2062-2064)AAC>AAT	p.N688N	TRIM9_uc001wyy.2_Silent_p.N769N	NM_015163	NP_055978	Q9C026	TRIM9_HUMAN	tripartite motif protein 9 isoform 1	688	B30.2/SPRY.				proteasomal ubiquitin-dependent protein catabolic process	cell junction|cytoskeleton|dendrite|synaptic vesicle	protein homodimerization activity|ubiquitin-protein ligase activity|zinc ion binding			skin(2)|lung(1)	3	all_epithelial(31;0.00418)|Breast(41;0.148)					TTACCTGCACGTTCCTGTTCA	0.512													65	203	---	---	---	---	PASS
CDC42BPB	9578	broad.mit.edu	37	14	103442220	103442220	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103442220C>G	uc001ymi.1	-	10	1619	c.1387G>C	c.(1387-1389)GAG>CAG	p.E463Q		NM_006035	NP_006026	Q9Y5S2	MRCKB_HUMAN	CDC42-binding protein kinase beta	463	Potential.				actin cytoskeleton reorganization|establishment or maintenance of cell polarity|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm|cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(3)|skin(3)|lung(2)|stomach(1)|breast(1)|ovary(1)	11		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		CTGCCCTCACCTTGCAGCTTC	0.662													13	154	---	---	---	---	PASS
KIAA0125	9834	broad.mit.edu	37	14	106363843	106363843	+	Intron	SNP	C	G	G			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106363843C>G	uc001ysq.2	+						ADAM6_uc010tyt.1_RNA|KIAA0125_uc001ysr.2_Intron					SubName: Full=HCG2029388, isoform CRA_d; SubName: Full=FAM30A protein;												0						ACTACAATATCCTCACAGTGA	0.567													4	38	---	---	---	---	PASS
CHP	11261	broad.mit.edu	37	15	41523608	41523608	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41523608C>T	uc001znl.2	+	1	172	c.28C>T	c.(28-30)CGG>TGG	p.R10W	EXD1_uc001znk.2_5'Flank|EXD1_uc010ucv.1_5'Flank	NM_007236	NP_009167	Q99653	CHP1_HUMAN	calcium binding protein P22	10					potassium ion transport|small GTPase mediated signal transduction		potassium channel regulator activity			ovary(1)	1		all_cancers(109;1.19e-18)|all_epithelial(112;5.87e-16)|Lung NSC(122;8.86e-12)|all_lung(180;2.47e-10)|Melanoma(134;0.0574)|Colorectal(260;0.0946)|Ovarian(310;0.143)		GBM - Glioblastoma multiforme(113;1.68e-06)|LUSC - Lung squamous cell carcinoma(244;0.008)|Lung(196;0.00802)|BRCA - Breast invasive adenocarcinoma(123;0.169)		CACGTTACTGCGGGACGAAGA	0.607													3	7	---	---	---	---	PASS
TBC1D2B	23102	broad.mit.edu	37	15	78290654	78290654	+	Missense_Mutation	SNP	G	C	C	rs142394567	by1000genomes	TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78290654G>C	uc002bcy.3	-	13	2740	c.2740C>G	c.(2740-2742)CTA>GTA	p.L914V	TBC1D2B_uc010bla.2_Intron	NM_144572	NP_653173	Q9UPU7	TBD2B_HUMAN	TBC1 domain family, member 2B isoform a	914						intracellular	protein binding|Rab GTPase activator activity			ovary(1)|large_intestine(1)|breast(1)	3						ATCTGGCGTAGGGGGAAAGGG	0.612													3	11	---	---	---	---	PASS
ZFHX3	463	broad.mit.edu	37	16	72821029	72821029	+	3'UTR	SNP	A	T	T			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72821029A>T	uc002fck.2	-	10					uc002fcj.1_Intron|ZFHX3_uc002fcl.2_3'UTR	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A						muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|skin(2)	4		Ovarian(137;0.13)				TTTTGTATTTAAATTCATTTG	0.308													8	272	---	---	---	---	PASS
GLG1	2734	broad.mit.edu	37	16	74566028	74566028	+	Silent	SNP	G	A	A	rs2550807		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74566028G>A	uc002fcy.3	-	2	512	c.462C>T	c.(460-462)GAC>GAT	p.D154D	GLG1_uc002fcx.2_Silent_p.D154D|GLG1_uc002fcw.3_Intron|GLG1_uc002fcz.3_5'UTR	NM_001145667	NP_001139139	Q92896	GSLG1_HUMAN	golgi apparatus protein 1 isoform 3	154	Cys-rich GLG1 2.|Extracellular (Potential).					Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2						CATGATTGCAGTCTGAAGAAA	0.323													5	104	---	---	---	---	PASS
ZNF778	197320	broad.mit.edu	37	16	89294346	89294346	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89294346G>T	uc002fmv.2	+	6	1905	c.1566G>T	c.(1564-1566)GAG>GAT	p.E522D	ZNF778_uc010vpf.1_Intron|ZNF778_uc002fmw.1_Missense_Mutation_p.E480D|ZNF778_uc010vpg.1_Missense_Mutation_p.E285D	NM_182531	NP_872337	Q96MU6	ZN778_HUMAN	zinc finger protein 778	522	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0269)		TACTGAATGAGCATGTGAAAA	0.458													7	108	---	---	---	---	PASS
WDR81	124997	broad.mit.edu	37	17	1633695	1633695	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1633695G>T	uc002fti.2	+	2	269	c.8G>T	c.(7-9)CGC>CTC	p.R3L	WDR81_uc002fth.2_Missense_Mutation_p.R179L|WDR81_uc010vqp.1_Missense_Mutation_p.R27L|WDR81_uc002ftj.2_Missense_Mutation_p.R1230L|WDR81_uc010vqq.1_5'UTR	NM_001163811	NP_001157283	Q562E7	WDR81_HUMAN	WD repeat domain 81 isoform 4	3										skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		AAGATGGTCCGCTGGCTGTCT	0.537													3	39	---	---	---	---	PASS
ASPA	443	broad.mit.edu	37	17	3402474	3402474	+	3'UTR	SNP	C	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3402474C>A	uc010ckg.2	+	7					SPATA22_uc010vrg.1_Intron|ASPA_uc002fvq.2_3'UTR	NM_001128085	NP_001121557	P45381	ACY2_HUMAN	aspartoacylase						aspartate catabolic process	cytoplasm|nucleus	aminoacylase activity|aspartoacylase activity|hydrolase activity, acting on ester bonds|metal ion binding				0					L-Aspartic Acid(DB00128)	tattcaactgcatacatagct	0.114													3	18	---	---	---	---	PASS
ALDH3A2	224	broad.mit.edu	37	17	19559759	19559759	+	Silent	SNP	G	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19559759G>A	uc002gwb.1	+	4	773	c.552G>A	c.(550-552)ACG>ACA	p.T184T	ALDH3A2_uc002gwa.1_Silent_p.T184T|ALDH3A2_uc010cqr.1_5'UTR|ALDH3A2_uc002gwc.1_Silent_p.T184T|ALDH3A2_uc002gwd.1_5'UTR	NM_000382	NP_000373	P51648	AL3A2_HUMAN	aldehyde dehydrogenase 3A2 isoform 2	184	Cytoplasmic.		T -> M (in SLS; severe loss of activity).|T -> R (in SLS; severe loss of activity).		cellular aldehyde metabolic process|central nervous system development|epidermis development|lipid metabolic process|peripheral nervous system development	endoplasmic reticulum membrane|integral to membrane	3-chloroallyl aldehyde dehydrogenase activity|aldehyde dehydrogenase (NAD) activity|aldehyde dehydrogenase			ovary(2)	2	all_cancers(12;1.39e-05)|all_epithelial(12;0.00158)|Breast(13;0.245)				NADH(DB00157)	TTTTCTATACGGGAAACACTG	0.438													32	167	---	---	---	---	PASS
KRT14	3861	broad.mit.edu	37	17	39741238	39741238	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39741238G>C	uc002hxf.1	-	2	658	c.597C>G	c.(595-597)GAC>GAG	p.D199E	JUP_uc010wfs.1_Intron|KRT14_uc010cxp.1_Missense_Mutation_p.D199E	NM_000526	NP_000517	P02533	K1C14_HUMAN	keratin 14	199	Coil 1B.|Rod.				epidermis development|hemidesmosome assembly|intermediate filament bundle assembly	cytosol|keratin filament|mitochondrion|nucleus	protein binding|structural constituent of cytoskeleton			ovary(1)	1		Breast(137;0.000307)				TGGTGCGGAAGTCATCCGCGG	0.502													4	96	---	---	---	---	PASS
GOSR2	9570	broad.mit.edu	37	17	45096329	45096329	+	Intron	SNP	C	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45096329C>A	uc010wkh.1	+						uc010wki.1_RNA	NM_004287	NP_004278	O14653	GOSR2_HUMAN	golgi SNAP receptor complex member 2 isoform A						cellular membrane fusion|ER to Golgi vesicle-mediated transport|protein transport	Golgi membrane|integral to membrane	transporter activity			ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(9;0.102)			GGTAACAAATCCAACACCAGG	0.483													12	302	---	---	---	---	PASS
GRP	2922	broad.mit.edu	37	18	56897840	56897840	+	3'UTR	SNP	C	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56897840C>A	uc002lhv.2	+	3					GRP_uc002lhu.2_3'UTR|GRP_uc002lhw.2_3'UTR	NM_002091	NP_002082	P07492	GRP_HUMAN	gastrin-releasing peptide isoform 1						neuropeptide signaling pathway	extracellular space	neuropeptide hormone activity				0		Colorectal(73;0.0946)				TGACTAAATTCGTGATTTTCA	0.358													12	6	---	---	---	---	PASS
ZNF516	9658	broad.mit.edu	37	18	74091047	74091047	+	Missense_Mutation	SNP	T	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74091047T>A	uc010dqx.1	-	3	3258	c.3023A>T	c.(3022-3024)CAG>CTG	p.Q1008L	ZNF516_uc002lme.2_RNA|ZNF516_uc002lmd.2_RNA	NM_014643	NP_055458	Q92618	ZN516_HUMAN	zinc finger protein 516	1008					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		CCTCAGCTCCTGGGCTGCCTT	0.706													25	29	---	---	---	---	PASS
FAM108A1	81926	broad.mit.edu	37	19	1881395	1881395	+	Silent	SNP	T	C	C			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1881395T>C	uc002lug.2	-	2	577	c.171A>G	c.(169-171)AGA>AGG	p.R57R	FAM108A1_uc002lud.2_Silent_p.R57R|FAM108A1_uc002lue.2_Silent_p.R57R|FAM108A1_uc002luf.2_Silent_p.R57R	NM_001130111	NP_001123583	Q96GS6	F18A1_HUMAN	hypothetical protein LOC81926 isoform 2	57						extracellular region	hydrolase activity				0		Ovarian(11;0.000137)		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)		CCGAGGAGGCTCTCAGGGTCC	0.726													4	39	---	---	---	---	PASS
TMEM145	284339	broad.mit.edu	37	19	42819344	42819344	+	Silent	SNP	C	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42819344C>A	uc002otk.1	+	7	562	c.510C>A	c.(508-510)ATC>ATA	p.I170I		NM_173633	NP_775904	Q8NBT3	TM145_HUMAN	transmembrane protein 145	170						integral to membrane					0		Prostate(69;0.00682)				CGGCAGGGATCCTGGAGACAG	0.448													5	129	---	---	---	---	PASS
GIPR	2696	broad.mit.edu	37	19	46181196	46181196	+	Silent	SNP	C	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46181196C>A	uc002pcu.1	+	11	1056	c.957C>A	c.(955-957)GGC>GGA	p.G319G	GIPR_uc002pct.1_Silent_p.G319G|GIPR_uc010xxp.1_Silent_p.G283G|GIPR_uc010xxq.1_RNA	NM_000164	NP_000155	P48546	GIPR_HUMAN	gastric inhibitory polypeptide receptor	319	Helical; Name=5; (Potential).				generation of precursor metabolites and energy|response to nutrient	integral to membrane|plasma membrane				skin(1)	1		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0056)|GBM - Glioblastoma multiforme(486;0.0832)|Epithelial(262;0.199)		GCATTCTTGGCATTCTCCTGT	0.597													8	121	---	---	---	---	PASS
LILRB3	11025	broad.mit.edu	37	19	54721090	54721090	+	Missense_Mutation	SNP	A	G	G	rs141841040	byFrequency	TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54721090A>G	uc002qef.1	-	13	1879	c.1768T>C	c.(1768-1770)TCC>CCC	p.S590P	LILRB3_uc002qee.1_Missense_Mutation_p.S591P|LILRB3_uc002qeh.1_Missense_Mutation_p.S590P|LILRB3_uc002qeg.1_RNA|LILRB3_uc002qei.1_Missense_Mutation_p.S590P|LILRA6_uc002qek.1_Missense_Mutation_p.S591P|LILRB3_uc010erh.1_Missense_Mutation_p.S607P|LILRB3_uc002qej.1_RNA|LILRA6_uc002qel.1_Missense_Mutation_p.S590P|LILRA6_uc002qem.1_RNA|LILRB3_uc002qen.1_RNA|LILRB3_uc002qeo.1_Missense_Mutation_p.S591P|LILRB3_uc002qep.1_Missense_Mutation_p.S591P|LILRB3_uc002qeq.1_Missense_Mutation_p.S590P|LILRB3_uc002qer.1_RNA|LILRB3_uc002qes.1_Missense_Mutation_p.S591P	NM_006864	NP_006855	O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor,	590	Cytoplasmic (Potential).				cell surface receptor linked signaling pathway|defense response	integral to plasma membrane	transmembrane receptor activity			skin(2)|ovary(1)	3	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ACATCCTGGGAGGCTTCAGAT	0.637													4	82	---	---	---	---	PASS
TP53TG5	27296	broad.mit.edu	37	20	44004137	44004137	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44004137C>T	uc002xny.2	-	4	391	c.310G>A	c.(310-312)GGG>AGG	p.G104R	SYS1_uc002xnw.1_3'UTR|SYS1-DBNDD2_uc002xnx.2_Intron	NM_014477	NP_055292	Q9Y2B4	T53G5_HUMAN	TP53-target gene 5 protein	104					intracellular signal transduction|negative regulation of cell growth	cytoplasm|nucleus				central_nervous_system(1)	1						TCGGAGCACCCGATCTCCTGG	0.502													43	326	---	---	---	---	PASS
ZNF334	55713	broad.mit.edu	37	20	45129836	45129836	+	3'UTR	SNP	A	T	T			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45129836A>T	uc002xsc.2	-	5					ZNF334_uc002xsa.2_3'UTR|ZNF334_uc002xsb.2_3'UTR|ZNF334_uc002xsd.2_3'UTR|ZNF334_uc010ghl.2_3'UTR	NM_018102	NP_060572	Q9HCZ1	ZN334_HUMAN	zinc finger protein 334 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2		Myeloproliferative disorder(115;0.0122)				CATATTCATTACATTTATAAG	0.269													5	77	---	---	---	---	PASS
MX1	4599	broad.mit.edu	37	21	42807818	42807818	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42807818G>A	uc002yzh.2	+	8	1107	c.160G>A	c.(160-162)GAC>AAC	p.D54N	MX1_uc002yzi.2_Missense_Mutation_p.D54N|MX1_uc010goq.2_Missense_Mutation_p.D54N	NM_001144925	NP_001138397	P20591	MX1_HUMAN	myxovirus resistance protein 1	54					induction of apoptosis|response to virus|type I interferon-mediated signaling pathway	cytosol	GTP binding|GTPase activity|protein binding			ovary(1)	1		Prostate(19;3.18e-07)|all_epithelial(19;0.0277)				CCCCTGCATCGACCTCATTGA	0.582													7	150	---	---	---	---	PASS
C21orf29	54084	broad.mit.edu	37	21	46011149	46011149	+	Intron	SNP	T	C	C	rs62220886	by1000genomes	TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46011149T>C	uc002zfe.1	-						C21orf29_uc010gpv.1_Intron	NM_144991	NP_659428	Q8WU66	TSEAR_HUMAN	chromosome 21 open reading frame 29 precursor						cell adhesion	extracellular region	structural molecule activity				0						TCCTGGTCCCTAAGACAAAGA	0.612													2	11	---	---	---	---	PASS
LOC644165	644165	broad.mit.edu	37	22	25046628	25046628	+	Intron	SNP	G	A	A	rs28533084	by1000genomes	TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25046628G>A	uc011ajv.1	+						POM121L10P_uc003aaz.3_RNA|POM121L10P_uc003abc.2_Intron	NR_024494				Homo sapiens cDNA FLJ57042 complete cds, moderately similar to Breakpoint cluster region protein (EC 2.7.11.1).												0						GGACTTGGGGGCTTGGGCCCC	0.622													3	2	---	---	---	---	PASS
DEPDC5	9681	broad.mit.edu	37	22	32229973	32229973	+	Intron	SNP	G	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32229973G>A	uc003als.2	+						DEPDC5_uc011als.1_Intron|DEPDC5_uc011alu.1_Intron|DEPDC5_uc011alv.1_Intron|DEPDC5_uc003alt.2_Intron|DEPDC5_uc003alu.2_Intron|DEPDC5_uc003alv.2_Intron|DEPDC5_uc011alw.1_Intron|DEPDC5_uc003alw.2_Intron|DEPDC5_uc011alx.1_Intron|DEPDC5_uc011alt.1_Missense_Mutation_p.R620K	NM_014662	NP_055477	O75140	DEPD5_HUMAN	DEP domain containing 5 isoform 1						intracellular signal transduction					ovary(4)|central_nervous_system(3)|pancreas(1)	8						CCAAGTAAGAGGGGGCAGCTG	0.502													23	452	---	---	---	---	PASS
TCF20	6942	broad.mit.edu	37	22	42610895	42610895	+	Silent	SNP	A	G	G			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42610895A>G	uc003bcj.1	-	1	551	c.417T>C	c.(415-417)TTT>TTC	p.F139F	TCF20_uc003bck.1_Silent_p.F139F|TCF20_uc003bnt.2_Silent_p.F139F	NM_005650	NP_005641	Q9UGU0	TCF20_HUMAN	transcription factor 20 isoform 1	139					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(4)|skin(1)	5						GCTGTGCTTGAAACTGGCCCA	0.577													56	162	---	---	---	---	PASS
BCOR	54880	broad.mit.edu	37	X	39914706	39914706	+	Silent	SNP	A	G	G			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:39914706A>G	uc004den.3	-	12	4948	c.4656T>C	c.(4654-4656)TAT>TAC	p.Y1552Y	BCOR_uc004dep.3_Silent_p.Y1518Y|BCOR_uc004deo.3_Silent_p.Y1500Y|BCOR_uc010nhb.2_Silent_p.Y260Y|BCOR_uc004dem.3_Silent_p.Y1518Y	NM_001123385	NP_001116857	Q6W2J9	BCOR_HUMAN	BCL-6 interacting corepressor isoform c	1552	ANK 3.				heart development|histone H2A monoubiquitination|negative regulation of bone mineralization|negative regulation of histone H3-K36 methylation|negative regulation of histone H3-K4 methylation|negative regulation of tooth mineralization|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|palate development|specification of axis polarity|transcription, DNA-dependent	nucleus	heat shock protein binding|histone deacetylase binding|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding			ovary(2)|kidney(1)|central_nervous_system(1)	4						GGTCAGCACCATAAGAGAGAA	0.453													8	83	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	10869	10869	+	RNA	SNP	T	C	C			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:10869T>C	uc004cov.3	+	1		c.292T>C			uc004cow.1_5'Flank|uc004cox.3_5'Flank					Homo sapiens potential LAG1 interactor mRNA, partial cds.																		TATTAGCATCATCCCCCTACT	0.398													2	3	---	---	---	---	PASS
RBP7	116362	broad.mit.edu	37	1	10068501	10068502	+	Intron	INS	-	T	T	rs112928878		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10068501_10068502insT	uc001aqq.2	+						RBP7_uc009vms.2_Intron	NM_052960	NP_443192	Q96R05	RET7_HUMAN	retinol binding protein 7, cellular							cytoplasm	retinal binding|retinol binding|transporter activity				0		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.5e-08)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;0.000249)|BRCA - Breast invasive adenocarcinoma(304;0.000302)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00856)|READ - Rectum adenocarcinoma(331;0.0419)	Vitamin A(DB00162)	catctctactattttttttttt	0.000													3	3	---	---	---	---	
CASZ1	54897	broad.mit.edu	37	1	10713982	10713982	+	Frame_Shift_Del	DEL	C	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10713982delC	uc001aro.2	-	11	2452	c.2132delG	c.(2131-2133)GGCfs	p.G711fs	CASZ1_uc001arp.1_Frame_Shift_Del_p.G711fs|CASZ1_uc009vmx.2_Frame_Shift_Del_p.G735fs	NM_001079843	NP_001073312	Q86V15	CASZ1_HUMAN	castor homolog 1, zinc finger isoform a	711					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			skin(1)	1	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		GTCCTTGGCGCCCAGCAGCGA	0.662													124	9	---	---	---	---	
SPEN	23013	broad.mit.edu	37	1	16242402	16242402	+	Intron	DEL	T	-	-	rs141272922		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16242402delT	uc001axk.1	+						SPEN_uc010obp.1_Intron	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator						interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		TTAGCCTTAATTTTTTTTTGA	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	36586349	36586349	+	IGR	DEL	A	-	-	rs146743730		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36586349delA								COL8A2 (20499 upstream) : TRAPPC3 (15826 downstream)																							actccgtctcaaaaaaaaaaa	0.005													6	3	---	---	---	---	
INADL	10207	broad.mit.edu	37	1	62237397	62237397	+	Intron	DEL	T	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62237397delT	uc001dab.2	+						INADL_uc009waf.1_Intron|INADL_uc001daa.2_Intron|INADL_uc001dad.3_Intron	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like						intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4						Ctttctttccttttttttttt	0.134													7	5	---	---	---	---	
SLC44A5	204962	broad.mit.edu	37	1	76084765	76084765	+	Intron	DEL	G	-	-	rs34647299		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76084765delG	uc010oqz.1	-						SLC44A5_uc010orb.1_Intron	NM_001130058	NP_001123530	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5 isoform B							integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4						caaaaaaaaagggggggggga	0.000													6	4	---	---	---	---	
C1orf161	126868	broad.mit.edu	37	1	116655015	116655015	+	Intron	DEL	A	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116655015delA	uc001egc.1	+							NM_152367	NP_689580	Q8N8X9	MB213_HUMAN	hypothetical protein LOC126868												0	Lung SC(450;0.184)	all_cancers(81;0.00142)|all_lung(203;0.000139)|all_epithelial(167;0.000401)|Lung NSC(69;0.000705)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		TTTTTTTTTTAATTTCCCAAA	0.343													4	2	---	---	---	---	
TCHH	7062	broad.mit.edu	37	1	152082957	152082959	+	In_Frame_Del	DEL	CTC	-	-	rs143222885	by1000genomes	TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152082957_152082959delCTC	uc001ezp.2	-	2	2734_2736	c.2734_2736delGAG	c.(2734-2736)GAGdel	p.E912del	TCHH_uc009wne.1_In_Frame_Del_p.E912del	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	912	4-1.|10 X 30 AA tandem repeats.				keratinization	cytoskeleton	calcium ion binding			ovary(3)|kidney(1)|central_nervous_system(1)	5	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCTCTGTAGCTCCTCCTCCTCC	0.586													513	7	---	---	---	---	
LBR	3930	broad.mit.edu	37	1	225592043	225592044	+	Intron	DEL	AC	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225592043_225592044delAC	uc001hoy.2	-						LBR_uc001hoz.2_Intron	NM_002296	NP_002287	Q14739	LBR_HUMAN	lamin B receptor						cholesterol biosynthetic process	integral to nuclear inner membrane	chromo shadow domain binding|delta14-sterol reductase activity|DNA binding|lamin binding|receptor activity			ovary(1)|skin(1)	2	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)		CACACAAAGGACACACACACAC	0.520													59	9	---	---	---	---	
GCC2	9648	broad.mit.edu	37	2	109087883	109087884	+	Frame_Shift_Ins	INS	-	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109087883_109087884insA	uc002tec.2	+	6	2252_2253	c.2098_2099insA	c.(2098-2100)GAAfs	p.E700fs	GCC2_uc002ted.2_Frame_Shift_Ins_p.E599fs	NM_181453	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain-containing 2	700	Potential.				Golgi ribbon formation|late endosome to Golgi transport|microtubule anchoring|microtubule organizing center organization|protein localization in Golgi apparatus|protein targeting to lysosome|recycling endosome to Golgi transport|regulation of protein exit from endoplasmic reticulum	membrane|trans-Golgi network	identical protein binding			ovary(1)	1						ACTCAGTTCAGAAAAAAAACAG	0.307													565	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	131236257	131236257	+	IGR	DEL	G	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131236257delG								PTPN18 (103276 upstream) : CFC1B (42579 downstream)																							TTTCTTTTCTGGCAGCTGTGA	0.428													5	4	---	---	---	---	
CCDC148	130940	broad.mit.edu	37	2	159077014	159077014	+	Intron	DEL	A	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159077014delA	uc002tzq.2	-						CCDC148_uc002tzr.2_Intron|CCDC148_uc010foh.2_Intron	NM_138803	NP_620158	Q8NFR7	CC148_HUMAN	coiled-coil domain containing 148											ovary(2)	2						TTAAGTATAGAAAAAAGTTCC	0.279													81	9	---	---	---	---	
MYO3B	140469	broad.mit.edu	37	2	171073549	171073549	+	Intron	DEL	A	-	-	rs35309592		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171073549delA	uc002ufy.2	+						MYO3B_uc002ufv.2_Intron|MYO3B_uc010fqb.1_Intron|MYO3B_uc002ufz.2_Intron|MYO3B_uc002ufw.2_Intron|MYO3B_uc002ufx.2_Intron|MYO3B_uc002uga.2_Intron	NM_138995	NP_620482	Q8WXR4	MYO3B_HUMAN	myosin IIIB isoform 2						response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(6)|skin(4)|central_nervous_system(1)	19						aaatgattggaaaaaaaaaac	0.010													4	2	---	---	---	---	
CCNYL1	151195	broad.mit.edu	37	2	208618360	208618362	+	In_Frame_Del	DEL	AGA	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208618360_208618362delAGA	uc002vci.2	+	8	1222_1224	c.865_867delAGA	c.(865-867)AGAdel	p.R290del	CCNYL1_uc002vch.2_In_Frame_Del_p.R271del	NM_001142300	NP_001135772	Q8N7R7	CCYL1_HUMAN	cyclin Y-like 1 isoform 1	341					regulation of cyclin-dependent protein kinase activity		protein kinase binding				0				LUSC - Lung squamous cell carcinoma(261;0.0731)|Epithelial(149;0.139)|Lung(261;0.14)		AGCCGCTATGAGAAGGTCTTTCA	0.404													356	72	---	---	---	---	
ACSL3	2181	broad.mit.edu	37	2	223786354	223786355	+	Intron	DEL	TT	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223786354_223786355delTT	uc002vni.2	+						ACSL3_uc002vnj.2_Intron	NM_004457	NP_004448	O95573	ACSL3_HUMAN	acyl-CoA synthetase long-chain family member 3						long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane	ATP binding|fatty-acyl-CoA synthase activity|long-chain fatty acid-CoA ligase activity|protein binding			ovary(2)	2		Renal(207;0.0183)		Epithelial(121;1.28e-10)|all cancers(144;8.06e-08)|Lung(261;0.00834)|LUSC - Lung squamous cell carcinoma(224;0.00864)	Icosapent(DB00159)	TATAGATATATTTTAAAAAGTA	0.238			T	ETV1	prostate								4	2	---	---	---	---	
CCDC36	339834	broad.mit.edu	37	3	49281663	49281663	+	Intron	DEL	T	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49281663delT	uc003cwk.2	+						CCDC36_uc003cwl.3_Intron|CCDC36_uc011bck.1_Intron	NM_178173	NP_835467	Q8IYA8	CCD36_HUMAN	coiled-coil domain containing 36											ovary(1)|kidney(1)	2				BRCA - Breast invasive adenocarcinoma(193;9.11e-05)|Kidney(197;0.00248)|KIRC - Kidney renal clear cell carcinoma(197;0.00262)		tgggaCTCTCTTTTTTTTTCC	0.214													4	2	---	---	---	---	
PFN2	5217	broad.mit.edu	37	3	149684633	149684634	+	Intron	INS	-	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149684633_149684634insA	uc003ext.1	-						PFN2_uc003exs.1_Intron|PFN2_uc003exu.1_Intron|PFN2_uc011bnu.1_Intron	NM_053024	NP_444252	P35080	PROF2_HUMAN	profilin 2 isoform a						actin cytoskeleton organization|regulation of actin polymerization or depolymerization	actin cytoskeleton|cytoplasm	actin binding|phosphatidylinositol-4,5-bisphosphate binding				0			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			ACTAGCTACAGAAAAAAAAAAA	0.307													4	2	---	---	---	---	
ATP11B	23200	broad.mit.edu	37	3	182598471	182598473	+	Intron	DEL	ATA	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182598471_182598473delATA	uc003flb.2	+						ATP11B_uc003flc.2_Intron|ATP11B_uc011bqm.1_Intron|ATP11B_uc010hxf.1_Intron	NM_014616	NP_055431	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B						aminophospholipid transport|ATP biosynthetic process	integral to membrane|nuclear inner membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			CTGTTTTATTATAACATTTCTGA	0.217													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	196395240	196395241	+	IGR	INS	-	AAGA	AAGA			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196395240_196395241insAAGA								LRRC33 (6368 upstream) : C3orf34 (37908 downstream)																							agagagaaatgaaggaaggaag	0.094													4	2	---	---	---	---	
ATP8A1	10396	broad.mit.edu	37	4	42424522	42424523	+	Intron	DEL	TT	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42424522_42424523delTT	uc003gwr.2	-						ATP8A1_uc003gwq.2_Intron|ATP8A1_uc003gws.2_Intron	NM_006095	NP_006086	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT),						ATP biosynthetic process	chromaffin granule membrane|integral to membrane|plasma membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			skin(2)|central_nervous_system(1)	3					Phosphatidylserine(DB00144)	cattaaagactttgcactatgc	0.084													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	43749393	43749395	+	IGR	DEL	TGG	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43749393_43749395delTGG								GRXCR1 (716720 upstream) : KCTD8 (426527 downstream)																							gaacaaggtatggtggtggtggt	0.000													5	3	---	---	---	---	
PDGFRA	5156	broad.mit.edu	37	4	54374598	54374599	+	Intron	INS	-	T	T	rs142889716	by1000genomes	TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54374598_54374599insT	uc003haa.2	+						LNX1_uc003haf.3_Intron|LNX1_uc003hag.3_Intron|LNX1_uc003hah.3_Intron	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	ATAATTTGAGATTTTTTAAAGA	0.396			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			4	3	---	---	---	---	
UBA6	55236	broad.mit.edu	37	4	68529609	68529610	+	Frame_Shift_Ins	INS	-	T	T			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68529609_68529610insT	uc003hdg.3	-	11	1005_1006	c.953_954insA	c.(952-954)AACfs	p.N318fs	UBA6_uc003hdi.2_Frame_Shift_Ins_p.N318fs|UBA6_uc003hdj.2_Frame_Shift_Ins_p.N318fs	NM_018227	NP_060697	A0AVT1	UBA6_HUMAN	ubiquitin-activating enzyme E1-like 2	318					protein ubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm	ATP binding|FAT10 activating enzyme activity|ligase activity|protein binding				0						TTACCTCAGGGTTGCTAAAATC	0.386													279	8	---	---	---	---	
CSN2	1447	broad.mit.edu	37	4	70825805	70825805	+	Intron	DEL	A	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70825805delA	uc003hes.3	-						CSN2_uc003het.3_Intron	NM_001891	NP_001882	P05814	CASB_HUMAN	casein beta precursor						calcium ion transport	extracellular region	calcium ion binding|enzyme inhibitor activity|transporter activity				0						GGTCTGTGGGAAAAAAAAATT	0.313													198	7	---	---	---	---	
NNT	23530	broad.mit.edu	37	5	43704689	43704690	+	3'UTR	INS	-	A	A	rs140114937	by1000genomes	TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43704689_43704690insA	uc003joe.2	+	22					NNT_uc003jof.2_3'UTR	NM_012343	NP_036475	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase						tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain	NAD binding|NAD(P)+ transhydrogenase (AB-specific) activity|NAD(P)+ transhydrogenase (B-specific) activity|NADP binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(6;2.58e-06)				NADH(DB00157)	CCCTCAATTTTAAAAAAGGATT	0.302													4	2	---	---	---	---	
C5orf44	80006	broad.mit.edu	37	5	64942853	64942853	+	Intron	DEL	T	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64942853delT	uc003jtz.3	+						C5orf44_uc003jua.3_Intron|C5orf44_uc003juc.3_Intron|C5orf44_uc010iwv.2_Intron	NM_024941	NP_079217	A5PLN9	CE044_HUMAN	hypothetical protein LOC80006 isoform 2											ovary(1)	1						tcattTGGACTTTTTTTTTTT	0.199													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	166471034	166471041	+	IGR	DEL	TAAGGACA	-	-	rs2910053		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166471034_166471041delTAAGGACA								None (None upstream) : ODZ2 (240802 downstream)																							aaataaaTAGTaaggacagaaggaagga	0.115													5	3	---	---	---	---	
FAM153B	202134	broad.mit.edu	37	5	175530031	175530031	+	Intron	DEL	G	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175530031delG	uc003mdk.2	+							NM_001079529	NP_001072997	P0C7A2	F153B_HUMAN	hypothetical protein LOC202134											ovary(1)	1	all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Kidney(146;0.0965)		CCTGCACTGCGTGGTGTGCAC	0.507													8	4	---	---	---	---	
TUBB	203068	broad.mit.edu	37	6	30692293	30692294	+	3'UTR	INS	-	G	G	rs150645240	by1000genomes	TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30692293_30692294insG	uc003nrl.2	+	4					TUBB_uc003nrk.1_3'UTR|TUBB_uc011dmq.1_3'UTR	NM_178014	NP_821133	P07437	TBB5_HUMAN	tubulin, beta						cellular component movement|G2/M transition of mitotic cell cycle|microtubule-based movement|natural killer cell mediated cytotoxicity|protein polymerization	cytosol|microtubule	GTP binding|GTPase activity|MHC class I protein binding			ovary(1)	1					Colchicine(DB01394)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)	ttttttcttctggggggggtct	0.277													4	2	---	---	---	---	
HLA-DRB5	3127	broad.mit.edu	37	6	32546929	32546929	+	Intron	DEL	A	-	-	rs67615547		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32546929delA	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						CTCTACTAACAGTTTCTTTTC	0.478													38	8	---	---	---	---	
C6orf106	64771	broad.mit.edu	37	6	34654281	34654281	+	Intron	DEL	A	-	-	rs74753449		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34654281delA	uc003ojr.2	-						C6orf106_uc003ojs.2_Intron	NM_024294	NP_077270	Q9H6K1	CF106_HUMAN	chromosome 6 open reading frame 106 isoform a											skin(2)|ovary(1)	3						cgtctcaaagaaaaaaaaaaa	0.085													5	3	---	---	---	---	
KIAA0776	23376	broad.mit.edu	37	6	96985621	96985621	+	Intron	DEL	G	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96985621delG	uc003por.2	+						KIAA0776_uc010kck.2_Intron	NM_015323	NP_056138	O94874	UFL1_HUMAN	hypothetical protein LOC23376						negative regulation of NF-kappaB transcription factor activity|negative regulation of protein ubiquitination|protein ufmylation	endoplasmic reticulum|nucleus	protein binding|UFM1 conjugating enzyme activity			ovary(1)	1		all_cancers(76;5.83e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0604)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0934)		TCAACATCCAGAATTCTATAA	0.343													4	2	---	---	---	---	
NCOA7	135112	broad.mit.edu	37	6	126240526	126240526	+	Intron	DEL	G	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126240526delG	uc010kes.2	+						NCOA7_uc003qae.3_Intron|NCOA7_uc003qah.2_Intron|NCOA7_uc003qai.2_Intron|NCOA7_uc010ket.2_Intron|NCOA7_uc003qak.2_Frame_Shift_Del_p.L8fs	NM_181782	NP_861447	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7 isoform 1						cell wall macromolecule catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		GATTACCCTTGGACATCCAGA	0.468													203	15	---	---	---	---	
MOXD1	26002	broad.mit.edu	37	6	132705420	132705420	+	Intron	DEL	C	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132705420delC	uc003qdf.2	-							NM_015529	NP_056344	Q6UVY6	MOXD1_HUMAN	monooxygenase, DBH-like 1 isoform 2						catecholamine metabolic process	endoplasmic reticulum membrane|integral to membrane	copper ion binding|dopamine beta-monooxygenase activity			ovary(1)	1	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)		ttccttccttccttccttcct	0.065													4	3	---	---	---	---	
MAP3K5	4217	broad.mit.edu	37	6	136878752	136878752	+	3'UTR	DEL	T	-	-	rs71747329		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136878752delT	uc003qhc.2	-	30					MAP3K5_uc011edj.1_3'UTR	NM_005923	NP_005914	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		GTTTTGTCTGTTTTTTTTTTT	0.343													8	4	---	---	---	---	
SYNJ2	8871	broad.mit.edu	37	6	158438438	158438438	+	Intron	DEL	T	-	-	rs3079514		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158438438delT	uc003qqx.1	+						SYNJ2_uc011efm.1_Intron|SYNJ2_uc003qqw.1_Intron|SYNJ2_uc003qqy.1_Intron|SYNJ2_uc011efn.1_5'Flank|SYNJ2_uc010kjo.1_5'Flank	NM_003898	NP_003889	O15056	SYNJ2_HUMAN	synaptojanin 2								nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		CTCTCTCttcttttttttttt	0.313													4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151944708	151944708	+	Intron	DEL	T	-	-	rs113407913		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151944708delT	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		ACTAAAAGAATTTTTAAAGTT	0.264			N		medulloblastoma								4	4	---	---	---	---	
VPS13A	23230	broad.mit.edu	37	9	79828414	79828414	+	Intron	DEL	T	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79828414delT	uc004akr.2	+						VPS13A_uc004akp.3_Intron|VPS13A_uc004akq.3_Intron|VPS13A_uc004aks.2_Intron	NM_033305	NP_150648	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13A isoform A						Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|skin(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	10						CCCCCATATCttttttttttt	0.174													4	2	---	---	---	---	
C9orf114	51490	broad.mit.edu	37	9	131586559	131586560	+	Intron	DEL	GT	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131586559_131586560delGT	uc004bwd.2	-						C9orf114_uc004bwe.2_Intron|C9orf114_uc010mym.2_Intron	NM_016390	NP_057474	Q5T280	CI114_HUMAN	hypothetical protein LOC51490												0						GAGCtgtgtggtgtgtgtgtgt	0.500													4	2	---	---	---	---	
SURF4	6836	broad.mit.edu	37	9	136231748	136231748	+	Frame_Shift_Del	DEL	T	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136231748delT	uc004cdj.2	-	5	641	c.511delA	c.(511-513)ACCfs	p.T171fs	SURF4_uc011mda.1_Frame_Shift_Del_p.T162fs|SURF4_uc010nal.2_Intron|SURF4_uc011mdb.1_Frame_Shift_Del_p.T128fs|SURF4_uc011mdc.1_Frame_Shift_Del_p.T128fs|SURF4_uc011mdd.1_Intron	NM_033161	NP_149351	O15260	SURF4_HUMAN	surfeit 4	171						endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	protein binding				0				OV - Ovarian serous cystadenocarcinoma(145;5.32e-07)|Epithelial(140;4.56e-06)|all cancers(34;4.25e-05)		TGAAGGAGGGTCATGAACATC	0.562													69	12	---	---	---	---	
CACNA1B	774	broad.mit.edu	37	9	140968697	140968697	+	Intron	DEL	T	-	-	rs78547363		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140968697delT	uc004cog.2	+						CACNA1B_uc004coi.2_Intron|CACNA1B_uc004cok.1_5'Flank|CACNA1B_uc010ncp.1_5'Flank	NM_000718	NP_000709	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type,						membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity			breast(3)|large_intestine(2)|ovary(1)	6	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)	tttcttactcttttttttttt	0.020													5	3	---	---	---	---	
AKR1C2	1646	broad.mit.edu	37	10	5045397	5045397	+	Intron	DEL	T	-	-	rs71929051		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5045397delT	uc010qan.1	-						AKR1E2_uc001ihl.1_Intron|AKR1C3_uc001ihr.2_Intron|AKR1C2_uc009xhy.2_Intron|AKR1C2_uc001ihs.2_Intron|AKR1C2_uc001iht.2_Intron|AKR1C2_uc010qao.1_Intron	NM_205845	NP_995317	P52895	AK1C2_HUMAN	aldo-keto reductase family 1, member C2						digestion|prostaglandin metabolic process|steroid metabolic process	cytoplasm	androsterone dehydrogenase (A-specific) activity|bile acid binding|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity				0					NADH(DB00157)|Ursodeoxycholic acid(DB01586)	TTGGTTCTAGTTTTTTTTTTT	0.289													6	3	---	---	---	---	
ITIH5	80760	broad.mit.edu	37	10	7697413	7697413	+	Intron	DEL	A	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7697413delA	uc001ijq.2	-						ITIH5_uc001ijr.1_Intron	NM_030569	NP_085046	Q86UX2	ITIH5_HUMAN	inter-alpha trypsin inhibitor heavy chain						hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4						CAGAAAAAAGAAAAAAAAAAT	0.284													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	35254677	35254677	+	IGR	DEL	T	-	-	rs150201909		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35254677delT								PARD3 (150754 upstream) : CUL2 (44131 downstream)																							CTGCAGGGGCttttttttttt	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	132769890	132769893	+	IGR	DEL	TCCT	-	-	rs148834263	by1000genomes	TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132769890_132769893delTCCT								GLRX3 (787106 upstream) : TCERG1L (120763 downstream)																							TCCTGGAATGtccttccttccttc	0.279													5	3	---	---	---	---	
FNBP4	23360	broad.mit.edu	37	11	47788664	47788669	+	In_Frame_Del	DEL	GGTGGT	-	-	rs59413596		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47788664_47788669delGGTGGT	uc009ylv.2	-	1	325_330	c.172_177delACCACC	c.(172-177)ACCACCdel	p.TT58del	FNBP4_uc001ngj.2_5'UTR|FNBP4_uc001ngl.2_RNA	NM_015308	NP_056123	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	58_59										ovary(1)	1						CAGTCACCGCGGTGGTGGTGGTCGTC	0.748													3	3	---	---	---	---	
MYO7A	4647	broad.mit.edu	37	11	76892819	76892825	+	Intron	DEL	TTTTTTG	-	-	rs12794459		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76892819_76892825delTTTTTTG	uc001oyb.2	+						MYO7A_uc010rsl.1_Intron|MYO7A_uc010rsm.1_Intron|MYO7A_uc001oyc.2_Intron|MYO7A_uc001oyd.2_Intron|MYO7A_uc009yus.1_Intron|MYO7A_uc009yut.1_Intron	NM_000260	NP_000251	Q13402	MYO7A_HUMAN	myosin VIIA isoform 1						actin filament-based movement|equilibrioception|lysosome organization|sensory perception of sound|visual perception	cytosol|lysosomal membrane|myosin complex|photoreceptor inner segment|photoreceptor outer segment|synapse	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|breast(1)	4						TCAAGtttttttttttgtttttttttt	0.290													4	2	---	---	---	---	
AASDHPPT	60496	broad.mit.edu	37	11	105961622	105961625	+	Intron	DEL	TACT	-	-	rs138293505		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105961622_105961625delTACT	uc001pjc.1	+						AASDHPPT_uc010rvn.1_Intron|AASDHPPT_uc001pjd.1_Intron	NM_015423	NP_056238	Q9NRN7	ADPPT_HUMAN	aminoadipate-semialdehyde						macromolecule biosynthetic process|pantothenate metabolic process	cytosol	holo-[acyl-carrier-protein] synthase activity|magnesium ion binding|protein binding				0		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.78e-05)|Epithelial(105;0.00622)|all cancers(92;0.041)		AGTTAGAAAGTACTTACTTAAAGC	0.225													9	5	---	---	---	---	
GUCY2C	2984	broad.mit.edu	37	12	14775148	14775148	+	Intron	DEL	A	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14775148delA	uc001rcd.2	-							NM_004963	NP_004954	P25092	GUC2C_HUMAN	guanylate cyclase 2C precursor						intracellular signal transduction|receptor guanylyl cyclase signaling pathway	integral to membrane	ATP binding|GTP binding|guanylate cyclase activity|protein binding|protein kinase activity|receptor activity			ovary(4)|skin(2)	6						GAACGAAGGGAAAAAAAATGC	0.378													63	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	16879340	16879350	+	IGR	DEL	TCCTTCCTTCC	-	-	rs71953318		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16879340_16879350delTCCTTCCTTCC								LMO3 (116582 upstream) : None (None downstream)																							cttccttccttccttccttccttccttcctt	0.175													5	3	---	---	---	---	
GDF11	10220	broad.mit.edu	37	12	56143019	56143020	+	Intron	INS	-	A	A			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56143019_56143020insA	uc001shq.2	+						GDF11_uc010spv.1_Intron	NM_005811	NP_005802	O95390	GDF11_HUMAN	growth differentiation factor 11 precursor						growth|mesoderm development|skeletal system development	extracellular space	cytokine activity|growth factor activity			kidney(1)	1						GCTGTGAGAACAAAAAAACTGG	0.460													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19492018	19492019	+	IGR	INS	-	GTGT	GTGT			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19492018_19492019insGTGT								OR11H12 (113446 upstream) : POTEG (61346 downstream)																							CAATAAACtgcgtgtgtgtgtg	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	46721941	46721944	+	IGR	DEL	GTGT	-	-	rs149690572		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46721941_46721944delGTGT								C14orf106 (999336 upstream) : RPL10L (398278 downstream)																							TCTGGAAtgcgtgtgtgtgtgtgt	0.142													4	2	---	---	---	---	
CASC5	57082	broad.mit.edu	37	15	40921694	40921705	+	Intron	DEL	TTTTTTTTTTTT	-	-	rs71104709		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40921694_40921705delTTTTTTTTTTTT	uc010bbs.1	+						CASC5_uc010bbt.1_Intron	NM_170589	NP_733468	Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5 isoform 1						acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint	acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm	protein binding			breast(3)|central_nervous_system(1)|skin(1)	5		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		ttgccttttctttttttttttttttttttttt	0.104													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	78202278	78202278	+	IGR	DEL	C	-	-	rs71145877		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78202278delC								LINGO1 (213803 upstream) : LOC645752 (4281 downstream)																							TTGACAGTGGCTCCCCCAGCC	0.577													9	4	---	---	---	---	
GSG1L	146395	broad.mit.edu	37	16	27990888	27990888	+	Intron	DEL	A	-	-	rs77066595		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27990888delA	uc002doz.2	-						GSG1L_uc010bya.1_Intron	NM_001109763	NP_001103233	Q6UXU4	GSG1L_HUMAN	GSG1-like isoform 1							integral to membrane				ovary(1)	1						agaatccatcaaaaaaaaaaa	0.000													4	3	---	---	---	---	
TEPP	374739	broad.mit.edu	37	16	58011464	58011465	+	Intron	INS	-	GTGTGTGTGT	GTGTGTGTGT	rs146374461		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58011464_58011465insGTGTGTGTGT	uc002emw.3	+						TEPP_uc002emv.3_Intron	NM_199456	NP_955535	Q6URK8	TEPP_HUMAN	testis/prostate/placenta-expressed protein							extracellular region				kidney(1)|central_nervous_system(1)|skin(1)	3						GCACAAtgtgagtgtgtgtgtg	0.327													3	3	---	---	---	---	
ATP2C2	9914	broad.mit.edu	37	16	84493954	84493955	+	Intron	INS	-	A	A	rs142178706	by1000genomes	TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84493954_84493955insA	uc002fhx.2	+						ATP2C2_uc010chj.2_Intron|ATP2C2_uc002fhy.2_Intron|ATP2C2_uc002fhz.2_Intron|ATP2C2_uc002fia.2_5'UTR	NM_014861	NP_055676	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2						ATP biosynthetic process	Golgi membrane|integral to membrane	ATP binding|calcium-transporting ATPase activity|metal ion binding|protein binding			breast(1)|central_nervous_system(1)	2						GCGCAACGTTGGGGGGGGTCCC	0.619													4	3	---	---	---	---	
TMEM132E	124842	broad.mit.edu	37	17	32965275	32965276	+	3'UTR	INS	-	C	C	rs71921875		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32965275_32965276insC	uc002hif.2	+	10						NM_207313	NP_997196	Q6IEE7	T132E_HUMAN	transmembrane protein 132E precursor							integral to membrane				central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(366;0.231)		AGTAGCAGGGACCCCCCCCCCC	0.644											OREG0024325	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	10	8	---	---	---	---	
KRT40	125115	broad.mit.edu	37	17	39138900	39138901	+	Intron	DEL	TG	-	-	rs5820382		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39138900_39138901delTG	uc010cxh.1	-						KRT40_uc002hvq.1_Intron	NM_182497	NP_872303	Q6A162	K1C40_HUMAN	type I hair keratin KA36							intermediate filament	structural molecule activity				0		Breast(137;0.00043)				AGAGAATATTtgtgtgtgtgtg	0.198													3	4	---	---	---	---	
MUM1	84939	broad.mit.edu	37	19	1376295	1376300	+	Intron	DEL	TTTTTT	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1376295_1376300delTTTTTT	uc010xgm.1	+						MUM1_uc002lrz.2_Intron|MUM1_uc002lsb.2_Intron|MUM1_uc002lsd.2_Intron			Q2TAK8	MUM1_HUMAN	SubName: Full=MUM1 protein;						chromatin organization|DNA repair	nucleus	nucleosome binding|protein binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|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)		cggctgtttgtttttttttttgtttg	0.000													4	3	---	---	---	---	
KIR3DX1	90011	broad.mit.edu	37	19	55044571	55044572	+	Intron	DEL	CT	-	-	rs72249234		TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55044571_55044572delCT	uc010yfa.1	+						KIR3DX1_uc010yfb.1_Intron|KIR3DX1_uc010yfc.1_Intron|KIR3DX1_uc010yfd.1_Intron	NR_026716				Homo sapiens mRNA for FLJ00060 protein, partial cds.											ovary(1)	1				GBM - Glioblastoma multiforme(193;0.099)		GGTAGGAGTACTCTCTGTCAGG	0.510													2	6	---	---	---	---	
TM9SF4	9777	broad.mit.edu	37	20	30748854	30748854	+	Intron	DEL	A	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30748854delA	uc002wxj.2	+						TM9SF4_uc010zts.1_Intron|TM9SF4_uc002wxk.2_Intron|TM9SF4_uc010gdz.2_Intron	NM_014742	NP_055557	Q92544	TM9S4_HUMAN	transmembrane 9 superfamily protein member 4							integral to membrane				central_nervous_system(1)|pancreas(1)	2			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			TTTTTTTtttaatgaggtata	0.015													4	2	---	---	---	---	
ZMYND8	23613	broad.mit.edu	37	20	45938512	45938512	+	Intron	DEL	A	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45938512delA	uc002xta.1	-						ZMYND8_uc010ghr.1_Intron|ZMYND8_uc002xst.1_Intron|ZMYND8_uc002xsu.1_Intron|ZMYND8_uc002xsv.1_Intron|ZMYND8_uc002xsw.1_Intron|ZMYND8_uc002xsx.1_Intron|ZMYND8_uc002xsy.1_Intron|ZMYND8_uc002xsz.1_Intron|ZMYND8_uc010zxy.1_Intron|ZMYND8_uc002xtb.1_Intron|ZMYND8_uc002xss.2_Intron|ZMYND8_uc010zxz.1_Intron|ZMYND8_uc002xtc.1_Intron|ZMYND8_uc002xtd.1_Intron|ZMYND8_uc002xte.1_Intron|ZMYND8_uc010zya.1_Intron|ZMYND8_uc002xtf.1_Intron|ZMYND8_uc002xtg.2_Intron|ZMYND8_uc010ghs.1_Intron|ZMYND8_uc002xth.2_Intron	NM_012408	NP_036540	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8 isoform b								protein binding|zinc ion binding			central_nervous_system(2)|urinary_tract(1)|ovary(1)|skin(1)	5			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)			TAAAAGCATGAAAAAAAAAAA	0.388													4	2	---	---	---	---	
KCNQ2	3785	broad.mit.edu	37	20	62074452	62074453	+	Intron	INS	-	CAC	CAC	rs139636562	by1000genomes	TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62074452_62074453insCAC	uc002yey.1	-						KCNQ2_uc002yez.1_Intron|KCNQ2_uc002yfa.1_Intron|KCNQ2_uc002yfb.1_Intron|KCNQ2_uc011aax.1_Intron|KCNQ2_uc002yfc.1_Intron	NM_172107	NP_742105	O43526	KCNQ2_HUMAN	potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)	atcaccaccatcaccatcacca	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	82130969	82130969	+	IGR	DEL	A	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:82130969delA								None (None upstream) : POU3F4 (632300 downstream)																							ATTATAAACTAAAAAAAAAAa	0.139													4	2	---	---	---	---	
SLITRK4	139065	broad.mit.edu	37	X	142717743	142717743	+	Frame_Shift_Del	DEL	T	-	-			TCGA-EJ-5527-01	TCGA-EJ-5527-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142717743delT	uc004fbx.2	-	2	1558	c.1182delA	c.(1180-1182)GTAfs	p.V394fs	SLITRK4_uc004fby.2_Frame_Shift_Del_p.V394fs	NM_173078	NP_775101	Q8IW52	SLIK4_HUMAN	slit and trk like 4 protein precursor	394	Extracellular (Potential).|LRR 7.					integral to membrane				upper_aerodigestive_tract(1)|large_intestine(1)	2	Acute lymphoblastic leukemia(192;6.56e-05)					TGAAGTCTGATACGTCCACAT	0.393													164	110	---	---	---	---	
