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
PRDM16	63976	broad.mit.edu	37	1	3328212	3328212	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3328212G>T	uc001akf.2	+	9	1531	c.1451G>T	c.(1450-1452)GGC>GTC	p.G484V	PRDM16_uc001akc.2_Missense_Mutation_p.G484V|PRDM16_uc001akd.2_Missense_Mutation_p.G484V|PRDM16_uc001ake.2_Missense_Mutation_p.G484V|PRDM16_uc009vlh.2_Missense_Mutation_p.G185V	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1	484	Pro-rich.				brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		GCCAGCCTGGGCTTCAACGAG	0.687			T	EVI1	MDS|AML								17	24	---	---	---	---	PASS
CLSTN1	22883	broad.mit.edu	37	1	9791432	9791432	+	Silent	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9791432C>A	uc001aqh.2	-	18	3339	c.2580G>T	c.(2578-2580)GCG>GCT	p.A860A	CLSTN1_uc001aqi.2_Silent_p.A850A|CLSTN1_uc010oag.1_Silent_p.A841A|CLSTN1_uc001aqf.2_Silent_p.A96A	NM_001009566	NP_001009566	O94985	CSTN1_HUMAN	calsyntenin 1 isoform 1	860	Helical; (Potential).				homophilic cell adhesion	cell junction|cell projection|endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nucleus|postsynaptic membrane	calcium ion binding			skin(1)	1	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		TCACAACTGTCGCAGTGCTGG	0.627													13	19	---	---	---	---	PASS
MTOR	2475	broad.mit.edu	37	1	11187830	11187830	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11187830A>C	uc001asd.2	-	44	6188	c.6067T>G	c.(6067-6069)TGG>GGG	p.W2023G	MTOR_uc001asc.2_Missense_Mutation_p.W228G	NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	2023					cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29						ATCTCATGCCAGAGGATGGCC	0.517													10	105	---	---	---	---	PASS
PLA2G2F	64600	broad.mit.edu	37	1	20466723	20466723	+	Intron	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20466723C>T	uc009vpp.1	+							NM_022819	NP_073730	Q9BZM2	PA2GF_HUMAN	phospholipase A2, group IIF						lipid catabolic process|phospholipid metabolic process	extracellular region	calcium ion binding|phospholipase A2 activity			ovary(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000247)|Lung NSC(340;0.000285)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.000524)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)		TGAGTAAAGACTCCAGAGGGC	0.577													7	15	---	---	---	---	PASS
EPHB2	2048	broad.mit.edu	37	1	23240007	23240007	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23240007A>T	uc009vqj.1	+	16	3050	c.2905A>T	c.(2905-2907)AAC>TAC	p.N969Y	EPHB2_uc001bge.2_Missense_Mutation_p.N970Y|EPHB2_uc001bgf.2_Missense_Mutation_p.N969Y|EPHB2_uc010odu.1_Missense_Mutation_p.N911Y	NM_017449	NP_059145	P29323	EPHB2_HUMAN	ephrin receptor EphB2 isoform 1 precursor	969	Cytoplasmic (Potential).|SAM.				axon guidance	integral to plasma membrane	ATP binding|transmembrane-ephrin receptor activity			ovary(3)|lung(1)|pancreas(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)		AAAAATCCTGAACAGTATCCA	0.557									Hereditary_Prostate_Cancer				8	20	---	---	---	---	PASS
ARID1A	8289	broad.mit.edu	37	1	27097600	27097600	+	Intron	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27097600G>A	uc001bmv.1	+						ARID1A_uc001bmt.1_Intron|ARID1A_uc001bmu.1_Intron|ARID1A_uc001bmw.1_Intron|ARID1A_uc001bmx.1_5'Flank|ARID1A_uc009vsm.1_5'Flank	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a						androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding			ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	142		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CCTTTGGTTTGGTTATACAGG	0.473			Mis|N|F|S|D		clear cell ovarian carcinoma|RCC								11	21	---	---	---	---	PASS
HMGB4	127540	broad.mit.edu	37	1	34330035	34330035	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34330035G>T	uc001bxp.2	+	2	1986	c.243G>T	c.(241-243)AAG>AAT	p.K81N	CSMD2_uc001bxm.1_Intron|CSMD2_uc001bxn.1_Intron|HMGB4_uc001bxq.2_Missense_Mutation_p.K7N	NM_145205	NP_660206	Q8WW32	HMGB4_HUMAN	HMG2 like isoform 1	81						nucleus	DNA binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				ATGTTGGCAAGAGGAAGAAAC	0.493													6	96	---	---	---	---	PASS
SNIP1	79753	broad.mit.edu	37	1	38019758	38019758	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38019758C>A	uc001cbi.2	-	1	146	c.73G>T	c.(73-75)GCG>TCG	p.A25S	SNIP1_uc010oid.1_RNA|DNALI1_uc001cbj.2_5'Flank|DNALI1_uc010oie.1_5'Flank	NM_024700	NP_078976	Q8TAD8	SNIP1_HUMAN	Smad nuclear interacting protein	25					production of miRNAs involved in gene silencing by miRNA	nucleus	protein binding			upper_aerodigestive_tract(1)|lung(1)	2		Myeloproliferative disorder(586;0.0393)				ACCACCCCCGCCGGCAGCACC	0.672													7	4	---	---	---	---	PASS
CDC20	991	broad.mit.edu	37	1	43825396	43825396	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43825396G>A	uc001cix.2	+	4	432	c.331G>A	c.(331-333)GAA>AAA	p.E111K	CDC20_uc001ciy.2_Missense_Mutation_p.E111K	NM_001255	NP_001246	Q12834	CDC20_HUMAN	cell division cycle 20	111					activation of anaphase-promoting complex activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of synapse maturation|positive regulation of synaptic plasticity|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle	cytosol|nucleoplasm|spindle	enzyme binding|protein C-terminus binding				0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				TTTATGCCAGGAACATCAGAA	0.502													60	94	---	---	---	---	PASS
CYP4X1	260293	broad.mit.edu	37	1	47504418	47504418	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47504418G>T	uc001cqt.2	+	7	1112	c.862G>T	c.(862-864)GAT>TAT	p.D288Y	CYP4X1_uc001cqr.2_Missense_Mutation_p.D287Y|CYP4X1_uc001cqs.2_Missense_Mutation_p.D223Y	NM_178033	NP_828847	Q8N118	CP4X1_HUMAN	cytochrome P450, family 4, subfamily X,	288						endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding			ovary(1)|skin(1)	2						GGATTTTCTGGATATTGTCCT	0.423													12	25	---	---	---	---	PASS
C1orf173	127254	broad.mit.edu	37	1	75055611	75055611	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75055611T>C	uc001dgg.2	-	12	2099	c.1880A>G	c.(1879-1881)GAT>GGT	p.D627G	uc001dgh.2_Intron|C1orf173_uc001dgi.3_Missense_Mutation_p.D421G	NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	627	Glu-rich.									ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5						TCTTGGCTTATCATTTTCACT	0.453													3	67	---	---	---	---	PASS
EVI5	7813	broad.mit.edu	37	1	92979449	92979449	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92979449C>A	uc001dox.2	-	18	2207	c.2197G>T	c.(2197-2199)GGA>TGA	p.G733*	EVI5_uc010otf.1_Nonsense_Mutation_p.G744*	NM_005665	NP_005656	O60447	EVI5_HUMAN	ecotropic viral integration site 5	733	Targeting to the centrosomes.|Interaction with AURKB and INCENP.				cell cycle|cell division|cell proliferation|multicellular organismal development	microtubule organizing center|nucleus|spindle	protein binding|Rab GTPase activator activity			ovary(1)|breast(1)	2		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)		TCATCATCTCCTATTAAATGG	0.408													4	28	---	---	---	---	PASS
COL11A1	1301	broad.mit.edu	37	1	103355028	103355028	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103355028C>A	uc001dul.2	-	59	4765	c.4447G>T	c.(4447-4449)GGA>TGA	p.G1483*	COL11A1_uc001duk.2_Nonsense_Mutation_p.G679*|COL11A1_uc001dum.2_Nonsense_Mutation_p.G1495*|COL11A1_uc001dun.2_Nonsense_Mutation_p.G1444*|COL11A1_uc009weh.2_Nonsense_Mutation_p.G1367*	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A	1483	Triple-helical region.				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		CCTTTTGCTCCTGGAGATCCT	0.383													24	27	---	---	---	---	PASS
CSF1	1435	broad.mit.edu	37	1	110466223	110466223	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110466223G>T	uc001dyu.2	+	6	1393	c.980G>T	c.(979-981)AGG>ATG	p.R327M	CSF1_uc001dyt.2_Missense_Mutation_p.R327M|CSF1_uc001dyv.3_Intron|CSF1_uc001dyw.3_Missense_Mutation_p.R327M	NM_172212	NP_757351	P09603	CSF1_HUMAN	colony stimulating factor 1 isoform a precursor	327	Lumenal (Potential).				cell proliferation|developmental process involved in reproduction|macrophage differentiation|monocyte activation|osteoclast differentiation|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of cellular protein metabolic process|positive regulation of gene expression|positive regulation of macrophage derived foam cell differentiation|positive regulation of macrophage differentiation|positive regulation of monocyte differentiation|positive regulation of mononuclear cell proliferation|positive regulation of protein kinase activity	extracellular space|integral to membrane|perinuclear region of cytoplasm|plasma membrane|receptor complex	cytokine activity|growth factor activity|macrophage colony-stimulating factor receptor binding|protein homodimerization activity			ovary(1)	1		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Acute lymphoblastic leukemia(138;0.204)		Lung(183;0.0238)|Colorectal(144;0.112)|all cancers(265;0.117)|Epithelial(280;0.127)|LUSC - Lung squamous cell carcinoma(189;0.135)		TCCCCCTCCAGGCCAGGAGGG	0.592											OREG0013645	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	16	22	---	---	---	---	PASS
RBM15	64783	broad.mit.edu	37	1	110888154	110888154	+	Intron	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110888154C>A	uc001dzl.1	+						RBM15_uc001dzm.1_Intron|uc001dzn.1_RNA	NM_022768	NP_073605	Q96T37	RBM15_HUMAN	RNA binding motif protein 15						interspecies interaction between organisms	nucleus	nucleotide binding|protein binding|RNA binding			ovary(3)	3		all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634)		BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135)		TTCTGTCTCTCTCACAGGGTT	0.383			T	MKL1	acute megakaryocytic leukemia								6	126	---	---	---	---	PASS
CTTNBP2NL	55917	broad.mit.edu	37	1	112999425	112999425	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112999425A>T	uc001ebx.2	+	6	1539	c.1311A>T	c.(1309-1311)TTA>TTT	p.L437F	CTTNBP2NL_uc001ebz.2_5'Flank	NM_018704	NP_061174	Q9P2B4	CT2NL_HUMAN	CTTNBP2 N-terminal like	437						actin cytoskeleton	protein binding			central_nervous_system(2)|ovary(1)	3		all_cancers(81;0.00064)|all_epithelial(167;0.000415)|all_lung(203;0.00045)|Lung NSC(69;0.000705)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTAAGCGTTTATTGGGGTCAT	0.552													51	110	---	---	---	---	PASS
THEM4	117145	broad.mit.edu	37	1	151861829	151861829	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151861829C>T	uc001ezj.1	-	3	486	c.307G>A	c.(307-309)GAA>AAA	p.E103K	THEM4_uc001ezk.1_RNA	NM_053055	NP_444283	Q5T1C6	THEM4_HUMAN	thioesterase superfamily member 4	103					insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol|ruffle membrane					0	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			GACATTTGTTCTTCTTTCATA	0.453													21	31	---	---	---	---	PASS
S100A11	6282	broad.mit.edu	37	1	152006196	152006196	+	Silent	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152006196A>G	uc001ezn.2	-	2	204	c.84T>C	c.(82-84)GAT>GAC	p.D28D	uc001ezm.1_Intron	NM_005620	NP_005611	P31949	S10AB_HUMAN	S100 calcium binding protein A11	28	1; low affinity (Potential).|EF-hand 1.				negative regulation of cell proliferation|negative regulation of DNA replication|signal transduction	cytoplasm|nucleus|ruffle	calcium ion binding|calcium-dependent protein binding|protein homodimerization activity|S100 beta binding				0	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)			AGTTATAACCATCCTTTCCAG	0.473													29	50	---	---	---	---	PASS
FLG2	388698	broad.mit.edu	37	1	152328465	152328465	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152328465G>T	uc001ezw.3	-	3	1870	c.1797C>A	c.(1795-1797)GGC>GGA	p.G599G	uc001ezv.2_Intron	NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	599	Ser-rich.						calcium ion binding|structural molecule activity			ovary(10)|skin(5)|upper_aerodigestive_tract(1)|breast(1)	17	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ATTGTCCTGAGCCAGACCCAT	0.522													76	122	---	---	---	---	PASS
YY1AP1	55249	broad.mit.edu	37	1	155657886	155657886	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155657886G>T	uc001fln.2	-	2	178	c.154C>A	c.(154-156)CTC>ATC	p.L52I	YY1AP1_uc010pgi.1_Missense_Mutation_p.L124I|YY1AP1_uc001flh.2_Missense_Mutation_p.L124I|YY1AP1_uc009wqt.2_5'UTR|YY1AP1_uc001flk.2_5'UTR|YY1AP1_uc001fll.2_Intron|YY1AP1_uc009wqv.2_5'UTR|YY1AP1_uc001flm.2_5'UTR|YY1AP1_uc001fli.2_5'UTR|YY1AP1_uc009wqu.2_5'UTR|YY1AP1_uc001flj.2_5'UTR|YY1AP1_uc009wqw.2_5'UTR|YY1AP1_uc001flo.2_Intron|YY1AP1_uc001flp.2_Intron|YY1AP1_uc010pgj.1_Missense_Mutation_p.L52I|YY1AP1_uc009wqx.2_Missense_Mutation_p.L124I|YY1AP1_uc010pgk.1_Missense_Mutation_p.L124I|DAP3_uc001flq.2_5'Flank|DAP3_uc001flr.2_5'Flank|DAP3_uc001fls.2_5'Flank|DAP3_uc010pgl.1_5'Flank|DAP3_uc001flt.2_5'Flank|DAP3_uc001flu.2_5'Flank|DAP3_uc010pgm.1_5'Flank	NM_139118	NP_620829	Q9H869	YYAP1_HUMAN	YY1-associated protein isoform 2	52					regulation of cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding			ovary(2)|skin(1)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					AGAGCGATGAGAGTACAGGGA	0.642													5	35	---	---	---	---	PASS
ARHGEF11	9826	broad.mit.edu	37	1	156926247	156926247	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156926247C>A	uc001fqo.2	-	18	2556	c.1516G>T	c.(1516-1518)GAC>TAC	p.D506Y	ARHGEF11_uc001fqn.2_Missense_Mutation_p.D546Y|ARHGEF11_uc001fqp.1_Missense_Mutation_p.D35Y	NM_014784	NP_055599	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	506					actin cytoskeleton organization|apoptosis|axon guidance|cellular component movement|cytokinesis|establishment of cell polarity|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of cell growth|regulation of Rho protein signal transduction|Rho protein signal transduction|striated muscle contraction	cytosol|Golgi apparatus|plasma membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			ovary(3)|skin(2)|pleura(1)|lung(1)|kidney(1)|pancreas(1)	9	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					AGCCACTTGTCCTTGTCAGGA	0.383													55	33	---	---	---	---	PASS
OR10T2	128360	broad.mit.edu	37	1	158369188	158369188	+	Silent	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158369188C>T	uc010pih.1	-	1	69	c.69G>A	c.(67-69)GAG>GAA	p.E23E		NM_001004475	NP_001004475	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T,	23	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3	all_hematologic(112;0.0378)					GCAGCTGGAGCTCCCCCAGGC	0.478													6	24	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158609362	158609362	+	Intron	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158609362C>A	uc001fst.1	-							NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1						actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					GGGATGCCAACACTACTTACC	0.468													14	86	---	---	---	---	PASS
NUF2	83540	broad.mit.edu	37	1	163295923	163295923	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163295923G>T	uc001gcq.1	+	2	382	c.82G>T	c.(82-84)GGT>TGT	p.G28C	NUF2_uc001gcp.2_Missense_Mutation_p.G28C|NUF2_uc001gcr.1_Missense_Mutation_p.G28C|NUF2_uc009wvc.1_Missense_Mutation_p.G28C	NM_145697	NP_663735	Q9BZD4	NUF2_HUMAN	NUF2, NDC80 kinetochore complex component	28	Interaction with the N-terminus of NDC80.				cell division|chromosome segregation|mitotic prometaphase	condensed chromosome kinetochore|cytosol|Ndc80 complex|nucleus	protein binding			ovary(3)|skin(1)	4	all_hematologic(923;0.101)					AGGAGCTGATGGTAAAAACCT	0.358													5	67	---	---	---	---	PASS
MAEL	84944	broad.mit.edu	37	1	166990397	166990397	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166990397G>T	uc001gdy.1	+	11	1188	c.1117G>T	c.(1117-1119)GGT>TGT	p.G373C	MAEL_uc001gdz.1_Missense_Mutation_p.G342C|MAEL_uc009wvf.1_RNA	NM_032858	NP_116247	Q96JY0	MAEL_HUMAN	maelstrom homolog	373					cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|multicellular organismal development|piRNA metabolic process|spermatogenesis	piP-body	DNA binding			skin(1)	1						CACACCCATTGGTAAGCAACT	0.363													5	42	---	---	---	---	PASS
POU2F1	5451	broad.mit.edu	37	1	167301757	167301757	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167301757G>A	uc001gec.2	+	3	205	c.43G>A	c.(43-45)GGA>AGA	p.G15R	POU2F1_uc010plg.1_RNA|POU2F1_uc001ged.2_5'UTR|POU2F1_uc001gee.2_Missense_Mutation_p.G15R|POU2F1_uc010plh.1_Missense_Mutation_p.G15R|POU2F1_uc001gef.2_Missense_Mutation_p.G27R	NM_002697	NP_002688	P14859	PO2F1_HUMAN	POU class 2 homeobox 1	15					negative regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|skin(2)|breast(1)	5						TATGGAGAGTGGAGATGGCAA	0.373													4	55	---	---	---	---	PASS
CD247	919	broad.mit.edu	37	1	167487640	167487640	+	Intron	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167487640C>T	uc001gei.3	-						CD247_uc001gej.3_Intron|CD247_uc001gek.2_Intron	NM_198053	NP_932170	P20963	CD3Z_HUMAN	T-cell receptor zeta chain isoform 1 precursor						interspecies interaction between organisms|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytoplasm|integral to membrane	protein homodimerization activity|transmembrane receptor activity				0			LUSC - Lung squamous cell carcinoma(543;0.236)			ACACGTCGGCCCTACCTGTAA	0.582													4	30	---	---	---	---	PASS
XCL2	6846	broad.mit.edu	37	1	168511224	168511224	+	Intron	SNP	G	T	T	rs147589659	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168511224G>T	uc001gfn.3	-							NM_003175	NP_003166	Q9UBD3	XCL2_HUMAN	chemokine (C motif) ligand 2 precursor						blood circulation|chemotaxis|immune response|signal transduction	extracellular space	chemokine activity			ovary(1)	1	all_hematologic(923;0.215)					TGAGGAGGCAGACTCACATTA	0.498													7	59	---	---	---	---	PASS
BAT2L2	23215	broad.mit.edu	37	1	171509367	171509367	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171509367C>T	uc010pmg.1	+	16	3022	c.2756C>T	c.(2755-2757)CCT>CTT	p.P919L	BAT2L2_uc010pmh.1_5'UTR	NM_015172	NP_055987	Q9Y520	PRC2C_HUMAN	HBxAg transactivated protein 2	919							protein C-terminus binding				0						GAAAGTCAGCCTTCCCGGAAA	0.453													12	70	---	---	---	---	PASS
PAPPA2	60676	broad.mit.edu	37	1	176564488	176564488	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176564488T>A	uc001gkz.2	+	3	2912	c.1748T>A	c.(1747-1749)CTT>CAT	p.L583H	PAPPA2_uc001gky.1_Missense_Mutation_p.L583H|PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	583	Metalloprotease.				cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16						CGGGTTGTGCTTGTGAACTGT	0.597													74	54	---	---	---	---	PASS
FAM5B	57795	broad.mit.edu	37	1	177247876	177247876	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177247876G>A	uc001glf.2	+	7	1502	c.1190G>A	c.(1189-1191)TGC>TAC	p.C397Y	FAM5B_uc010pna.1_Missense_Mutation_p.C147Y|FAM5B_uc001glg.2_Missense_Mutation_p.C292Y	NM_021165	NP_066988	Q9C0B6	FAM5B_HUMAN	family with sequence similarity 5, member B	397						extracellular region				skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6						TTCAACCTCTGCAAGCGCTGC	0.617													48	48	---	---	---	---	PASS
C1orf125	126859	broad.mit.edu	37	1	179462086	179462086	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179462086G>C	uc001gmo.2	+	20	2515	c.2388G>C	c.(2386-2388)AAG>AAC	p.K796N	C1orf125_uc009wxg.2_RNA|C1orf125_uc001gmp.2_Missense_Mutation_p.K796N|C1orf125_uc009wxh.2_RNA	NM_144696	NP_653297	Q5T1B0	AXDN1_HUMAN	hypothetical protein LOC126859 isoform 1	796											0						ATAAGTTGAAGGTAATAACTC	0.279													26	35	---	---	---	---	PASS
TDRD5	163589	broad.mit.edu	37	1	179632621	179632621	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179632621C>T	uc001gnf.1	+	15	2732	c.2482C>T	c.(2482-2484)CAA>TAA	p.Q828*	TDRD5_uc010pnp.1_Nonsense_Mutation_p.Q882*|TDRD5_uc001gnh.1_Nonsense_Mutation_p.Q383*	NM_173533	NP_775804	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	828					DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|skin(2)|central_nervous_system(1)	5						AAACAGGACTCAAAAGGTAAA	0.348													19	26	---	---	---	---	PASS
SMG7	9887	broad.mit.edu	37	1	183518931	183518931	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183518931G>T	uc001gqg.2	+	19	2978	c.2856G>T	c.(2854-2856)GAG>GAT	p.E952D	SMG7_uc001gqf.2_Missense_Mutation_p.E956D|SMG7_uc001gqh.2_Missense_Mutation_p.E906D|SMG7_uc001gqi.2_Missense_Mutation_p.E864D|SMG7_uc010poc.1_Missense_Mutation_p.E960D	NM_173156	NP_775179	Q92540	SMG7_HUMAN	SMG-7 homolog isoform 1	952	Ser-rich.				mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|intermediate filament cytoskeleton|nucleus	protein phosphatase 2A binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						TGTTCAATGAGGTATATGGGA	0.418													5	85	---	---	---	---	PASS
C1orf26	54823	broad.mit.edu	37	1	185143653	185143653	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185143653A>G	uc001grg.3	+	5	488	c.374A>G	c.(373-375)CAT>CGT	p.H125R	C1orf26_uc001grh.3_Missense_Mutation_p.H125R	NM_001105518	NP_001098988	Q5T5J6	SWT1_HUMAN	hypothetical protein LOC54823	125											0						AAAGACATACATAAATGTGTA	0.328													20	19	---	---	---	---	PASS
PLA2G4A	5321	broad.mit.edu	37	1	186946790	186946790	+	Silent	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186946790T>C	uc001gsc.2	+	16	2035	c.1830T>C	c.(1828-1830)TAT>TAC	p.Y610Y	PLA2G4A_uc010pos.1_Silent_p.Y550Y	NM_024420	NP_077734	P47712	PA24A_HUMAN	cytosolic phospholipase A2, group IVA	610	PLA2c.				phospholipid catabolic process|platelet activating factor biosynthetic process|platelet activation	cytosol|endoplasmic reticulum membrane	calcium ion binding|calcium-dependent phospholipid binding|lysophospholipase activity			lung(2)|breast(1)	3					Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Medrysone(DB00253)|Quinacrine(DB01103)	TTGATCCTTATGTGTTTGATC	0.413													9	66	---	---	---	---	PASS
KIF21B	23046	broad.mit.edu	37	1	200946367	200946367	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200946367T>A	uc001gvs.1	-	31	4615	c.4298A>T	c.(4297-4299)AAT>ATT	p.N1433I	KIF21B_uc001gvr.1_Missense_Mutation_p.N1420I|KIF21B_uc009wzl.1_Missense_Mutation_p.N1433I|KIF21B_uc010ppn.1_Missense_Mutation_p.N1420I	NM_017596	NP_060066	O75037	KI21B_HUMAN	kinesin family member 21B	1433	WD 3.				microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(3)	6						GCGGACGGCATTGCCCGAGGC	0.637													8	75	---	---	---	---	PASS
KDM5B	10765	broad.mit.edu	37	1	202711560	202711560	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202711560A>G	uc001gyf.2	-	18	2664	c.2548T>C	c.(2548-2550)TAT>CAT	p.Y850H	KDM5B_uc009xag.2_Missense_Mutation_p.Y886H|KDM5B_uc001gyg.1_Missense_Mutation_p.Y692H	NM_006618	NP_006609	Q9UGL1	KDM5B_HUMAN	jumonji, AT rich interactive domain 1B	850					negative regulation of transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-trimethyl-K4 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(2)|breast(2)|urinary_tract(1)	5						GGAAGAGCATACAGCTGTGTT	0.433													12	78	---	---	---	---	PASS
PIGR	5284	broad.mit.edu	37	1	207107865	207107865	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207107865G>T	uc001hez.2	-	6	1789	c.1605C>A	c.(1603-1605)ACC>ACA	p.T535T	PIGR_uc009xbz.2_Silent_p.T535T	NM_002644	NP_002635	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor precursor	535	Ig-like V-type 5.|Extracellular (Potential).					extracellular region|integral to plasma membrane	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3						CATCAGCCCTGGTCACCAGGT	0.612													14	62	---	---	---	---	PASS
PIGR	5284	broad.mit.edu	37	1	207107996	207107996	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207107996C>A	uc001hez.2	-	6	1658	c.1474G>T	c.(1474-1476)GAG>TAG	p.E492*	PIGR_uc009xbz.2_Nonsense_Mutation_p.E492*	NM_002644	NP_002635	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor precursor	492	Ig-like V-type 5.|Extracellular (Potential).					extracellular region|integral to plasma membrane	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3						CAGTATTTCTCGTACGAGGAG	0.562													4	44	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	215848148	215848148	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215848148C>A	uc001hku.1	-	63	13492	c.13105G>T	c.(13105-13107)GCC>TCC	p.A4369S		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	4369	Extracellular (Potential).|Fibronectin type-III 29.				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ATTTGAGTGGCACTGACGGCC	0.483										HNSCC(13;0.011)			22	22	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	215848713	215848713	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215848713G>T	uc001hku.1	-	63	12927	c.12540C>A	c.(12538-12540)AAC>AAA	p.N4180K		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	4180	Extracellular (Potential).|Fibronectin type-III 27.				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TTCCATTTGGGTTAACAGGCT	0.488										HNSCC(13;0.011)			29	56	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	216405331	216405331	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216405331T>A	uc001hku.1	-	14	3344	c.2957A>T	c.(2956-2958)AAA>ATA	p.K986I	USH2A_uc001hkv.2_Missense_Mutation_p.K986I	NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	986	Extracellular (Potential).|Laminin EGF-like 9.				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GTAATGGTCTTTGCATTGGTC	0.393										HNSCC(13;0.011)			21	137	---	---	---	---	PASS
OBSCN	84033	broad.mit.edu	37	1	228437810	228437810	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228437810G>T	uc009xez.1	+	14	4222	c.4178G>T	c.(4177-4179)AGC>ATC	p.S1393I	OBSCN_uc001hsn.2_Missense_Mutation_p.S1393I	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	1393	Poly-Ser.|Ig-like 14.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)				CTGAGCTCCAGCTCGAAAGTT	0.672													6	84	---	---	---	---	PASS
KIAA1804	84451	broad.mit.edu	37	1	233507859	233507859	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233507859G>T	uc001hvt.3	+	6	1889	c.1628G>T	c.(1627-1629)AGT>ATT	p.S543I	KIAA1804_uc001hvs.1_Missense_Mutation_p.S543I	NM_032435	NP_115811	Q5TCX8	M3KL4_HUMAN	mixed lineage kinase 4	543					activation of JUN kinase activity|protein autophosphorylation		ATP binding|MAP kinase kinase kinase activity|protein homodimerization activity			lung(5)|central_nervous_system(2)|skin(1)	8		all_cancers(173;0.000405)|all_epithelial(177;0.0345)|Prostate(94;0.122)				AGCAGTTCCAGTCCCCCGAGC	0.567													5	45	---	---	---	---	PASS
FMN2	56776	broad.mit.edu	37	1	240372043	240372043	+	Intron	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240372043A>T	uc010pyd.1	+						FMN2_uc010pye.1_Intron	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2						actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			GTAACATGAAAGTGAGCTCGT	0.413													28	43	---	---	---	---	PASS
RGS7	6000	broad.mit.edu	37	1	240969634	240969634	+	Intron	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240969634G>T	uc001hyv.2	-						RGS7_uc010pyh.1_Intron|RGS7_uc010pyj.1_Intron|RGS7_uc001hyu.2_Intron|RGS7_uc009xgn.1_Intron|RGS7_uc001hyw.2_Intron|RGS7_uc001hyt.2_Intron	NM_002924	NP_002915	P49802	RGS7_HUMAN	regulator of G-protein signaling 7						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			AATCTATGCAGAATGTGAGAT	0.468													7	39	---	---	---	---	PASS
RGS7	6000	broad.mit.edu	37	1	240969638	240969638	+	Intron	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240969638G>T	uc001hyv.2	-						RGS7_uc010pyh.1_Intron|RGS7_uc010pyj.1_Intron|RGS7_uc001hyu.2_Intron|RGS7_uc009xgn.1_Intron|RGS7_uc001hyw.2_Intron|RGS7_uc001hyt.2_Intron	NM_002924	NP_002915	P49802	RGS7_HUMAN	regulator of G-protein signaling 7						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			TATGCAGAATGTGAGATCGGG	0.453													14	27	---	---	---	---	PASS
WDR64	128025	broad.mit.edu	37	1	241901793	241901793	+	Splice_Site	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241901793T>C	uc001hze.1	+	10	1498	c.1291_splice	c.e10+2	p.G431_splice	WDR64_uc001hzf.1_Splice_Site_p.G151_splice			B1ANS9	WDR64_HUMAN	RecName: Full=WD repeat-containing protein 64;											skin(1)	1	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			TTATTACGGGTAAGTGTACCC	0.368													7	27	---	---	---	---	PASS
ZNF670	93474	broad.mit.edu	37	1	247202712	247202712	+	Splice_Site	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247202712C>A	uc001icd.1	-	2	301	c.130_splice	c.e2+1	p.G44_splice	ZNF695_uc001ica.2_Intron|ZNF695_uc001icb.1_Intron	NM_033213	NP_149990	Q9BS34	ZN670_HUMAN	zinc finger protein 670						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00427)			GTTATTCTTACCTACAGAAGC	0.313													13	35	---	---	---	---	PASS
VN1R5	317705	broad.mit.edu	37	1	247419472	247419472	+	Silent	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247419472T>A	uc010pyu.1	+	1	99	c.99T>A	c.(97-99)CCT>CCA	p.P33P		NM_173858	NP_776257	Q7Z5H4	VN1R5_HUMAN	vomeronasal 1 receptor 5	33	Cytoplasmic (Potential).				response to pheromone	integral to membrane|plasma membrane	pheromone receptor activity				0	all_cancers(71;5.7e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)	all_cancers(173;0.0314)	OV - Ovarian serous cystadenocarcinoma(106;0.00854)			TTAATTTTCCTTCTAAGATGA	0.333													7	58	---	---	---	---	PASS
OR2C3	81472	broad.mit.edu	37	1	247695176	247695176	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247695176C>A	uc009xgy.2	-	2	1000	c.638G>T	c.(637-639)GGG>GTG	p.G213V	C1orf150_uc009xgw.2_Intron|C1orf150_uc001ida.3_Intron|C1orf150_uc001idb.3_Intron|C1orf150_uc009xgx.2_Intron|LOC148824_uc001idd.2_5'Flank	NM_198074	NP_932340	Q8N628	OR2C3_HUMAN	olfactory receptor, family 2, subfamily C,	213	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0242)	OV - Ovarian serous cystadenocarcinoma(106;0.0241)			CAGGATGAGCCCCAGAGGCAG	0.547													26	18	---	---	---	---	PASS
OR13G1	441933	broad.mit.edu	37	1	247835814	247835814	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247835814T>A	uc001idi.1	-	1	530	c.530A>T	c.(529-531)GAG>GTG	p.E177V		NM_001005487	NP_001005487	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G,	177	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			TGGGGGTATCTCACAGAAGAA	0.468													17	83	---	---	---	---	PASS
OR2M2	391194	broad.mit.edu	37	1	248343551	248343551	+	Silent	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248343551C>A	uc010pzf.1	+	1	264	c.264C>A	c.(262-264)GGC>GGA	p.G88G		NM_001004688	NP_001004688	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M,	88	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|skin(1)	4	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			ACCTGTCTGGCAGCAAGTCCA	0.478													21	171	---	---	---	---	PASS
OR2M3	127062	broad.mit.edu	37	1	248366465	248366465	+	Silent	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248366465G>C	uc010pzg.1	+	1	96	c.96G>C	c.(94-96)CTG>CTC	p.L32L		NM_001004689	NP_001004689	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M,	32	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			TTCTGGTCCTGGCCATCTTTT	0.532													25	125	---	---	---	---	PASS
OR2T4	127074	broad.mit.edu	37	1	248525048	248525048	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248525048C>A	uc001ieh.1	+	1	166	c.166C>A	c.(166-168)CCA>ACA	p.P56T		NM_001004696	NP_001004696	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T,	56	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ATCCAAACATCCAGCACTACT	0.483													15	102	---	---	---	---	PASS
OR2T4	127074	broad.mit.edu	37	1	248525049	248525049	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248525049C>T	uc001ieh.1	+	1	167	c.167C>T	c.(166-168)CCA>CTA	p.P56L		NM_001004696	NP_001004696	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T,	56	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCCAAACATCCAGCACTACTT	0.483													15	103	---	---	---	---	PASS
OR2T3	343173	broad.mit.edu	37	1	248637406	248637406	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248637406T>C	uc001iel.1	+	1	755	c.755T>C	c.(754-756)ATA>ACA	p.I252T		NM_001005495	NP_001005495	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T,	252	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CACATGATCATAGTGCTGCTG	0.547													42	111	---	---	---	---	PASS
MYT1L	23040	broad.mit.edu	37	2	1926334	1926334	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1926334C>A	uc002qxe.2	-	10	2034	c.1207G>T	c.(1207-1209)GAT>TAT	p.D403Y	MYT1L_uc002qxd.2_Missense_Mutation_p.D403Y|MYT1L_uc010ewl.1_RNA	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	403					cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		TGACACCCATCCTCCTTCGCA	0.582													7	50	---	---	---	---	PASS
NBAS	51594	broad.mit.edu	37	2	15374743	15374743	+	Silent	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15374743C>A	uc002rcc.1	-	46	6098	c.6072G>T	c.(6070-6072)GTG>GTT	p.V2024V	NBAS_uc002rcb.1_5'UTR|NBAS_uc010exl.1_Silent_p.V1096V|NBAS_uc002rcd.1_RNA	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein	2024										ovary(2)|liver(1)|skin(1)	4						GGCCAACTGCCACCTCTAGCA	0.433													6	29	---	---	---	---	PASS
MATN3	4148	broad.mit.edu	37	2	20206074	20206074	+	Intron	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20206074G>T	uc002rdl.2	-						MATN3_uc010exu.1_Intron	NM_002381	NP_002372	O15232	MATN3_HUMAN	matrilin 3 precursor						skeletal system development	proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCAAACACCTGCAAAAGACCA	0.478													7	15	---	---	---	---	PASS
CAD	790	broad.mit.edu	37	2	27454372	27454372	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27454372C>T	uc002rji.2	+	16	2486	c.2324C>T	c.(2323-2325)GCC>GTC	p.A775V	CAD_uc010eyw.2_Missense_Mutation_p.A712V	NM_004341	NP_004332	P27708	PYR1_HUMAN	carbamoylphosphate synthetase 2/aspartate	775	CPSase (Carbamoyl-phosphate synthase).|CPSase A.				'de novo' pyrimidine base biosynthetic process|drug metabolic process|glutamine metabolic process|peptidyl-threonine phosphorylation|protein autophosphorylation|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide biosynthetic process	cytosol|neuronal cell body|nuclear matrix|terminal button	aspartate binding|aspartate carbamoyltransferase activity|ATP binding|carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity|dihydroorotase activity|enzyme binding|identical protein binding|metal ion binding|protein kinase activity			ovary(4)|large_intestine(2)|kidney(2)|lung(1)|pancreas(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				L-Aspartic Acid(DB00128)|L-Glutamine(DB00130)	TTTGAGGAGGCCTTCCAGAAG	0.547													5	28	---	---	---	---	PASS
C2orf16	84226	broad.mit.edu	37	2	27799968	27799968	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27799968A>C	uc002rkz.3	+	1	580	c.529A>C	c.(529-531)AAA>CAA	p.K177Q		NM_032266	NP_115642	Q68DN1	CB016_HUMAN	hypothetical protein LOC84226	177										large_intestine(1)	1	Acute lymphoblastic leukemia(172;0.155)					TACTGTAGAGAAATCTGTGGG	0.418													5	46	---	---	---	---	PASS
SUPT7L	9913	broad.mit.edu	37	2	27876565	27876565	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27876565C>T	uc002rlh.1	-	6	1375	c.1032G>A	c.(1030-1032)ATG>ATA	p.M344I	SUPT7L_uc002rli.1_Missense_Mutation_p.M344I|SUPT7L_uc010ymf.1_Missense_Mutation_p.M209I|SUPT7L_uc002rlj.1_Missense_Mutation_p.M342I|SUPT7L_uc010ezh.1_Missense_Mutation_p.M342I	NM_014860	NP_055675	O94864	ST65G_HUMAN	SPTF-associated factor 65 gamma	344					histone H3 acetylation|maintenance of protein location in nucleus|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			skin(2)	2	Acute lymphoblastic leukemia(172;0.155)					CTTGAGGCTCCATTTTCACAT	0.483													86	133	---	---	---	---	PASS
CLIP4	79745	broad.mit.edu	37	2	29404610	29404610	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29404610G>A	uc002rmv.2	+	16	2208	c.1969G>A	c.(1969-1971)GAG>AAG	p.E657K	CLIP4_uc002rmw.2_RNA	NM_024692	NP_078968	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family,	657	CAP-Gly 3.									ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)					GCTTGGACTTGAGCTCCGAAG	0.537													28	54	---	---	---	---	PASS
ABCG8	64241	broad.mit.edu	37	2	44078879	44078879	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44078879A>G	uc002rtq.2	+	4	569	c.479A>G	c.(478-480)AAC>AGC	p.N160S	ABCG8_uc010yoa.1_Missense_Mutation_p.N160S	NM_022437	NP_071882	Q9H221	ABCG8_HUMAN	ATP-binding cassette sub-family G member 8	160	ABC transporter.|Cytoplasmic (Potential).				cholesterol efflux|cholesterol homeostasis|excretion|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			skin(3)|ovary(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				CTGCTCCCCAACTTGACTGTG	0.602													10	83	---	---	---	---	PASS
SIX2	10736	broad.mit.edu	37	2	45235678	45235678	+	Intron	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45235678A>T	uc002ruo.2	-						SIX2_uc002rup.2_Intron	NM_016932	NP_058628	Q9NPC8	SIX2_HUMAN	SIX homeobox 2							nucleus	sequence-specific DNA binding transcription factor activity			pancreas(1)	1		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				AAGAAGGTCTACTTACTCGTA	0.701													15	18	---	---	---	---	PASS
SRBD1	55133	broad.mit.edu	37	2	45616719	45616719	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45616719G>T	uc002rus.2	-	21	2794	c.2718C>A	c.(2716-2718)TTC>TTA	p.F906L	SRBD1_uc010yoc.1_Missense_Mutation_p.F425L	NM_018079	NP_060549	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1	906					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		hydrolase activity, acting on ester bonds|RNA binding			central_nervous_system(1)	1		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)			TGCTTCTCTTGAAATCAGGTT	0.353													7	37	---	---	---	---	PASS
USP34	9736	broad.mit.edu	37	2	61546343	61546343	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61546343C>A	uc002sbe.2	-	22	3155	c.3133G>T	c.(3133-3135)GGT>TGT	p.G1045C		NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	1045					positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			GTTTCCATACCCATAGCATGT	0.333													15	39	---	---	---	---	PASS
DCTN1	1639	broad.mit.edu	37	2	74593124	74593124	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74593124C>T	uc002skx.2	-	24	3093	c.2782G>A	c.(2782-2784)GCT>ACT	p.A928T	SLC4A5_uc002skl.2_5'Flank|DCTN1_uc002skt.1_5'Flank|DCTN1_uc002skv.2_Missense_Mutation_p.A794T|DCTN1_uc002sku.2_Missense_Mutation_p.A794T|DCTN1_uc002skw.1_Missense_Mutation_p.A904T|DCTN1_uc010ffd.2_Missense_Mutation_p.A908T|DCTN1_uc002sky.2_Missense_Mutation_p.A891T	NM_004082	NP_004073	Q14203	DCTN1_HUMAN	dynactin 1 isoform 1	928					cell death|G2/M transition of mitotic cell cycle|mitosis|nervous system development	centrosome|cytosol|kinetochore|microtubule|spindle pole	motor activity|protein binding			ovary(3)|skin(2)	5						AGGGCAGCAGCCCGCAGTTCA	0.512													21	25	---	---	---	---	PASS
REG3A	5068	broad.mit.edu	37	2	79384706	79384706	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79384706C>T	uc002sod.1	-	4	707	c.452G>A	c.(451-453)AGA>AAA	p.R151K	REG3A_uc002soe.1_Missense_Mutation_p.R151K|REG3A_uc002sof.1_Missense_Mutation_p.R151K	NM_138938	NP_620355	Q06141	REG3A_HUMAN	pancreatitis-associated protein precursor	151	C-type lectin.				acute-phase response|cell proliferation|heterophilic cell-cell adhesion|multicellular organismal development	cytoplasm|extracellular space|soluble fraction	sugar binding			skin(1)	1						ACCTGTGCTTCTCGACAGGCT	0.517													7	84	---	---	---	---	PASS
CTNNA2	1496	broad.mit.edu	37	2	80096942	80096942	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80096942G>T	uc010ysh.1	+	4	471	c.466G>T	c.(466-468)GTG>TTG	p.V156L	CTNNA2_uc010yse.1_Missense_Mutation_p.V156L|CTNNA2_uc010ysf.1_Missense_Mutation_p.V156L|CTNNA2_uc010ysg.1_Missense_Mutation_p.V156L	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1	156					axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9						ACCACTGCAGGTGGAAGAGGC	0.353													18	52	---	---	---	---	PASS
LRRTM1	347730	broad.mit.edu	37	2	80530054	80530054	+	Silent	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80530054G>C	uc002sok.1	-	2	1161	c.891C>G	c.(889-891)CCC>CCG	p.P297P	CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron|CTNNA2_uc010ysh.1_Intron|CTNNA2_uc010ysi.1_5'Flank|LRRTM1_uc002soj.3_RNA	NM_178839	NP_849161	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	297	LRR 9.|Lumenal (Potential).					axon|endoplasmic reticulum membrane|growth cone|integral to membrane				ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5						TGAGGATCCGGGGCTCGATGT	0.622										HNSCC(69;0.2)			5	26	---	---	---	---	PASS
PTCD3	55037	broad.mit.edu	37	2	86359468	86359468	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86359468G>A	uc002sqw.2	+	17	1360	c.1294G>A	c.(1294-1296)GCC>ACC	p.A432T	PTCD3_uc002sqx.1_Missense_Mutation_p.A22T	NM_017952	NP_060422	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3 precursor	432	PPR 7.					mitochondrion	protein binding			ovary(1)	1						TCTAGAACTTGCCTACCAAGT	0.378													27	100	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	89416871	89416871	+	RNA	SNP	A	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89416871A>C	uc010ytr.1	-	42		c.4731T>G			uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																		TAAGTTGCAAAATCTTCAGGC	0.507													28	73	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	90078209	90078209	+	RNA	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90078209G>C	uc010fhm.2	+	14		c.1599G>C								Parts of antibodies, mostly variable regions.																		TCCCAGACAGGTTCAGTGGCA	0.547													18	42	---	---	---	---	PASS
SLC5A7	60482	broad.mit.edu	37	2	108608572	108608572	+	Silent	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108608572C>T	uc002tdv.2	+	3	465	c.189C>T	c.(187-189)GTC>GTT	p.V63V	SLC5A7_uc010ywm.1_5'UTR|SLC5A7_uc010fjj.2_Silent_p.V63V|SLC5A7_uc010ywn.1_5'UTR	NM_021815	NP_068587	Q9GZV3	SC5A7_HUMAN	solute carrier family 5 (choline transporter),	63	Helical; (Potential).				acetylcholine biosynthetic process|neurotransmitter secretion	integral to membrane|plasma membrane	choline:sodium symporter activity			ovary(2)|central_nervous_system(1)|skin(1)	4					Choline(DB00122)	CTACCTGGGTCGGAGGAGGGT	0.368													20	38	---	---	---	---	PASS
GLI2	2736	broad.mit.edu	37	2	121708906	121708906	+	Silent	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121708906C>T	uc010flp.2	+	3	372	c.342C>T	c.(340-342)CCC>CCT	p.P114P	GLI2_uc010yyu.1_Silent_p.P114P|GLI2_uc002tmq.1_Intron|GLI2_uc002tmr.1_Intron|GLI2_uc002tmt.3_Intron|GLI2_uc002tmu.3_Intron|GLI2_uc002tmv.1_Intron|GLI2_uc010flo.1_5'UTR|GLI2_uc002tmw.1_Silent_p.P114P	NM_005270	NP_005261	P10070	GLI2_HUMAN	GLI-Kruppel family member GLI2	114					axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)				GGGAGTCCCCCTTCAACGCCC	0.657													12	32	---	---	---	---	PASS
CNTNAP5	129684	broad.mit.edu	37	2	125405330	125405330	+	Intron	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125405330G>T	uc002tno.2	+						CNTNAP5_uc010flu.2_Intron	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		GTGTTGTCTGGGCAGAGGACA	0.512													4	15	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141245278	141245278	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141245278C>A	uc002tvj.1	-	58	10123	c.9151G>T	c.(9151-9153)GAT>TAT	p.D3051Y		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	3051	Extracellular (Potential).				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TCTCTGTAATCAAAGTCTATA	0.299										TSP Lung(27;0.18)			10	27	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141260667	141260667	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141260667G>T	uc002tvj.1	-	54	9499	c.8527C>A	c.(8527-8529)CGA>AGA	p.R2843R		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	2843	Extracellular (Potential).				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CCACACTGTCGATATCCTAGA	0.398										TSP Lung(27;0.18)			9	27	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141806660	141806660	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141806660C>T	uc002tvj.1	-	11	2656	c.1684G>A	c.(1684-1686)GAC>AAC	p.D562N	LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	562	Extracellular (Potential).				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GCGTGAAAGTCTAAAGCACGA	0.438										TSP Lung(27;0.18)			14	89	---	---	---	---	PASS
ZEB2	9839	broad.mit.edu	37	2	145157345	145157345	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145157345G>T	uc002tvu.2	-	8	1889	c.1409C>A	c.(1408-1410)ACT>AAT	p.T470N	ZEB2_uc002tvv.2_Missense_Mutation_p.T464N|ZEB2_uc010zbm.1_Missense_Mutation_p.T441N|ZEB2_uc010fnp.2_Intron|ZEB2_uc010fnq.1_Missense_Mutation_p.T499N	NM_014795	NP_055610	O60315	ZEB2_HUMAN	zinc finger homeobox 1b	470	SMAD-MH2 binding domain (By similarity).					cytoplasm|nucleolus	phosphatase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|SMAD binding|zinc ion binding			ovary(5)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.112)		CCTGGAAACAGTATTGTCCAC	0.418													9	53	---	---	---	---	PASS
MBD5	55777	broad.mit.edu	37	2	149227994	149227994	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149227994A>T	uc002twm.3	+	9	3470	c.2482A>T	c.(2482-2484)ATT>TTT	p.I828F	MBD5_uc010zbs.1_RNA|MBD5_uc010fns.2_Missense_Mutation_p.I828F|MBD5_uc002twn.1_Missense_Mutation_p.I269F	NM_018328	NP_060798	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	828						chromosome|nucleus	chromatin binding|DNA binding			skin(3)|ovary(2)	5				BRCA - Breast invasive adenocarcinoma(221;0.0569)		ACCAAACAGCATTGTTAGCAG	0.378													5	30	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152385743	152385743	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152385743G>T	uc010fnx.2	-	118	16804	c.16613C>A	c.(16612-16614)GCC>GAC	p.A5538D	NEB_uc002txr.2_Missense_Mutation_p.A1961D|NEB_uc002txt.3_Missense_Mutation_p.A43D	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	5538	Nebulin 151.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		GACTTTGTAGGCGTCCTTGGC	0.438													10	49	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152402505	152402505	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152402505T>A	uc010fnx.2	-	107	15562	c.15371A>T	c.(15370-15372)TAC>TTC	p.Y5124F	NEB_uc002txr.2_Missense_Mutation_p.Y1547F	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	5124					muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		AGTGTATAGGTAATTAGACTT	0.338													3	4	---	---	---	---	PASS
SCN1A	6323	broad.mit.edu	37	2	166848156	166848156	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166848156C>T	uc010zcz.1	-	26	5614	c.5596G>A	c.(5596-5598)GGA>AGA	p.G1866R		NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha	1877						voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|skin(6)|large_intestine(1)	13					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)	CCACTCTCTCCTAGAACCCGC	0.458													19	46	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	167760089	167760089	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167760089T>A	uc002udx.2	+	1	115	c.97T>A	c.(97-99)TGT>AGT	p.C33S	XIRP2_uc010fpn.2_Missense_Mutation_p.C33S|XIRP2_uc010fpo.2_Missense_Mutation_p.C33S|XIRP2_uc010fpp.2_Missense_Mutation_p.C33S	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	Error:Variant_position_missing_in_A4UGR9_after_alignment					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						GGACAGCCATTGTACAATTTT	0.488													4	27	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	168115219	168115219	+	3'UTR	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168115219C>A	uc002udx.2	+	10					XIRP2_uc010fpn.2_Nonsense_Mutation_p.C754*|XIRP2_uc010fpo.2_Nonsense_Mutation_p.C721*|XIRP2_uc010fpp.2_Nonsense_Mutation_p.C721*|XIRP2_uc010fpq.2_3'UTR|XIRP2_uc010fpr.2_Nonsense_Mutation_p.C499*	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1						actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						TGAATAATTGCAGGCAGAAGA	0.294													9	28	---	---	---	---	PASS
LASS6	253782	broad.mit.edu	37	2	169626093	169626093	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169626093C>A	uc002ueb.1	+	10	1200	c.1076C>A	c.(1075-1077)CCC>CAC	p.P359H	LASS6_uc002uec.1_Missense_Mutation_p.P367H	NM_203463	NP_982288	Q6ZMG9	CERS6_HUMAN	longevity assurance homolog 6	359	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			skin(1)	1						GGAAAGAATCCCCACACTGCG	0.493													6	45	---	---	---	---	PASS
LRP2	4036	broad.mit.edu	37	2	170175293	170175293	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170175293A>T	uc002ues.2	-	3	502	c.289T>A	c.(289-291)TCA>ACA	p.S97T	LRP2_uc010zdf.1_Missense_Mutation_p.S97T	NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	97	LDL-receptor class A 2.|Extracellular (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	CGTTCATCTGAGCCATCATCA	0.478													9	61	---	---	---	---	PASS
NFE2L2	4780	broad.mit.edu	37	2	178098804	178098804	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178098804C>T	uc002ulh.3	-	2	796	c.241G>A	c.(241-243)GGT>AGT	p.G81S	NFE2L2_uc002ulg.3_Missense_Mutation_p.G65S|NFE2L2_uc010zfa.1_Missense_Mutation_p.G65S|NFE2L2_uc002uli.3_Missense_Mutation_p.G65S|NFE2L2_uc010fra.2_Missense_Mutation_p.G65S|NFE2L2_uc010frb.2_Missense_Mutation_p.G65S	NM_006164	NP_006155	Q16236	NF2L2_HUMAN	nuclear factor erythroid 2-like 2 isoform 1	81					transcription from RNA polymerase II promoter	centrosome|cytosol|nucleus|plasma membrane	protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			AGAAATTCACCTGTCTCTTCA	0.438			Mis		NSCLC|HNSCC					HNSCC(56;0.16)			12	29	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179426284	179426284	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179426284T>C	uc010zfg.1	-	275	77095	c.76871A>G	c.(76870-76872)GAG>GGG	p.E25624G	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.E19319G|TTN_uc010zfi.1_Missense_Mutation_p.E19252G|TTN_uc010zfj.1_Missense_Mutation_p.E19127G	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	26551							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCTTTATACTCAAGATGATA	0.403													7	25	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179472319	179472319	+	Missense_Mutation	SNP	C	T	T	rs72646808	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179472319C>T	uc010zfg.1	-	226	45616	c.45392G>A	c.(45391-45393)CGC>CAC	p.R15131H	uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.R8826H|TTN_uc010zfi.1_Missense_Mutation_p.R8759H|TTN_uc010zfj.1_Missense_Mutation_p.R8634H	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	16058							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGGTACAGGGCGACCAGTCAC	0.448													24	161	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179553856	179553856	+	Silent	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179553856A>T	uc010zfg.1	-	122	28511	c.28287T>A	c.(28285-28287)GCT>GCA	p.A9429A	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Silent_p.A6090A|TTN_uc010fre.1_Silent_p.A540A	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	10356							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTTAGGCAGAGCTGGCACTT	0.458													8	51	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179581848	179581848	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179581848G>T	uc010zfg.1	-	85	22105	c.21881C>A	c.(21880-21882)TCT>TAT	p.S7294Y	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.S3955Y	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	8221							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGCAGAACAAGAGTCTTTTCC	0.448													7	26	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179590510	179590510	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179590510T>C	uc010zfg.1	-	67	17031	c.16807A>G	c.(16807-16809)ACT>GCT	p.T5603A	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.T2264A	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	6530							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AATTTTACAGTACAAACACAA	0.378													7	73	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179598616	179598616	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179598616G>T	uc010zfg.1	-	50	11992	c.11768C>A	c.(11767-11769)CCT>CAT	p.P3923H	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.P584H	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	4850							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAAGGTTGGAGGTTCTAGTTA	0.368													12	32	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179616020	179616020	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179616020G>T	uc002unb.2	-	46	11331	c.11107C>A	c.(11107-11109)CAA>AAA	p.Q3703K	TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron	NM_133379	NP_596870	Q8WZ42	TITIN_HUMAN	titin isoform novex-3	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTAAACGTTGCAACTTCACT	0.343													11	51	---	---	---	---	PASS
CWC22	57703	broad.mit.edu	37	2	180815259	180815259	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180815259C>A	uc010frh.1	-	19	2420	c.2120G>T	c.(2119-2121)AGT>ATT	p.S707I	CWC22_uc002uno.2_Missense_Mutation_p.S229I|CWC22_uc002unp.2_Missense_Mutation_p.S707I	NM_020943	NP_065994	Q9HCG8	CWC22_HUMAN	CWC22 spliceosome-associated protein homolog	707	Ser-rich.					catalytic step 2 spliceosome	protein binding|RNA binding				0						GCTATGACTACTGATGGATGA	0.408													5	14	---	---	---	---	PASS
SSFA2	6744	broad.mit.edu	37	2	182787078	182787078	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182787078C>T	uc002uoi.2	+	16	3936	c.3614C>T	c.(3613-3615)CCA>CTA	p.P1205L	SSFA2_uc002uoh.2_Missense_Mutation_p.P1205L|SSFA2_uc002uoj.2_Missense_Mutation_p.P1183L|SSFA2_uc002uok.2_RNA|SSFA2_uc010zfo.1_Missense_Mutation_p.P1030L|SSFA2_uc002uol.2_Missense_Mutation_p.P1052L|SSFA2_uc002uom.2_Missense_Mutation_p.P669L	NM_001130445	NP_001123917	P28290	SSFA2_HUMAN	sperm specific antigen 2 isoform 1	1205						cytoplasm|plasma membrane	actin binding			breast(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			CCATCAATGCCAGCTGCTGAG	0.443													6	32	---	---	---	---	PASS
FRZB	2487	broad.mit.edu	37	2	183699610	183699610	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183699610C>A	uc002upa.1	-	6	1162	c.944G>T	c.(943-945)GGC>GTC	p.G315V		NM_001463	NP_001454	Q92765	SFRP3_HUMAN	frizzled-related protein precursor	315	Ser-rich.				brain development|cochlea morphogenesis|gonad development|mammary gland involution|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cartilage development|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of hepatocyte differentiation|positive regulation of apoptosis|positive regulation of fat cell differentiation|skeletal system development|vasculature development|Wnt receptor signaling pathway	cytoplasm|extracellular space|membrane	PDZ domain binding|Wnt receptor activity|Wnt-protein binding			ovary(2)|lung(1)|central_nervous_system(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.109)|Epithelial(96;0.231)			CGAGTTCCTGCCAGACTTCTG	0.433													17	46	---	---	---	---	PASS
SLC39A10	57181	broad.mit.edu	37	2	196599666	196599666	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196599666G>T	uc002utg.3	+	10	2611	c.2397G>T	c.(2395-2397)GGG>GGT	p.G799G	SLC39A10_uc002uth.3_Silent_p.G799G|SLC39A10_uc010zgp.1_Silent_p.G349G	NM_001127257	NP_001120729	Q9ULF5	S39AA_HUMAN	solute carrier family 39 (zinc transporter),	799					zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			pancreas(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.221)			GTCCTGTGGGGCAATTCATCC	0.363													31	65	---	---	---	---	PASS
DNAH7	56171	broad.mit.edu	37	2	196619071	196619071	+	Silent	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196619071A>T	uc002utj.3	-	63	11855	c.11754T>A	c.(11752-11754)CCT>CCA	p.P3918P	DNAH7_uc002uti.3_Silent_p.P401P	NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3918					ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12						CATCCTCAGGAGGATGCTTGT	0.438													16	45	---	---	---	---	PASS
HECW2	57520	broad.mit.edu	37	2	197194300	197194300	+	Silent	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197194300T>A	uc002utm.1	-	5	753	c.570A>T	c.(568-570)TCA>TCT	p.S190S	HECW2_uc002utl.1_5'UTR	NM_020760	NP_065811	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin	190	C2.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18						CATTCTTACCTGACAATGTAA	0.398													15	59	---	---	---	---	PASS
RFTN2	130132	broad.mit.edu	37	2	198495730	198495730	+	Intron	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198495730C>G	uc002uuo.3	-							NM_144629	NP_653230	Q52LD8	RFTN2_HUMAN	raftlin family member 2							plasma membrane					0						TAACATAAAACTTACCTTTAG	0.308													7	24	---	---	---	---	PASS
PLCL1	5334	broad.mit.edu	37	2	198949214	198949214	+	Nonsense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198949214A>T	uc010fsp.2	+	2	1264	c.973A>T	c.(973-975)AAA>TAA	p.K325*	PLCL1_uc002uuv.3_Nonsense_Mutation_p.K246*	NM_001114661	NP_001108133	Q15111	PLCL1_HUMAN	RecName: Full=Inactive phospholipase C-like protein 1;          Short=PLC-L1; AltName: Full=Phospholipase C-deleted in lung carcinoma; AltName: Full=Phospholipase C-related but catalytically inactive protein;          Short=PRIP;	325					intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|skin(1)	2					Quinacrine(DB01103)	ACAGATATCTAAAAACAAAGA	0.398													15	46	---	---	---	---	PASS
C2orf69	205327	broad.mit.edu	37	2	200789838	200789838	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200789838G>T	uc010zhb.1	+	2	570	c.387G>T	c.(385-387)TGG>TGT	p.W129C		NM_153689	NP_710156	Q8N8R5	CB069_HUMAN	hypothetical protein LOC205327 precursor	129						extracellular region				central_nervous_system(1)	1						GGGAAAACTGGAGTCTAGAAA	0.343													4	26	---	---	---	---	PASS
ZDBF2	57683	broad.mit.edu	37	2	207176006	207176006	+	Nonsense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207176006A>T	uc002vbp.2	+	5	7004	c.6754A>T	c.(6754-6756)AAA>TAA	p.K2252*		NM_020923	NP_065974	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	2252	Poly-Lys.						nucleic acid binding|zinc ion binding			ovary(3)	3						TCTGAAGAAGAAAAAATCTGT	0.413													8	12	---	---	---	---	PASS
PIKFYVE	200576	broad.mit.edu	37	2	209163433	209163433	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209163433C>T	uc002vcz.2	+	8	1138	c.980C>T	c.(979-981)TCT>TTT	p.S327F	PIKFYVE_uc010fun.1_Missense_Mutation_p.S8F|PIKFYVE_uc002vcy.1_Missense_Mutation_p.S327F|PIKFYVE_uc002vcv.2_Missense_Mutation_p.S230F|PIKFYVE_uc002vcw.2_Missense_Mutation_p.S327F|PIKFYVE_uc002vcx.2_Missense_Mutation_p.S241F	NM_015040	NP_055855	Q9Y2I7	FYV1_HUMAN	phosphatidylinositol-3-phosphate 5-kinase type	327					cellular protein metabolic process|intracellular signal transduction|protein localization to nucleus|retrograde transport, endosome to Golgi	early endosome membrane|membrane raft	1-phosphatidylinositol-3-phosphate 5-kinase activity|1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|metal ion binding|protein binding			ovary(5)|kidney(2)|pancreas(1)|central_nervous_system(1)|skin(1)	10						TATGAGACATCTGTCAGTCCC	0.438													3	17	---	---	---	---	PASS
SPAG16	79582	broad.mit.edu	37	2	214181983	214181983	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214181983G>C	uc002veq.2	+	5	531	c.439G>C	c.(439-441)GTT>CTT	p.V147L	SPAG16_uc010fuz.1_Intron|SPAG16_uc002ver.2_Missense_Mutation_p.V93L|SPAG16_uc010zjk.1_Missense_Mutation_p.V53L|SPAG16_uc002veo.2_Missense_Mutation_p.V147L|SPAG16_uc002vep.1_Intron|SPAG16_uc002ves.1_Missense_Mutation_p.V116L	NM_024532	NP_078808	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16 isoform 1	147					cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		ACTTAGAACTGTTGGGAATGT	0.333													12	26	---	---	---	---	PASS
ALPP	250	broad.mit.edu	37	2	233245187	233245187	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233245187G>T	uc002vsq.2	+	7	1015	c.850G>T	c.(850-852)GTG>TTG	p.V284L	ALPP_uc002vsr.2_5'Flank	NM_001632	NP_001623	P05187	PPB1_HUMAN	placental alkaline phosphatase preproprotein	284						anchored to membrane|cell surface|integral to membrane|plasma membrane	alkaline phosphatase activity|metal ion binding			ovary(1)	1		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		GGACCCGTCTGTGACCCATCT	0.637													5	80	---	---	---	---	PASS
CNTN6	27255	broad.mit.edu	37	3	1443184	1443184	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1443184G>T	uc003boz.2	+	21	3039	c.2772G>T	c.(2770-2772)GAG>GAT	p.E924D	CNTN6_uc011asj.1_Missense_Mutation_p.E852D|CNTN6_uc003bpa.2_Missense_Mutation_p.E924D	NM_014461	NP_055276	Q9UQ52	CNTN6_HUMAN	contactin 6 precursor	924	Fibronectin type-III 4.				axon guidance|cell adhesion|central nervous system development|Notch signaling pathway	anchored to membrane|plasma membrane				skin(3)|lung(2)|breast(2)|pancreas(1)	8		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		TGAACTGGGAGCATGTAAAAA	0.358													7	18	---	---	---	---	PASS
THUMPD3	25917	broad.mit.edu	37	3	9426217	9426217	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9426217G>T	uc003bro.3	+	10	1517	c.1369G>T	c.(1369-1371)GGA>TGA	p.G457*	LOC440944_uc003brm.2_Intron|THUMPD3_uc003brn.3_Nonsense_Mutation_p.G457*	NM_001114092	NP_001107564	Q9BV44	THUM3_HUMAN	THUMP domain containing 3	457							methyltransferase activity|protein binding|RNA binding			ovary(1)	1	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.101)		GGCGTTATCTGGAATGCGACA	0.428													6	147	---	---	---	---	PASS
MTMR14	64419	broad.mit.edu	37	3	9731795	9731795	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9731795G>T	uc003brz.2	+	17	1705	c.1581G>T	c.(1579-1581)ATG>ATT	p.M527I	MTMR14_uc003bsa.2_Missense_Mutation_p.M527I|MTMR14_uc003bsb.2_Intron|MTMR14_uc011ath.1_Intron|MTMR14_uc010hcl.2_Intron|MTMR14_uc003bsc.2_Intron	NM_001077525	NP_001070993	Q8NCE2	MTMRE_HUMAN	jumpy isoform 2	527						perinuclear region of cytoplasm|ruffle	phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity			skin(1)	1	Medulloblastoma(99;0.227)					TTTTCAGGATGGGTAGCAGTC	0.567													4	17	---	---	---	---	PASS
COLQ	8292	broad.mit.edu	37	3	15512050	15512050	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15512050C>A	uc003bzx.2	-	11	836	c.710G>T	c.(709-711)GGC>GTC	p.G237V	COLQ_uc003bzv.2_Missense_Mutation_p.G227V|COLQ_uc003bzz.2_Missense_Mutation_p.G228V|COLQ_uc010heo.2_Missense_Mutation_p.G203V|COLQ_uc003cac.1_RNA|COLQ_uc003cae.1_Missense_Mutation_p.G96V|COLQ_uc003cad.1_RNA	NM_005677	NP_005668	Q9Y215	COLQ_HUMAN	acetylcholinesterase collagen-like tail subunit	237	Heparan sulfate proteoglycan binding (Potential).|Collagen-like 1.				acetylcholine catabolic process in synaptic cleft|asymmetric protein localization	basal lamina|cell junction|collagen|extracellular space|synaptic cleft					0						TACCTGCTTGCCTCGTTTTCC	0.547													23	28	---	---	---	---	PASS
CLASP2	23122	broad.mit.edu	37	3	33633993	33633993	+	Intron	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33633993G>T	uc003cfu.2	-						CLASP2_uc003cft.2_Intron|CLASP2_uc010hgb.2_Intron|CLASP2_uc011axt.1_Intron	NM_015097	NP_055912	B2RTR1	B2RTR1_HUMAN	CLIP-associating protein 2											ovary(3)|central_nervous_system(1)	4						CCCGGCCTGAGaaataaaata	0.323													8	9	---	---	---	---	PASS
SCN11A	11280	broad.mit.edu	37	3	38938418	38938418	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38938418C>T	uc011ays.1	-	14	2520	c.2321G>A	c.(2320-2322)TGG>TAG	p.W774*	SCN11A_uc010hhn.1_5'Flank	NM_014139	NP_054858	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha	774	II.				response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			skin(6)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)|pancreas(1)	9				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)	CATACATTCCCACATATTTTC	0.443													20	21	---	---	---	---	PASS
ZBTB47	92999	broad.mit.edu	37	3	42703103	42703103	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42703103C>T	uc003clu.1	+	2	574	c.472C>T	c.(472-474)CAC>TAC	p.H158Y		NM_145166	NP_660149	Q9UFB7	ZBT47_HUMAN	zinc finger protein 651	158	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				KIRC - Kidney renal clear cell carcinoma(284;0.216)		CACCATGGCCCACGTGCGTAA	0.527													10	27	---	---	---	---	PASS
CCR1	1230	broad.mit.edu	37	3	46244987	46244987	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46244987C>A	uc003cph.1	-	2	889	c.818G>T	c.(817-819)TGT>TTT	p.C273F	CCR3_uc003cpg.1_Intron	NM_001295	NP_001286	P32246	CCR1_HUMAN	chemokine (C-C motif) receptor 1	273	Extracellular (Potential).				cell adhesion|cell-cell signaling|cytokine-mediated signaling pathway|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|G-protein signaling, coupled to cyclic nucleotide second messenger|immune response|inflammatory response	integral to plasma membrane	C-C chemokine receptor activity			skin(2)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)		GCTCTGCTCACACTCATGGGT	0.458													6	28	---	---	---	---	PASS
ADAMTS9	56999	broad.mit.edu	37	3	64601826	64601826	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64601826C>A	uc003dmg.2	-	20	2866	c.2834G>T	c.(2833-2835)AGT>ATT	p.S945I	ADAMTS9_uc011bfo.1_Missense_Mutation_p.S917I|ADAMTS9_uc003dmh.1_Missense_Mutation_p.S774I|ADAMTS9_uc003dmk.1_Missense_Mutation_p.S945I|ADAMTS9_uc011bfp.1_5'UTR	NM_182920	NP_891550	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1	945	TSP type-1 3.				glycoprotein catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)|skin(1)	4		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		ACTACATTCACTCCTGCTGGC	0.428													26	95	---	---	---	---	PASS
EIF4E3	317649	broad.mit.edu	37	3	71739215	71739215	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71739215C>G	uc003dov.3	-	6	582	c.574G>C	c.(574-576)GAA>CAA	p.E192Q	EIF4E3_uc011bgc.1_Missense_Mutation_p.E86Q|EIF4E3_uc003dox.2_Missense_Mutation_p.E86Q|EIF4E3_uc011bgd.1_Missense_Mutation_p.E86Q|EIF4E3_uc010hoc.2_Missense_Mutation_p.E86Q	NM_001134651	NP_001128123	Q8N5X7	IF4E3_HUMAN	eukaryotic translation initiation factor 4E	192					regulation of translation	cytoplasm|mRNA cap binding complex	translation initiation factor activity				0		Prostate(10;0.0166)		BRCA - Breast invasive adenocarcinoma(55;2.56e-05)|Epithelial(33;2.9e-05)|Lung(16;9.28e-05)|LUSC - Lung squamous cell carcinoma(21;0.00227)		TAGATCTTTTCTAAAACAGTC	0.383													9	30	---	---	---	---	PASS
GBE1	2632	broad.mit.edu	37	3	81719992	81719992	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81719992T>G	uc003dqg.2	-	4	709	c.426A>C	c.(424-426)TTA>TTC	p.L142F	GBE1_uc011bgm.1_Missense_Mutation_p.L101F	NM_000158	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1	142					glucose metabolic process|glycogen biosynthetic process	cytosol	1,4-alpha-glucan branching enzyme activity|cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(3)	3		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)		AAAGTACCTTTAATTTGGATC	0.343									Glycogen_Storage_Disease_type_IV				3	11	---	---	---	---	PASS
EPHA6	285220	broad.mit.edu	37	3	96706678	96706678	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96706678G>T	uc010how.1	+	3	998	c.955G>T	c.(955-957)GAT>TAT	p.D319Y	EPHA6_uc003drp.1_Missense_Mutation_p.D319Y	NM_001080448	NP_001073917	Q9UF33	EPHA6_HUMAN	EPH receptor A6 isoform a	224	Extracellular (Potential).					integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16						TCCAAGGGTTGATTCCTCCTC	0.488													22	192	---	---	---	---	PASS
GPR15	2838	broad.mit.edu	37	3	98250924	98250924	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98250924C>A	uc011bgy.1	+	1	47	c.47C>A	c.(46-48)ACG>AAG	p.T16K		NM_005290	NP_005281	P49685	GPR15_HUMAN	G protein-coupled receptor 15	16	Extracellular (Potential).					integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(1)	1		Lung NSC(201;7.93e-06)|all_neural(597;0.00172)|Hepatocellular(537;0.00825)|Myeloproliferative disorder(1037;0.0255)		Lung(72;0.246)		TACTATGCTACGAGCCCAAAC	0.438													6	34	---	---	---	---	PASS
DPPA2	151871	broad.mit.edu	37	3	109028117	109028117	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109028117G>A	uc003dxo.2	-	4	489	c.242C>T	c.(241-243)CCA>CTA	p.P81L		NM_138815	NP_620170	Q7Z7J5	DPPA2_HUMAN	developmental pluripotency associated 2	81						nucleus	nucleic acid binding			ovary(2)|upper_aerodigestive_tract(1)	3						GGGAAGGGCTGGTATTTTGCA	0.418													18	122	---	---	---	---	PASS
CD96	10225	broad.mit.edu	37	3	111357003	111357003	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111357003G>T	uc003dxw.2	+	13	1683	c.1513G>T	c.(1513-1515)GTC>TTC	p.V505F	CD96_uc003dxx.2_Missense_Mutation_p.V489F|CD96_uc010hpy.1_Missense_Mutation_p.V488F	NM_198196	NP_937839	P40200	TACT_HUMAN	CD96 antigen isoform 1 precursor	505	Extracellular (Potential).				cell adhesion|immune response|regulation of immune response	integral to plasma membrane				skin(2)|central_nervous_system(1)	3						AACTAATCACGTCCATATCAC	0.303									Opitz_Trigonocephaly_syndrome				19	74	---	---	---	---	PASS
CD200R1L	344807	broad.mit.edu	37	3	112548240	112548240	+	Intron	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112548240C>T	uc003dzi.1	-						CD200R1L_uc011bhw.1_Intron|CD200R1L_uc010hqf.1_Intron	NM_001008784	NP_001008784	Q6Q8B3	MO2R2_HUMAN	CD200 cell surface glycoprotein receptor 2							integral to membrane	receptor activity			ovary(1)	1						AGCTAGAAAACATTTAGAGAA	0.363													13	56	---	---	---	---	PASS
GAP43	2596	broad.mit.edu	37	3	115439702	115439702	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115439702A>C	uc003ebq.2	+	3	1076	c.690A>C	c.(688-690)GAA>GAC	p.E230D	GAP43_uc003ebr.2_Missense_Mutation_p.E266D	NM_002045	NP_002036	P17677	NEUM_HUMAN	growth associated protein 43 isoform 2	230					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell differentiation|nervous system development|regulation of filopodium assembly|regulation of growth|response to wounding	cell junction|filopodium membrane|growth cone membrane|synapse	calmodulin binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.164)		AAGAAGAGGAACCTGAGGCTG	0.512													7	252	---	---	---	---	PASS
C3orf1	51300	broad.mit.edu	37	3	119219532	119219532	+	Intron	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119219532G>T	uc003ecn.2	+						C3orf1_uc003eco.2_Intron|C3orf1_uc003ecp.2_Intron	NM_016589	NP_057673	Q9NPL8	TIDC1_HUMAN	hypothetical protein LOC51300							integral to membrane|mitochondrial inner membrane	protein transporter activity				0				GBM - Glioblastoma multiforme(114;0.186)		TTGTCTTTTTGATGTTGTAGT	0.408													13	53	---	---	---	---	PASS
C3orf15	89876	broad.mit.edu	37	3	119462960	119462960	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119462960C>G	uc003ede.3	+	14	1896	c.1819C>G	c.(1819-1821)CGG>GGG	p.R607G	C3orf15_uc010hqz.2_Missense_Mutation_p.R545G|C3orf15_uc011bjd.1_Missense_Mutation_p.R481G|C3orf15_uc011bje.1_Missense_Mutation_p.R587G	NM_033364	NP_203528	Q7Z4T9	AAT1_HUMAN	AAT1-alpha	443						mitochondrion	protein binding			ovary(2)|pancreas(1)	3				GBM - Glioblastoma multiforme(114;0.186)		TGAGCGCCAGCGGCGGGTACG	0.582													13	39	---	---	---	---	PASS
GPR156	165829	broad.mit.edu	37	3	119887051	119887051	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119887051G>C	uc011bjf.1	-	9	1273	c.1273C>G	c.(1273-1275)CCT>GCT	p.P425A	GPR156_uc011bjg.1_Missense_Mutation_p.P421A	NM_153002	NP_694547	Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156	425	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(114;0.19)		TGACCCGAAGGCCCCTGAGCA	0.627													7	22	---	---	---	---	PASS
EAF2	55840	broad.mit.edu	37	3	121554135	121554135	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121554135G>T	uc003een.2	+	1	102	c.3G>T	c.(1-3)ATG>ATT	p.M1I	IQCB1_uc010hre.1_5'Flank|IQCB1_uc003eek.2_5'Flank|IQCB1_uc010hrf.1_5'Flank|EAF2_uc003eem.2_RNA|EAF2_uc003eeo.2_5'UTR	NM_018456	NP_060926	Q96CJ1	EAF2_HUMAN	ELL associated factor 2	1					apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck	protein binding				0				GBM - Glioblastoma multiforme(114;0.0972)		GAGTAATTATGAATAGCGCAG	0.572													9	60	---	---	---	---	PASS
UMPS	7372	broad.mit.edu	37	3	124462860	124462860	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124462860G>C	uc003ehl.3	+	6	1478	c.1372G>C	c.(1372-1374)GAT>CAT	p.D458H	UMPS_uc003ehm.3_RNA|UMPS_uc011bka.1_Missense_Mutation_p.D280H|UMPS_uc011bkb.1_Missense_Mutation_p.D366H|UMPS_uc011bkc.1_Missense_Mutation_p.D280H|UMPS_uc003ehn.3_Missense_Mutation_p.D280H|UMPS_uc011bkd.1_Missense_Mutation_p.D183H	NM_000373	NP_000364	P11172	UMPS_HUMAN	uridine monophosphate synthase	458	OMPdecase.				'de novo' pyrimidine base biosynthetic process|'de novo' UMP biosynthetic process|pyrimidine nucleoside biosynthetic process	cytosol|nucleus	orotate phosphoribosyltransferase activity|orotidine-5'-phosphate decarboxylase activity			kidney(1)	1				GBM - Glioblastoma multiforme(114;0.146)		CTCAGCAGCTGATCGTCTGGA	0.428													18	72	---	---	---	---	PASS
SLC12A8	84561	broad.mit.edu	37	3	124826404	124826404	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124826404G>C	uc003ehv.3	-	10	1737	c.1626C>G	c.(1624-1626)AGC>AGG	p.S542R	SLC12A8_uc003ehw.3_Missense_Mutation_p.S571R|SLC12A8_uc003eht.3_Missense_Mutation_p.S343R|SLC12A8_uc003ehu.3_Missense_Mutation_p.S295R|SLC12A8_uc010hry.2_Missense_Mutation_p.S295R	NM_024628	NP_078904	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8	542					potassium ion transport	integral to membrane	symporter activity				0						GAGTCCCTTCGCTCTTGGAAG	0.552													18	93	---	---	---	---	PASS
ACAD9	28976	broad.mit.edu	37	3	128631463	128631463	+	3'UTR	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128631463T>C	uc003ela.3	+	18					KIAA1257_uc003elg.1_Intron|ACAD9_uc011bks.1_3'UTR|ACAD9_uc003elb.2_3'UTR|ACAD9_uc003eld.1_RNA|ACAD9_uc003ele.2_3'UTR|uc003elf.1_Intron	NM_014049	NP_054768	Q9H845	ACAD9_HUMAN	acyl-Coenzyme A dehydrogenase family, member 9							mitochondrion	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding			ovary(2)|central_nervous_system(1)	3						CAGGGGACAGTGTCCCCTGCT	0.527													4	58	---	---	---	---	PASS
IFT122	55764	broad.mit.edu	37	3	129221605	129221605	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129221605G>T	uc003emm.2	+	20	2633	c.2427G>T	c.(2425-2427)CTG>CTT	p.L809L	IFT122_uc003eml.2_Silent_p.L860L|IFT122_uc003emn.2_Silent_p.L750L|IFT122_uc003emo.2_Silent_p.L698L|IFT122_uc003emp.2_Silent_p.L659L|IFT122_uc010htc.2_Silent_p.L801L|IFT122_uc011bky.1_Silent_p.L600L|IFT122_uc003emq.2_Silent_p.L649L|IFT122_uc003emr.2_Silent_p.L561L|IFT122_uc011bla.1_Silent_p.L582L|IFT122_uc010hte.2_Silent_p.L135L|IFT122_uc003ems.2_Silent_p.L190L|IFT122_uc011bkx.1_Silent_p.L649L|IFT122_uc010htd.1_Silent_p.L288L	NM_052989	NP_443715	Q9HBG6	IF122_HUMAN	WD repeat domain 10 isoform 2	809					camera-type eye morphogenesis|cilium morphogenesis|embryonic body morphogenesis|embryonic heart tube development|limb development|neural tube closure	microtubule basal body|photoreceptor connecting cilium				ovary(1)|skin(1)	2						AGCCCCTGCTGCTGTGCGCTA	0.552													9	101	---	---	---	---	PASS
NEK11	79858	broad.mit.edu	37	3	130852747	130852747	+	Silent	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130852747T>C	uc003eny.2	+	7	920	c.594T>C	c.(592-594)TAT>TAC	p.Y198Y	NEK11_uc003enx.2_Silent_p.Y198Y|NEK11_uc003eoa.2_Silent_p.Y198Y|NEK11_uc003enz.2_Silent_p.Y16Y|NEK11_uc010htn.2_RNA|NEK11_uc011blk.1_Silent_p.Y50Y|NEK11_uc011bll.1_Silent_p.Y198Y|NEK11_uc003enw.1_Silent_p.Y198Y|NEK11_uc011blm.1_Silent_p.Y198Y|NEK11_uc010hto.1_Silent_p.Y50Y	NM_024800	NP_079076	Q8NG66	NEK11_HUMAN	NIMA-related kinase 11 isoform 1	198	Protein kinase.				cell cycle|intra-S DNA damage checkpoint|intracellular protein kinase cascade	nucleolus	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(4)|stomach(1)|central_nervous_system(1)	6						CTCCCCATTATATGAGTCCTG	0.423													55	56	---	---	---	---	PASS
TMEM108	66000	broad.mit.edu	37	3	133098855	133098855	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133098855C>G	uc003eph.2	+	4	574	c.300C>G	c.(298-300)ATC>ATG	p.I100M	TMEM108_uc003epi.2_Missense_Mutation_p.I100M|TMEM108_uc003epj.1_Missense_Mutation_p.I100M|TMEM108_uc003epk.2_Intron|TMEM108_uc003epm.2_Missense_Mutation_p.I51M	NM_023943	NP_076432	Q6UXF1	TM108_HUMAN	transmembrane protein 108 precursor	100	Pro-rich.|Extracellular (Potential).					integral to membrane				ovary(2)|skin(2)	4						TCTCCACCATCGCTGCGACAG	0.662													5	77	---	---	---	---	PASS
EPHB1	2047	broad.mit.edu	37	3	134873074	134873074	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134873074C>A	uc003eqt.2	+	6	1598	c.1378C>A	c.(1378-1380)CCC>ACC	p.P460T	EPHB1_uc003equ.2_Missense_Mutation_p.P21T	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor	460	Fibronectin type-III 2.|Extracellular (Potential).					integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30						GCCGGAGCAGCCCAATGGCAT	0.557													19	143	---	---	---	---	PASS
PCCB	5096	broad.mit.edu	37	3	136016830	136016830	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136016830C>G	uc003eqy.1	+	8	851	c.800C>G	c.(799-801)GCC>GGC	p.A267G	PCCB_uc003eqz.1_Missense_Mutation_p.A267G|PCCB_uc011bmc.1_Missense_Mutation_p.A287G|PCCB_uc011bmd.1_Missense_Mutation_p.A184G	NM_000532	NP_000523	P05166	PCCB_HUMAN	propionyl Coenzyme A carboxylase, beta	267	Carboxyltransferase.				fatty acid beta-oxidation	mitochondrial matrix	ATP binding|propionyl-CoA carboxylase activity				0					Biotin(DB00121)|L-Valine(DB00161)	GATGTTGATGCCTTGTGTAAT	0.542													23	160	---	---	---	---	PASS
STAG1	10274	broad.mit.edu	37	3	136082280	136082280	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136082280C>A	uc003era.1	-	26	3007	c.2715G>T	c.(2713-2715)AAG>AAT	p.K905N	STAG1_uc003erb.1_Missense_Mutation_p.K905N	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1	905					cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2						TCAGTGTTTCCTTAATAATAT	0.353													5	44	---	---	---	---	PASS
ARMC8	25852	broad.mit.edu	37	3	137993288	137993288	+	Intron	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137993288C>T	uc003esa.1	+						TXNDC6_uc003esd.1_Intron|TXNDC6_uc010huf.1_Intron|TXNDC6_uc003ese.1_Intron|ARMC8_uc011bmf.1_Intron|ARMC8_uc011bmg.1_Intron|ARMC8_uc011bmh.1_Intron|ARMC8_uc003esb.1_Intron|ARMC8_uc003esc.1_Intron|ARMC8_uc003esf.1_Intron	NM_015396	NP_056211	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8 isoform 2								binding				0						CATTGTTTTACAGCATATAGA	0.348													14	91	---	---	---	---	PASS
ZBTB38	253461	broad.mit.edu	37	3	141163969	141163969	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141163969C>A	uc003etw.2	+	8	3721	c.2739C>A	c.(2737-2739)GAC>GAA	p.D913E	ZBTB38_uc010hun.2_Missense_Mutation_p.D910E|ZBTB38_uc010huo.2_Missense_Mutation_p.D913E|ZBTB38_uc003ety.2_Missense_Mutation_p.D913E|ZBTB38_uc010hup.2_Missense_Mutation_p.D914E	NM_001080412	NP_001073881	Q8NAP3	ZBT38_HUMAN	zinc finger and BTB domain containing 38	913					positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3						ATTCCACTGACAAACCGTGGC	0.498													8	49	---	---	---	---	PASS
ZBTB38	253461	broad.mit.edu	37	3	141164615	141164615	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141164615C>T	uc003etw.2	+	8	4367	c.3385C>T	c.(3385-3387)CAG>TAG	p.Q1129*	ZBTB38_uc010hun.2_Nonsense_Mutation_p.Q1126*|ZBTB38_uc010huo.2_Nonsense_Mutation_p.Q1129*|ZBTB38_uc003ety.2_Nonsense_Mutation_p.Q1129*|ZBTB38_uc010hup.2_Nonsense_Mutation_p.Q1130*	NM_001080412	NP_001073881	Q8NAP3	ZBT38_HUMAN	zinc finger and BTB domain containing 38	1129	C2H2-type 10.				positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3						TGCCTGCTTCCAGTGCCCCAA	0.463													13	181	---	---	---	---	PASS
TRPC1	7220	broad.mit.edu	37	3	142511813	142511813	+	Intron	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142511813A>T	uc003evc.2	+						TRPC1_uc003evb.2_Intron|TRPC1_uc011bni.1_Intron	NM_003304	NP_003295	P48995	TRPC1_HUMAN	transient receptor potential cation channel,						axon guidance|cytosolic calcium ion homeostasis|positive regulation of release of sequestered calcium ion into cytosol|response to calcium ion	cytosol|integral to plasma membrane	protein binding|store-operated calcium channel activity			ovary(2)	2						ATTACAGGTAAATAATTAAAA	0.323													6	52	---	---	---	---	PASS
SLC9A9	285195	broad.mit.edu	37	3	142985708	142985708	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142985708G>T	uc003evn.2	-	16	1956	c.1774C>A	c.(1774-1776)CAG>AAG	p.Q592K		NM_173653	NP_775924	Q8IVB4	SL9A9_HUMAN	solute carrier family 9 (sodium/hydrogen	592					regulation of pH	integral to membrane|late endosome membrane|recycling endosome	sodium:hydrogen antiporter activity			ovary(2)|skin(1)	3						GCTTGCTCCTGGTAATTTATG	0.488													17	80	---	---	---	---	PASS
COMMD2	51122	broad.mit.edu	37	3	149459448	149459448	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149459448G>T	uc003exk.2	-	5	507	c.460C>A	c.(460-462)CTT>ATT	p.L154I	COMMD2_uc003exj.1_5'Flank	NM_016094	NP_057178	Q86X83	COMD2_HUMAN	COMM domain containing 2	154	COMM.						protein binding				0			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			TTTTGATTAAGGTGTAGCTTT	0.393													6	156	---	---	---	---	PASS
CLRN1	7401	broad.mit.edu	37	3	150690325	150690325	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150690325A>T	uc003eyk.1	-	1	462	c.171T>A	c.(169-171)TTT>TTA	p.F57L	CLRN1OS_uc011bny.1_Intron|CLRN1OS_uc003eyl.2_5'Flank	NM_174878	NP_777367	P58418	CLRN1_HUMAN	clarin 1 isoform a	57					equilibrioception|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	integral to membrane					0			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			TTTCACCCATAAACTTGTCCA	0.537													11	98	---	---	---	---	PASS
IGSF10	285313	broad.mit.edu	37	3	151163652	151163652	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151163652C>A	uc011bod.1	-	4	4117	c.4117G>T	c.(4117-4119)GCT>TCT	p.A1373S		NM_178822	NP_849144	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10 precursor	1373					cell differentiation|multicellular organismal development|ossification	extracellular region				skin(7)|ovary(5)|central_nervous_system(1)	13			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GGTGTCATAGCAGTGGGTGTA	0.473													30	146	---	---	---	---	PASS
VEPH1	79674	broad.mit.edu	37	3	157188180	157188180	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157188180T>G	uc003fbj.1	-	3	594	c.277A>C	c.(277-279)AAC>CAC	p.N93H	VEPH1_uc003fbk.1_Missense_Mutation_p.N93H|VEPH1_uc010hvu.1_Missense_Mutation_p.N93H|VEPH1_uc003fbm.2_Missense_Mutation_p.N93H|VEPH1_uc003fbn.2_Missense_Mutation_p.N93H	NM_024621	NP_078897	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain homolog 1	93						plasma membrane				breast(3)|ovary(1)|lung(1)	5			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			GGTCTCAGGTTATGTTCCAAG	0.458													33	45	---	---	---	---	PASS
IFT80	57560	broad.mit.edu	37	3	159997010	159997010	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159997010C>G	uc011boy.1	-	16	2240	c.1807G>C	c.(1807-1809)GAT>CAT	p.D603H	IFT80_uc003fda.2_RNA|IFT80_uc003fdb.1_Missense_Mutation_p.D466H|IFT80_uc003fdd.1_Missense_Mutation_p.D286H|IFT80_uc003fde.1_Missense_Mutation_p.D466H	NM_020800	NP_065851	Q9P2H3	IFT80_HUMAN	WD repeat domain 56	603						cilium axoneme|microtubule basal body				ovary(1)	1			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			CTCACAGCATCTTCCCATTTT	0.343													18	71	---	---	---	---	PASS
SI	6476	broad.mit.edu	37	3	164766995	164766995	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164766995G>T	uc003fei.2	-	15	1697	c.1635C>A	c.(1633-1635)TGC>TGA	p.C545*		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	545	Lumenal.|Isomaltase.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)	CAGCATCCATGCAAATTGTTT	0.328										HNSCC(35;0.089)			6	27	---	---	---	---	PASS
SLITRK3	22865	broad.mit.edu	37	3	164906058	164906058	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164906058C>G	uc003fej.3	-	2	3005	c.2561G>C	c.(2560-2562)GGG>GCG	p.G854A	SLITRK3_uc003fek.2_Missense_Mutation_p.G854A	NM_014926	NP_055741	O94933	SLIK3_HUMAN	slit and trk like 3 protein precursor	854	Cytoplasmic (Potential).					integral to membrane				ovary(6)|skin(3)|pancreas(1)	10						CAAGTCTCCCCCAGTTCCCCC	0.567										HNSCC(40;0.11)			19	99	---	---	---	---	PASS
SLITRK3	22865	broad.mit.edu	37	3	164906748	164906748	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164906748G>A	uc003fej.3	-	2	2315	c.1871C>T	c.(1870-1872)CCA>CTA	p.P624L	SLITRK3_uc003fek.2_Missense_Mutation_p.P624L	NM_014926	NP_055741	O94933	SLIK3_HUMAN	slit and trk like 3 protein precursor	624	Extracellular (Potential).					integral to membrane				ovary(6)|skin(3)|pancreas(1)	10						AGGCTGGGCTGGGGATTCTCC	0.547										HNSCC(40;0.11)			7	27	---	---	---	---	PASS
ZBBX	79740	broad.mit.edu	37	3	167000262	167000262	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167000262G>T	uc003fep.2	-	19	2224	c.1901C>A	c.(1900-1902)TCA>TAA	p.S634*	ZBBX_uc011bpc.1_Nonsense_Mutation_p.S673*|ZBBX_uc003feq.2_Nonsense_Mutation_p.S605*	NM_024687	NP_078963	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	634						intracellular	zinc ion binding			ovary(2)	2						ATTTGCTGTTGAAGGTCTCTG	0.343													33	151	---	---	---	---	PASS
NLGN1	22871	broad.mit.edu	37	3	173525632	173525632	+	Intron	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173525632G>T	uc003fio.1	+						NLGN1_uc010hww.1_Intron|NLGN1_uc003fip.1_Intron	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			GGTAAGAAGAGTCTCTCTTTT	0.318													4	48	---	---	---	---	PASS
ZNF639	51193	broad.mit.edu	37	3	179052110	179052110	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179052110A>G	uc003fjq.1	+	6	1701	c.1358A>G	c.(1357-1359)AAG>AGG	p.K453R	ZNF639_uc003fjr.1_Missense_Mutation_p.K453R	NM_016331	NP_057415	Q9UID6	ZN639_HUMAN	zinc finger protein 639	453	Interaction with CTNNA2.|C2H2-type 7.				initiation of viral infection|negative regulation by host of viral transcription|negative regulation of transcription, DNA-dependent|positive regulation by host of viral transcription|positive regulation of cell growth|positive regulation of transcription, DNA-dependent	nucleus	protein self-association|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding				0	all_cancers(143;7.9e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			CTAGATTTCAAGCATTCAGCT	0.328													9	40	---	---	---	---	PASS
MCCC1	56922	broad.mit.edu	37	3	182756857	182756857	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182756857T>C	uc003fle.2	-	12	1471	c.1334A>G	c.(1333-1335)CAG>CGG	p.Q445R	MCCC1_uc010hxi.2_RNA|MCCC1_uc011bqo.1_RNA|MCCC1_uc003flf.2_Missense_Mutation_p.Q328R|MCCC1_uc003flg.2_Missense_Mutation_p.Q336R|MCCC1_uc011bqp.1_Missense_Mutation_p.Q398R	NM_020166	NP_064551	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)	445	Biotin carboxylation.				biotin metabolic process|leucine catabolic process	mitochondrial inner membrane|mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|metal ion binding|methylcrotonoyl-CoA carboxylase activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	CAATGCCGCCTGGCGATCTGC	0.512													50	38	---	---	---	---	PASS
C3orf59	151963	broad.mit.edu	37	3	192635441	192635441	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192635441C>A	uc011bsp.1	-	1	510	c.189G>T	c.(187-189)AAG>AAT	p.K63N		NM_178496	NP_848591	Q8IYB1	M21D2_HUMAN	hypothetical protein LOC151963	63											0	all_cancers(143;1.56e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.8e-18)|LUSC - Lung squamous cell carcinoma(58;8.04e-06)|Lung(62;8.62e-06)	GBM - Glioblastoma multiforme(46;3.86e-05)		AGATGAAATCCTTGGCTGTGT	0.453													6	78	---	---	---	---	PASS
CPN2	1370	broad.mit.edu	37	3	194062993	194062993	+	Silent	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194062993G>A	uc003fts.2	-	2	529	c.439C>T	c.(439-441)CTG>TTG	p.L147L		NM_001080513	NP_001073982	P22792	CPN2_HUMAN	carboxypeptidase N, polypeptide 2	147	LRR 3.				protein stabilization	extracellular region	enzyme regulator activity			ovary(5)	5	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.65e-05)		AGGGACTCCAGGGCAGCCAGG	0.612													8	32	---	---	---	---	PASS
LRRC15	131578	broad.mit.edu	37	3	194080603	194080603	+	Silent	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194080603G>C	uc003ftu.2	-	2	1256	c.1170C>G	c.(1168-1170)GGC>GGG	p.G390G	LRRC15_uc003ftt.2_Silent_p.G396G	NM_130830	NP_570843	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15 isoform b	390	LRR 15.|Extracellular (Potential).					integral to membrane				ovary(3)	3	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		TGGCCATGAGGCCATTGACGT	0.562													8	32	---	---	---	---	PASS
TM4SF19	116211	broad.mit.edu	37	3	196050764	196050764	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196050764A>T	uc003fwl.1	-	5	679	c.554T>A	c.(553-555)CTG>CAG	p.L185Q	TM4SF19_uc003fwj.2_RNA|uc003fwk.1_Missense_Mutation_p.Q10L|TM4SF19_uc010iad.1_Missense_Mutation_p.C184S|TM4SF19_uc011btv.1_Missense_Mutation_p.L159Q	NM_138461	NP_612470	Q96DZ7	T4S19_HUMAN	transmembrane 4 L six family member 19	185	Helical; (Potential).					integral to membrane					0	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;3.94e-24)|all cancers(36;4.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.53e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		AAGCTGGAGCAGGCTGATGCA	0.572													11	73	---	---	---	---	PASS
KIAA0226	9711	broad.mit.edu	37	3	197410253	197410253	+	Silent	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197410253C>T	uc003fyc.2	-	13	2088	c.1905G>A	c.(1903-1905)AAG>AAA	p.K635K	KIAA0226_uc003fyd.3_Silent_p.K590K|KIAA0226_uc003fye.1_Silent_p.K367K	NM_014687	NP_055502	Q92622	RUBIC_HUMAN	hypothetical protein LOC9711 isoform 2.	635					autophagy|endocytosis|negative regulation of autophagy|negative regulation of endocytosis	early endosome|late endosome|lysosome	protein binding				0	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		CCTCAAACTGCTTCAGGAGCC	0.597													15	53	---	---	---	---	PASS
ZFYVE28	57732	broad.mit.edu	37	4	2274976	2274976	+	Silent	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2274976C>G	uc003gex.1	-	10	2566	c.2247G>C	c.(2245-2247)CTG>CTC	p.L749L	ZFYVE28_uc011bvk.1_Silent_p.L679L|ZFYVE28_uc011bvl.1_Silent_p.L719L|ZFYVE28_uc003gew.1_Silent_p.L635L	NM_020972	NP_066023	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28	749					negative regulation of epidermal growth factor receptor activity	cytosol|early endosome membrane	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			skin(2)|ovary(1)	3						GAATACTTCTCAGGTCACTGG	0.527													4	47	---	---	---	---	PASS
EVC2	132884	broad.mit.edu	37	4	5699318	5699318	+	Splice_Site	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5699318A>G	uc003gij.2	-	2	337	c.283_splice	c.e2+1	p.V95_splice	EVC2_uc011bwb.1_Splice_Site|EVC2_uc003gik.2_Splice_Site_p.V15_splice	NM_147127	NP_667338	Q86UK5	LBN_HUMAN	limbin							integral to membrane				large_intestine(3)|ovary(2)	5						AGAAAAACTCACCTGCAGTCT	0.448													13	17	---	---	---	---	PASS
JAKMIP1	152789	broad.mit.edu	37	4	6080723	6080723	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6080723C>A	uc003giu.3	-	8	1521	c.1245G>T	c.(1243-1245)GAG>GAT	p.E415D	JAKMIP1_uc010idb.1_Missense_Mutation_p.E415D|JAKMIP1_uc010idc.1_Intron|JAKMIP1_uc010idd.1_Missense_Mutation_p.E415D|JAKMIP1_uc011bwc.1_Missense_Mutation_p.E250D|JAKMIP1_uc003giv.3_Missense_Mutation_p.E415D|JAKMIP1_uc010ide.2_Missense_Mutation_p.E415D	NM_144720	NP_653321	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein	415	Mediates interaction with TYK2 and GABBR1.				protein transport	cytoplasm|membrane|microtubule|peripheral to membrane of membrane fraction|ribonucleoprotein complex	GABA receptor binding|RNA binding			large_intestine(1)|pancreas(1)|ovary(1)|skin(1)	4						GCCGTTCTCTCTCCTAGAAGG	0.577													7	18	---	---	---	---	PASS
PPP2R2C	5522	broad.mit.edu	37	4	6374278	6374278	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6374278C>A	uc003gjc.2	-	5	967	c.597G>T	c.(595-597)TGG>TGT	p.W199C	PPP2R2C_uc003gjb.2_Missense_Mutation_p.W182C|PPP2R2C_uc011bwd.1_Missense_Mutation_p.W192C|PPP2R2C_uc011bwe.1_Missense_Mutation_p.W192C|PPP2R2C_uc003gja.2_Missense_Mutation_p.W199C|PPP2R2C_uc003gjd.1_Missense_Mutation_p.W287C	NM_020416	NP_065149	Q9Y2T4	2ABG_HUMAN	gamma isoform of regulatory subunit B55, protein	199	WD 3.				signal transduction	protein phosphatase type 2A complex	protein phosphatase type 2A regulator activity			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4						TGGCCAGGTGCCAGAGGTTGA	0.577													15	55	---	---	---	---	PASS
BOD1L	259282	broad.mit.edu	37	4	13603499	13603499	+	Silent	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13603499T>C	uc003gmz.1	-	10	5142	c.5025A>G	c.(5023-5025)GAA>GAG	p.E1675E	BOD1L_uc010idr.1_Silent_p.E1012E	NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN	biorientation of chromosomes in cell division	1675							DNA binding			ovary(5)|breast(1)	6						TAATAGTTCCTTCAACTATTT	0.393													27	129	---	---	---	---	PASS
FGFBP1	9982	broad.mit.edu	37	4	15937711	15937711	+	Missense_Mutation	SNP	G	C	C	rs143807110	byFrequency	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15937711G>C	uc003gom.2	-	2	663	c.545C>G	c.(544-546)TCT>TGT	p.S182C		NM_005130	NP_005121	Q14512	FGFP1_HUMAN	fibroblast growth factor binding protein 1	182					cell-cell signaling|negative regulation of cell proliferation|signal transduction	extracellular space|plasma membrane	heparin binding				0						TGCTAGGCTAGAGGGGGTGGT	0.547													13	56	---	---	---	---	PASS
LDB2	9079	broad.mit.edu	37	4	16504481	16504481	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16504481C>A	uc003goz.2	-	8	1223	c.907G>T	c.(907-909)GGA>TGA	p.G303*	LDB2_uc003gpa.2_3'UTR|LDB2_uc003gpb.2_Nonsense_Mutation_p.G301*|LDB2_uc011bxh.1_Nonsense_Mutation_p.G275*|LDB2_uc010iee.2_3'UTR|LDB2_uc003goy.2_Nonsense_Mutation_p.G178*|LDB2_uc011bxi.1_3'UTR	NM_001290	NP_001281	O43679	LDB2_HUMAN	LIM domain binding 2 isoform a	303	LIM-binding domain (LID) (By similarity).						LIM domain binding|transcription cofactor activity				0						GTTGGCTCTCCTACCACCATC	0.493													10	73	---	---	---	---	PASS
SLIT2	9353	broad.mit.edu	37	4	20620527	20620527	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20620527G>T	uc003gpr.1	+	37	4689	c.4485G>T	c.(4483-4485)CTG>CTT	p.L1495L	SLIT2_uc003gps.1_Silent_p.L1487L	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor	1495	CTCK.				apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11						GTGGACCGCTGAGGAGCAAGC	0.557													10	17	---	---	---	---	PASS
GABRA2	2555	broad.mit.edu	37	4	46388100	46388100	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46388100C>A	uc003gxc.3	-	2	851	c.178G>T	c.(178-180)GGA>TGA	p.G60*	GABRA2_uc010igc.2_Nonsense_Mutation_p.G60*|GABRA2_uc011bzc.1_Missense_Mutation_p.Q27H|GABRA2_uc003gxe.2_Nonsense_Mutation_p.G60*|GABRA2_uc010igd.1_Nonsense_Mutation_p.G60*	NM_001114175	NP_001107647	P47869	GBRA2_HUMAN	gamma-aminobutyric acid A receptor, alpha 2	60	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway|neurotransmitter transport|regulation of neurotransmitter levels	cell junction|chloride channel complex|integral to synaptic vesicle membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)|skin(2)	4					Alprazolam(DB00404)|Bromazepam(DB01558)|Diazepam(DB00829)|Ethchlorvynol(DB00189)|Fludiazepam(DB01567)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	CCTCCCAGTCCTGGTCTAAGC	0.333													11	27	---	---	---	---	PASS
TEC	7006	broad.mit.edu	37	4	48230636	48230636	+	Translation_Start_Site	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48230636G>A	uc003gxz.2	-	2	87	c.-4C>T	c.(-6--2)GACGG>GATGG			NM_003215	NP_003206	P42680	TEC_HUMAN	tec protein tyrosine kinase						intracellular protein kinase cascade	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(4)|stomach(1)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)	9						ATTCATCTCCGTCTTCTGATT	0.353													5	56	---	---	---	---	PASS
CWH43	80157	broad.mit.edu	37	4	49052848	49052848	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49052848A>C	uc003gyv.2	+	15	2185	c.2003A>C	c.(2002-2004)AAA>ACA	p.K668T	CWH43_uc011bzl.1_Missense_Mutation_p.K641T	NM_025087	NP_079363	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog	668					GPI anchor biosynthetic process	integral to membrane				skin(2)|ovary(1)	3						GTTTCTGAGAAAATTCATTTT	0.393													8	39	---	---	---	---	PASS
LRRC66	339977	broad.mit.edu	37	4	52883611	52883611	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:52883611C>A	uc003gzi.2	-	1	182	c.169G>T	c.(169-171)GAC>TAC	p.D57Y		NM_001024611	NP_001019782	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	57						integral to membrane				ovary(1)|central_nervous_system(1)|skin(1)	3						TGTGATATGTCCACAGGTATA	0.338													18	23	---	---	---	---	PASS
KIT	3815	broad.mit.edu	37	4	55602887	55602887	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55602887G>C	uc010igr.2	+	19	2684	c.2597G>C	c.(2596-2598)GGA>GCA	p.G866A	KIT_uc010igs.2_Missense_Mutation_p.G862A	NM_000222	NP_000213	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral	866	Protein kinase.|Cytoplasmic (Potential).				male gonad development|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular space|integral to membrane	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity			soft_tissue(3273)|haematopoietic_and_lymphoid_tissue(1572)|skin(99)|testis(49)|bone(21)|genital_tract(18)|kidney(17)|ovary(16)|salivary_gland(15)|large_intestine(11)|thymus(6)|lung(6)|central_nervous_system(4)|NS(3)|eye(2)|endometrium(2)|breast(1)|stomach(1)|autonomic_ganglia(1)|pancreas(1)	5118	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Sorafenib(DB00398)|Sunitinib(DB01268)	TGTGTCTCAGGAAGCAGCCCC	0.473		1	Mis|O		GIST|AML|TGCT|mastocytosis|mucosal melanoma	GIST|epithelioma	Piebald trait		Mast_Cell_disease_Familial_Clustering_of|Piebaldism|Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Gastrointestinal_Stromal_Tumors				35	96	---	---	---	---	PASS
EXOC1	55763	broad.mit.edu	37	4	56768606	56768606	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56768606G>T	uc003hbe.1	+	18	2592	c.2434G>T	c.(2434-2436)GTC>TTC	p.V812F	EXOC1_uc003hbf.1_Missense_Mutation_p.V812F|EXOC1_uc003hbg.1_Missense_Mutation_p.V797F	NM_018261	NP_060731	Q9NV70	EXOC1_HUMAN	exocyst complex component 1 isoform 1	812					exocytosis|protein transport	exocyst	protein binding			ovary(2)|skin(2)|lung(1)|central_nervous_system(1)	6	Glioma(25;0.08)|all_neural(26;0.101)					ACTTCGTAAAGTCATTAAGGA	0.388													8	109	---	---	---	---	PASS
EPHA5	2044	broad.mit.edu	37	4	66189906	66189906	+	Missense_Mutation	SNP	C	T	T	rs149835568		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66189906C>T	uc003hcy.2	-	18	3233	c.3040G>A	c.(3040-3042)GGT>AGT	p.G1014S	EPHA5_uc003hcx.2_Missense_Mutation_p.G946S|EPHA5_uc003hcz.2_Missense_Mutation_p.G992S|EPHA5_uc011cah.1_Missense_Mutation_p.G1015S|EPHA5_uc011cai.1_Missense_Mutation_p.G993S	NM_004439	NP_004430	P54756	EPHA5_HUMAN	ephrin receptor EphA5 isoform a precursor	1014	Cytoplasmic (Potential).|SAM.				cAMP-mediated signaling|neuron development	dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum	ATP binding|transmembrane-ephrin receptor activity			lung(19)|stomach(2)|ovary(2)|central_nervous_system(1)	24						TTCTGGTGACCGACAAGAGTC	0.428										TSP Lung(17;0.13)			12	17	---	---	---	---	PASS
TMPRSS11D	9407	broad.mit.edu	37	4	68725388	68725388	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68725388C>T	uc003hdq.2	-	2	82	c.17G>A	c.(16-18)CGT>CAT	p.R6H	LOC550112_uc003hdl.3_Intron|TMPRSS11D_uc011caj.1_Intron	NM_004262	NP_004253	O60235	TM11D_HUMAN	transmembrane protease, serine 11D	6	Cytoplasmic (Potential).				proteolysis|respiratory gaseous exchange	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1						CGAAGTTACACGTGCTGGCCT	0.413													14	34	---	---	---	---	PASS
AMBN	258	broad.mit.edu	37	4	71469636	71469636	+	Missense_Mutation	SNP	G	T	T	rs141521373		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71469636G>T	uc003hfl.2	+	12	871	c.796G>T	c.(796-798)GCA>TCA	p.A266S		NM_016519	NP_057603	Q9NP70	AMBN_HUMAN	ameloblastin precursor	266					bone mineralization|cell adhesion|cell proliferation|odontogenesis of dentine-containing tooth	proteinaceous extracellular matrix	growth factor activity|structural constituent of tooth enamel			ovary(3)|skin(1)	4			Lung(101;0.235)			AGAAGAAGTGGCAGTGAGTAA	0.423													8	19	---	---	---	---	PASS
SLC4A4	8671	broad.mit.edu	37	4	72332198	72332198	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72332198G>A	uc003hfy.2	+	13	1652	c.1535G>A	c.(1534-1536)GGA>GAA	p.G512E	SLC4A4_uc010iic.2_Missense_Mutation_p.G512E|SLC4A4_uc010iib.2_Missense_Mutation_p.G512E|SLC4A4_uc003hfz.2_Missense_Mutation_p.G512E|SLC4A4_uc003hgc.3_Missense_Mutation_p.G468E|SLC4A4_uc010iid.2_Intron|SLC4A4_uc003hga.2_Missense_Mutation_p.G390E|SLC4A4_uc003hgb.3_Missense_Mutation_p.G468E	NM_001098484	NP_001091954	Q9Y6R1	S4A4_HUMAN	solute carrier family 4, sodium bicarbonate	512	Helical; (Potential).					basolateral plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|kidney(1)|skin(1)	5			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)			GCTGTCTCTGGAGCCATCTTT	0.403													23	40	---	---	---	---	PASS
ANTXR2	118429	broad.mit.edu	37	4	80899154	80899154	+	Intron	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80899154C>A	uc003hlz.3	-						ANTXR2_uc003hly.3_Intron|ANTXR2_uc003hlx.1_Intron|ANTXR2_uc010ijn.2_Intron	NM_001145794	NP_001139266	P58335	ANTR2_HUMAN	anthrax toxin receptor 2 isoform 2							endoplasmic reticulum membrane|extracellular region|integral to membrane|plasma membrane	metal ion binding|protein binding|receptor activity			ovary(1)	1						AAAATCTGGACACATACCTTA	0.443									Juvenile_Hyaline_Fibromatosis				7	17	---	---	---	---	PASS
GPRIN3	285513	broad.mit.edu	37	4	90169902	90169902	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90169902T>C	uc003hsm.1	-	2	1879	c.1360A>G	c.(1360-1362)AAG>GAG	p.K454E		NM_198281	NP_938022	Q6ZVF9	GRIN3_HUMAN	G protein-regulated inducer of neurite outgrowth	454										ovary(3)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		CCTGCGAGCTTTTTAGCAGTT	0.453													6	43	---	---	---	---	PASS
UNC5C	8633	broad.mit.edu	37	4	96222890	96222890	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96222890G>T	uc003htp.1	-	3	511	c.357C>A	c.(355-357)GTC>GTA	p.V119V	UNC5C_uc010ilc.1_Silent_p.V119V|UNC5C_uc003htq.2_Silent_p.V119V	NM_003728	NP_003719	O95185	UNC5C_HUMAN	unc5C precursor	119	Extracellular (Potential).|Ig-like.				apoptosis|axon guidance|brain development	integral to membrane	netrin receptor activity			ovary(3)|pancreas(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		TCACTTCCCGGACAATGAGAC	0.448													5	17	---	---	---	---	PASS
METAP1	23173	broad.mit.edu	37	4	99960601	99960601	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99960601G>A	uc003huf.3	+	5	534	c.417G>A	c.(415-417)ATG>ATA	p.M139I	METAP1_uc003hug.2_RNA	NM_015143	NP_055958	P53582	AMPM1_HUMAN	methionyl aminopeptidase 1	139					N-terminal protein amino acid modification|peptidyl-methionine modification|proteolysis|regulation of translation	cytoplasm	aminopeptidase activity|metal ion binding|metalloexopeptidase activity|protein binding				0				OV - Ovarian serous cystadenocarcinoma(123;3.12e-07)		TAGAAGGGATGCGACTTGTAT	0.363													15	48	---	---	---	---	PASS
FAT4	79633	broad.mit.edu	37	4	126239869	126239869	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126239869G>A	uc003ifj.3	+	1	2303	c.2303G>A	c.(2302-2304)GGT>GAT	p.G768D		NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	768	Cadherin 7.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18						GCTACTGATGGTGGCAATTTA	0.438													42	23	---	---	---	---	PASS
FAT4	79633	broad.mit.edu	37	4	126369935	126369935	+	Silent	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126369935C>T	uc003ifj.3	+	9	7764	c.7764C>T	c.(7762-7764)ACC>ACT	p.T2588T	FAT4_uc011cgp.1_Silent_p.T886T|FAT4_uc003ifi.1_Silent_p.T66T	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	2588	Extracellular (Potential).|Cadherin 25.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18						TTGTCACCACCATCACAGGAT	0.333													13	28	---	---	---	---	PASS
RNF150	57484	broad.mit.edu	37	4	142053810	142053810	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142053810G>T	uc003iio.1	-	1	807	c.153C>A	c.(151-153)CCC>CCA	p.P51P	RNF150_uc010iok.1_Silent_p.P51P|RNF150_uc003iip.1_Silent_p.P51P	NM_020724	NP_065775	Q9ULK6	RN150_HUMAN	ring finger protein 150 precursor	51	Extracellular (Potential).					integral to membrane	zinc ion binding			ovary(1)	1	all_hematologic(180;0.162)					ggtccggcgcgggcTCGGCGT	0.448													3	14	---	---	---	---	PASS
SLC10A7	84068	broad.mit.edu	37	4	147247142	147247142	+	Missense_Mutation	SNP	C	A	A	rs147461877	byFrequency	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147247142C>A	uc010ioz.2	-	6	696	c.442G>T	c.(442-444)GTT>TTT	p.V148F	SLC10A7_uc003ikr.2_Missense_Mutation_p.V148F|SLC10A7_uc010ipa.2_Missense_Mutation_p.V135F|SLC10A7_uc003iks.2_RNA	NM_001029998	NP_001025169	Q0GE19	NTCP7_HUMAN	solute carrier family 10 (sodium/bile acid	148	Helical; (Potential).					integral to membrane	bile acid:sodium symporter activity				0	all_hematologic(180;0.151)					GGTGTTATAACGATGCCCTGA	0.358													6	10	---	---	---	---	PASS
DCLK2	166614	broad.mit.edu	37	4	151153526	151153526	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151153526G>T	uc003ilm.3	+	9	1437	c.1337G>T	c.(1336-1338)CGA>CTA	p.R446L	DCLK2_uc003iln.3_Missense_Mutation_p.R445L|DCLK2_uc003ilo.3_Missense_Mutation_p.R463L|DCLK2_uc003ilp.3_RNA	NM_001040260	NP_001035350	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2 isoform a	446	Protein kinase.				intracellular signal transduction	cytoplasm|cytoskeleton	ATP binding|protein serine/threonine kinase activity			ovary(3)	3	all_hematologic(180;0.151)					ATACTGCGCCGAGTGAAACAT	0.448													44	73	---	---	---	---	PASS
PDGFC	56034	broad.mit.edu	37	4	157688921	157688921	+	Intron	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157688921C>A	uc003iph.1	-						PDGFC_uc003ipi.1_Intron|PDGFC_uc011cis.1_Intron|PDGFC_uc011cir.1_Intron	NM_016205	NP_057289	Q9NRA1	PDGFC_HUMAN	platelet-derived growth factor C precursor						central nervous system development|platelet-derived growth factor receptor signaling pathway|positive regulation of cell division|positive regulation of DNA replication|positive regulation of fibroblast proliferation|vascular endothelial growth factor receptor signaling pathway	endoplasmic reticulum lumen|extracellular space|Golgi membrane|nucleus	cell surface binding|growth factor activity|platelet-derived growth factor receptor binding|protein homodimerization activity			ovary(1)|lung(1)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)		AATTGTATACCTACCTCGTGG	0.378													5	11	---	---	---	---	PASS
KLKB1	3818	broad.mit.edu	37	4	187172721	187172721	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187172721G>C	uc003iyy.2	+	9	1020	c.949G>C	c.(949-951)GTT>CTT	p.V317L	KLKB1_uc011clc.1_Missense_Mutation_p.V115L|KLKB1_uc011cld.1_Missense_Mutation_p.V279L	NM_000892	NP_000883	P03952	KLKB1_HUMAN	plasma kallikrein B1 precursor	317	Apple 4.				blood coagulation, intrinsic pathway|Factor XII activation|fibrinolysis|plasminogen activation|positive regulation of fibrinolysis	cytoplasm|extracellular space|plasma membrane	serine-type endopeptidase activity			ovary(1)	1		all_cancers(14;1.55e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00664)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.29e-10)|BRCA - Breast invasive adenocarcinoma(30;3.8e-05)|GBM - Glioblastoma multiforme(59;0.000131)|STAD - Stomach adenocarcinoma(60;0.000292)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.168)		AGGAGTGAATGTTTGCCAAGA	0.363													3	30	---	---	---	---	PASS
F11	2160	broad.mit.edu	37	4	187197555	187197555	+	Intron	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187197555A>T	uc003iza.1	+							NM_000128	NP_000119	P03951	FA11_HUMAN	coagulation factor XI precursor						blood coagulation, intrinsic pathway|plasminogen activation|positive regulation of fibrinolysis	extracellular space|plasma membrane	heparin binding|serine-type endopeptidase activity				0		all_cancers(14;6.2e-52)|all_epithelial(14;1.62e-38)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;2.13e-11)|BRCA - Breast invasive adenocarcinoma(30;4.59e-06)|GBM - Glioblastoma multiforme(59;0.000149)|STAD - Stomach adenocarcinoma(60;0.000314)|LUSC - Lung squamous cell carcinoma(40;0.00112)|READ - Rectum adenocarcinoma(43;0.176)	Coagulation Factor IX(DB00100)	GTAAGGAGTTAACAAGTAAGG	0.348													18	30	---	---	---	---	PASS
ADAMTS16	170690	broad.mit.edu	37	5	5186325	5186325	+	Silent	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5186325T>C	uc003jdl.2	+	5	1062	c.924T>C	c.(922-924)CAT>CAC	p.H308H	ADAMTS16_uc003jdk.1_Silent_p.H308H|ADAMTS16_uc003jdj.1_Silent_p.H308H	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1	308	Peptidase M12B.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8						ACCATGGCCATGAAAATATCA	0.453													13	36	---	---	---	---	PASS
FASTKD3	79072	broad.mit.edu	37	5	7867883	7867883	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7867883C>A	uc003jeb.2	-	2	451	c.314G>T	c.(313-315)AGA>ATA	p.R105I	FASTKD3_uc011cmp.1_Intron|FASTKD3_uc003jec.2_Intron|MTRR_uc010itn.1_5'Flank|MTRR_uc003jee.3_5'Flank|MTRR_uc003jed.2_5'Flank|MTRR_uc003jef.3_5'Flank|MTRR_uc003jeg.3_5'Flank|MTRR_uc010ito.2_5'Flank	NM_024091	NP_076996	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	105					apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity			ovary(2)|breast(1)|pancreas(1)	4						GTTGCTCAGTCTCCTGTAAAA	0.438													10	27	---	---	---	---	PASS
DNAH5	1767	broad.mit.edu	37	5	13735337	13735337	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13735337G>T	uc003jfd.2	-	68	11706	c.11664C>A	c.(11662-11664)TAC>TAA	p.Y3888*	DNAH5_uc003jfc.2_Nonsense_Mutation_p.Y56*	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3888					microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					TGTGCTCCTCGTACAGCCCTC	0.458									Kartagener_syndrome				15	37	---	---	---	---	PASS
DNAH5	1767	broad.mit.edu	37	5	13864711	13864711	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13864711T>A	uc003jfd.2	-	28	4433	c.4391A>T	c.(4390-4392)CAG>CTG	p.Q1464L		NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1464	Potential.|Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					CAAAAAAGCCTGCCAGTCCTT	0.502									Kartagener_syndrome				5	38	---	---	---	---	PASS
MYO10	4651	broad.mit.edu	37	5	16818205	16818205	+	Silent	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16818205G>A	uc003jft.3	-	3	660	c.192C>T	c.(190-192)GGC>GGT	p.G64G	MYO10_uc003jfu.2_Silent_p.G31G|MYO10_uc003jfv.2_Silent_p.G64G	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X	64	Myosin head-like.				axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						TGTCATCCACGCCCTCCTCGT	0.463													5	30	---	---	---	---	PASS
CDH12	1010	broad.mit.edu	37	5	21975358	21975358	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21975358G>A	uc010iuc.2	-	3	826	c.368C>T	c.(367-369)CCT>CTT	p.P123L	CDH12_uc011cno.1_Missense_Mutation_p.P123L|CDH12_uc003jgk.2_Missense_Mutation_p.P123L	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein	123	Cadherin 1.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						AGTGTAGAAAGGTTTCTCTTC	0.443										HNSCC(59;0.17)			11	50	---	---	---	---	PASS
CDH9	1007	broad.mit.edu	37	5	26881271	26881271	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26881271C>A	uc003jgs.1	-	12	2513	c.2344G>T	c.(2344-2346)GGG>TGG	p.G782W	CDH9_uc011cnv.1_Missense_Mutation_p.G375W	NM_016279	NP_057363	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 preproprotein	782	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|skin(2)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)	9						TCATCACCCCCATACATATCG	0.408													23	95	---	---	---	---	PASS
SPEF2	79925	broad.mit.edu	37	5	35705881	35705881	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35705881C>T	uc003jjo.2	+	18	2747	c.2636C>T	c.(2635-2637)ACG>ATG	p.T879M	SPEF2_uc003jjq.3_Missense_Mutation_p.T874M|SPEF2_uc003jjp.1_Missense_Mutation_p.T365M	NM_024867	NP_079143	Q9C093	SPEF2_HUMAN	KPL2 protein isoform 1	879	Potential.				nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity			skin(2)|ovary(1)|central_nervous_system(1)	4	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GAAATTCTTACGACTGAAATA	0.269													6	24	---	---	---	---	PASS
DDX4	54514	broad.mit.edu	37	5	55110787	55110787	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55110787C>A	uc003jqg.3	+	20	1848	c.1774C>A	c.(1774-1776)CCA>ACA	p.P592T	DDX4_uc010ivz.2_Missense_Mutation_p.P572T|DDX4_uc003jqh.3_Missense_Mutation_p.P558T|DDX4_uc003jqj.2_Missense_Mutation_p.P443T	NM_001136034	NP_001129506	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 isoform	592	Helicase C-terminal.				multicellular organismal development|sperm motility	perinuclear region of cytoplasm|pi-body|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(1)|skin(1)	2		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				TGGAAAGTGCCCAGTTCTTGT	0.403													16	43	---	---	---	---	PASS
MAP3K1	4214	broad.mit.edu	37	5	56184162	56184162	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56184162A>G	uc003jqw.3	+	19	4868	c.4367A>G	c.(4366-4368)AAT>AGT	p.N1456S		NM_005921	NP_005912	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase	1456	Protein kinase.				cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|zinc ion binding			ovary(1)|skin(1)	2		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		AAACACTCCAATCATCTTGCT	0.388													8	23	---	---	---	---	PASS
TRIM23	373	broad.mit.edu	37	5	64905270	64905270	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64905270C>T	uc003jty.2	-	6	930	c.844G>A	c.(844-846)GAG>AAG	p.E282K	TRIM23_uc003jtw.2_Missense_Mutation_p.E282K|TRIM23_uc003jtx.2_Missense_Mutation_p.E282K	NM_001656	NP_001647	P36406	TRI23_HUMAN	ADP-ribosylation factor domain protein 1 isoform	282					interspecies interaction between organisms|small GTPase mediated signal transduction	Golgi membrane|lysosomal membrane	enzyme activator activity|GDP binding|GTP binding|GTPase activity|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|lung(1)	4		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Breast(144;0.0433)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.00473)		CGGGCATTCTCTGCAGTCCCT	0.313													8	17	---	---	---	---	PASS
ERBB2IP	55914	broad.mit.edu	37	5	65342183	65342183	+	Silent	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65342183C>A	uc003juk.1	+	18	1913	c.1605C>A	c.(1603-1605)ACC>ACA	p.T535T	ERBB2IP_uc003juh.1_Silent_p.T531T|ERBB2IP_uc003jui.1_Silent_p.T535T|ERBB2IP_uc003juj.1_Silent_p.T535T|ERBB2IP_uc011cqx.1_Silent_p.T535T|ERBB2IP_uc011cqy.1_Silent_p.T535T|ERBB2IP_uc011cqz.1_Intron|ERBB2IP_uc010iwx.1_Silent_p.T531T|ERBB2IP_uc003jul.1_Silent_p.T531T	NM_018695	NP_061165	Q96RT1	LAP2_HUMAN	ERBB2 interacting protein isoform 2	535					basal protein localization|cell adhesion|cell cycle|cell growth|epidermal growth factor receptor signaling pathway|establishment or maintenance of epithelial cell apical/basal polarity|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization	basement membrane|cytoplasm|hemidesmosome|nucleus	ErbB-2 class receptor binding|integrin binding|structural constituent of cytoskeleton			ovary(3)|lung(2)|central_nervous_system(2)	7		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		TTACTTAGACCTCAGAAAGTA	0.289													30	58	---	---	---	---	PASS
GPR98	84059	broad.mit.edu	37	5	89989742	89989742	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89989742G>C	uc003kju.2	+	33	7265	c.7169G>C	c.(7168-7170)AGT>ACT	p.S2390T	GPR98_uc003kjt.2_Missense_Mutation_p.S96T|GPR98_uc003kjv.2_5'UTR	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	2390	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TTGTTCTACAGTACTTCCGAC	0.438													5	11	---	---	---	---	PASS
GPR98	84059	broad.mit.edu	37	5	90368330	90368330	+	Silent	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90368330G>A	uc003kju.2	+	86	18315	c.18219G>A	c.(18217-18219)GTG>GTA	p.V6073V	GPR98_uc003kjt.2_Silent_p.V3779V|GPR98_uc003kjw.2_Silent_p.V1734V|GPR98_uc003kjx.2_Silent_p.V101V	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	6073	Helical; (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CGTGCCTCGTGGTGGTGTTCG	0.463													42	74	---	---	---	---	PASS
CHD1	1105	broad.mit.edu	37	5	98232003	98232003	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98232003T>G	uc003knf.2	-	11	1785	c.1637A>C	c.(1636-1638)CAA>CCA	p.Q546P		NM_001270	NP_001261	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	546	Helicase ATP-binding.				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding			lung(2)|ovary(1)|breast(1)|pancreas(1)	5		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	AATTTCCCTTTGCCAGGAAGT	0.363													11	23	---	---	---	---	PASS
FER	2241	broad.mit.edu	37	5	108207163	108207163	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108207163G>C	uc003kop.1	+	7	1147	c.763G>C	c.(763-765)GAT>CAT	p.D255H	FER_uc011cve.1_Missense_Mutation_p.D195H|FER_uc011cvf.1_RNA|FER_uc011cvg.1_Missense_Mutation_p.D80H	NM_005246	NP_005237	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	255	Important for interaction with membranes containing phosphoinositides.				intracellular signal transduction|peptidyl-tyrosine phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|kidney(1)	5		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		TGAACAGATAGATCCTAGTAC	0.323													14	22	---	---	---	---	PASS
WDR36	134430	broad.mit.edu	37	5	110461440	110461440	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110461440G>A	uc003kpd.2	+	22	2770	c.2653G>A	c.(2653-2655)GAC>AAC	p.D885N	WDR36_uc010jbu.2_RNA	NM_139281	NP_644810	Q8NI36	WDR36_HUMAN	WD repeat domain 36	885					response to stimulus|rRNA processing|visual perception	small-subunit processome				ovary(1)|skin(1)	2		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)		GATGATGCTGGACAGAAAGCG	0.453													11	40	---	---	---	---	PASS
KCNN2	3781	broad.mit.edu	37	5	113822787	113822787	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113822787T>A	uc003kqo.2	+	6	1752	c.1295T>A	c.(1294-1296)CTA>CAA	p.L432Q	KCNN2_uc003kqp.2_Missense_Mutation_p.L84Q|KCNN2_uc010jcg.2_RNA|uc003kqr.1_Intron	NM_021614	NP_067627	Q9H2S1	KCNN2_HUMAN	small conductance calcium-activated potassium	432	Calmodulin-binding (By similarity).					integral to membrane	calmodulin binding|small conductance calcium-activated potassium channel activity			ovary(2)	2		all_cancers(142;2.86e-05)|all_epithelial(76;9.33e-06)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Breast(839;0.159)|Lung NSC(810;0.174)|all_lung(232;0.206)		OV - Ovarian serous cystadenocarcinoma(64;1.89e-08)|Epithelial(69;2.04e-08)|all cancers(49;3.74e-06)|COAD - Colon adenocarcinoma(37;0.142)|Colorectal(14;0.195)		GAAACATGGCTAATTTACAAA	0.333													22	34	---	---	---	---	PASS
FBN2	2201	broad.mit.edu	37	5	127702111	127702111	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127702111C>A	uc003kuu.2	-	17	2700	c.2261G>T	c.(2260-2262)GGC>GTC	p.G754V	FBN2_uc003kuv.2_Missense_Mutation_p.G721V	NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	754	TB 3.		G -> S (in CCA).		bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		ACTACAAAGGCCGTGGAATTC	0.323													7	10	---	---	---	---	PASS
SLC27A6	28965	broad.mit.edu	37	5	128320941	128320941	+	Silent	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128320941C>A	uc003kuy.2	+	3	993	c.597C>A	c.(595-597)ACC>ACA	p.T199T	SLC27A6_uc003kuz.2_Silent_p.T199T	NM_014031	NP_054750	Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid	199					long-chain fatty acid transport|transmembrane transport|very long-chain fatty acid metabolic process	integral to membrane|sarcolemma	fatty acid transporter activity|long-chain fatty acid-CoA ligase activity|nucleotide binding				0		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)		AACTGAGCACCTCACCTGATG	0.433													19	23	---	---	---	---	PASS
IL4	3565	broad.mit.edu	37	5	132015524	132015524	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132015524A>G	uc003kxk.1	+	3	672	c.302A>G	c.(301-303)AAG>AGG	p.K101R	IL4_uc003kxl.1_Missense_Mutation_p.K85R	NM_000589	NP_000580	P05112	IL4_HUMAN	interleukin 4 isoform 1 precursor	101					B cell differentiation|cellular defense response|chemotaxis|cholesterol metabolic process|connective tissue growth factor biosynthetic process|negative regulation of apoptosis|negative regulation of osteoclast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of B cell proliferation|positive regulation of interleukin-13 production|positive regulation of isotype switching to IgE isotypes|positive regulation of isotype switching to IgG isotypes|positive regulation of MHC class II biosynthetic process|positive regulation of T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|T-helper 2 cell cytokine production	extracellular space	cytokine activity|growth factor activity|interleukin-4 receptor binding				0		all_cancers(142;2.81e-05)|all_lung(232;1.47e-05)|Lung NSC(810;2.31e-05)|all_neural(839;0.0459)|Ovarian(839;0.0481)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	GBM - Glioblastoma multiforme(465;0.00245)		CACAGGCACAAGCAGCTGATC	0.622													15	33	---	---	---	---	PASS
FBXL21	26223	broad.mit.edu	37	5	135276949	135276949	+	Silent	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135276949C>T	uc010jec.1	+	5	915	c.894C>T	c.(892-894)CAC>CAT	p.H298H	FBXL21_uc003lbc.2_Intron	NM_012159	NP_036291	Q9UKT6	FXL21_HUMAN	F-box and leucine-rich repeat protein 21	298					rhythmic process	ubiquitin ligase complex	ubiquitin-protein ligase activity			lung(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TTGTTATGCACTTCTTTCTAT	0.368													20	32	---	---	---	---	PASS
MIR886	100126299	broad.mit.edu	37	5	135416216	135416216	+	RNA	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135416216A>T	hsa-mir-886|MI0005527	-			c.82A>T																				0						GCGGGTCTCGAACCCCAGCAC	0.458													6	26	---	---	---	---	PASS
NRG2	9542	broad.mit.edu	37	5	139267090	139267090	+	Missense_Mutation	SNP	C	G	G	rs146573130	byFrequency	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139267090C>G	uc003lex.1	-	2	932	c.707G>C	c.(706-708)CGG>CCG	p.R236P	NRG2_uc003lev.1_Missense_Mutation_p.R236P|NRG2_uc003lew.1_Missense_Mutation_p.R236P|NRG2_uc003ley.1_Missense_Mutation_p.R236P	NM_004883	NP_004874	O14511	NRG2_HUMAN	neuregulin 2 isoform 1	236	Extracellular (Potential).				embryo development	extracellular region|integral to membrane|plasma membrane	growth factor activity			pancreas(2)|breast(2)|ovary(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAACTTGGGCCGGGTGGCTGT	0.587													7	4	---	---	---	---	PASS
PCDHA2	56146	broad.mit.edu	37	5	140176274	140176274	+	Silent	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140176274C>A	uc003lhd.2	+	1	1831	c.1725C>A	c.(1723-1725)GGC>GGA	p.G575G	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhc.1_Silent_p.G575G|PCDHA2_uc011czy.1_Silent_p.G575G	NM_018905	NP_061728	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2 isoform 1 precursor	575	Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGCTGCTGGCGCAGTGAGTG	0.672													30	55	---	---	---	---	PASS
PCDHA3	56145	broad.mit.edu	37	5	140180879	140180879	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140180879T>A	uc003lhf.2	+	1	97	c.97T>A	c.(97-99)TAC>AAC	p.Y33N	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA2_uc011czy.1_Intron|PCDHA3_uc011czz.1_Missense_Mutation_p.Y33N	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3 isoform 1 precursor	33	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(6)|skin(2)	8			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCAGCTCCACTACTCCGTCTC	0.657													10	27	---	---	---	---	PASS
PCDHA4	56144	broad.mit.edu	37	5	140188675	140188675	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140188675C>G	uc003lhi.2	+	1	2004	c.1903C>G	c.(1903-1905)CGT>GGT	p.R635G	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhh.1_Missense_Mutation_p.R635G|PCDHA4_uc011daa.1_Missense_Mutation_p.R635G	NM_018907	NP_061730	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4 isoform 1 precursor	635	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(4)|skin(2)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGCACAACGCGTGCCCTGGA	0.687													30	46	---	---	---	---	PASS
PCDHA13	56136	broad.mit.edu	37	5	140263823	140263823	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140263823C>A	uc003lif.2	+	1	1970	c.1970C>A	c.(1969-1971)CCC>CAC	p.P657H	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Missense_Mutation_p.P657H|PCDHA13_uc003lid.2_Missense_Mutation_p.P657H	NM_018904	NP_061727	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13 isoform 1 precursor	657	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CACGGTGAGCCCGCGCTGACG	0.692													16	32	---	---	---	---	PASS
PCDHB9	56127	broad.mit.edu	37	5	140567751	140567751	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140567751G>A	uc003liw.1	+	1	859	c.859G>A	c.(859-861)GAT>AAT	p.D287N		NM_019119	NP_061992	Q9Y5E1	PCDB9_HUMAN	protocadherin beta 9 precursor	287	Extracellular (Potential).|Cadherin 3.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGCTTCTGAAGATATTTTAAC	0.338													5	12	---	---	---	---	PASS
SH3TC2	79628	broad.mit.edu	37	5	148427424	148427424	+	Splice_Site	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148427424C>A	uc003lpu.2	-	3	431	c.279_splice	c.e3+1	p.K93_splice	SH3TC2_uc003lpp.1_Splice_Site|SH3TC2_uc003lpt.2_Splice_Site|SH3TC2_uc010jgx.2_Splice_Site_p.K93_splice|SH3TC2_uc003lpv.1_Splice_Site|SH3TC2_uc011dbz.1_Splice_Site|SH3TC2_uc003lpw.1_Missense_Mutation_p.V94L	NM_024577	NP_078853	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2								binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ttcatgctcacCTTAAACAGC	0.299													19	34	---	---	---	---	PASS
NDST1	3340	broad.mit.edu	37	5	149912589	149912589	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149912589A>C	uc003lsk.3	+	4	1593	c.1091A>C	c.(1090-1092)CAC>CCC	p.H364P	NDST1_uc011dcj.1_Missense_Mutation_p.H364P|NDST1_uc003lsl.2_Missense_Mutation_p.H364P	NM_001543	NP_001534	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan	364	Heparan sulfate N-deacetylase 1.|Lumenal (Potential).			H -> Q (in Ref. 4; AAH12888).	heparan sulfate proteoglycan biosynthetic process|inflammatory response	Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			breast(1)|skin(1)	2		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AAATTCTTCCACACAGGTAAG	0.572													21	37	---	---	---	---	PASS
C5orf4	10826	broad.mit.edu	37	5	154200021	154200021	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154200021C>A	uc003lvs.3	-	9	1028	c.857G>T	c.(856-858)TGC>TTC	p.C286F	C5orf4_uc003lvq.2_5'Flank|C5orf4_uc003lvr.2_Missense_Mutation_p.A26S|C5orf4_uc011dde.1_Missense_Mutation_p.C263F	NM_032385	NP_115761	Q96IV6	CE004_HUMAN	hypothetical protein LOC10826	286					fatty acid biosynthetic process	integral to membrane	iron ion binding|oxidoreductase activity			ovary(1)	1	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CACCCCATAGCACTGGTTGAA	0.562													14	30	---	---	---	---	PASS
DOCK2	1794	broad.mit.edu	37	5	169461420	169461420	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169461420C>A	uc003maf.2	+	35	3565	c.3485C>A	c.(3484-3486)GCA>GAA	p.A1162E	DOCK2_uc011der.1_RNA|DOCK2_uc010jjm.2_Missense_Mutation_p.A654E	NM_004946	NP_004937	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1162	DHR-2.|Interaction with CRKL.				actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GAATGTGCTGCAGAGCACCCA	0.592													19	30	---	---	---	---	PASS
COL23A1	91522	broad.mit.edu	37	5	177690210	177690210	+	Missense_Mutation	SNP	G	T	T	rs112924647		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177690210G>T	uc003mje.2	-	9	996	c.638C>A	c.(637-639)GCG>GAG	p.A213E	COL23A1_uc010jkt.2_Silent_p.R61R	NM_173465	NP_775736	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1	213	Extracellular (Potential).|Collagen-like 1.|Gly-rich.					collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)		CTCTCTTACCGCTGGGCCTTG	0.552													6	25	---	---	---	---	PASS
TBC1D9B	23061	broad.mit.edu	37	5	179305398	179305398	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179305398G>T	uc003mlh.2	-	10	1730	c.1693C>A	c.(1693-1695)CCT>ACT	p.P565T	TBC1D9B_uc003mli.2_Missense_Mutation_p.P565T|TBC1D9B_uc003mlj.2_Missense_Mutation_p.P565T	NM_198868	NP_942568	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	565	Rab-GAP TBC.					integral to membrane|intracellular	calcium ion binding|Rab GTPase activator activity			breast(1)|skin(1)	2	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGGAAGGCAGGGTGCTCGGGC	0.642													4	8	---	---	---	---	PASS
BTNL8	79908	broad.mit.edu	37	5	180338406	180338406	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180338406G>T	uc003mmp.2	+	3	699	c.465G>T	c.(463-465)CAG>CAT	p.Q155H	BTNL8_uc003mmq.2_Missense_Mutation_p.Q155H|BTNL8_uc011dhg.1_Missense_Mutation_p.Q30H|BTNL8_uc010jll.2_Missense_Mutation_p.Q155H|BTNL8_uc010jlm.2_Missense_Mutation_p.Q39H|BTNL8_uc011dhh.1_5'UTR	NM_001040462	NP_001035552	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8 isoform 2 precursor	155	Ig-like V-type 2.|Extracellular (Potential).					integral to membrane				upper_aerodigestive_tract(1)|skin(1)	2	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TACTCTGTCAGTCCTCGGGCT	0.532													54	93	---	---	---	---	PASS
PRPF4B	8899	broad.mit.edu	37	6	4032634	4032634	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4032634C>T	uc003mvv.2	+	2	974	c.883C>T	c.(883-885)CCA>TCA	p.P295S	PRPF4B_uc011dhv.1_RNA	NM_003913	NP_003904	Q13523	PRP4B_HUMAN	serine/threonine-protein kinase PRP4K	295	Arg/Lys-rich (basic).					catalytic step 2 spliceosome	ATP binding|protein binding|protein serine/threonine kinase activity			breast(5)	5	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				ATCCAGATCCCCAGTTGATTT	0.333													51	135	---	---	---	---	PASS
F13A1	2162	broad.mit.edu	37	6	6266881	6266881	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6266881A>T	uc003mwv.2	-	4	604	c.481T>A	c.(481-483)TAT>AAT	p.Y161N	F13A1_uc011dib.1_Missense_Mutation_p.Y98N	NM_000129	NP_000120	P00488	F13A_HUMAN	coagulation factor XIII A1 subunit precursor	161					peptide cross-linking|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)|skin(1)	6	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	ACAGCAACATACATGCGGAAT	0.502													18	31	---	---	---	---	PASS
CAGE1	285782	broad.mit.edu	37	6	7365779	7365779	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7365779C>A	uc003mxi.2	-	7	2347	c.1626G>T	c.(1624-1626)AAG>AAT	p.K542N	CAGE1_uc003mxh.2_RNA|CAGE1_uc003mxj.2_Missense_Mutation_p.K460N|CAGE1_uc003mxk.1_Missense_Mutation_p.K460N	NM_205864	NP_995586	Q8TC20	CAGE1_HUMAN	cancer antigen 1	678											0	Ovarian(93;0.0418)					CTCTGATACTCTTGGCTTCAT	0.368													4	34	---	---	---	---	PASS
NHLRC1	378884	broad.mit.edu	37	6	18121939	18121939	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18121939C>G	uc003ncl.1	-	1	913	c.899G>C	c.(898-900)AGT>ACT	p.S300T		NM_198586	NP_940988	Q6VVB1	NHLC1_HUMAN	NHL repeat containing 1	300	NHL 4.				proteasomal ubiquitin-dependent protein catabolic process|protein polyubiquitination	endoplasmic reticulum|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0	Ovarian(93;0.016)|Breast(50;0.0245)	all_hematologic(90;0.165)	all cancers(50;0.0451)|Epithelial(50;0.0493)			AAGCTGCATACTTGAGCTAAA	0.572													16	50	---	---	---	---	PASS
HIST1H4C	8364	broad.mit.edu	37	6	26104290	26104290	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26104290G>T	uc003ngi.2	+	1	115	c.115G>T	c.(115-117)GCT>TCT	p.A39S		NM_003542	NP_003533	P62805	H4_HUMAN	histone cluster 1, H4c	39					CenH3-containing nucleosome assembly at centromere|negative regulation of megakaryocyte differentiation|phosphatidylinositol-mediated signaling|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding				0						TCGCCGTTTGGCTCGGCGCGG	0.542													9	35	---	---	---	---	PASS
HIST1H3E	8353	broad.mit.edu	37	6	26225436	26225436	+	Silent	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26225436C>A	uc003nhb.2	+	2	414	c.54C>A	c.(52-54)CGC>CGA	p.R18R	HIST1H3E_uc003nhc.3_Silent_p.R18R	NM_021018	NP_066298	P68431	H31_HUMAN	histone cluster 1, H3f	18					blood coagulation|nucleosome assembly|regulation of gene silencing|S phase	nucleoplasm|nucleosome	DNA binding|protein binding				0		all_hematologic(11;0.0223)|Acute lymphoblastic leukemia(11;0.0351)				AAGCACCGCGCAAACAGCTGG	0.592													14	36	---	---	---	---	PASS
ZNF391	346157	broad.mit.edu	37	6	27368915	27368915	+	Nonsense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27368915A>T	uc003njf.1	+	3	1284	c.766A>T	c.(766-768)AAA>TAA	p.K256*		NM_001076781	NP_001070249	Q9UJN7	ZN391_HUMAN	zinc finger protein 391	256	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(2)|skin(1)	3						TAAATGTGGAAAAGCTTTCAG	0.443													10	25	---	---	---	---	PASS
OR14J1	442191	broad.mit.edu	37	6	29275320	29275320	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29275320C>A	uc011dln.1	+	1	854	c.854C>A	c.(853-855)CCA>CAA	p.P285Q		NM_030946	NP_112208	Q9UGF5	O14J1_HUMAN	olfactory receptor, family 5, subfamily U member	285	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						ACACTCAATCCAGTCATTTAT	0.408													22	68	---	---	---	---	PASS
MOG	4340	broad.mit.edu	37	6	29638970	29638970	+	3'UTR	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29638970C>G	uc003nnf.2	+	8					MOG_uc003nmz.2_Intron|MOG_uc011dlt.1_3'UTR|MOG_uc003nna.2_3'UTR|MOG_uc011dlu.1_3'UTR|MOG_uc011dlv.1_3'UTR|MOG_uc003nnd.2_3'UTR|MOG_uc003nne.2_Intron|MOG_uc003nng.2_Intron|MOG_uc003nnh.2_Intron|MOG_uc003nni.2_3'UTR|MOG_uc003nnj.2_3'UTR|MOG_uc003nnk.2_Intron	NM_206809	NP_996532	Q16653	MOG_HUMAN	myelin oligodendrocyte glycoprotein isoform						cell adhesion|central nervous system development|positive regulation of MyD88-dependent toll-like receptor signaling pathway	integral to membrane|plasma membrane				ovary(1)	1						TGAGTGATGTCACATCTTGGC	0.398													14	41	---	---	---	---	PASS
KIFC1	3833	broad.mit.edu	37	6	33371295	33371295	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33371295C>A	uc003oef.3	+	5	788	c.338C>A	c.(337-339)CCT>CAT	p.P113H	KIFC1_uc011drf.1_Missense_Mutation_p.P113H	NM_002263	NP_002254	Q9BW19	KIFC1_HUMAN	kinesin family member C1	113					blood coagulation|cell division|microtubule-based movement|mitotic sister chromatid segregation	early endosome|microtubule|microtubule associated complex|microtubule organizing center|nucleus|spindle	ATP binding|microtubule motor activity				0						CCTGCTGTTCCTGTCCAGAAG	0.488													5	60	---	---	---	---	PASS
DNAH8	1769	broad.mit.edu	37	6	38802366	38802366	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38802366G>T	uc003ooe.1	+	30	4263	c.3663G>T	c.(3661-3663)ATG>ATT	p.M1221I		NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						AAGGACCTATGGTTCCAAATA	0.308													27	68	---	---	---	---	PASS
DNAH8	1769	broad.mit.edu	37	6	38906009	38906009	+	Intron	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38906009C>T	uc003ooe.1	+						DNAH8_uc003oog.1_Intron|uc003oof.1_Intron	NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						CCAGGTGAGTCCTCACTACCT	0.348													18	43	---	---	---	---	PASS
KCNK5	8645	broad.mit.edu	37	6	39162006	39162006	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39162006G>T	uc003oon.2	-	4	937	c.573C>A	c.(571-573)ATC>ATA	p.I191I		NM_003740	NP_003731	O95279	KCNK5_HUMAN	potassium channel, subfamily K, member 5	191					excretion	integral to plasma membrane	potassium channel activity|voltage-gated ion channel activity			central_nervous_system(1)|skin(1)	2						AGAGGCCCTCGATGTAGTTCC	0.562													18	50	---	---	---	---	PASS
LRFN2	57497	broad.mit.edu	37	6	40399687	40399687	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40399687G>C	uc003oph.1	-	2	1631	c.1166C>G	c.(1165-1167)ACT>AGT	p.T389S		NM_020737	NP_065788	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III	389	Extracellular (Potential).					cell junction|integral to membrane|postsynaptic membrane				ovary(2)|skin(1)	3	Ovarian(28;0.0418)|Colorectal(47;0.196)					GGGGGGTGCAGTGCGGCTGGT	0.667													5	22	---	---	---	---	PASS
TDRD6	221400	broad.mit.edu	37	6	46656980	46656980	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46656980T>A	uc003oyj.2	+	1	1115	c.1115T>A	c.(1114-1116)GTG>GAG	p.V372E	TDRD6_uc010jze.2_Missense_Mutation_p.V366E	NM_001010870	NP_001010870	O60522	TDRD6_HUMAN	tudor domain containing 6	372					cell differentiation|multicellular organismal development|spermatogenesis	chromatoid body	nucleic acid binding			breast(3)|ovary(2)|skin(1)	6			Lung(136;0.192)			ATGCCGGTGGTGACCTACCCT	0.547													14	56	---	---	---	---	PASS
CRISP1	167	broad.mit.edu	37	6	49816007	49816007	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49816007C>A	uc003ozw.2	-	4	280	c.201G>T	c.(199-201)TGG>TGT	p.W67C	CRISP1_uc003ozx.2_Missense_Mutation_p.W67C	NM_001131	NP_001122	P54107	CRIS1_HUMAN	acidic epididymal glycoprotein-like 1 isoform 1	67					fusion of sperm to egg plasma membrane	extracellular space					0	Lung NSC(77;0.0358)					CCTCTTCACTCCAACTCTGTA	0.328													8	34	---	---	---	---	PASS
DEFB112	245915	broad.mit.edu	37	6	50011464	50011464	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50011464C>G	uc011dws.1	-	2	166	c.166G>C	c.(166-168)GCG>CCG	p.A56P		NM_001037498	NP_001032587	Q30KQ8	DB112_HUMAN	beta-defensin 112 precursor	56					defense response to bacterium	extracellular region				central_nervous_system(1)	1	Lung NSC(77;0.042)					CCTCCAATCGCTGTACATGAC	0.438													15	53	---	---	---	---	PASS
PKHD1	5314	broad.mit.edu	37	6	51907739	51907739	+	Silent	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51907739G>C	uc003pah.1	-	27	3291	c.3015C>G	c.(3013-3015)GCC>GCG	p.A1005A	PKHD1_uc003pai.2_Silent_p.A1005A	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	1005	IPT/TIG 4.|Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					TGGCACTGATGGCAAGACCAG	0.473													34	48	---	---	---	---	PASS
PKHD1	5314	broad.mit.edu	37	6	51907740	51907740	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51907740G>T	uc003pah.1	-	27	3290	c.3014C>A	c.(3013-3015)GCC>GAC	p.A1005D	PKHD1_uc003pai.2_Missense_Mutation_p.A1005D	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	1005	IPT/TIG 4.|Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					GGCACTGATGGCAAGACCAGA	0.473													34	49	---	---	---	---	PASS
GSTA1	2938	broad.mit.edu	37	6	52661110	52661110	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52661110C>A	uc003paz.2	-	4	254	c.142G>T	c.(142-144)GGA>TGA	p.G48*		NM_145740	NP_665683	P08263	GSTA1_HUMAN	glutathione S-transferase alpha 1	48	GST N-terminal.				glutathione metabolic process|xenobiotic metabolic process	cytosol	glutathione transferase activity			ovary(1)	1	Lung NSC(77;0.118)				Amsacrine(DB00276)|Busulfan(DB01008)|Glutathione(DB00143)	ATCAAATATCCATCTTTAGAA	0.403													5	119	---	---	---	---	PASS
DST	667	broad.mit.edu	37	6	56394534	56394534	+	Silent	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56394534T>C	uc003pdf.2	-	60	10978	c.10950A>G	c.(10948-10950)TTA>TTG	p.L3650L	DST_uc003pcz.3_Silent_p.L3472L|DST_uc011dxj.1_Silent_p.L3501L|DST_uc011dxk.1_Silent_p.L3512L|DST_uc003pcy.3_Silent_p.L3146L	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	5558	Spectrin 9.				cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CAGCCTGGTGTAAATGTTTAT	0.299													9	21	---	---	---	---	PASS
BAI3	577	broad.mit.edu	37	6	69666600	69666600	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69666600G>T	uc003pev.3	+	8	1872	c.1424G>T	c.(1423-1425)TGG>TTG	p.W475L	BAI3_uc010kak.2_Missense_Mutation_p.W475L	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	475	TSP type-1 4.|Extracellular (Potential).				negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)				GATGGCGGCTGGGAAAGGCGA	0.498													15	62	---	---	---	---	PASS
EEF1A1	1915	broad.mit.edu	37	6	74228328	74228328	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74228328C>A	uc003phi.2	-	5	815	c.778G>T	c.(778-780)GGT>TGT	p.G260C	EEF1A1_uc003phd.2_5'UTR|EEF1A1_uc003phe.2_Missense_Mutation_p.G250C|EEF1A1_uc003phf.2_Missense_Mutation_p.G260C|EEF1A1_uc003phg.2_Missense_Mutation_p.G260C|EEF1A1_uc003phh.2_Missense_Mutation_p.G106C|EEF1A1_uc003phj.2_Missense_Mutation_p.G260C|EEF1A1_uc003phk.2_Missense_Mutation_p.G260C|EEF1A1_uc003phl.2_Intron|EEF1A1_uc003phm.1_Intron	NM_001402	NP_001393	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha	260						cytosol|eukaryotic translation elongation factor 1 complex	GTP binding|GTPase activity|protein binding|translation elongation factor activity				0						GGAACAGTACCAATACCTAAA	0.413											OREG0003895	type=REGULATORY REGION|Gene=D16891|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	5	38	---	---	---	---	PASS
COL12A1	1303	broad.mit.edu	37	6	75825592	75825592	+	Silent	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75825592A>T	uc003phs.2	-	49	7771	c.7605T>A	c.(7603-7605)GCT>GCA	p.A2535A	COL12A1_uc003pht.2_Silent_p.A1371A	NM_004370	NP_004361	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1 long isoform	2535	TSP N-terminal.|Nonhelical region (NC3).				cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)|skin(1)	9						CTTGTACAGAAGCAAAATTCT	0.363													16	80	---	---	---	---	PASS
HTR1E	3354	broad.mit.edu	37	6	87726039	87726039	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87726039G>T	uc003pli.2	+	2	1690	c.987G>T	c.(985-987)CTG>CTT	p.L329L		NM_000865	NP_000856	P28566	5HT1E_HUMAN	5-hydroxytryptamine (serotonin) receptor 1E	329	Helical; Name=7; (By similarity).				G-protein signaling, coupled to cyclic nucleotide second messenger|synaptic transmission	integral to plasma membrane	protein binding|serotonin binding|serotonin receptor activity			ovary(2)|skin(1)	3		all_cancers(76;7.11e-06)|Acute lymphoblastic leukemia(125;1.2e-09)|Prostate(29;3.51e-09)|all_hematologic(105;7.43e-06)|all_epithelial(107;0.00819)		BRCA - Breast invasive adenocarcinoma(108;0.055)	Eletriptan(DB00216)	CCGACTTTCTGACGTGGCTCG	0.443													23	91	---	---	---	---	PASS
CNR1	1268	broad.mit.edu	37	6	88853983	88853983	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88853983C>A	uc011dzq.1	-	2	4574	c.1011G>T	c.(1009-1011)ATG>ATT	p.M337I	CNR1_uc010kbz.2_Missense_Mutation_p.M337I|CNR1_uc011dzr.1_Missense_Mutation_p.M337I|CNR1_uc011dzs.1_Missense_Mutation_p.M337I|CNR1_uc003pmq.3_Missense_Mutation_p.M337I|CNR1_uc011dzt.1_Missense_Mutation_p.M337I|CNR1_uc010kca.2_Missense_Mutation_p.M304I	NM_001160260	NP_001153732	P21554	CNR1_HUMAN	cannabinoid receptor 1 isoform a	337	Cytoplasmic (Potential).				G-protein signaling, coupled to cAMP nucleotide second messenger	integral to plasma membrane	cannabinoid receptor activity|protein binding			skin(2)	2		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.15)	Marinol(DB00470)|Nabilone(DB00486)|Rimonabant(DB06155)	ACCTAATGTCCATGCGGGCTT	0.557													23	64	---	---	---	---	PASS
EPHA7	2045	broad.mit.edu	37	6	93969136	93969136	+	Silent	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93969136A>T	uc003poe.2	-	10	2101	c.1860T>A	c.(1858-1860)GCT>GCA	p.A620A	EPHA7_uc003pof.2_Silent_p.A615A|EPHA7_uc011eac.1_Silent_p.A616A	NM_004440	NP_004431	Q15375	EPHA7_HUMAN	ephrin receptor EphA7 precursor	620	Cytoplasmic (Potential).					integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|ovary(7)|upper_aerodigestive_tract(3)|central_nervous_system(3)|skin(3)|large_intestine(2)|stomach(1)|pancreas(1)	28		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		ATTGATGGACAGCTCTATTTG	0.433													8	60	---	---	---	---	PASS
BEND3	57673	broad.mit.edu	37	6	107391211	107391211	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107391211T>A	uc003prs.2	-	5	1834	c.1184A>T	c.(1183-1185)CAG>CTG	p.Q395L		NM_001080450	NP_001073919	Q5T5X7	BEND3_HUMAN	BEN domain containing 3	395	BEN 2.									ovary(3)	3						AGTGAGGTCCTGCGTGTCCAC	0.632													12	57	---	---	---	---	PASS
FRK	2444	broad.mit.edu	37	6	116288787	116288787	+	Silent	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116288787A>T	uc003pwi.1	-	4	1173	c.726T>A	c.(724-726)TCT>TCA	p.S242S		NM_002031	NP_002022	P42685	FRK_HUMAN	fyn-related kinase	242	ATP (By similarity).|Protein kinase.				negative regulation of cell proliferation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			ovary(3)|lung(3)	6		all_cancers(87;0.00559)|all_epithelial(87;0.00738)|Colorectal(196;0.0465)		all cancers(137;0.0128)|OV - Ovarian serous cystadenocarcinoma(136;0.0209)|GBM - Glioblastoma multiforme(226;0.0459)|Epithelial(106;0.0625)		CAAACTGACCAGATCCCAATC	0.458													15	84	---	---	---	---	PASS
RFX6	222546	broad.mit.edu	37	6	117240292	117240292	+	Intron	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117240292C>G	uc003pxm.2	+							NM_173560	NP_775831	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6						glucose homeostasis|pancreatic A cell differentiation|pancreatic D cell differentiation|pancreatic E cell differentiation|positive regulation of transcription, DNA-dependent|regulation of insulin secretion|transcription, DNA-dependent|type B pancreatic cell differentiation	nucleus	protein binding|transcription regulatory region DNA binding			ovary(1)|pancreas(1)|skin(1)	3						ACATAGCCTTCTTTGTAGCTT	0.308													9	27	---	---	---	---	PASS
ROS1	6098	broad.mit.edu	37	6	117714485	117714485	+	Splice_Site	SNP	C	G	G	rs150002762		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117714485C>G	uc003pxp.1	-	11	1364	c.1165_splice	c.e11-1	p.V389_splice	ROS1_uc011ebi.1_Splice_Site|GOPC_uc003pxq.1_Intron	NM_002944	NP_002935	P08922	ROS_HUMAN	proto-oncogene c-ros-1 protein precursor						transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1)	25		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		AGACACATACCTAAAAAAATA	0.368			T	GOPC|ROS1	glioblastoma|NSCLC								5	139	---	---	---	---	PASS
MAN1A1	4121	broad.mit.edu	37	6	119514988	119514988	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119514988T>A	uc003pym.1	-	9	1722	c.1280A>T	c.(1279-1281)GAC>GTC	p.D427V		NM_005907	NP_005898	P33908	MA1A1_HUMAN	mannosidase, alpha, class 1A, member 1	427	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum|ER-Golgi intermediate compartment|Golgi membrane|integral to membrane|membrane fraction	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			ovary(2)|central_nervous_system(1)|skin(1)	4		all_epithelial(87;0.173)		OV - Ovarian serous cystadenocarcinoma(136;0.0612)|GBM - Glioblastoma multiforme(226;0.0702)|all cancers(137;0.115)		ATCTGTCTTGTCAGACATTAA	0.383													8	39	---	---	---	---	PASS
C6orf170	221322	broad.mit.edu	37	6	121577251	121577251	+	Silent	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121577251A>G	uc003pyo.1	-	16	1982	c.1914T>C	c.(1912-1914)TCT>TCC	p.S638S	C6orf170_uc003pyq.1_RNA|C6orf170_uc003pyp.1_Silent_p.S157S	NM_152730	NP_689943	Q96NH3	BROMI_HUMAN	hypothetical protein LOC221322	638					multicellular organismal development	cilium|cytoplasm	Rab GTPase activator activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(226;0.00521)		CCTTTGCTATAGATTCATGCA	0.338													8	20	---	---	---	---	PASS
GJA1	2697	broad.mit.edu	37	6	121768886	121768886	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121768886G>C	uc003pyr.2	+	2	1143	c.893G>C	c.(892-894)TGC>TCC	p.C298S	GJA1_uc011ebo.1_Missense_Mutation_p.C199S|GJA1_uc011ebp.1_Missense_Mutation_p.C86S	NM_000165	NP_000156	P17302	CXA1_HUMAN	connexin 43	298	Cytoplasmic (Potential).				cell-cell signaling|cellular membrane organization|gap junction assembly|heart development|muscle contraction|positive regulation of I-kappaB kinase/NF-kappaB cascade	connexon complex|Golgi-associated vesicle membrane|integral to plasma membrane|membrane raft	ion transmembrane transporter activity|signal transducer activity			ovary(2)	2				GBM - Glioblastoma multiforme(226;0.00252)	Carvedilol(DB01136)	AATTCTTCTTGCCGCAATTAC	0.493													28	68	---	---	---	---	PASS
FABP7	2173	broad.mit.edu	37	6	123101603	123101603	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123101603T>C	uc003pzf.2	+	2	535	c.241T>C	c.(241-243)TGT>CGT	p.C81R	FABP7_uc003pzd.2_Missense_Mutation_p.C81R|FABP7_uc003pze.1_Missense_Mutation_p.C81R	NM_001446	NP_001437	O15540	FABP7_HUMAN	fatty acid binding protein 7, brain	81					negative regulation of cell proliferation	cytoplasm	lipid binding|transporter activity				0				GBM - Glioblastoma multiforme(226;0.226)	Alpha-Linolenic Acid(DB00132)|gamma-Homolinolenic acid(DB00154)|Icosapent(DB00159)	TGATAGAAACTGTAAGGTGAG	0.413													10	37	---	---	---	---	PASS
CLVS2	134829	broad.mit.edu	37	6	123376952	123376952	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123376952T>G	uc003pzi.1	+	5	1546	c.677T>G	c.(676-678)ATA>AGA	p.I226R		NM_001010852	NP_001010852	Q5SYC1	CLVS2_HUMAN	retinaldehyde binding protein 1-like 2	226	CRAL-TRIO.				lysosome organization	clathrin-coated vesicle|early endosome membrane|trans-Golgi network	phosphatidylinositol-3,5-bisphosphate binding|transporter activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5						CATTTATAGATATTTTTGCAT	0.433													14	31	---	---	---	---	PASS
THEMIS	387357	broad.mit.edu	37	6	128134372	128134372	+	Missense_Mutation	SNP	C	A	A	rs144858181		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128134372C>A	uc003qbi.2	-	5	1733	c.1414G>T	c.(1414-1416)GTG>TTG	p.V472L	THEMIS_uc010kfa.2_Missense_Mutation_p.V375L|THEMIS_uc011ebt.1_Missense_Mutation_p.V472L|THEMIS_uc010kfb.2_Missense_Mutation_p.V437L	NM_001010923	NP_001010923	Q8N1K5	THMS1_HUMAN	thymocyte selection pathway associated isoform	472	CABIT 2.				negative T cell selection|positive T cell selection|T cell receptor signaling pathway	cytoplasm|nucleus				ovary(2)|skin(2)	4						GCAGCCAACACGTCCTCTTCA	0.483													5	22	---	---	---	---	PASS
THEMIS	387357	broad.mit.edu	37	6	128150997	128150997	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128150997T>A	uc003qbi.2	-	4	652	c.333A>T	c.(331-333)AGA>AGT	p.R111S	THEMIS_uc010kfa.2_Missense_Mutation_p.R14S|THEMIS_uc011ebt.1_Missense_Mutation_p.R111S|THEMIS_uc010kfb.2_Missense_Mutation_p.R76S	NM_001010923	NP_001010923	Q8N1K5	THMS1_HUMAN	thymocyte selection pathway associated isoform	111	CABIT 1.				negative T cell selection|positive T cell selection|T cell receptor signaling pathway	cytoplasm|nucleus				ovary(2)|skin(2)	4						GATGCCCTAGTCTACTTGGTC	0.383													12	34	---	---	---	---	PASS
LAMA2	3908	broad.mit.edu	37	6	129759879	129759879	+	Silent	SNP	T	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129759879T>G	uc003qbn.2	+	42	6162	c.6057T>G	c.(6055-6057)ACT>ACG	p.T2019T	LAMA2_uc003qbo.2_Silent_p.T2019T	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	2019	Domain II and I.|Potential.				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		TGAATGACACTTTGGGAAAGT	0.368													10	57	---	---	---	---	PASS
TMEM200A	114801	broad.mit.edu	37	6	130762800	130762800	+	Silent	SNP	A	G	G	rs141922342	byFrequency	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130762800A>G	uc003qca.2	+	3	2104	c.1233A>G	c.(1231-1233)GCA>GCG	p.A411A	TMEM200A_uc010kfh.2_Silent_p.A411A|TMEM200A_uc010kfi.2_Silent_p.A411A|TMEM200A_uc003qcb.2_Silent_p.A411A	NM_052913	NP_443145	Q86VY9	T200A_HUMAN	transmembrane protein 200A	411	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)		CTGTTCAGGCAGAACAACGGA	0.478													18	43	---	---	---	---	PASS
ENPP1	5167	broad.mit.edu	37	6	132197013	132197013	+	Intron	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132197013A>G	uc011ecf.1	+						ENPP1_uc003qcy.2_Intron	NM_006208	NP_006199	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase						3'-phosphoadenosine 5'-phosphosulfate metabolic process|biomineral tissue development|cellular phosphate ion homeostasis|cellular response to insulin stimulus|generation of precursor metabolites and energy|immune response|inorganic diphosphate transport|negative regulation of cell growth|negative regulation of fat cell differentiation|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of protein autophosphorylation|nucleoside triphosphate catabolic process|phosphate metabolic process|sequestering of triglyceride|water-soluble vitamin metabolic process	basolateral plasma membrane|cell surface|extracellular space|integral to membrane	ATP binding|insulin receptor binding|metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|protein homodimerization activity|scavenger receptor activity			upper_aerodigestive_tract(2)|ovary(2)	4	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)	GGTAAGTGTGAACAGGTGCCT	0.423													8	31	---	---	---	---	PASS
TXLNB	167838	broad.mit.edu	37	6	139609763	139609763	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139609763C>A	uc011eds.1	-	2	439	c.274G>T	c.(274-276)GCA>TCA	p.A92S		NM_153235	NP_694967	Q8N3L3	TXLNB_HUMAN	taxilin beta	92						cytoplasm				large_intestine(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)		GGTGATTCTGCATTCTCAGGC	0.547													23	41	---	---	---	---	PASS
SHPRH	257218	broad.mit.edu	37	6	146264293	146264293	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146264293A>T	uc003qlf.2	-	9	2623	c.2224T>A	c.(2224-2226)TCT>ACT	p.S742T	SHPRH_uc003qld.2_Missense_Mutation_p.S742T|SHPRH_uc003qle.2_Missense_Mutation_p.S742T|SHPRH_uc003qlg.1_Missense_Mutation_p.S298T|SHPRH_uc003qlj.1_Missense_Mutation_p.S631T	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a	742	Helicase ATP-binding; second part.				DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)|central_nervous_system(1)	3		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		ACTCGAAGAGATGACGACCTC	0.438													13	42	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152644691	152644691	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152644691T>C	uc010kiw.2	-	82	16441	c.15839A>G	c.(15838-15840)CAG>CGG	p.Q5280R	SYNE1_uc003qot.3_Missense_Mutation_p.Q5209R|SYNE1_uc003qou.3_Missense_Mutation_p.Q5280R|SYNE1_uc010kiz.2_Missense_Mutation_p.Q1035R	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5280	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GGCTCCATCCTGGAGCATGCT	0.562										HNSCC(10;0.0054)			4	15	---	---	---	---	PASS
SLC22A2	6582	broad.mit.edu	37	6	160671686	160671686	+	Silent	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160671686T>A	uc003qtf.2	-	3	737	c.567A>T	c.(565-567)GCA>GCT	p.A189A	SLC22A2_uc003qte.1_Silent_p.A189A|SLC22A2_uc003qth.1_Silent_p.A189A	NM_003058	NP_003049	O15244	S22A2_HUMAN	solute carrier family 22 member 2	189	Helical; (Potential).				body fluid secretion|neurotransmitter biosynthetic process|neurotransmitter secretion	integral to plasma membrane|membrane fraction	neurotransmitter transporter activity|organic cation transmembrane transporter activity			breast(1)|skin(1)	2		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.28e-17)|BRCA - Breast invasive adenocarcinoma(81;6.29e-06)		GAACTCCAGCTGCAGCATTTA	0.433													26	33	---	---	---	---	PASS
RPS6KA2	6196	broad.mit.edu	37	6	166952269	166952269	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166952269C>G	uc003qvb.1	-	2	322	c.103G>C	c.(103-105)GAA>CAA	p.E35Q	RPS6KA2_uc011ego.1_5'UTR|RPS6KA2_uc010kkl.1_5'UTR|RPS6KA2_uc003qvc.1_Missense_Mutation_p.E43Q|RPS6KA2_uc003qvd.1_Missense_Mutation_p.E60Q	NM_021135	NP_066958	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide	35					axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		ACGACGCCTTCTTCCTGCAAG	0.557													13	59	---	---	---	---	PASS
TCP10	6953	broad.mit.edu	37	6	167791471	167791471	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167791471C>A	uc003qvv.1	-	4	601	c.389G>T	c.(388-390)TGG>TTG	p.W130L	TCP10_uc003qvu.2_Missense_Mutation_p.W130L|TCP10_uc003qvw.2_Missense_Mutation_p.W106L	NM_004610	NP_004601	Q12799	TCP10_HUMAN	t-complex 10	157						cytosol				breast(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)|GBM - Glioblastoma multiforme(31;0.0386)		GTTAGATGACCATCTTTGTCC	0.493													18	71	---	---	---	---	PASS
MLLT4	4301	broad.mit.edu	37	6	168352705	168352705	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168352705C>G	uc003qwd.2	+	29	4789	c.4647C>G	c.(4645-4647)AGC>AGG	p.S1549R	MLLT4_uc003qwb.1_Missense_Mutation_p.S1534R|MLLT4_uc003qwc.1_Missense_Mutation_p.S1550R|MLLT4_uc003qwg.1_Missense_Mutation_p.S859R	NM_001040001	NP_001035090	P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	1550	Potential.				adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		CGGACCGCAGCGCCGAGGAGA	0.498			T	MLL	AL								5	19	---	---	---	---	PASS
DNAH11	8701	broad.mit.edu	37	7	21630856	21630856	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21630856G>T	uc003svc.2	+	14	2359	c.2328G>T	c.(2326-2328)ACG>ACT	p.T776T		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	776	Stem (By similarity).				microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15						TCAAACAGACGCTCCTGGAAG	0.448									Kartagener_syndrome				10	17	---	---	---	---	PASS
DNAH11	8701	broad.mit.edu	37	7	21775367	21775367	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21775367C>A	uc003svc.2	+	47	7602	c.7571C>A	c.(7570-7572)ACA>AAA	p.T2524K		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2524	AAA 3 (By similarity).|ATP (Potential).				microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15						GTGGGAAAAACAGTCTTTGTA	0.433									Kartagener_syndrome				18	34	---	---	---	---	PASS
HOXA2	3199	broad.mit.edu	37	7	27142129	27142129	+	5'UTR	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27142129C>G	uc003syh.2	-	1						NM_006735	NP_006726	O43364	HXA2_HUMAN	homeobox A2							nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2						TGGCCTTCTCCTTGGAGCCCC	0.502													14	9	---	---	---	---	PASS
FAM188B	84182	broad.mit.edu	37	7	30915170	30915170	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30915170G>T	uc003tbt.2	+	15	1947	c.1870G>T	c.(1870-1872)GAG>TAG	p.E624*	FAM188B_uc010kwe.2_Nonsense_Mutation_p.E595*|AQP1_uc011kac.1_5'UTR|FAM188B_uc003tbu.2_Nonsense_Mutation_p.E144*	NM_032222	NP_115598	Q4G0A6	F188B_HUMAN	hypothetical protein LOC84182	624											0						CGATGTGGTTGAGCTGGATTC	0.468													56	89	---	---	---	---	PASS
RALA	5898	broad.mit.edu	37	7	39730117	39730117	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39730117G>A	uc003thd.2	+	3	551	c.251G>A	c.(250-252)CGA>CAA	p.R84Q		NM_005402	NP_005393	P11233	RALA_HUMAN	ras related v-ral simian leukemia viral oncogene	84					actin cytoskeleton reorganization|cell cycle|chemotaxis|cytokinesis|exocytosis|interspecies interaction between organisms|membrane raft localization|nerve growth factor receptor signaling pathway|positive regulation of filopodium assembly|Ras protein signal transduction|regulation of exocytosis	cell surface|cleavage furrow|cytosol|midbody|plasma membrane	Edg-2 lysophosphatidic acid receptor binding|GTP binding|GTPase activity			lung(1)|skin(1)	2						AACTACTTCCGAAGTGGGGAG	0.463													18	35	---	---	---	---	PASS
C7orf10	79783	broad.mit.edu	37	7	40899991	40899991	+	Silent	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40899991C>T	uc003thn.1	+	14	1275	c.1230C>T	c.(1228-1230)CAC>CAT	p.H410H	C7orf10_uc003thm.1_Silent_p.H406H|C7orf10_uc003tho.1_Silent_p.H362H|C7orf10_uc003thp.1_RNA	NM_024728	NP_079004	Q9HAC7	CG010_HUMAN	dermal papilla derived protein 13	417							transferase activity			ovary(2)	2						ACACAACGCACATCCTGAAGG	0.577													14	48	---	---	---	---	PASS
SUN3	256979	broad.mit.edu	37	7	48026964	48026964	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48026964C>A	uc003tof.2	-	11	1134	c.1037G>T	c.(1036-1038)CGA>CTA	p.R346L	SUN3_uc010kyq.2_Missense_Mutation_p.R258L|SUN3_uc003tog.2_Missense_Mutation_p.R346L|SUN3_uc011kcf.1_Missense_Mutation_p.R334L	NM_152782	NP_689995	Q8TAQ9	SUN3_HUMAN	Sad1 and UNC84 domain containing 1	346	SUN.					integral to membrane				central_nervous_system(1)	1						GACCCTGAATCGATATAAACA	0.383													4	76	---	---	---	---	PASS
SRCRB4D	136853	broad.mit.edu	37	7	76033672	76033672	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76033672G>C	uc003ufb.2	-	2	433	c.85C>G	c.(85-87)CCT>GCT	p.P29A	ZP3_uc003ufc.3_Intron	NM_080744	NP_542782	Q8WTU2	SRB4D_HUMAN	scavenger receptor cysteine rich domain	29						extracellular region|membrane	scavenger receptor activity			pancreas(1)	1						AGGAAGGGAGGGGCAGCACTC	0.507													3	20	---	---	---	---	PASS
HGF	3082	broad.mit.edu	37	7	81331913	81331913	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81331913T>A	uc003uhl.2	-	18	2336	c.2171A>T	c.(2170-2172)AAG>ATG	p.K724M	HGF_uc003uhm.2_Missense_Mutation_p.K719M	NM_000601	NP_000592	P14210	HGF_HUMAN	hepatocyte growth factor isoform 1	724					epithelial to mesenchymal transition|mitosis|platelet activation|platelet degranulation|proteolysis|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling	platelet alpha granule lumen	growth factor activity|serine-type endopeptidase activity			ovary(2)|central_nervous_system(2)	4						CTGTGGTACCTTATATGTTAA	0.368													35	27	---	---	---	---	PASS
C7orf63	79846	broad.mit.edu	37	7	89874839	89874839	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89874839C>A	uc010lep.2	+	1	352	c.101C>A	c.(100-102)ACG>AAG	p.T34K	C7orf63_uc003ukf.2_RNA|C7orf63_uc003ukg.2_5'UTR|C7orf63_uc011khj.1_Missense_Mutation_p.T34K|C7orf63_uc010leo.2_Missense_Mutation_p.T34K	NM_001039706	NP_001034795	A5D8W1	CG063_HUMAN	hypothetical protein LOC79846 isoform 1	34							binding			ovary(1)	1						GGGGTGGTGACGGAGGACGAT	0.622													61	65	---	---	---	---	PASS
CDK14	5218	broad.mit.edu	37	7	90419888	90419888	+	Silent	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90419888G>A	uc003uky.2	+	5	687	c.465G>A	c.(463-465)AAG>AAA	p.K155K	CDK14_uc003ukt.1_Silent_p.K109K|CDK14_uc003ukv.1_Silent_p.K109K|CDK14_uc003uku.1_Silent_p.K109K|CDK14_uc003ukx.1_RNA|CDK14_uc003ukz.1_Silent_p.K137K|CDK14_uc010les.1_Silent_p.K109K|CDK14_uc011khl.1_Silent_p.R26R	NM_012395	NP_036527	O94921	CDK14_HUMAN	PFTAIRE protein kinase 1	155	Protein kinase.				cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4						TTTCTCACAGGGTAAATGGGA	0.358													14	20	---	---	---	---	PASS
HEPACAM2	253012	broad.mit.edu	37	7	92848755	92848755	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92848755G>T	uc003umm.2	-	2	112	c.89C>A	c.(88-90)TCG>TAG	p.S30*	HEPACAM2_uc003uml.2_Nonsense_Mutation_p.S18*|HEPACAM2_uc010lff.2_Nonsense_Mutation_p.S18*|HEPACAM2_uc011khy.1_Nonsense_Mutation_p.S53*	NM_001039372	NP_001034461	A8MVW5	HECA2_HUMAN	HEPACAM family member 2 isoform 1	30						integral to membrane				ovary(3)|breast(1)|kidney(1)	5						CTTCAGCCCCGAGCAAGCACC	0.517													5	114	---	---	---	---	PASS
COL1A2	1278	broad.mit.edu	37	7	94058503	94058503	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94058503G>T	uc003ung.1	+	51	4186	c.3715G>T	c.(3715-3717)GAA>TAA	p.E1239*	COL1A2_uc011kib.1_Intron	NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen precursor	1239	Fibrillar collagen NC1.				axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging		COL1A2/PLAG1(3)	soft_tissue(3)|central_nervous_system(3)|ovary(2)|skin(1)	9	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	TCTGTAGTTTGAATATAATGT	0.383										HNSCC(75;0.22)			17	21	---	---	---	---	PASS
TRRAP	8295	broad.mit.edu	37	7	98601940	98601940	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98601940C>A	uc003upp.2	+	67	10604	c.10395C>A	c.(10393-10395)TGC>TGA	p.C3465*	TRRAP_uc011kis.1_Nonsense_Mutation_p.C3436*|TRRAP_uc003upr.2_Nonsense_Mutation_p.C3171*	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	3465					histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			AGGAAAAGTGCCGGTTCTTGA	0.428													5	161	---	---	---	---	PASS
C7orf51	222950	broad.mit.edu	37	7	100086350	100086350	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100086350C>A	uc003uvd.1	+	4	1165	c.1006C>A	c.(1006-1008)CCA>ACA	p.P336T	C7orf51_uc003uve.1_Missense_Mutation_p.P118T	NM_173564	NP_775835	Q6ZVC0	CG051_HUMAN	hypothetical protein FLJ37538	336	Pro-rich.									skin(1)	1	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GCACCGGCCTCCACTCCTGGC	0.667													27	18	---	---	---	---	PASS
ACHE	43	broad.mit.edu	37	7	100490928	100490928	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100490928G>C	uc003uxd.2	-	1	1082	c.926C>G	c.(925-927)GCG>GGG	p.A309G	ACHE_uc003uxe.2_Missense_Mutation_p.A309G|ACHE_uc003uxf.2_Missense_Mutation_p.A309G|ACHE_uc003uxg.2_Missense_Mutation_p.A309G|ACHE_uc003uxh.2_Missense_Mutation_p.A309G|ACHE_uc003uxi.2_Missense_Mutation_p.A309G|ACHE_uc003uxj.1_Missense_Mutation_p.A428G	NM_000665	NP_000656	P22303	ACES_HUMAN	acetylcholinesterase isoform E4-E6 precursor	309					acetylcholine catabolic process in synaptic cleft|amyloid precursor protein metabolic process|cell adhesion|cell proliferation|choline metabolic process|DNA replication|muscle organ development|neurotransmitter biosynthetic process|osteoblast development|positive regulation of protein secretion|regulation of axonogenesis|regulation of dendrite morphogenesis|response to wounding|synapse assembly	anchored to membrane|axon|basal lamina|cell junction|cell surface|dendrite|endoplasmic reticulum lumen|extracellular space|Golgi apparatus|neuromuscular junction|nucleus|perinuclear region of cytoplasm|postsynaptic membrane|presynaptic membrane|synaptic cleft	acetylcholine binding|acetylcholinesterase activity|beta-amyloid binding|carboxylesterase activity|cholinesterase activity|collagen binding|laminin-1 binding|protein homodimerization activity|serine hydrolase activity			skin(2)	2	Lung NSC(181;0.041)|all_lung(186;0.0581)				Ambenonium(DB01122)|Atropine(DB00572)|Choline(DB00122)|Decamethonium(DB01245)|Demecarium bromide(DB00944)|Donepezil(DB00843)|Edrophonium(DB01010)|Ephedrine(DB01364)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Isoflurophate(DB00677)|Neostigmine(DB01400)|Physostigmine(DB00981)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Tacrine(DB00382)|Tubocurarine(DB01199)	CAGGACCTGCGCTGGTCGTGT	0.622													11	9	---	---	---	---	PASS
PSMC2	5701	broad.mit.edu	37	7	103004624	103004624	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103004624C>A	uc003vbs.2	+	8	696	c.626C>A	c.(625-627)CCC>CAC	p.P209H	SLC26A5_uc003vbt.1_Intron|SLC26A5_uc003vbu.1_Intron|SLC26A5_uc003vbv.1_Intron|PSMC2_uc011klo.1_Missense_Mutation_p.P72H	NM_002803	NP_002794	P35998	PRS7_HUMAN	proteasome 26S ATPase subunit 2	209					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	mitochondrion|nucleus|proteasome complex	ATP binding|ATPase activity|protein binding				0						ATTGAGCCTCCCAAGGGCGTG	0.478													5	43	---	---	---	---	PASS
SLC13A1	6561	broad.mit.edu	37	7	122774567	122774567	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122774567G>T	uc003vkm.2	-	8	854	c.829C>A	c.(829-831)CGT>AGT	p.R277S	SLC13A1_uc010lks.2_Missense_Mutation_p.R153S	NM_022444	NP_071889	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate	277						integral to membrane|plasma membrane	sodium:sulfate symporter activity			ovary(2)	2					Succinic acid(DB00139)	TTGAGGCAACGACAGTCAGGA	0.483													39	23	---	---	---	---	PASS
PLXNA4	91584	broad.mit.edu	37	7	131817907	131817907	+	Silent	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131817907G>A	uc003vra.3	-	31	5719	c.5490C>T	c.(5488-5490)AAC>AAT	p.N1830N	PLXNA4_uc003vqz.3_Silent_p.N115N	NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	1830	Cytoplasmic (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1						CCAGGTATGCGTTCATGTCTT	0.507													28	56	---	---	---	---	PASS
PLXNA4	91584	broad.mit.edu	37	7	131872222	131872222	+	Intron	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131872222T>A	uc003vra.3	-							NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1						AGGGGCCCTCTGAGTTACCTG	0.507													140	135	---	---	---	---	PASS
KIAA1549	57670	broad.mit.edu	37	7	138591710	138591710	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138591710C>A	uc011kql.1	-	6	3464	c.3415G>T	c.(3415-3417)GAG>TAG	p.E1139*	KIAA1549_uc003vuk.3_Nonsense_Mutation_p.E1089*|KIAA1549_uc011kqj.1_Nonsense_Mutation_p.E1139*	NM_020910	NP_065961	Q9HCM3	K1549_HUMAN	hypothetical protein LOC57670 isoform 1	1139						integral to membrane			KIAA1549/BRAF(229)	central_nervous_system(229)|pancreas(1)	230						AAACTGAACTCCACCACACTC	0.537			O	BRAF	pilocytic astrocytoma								46	56	---	---	---	---	PASS
MGAM	8972	broad.mit.edu	37	7	141722156	141722156	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141722156G>T	uc003vwy.2	+	7	853	c.799G>T	c.(799-801)GGA>TGA	p.G267*		NM_004668	NP_004659	O43451	MGA_HUMAN	maltase-glucoamylase	267	Lumenal (Potential).|Maltase.				polysaccharide digestion|starch catabolic process	apical plasma membrane|integral to membrane	carbohydrate binding|glucan 1,4-alpha-glucosidase activity|maltose alpha-glucosidase activity			ovary(2)	2	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GTATGGCCTGGGAGAGCATGT	0.502													66	75	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	142364538	142364538	+	Intron	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142364538C>T	uc011krp.1	+						uc011krr.1_Intron|uc003vzp.2_Intron|uc011ksh.1_Intron|uc011ksi.1_Intron|uc003vzw.1_Intron|uc010loj.1_5'Flank|uc011ksg.1_Intron|uc003vzx.3_Missense_Mutation_p.P58L					Homo sapiens mRNA for T cell receptor beta variable 3, partial cds, clone: un 191.																		CGACAAGACCCAGGACTGGGC	0.448													19	13	---	---	---	---	PASS
EPHB6	2051	broad.mit.edu	37	7	142562440	142562440	+	Silent	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142562440A>T	uc011kst.1	+	7	1669	c.882A>T	c.(880-882)GTA>GTT	p.V294V	EPHB6_uc011ksu.1_Silent_p.V294V|EPHB6_uc003wbs.2_Silent_p.V2V|EPHB6_uc003wbt.2_5'UTR|EPHB6_uc003wbu.2_Silent_p.V2V|EPHB6_uc003wbv.2_5'Flank	NM_004445	NP_004436	O15197	EPHB6_HUMAN	ephrin receptor EphB6 precursor	294	Extracellular (Potential).|Cys-rich.					extracellular region|integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1)	19	Melanoma(164;0.059)					AGTGGATGGTAGCTGTCGGGG	0.657													9	11	---	---	---	---	PASS
TRPV5	56302	broad.mit.edu	37	7	142609900	142609900	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142609900G>T	uc003wby.1	-	13	1800	c.1536C>A	c.(1534-1536)TTC>TTA	p.F512L		NM_019841	NP_062815	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel,	512	Helical; (Potential).				protein tetramerization	apical plasma membrane|integral to plasma membrane	calcium channel activity			ovary(3)|central_nervous_system(2)|skin(1)	6	Melanoma(164;0.059)					CCTCTGTCTGGAAAATGATAT	0.463													9	83	---	---	---	---	PASS
OR2A7	401427	broad.mit.edu	37	7	143956017	143956017	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143956017T>A	uc011kuc.1	-	1	705	c.705A>T	c.(703-705)AAA>AAT	p.K235N	OR2A9P_uc003wec.1_Intron|uc003wed.2_5'Flank	NM_001005328	NP_001005328	Q96R45	OR2A7_HUMAN	olfactory receptor, family 2, subfamily A,	235	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	Melanoma(164;0.14)					TGCAGAAGGCTTTCCTCTGAA	0.478													8	81	---	---	---	---	PASS
ZNF746	155061	broad.mit.edu	37	7	149191124	149191124	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149191124T>C	uc003wfw.2	-	3	633	c.362A>G	c.(361-363)TAC>TGC	p.Y121C	ZNF746_uc010lpi.2_Missense_Mutation_p.Y121C	NM_152557	NP_689770	Q6NUN9	ZN746_HUMAN	zinc finger protein 746 isoform 2	121	KRAB.				negative regulation of transcription, DNA-dependent|neuron death|regulation of cell death|transcription, DNA-dependent	cytoplasm|nucleus	transcription regulatory region DNA binding|ubiquitin protein ligase binding|zinc ion binding			ovary(2)|breast(1)	3	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			CACGTGCTTGTAGAGCTCCTT	0.532													7	130	---	---	---	---	PASS
SSPO	23145	broad.mit.edu	37	7	149478003	149478003	+	Silent	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149478003C>T	uc010lpk.2	+	13	1774	c.1774C>T	c.(1774-1776)CTG>TTG	p.L592L	SSPO_uc010lpl.1_Intron	NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	592	VWFD 2.				cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CCGCTACAGCCTGGTGCAGGT	0.642													15	7	---	---	---	---	PASS
GBX1	2636	broad.mit.edu	37	7	150846205	150846205	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150846205T>C	uc011kvg.1	-	2	795	c.563A>G	c.(562-564)GAT>GGT	p.D188G		NM_001098834	NP_001092304	Q14549	GBX1_HUMAN	gastrulation brain homeo box 1	188						nuclear chromosome	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CTTCTCCTCATCTGAGCTGTA	0.572													55	181	---	---	---	---	PASS
ASB10	136371	broad.mit.edu	37	7	150883938	150883938	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150883938G>T	uc003wjm.1	-	1	541	c.415C>A	c.(415-417)CGA>AGA	p.R139R	ASB10_uc003wjl.1_Silent_p.R139R|ASB10_uc003wjn.1_Intron	NM_001142459	NP_001135931	Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box-containing 10	94					intracellular signal transduction						0			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TCCCTCCATCGCTCTGGGTCG	0.642													10	8	---	---	---	---	PASS
ASB10	136371	broad.mit.edu	37	7	150884185	150884185	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150884185C>G	uc003wjm.1	-	1	294	c.168G>C	c.(166-168)AAG>AAC	p.K56N	ASB10_uc003wjl.1_Missense_Mutation_p.K56N|ASB10_uc003wjn.1_Intron	NM_001142459	NP_001135931	Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box-containing 10	11					intracellular signal transduction						0			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CTCCCTGCCCCTTGCACTCTT	0.562													4	1	---	---	---	---	PASS
GALNT11	63917	broad.mit.edu	37	7	151791434	151791434	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151791434C>T	uc010lqg.1	+	2	352	c.122C>T	c.(121-123)CCC>CTC	p.P41L	GALNT11_uc011kvm.1_Intron|GALNT11_uc003wku.2_Missense_Mutation_p.P41L|GALNT11_uc003wkv.1_Missense_Mutation_p.P41L|GALNT11_uc011kvn.1_RNA	NM_022087	NP_071370	Q8NCW6	GLT11_HUMAN	N-acetylgalactosaminyltransferase 11	41	Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.214)	OV - Ovarian serous cystadenocarcinoma(82;0.00168)	UCEC - Uterine corpus endometrioid carcinoma (81;0.177)|BRCA - Breast invasive adenocarcinoma(188;0.0932)		AAGAATGTGCCCGTCAAGGGG	0.473													6	106	---	---	---	---	PASS
MLL3	58508	broad.mit.edu	37	7	151851428	151851428	+	Silent	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151851428C>A	uc003wla.2	-	47	12282	c.12063G>T	c.(12061-12063)CTG>CTT	p.L4021L	MLL3_uc003wkz.2_Silent_p.L3139L|MLL3_uc003wkx.2_Silent_p.L179L|MLL3_uc003wky.2_Silent_p.L1585L	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	4021					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)		TGACCAATGACAGATCTGGAT	0.488			N		medulloblastoma								34	82	---	---	---	---	PASS
MLL3	58508	broad.mit.edu	37	7	151962250	151962250	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151962250G>A	uc003wla.2	-	8	1276	c.1057C>T	c.(1057-1059)CTC>TTC	p.L353F		NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	353	PHD-type 1.|RING-type.				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)		TGATCTAAGAGGTCTCCCGGG	0.403			N		medulloblastoma								8	202	---	---	---	---	PASS
ARHGEF10	9639	broad.mit.edu	37	8	1851599	1851599	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1851599C>A	uc003wpr.2	+	16	1981	c.1803C>A	c.(1801-1803)AAC>AAA	p.N601K	ARHGEF10_uc003wpq.1_Missense_Mutation_p.N625K|ARHGEF10_uc003wps.2_Missense_Mutation_p.N563K|ARHGEF10_uc003wpt.2_Missense_Mutation_p.N477K|ARHGEF10_uc003wpv.2_Missense_Mutation_p.N334K|ARHGEF10_uc010lre.2_Missense_Mutation_p.N281K	NM_014629	NP_055444	O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor 10	626					centrosome duplication|myelination in peripheral nervous system|positive regulation of GTP catabolic process|positive regulation of stress fiber assembly|regulation of Rho protein signal transduction|spindle assembly involved in mitosis	centrosome|cytosol|soluble fraction	kinesin binding|Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		AAGCCATAAACGAAAGATACC	0.393													13	47	---	---	---	---	PASS
CSMD1	64478	broad.mit.edu	37	8	2796240	2796240	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2796240C>T	uc011kwk.1	-	70	10955	c.10565G>A	c.(10564-10566)GGC>GAC	p.G3522D	CSMD1_uc011kwj.1_Missense_Mutation_p.G2836D|CSMD1_uc010lrg.2_Missense_Mutation_p.G1413D	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	3522	Cytoplasmic (Potential).					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CCCAGCATAGCCATTGTATTG	0.418													7	17	---	---	---	---	PASS
CSMD1	64478	broad.mit.edu	37	8	2965277	2965277	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2965277C>A	uc011kwk.1	-	45	7191	c.6801G>T	c.(6799-6801)CAG>CAT	p.Q2267H	CSMD1_uc011kwj.1_Missense_Mutation_p.Q1659H|CSMD1_uc010lrg.2_Missense_Mutation_p.Q335H	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	2267	Extracellular (Potential).|Sushi 13.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GCATTTCTGCCTGTGGAACCG	0.358													8	53	---	---	---	---	PASS
BLK	640	broad.mit.edu	37	8	11403590	11403590	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11403590G>T	uc003wty.2	+	3	734	c.153G>T	c.(151-153)CCG>CCT	p.P51P	BLK_uc003wtz.2_5'UTR	NM_001715	NP_001706	P51451	BLK_HUMAN	B lymphoid tyrosine kinase	51					intracellular protein kinase cascade|positive regulation of insulin secretion		ATP binding|non-membrane spanning protein tyrosine kinase activity			large_intestine(1)|stomach(1)|ovary(1)	3			STAD - Stomach adenocarcinoma(15;0.00391)	COAD - Colon adenocarcinoma(149;0.207)		CTCCTCCACCGCCCGATGAAC	0.547													18	117	---	---	---	---	PASS
PCM1	5108	broad.mit.edu	37	8	17822100	17822100	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17822100C>G	uc003wyi.3	+	18	3100	c.2678C>G	c.(2677-2679)TCT>TGT	p.S893C	PCM1_uc011kyh.1_Missense_Mutation_p.S893C|PCM1_uc003wyj.3_Missense_Mutation_p.S894C	NM_006197	NP_006188	Q15154	PCM1_HUMAN	pericentriolar material 1	893					centrosome organization|cilium assembly|G2/M transition of mitotic cell cycle|interkinetic nuclear migration|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome	centriolar satellite|cytosol|nuclear membrane|pericentriolar material	identical protein binding		PCM1/JAK2(30)	haematopoietic_and_lymphoid_tissue(30)|breast(4)|ovary(2)	36				Colorectal(111;0.0789)		TGGGGAGGGTCTACCCAGTGT	0.393			T	RET|JAK2	papillary thyroid|CML|MPD								5	41	---	---	---	---	PASS
INTS10	55174	broad.mit.edu	37	8	19700393	19700393	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19700393G>T	uc003wzj.2	+	14	1805	c.1674G>T	c.(1672-1674)AAG>AAT	p.K558N		NM_018142	NP_060612	Q9NVR2	INT10_HUMAN	integrator complex subunit 10	558					snRNA processing	integrator complex	protein binding			ovary(1)	1				Colorectal(111;0.057)|COAD - Colon adenocarcinoma(73;0.215)		GTACCAGCAAGGCTATCATGC	0.348													20	53	---	---	---	---	PASS
DOCK5	80005	broad.mit.edu	37	8	25258515	25258515	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25258515A>T	uc003xeg.2	+	47	4996	c.4859A>T	c.(4858-4860)GAG>GTG	p.E1620V	PPP2R2A_uc003xek.2_Intron|DOCK5_uc003xej.2_RNA	NM_024940	NP_079216	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1620	DHR-2.					cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		CCGCTGCATGAGCGGTTGTCT	0.483													13	104	---	---	---	---	PASS
TEX15	56154	broad.mit.edu	37	8	30700808	30700808	+	Nonsense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30700808G>C	uc003xil.2	-	1	5726	c.5726C>G	c.(5725-5727)TCA>TGA	p.S1909*		NM_031271	NP_112561	Q9BXT5	TEX15_HUMAN	testis expressed 15	1909										ovary(3)|upper_aerodigestive_tract(2)|skin(2)	7				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		CTTCTTTTGTGAGTATTTTTT	0.323													10	46	---	---	---	---	PASS
ADAM2	2515	broad.mit.edu	37	8	39624568	39624568	+	Intron	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39624568G>C	uc003xnj.2	-						ADAM2_uc003xnk.2_Intron|ADAM2_uc011lck.1_Intron|ADAM2_uc003xnl.2_Intron	NM_001464	NP_001455	Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2 proprotein						cell adhesion|fusion of sperm to egg plasma membrane|proteolysis	integral to plasma membrane	integrin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)		ATAAACTGATGGGATGAGGTA	0.338													6	43	---	---	---	---	PASS
CHD7	55636	broad.mit.edu	37	8	61693855	61693855	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61693855G>T	uc003xue.2	+	3	2439	c.1962G>T	c.(1960-1962)AAG>AAT	p.K654N		NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	654	Lys-rich.				central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity	p.556_871dup(1)		ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			AAGACCCGAAGGAACCGAAAG	0.438													8	20	---	---	---	---	PASS
C8orf34	116328	broad.mit.edu	37	8	69688635	69688635	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69688635G>T	uc010lyz.2	+	11	1197	c.1148G>T	c.(1147-1149)GGA>GTA	p.G383V	C8orf34_uc003xyb.2_Missense_Mutation_p.G358V	NM_052958	NP_443190	Q49A92	CH034_HUMAN	hypothetical protein LOC116328	383					signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			TACTTCTAGGGAGAAGCCTCC	0.398													9	50	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77765818	77765818	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77765818G>C	uc003yav.2	+	10	6913	c.6526G>C	c.(6526-6528)GAT>CAT	p.D2176H	ZFHX4_uc003yau.1_Missense_Mutation_p.D2221H|ZFHX4_uc003yaw.1_Missense_Mutation_p.D2176H	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	2176						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TTACAAATCTGATGCATCATT	0.373										HNSCC(33;0.089)			14	47	---	---	---	---	PASS
ZNF704	619279	broad.mit.edu	37	8	81555340	81555340	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81555340C>A	uc003yby.1	-	8	1289	c.1057G>T	c.(1057-1059)GGC>TGC	p.G353C		NM_001033723	NP_001028895	Q6ZNC4	ZN704_HUMAN	zinc finger protein 704	353						intracellular	zinc ion binding				0	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)			TCTCCTGTGCCCACCGGATGA	0.527													5	22	---	---	---	---	PASS
WWP1	11059	broad.mit.edu	37	8	87423938	87423938	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87423938C>G	uc003ydt.2	+	9	1176	c.896C>G	c.(895-897)ACC>AGC	p.T299S	WWP1_uc010mai.2_Missense_Mutation_p.T75S	NM_007013	NP_008944	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase	299					central nervous system development|entry of virus into host cell|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|signal transduction	cytoplasm|nucleus|plasma membrane|ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			lung(1)|liver(1)	2						ATTCCTTCTACCAGTGCAGAA	0.393													13	28	---	---	---	---	PASS
DCAF4L2	138009	broad.mit.edu	37	8	88885776	88885776	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88885776G>A	uc003ydz.2	-	1	521	c.424C>T	c.(424-426)CTT>TTT	p.L142F		NM_152418	NP_689631	Q8NA75	DC4L2_HUMAN	WD repeat domain 21C	142										ovary(1)	1						CACAGCAGAAGGTGGGAATCC	0.567													4	50	---	---	---	---	PASS
SLC26A7	115111	broad.mit.edu	37	8	92378817	92378817	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92378817C>A	uc003yex.2	+	15	1776	c.1498C>A	c.(1498-1500)CAG>AAG	p.Q500K	SLC26A7_uc003yey.2_RNA|SLC26A7_uc003yez.2_Missense_Mutation_p.Q500K|SLC26A7_uc003yfa.2_Missense_Mutation_p.Q500K	NM_052832	NP_439897	Q8TE54	S26A7_HUMAN	solute carrier family 26, member 7 isoform a	500	STAS.|Cytoplasmic (Potential).					basolateral plasma membrane|integral to membrane|recycling endosome membrane	anion:anion antiporter activity|bicarbonate transmembrane transporter activity|chloride channel activity|oxalate transmembrane transporter activity|sulfate transmembrane transporter activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(11;0.00802)			GGAAACCCTGCAGCAGGTGAA	0.318													9	17	---	---	---	---	PASS
UBR5	51366	broad.mit.edu	37	8	103284843	103284843	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103284843T>C	uc003ykr.1	-	48	6920	c.6887A>G	c.(6886-6888)TAT>TGT	p.Y2296C	UBR5_uc003yks.1_Missense_Mutation_p.Y2296C	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	2296					cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			AATGGCTGTATAAAAACTTCG	0.408													17	35	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113569084	113569084	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113569084C>A	uc003ynu.2	-	25	4301	c.4142G>T	c.(4141-4143)TGC>TTC	p.C1381F	CSMD3_uc003yns.2_Missense_Mutation_p.C653F|CSMD3_uc003ynt.2_Missense_Mutation_p.C1341F|CSMD3_uc011lhx.1_Missense_Mutation_p.C1277F	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	1381	Extracellular (Potential).|Sushi 7.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						GCCTGGATTGCATCCATAAAT	0.483										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			8	43	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113697808	113697808	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113697808G>C	uc003ynu.2	-	15	2468	c.2309C>G	c.(2308-2310)TCC>TGC	p.S770C	CSMD3_uc003yns.2_Missense_Mutation_p.S42C|CSMD3_uc003ynt.2_Missense_Mutation_p.S730C|CSMD3_uc011lhx.1_Missense_Mutation_p.S666C	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	770	Extracellular (Potential).|CUB 4.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						ATCAAACTGGGATTCCAGGTC	0.428										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			13	58	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	114290852	114290852	+	Silent	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114290852A>G	uc003ynu.2	-	3	642	c.483T>C	c.(481-483)GTT>GTC	p.V161V	CSMD3_uc003ynt.2_Silent_p.V121V|CSMD3_uc011lhx.1_Silent_p.V161V|CSMD3_uc010mcx.1_Silent_p.V161V	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	161	Extracellular (Potential).|CUB 1.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						CATGAGCACTAACTGCAAAAT	0.373										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			15	26	---	---	---	---	PASS
ENPP2	5168	broad.mit.edu	37	8	120608089	120608089	+	Intron	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120608089T>C	uc003yot.1	-						ENPP2_uc003yor.1_5'Flank|ENPP2_uc003yos.1_Missense_Mutation_p.K376E|ENPP2_uc010mdd.1_Intron	NM_001040092	NP_001035181	Q13822	ENPP2_HUMAN	autotaxin isoform 2 preproprotein						cellular component movement|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|phosphate metabolic process|phosphatidylcholine catabolic process|regulation of cell migration	extracellular space|integral to plasma membrane	alkylglycerophosphoethanolamine phosphodiesterase activity|calcium ion binding|lysophospholipase activity|nucleic acid binding|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)|kidney(1)	7	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			AAACTTACTTTGTCCTGACGA	0.448													7	86	---	---	---	---	PASS
PHF20L1	51105	broad.mit.edu	37	8	133856422	133856422	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133856422G>A	uc003ytt.2	+	20	3095	c.2770G>A	c.(2770-2772)GTA>ATA	p.V924I	PHF20L1_uc011lja.1_Missense_Mutation_p.V898I	NM_016018	NP_057102	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1 isoform 1	924							nucleic acid binding|zinc ion binding			ovary(2)	2	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			AGGGAATACAGTATTTGTTTA	0.408													9	43	---	---	---	---	PASS
WISP1	8840	broad.mit.edu	37	8	134239682	134239682	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134239682A>T	uc003yub.2	+	5	909	c.833A>T	c.(832-834)CAG>CTG	p.Q278L	WISP1_uc003yuc.2_Missense_Mutation_p.Q191L|WISP1_uc010meb.2_Missense_Mutation_p.Q106L|WISP1_uc010mec.2_Silent_p.P126P|WISP1_uc010med.2_Missense_Mutation_p.Q33L|WISP1_uc003yud.2_RNA	NM_003882	NP_003873	O95388	WISP1_HUMAN	WNT1 inducible signaling pathway protein 1	278	CTCK.				cell adhesion|cell-cell signaling|regulation of cell growth|Wnt receptor signaling pathway	extracellular region|soluble fraction	insulin-like growth factor binding			central_nervous_system(1)|kidney(1)	2	all_epithelial(106;5.39e-23)|Lung NSC(106;7.26e-07)|all_lung(105;2.77e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0107)			GCTGTGTACCAGCCAGAGGCA	0.537													16	16	---	---	---	---	PASS
FAM135B	51059	broad.mit.edu	37	8	139180280	139180280	+	Silent	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139180280G>A	uc003yuy.2	-	12	1287	c.1116C>T	c.(1114-1116)CAC>CAT	p.H372H	FAM135B_uc003yux.2_Silent_p.H273H|FAM135B_uc003yuz.2_RNA	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	372										ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			ACAGCTGGCTGTGCGTCTGTA	0.592										HNSCC(54;0.14)			20	65	---	---	---	---	PASS
FAM135B	51059	broad.mit.edu	37	8	139263259	139263259	+	Splice_Site	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139263259T>A	uc003yuy.2	-	6	540	c.369_splice	c.e6-1	p.Q123_splice	FAM135B_uc003yux.2_Splice_Site_p.Q24_splice|FAM135B_uc003yuz.2_Splice_Site	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059											ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			TCCCTCAACCTAGAAGGCAAG	0.532										HNSCC(54;0.14)			6	30	---	---	---	---	PASS
HEATR7A	727957	broad.mit.edu	37	8	145278049	145278049	+	Silent	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145278049C>T	uc003zbk.3	+	14	1491	c.1254C>T	c.(1252-1254)GCC>GCT	p.A418A	HEATR7A_uc011lla.1_Silent_p.A418A|HEATR7A_uc010mft.2_Silent_p.A418A	NM_032450	NP_115826	Q8NDA8	HTR7A_HUMAN	HEAT repeat containing 7A isoform 1	418	HEAT 4.						binding				0						GCGCCATGGCCCACCACGGCT	0.642													5	7	---	---	---	---	PASS
GLIS3	169792	broad.mit.edu	37	9	3898798	3898798	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3898798G>T	uc003zhw.1	-	6	1750	c.1556C>A	c.(1555-1557)ACA>AAA	p.T519K	GLIS3_uc003zhx.1_Missense_Mutation_p.T674K|GLIS3_uc010mhf.1_Missense_Mutation_p.T68K|GLIS3_uc003zhv.1_RNA|GLIS3_uc003zhy.1_Missense_Mutation_p.T452K|GLIS3_uc003zhz.1_Missense_Mutation_p.T452K|C9orf70_uc003zia.2_RNA	NM_152629	NP_689842	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3 isoform b	519					negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		GAGGCAATCTGTGAGCAGGTC	0.597													4	27	---	---	---	---	PASS
TTC39B	158219	broad.mit.edu	37	9	15192619	15192619	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15192619C>A	uc003zlr.1	-	9	822	c.701G>T	c.(700-702)GGT>GTT	p.G234V	TTC39B_uc003zlq.1_Missense_Mutation_p.G203V|TTC39B_uc011lmp.1_Missense_Mutation_p.G135V|TTC39B_uc010mie.1_Missense_Mutation_p.G232V|TTC39B_uc011lmq.1_Missense_Mutation_p.G234V|TTC39B_uc011lmr.1_Missense_Mutation_p.G165V|TTC39B_uc010mif.1_Missense_Mutation_p.G234V|TTC39B_uc003zls.1_Missense_Mutation_p.G135V|TTC39B_uc010mig.1_Missense_Mutation_p.G203V|TTC39B_uc011lms.1_RNA	NM_152574	NP_689787	Q5VTQ0	TT39B_HUMAN	tetratricopeptide repeat domain 39B	234							binding			ovary(1)	1						AAGCTTGACACCCCCTTCAAA	0.408													28	53	---	---	---	---	PASS
CDKN2A	1029	broad.mit.edu	37	9	21974677	21974677	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21974677C>G	uc003zpk.2	-	1	362	c.150G>C	c.(148-150)CAG>CAC	p.Q50H	MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_Missense_Mutation_p.Q50H|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_Intron	NM_000077	NP_000068	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A isoform 1	50	ANK 2.		Q -> R (in CMM2).		cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding	p.0?(1112)|p.?(25)|p.Q50*(5)|p.Q50R(1)|p.V28_V51del(1)		haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1)	3678		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		CTCTACCCACCTGGATCGGCC	0.677		17							Uveal_Melanoma_Familial|Familial_Malignant_Melanoma_and_Tumors_of_the_Nervous_System|Hereditary_Melanoma	HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)			45	46	---	---	---	---	PASS
C9orf72	203228	broad.mit.edu	37	9	27567113	27567113	+	Silent	SNP	C	T	T	rs138028443		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27567113C>T	uc003zqq.2	-	2	103	c.6G>A	c.(4-6)TCG>TCA	p.S2S	C9orf72_uc003zqr.1_Silent_p.S2S	NM_018325	NP_060795	Q96LT7	CI072_HUMAN	hypothetical protein LOC203228 isoform a	2										ovary(3)|central_nervous_system(1)	4		all_neural(11;7.57e-10)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)		GGCAAAGAGTCGACATCACTG	0.403													14	21	---	---	---	---	PASS
ARID3C	138715	broad.mit.edu	37	9	34623546	34623546	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34623546G>T	uc011lon.1	-	4	741	c.741C>A	c.(739-741)GAC>GAA	p.D247E		NM_001017363	NP_001017363	A6NKF2	ARI3C_HUMAN	AT rich interactive domain 3C (BRIGHT- like)	247	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.175)		CCAAGGCTGGGTCCTGAGCGC	0.736													6	5	---	---	---	---	PASS
RECK	8434	broad.mit.edu	37	9	36100327	36100327	+	Splice_Site	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36100327G>T	uc003zyv.2	+	11	1172	c.1086_splice	c.e11-1	p.R362_splice	RECK_uc003zyw.2_Splice_Site_p.R234_splice|RECK_uc003zyx.2_Splice_Site	NM_021111	NP_066934	O95980	RECK_HUMAN	RECK protein precursor							anchored to membrane|peripheral to membrane of membrane fraction|plasma membrane	metalloendopeptidase inhibitor activity|serine-type endopeptidase inhibitor activity			skin(2)|ovary(1)	3			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)			TTTCTCTTTAGGCCAACAGAA	0.378													4	16	---	---	---	---	PASS
CCIN	881	broad.mit.edu	37	9	36170237	36170237	+	Silent	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36170237C>A	uc003zzb.3	+	1	849	c.738C>A	c.(736-738)ACC>ACA	p.T246T		NM_005893	NP_005884	Q13939	CALI_HUMAN	calicin	246					cell differentiation|multicellular organismal development|spermatogenesis	cytoskeletal calyx	structural constituent of cytoskeleton			ovary(1)|skin(1)	2			STAD - Stomach adenocarcinoma(86;0.228)			TGGAGAACACCTCATCCCATA	0.507													9	24	---	---	---	---	PASS
TRPM3	80036	broad.mit.edu	37	9	73151786	73151786	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73151786A>G	uc004aid.2	-	25	4451	c.4207T>C	c.(4207-4209)TAT>CAT	p.Y1403H	TRPM3_uc004ahu.2_Missense_Mutation_p.Y1245H|TRPM3_uc004ahv.2_Missense_Mutation_p.Y1205H|TRPM3_uc004ahw.2_Missense_Mutation_p.Y1275H|TRPM3_uc004ahx.2_Missense_Mutation_p.Y1262H|TRPM3_uc004ahy.2_Missense_Mutation_p.Y1265H|TRPM3_uc004ahz.2_Missense_Mutation_p.Y1252H|TRPM3_uc004aia.2_Missense_Mutation_p.Y1250H|TRPM3_uc004aib.2_Missense_Mutation_p.Y1240H|TRPM3_uc004aic.2_Intron	NM_001007471	NP_001007472	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel,	1428	Cytoplasmic (Potential).					integral to membrane	calcium channel activity			ovary(3)|pancreas(2)|central_nervous_system(2)|skin(2)	9						GCAGAGACATAGATGTCTATA	0.502													23	33	---	---	---	---	PASS
TRPM6	140803	broad.mit.edu	37	9	77457212	77457212	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77457212G>A	uc004ajl.1	-	4	438	c.200C>T	c.(199-201)TCC>TTC	p.S67F	TRPM6_uc004ajk.1_Missense_Mutation_p.S62F|TRPM6_uc010mpb.1_RNA|TRPM6_uc010mpc.1_Missense_Mutation_p.S67F|TRPM6_uc010mpd.1_Missense_Mutation_p.S67F|TRPM6_uc010mpe.1_Missense_Mutation_p.S67F|TRPM6_uc004ajn.1_Missense_Mutation_p.S67F	NM_017662	NP_060132	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel,	67	Cytoplasmic (Potential).				response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	8						GATGGTCCAGGAATAATCTAT	0.393													24	70	---	---	---	---	PASS
PRUNE2	158471	broad.mit.edu	37	9	79322427	79322427	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79322427G>C	uc010mpk.2	-	8	4887	c.4763C>G	c.(4762-4764)ACC>AGC	p.T1588S		NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	1588					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0						GCCATCAGTGGTAATTAGTTC	0.408													16	40	---	---	---	---	PASS
PRUNE2	158471	broad.mit.edu	37	9	79403320	79403320	+	Intron	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79403320C>G	uc010mpk.2	-							NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2						apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0						CTACTTTCCTCTTTGTAAACT	0.204													4	14	---	---	---	---	PASS
PRUNE2	158471	broad.mit.edu	37	9	79441626	79441626	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79441626C>G	uc010mpk.2	-	5	655	c.531G>C	c.(529-531)ATG>ATC	p.M177I	PRUNE2_uc004akn.2_Missense_Mutation_p.M177I	NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	177					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0						ATTCCATGGTCATCCACTTGA	0.418													6	57	---	---	---	---	PASS
PRUNE2	158471	broad.mit.edu	37	9	79441638	79441638	+	Silent	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79441638A>G	uc010mpk.2	-	5	643	c.519T>C	c.(517-519)CTT>CTC	p.L173L	PRUNE2_uc004akn.2_Silent_p.L173L	NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	173					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0						TCCACTTGAAAAGAATGCTAC	0.423													5	55	---	---	---	---	PASS
PHF2	5253	broad.mit.edu	37	9	96418814	96418814	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96418814C>G	uc004aub.2	+	9	1231	c.1084C>G	c.(1084-1086)CAG>GAG	p.Q362E	PHF2_uc011lug.1_Missense_Mutation_p.Q245E	NM_005392	NP_005383	O75151	PHF2_HUMAN	PHD finger protein 2	362					liver development|negative regulation of chromatin silencing at rDNA|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K9 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		CAGCCTGACTCAGTTTCCCAA	0.557													35	70	---	---	---	---	PASS
KIAA1529	57653	broad.mit.edu	37	9	100119949	100119949	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100119949C>A	uc011lut.1	+	37	4627	c.3854C>A	c.(3853-3855)TCT>TAT	p.S1285Y	KIAA1529_uc004axe.1_Missense_Mutation_p.S1117Y|KIAA1529_uc004axg.1_Missense_Mutation_p.S1146Y|KIAA1529_uc004axh.1_RNA|KIAA1529_uc011luw.1_Missense_Mutation_p.S302Y	NM_020893	NP_065944			hypothetical protein LOC57653											ovary(4)|large_intestine(2)|skin(1)	7		Acute lymphoblastic leukemia(62;0.154)				TTAAATTTCTCTCTGCAACAG	0.358													6	112	---	---	---	---	PASS
ANKS6	203286	broad.mit.edu	37	9	101518738	101518738	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101518738T>A	uc004ayu.2	-	12	2311	c.2290A>T	c.(2290-2292)AGT>TGT	p.S764C	ANKS6_uc004ayt.2_Missense_Mutation_p.S463C|ANKS6_uc004ayv.1_Missense_Mutation_p.S227C|ANKS6_uc004ayw.1_Missense_Mutation_p.S347C|ANKS6_uc004ayx.1_RNA|ANKS6_uc004ayy.1_RNA	NM_173551	NP_775822	Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain	764	Ser-rich.									ovary(2)	2		Acute lymphoblastic leukemia(62;0.0527)				GAGCCCCCACTGCTCTTGGAC	0.602													13	24	---	---	---	---	PASS
CYLC2	1539	broad.mit.edu	37	9	105767117	105767117	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105767117G>T	uc004bbs.2	+	4	391	c.321G>T	c.(319-321)GTG>GTT	p.V107V		NM_001340	NP_001331	Q14093	CYLC2_HUMAN	cylicin 2	107	31 X 3 AA repeats of K-K-X.				cell differentiation|multicellular organismal development|spermatogenesis	cytoskeletal calyx	structural constituent of cytoskeleton			skin(1)	1		all_hematologic(171;0.125)				CTGTCGAGGTGGATTCTAAAG	0.363													4	19	---	---	---	---	PASS
PALM2-AKAP2	445815	broad.mit.edu	37	9	112918631	112918631	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112918631C>G	uc004bej.3	+	9	3208	c.3028C>G	c.(3028-3030)CCC>GCC	p.P1010A	PALM2-AKAP2_uc004bek.3_Missense_Mutation_p.P1010A|AKAP2_uc011lwi.1_Missense_Mutation_p.P868A|AKAP2_uc004bem.2_Missense_Mutation_p.P868A|AKAP2_uc011lwj.1_Missense_Mutation_p.P779A|PALM2-AKAP2_uc004ben.2_Intron	NM_007203	NP_009134	Q9Y2D5	AKAP2_HUMAN	PALM2-AKAP2 protein isoform 1	779							enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6						TCCTCCATCCCCCACCACTGA	0.498													8	52	---	---	---	---	PASS
AKNA	80709	broad.mit.edu	37	9	117103916	117103916	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117103916G>T	uc004biq.3	-	20	4099	c.3964C>A	c.(3964-3966)CCC>ACC	p.P1322T	AKNA_uc004bin.3_Missense_Mutation_p.P569T|AKNA_uc004bio.3_Missense_Mutation_p.P782T|AKNA_uc004bip.3_Missense_Mutation_p.P1241T|AKNA_uc004bir.3_Missense_Mutation_p.P1322T|AKNA_uc004bis.3_Missense_Mutation_p.P1322T|AKNA_uc010mve.2_Missense_Mutation_p.P1203T	NM_030767	NP_110394	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1322					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(4)|central_nervous_system(2)	6						AGTCCGGGGGGTGGGCGTGGC	0.637													4	23	---	---	---	---	PASS
TNC	3371	broad.mit.edu	37	9	117810681	117810681	+	Silent	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117810681C>G	uc004bjj.3	-	16	5072	c.4710G>C	c.(4708-4710)CTG>CTC	p.L1570L	TNC_uc010mvf.2_Intron	NM_002160	NP_002151	P24821	TENA_HUMAN	tenascin C precursor	1570	Fibronectin type-III 11.				cell adhesion|response to wounding|signal transduction	extracellular space	receptor binding|syndecan binding			central_nervous_system(4)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	7						CCTGGGGGTCCAGCAGCTTCC	0.512													5	37	---	---	---	---	PASS
ASTN2	23245	broad.mit.edu	37	9	120176822	120176822	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120176822G>T	uc004bjs.1	-	1	496	c.395C>A	c.(394-396)GCG>GAG	p.A132E	ASTN2_uc004bjr.1_Missense_Mutation_p.A132E|ASTN2_uc004bjt.1_Missense_Mutation_p.A132E	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c	132	Extracellular (Potential).					integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						GTCCTGCACCGCGATGCGCCC	0.721													6	7	---	---	---	---	PASS
RC3H2	54542	broad.mit.edu	37	9	125613661	125613661	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125613661C>A	uc010mwc.1	-	19	3413	c.3172G>T	c.(3172-3174)GAG>TAG	p.E1058*	uc004bnb.1_5'Flank|RC3H2_uc004bnc.2_RNA|RC3H2_uc004bnd.1_Nonsense_Mutation_p.E1058*	NM_001100588	NP_001094058	Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type zinc finger domains 2	1058						cell surface|endomembrane system|membrane|membrane fraction|perinuclear region of cytoplasm	DNA binding|zinc ion binding			ovary(2)|lung(2)	4						AGCTCTAACTCGATATCCCTA	0.308													12	31	---	---	---	---	PASS
TAF3	83860	broad.mit.edu	37	10	8055717	8055717	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8055717G>T	uc010qbd.1	+	6	2592	c.2592G>T	c.(2590-2592)CAG>CAT	p.Q864H		NM_031923	NP_114129	Q5VWG9	TAF3_HUMAN	RNA polymerase II transcription factor TAFII140	864					maintenance of protein location in nucleus|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding			ovary(1)	1						GGGGCAATCAGATCTGGATCT	0.517													28	41	---	---	---	---	PASS
UPF2	26019	broad.mit.edu	37	10	11997498	11997498	+	Silent	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11997498T>C	uc001ila.2	-	13	3057	c.2583A>G	c.(2581-2583)CAA>CAG	p.Q861Q	UPF2_uc001ilb.2_Silent_p.Q861Q|UPF2_uc001ilc.2_Silent_p.Q861Q|UPF2_uc009xiz.1_Silent_p.Q861Q	NM_080599	NP_542166	Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog	861	Sufficient for interaction with UPF3A and UPF3B.|MIF4G 3.|Sufficient for interaction with EIF4A1 and EIF1.				mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	exon-exon junction complex|perinuclear region of cytoplasm	identical protein binding|RNA binding			central_nervous_system(2)|ovary(1)	3		Renal(717;0.228)				TAAATTTAGGTTGATTAACCT	0.343													12	32	---	---	---	---	PASS
FAM107B	83641	broad.mit.edu	37	10	14572459	14572459	+	5'UTR	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14572459G>A	uc001imx.1	-	2					FAM107B_uc001ina.1_Silent_p.I175I|FAM107B_uc010qbu.1_RNA|FAM107B_uc009xjg.1_5'UTR|FAM107B_uc001imy.1_5'UTR|FAM107B_uc001imz.1_5'UTR	NM_031453	NP_113641	Q9H098	F107B_HUMAN	hypothetical protein LOC83641											breast(4)	4						GCTCGGCCATGATGCTTCTTG	0.423													5	35	---	---	---	---	PASS
RPP38	10557	broad.mit.edu	37	10	15145543	15145543	+	Missense_Mutation	SNP	G	T	T	rs141142473		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15145543G>T	uc001iny.3	+	3	943	c.230G>T	c.(229-231)AGA>ATA	p.R77I	RPP38_uc009xjm.2_Missense_Mutation_p.R77I|RPP38_uc001inx.3_Missense_Mutation_p.R77I	NM_183005	NP_892117	P78345	RPP38_HUMAN	ribonuclease P/MRP 38 subunit	77					tRNA processing	nucleolar ribonuclease P complex	protein binding|ribonuclease P activity			ovary(1)	1						AAAGAAAGCAGAGAGAAATGC	0.418													5	9	---	---	---	---	PASS
PLXDC2	84898	broad.mit.edu	37	10	20453385	20453385	+	Intron	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20453385G>C	uc001iqg.1	+						PLXDC2_uc001iqh.1_Intron|PLXDC2_uc009xkc.1_Intron	NM_032812	NP_116201	Q6UX71	PXDC2_HUMAN	plexin domain containing 2 precursor							integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4						TACCTGCTTTGTTTTTTTCCA	0.413													12	9	---	---	---	---	PASS
NEBL	10529	broad.mit.edu	37	10	21115440	21115440	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21115440C>T	uc001iqi.2	-	18	2202	c.1805G>A	c.(1804-1806)GGC>GAC	p.G602D	NEBL_uc001iqj.2_RNA|NEBL_uc001iqk.2_Intron|NEBL_uc001iql.1_RNA	NM_006393	NP_006384	O76041	NEBL_HUMAN	nebulette sarcomeric isoform	602	Nebulin 17.				regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2						CACTGCAGTGCCAGCTCCCAC	0.343													32	42	---	---	---	---	PASS
ANKRD26	22852	broad.mit.edu	37	10	27306604	27306604	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27306604C>A	uc001ith.2	-	30	4502	c.4330G>T	c.(4330-4332)GAA>TAA	p.E1444*	ANKRD26_uc001itg.2_Nonsense_Mutation_p.E1131*|ANKRD26_uc009xku.1_Nonsense_Mutation_p.E1445*	NM_014915	NP_055730	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1444	Potential.					centrosome				large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|skin(1)	4						TGTAGTTTTTCACATTTCTTT	0.343													20	16	---	---	---	---	PASS
ZEB1	6935	broad.mit.edu	37	10	31809581	31809581	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31809581G>A	uc001ivs.3	+	7	1381	c.1318G>A	c.(1318-1320)GAA>AAA	p.E440K	ZEB1_uc001ivr.3_Missense_Mutation_p.E222K|ZEB1_uc010qee.1_Missense_Mutation_p.E222K|ZEB1_uc010qef.1_Missense_Mutation_p.E222K|ZEB1_uc009xlj.1_Missense_Mutation_p.E366K|ZEB1_uc010qeg.1_Missense_Mutation_p.E299K|ZEB1_uc009xlk.1_Missense_Mutation_p.E222K|ZEB1_uc001ivt.3_Missense_Mutation_p.E222K|ZEB1_uc001ivu.3_Missense_Mutation_p.E441K|ZEB1_uc001ivv.3_Missense_Mutation_p.E420K|ZEB1_uc010qeh.1_Missense_Mutation_p.E373K|ZEB1_uc009xlo.1_Missense_Mutation_p.E423K|ZEB1_uc009xlp.2_Missense_Mutation_p.E424K	NM_030751	NP_110378	P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1 isoform b	440					cell proliferation|immune response|negative regulation of transcription from RNA polymerase II promoter|positive regulation of neuron differentiation	cytoplasm	E-box binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(3)|central_nervous_system(2)	5		Prostate(175;0.0156)				TGCATCCAAAGAACAAGAAAC	0.368													15	13	---	---	---	---	PASS
CCDC7	221016	broad.mit.edu	37	10	32780844	32780844	+	Intron	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32780844T>A	uc001iwj.2	+						CCDC7_uc009xlu.1_Intron|CCDC7_uc001iwk.2_Intron|CCDC7_uc009xlv.2_Intron|CCDC7_uc009xlw.1_Intron|CCDC7_uc009xlx.1_Intron|CCDC7_uc009xly.1_Intron	NM_145023	NP_659460	Q96M83	CCDC7_HUMAN	coiled-coil domain containing 7												0		Breast(68;0.000207)|Prostate(175;0.0107)				ACTTTTTAAATAATAGAAACT	0.279													11	42	---	---	---	---	PASS
ANKRD30A	91074	broad.mit.edu	37	10	37508167	37508167	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37508167C>G	uc001iza.1	+	34	3458	c.3359C>G	c.(3358-3360)ACA>AGA	p.T1120R		NM_052997	NP_443723	Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1176	Potential.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(7)|breast(1)|skin(1)	9						GCTGAGAACACAATGCTCACT	0.383													45	79	---	---	---	---	PASS
GDF2	2658	broad.mit.edu	37	10	48413941	48413941	+	Silent	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48413941A>T	uc001jfa.1	-	2	1090	c.927T>A	c.(925-927)GCT>GCA	p.A309A		NM_016204	NP_057288	Q9UK05	GDF2_HUMAN	growth differentiation factor 2 precursor	309					activin receptor signaling pathway|BMP signaling pathway|cartilage development|cellular iron ion homeostasis|growth|negative regulation of angiogenesis|negative regulation of blood vessel endothelial cell migration|negative regulation of cell growth|negative regulation of DNA replication|negative regulation of endothelial cell proliferation|ossification|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|positive regulation of angiogenesis|positive regulation of endothelial cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of transcription, DNA-dependent	extracellular space	cytokine activity|growth factor activity			ovary(2)|skin(1)	3						TCGACCCCGCAGCCACGTGGC	0.612													11	12	---	---	---	---	PASS
MAPK8	5599	broad.mit.edu	37	10	49628312	49628312	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49628312C>T	uc009xnz.2	+	6	789	c.565C>T	c.(565-567)CGC>TGC	p.R189C	MAPK8_uc001jgl.2_Missense_Mutation_p.R189C|MAPK8_uc001jgm.2_Missense_Mutation_p.R189C|MAPK8_uc001jgo.2_Missense_Mutation_p.R189C|MAPK8_uc009xoa.2_Missense_Mutation_p.R189C|MAPK8_uc001jgn.2_Missense_Mutation_p.R189C|MAPK8_uc010qgk.1_Missense_Mutation_p.R189C|MAPK8_uc001jgp.2_Missense_Mutation_p.R189C|MAPK8_uc001jgq.2_Missense_Mutation_p.R189C	NM_139047	NP_620635	P45983	MK08_HUMAN	mitogen-activated protein kinase 8 isoform JNK1	189	Protein kinase.				activation of pro-apoptotic gene products|cellular response to mechanical stimulus|induction of apoptosis by intracellular signals|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of apoptosis|negative regulation of protein binding|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of deacetylase activity|regulation of protein localization|regulation of sequence-specific DNA binding transcription factor activity|response to UV|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|histone deacetylase binding|histone deacetylase regulator activity|JUN kinase activity|protein binding			central_nervous_system(3)|lung(2)|stomach(1)|ovary(1)|kidney(1)	8		Ovarian(717;0.0221)|Lung SC(717;0.113)|all_neural(218;0.116)		Epithelial(53;3.46e-65)|Lung(62;0.125)		TGTAGTGACTCGCTACTACAG	0.408													22	35	---	---	---	---	PASS
MAPK8	5599	broad.mit.edu	37	10	49628313	49628313	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49628313G>T	uc009xnz.2	+	6	790	c.566G>T	c.(565-567)CGC>CTC	p.R189L	MAPK8_uc001jgl.2_Missense_Mutation_p.R189L|MAPK8_uc001jgm.2_Missense_Mutation_p.R189L|MAPK8_uc001jgo.2_Missense_Mutation_p.R189L|MAPK8_uc009xoa.2_Missense_Mutation_p.R189L|MAPK8_uc001jgn.2_Missense_Mutation_p.R189L|MAPK8_uc010qgk.1_Missense_Mutation_p.R189L|MAPK8_uc001jgp.2_Missense_Mutation_p.R189L|MAPK8_uc001jgq.2_Missense_Mutation_p.R189L	NM_139047	NP_620635	P45983	MK08_HUMAN	mitogen-activated protein kinase 8 isoform JNK1	189	Protein kinase.				activation of pro-apoptotic gene products|cellular response to mechanical stimulus|induction of apoptosis by intracellular signals|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of apoptosis|negative regulation of protein binding|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of deacetylase activity|regulation of protein localization|regulation of sequence-specific DNA binding transcription factor activity|response to UV|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|histone deacetylase binding|histone deacetylase regulator activity|JUN kinase activity|protein binding			central_nervous_system(3)|lung(2)|stomach(1)|ovary(1)|kidney(1)	8		Ovarian(717;0.0221)|Lung SC(717;0.113)|all_neural(218;0.116)		Epithelial(53;3.46e-65)|Lung(62;0.125)		GTAGTGACTCGCTACTACAGA	0.408													22	35	---	---	---	---	PASS
C10orf71	118461	broad.mit.edu	37	10	50530641	50530641	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50530641C>G	uc010qgp.1	+	3	390	c.51C>G	c.(49-51)AGC>AGG	p.S17R		NM_199459	NP_955629	Q711Q0	CJ071_HUMAN	hypothetical protein LOC118461 isoform 2	17											0						ACTCCTCCAGCATCGGCAGCG	0.552													6	15	---	---	---	---	PASS
AGAP7	653268	broad.mit.edu	37	10	51465367	51465367	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51465367G>C	uc001jio.2	-	7	1215	c.1089C>G	c.(1087-1089)ATC>ATG	p.I363M	PARG_uc001jih.2_Intron|uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron	NM_001077685	NP_001071153	Q5VUJ5	AGAP7_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH	363	PH.				regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding				0						TGAGCTTGGGGATGGTGGTGC	0.517													4	96	---	---	---	---	PASS
USP54	159195	broad.mit.edu	37	10	75290488	75290488	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75290488G>A	uc001juo.2	-	11	1438	c.1421C>T	c.(1420-1422)CCC>CTC	p.P474L	USP54_uc001juk.2_5'UTR|USP54_uc001jul.2_5'UTR|USP54_uc001jum.2_RNA|USP54_uc001jun.2_RNA|USP54_uc001jup.2_Missense_Mutation_p.P474L|USP54_uc010qkl.1_Missense_Mutation_p.P474L	NM_152586	NP_689799	Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	474					ubiquitin-dependent protein catabolic process		protein binding|ubiquitin thiolesterase activity			breast(3)|lung(2)|kidney(1)	6	Prostate(51;0.0112)					CGAGGCCTGGGGCTCATCGCC	0.502													9	31	---	---	---	---	PASS
LRIT1	26103	broad.mit.edu	37	10	85992438	85992438	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85992438C>A	uc001kcz.1	-	4	1139	c.1117G>T	c.(1117-1119)GCT>TCT	p.A373S		NM_015613	NP_056428	Q9P2V4	LRIT1_HUMAN	retina specific protein PAL	373	Lumenal (Potential).					integral to endoplasmic reticulum membrane					0						TTGTTGTAAGCAGCAGCTTCC	0.587													3	7	---	---	---	---	PASS
PANK1	53354	broad.mit.edu	37	10	91405006	91405006	+	Silent	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91405006C>G	uc001kgp.1	-	1	210	c.54G>C	c.(52-54)GCG>GCC	p.A18A	PANK1_uc001kgn.1_5'Flank|PANK1_uc001kgo.1_5'Flank|PANK1_uc009xtu.1_5'Flank	NM_148977	NP_683878	Q8TE04	PANK1_HUMAN	pantothenate kinase 1 isoform alpha	18					coenzyme A biosynthetic process|pantothenate metabolic process	cytosol|nucleus	ATP binding|pantothenate kinase activity				0					Bezafibrate(DB01393)	GACTGGTCCCCGCCACTGAGC	0.692													4	4	---	---	---	---	PASS
NT5C2	22978	broad.mit.edu	37	10	104854165	104854165	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104854165C>A	uc001kwo.2	-	13	1047	c.861G>T	c.(859-861)TTG>TTT	p.L287F	NT5C2_uc010qqp.1_Missense_Mutation_p.L258F|NT5C2_uc001kwq.2_Missense_Mutation_p.L287F|NT5C2_uc001kwp.2_Missense_Mutation_p.L134F	NM_012229	NP_036361	P49902	5NTC_HUMAN	5'-nucleotidase, cytosolic II	287					purine base metabolic process|purine nucleotide catabolic process	cytosol	5'-nucleotidase activity|metal ion binding|nucleotide binding|protein binding				0		all_hematologic(284;0.176)|Colorectal(252;0.178)		Epithelial(162;1.33e-08)|all cancers(201;1.04e-07)|BRCA - Breast invasive adenocarcinoma(275;0.159)	Adenosine triphosphate(DB00171)|Ribavirin(DB00811)	GTGCATCCACCAAGATCAAGT	0.473													4	27	---	---	---	---	PASS
GPAM	57678	broad.mit.edu	37	10	113924340	113924340	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113924340G>A	uc009xxy.1	-	13	1448	c.1250C>T	c.(1249-1251)CCG>CTG	p.P417L	GPAM_uc001kzp.2_Missense_Mutation_p.P417L|GPAM_uc001kzq.1_Missense_Mutation_p.P417L	NM_020918	NP_065969	Q9HCL2	GPAT1_HUMAN	mitochondrial glycerol 3-phosphate	417					phospholipid biosynthetic process|triglyceride biosynthetic process	integral to membrane|mitochondrial outer membrane	glycerol-3-phosphate O-acyltransferase activity			ovary(1)|skin(1)	2				Epithelial(162;0.0306)|all cancers(201;0.123)		AGCAGACACCGGTTTCTGACT	0.368													13	25	---	---	---	---	PASS
NRAP	4892	broad.mit.edu	37	10	115348836	115348836	+	Silent	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115348836C>G	uc001laj.2	-	42	5255	c.5091G>C	c.(5089-5091)CGG>CGC	p.R1697R	HABP2_uc001lai.3_3'UTR|NRAP_uc009xyb.2_Silent_p.R450R|NRAP_uc001lak.2_Silent_p.R1662R|NRAP_uc001lal.3_Silent_p.R1698R	NM_198060	NP_932326	Q86VF7	NRAP_HUMAN	nebulin-related anchoring protein isoform S	1697				R -> Q (in Ref. 3; CAD89899).		fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)|upper_aerodigestive_tract(1)	10		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		CTTCTGCCCCCCGCTGCTGAA	0.562													12	14	---	---	---	---	PASS
FANK1	92565	broad.mit.edu	37	10	127685989	127685989	+	Silent	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127685989G>A	uc001ljh.3	+	6	578	c.474G>A	c.(472-474)AGG>AGA	p.R158R	FANK1_uc009yan.2_Silent_p.R184R|FANK1_uc001lji.2_Silent_p.R152R	NM_145235	NP_660278	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains	158	ANK 2.					cytoplasm|nucleus				ovary(1)	1		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				TTTCCTTTAGGCTTGTGAAAA	0.408													12	26	---	---	---	---	PASS
PPP2R2D	55844	broad.mit.edu	37	10	133769242	133769242	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133769242G>T	uc001lks.2	+	7	1281	c.1038G>T	c.(1036-1038)ACG>ACT	p.T346T	PPP2R2D_uc001lkr.2_Silent_p.T152T|PPP2R2D_uc001lkt.2_Silent_p.T152T|PPP2R2D_uc009yay.2_Silent_p.T214T	NM_018461	NP_060931	Q66LE6	2ABD_HUMAN	protein phosphatase 2, regulatory subunit B,	379	WD 6.				cell division|exit from mitosis|mitosis|signal transduction	cytoplasm|protein phosphatase type 2A complex	protein phosphatase type 2A regulator activity			skin(1)	1		all_cancers(35;2.16e-12)|all_epithelial(44;2.77e-09)|Lung NSC(174;0.00237)|all_lung(145;0.00354)|Colorectal(31;0.0124)|Breast(234;0.023)|all_neural(114;0.0299)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;7.86e-05)|Epithelial(32;8.82e-05)|all cancers(32;0.000106)|BRCA - Breast invasive adenocarcinoma(275;0.21)		ATAGAGACACGCGGAGGGATG	0.582													4	16	---	---	---	---	PASS
MUC5B	727897	broad.mit.edu	37	11	1267049	1267049	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1267049C>T	uc009ycr.1	+	49	10814	c.10688C>T	c.(10687-10689)ACG>ATG	p.T3563M	MUC5B_uc001ltb.2_Missense_Mutation_p.T2983M	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	2980	7 X Cys-rich subdomain repeats.|Thr-rich.|17 X approximate tandem repeats, Ser/Thr- rich.			Missing (in Ref. 6; AAB61398).	cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		ACCAGCTCTACGGCCACGCCC	0.617													11	100	---	---	---	---	PASS
OR51L1	119682	broad.mit.edu	37	11	5020998	5020998	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5020998G>C	uc010qyu.1	+	1	786	c.786G>C	c.(784-786)ATG>ATC	p.M262I		NM_001004755	NP_001004755	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L,	262	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		GGGTGTCAATGGTCCATCGCT	0.463													4	30	---	---	---	---	PASS
OR52A4	390053	broad.mit.edu	37	11	5142501	5142501	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5142501A>G	uc001lzz.1	-	1	308	c.308T>C	c.(307-309)TTT>TCT	p.F103S	OR52A4_uc001maa.2_RNA	NM_001005222	NP_001005222			olfactory receptor, family 52, subfamily A,											ovary(2)	2		Medulloblastoma(188;0.0049)|all_neural(188;0.0442)|Breast(177;0.0675)		Epithelial(150;1.7e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.2)		CCACATCTGAAAGAGGCAAGC	0.463													5	40	---	---	---	---	PASS
UBQLNL	143630	broad.mit.edu	37	11	5537174	5537174	+	Silent	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5537174C>A	uc001maz.3	-	1	783	c.498G>T	c.(496-498)GTG>GTT	p.V166V	HBG2_uc001mak.1_Intron	NM_145053	NP_659490	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	166										large_intestine(2)|skin(1)	3		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)		CTGGGTGGCTCACTTCCAAGT	0.507													16	40	---	---	---	---	PASS
FAM160A2	84067	broad.mit.edu	37	11	6238899	6238899	+	Silent	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6238899T>A	uc001mcl.3	-	9	2276	c.1917A>T	c.(1915-1917)CCA>CCT	p.P639P	FAM160A2_uc001mck.3_Silent_p.P653P|FAM160A2_uc001mcm.2_Silent_p.P639P	NM_001098794	NP_001092264	Q8N612	F16A2_HUMAN	hypothetical protein LOC84067 isoform 2	639					early endosome to late endosome transport|endosome organization|endosome to lysosome transport|lysosome organization|protein transport	FHF complex	protein binding			skin(2)	2						GCCATGATCCTGGCACTCCAT	0.443													8	18	---	---	---	---	PASS
FAM160A2	84067	broad.mit.edu	37	11	6243821	6243821	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6243821T>A	uc001mcl.3	-	6	1401	c.1042A>T	c.(1042-1044)ATC>TTC	p.I348F	FAM160A2_uc001mck.3_Missense_Mutation_p.I348F|FAM160A2_uc001mcm.2_Missense_Mutation_p.I348F	NM_001098794	NP_001092264	Q8N612	F16A2_HUMAN	hypothetical protein LOC84067 isoform 2	348					early endosome to late endosome transport|endosome organization|endosome to lysosome transport|lysosome organization|protein transport	FHF complex	protein binding			skin(2)	2						GTACTGGCGATCATCTCCTCC	0.502													9	29	---	---	---	---	PASS
CCKBR	887	broad.mit.edu	37	11	6290904	6290904	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6290904G>T	uc001mcp.2	+	2	350	c.157G>T	c.(157-159)GAG>TAG	p.E53*	CCKBR_uc001mcq.2_5'UTR|CCKBR_uc001mcr.2_Nonsense_Mutation_p.E53*|CCKBR_uc001mcs.2_Nonsense_Mutation_p.E53*	NM_176875	NP_795344	P32239	GASR_HUMAN	cholecystokinin B receptor	53	Extracellular (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|cell proliferation|digestion|elevation of cytosolic calcium ion concentration|feeding behavior|positive regulation of cell proliferation|sensory perception		1-phosphatidylinositol-3-kinase regulator activity|gastrin receptor activity|phosphatidylinositol phospholipase C activity|type B gastrin/cholecystokinin receptor binding			lung(5)|ovary(2)|breast(1)	8		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139)	Pentagastrin(DB00183)	CCCAGAATTGGAGCTGGCCAT	0.537													8	20	---	---	---	---	PASS
APBB1	322	broad.mit.edu	37	11	6423795	6423795	+	Intron	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6423795C>A	uc001mdb.1	-						APBB1_uc001mcz.1_Intron|APBB1_uc001mdd.3_Intron|APBB1_uc001mda.2_Intron|APBB1_uc001mdc.1_Intron|APBB1_uc010rab.1_5'Flank|APBB1_uc010rac.1_5'Flank|APBB1_uc010rad.1_Intron|APBB1_uc010rae.1_Intron|APBB1_uc010raf.1_Nonstop_Mutation_p.*163L|APBB1_uc009yfa.2_Intron|APBB1_uc009yey.2_Intron|APBB1_uc010rag.1_Intron|APBB1_uc009yfb.2_Intron|APBB1_uc001mde.2_Intron|APBB1_uc010rah.1_Intron	NM_001164	NP_001155	O00213	APBB1_HUMAN	amyloid beta A4 precursor protein-binding,						apoptosis|axonogenesis|cell cycle arrest|histone H4 acetylation|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of thymidylate synthase biosynthetic process|positive regulation of apoptosis|positive regulation of transcription, DNA-dependent|response to DNA damage stimulus|signal transduction|transcription, DNA-dependent	cytoplasm|growth cone|lamellipodium|nucleus|plasma membrane|synapse	beta-amyloid binding|chromatin binding|histone binding|proline-rich region binding|transcription factor binding			breast(2)	2		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		ACCCCCGGCTCAGGTCCTTAC	0.572													11	21	---	---	---	---	PASS
DCHS1	8642	broad.mit.edu	37	11	6661842	6661842	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6661842G>T	uc001mem.1	-	2	1413	c.1003C>A	c.(1003-1005)CGA>AGA	p.R335R		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	335	Extracellular (Potential).|Cadherin 3.				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCACCATCTCGTGCTTGCACC	0.587													12	54	---	---	---	---	PASS
OR6A2	8590	broad.mit.edu	37	11	6816414	6816414	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6816414G>T	uc001mes.1	-	1	726	c.526C>A	c.(526-528)CCC>ACC	p.P176T		NM_003696	NP_003687	O95222	OR6A2_HUMAN	olfactory receptor, family 6, subfamily A,	176	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		ATGATGTTGGGGCCACAGTAA	0.493													14	86	---	---	---	---	PASS
NAV2	89797	broad.mit.edu	37	11	20005798	20005798	+	Intron	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20005798G>C	uc010rdm.1	+						NAV2_uc001mpp.2_Intron|NAV2_uc001mpr.3_Intron	NM_145117	NP_660093	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 2							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6						TGACAGGTAAGCTTGCTGCAC	0.577													10	35	---	---	---	---	PASS
KCNA4	3739	broad.mit.edu	37	11	30033705	30033705	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30033705C>A	uc001msk.2	-	2	1673	c.521G>T	c.(520-522)TGT>TTT	p.C174F		NM_002233	NP_002224	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related	174						voltage-gated potassium channel complex	potassium ion binding|protein binding|voltage-gated potassium channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4						ACGTTCACAACAGTCACTGTA	0.502													7	24	---	---	---	---	PASS
PAX6	5080	broad.mit.edu	37	11	31822244	31822244	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31822244G>A	uc001mtd.3	-	6	1408	c.518C>T	c.(517-519)ACG>ATG	p.T173M	PAX6_uc001mte.3_Missense_Mutation_p.T173M|PAX6_uc001mtg.3_Missense_Mutation_p.T187M|PAX6_uc001mtf.3_Missense_Mutation_p.T173M|PAX6_uc001mth.3_Missense_Mutation_p.T173M|PAX6_uc009yjr.2_Missense_Mutation_p.T173M	NM_001127612	NP_001121084	P26367	PAX6_HUMAN	paired box gene 6 isoform a	173	Gln/Gly-rich.				blood vessel development|central nervous system development|cornea development in camera-type eye|glucose homeostasis|iris morphogenesis|negative regulation of neurogenesis|neuron fate commitment|pancreatic A cell development|positive regulation of transcription, DNA-dependent|response to wounding|visual perception	cytoplasm|nuclear chromatin	R-SMAD binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|ubiquitin-protein ligase activity			lung(4)|ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	9	Lung SC(675;0.225)					TTTACCTTGCGTAGGTTGCCC	0.572									Wilms_tumor-Aniridia-ambiguous_Genitals-mental_Retardation				41	74	---	---	---	---	PASS
FOLH1	2346	broad.mit.edu	37	11	49214371	49214371	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49214371C>A	uc001ngy.2	-	4	748	c.487G>T	c.(487-489)GCT>TCT	p.A163S	FOLH1_uc001ngz.2_Missense_Mutation_p.A163S|FOLH1_uc009yly.2_Missense_Mutation_p.A148S|FOLH1_uc009ylz.2_Missense_Mutation_p.A148S|FOLH1_uc009yma.2_5'UTR|FOLH1_uc001nha.2_Missense_Mutation_p.A148S	NM_004476	NP_004467	Q04609	FOLH1_HUMAN	folate hydrolase 1 isoform 1	163	Extracellular (Probable).				proteolysis	cytoplasm|integral to plasma membrane|membrane fraction|nucleus	carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity			large_intestine(1)|ovary(1)|skin(1)	3					Capromab(DB00089)|L-Glutamic Acid(DB00142)	GGAGAGAAAGCACTGAAAGGT	0.348													11	41	---	---	---	---	PASS
OR5D13	390142	broad.mit.edu	37	11	55541493	55541493	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55541493C>A	uc010ril.1	+	1	580	c.580C>A	c.(580-582)CCC>ACC	p.P194T		NM_001001967	NP_001001967	Q8NGL4	OR5DD_HUMAN	olfactory receptor, family 5, subfamily D,	194	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)|skin(1)	3		all_epithelial(135;0.196)				CTACTCAGACCCCTATATCAG	0.353													23	73	---	---	---	---	PASS
OR5L1	219437	broad.mit.edu	37	11	55578934	55578934	+	5'Flank	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55578934A>T	uc001nhw.1	+							NM_001004738	NP_001004738	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)|ovary(2)	5		all_epithelial(135;0.208)				TCTCATATAAATTGGAGACAT	0.383													12	101	---	---	---	---	PASS
OR5W2	390148	broad.mit.edu	37	11	55681780	55681780	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55681780G>T	uc010rir.1	-	1	279	c.279C>A	c.(277-279)CCC>CCA	p.P93P		NM_001001960	NP_001001960	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W,	93	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						AGCCATAGAAGGGTATTGACT	0.453													21	90	---	---	---	---	PASS
OR5F1	338674	broad.mit.edu	37	11	55761640	55761640	+	Silent	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55761640C>T	uc010riv.1	-	1	462	c.462G>A	c.(460-462)CTG>CTA	p.L154L		NM_003697	NP_003688	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F,	154	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2	Esophageal squamous(21;0.00448)					CCATGAAGTTCAGCAACCCTG	0.507													14	34	---	---	---	---	PASS
OR8K5	219453	broad.mit.edu	37	11	55926940	55926940	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55926940A>G	uc010rja.1	-	1	854	c.854T>C	c.(853-855)CTT>CCT	p.L285P		NM_001004058	NP_001004058	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K,	285	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|pancreas(1)|skin(1)	4	Esophageal squamous(21;0.00693)	Lung NSC(402;0.197)|all_epithelial(135;0.236)				CAAAGGGTTAAGCATGGGGAT	0.343													4	43	---	---	---	---	PASS
OR5T1	390155	broad.mit.edu	37	11	56043811	56043811	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56043811A>T	uc001nio.1	+	1	697	c.697A>T	c.(697-699)ATT>TTT	p.I233F		NM_001004745	NP_001004745	Q8NG75	OR5T1_HUMAN	olfactory receptor, family 5, subfamily T,	233	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|pancreas(1)	3	Esophageal squamous(21;0.00448)					CTATGGTTTTATTCTGTTGGC	0.428													43	119	---	---	---	---	PASS
OR9I1	219954	broad.mit.edu	37	11	57886523	57886523	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57886523A>G	uc001nml.1	-	1	394	c.394T>C	c.(394-396)TAT>CAT	p.Y132H	OR9Q1_uc001nmj.2_Intron	NM_001005211	NP_001005211	Q8NGQ6	OR9I1_HUMAN	olfactory receptor, family 9, subfamily I,	132	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1		Breast(21;0.0589)				GCCACGGTATAGAGCAGTGGG	0.552													11	22	---	---	---	---	PASS
OR5B12	390191	broad.mit.edu	37	11	58206843	58206843	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58206843T>A	uc010rkh.1	-	1	782	c.782A>T	c.(781-783)AAC>ATC	p.N261I		NM_001004733	NP_001004733	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B,	261	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				ATGGCTGGAGTTAGGTCGTAA	0.458													11	40	---	---	---	---	PASS
MS4A6E	245802	broad.mit.edu	37	11	60102436	60102436	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60102436A>T	uc001npd.2	+	1	82	c.68A>T	c.(67-69)CAA>CTA	p.Q23L		NM_139249	NP_640342	Q96DS6	M4A6E_HUMAN	membrane-spanning 4-domains, subfamily A, member	23	Cytoplasmic (Potential).					integral to membrane	receptor activity				0						AACTTCTCCCAAGCAGAGAAA	0.423													36	54	---	---	---	---	PASS
MS4A6E	245802	broad.mit.edu	37	11	60102450	60102450	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60102450G>T	uc001npd.2	+	1	96	c.82G>T	c.(82-84)GAA>TAA	p.E28*		NM_139249	NP_640342	Q96DS6	M4A6E_HUMAN	membrane-spanning 4-domains, subfamily A, member	28	Cytoplasmic (Potential).					integral to membrane	receptor activity				0						AGAGAAACCCGAACCCACCAA	0.443													25	57	---	---	---	---	PASS
MS4A7	58475	broad.mit.edu	37	11	60150658	60150658	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60150658C>A	uc001npe.2	+	2	189	c.44C>A	c.(43-45)ACA>AAA	p.T15K	MS4A7_uc001npf.2_Missense_Mutation_p.T15K|MS4A7_uc001npg.2_Missense_Mutation_p.T15K|MS4A7_uc001nph.2_Missense_Mutation_p.T15K|MS4A14_uc001npi.2_Intron|MS4A7_uc009ymx.1_Missense_Mutation_p.T15K	NM_206939	NP_996822	Q9GZW8	MS4A7_HUMAN	membrane-spanning 4-domains, subfamily A, member	15	Cytoplasmic (Potential).					integral to membrane	receptor activity			ovary(1)|central_nervous_system(1)	2						CACAGCTTTACACCAAAGGGC	0.458													19	62	---	---	---	---	PASS
SLC22A9	114571	broad.mit.edu	37	11	63175607	63175607	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63175607T>A	uc001nww.2	+	8	1580	c.1312T>A	c.(1312-1314)TTG>ATG	p.L438M	SLC22A9_uc001nwx.2_Intron	NM_080866	NP_543142	Q8IVM8	S22A9_HUMAN	solute carrier family 22 (organic anion/cation	438	Helical; (Potential).				transmembrane transport	integral to membrane				breast(2)|large_intestine(1)	3						GCGTGAGGTTTTGGCAACACT	0.478													21	14	---	---	---	---	PASS
MOGAT2	80168	broad.mit.edu	37	11	75442217	75442217	+	Silent	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75442217G>A	uc010rru.1	+	6	891	c.891G>A	c.(889-891)TCG>TCA	p.S297S	MOGAT2_uc010rrv.1_Silent_p.S215S	NM_025098	NP_079374	Q3SYC2	MOGT2_HUMAN	monoacylglycerol O-acyltransferase 2	297					glycerol metabolic process	endoplasmic reticulum membrane|integral to membrane	2-acylglycerol O-acyltransferase activity			ovary(2)	2	Ovarian(111;0.103)					TGCATCCCTCGGAGGAGGAGG	0.572													25	32	---	---	---	---	PASS
GRM5	2915	broad.mit.edu	37	11	88338018	88338018	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88338018C>A	uc001pcq.2	-	4	1462	c.1262G>T	c.(1261-1263)GGC>GTC	p.G421V	GRM5_uc009yvm.2_Missense_Mutation_p.G421V	NM_001143831	NP_001137303	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5 isoform a	421	Extracellular (Potential).				activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(2)|lung(2)|breast(1)	9		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)	TCCTGCATAGCCTGGGCAGAG	0.463													15	22	---	---	---	---	PASS
NOX4	50507	broad.mit.edu	37	11	89059961	89059961	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89059961C>A	uc001pct.2	-	18	1939	c.1700G>T	c.(1699-1701)GGG>GTG	p.G567V	NOX4_uc009yvr.2_Missense_Mutation_p.G542V|NOX4_uc001pcu.2_Missense_Mutation_p.G493V|NOX4_uc001pcw.2_Missense_Mutation_p.G260V|NOX4_uc001pcx.2_Missense_Mutation_p.G220V|NOX4_uc001pcv.2_Missense_Mutation_p.G527V|NOX4_uc009yvo.2_RNA|NOX4_uc010rtu.1_Missense_Mutation_p.G380V|NOX4_uc009yvp.2_Missense_Mutation_p.G331V|NOX4_uc010rtv.1_Missense_Mutation_p.G503V|NOX4_uc009yvq.2_Missense_Mutation_p.G543V	NM_016931	NP_058627	Q9NPH5	NOX4_HUMAN	NADPH oxidase 4 isoform a	567	Cytoplasmic (Potential).|Mediates interaction with TLR4.				cell aging|cell morphogenesis|inflammatory response|negative regulation of cell proliferation|superoxide anion generation	endoplasmic reticulum membrane|focal adhesion|integral to membrane|nucleus	electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|nucleotide binding|oxygen sensor activity			ovary(1)|central_nervous_system(1)	2		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				AAATCTTGTCCCATATGAGTT	0.373													18	16	---	---	---	---	PASS
MTNR1B	4544	broad.mit.edu	37	11	92715302	92715302	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92715302G>A	uc001pdk.1	+	2	1016	c.913G>A	c.(913-915)GCC>ACC	p.A305T		NM_005959	NP_005950	P49286	MTR1B_HUMAN	melatonin receptor 1B	305	Helical; Name=7; (Potential).				G-protein signaling, coupled to cyclic nucleotide second messenger|glucose homeostasis|regulation of insulin secretion|synaptic transmission	integral to plasma membrane	melatonin receptor activity			ovary(1)|central_nervous_system(1)	2		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Ramelteon(DB00980)	CTGCCTGAATGCCATTGTCTA	0.512													14	210	---	---	---	---	PASS
HEPHL1	341208	broad.mit.edu	37	11	93797542	93797542	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93797542A>G	uc001pep.2	+	4	831	c.674A>G	c.(673-675)GAG>GGG	p.E225G		NM_001098672	NP_001092142	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1 precursor	225	Plastocyanin-like 2.|Extracellular (Potential).				copper ion transport	integral to membrane	copper ion binding|oxidoreductase activity			ovary(3)	3		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				GTGGATCGAGAGTTTGTTATA	0.378													10	32	---	---	---	---	PASS
DYNC2H1	79659	broad.mit.edu	37	11	103325989	103325989	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103325989A>T	uc001pho.2	+	86	12676	c.12532A>T	c.(12532-12534)ACA>TCA	p.T4178S	DYNC2H1_uc001phn.1_Missense_Mutation_p.T4185S|DYNC2H1_uc009yxe.1_Missense_Mutation_p.T791S	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	4178					cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		CCATCCAGACACATTTCTTAA	0.383													25	31	---	---	---	---	PASS
RAB39	54734	broad.mit.edu	37	11	107833106	107833106	+	3'UTR	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107833106C>A	uc001pjt.2	+	2						NM_017516	NP_059986	Q14964	RB39A_HUMAN	RAB39, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding				0				BRCA - Breast invasive adenocarcinoma(274;3.04e-05)|Epithelial(105;8.56e-05)|all cancers(92;0.00179)		TGACTTCAAACATGCTGAAGA	0.393													15	14	---	---	---	---	PASS
APOC3	345	broad.mit.edu	37	11	116703578	116703578	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116703578C>A	uc001ppt.1	+	4	324	c.278C>A	c.(277-279)CCA>CAA	p.P93Q		NM_000040	NP_000031	P02656	APOC3_HUMAN	apolipoprotein C-III precursor	93	Lipid-binding.				Cdc42 protein signal transduction|cholesterol efflux|cholesterol homeostasis|chylomicron remnant clearance|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle remodeling|lipoprotein metabolic process|negative regulation of cholesterol import|negative regulation of fatty acid biosynthetic process|negative regulation of high-density lipoprotein particle clearance|negative regulation of lipoprotein lipase activity|negative regulation of low-density lipoprotein particle clearance|negative regulation of receptor-mediated endocytosis|negative regulation of triglyceride catabolic process|negative regulation of very-low-density lipoprotein particle clearance|negative regulation of very-low-density lipoprotein particle remodeling|phospholipid efflux|triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle assembly	chylomicron|intermediate-density lipoprotein particle|spherical high-density lipoprotein particle|very-low-density lipoprotein particle	high-density lipoprotein particle receptor binding|lipase inhibitor activity|phospholipid binding				0	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		GAGGTCAGACCAACTTCAGCC	0.572													11	10	---	---	---	---	PASS
MFRP	83552	broad.mit.edu	37	11	119215587	119215587	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119215587G>T	uc001pwj.2	-	6	929	c.769C>A	c.(769-771)CGC>AGC	p.R257S	MFRP_uc010rzf.1_RNA|MFRP_uc010rzg.1_Missense_Mutation_p.R257S	NM_031433	NP_113621	Q9BXJ0	C1QT5_HUMAN	membrane frizzled-related protein	Error:Variant_position_missing_in_Q9BXJ0_after_alignment						collagen					0		Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.84e-05)		CACTCACCGCGCCCAGGGGCC	0.602													8	4	---	---	---	---	PASS
UBASH3B	84959	broad.mit.edu	37	11	122678809	122678809	+	Silent	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122678809C>A	uc001pyi.3	+	13	2097	c.1737C>A	c.(1735-1737)TCC>TCA	p.S579S		NM_032873	NP_116262	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing,	579	Protein tyrosine phosphatase (By similarity).					cytoplasm|nucleus	protein tyrosine phosphatase activity			central_nervous_system(1)	1		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)		ACGCATCTTCCCTTGAAGCGT	0.463													10	328	---	---	---	---	PASS
OR10G7	390265	broad.mit.edu	37	11	123909083	123909083	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123909083C>A	uc001pzq.1	-	1	626	c.626G>T	c.(625-627)TGC>TTC	p.C209F		NM_001004463	NP_001004463	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G,	209	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		CAGGACAAAGCAGCCCGAGGC	0.562													37	41	---	---	---	---	PASS
OR8A1	390275	broad.mit.edu	37	11	124440836	124440836	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124440836C>G	uc010san.1	+	1	872	c.872C>G	c.(871-873)TCT>TGT	p.S291C		NM_001005194	NP_001005194	Q8NGG7	OR8A1_HUMAN	olfactory receptor, family 8, subfamily A,	291	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0214)		AATGTGGCCTCTGTGTTCTAC	0.493													6	42	---	---	---	---	PASS
PANX3	116337	broad.mit.edu	37	11	124481592	124481592	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124481592T>C	uc001qah.2	+	1	140	c.140T>C	c.(139-141)TTG>TCG	p.L47S		NM_052959	NP_443191	Q96QZ0	PANX3_HUMAN	pannexin 3	47	Helical; (Potential).				protein hexamerization	gap junction|integral to membrane	gap junction hemi-channel activity|ion channel activity				0	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0219)		GGCTCCCCCTTGTTGCTGATG	0.602													10	21	---	---	---	---	PASS
GLB1L2	89944	broad.mit.edu	37	11	134212647	134212647	+	Splice_Site	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134212647G>T	uc001qhp.2	+	2	275	c.87_splice	c.e2-1	p.R29_splice		NM_138342	NP_612351	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2 precursor						carbohydrate metabolic process	extracellular region	cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(1)|pancreas(1)|skin(1)	3	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)		TGTCTTTCCAGGCTGGACTGG	0.637													10	10	---	---	---	---	PASS
IQSEC3	440073	broad.mit.edu	37	12	247987	247987	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:247987G>T	uc001qhw.1	+	1	555	c.549G>T	c.(547-549)CGG>CGT	p.R183R	IQSEC3_uc001qhu.1_Silent_p.R183R|IQSEC3_uc001qht.1_Silent_p.R268R|uc001qhv.1_Intron	NM_015232	NP_056047	Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	486					regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity			central_nervous_system(2)|large_intestine(1)|skin(1)	4	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		TGGCTTTCCGGGACGTCACGG	0.567													7	7	---	---	---	---	PASS
SLC6A13	6540	broad.mit.edu	37	12	330116	330116	+	Nonstop_Mutation	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:330116A>G	uc001qic.1	-	15	1860	c.1807T>C	c.(1807-1809)TAG>CAG	p.*603Q	SLC6A13_uc009zdj.1_Nonstop_Mutation_p.*593Q|SLC6A13_uc010sdl.1_Nonstop_Mutation_p.*511Q	NM_016615	NP_057699	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter	603					neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity				0	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			CCTGCCCCCTAGCAGTGAGAC	0.677													4	12	---	---	---	---	PASS
CHD4	1108	broad.mit.edu	37	12	6710699	6710699	+	Intron	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6710699G>C	uc001qpo.2	-						CHD4_uc001qpn.2_Intron|CHD4_uc001qpp.2_Intron	NM_001273	NP_001264	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4						chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding			central_nervous_system(2)	2						TGAGGGGTCTGGTGGAGAAAT	0.443													47	203	---	---	---	---	PASS
LAG3	3902	broad.mit.edu	37	12	6884475	6884475	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6884475G>T	uc001qqt.3	+	5	1167	c.818G>T	c.(817-819)GGA>GTA	p.G273V	LAG3_uc001qqs.2_Missense_Mutation_p.G273V|LAG3_uc001qqu.2_Missense_Mutation_p.G103V	NM_002286	NP_002277	P18627	LAG3_HUMAN	lymphocyte-activation protein 3 precursor	273	Extracellular (Potential).|Ig-like C2-type 2.					integral to membrane	antigen binding|MHC class II protein binding				0						GTGTACGCTGGAGCAGGTTCC	0.627													26	58	---	---	---	---	PASS
TAS2R19	259294	broad.mit.edu	37	12	11174863	11174863	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11174863C>A	uc010shj.1	-	1	308	c.308G>T	c.(307-309)AGC>ATC	p.S103I	PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRB4_uc001qzf.1_Intron|PRH1_uc001qzj.2_Intron	NM_176888	NP_795369	P59542	T2R19_HUMAN	taste receptor, type 2, member 19	103	Helical; Name=3; (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity			skin(1)	1						ACAAAATATGCTGAGGCTAGC	0.408													24	72	---	---	---	---	PASS
PRB2	653247	broad.mit.edu	37	12	11546701	11546701	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11546701T>A	uc010shk.1	-	3	346	c.311A>T	c.(310-312)CAA>CTA	p.Q104L		NM_006248	NP_006239			proline-rich protein BstNI subfamily 2												0		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			CTTGTCTCCTTGTGGGGGTGG	0.617													9	450	---	---	---	---	PASS
SLCO1B3	28234	broad.mit.edu	37	12	21069129	21069129	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21069129C>G	uc001rek.2	+	15	2183	c.2057C>G	c.(2056-2058)ACA>AGA	p.T686R	SLCO1B3_uc001rel.2_Missense_Mutation_p.T686R|SLCO1B3_uc010sil.1_Intron|LST-3TM12_uc010sim.1_Intron	NM_019844	NP_062818	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family,	686	Cytoplasmic (Potential).				bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)					TCTGCTGGAACAGATAGTAAA	0.353													13	29	---	---	---	---	PASS
ITPR2	3709	broad.mit.edu	37	12	26775186	26775186	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26775186T>C	uc001rhg.2	-	25	3692	c.3275A>G	c.(3274-3276)CAG>CGG	p.Q1092R		NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2	1092	Cytoplasmic (Potential).				activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)					CTTAAATGCCTGTAAAACCTC	0.488													3	42	---	---	---	---	PASS
CCDC91	55297	broad.mit.edu	37	12	28515395	28515395	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28515395G>T	uc001riq.2	+	6	617	c.601G>T	c.(601-603)GAC>TAC	p.D201Y	CCDC91_uc001rio.2_Missense_Mutation_p.D171Y|CCDC91_uc009zjk.2_RNA|CCDC91_uc001rip.1_Missense_Mutation_p.D201Y|CCDC91_uc001rir.2_Missense_Mutation_p.D39Y|CCDC91_uc009zjl.2_Missense_Mutation_p.D39Y	NM_018318	NP_060788	Q7Z6B0	CCD91_HUMAN	GGA binding partner	201	Potential.				protein transport	Golgi apparatus|membrane				central_nervous_system(1)	1	Acute lymphoblastic leukemia(23;0.00718)|all_hematologic(23;0.0113)|Lung SC(9;0.184)					AGAATTGGAAGACATGAGGAA	0.303													6	4	---	---	---	---	PASS
ABCD2	225	broad.mit.edu	37	12	39967558	39967558	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39967558C>A	uc001rmb.2	-	9	2389	c.1963G>T	c.(1963-1965)GGA>TGA	p.G655*		NM_005164	NP_005155	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D, member 2	655	ABC transporter.				fatty acid metabolic process|transport	ATP-binding cassette (ABC) transporter complex|integral to plasma membrane|peroxisomal membrane	ATP binding|ATPase activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)|central_nervous_system(1)|skin(1)	6						AAGGAAATTCCAGCCCCTTTT	0.368													10	67	---	---	---	---	PASS
CNTN1	1272	broad.mit.edu	37	12	41318436	41318436	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41318436C>A	uc001rmm.1	+	6	591	c.478C>A	c.(478-480)CCC>ACC	p.P160T	CNTN1_uc009zjy.1_Missense_Mutation_p.P160T|CNTN1_uc001rmn.1_Missense_Mutation_p.P149T|CNTN1_uc001rmo.2_Missense_Mutation_p.P160T	NM_001843	NP_001834	Q12860	CNTN1_HUMAN	contactin 1 isoform 1 precursor	160	Ig-like C2-type 2.				axon guidance|cell adhesion|Notch signaling pathway	anchored to membrane|membrane fraction|plasma membrane				lung(4)|ovary(3)|large_intestine(1)|skin(1)	9	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				TCTCTGTGACCCCCCATACCA	0.383													8	28	---	---	---	---	PASS
RPAP3	79657	broad.mit.edu	37	12	48090107	48090107	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48090107T>G	uc001rpr.2	-	5	613	c.497A>C	c.(496-498)AAT>ACT	p.N166T	RPAP3_uc010slk.1_Missense_Mutation_p.N7T|RPAP3_uc001rps.2_Missense_Mutation_p.N166T	NM_024604	NP_078880	Q9H6T3	RPAP3_HUMAN	RNA polymerase II associated protein 3 isoform	166	TPR 2.						binding			ovary(1)	1	Lung SC(27;0.192)					CAACACGGGATTATATGGATC	0.358													17	50	---	---	---	---	PASS
MIR1291	100302221	broad.mit.edu	37	12	49048286	49048286	+	RNA	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49048286C>T	hsa-mir-1291|MI0006353	-			c.28C>T			C12orf41_uc001rrw.2_Intron|C12orf41_uc001rrz.2_Intron|C12orf41_uc001rrx.2_Intron|C12orf41_uc001rry.2_Intron|C12orf41_uc001rru.2_Intron|C12orf41_uc001rrv.2_Intron|SNORA34_uc001rsa.1_RNA																	0						AACTGCTGGTCTTCAGTCAGG	0.478													7	29	---	---	---	---	PASS
MCRS1	10445	broad.mit.edu	37	12	49952448	49952448	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49952448G>T	uc001ruk.1	-	15	1558	c.1367C>A	c.(1366-1368)GCT>GAT	p.A456D	MCRS1_uc001rui.1_Missense_Mutation_p.A469D|MCRS1_uc001ruj.1_Missense_Mutation_p.A443D|MCRS1_uc001rul.1_Missense_Mutation_p.A456D|MCRS1_uc009zlj.1_Missense_Mutation_p.A265D|MCRS1_uc001rum.1_Missense_Mutation_p.A443D	NM_006337	NP_006328	Q96EZ8	MCRS1_HUMAN	microspherule protein 1 isoform 1	456					DNA recombination|DNA repair|protein modification process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|Ino80 complex|MLL1 complex|nucleolus	protein binding			large_intestine(1)	1						GATCTTGGCAGCCTCAGCCCT	0.602													22	30	---	---	---	---	PASS
KRT3	3850	broad.mit.edu	37	12	53189723	53189723	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53189723G>T	uc001say.2	-	1	170	c.104C>A	c.(103-105)TCT>TAT	p.S35Y		NM_057088	NP_476429	P12035	K2C3_HUMAN	keratin 3	35	Gly-rich.|Head.				epithelial cell differentiation|intermediate filament cytoskeleton organization	keratin filament	structural molecule activity				0						AGCTCCCCCAGAGTGGGCCAC	0.647													10	25	---	---	---	---	PASS
EIF4B	1975	broad.mit.edu	37	12	53410353	53410353	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53410353C>A	uc001sbh.3	+	2	316	c.110C>A	c.(109-111)CCA>CAA	p.P37Q	EIF4B_uc009zmp.1_RNA|EIF4B_uc010snu.1_Missense_Mutation_p.P37Q|EIF4B_uc010snv.1_Missense_Mutation_p.P37Q|EIF4B_uc001sbi.2_5'UTR	NM_001417	NP_001408	P23588	IF4B_HUMAN	eukaryotic translation initiation factor 4B	37					insulin receptor signaling pathway|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	nucleotide binding|translation initiation factor activity			breast(1)|kidney(1)	2						GTTTCCAAACCAGTCAGCTGG	0.423													7	54	---	---	---	---	PASS
NEUROD4	58158	broad.mit.edu	37	12	55421039	55421039	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55421039C>A	uc001sgp.3	+	2	1194	c.816C>A	c.(814-816)GAC>GAA	p.D272E		NM_021191	NP_067014	Q9HD90	NDF4_HUMAN	neurogenic differentiation 4	272					amacrine cell differentiation|positive regulation of cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(3)|skin(1)	4						GGTCTCCTGACCTAGAAAAAT	0.522													41	146	---	---	---	---	PASS
OR10P1	121130	broad.mit.edu	37	12	56031355	56031355	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56031355T>C	uc010spq.1	+	1	680	c.680T>C	c.(679-681)CTA>CCA	p.L227P		NM_206899	NP_996782	Q8NGE3	O10P1_HUMAN	olfactory receptor, family 10, subfamily P,	227	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)|pancreas(1)	2						GGTGCCATCCTAGCAATGGCC	0.552													19	53	---	---	---	---	PASS
KIF5A	3798	broad.mit.edu	37	12	57957891	57957891	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57957891G>T	uc001sor.1	+	4	500	c.292G>T	c.(292-294)GGA>TGA	p.G98*	KIF5A_uc010srr.1_Intron	NM_004984	NP_004975	Q12840	KIF5A_HUMAN	kinesin family member 5A	98	Kinesin-motor.				blood coagulation|cell death|microtubule-based movement|synaptic transmission	cytosol|kinesin complex|membrane fraction|microtubule|perinuclear region of cytoplasm	ATP binding|microtubule motor activity			ovary(2)|skin(1)	3						CACTCGCCAGGGAAAGCTGCA	0.488													4	33	---	---	---	---	PASS
USP15	9958	broad.mit.edu	37	12	62708564	62708564	+	Intron	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62708564A>G	uc001src.1	+						USP15_uc001srb.1_Intron|USP15_uc001sra.2_Intron	NM_006313	NP_006304	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15						protein deubiquitination|ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|lung(1)	3			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		TTGTTTCATTATTTTAGGTGG	0.308													49	139	---	---	---	---	PASS
CAND1	55832	broad.mit.edu	37	12	67700314	67700314	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67700314G>C	uc001stn.2	+	10	3303	c.2866G>C	c.(2866-2868)GGA>CGA	p.G956R	CAND1_uc001sto.2_Missense_Mutation_p.G466R	NM_018448	NP_060918	Q86VP6	CAND1_HUMAN	TIP120 protein	956	HEAT 22.				cell differentiation|negative regulation of catalytic activity|protein ubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|ubiquitin ligase complex	protein binding			central_nervous_system(1)|skin(1)	2			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		TGAATGTCTAGGAAAACTCAC	0.393													17	35	---	---	---	---	PASS
RAB3IP	117177	broad.mit.edu	37	12	70150440	70150440	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70150440G>T	uc001svp.2	+	3	1002	c.555G>T	c.(553-555)CAG>CAT	p.Q185H	RAB3IP_uc001svl.1_Missense_Mutation_p.Q169H|RAB3IP_uc001svm.2_Missense_Mutation_p.Q169H|RAB3IP_uc001svn.2_Missense_Mutation_p.Q169H|RAB3IP_uc001svo.2_RNA|RAB3IP_uc001svq.2_Missense_Mutation_p.Q185H|RAB3IP_uc001svr.2_RNA|RAB3IP_uc001svs.2_RNA	NM_175623	NP_783322	Q96QF0	RAB3I_HUMAN	RAB3A interacting protein isoform alpha 2	185	Potential.				cilium assembly|Golgi to plasma membrane transport|protein localization to organelle|protein transport	actin cortical patch|centrosome|cytosol|lamellipodium|microtubule basal body|nucleus	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1	Esophageal squamous(21;0.187)		Lung(24;0.000381)|OV - Ovarian serous cystadenocarcinoma(12;0.00168)|STAD - Stomach adenocarcinoma(21;0.00694)			CAAAAGCTCAGAGGGTAAGAA	0.373													8	57	---	---	---	---	PASS
LGR5	8549	broad.mit.edu	37	12	71833879	71833879	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71833879G>C	uc001swl.2	+	1	67	c.19G>C	c.(19-21)GGT>CGT	p.G7R	TSPAN8_uc001swk.1_Intron|LGR5_uc001swm.2_Missense_Mutation_p.G7R|LGR5_uc001swn.1_RNA	NM_003667	NP_003658	O75473	LGR5_HUMAN	leucine-rich repeat-containing G protein-coupled	7						integral to plasma membrane	protein-hormone receptor activity			lung(4)|skin(3)|ovary(1)|pancreas(1)	9						CTCCCGGCTCGGTGTGCTCCT	0.711													4	9	---	---	---	---	PASS
TRHDE	29953	broad.mit.edu	37	12	72893378	72893378	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72893378A>T	uc001sxa.2	+	6	1580	c.1550A>T	c.(1549-1551)GAT>GTT	p.D517V		NM_013381	NP_037513	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	517	Extracellular (Potential).				cell-cell signaling|proteolysis|signal transduction	integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(2)|skin(1)	3						CAGGCAACAGATATTGACAGG	0.423													11	17	---	---	---	---	PASS
NAV3	89795	broad.mit.edu	37	12	78513023	78513023	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78513023C>A	uc001syp.2	+	15	3220	c.3047C>A	c.(3046-3048)ACC>AAC	p.T1016N	NAV3_uc001syo.2_Missense_Mutation_p.T1016N|NAV3_uc010sub.1_Missense_Mutation_p.T516N|NAV3_uc009zsf.2_Missense_Mutation_p.T24N	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	1016						nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						TTAGGGAAAACCGATGATGCC	0.388										HNSCC(70;0.22)			29	94	---	---	---	---	PASS
MYF5	4617	broad.mit.edu	37	12	81112685	81112685	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81112685C>G	uc001szg.2	+	3	758	c.623C>G	c.(622-624)TCC>TGC	p.S208C		NM_005593	NP_005584	P13349	MYF5_HUMAN	myogenic factor 5	208					muscle cell fate commitment|positive regulation of muscle cell differentiation|skeletal muscle tissue development	nucleoplasm	DNA binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(1)	1						GATTGCTTATCCAACATAGTG	0.453													18	53	---	---	---	---	PASS
SLC6A15	55117	broad.mit.edu	37	12	85255584	85255584	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85255584T>A	uc001szv.2	-	12	2513	c.2020A>T	c.(2020-2022)ACA>TCA	p.T674S	SLC6A15_uc010sul.1_Missense_Mutation_p.T567S|SLC6A15_uc001szw.1_3'UTR	NM_182767	NP_877499	Q9H2J7	S6A15_HUMAN	solute carrier family 6, member 15 isoform 1	674	Cytoplasmic (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						ATGAGGCTTGTATCATCGCCC	0.423													18	60	---	---	---	---	PASS
ALX1	8092	broad.mit.edu	37	12	85674127	85674127	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85674127C>T	uc001tae.3	+	1	92	c.88C>T	c.(88-90)CAC>TAC	p.H30Y		NM_006982	NP_008913	Q15699	ALX1_HUMAN	cartilage paired-class homeoprotein 1	30					brain development|cartilage condensation|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(134;0.134)		TCCTCTGGAGCACGTTATGGA	0.552													9	56	---	---	---	---	PASS
SLC25A3	5250	broad.mit.edu	37	12	98989309	98989309	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98989309C>A	uc001tfo.2	+	3	376	c.256C>A	c.(256-258)CTA>ATA	p.L86I	SLC25A3_uc001tfm.2_Intron|SLC25A3_uc001tfn.2_Intron|SLC25A3_uc001tfp.2_Intron|SLC25A3_uc001tfq.2_5'UTR|SLC25A3_uc001tfr.2_Missense_Mutation_p.L86I|SLC25A3_uc001tfs.2_5'UTR|SLC25A3_uc009ztn.2_Intron|SLC25A3_uc001tft.2_Intron	NM_005888	NP_005879	Q00325	MPCP_HUMAN	solute carrier family 25 member 3 isoform a	86	Helical; Name=1; (Potential).|Solcar 1.				generation of precursor metabolites and energy	integral to plasma membrane|mitochondrial inner membrane	phosphate carrier activity|symporter activity				0		Lung NSC(355;4.08e-05)|Breast(359;0.00191)|Colorectal(145;0.00205)|Myeloproliferative disorder(1001;0.0255)		GBM - Glioblastoma multiforme(134;1.36e-23)|BRCA - Breast invasive adenocarcinoma(302;0.000115)		ATTGGTTCCTCTAGATCTGGT	0.398													5	67	---	---	---	---	PASS
SCYL2	55681	broad.mit.edu	37	12	100732317	100732317	+	Silent	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100732317G>A	uc001thn.2	+	18	2207	c.2157G>A	c.(2155-2157)TTG>TTA	p.L719L		NM_017988	NP_060458	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 protein	719	Necessary for interaction with AP2 complex and clathrin, interaction with clathrin is necessary for its targeting to the TGN and endosomal membranes.				endosome to lysosome transport|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of clathrin-mediated endocytosis|positive regulation of receptor internalization	clathrin-coated vesicle|endosome membrane|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|protein kinase activity|receptor binding			lung(3)|ovary(2)|skin(1)	6						CTAAGGACTTGACAGACACAC	0.323													17	35	---	---	---	---	PASS
SLC17A8	246213	broad.mit.edu	37	12	100806574	100806574	+	Missense_Mutation	SNP	C	A	A	rs138338989		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100806574C>A	uc010svi.1	+	10	1526	c.1213C>A	c.(1213-1215)CTG>ATG	p.L405M	SLC17A8_uc009ztx.2_Missense_Mutation_p.L355M	NM_139319	NP_647480	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (sodium-dependent	405	Helical; (Potential).				neurotransmitter transport|sensory perception of sound|sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)	3						AACCTTACTCCTGGTGGTTGG	0.423													11	53	---	---	---	---	PASS
NUP37	79023	broad.mit.edu	37	12	102468805	102468805	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102468805G>T	uc001tjc.2	-	8	906	c.841C>A	c.(841-843)CAA>AAA	p.Q281K		NM_024057	NP_076962	Q8NFH4	NUP37_HUMAN	nucleoporin 37kDa	281					carbohydrate metabolic process|cell division|chromosome segregation|glucose transport|mitotic prometaphase|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	protein binding			ovary(1)	1						TGATGAATTTGAAACTGGCTT	0.348													15	26	---	---	---	---	PASS
RPL6	6128	broad.mit.edu	37	12	112846149	112846149	+	Intron	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112846149G>T	uc001ttu.2	-						RPL6_uc001ttv.2_Intron|RPL6_uc009zwd.1_Silent_p.S104S	NM_001024662	NP_001019833	Q02878	RL6_HUMAN	ribosomal protein L6						endocrine pancreas development|regulation of transcription, DNA-dependent|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	DNA binding|RNA binding|structural constituent of ribosome			large_intestine(1)	1						CAACCTACAAGGACACAAATG	0.453													5	69	---	---	---	---	PASS
RNFT2	84900	broad.mit.edu	37	12	117287248	117287248	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117287248T>C	uc009zwn.2	+	11	1563	c.1330T>C	c.(1330-1332)TAC>CAC	p.Y444H	RNFT2_uc001twb.3_Intron|RNFT2_uc001twa.3_Intron|RNFT2_uc001twc.3_Missense_Mutation_p.Y192H|RNFT2_uc001twd.2_5'Flank	NM_001109903	NP_001103373	Q96EX2	RNFT2_HUMAN	transmembrane protein 118 isoform 1	444	Extracellular (Potential).					integral to membrane	zinc ion binding				0	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.034)		CTTCCAGGTGTACTAGGACCG	0.667													5	6	---	---	---	---	PASS
NOS1	4842	broad.mit.edu	37	12	117672400	117672400	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117672400C>A	uc001twm.1	-	21	3891	c.3205G>T	c.(3205-3207)GAA>TAA	p.E1069*		NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1, neuronal	1069	FAD-binding FR-type.				multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(3)|skin(3)|pancreas(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)	TCCAGCAGTTCCACTTTCACC	0.607													8	30	---	---	---	---	PASS
SLC15A4	121260	broad.mit.edu	37	12	129299466	129299466	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129299466G>T	uc001uhu.2	-	2	749	c.696C>A	c.(694-696)TGC>TGA	p.C232*	SLC15A4_uc001uhv.2_RNA|MGC16384_uc001uhw.2_5'Flank	NM_145648	NP_663623	Q8N697	S15A4_HUMAN	solute carrier family 15, member 4	232	Helical; (Potential).				oligopeptide transport|protein transport	integral to membrane|lysosomal membrane	peptide:hydrogen symporter activity				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.69e-06)|Epithelial(86;1.17e-05)|all cancers(50;5.07e-05)		CAAGGCCGACGCAGACAGTGG	0.517													31	81	---	---	---	---	PASS
TMEM132D	121256	broad.mit.edu	37	12	129569127	129569127	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129569127G>A	uc009zyl.1	-	6	1892	c.1564C>T	c.(1564-1566)CCC>TCC	p.P522S	TMEM132D_uc001uia.2_Missense_Mutation_p.P60S	NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	522	Extracellular (Potential).					integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		GGAAGCCGGGGCACCCACACC	0.577													6	20	---	---	---	---	PASS
TMEM132D	121256	broad.mit.edu	37	12	129822289	129822289	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129822289G>C	uc009zyl.1	-	4	1517	c.1189C>G	c.(1189-1191)CAG>GAG	p.Q397E		NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	397	Extracellular (Potential).					integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		GTGACCAGCTGTGTGGCTGGC	0.572													16	91	---	---	---	---	PASS
PABPC3	5042	broad.mit.edu	37	13	25671601	25671601	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25671601T>C	uc001upy.2	+	1	1326	c.1265T>C	c.(1264-1266)ATT>ACT	p.I422T		NM_030979	NP_112241	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	422					mRNA metabolic process	cytoplasm	nucleotide binding|poly(A) RNA binding			ovary(3)|skin(1)	4		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		CCTAGCCAAATTGCTCGACTA	0.537													48	98	---	---	---	---	PASS
BRCA2	675	broad.mit.edu	37	13	32911471	32911471	+	Missense_Mutation	SNP	G	C	C	rs80358544		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32911471G>C	uc001uub.1	+	11	3206	c.2979G>C	c.(2977-2979)TGG>TGC	p.W993C		NM_000059	NP_000050	P51587	BRCA2_HUMAN	breast cancer 2, early onset	993	Interaction with NPM1.				cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding			ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1)	64		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TGAACAAATGGGCAGGACTCT	0.333			D|Mis|N|F|S		breast|ovarian|pancreatic	breast|ovarian|pancreatic|leukemia  (FANCB|FANCD1)		Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome	TCGA Ovarian(8;0.087)			18	32	---	---	---	---	PASS
HTR2A	3356	broad.mit.edu	37	13	47409740	47409740	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47409740C>A	uc001vbq.2	-	3	782	c.648G>T	c.(646-648)CAG>CAT	p.Q216H	HTR2A_uc001vbr.2_Missense_Mutation_p.Q116H|HTR2A_uc010acr.2_Missense_Mutation_p.Q216H	NM_000621	NP_000612	P28223	5HT2A_HUMAN	5-hydroxytryptamine receptor 2A isoform 1	216	Extracellular (By similarity).				ERK1 and ERK2 cascade|phosphatidylinositol 3-kinase cascade|phosphatidylinositol biosynthetic process|release of sequestered calcium ion into cytosol|response to drug|synaptic transmission	integral to plasma membrane	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding|drug binding|phosphatidylinositol phospholipase C activity|serotonin binding|serotonin receptor activity			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6		all_lung(13;7.2e-10)|Lung NSC(96;3.77e-07)|Breast(56;2.06e-05)|Prostate(109;0.00116)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Myeloproliferative disorder(33;0.0333)		GBM - Glioblastoma multiforme(144;4.67e-05)|COAD - Colon adenocarcinoma(199;0.224)	Aripiprazole(DB01238)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cisapride(DB00604)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyclobenzaprine(DB00924)|Cyproheptadine(DB00434)|Dihydroergotamine(DB00320)|Donepezil(DB00843)|Epinastine(DB00751)|Ergotamine(DB00696)|Fluvoxamine(DB00176)|Mesoridazine(DB00933)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Olanzapine(DB00334)|Paliperidone(DB01267)|Paroxetine(DB00715)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Sertindole(DB06144)|Thiethylperazine(DB00372)|Thioridazine(DB00679)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Venlafaxine(DB00285)|Ziprasidone(DB00246)	TCGAATCGTCCTGTAGCCCAA	0.403													6	44	---	---	---	---	PASS
RB1	5925	broad.mit.edu	37	13	49039250	49039250	+	Intron	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49039250A>T	uc001vcb.2	+							NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1						androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.?(7)		lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	CCACCAGGGTAGGTCAAAAGT	0.343		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			16	18	---	---	---	---	PASS
PCDH8	5100	broad.mit.edu	37	13	53422133	53422133	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53422133C>A	uc001vhi.2	-	1	642	c.439G>T	c.(439-441)GGT>TGT	p.G147C	PCDH8_uc001vhj.2_Missense_Mutation_p.G147C	NM_002590	NP_002581	O95206	PCDH8_HUMAN	protocadherin 8 isoform 1 precursor	147	Extracellular (Potential).|Cadherin 2.				cell-cell signaling|homophilic cell adhesion	cell junction|dendrite|integral to plasma membrane|postsynaptic membrane|presynaptic membrane	calcium ion binding			breast(1)	1		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)		ACTGCCGCACCCTCGGACACC	0.716													10	6	---	---	---	---	PASS
RBM26	64062	broad.mit.edu	37	13	79939704	79939704	+	Intron	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79939704T>A	uc001vkz.2	-						RBM26_uc001vky.2_Intron|RBM26_uc001vla.2_Intron|RBM26_uc001vkx.2_Intron	NM_022118	NP_071401	Q5T8P6	RBM26_HUMAN	RNA binding motif protein 26						mRNA processing		nucleotide binding|protein binding|RNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(28;0.0279)		GBM - Glioblastoma multiforme(99;0.0188)		GAAAGATTAATTATAGTACCT	0.398													17	45	---	---	---	---	PASS
DOCK9	23348	broad.mit.edu	37	13	99489835	99489835	+	Silent	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99489835C>A	uc001vnt.2	-	39	4216	c.4161G>T	c.(4159-4161)CTG>CTT	p.L1387L	DOCK9_uc001vnw.2_Silent_p.L1386L|DOCK9_uc001vnv.1_RNA|DOCK9_uc010tir.1_Silent_p.L1387L|DOCK9_uc001vnq.2_5'UTR|DOCK9_uc001vnr.2_Silent_p.L30L|DOCK9_uc010tin.1_Silent_p.L30L|DOCK9_uc001vns.2_5'UTR|DOCK9_uc010tio.1_Silent_p.L79L|DOCK9_uc010tip.1_Silent_p.L97L|DOCK9_uc001vnu.1_5'UTR|DOCK9_uc010tiq.1_Silent_p.L365L	NM_015296	NP_056111	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9 isoform a	1387					blood coagulation	cytosol|endomembrane system|membrane	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					ATGACTGGTGCAGAACATCTG	0.478													10	21	---	---	---	---	PASS
BIVM	54841	broad.mit.edu	37	13	103492203	103492203	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103492203T>A	uc001vps.2	+	11	2179	c.1500T>A	c.(1498-1500)GAT>GAA	p.D500E	BIVM_uc010agc.2_Missense_Mutation_p.D278E|ERCC5_uc001vpu.1_Intron|BIVM_uc001vpv.2_Missense_Mutation_p.D271E	NM_017693	NP_060163	Q86UB2	BIVM_HUMAN	basic, immunoglobulin-like variable motif	500						cytoplasm|nucleus					0	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					GTGATTACGATGGGAATGATT	0.403													29	59	---	---	---	---	PASS
ABHD13	84945	broad.mit.edu	37	13	108882199	108882199	+	Silent	SNP	A	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108882199A>C	uc001vqq.2	+	2	898	c.633A>C	c.(631-633)TCA>TCC	p.S211S		NM_032859	NP_116248	Q7L211	ABHDD_HUMAN	abhydrolase domain containing 13	211						integral to membrane	hydrolase activity			ovary(2)|upper_aerodigestive_tract(1)	3	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					ATAGGATTTCAGCCATTATGG	0.388													17	16	---	---	---	---	PASS
COL4A1	1282	broad.mit.edu	37	13	110862183	110862183	+	Intron	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110862183G>T	uc001vqw.3	-						COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein						angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			CAAACGTTTAGTAAGAGGGAA	0.393													13	16	---	---	---	---	PASS
OXA1L	5018	broad.mit.edu	37	14	23239049	23239049	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23239049G>C	uc001wgn.2	+	4	669	c.669G>C	c.(667-669)CAG>CAC	p.Q223H	OXA1L_uc001wgo.2_RNA|OXA1L_uc010akc.2_Missense_Mutation_p.Q223H|OXA1L_uc001wgp.2_Missense_Mutation_p.Q147H|OXA1L_uc001wgq.2_5'UTR	NM_005015	NP_005006	Q15070	OXA1L_HUMAN	oxidase (cytochrome c) assembly 1-like	163	Mitochondrial intermembrane (Potential).				aerobic respiration|mitochondrial proton-transporting ATP synthase complex assembly|mitochondrial respiratory chain complex I assembly|negative regulation of ATPase activity|negative regulation of oxidoreductase activity|protein insertion into membrane|protein tetramerization	integral to mitochondrial membrane|mitochondrial respiratory chain|protein complex	protein homodimerization activity|ribosome binding			central_nervous_system(1)	1	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.0096)		TGACGGGCCAGCGAGAGGCAG	0.483													13	428	---	---	---	---	PASS
HOMEZ	57594	broad.mit.edu	37	14	23745067	23745067	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23745067G>C	uc001wja.2	-	2	1518	c.1370C>G	c.(1369-1371)CCT>CGT	p.P457R	HOMEZ_uc001wjb.2_Missense_Mutation_p.P459R	NM_020834	NP_065885	Q8IX15	HOMEZ_HUMAN	homeodomain leucine zipper protein	457	Pro-rich.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)		TGGGGGTGGAGGGATCGGCAG	0.557													5	18	---	---	---	---	PASS
DHRS4L1	728635	broad.mit.edu	37	14	24517437	24517437	+	Splice_Site	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24517437T>A	uc010alc.2	+	6	488	c.488_splice	c.e6+2	p.G163_splice	DHRS4L1_uc010tnu.1_RNA	NM_001082488	NP_001075957	P0CG22	DR4L1_HUMAN	dehydrogenase/reductase (SDR family) member 4								binding|oxidoreductase activity				0						GAAACGAGGGTACAGAGAGTG	0.527													7	35	---	---	---	---	PASS
G2E3	55632	broad.mit.edu	37	14	31055950	31055950	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31055950G>A	uc001wqk.2	+	3	218	c.64G>A	c.(64-66)GAC>AAC	p.D22N	G2E3_uc010tpe.1_5'UTR|G2E3_uc010tpf.1_5'UTR	NM_017769	NP_060239	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin ligase	22					apoptosis|multicellular organismal development|protein modification process	Golgi apparatus|nucleolus	acid-amino acid ligase activity|protein binding|zinc ion binding			ovary(2)|skin(1)	3						AAAACATGATGACTGTCCTAA	0.274													6	19	---	---	---	---	PASS
SEC23A	10484	broad.mit.edu	37	14	39514366	39514366	+	Splice_Site	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39514366C>A	uc001wup.1	-	16	2122	c.1899_splice	c.e16+1	p.E633_splice	SEC23A_uc010tqa.1_Splice_Site_p.E519_splice|SEC23A_uc010tqb.1_Splice_Site_p.E604_splice	NM_006364	NP_006355	Q15436	SC23A_HUMAN	SEC23-related protein A						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|Golgi membrane|smooth endoplasmic reticulum membrane	protein binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)	5	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)		GTCCCTCTTACCTCTGGTGGT	0.333													7	37	---	---	---	---	PASS
FSCB	84075	broad.mit.edu	37	14	44975700	44975700	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44975700A>G	uc001wvn.2	-	1	800	c.491T>C	c.(490-492)ATA>ACA	p.I164T		NM_032135	NP_115511	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	164						cilium				lung(3)|breast(3)|ovary(2)|central_nervous_system(1)	9				GBM - Glioblastoma multiforme(112;0.128)		AATAACCACTATTTCTGATTC	0.428													15	75	---	---	---	---	PASS
C14orf106	55320	broad.mit.edu	37	14	45687519	45687519	+	Silent	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45687519A>G	uc001wwf.2	-	12	3267	c.2808T>C	c.(2806-2808)ACT>ACC	p.T936T		NM_018353	NP_060823	Q6P0N0	M18BP_HUMAN	chromosome 14 open reading frame 106	936					cell division|CenH3-containing nucleosome assembly at centromere|mitosis	chromosome, centromeric region|nucleoplasm	DNA binding				0						GCTTCTTCTTAGTGACATGTT	0.428													4	37	---	---	---	---	PASS
MDGA2	161357	broad.mit.edu	37	14	47530539	47530539	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47530539C>A	uc001wwj.3	-	7	1427	c.1231G>T	c.(1231-1233)GAT>TAT	p.D411Y	MDGA2_uc001wwi.3_Missense_Mutation_p.D182Y|MDGA2_uc010ani.2_5'UTR	NM_001113498	NP_001106970	Q7Z553	MDGA2_HUMAN	MAM domain containing 1 isoform 1	411	Ig-like 4.				spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(4)|large_intestine(1)|pancreas(1)	6						GTCCCAAAATCCGTGAATTTT	0.418													19	66	---	---	---	---	PASS
NIN	51199	broad.mit.edu	37	14	51223968	51223968	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51223968G>T	uc001wym.2	-	18	3971	c.3780C>A	c.(3778-3780)GAC>GAA	p.D1260E	NIN_uc001wyi.2_Missense_Mutation_p.D1260E|NIN_uc001wyj.2_Intron|NIN_uc001wyk.2_Intron|NIN_uc010tqp.1_Missense_Mutation_p.D1266E|NIN_uc001wyo.2_Missense_Mutation_p.D1260E	NM_182946	NP_891991	Q8N4C6	NIN_HUMAN	ninein isoform 5	1260	Potential.				centrosome localization	centrosome|microtubule	calcium ion binding|GTP binding|protein binding			skin(3)|ovary(1)|kidney(1)|central_nervous_system(1)	6	all_epithelial(31;0.00244)|Breast(41;0.127)					CCTGAAGGCAGTCATTTTCTC	0.433			T	PDGFRB	MPD								12	77	---	---	---	---	PASS
NID2	22795	broad.mit.edu	37	14	52520461	52520461	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52520461G>T	uc001wzo.2	-	5	1499	c.1265C>A	c.(1264-1266)CCC>CAC	p.P422H	NID2_uc010tqs.1_Missense_Mutation_p.P422H|NID2_uc010tqt.1_Missense_Mutation_p.P422H|NID2_uc001wzp.2_Missense_Mutation_p.P422H	NM_007361	NP_031387	Q14112	NID2_HUMAN	nidogen 2 precursor	422						basement membrane	calcium ion binding|collagen binding			pancreas(2)|breast(2)|ovary(1)|liver(1)|skin(1)	7	Breast(41;0.0639)|all_epithelial(31;0.123)					ATCTGGGTAGGGCTGGATGCT	0.547													7	34	---	---	---	---	PASS
SLC10A1	6554	broad.mit.edu	37	14	70245071	70245071	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70245071C>A	uc001xlr.2	-	4	1056	c.922G>T	c.(922-924)GAG>TAG	p.E308*		NM_003049	NP_003040	Q14973	NTCP_HUMAN	solute carrier family 10, member 1	308					bile acid metabolic process|organic anion transport	integral to plasma membrane	bile acid:sodium symporter activity			ovary(1)	1				all cancers(60;0.00228)|BRCA - Breast invasive adenocarcinoma(234;0.0137)|OV - Ovarian serous cystadenocarcinoma(108;0.0226)		TTGAATTTCTCATAGCACCAA	0.448													6	118	---	---	---	---	PASS
RGS6	9628	broad.mit.edu	37	14	72944990	72944990	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72944990C>A	uc001xna.3	+	12	1330	c.807C>A	c.(805-807)AAC>AAA	p.N269K	RGS6_uc010ttn.1_Missense_Mutation_p.N269K|RGS6_uc001xmx.3_Missense_Mutation_p.N269K|RGS6_uc010tto.1_RNA|RGS6_uc001xmy.3_Missense_Mutation_p.N269K|RGS6_uc010ttp.1_Missense_Mutation_p.N200K|RGS6_uc001xmz.1_Missense_Mutation_p.N130K	NM_004296	NP_004287	P49758	RGS6_HUMAN	regulator of G-protein signalling 6	269	G protein gamma.				G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			upper_aerodigestive_tract(1)|lung(1)|skin(1)	3				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)		CATTTTTGAACGCACAGATCG	0.343													5	20	---	---	---	---	PASS
DPF3	8110	broad.mit.edu	37	14	73238597	73238597	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73238597C>A	uc001xnc.2	-	2	50	c.37G>T	c.(37-39)GGG>TGG	p.G13W	DPF3_uc001xnf.2_RNA|DPF3_uc010ari.1_Missense_Mutation_p.G13W|DPF3_uc010ttq.1_Missense_Mutation_p.G23W	NM_012074	NP_036206	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3	13					chromatin modification|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nBAF complex	nucleic acid binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		AACTGGTCCCCGAGCCTGCCA	0.577													3	16	---	---	---	---	PASS
PROX2	283571	broad.mit.edu	37	14	75329286	75329286	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75329286C>T	uc001xqr.1	-	1	1252	c.1252G>A	c.(1252-1254)GAA>AAA	p.E418K	PROX2_uc001xqq.1_Intron	NM_001080408	NP_001073877	Q3B8N5	PROX2_HUMAN	prospero homeobox 2	418					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00652)		CCTCTCTGTTCCATCTTCACC	0.468													7	60	---	---	---	---	PASS
C14orf145	145508	broad.mit.edu	37	14	80993276	80993276	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80993276C>A	uc001xux.2	-	22	3180	c.3009G>T	c.(3007-3009)AGG>AGT	p.R1003S	C14orf145_uc010asz.1_RNA	NM_152446	NP_689659	Q6ZU80	CE128_HUMAN	hypothetical protein LOC145508	1003						centriole|spindle pole					0				BRCA - Breast invasive adenocarcinoma(234;0.0586)		TTCTGCGAACCCTGTATTTGG	0.348													7	19	---	---	---	---	PASS
EML5	161436	broad.mit.edu	37	14	89154820	89154820	+	Intron	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89154820A>G	uc001xxg.2	-						EML5_uc001xxh.1_Intron	NM_183387	NP_899243	Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like							cytoplasm|microtubule				ovary(3)	3						TCCTCCCCCTAGTTCACAAAA	0.353													34	83	---	---	---	---	PASS
TRIP11	9321	broad.mit.edu	37	14	92488010	92488010	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92488010C>T	uc001xzy.2	-	4	1266	c.478G>A	c.(478-480)GAT>AAT	p.D160N		NM_004239	NP_004230	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	160	Potential.				transcription from RNA polymerase II promoter	cytoskeleton|Golgi apparatus|membrane|nucleus	protein binding|transcription coactivator activity			ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1)	13				COAD - Colon adenocarcinoma(157;0.223)		TCCATGTCATCGTCATGGAAA	0.438			T	PDGFRB	AML								15	25	---	---	---	---	PASS
ATG2B	55102	broad.mit.edu	37	14	96775918	96775918	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96775918C>A	uc001yfi.2	-	29	4540	c.4175G>T	c.(4174-4176)GGT>GTT	p.G1392V		NM_018036	NP_060506	Q96BY7	ATG2B_HUMAN	ATG2 autophagy related 2 homolog B	1392										ovary(1)|kidney(1)|skin(1)	3		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		GGATGATCGACCACTGGAATC	0.368													8	45	---	---	---	---	PASS
MIR655	724025	broad.mit.edu	37	14	101515983	101515983	+	RNA	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101515983C>T	hsa-mir-655|MI0003677	+			c.97C>T			MIR487A_hsa-mir-487a|MI0002471_5'Flank																	0						ATATCAGACTCTGCCTCGGAG	0.517													7	11	---	---	---	---	PASS
RAGE	5891	broad.mit.edu	37	14	102698904	102698904	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102698904C>A	uc001ylm.2	-	9	1060	c.834G>T	c.(832-834)CAG>CAT	p.Q278H	RAGE_uc010txv.1_Missense_Mutation_p.Q248H|RAGE_uc001yln.2_Missense_Mutation_p.Q96H|RAGE_uc001ylh.2_RNA|RAGE_uc001yli.2_RNA|RAGE_uc001yll.2_RNA|RAGE_uc001ylj.2_RNA|RAGE_uc001ylk.2_RNA	NM_014226	NP_055041	Q9UQ07	MOK_HUMAN	MAPK/MAK/MRK overlapping kinase	278	Protein kinase.				signal transduction	Golgi apparatus	ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4						GCTGCAGGGCCTGGTGGGCGG	0.572													22	44	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106494219	106494219	+	RNA	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106494219G>A	uc010tyt.1	-	1760		c.34779C>T								Parts of antibodies, mostly variable regions.												0						AGGTGTCCTTGGTGATGGTGA	0.522													16	46	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106494220	106494220	+	RNA	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106494220G>T	uc010tyt.1	-	1760		c.34778C>A								Parts of antibodies, mostly variable regions.												0						GGTGTCCTTGGTGATGGTGAG	0.517													16	44	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106963072	106963072	+	RNA	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106963072G>T	uc010tyt.1	-	207		c.9612C>A								Parts of antibodies, mostly variable regions.												0						TGAAAGGTGTGATCCATCCCA	0.542													25	63	---	---	---	---	PASS
NIPA1	123606	broad.mit.edu	37	15	23048951	23048951	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23048951C>G	uc001yvc.2	-	5	893	c.868G>C	c.(868-870)GAC>CAC	p.D290H	NIPA1_uc001yvd.2_Missense_Mutation_p.D120H|NIPA1_uc001yve.2_Missense_Mutation_p.D215H	NM_144599	NP_653200	Q7RTP0	NIPA1_HUMAN	non-imprinted in Prader-Willi/Angelman syndrome	290	Extracellular (Potential).				cell death	early endosome|integral to membrane|plasma membrane					0		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;4.18e-06)|Epithelial(43;3.97e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00165)		CCCAAGAAGTCCACCAGGCCC	0.557													13	7	---	---	---	---	PASS
RASGRP1	10125	broad.mit.edu	37	15	38794623	38794623	+	Splice_Site	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38794623C>T	uc001zke.3	-	12	1607	c.1429_splice	c.e12-1	p.S477_splice	RASGRP1_uc010bbe.2_Splice_Site|RASGRP1_uc010bbf.2_Splice_Site_p.S304_splice|RASGRP1_uc010bbg.2_Splice_Site_p.S304_splice|RASGRP1_uc001zkd.3_Splice_Site_p.S442_splice	NM_005739	NP_005730	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 isoform a						cell differentiation|platelet activation|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|lipid binding|protein binding			large_intestine(1)|ovary(1)	2		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)		TGAAGACAGACTGTGAAAAAG	0.398													7	21	---	---	---	---	PASS
TMEM87A	25963	broad.mit.edu	37	15	42519099	42519099	+	Silent	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42519099C>A	uc010udd.1	-	15	1467	c.1308G>T	c.(1306-1308)CGG>CGT	p.R436R		NM_015497	NP_056312	Q8NBN3	TM87A_HUMAN	transmembrane protein 87A isoform 1	436						integral to membrane				ovary(1)	1		all_cancers(109;4.28e-16)|all_epithelial(112;1.04e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;1.03e-06)		CCCACAGCTCCCGCCAGTCCT	0.443													5	55	---	---	---	---	PASS
TGM7	116179	broad.mit.edu	37	15	43574172	43574172	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43574172C>G	uc001zrf.1	-	9	1226	c.1221G>C	c.(1219-1221)TGG>TGC	p.W407C		NM_052955	NP_443187	Q96PF1	TGM7_HUMAN	transglutaminase 7	407					peptide cross-linking		acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)	2		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	CCCCAAGGAGCCAAATGACTT	0.587													5	22	---	---	---	---	PASS
CYP19A1	1588	broad.mit.edu	37	15	51503140	51503140	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51503140G>T	uc001zyz.3	-	11	1628	c.1377C>A	c.(1375-1377)CAC>CAA	p.H459Q	CYP19A1_uc001zza.3_Missense_Mutation_p.H459Q	NM_031226	NP_112503	P11511	CP19A_HUMAN	cytochrome P450, family 19	459					estrogen biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|membrane fraction	aromatase activity|electron carrier activity|heme binding|oxygen binding|steroid hydroxylase activity			skin(3)	3				all cancers(107;0.000372)|GBM - Glioblastoma multiforme(94;0.0128)	Aminoglutethimide(DB00357)|Anastrozole(DB01217)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Diethylstilbestrol(DB00255)|Exemestane(DB00990)|Letrozole(DB01006)|Testolactone(DB00894)|Testosterone(DB00624)	ATGTCTTCACGTGGAATCGTC	0.468													15	27	---	---	---	---	PASS
ADAM10	102	broad.mit.edu	37	15	58891797	58891797	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58891797C>A	uc002afd.1	-	15	2596	c.2152G>T	c.(2152-2154)GGC>TGC	p.G718C	ADAM10_uc010bgc.1_RNA|ADAM10_uc010ugz.1_Missense_Mutation_p.G417C|ADAM10_uc002afe.1_Intron	NM_001110	NP_001101	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10 precursor	718	Cytoplasmic (Potential).				cell-cell signaling|constitutive protein ectodomain proteolysis|epidermal growth factor receptor signaling pathway|in utero embryonic development|integrin-mediated signaling pathway|monocyte activation|negative regulation of cell adhesion|Notch receptor processing|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of T cell chemotaxis|protein phosphorylation|response to tumor necrosis factor	cell surface|endomembrane system|Golgi-associated vesicle|integral to membrane|nucleus|plasma membrane	integrin binding|metalloendopeptidase activity|protein homodimerization activity|protein kinase binding|SH3 domain binding|zinc ion binding			skin(2)	2				GBM - Glioblastoma multiforme(80;0.202)		ATATTCTTACCTGGAAGTGGT	0.348													5	88	---	---	---	---	PASS
DPP8	54878	broad.mit.edu	37	15	65771329	65771329	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65771329C>T	uc002aov.2	-	11	2971	c.1393G>A	c.(1393-1395)GAG>AAG	p.E465K	DPP8_uc002aow.2_Missense_Mutation_p.E465K|DPP8_uc010uiv.1_RNA|DPP8_uc002aox.2_Missense_Mutation_p.E449K|DPP8_uc002aoy.2_Missense_Mutation_p.E465K|DPP8_uc002aoz.2_Missense_Mutation_p.E449K|DPP8_uc010bhj.2_Missense_Mutation_p.E465K|DPP8_uc002apa.2_Missense_Mutation_p.E362K|DPP8_uc010bhk.1_Intron	NM_130434	NP_569118	Q6V1X1	DPP8_HUMAN	dipeptidyl peptidase 8 isoform 1	465					immune response|proteolysis	cytoplasm|membrane|nucleus	aminopeptidase activity|dipeptidyl-peptidase activity|serine-type peptidase activity			ovary(1)	1						AAAATAAACTCAATTTCCTCT	0.308													5	12	---	---	---	---	PASS
LCTL	197021	broad.mit.edu	37	15	66857146	66857146	+	Silent	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66857146G>A	uc002aqc.2	-	2	282	c.150C>T	c.(148-150)TAC>TAT	p.Y50Y	LCTL_uc002aqd.3_Intron|LCTL_uc010bhw.2_5'UTR	NM_207338	NP_997221	Q6UWM7	LCTL_HUMAN	lactase-like precursor	50	Extracellular (Potential).				carbohydrate metabolic process	endoplasmic reticulum membrane|integral to membrane	cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(2)	2						CCTCCGTCTGGTAGGCAGAAC	0.647													8	40	---	---	---	---	PASS
FAH	2184	broad.mit.edu	37	15	80478522	80478522	+	Nonsense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80478522A>T	uc002bfj.2	+	15	1313	c.1231A>T	c.(1231-1233)AAA>TAA	p.K411*	FAH_uc002bfk.1_Nonsense_Mutation_p.K411*|FAH_uc002bfm.1_Nonsense_Mutation_p.K411*|FAH_uc002bfn.1_Nonsense_Mutation_p.K341*	NM_000137	NP_000128	P16930	FAAA_HUMAN	fumarylacetoacetase	411					L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	fumarylacetoacetase activity|metal ion binding				0						GTGTGCTGGAAAAGTGCTGCC	0.562									Tyrosinemia_type_1				20	30	---	---	---	---	PASS
ARNT2	9915	broad.mit.edu	37	15	80884056	80884056	+	Intron	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80884056C>A	uc002bfr.2	+						ARNT2_uc010unm.1_Intron|ARNT2_uc002bfs.2_Intron	NM_014862	NP_055677	Q9HBZ2	ARNT2_HUMAN	aryl hydrocarbon receptor nuclear translocator						central nervous system development|in utero embryonic development|response to hypoxia		aryl hydrocarbon receptor binding|DNA binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(3)|ovary(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.134)			GTAAATCGAGCGAGCACCGCC	0.632													26	36	---	---	---	---	PASS
CPEB1	64506	broad.mit.edu	37	15	83218354	83218354	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83218354G>T	uc002bit.2	-	9	1587	c.1450C>A	c.(1450-1452)CAG>AAG	p.Q484K	CPEB1_uc002biq.2_Missense_Mutation_p.Q344K|CPEB1_uc002bir.2_Missense_Mutation_p.Q349K|CPEB1_uc002bis.2_Missense_Mutation_p.Q344K|CPEB1_uc010uod.1_Missense_Mutation_p.Q193K|CPEB1_uc010uoe.1_Missense_Mutation_p.Q422K|CPEB1_uc002biu.2_Missense_Mutation_p.Q446K|CPEB1_uc010uof.1_Missense_Mutation_p.Q344K|CPEB1_uc002biv.2_Missense_Mutation_p.Q419K|CPEB1_uc002bip.2_Missense_Mutation_p.Q193K	NM_001079533	NP_001073001	Q9BZB8	CPEB1_HUMAN	cytoplasmic polyadenylation element binding	424	Necessary for stress granule assembly and correct localization in dcp1 bodies.				mRNA processing|regulation of translation	cell junction|cytoplasmic mRNA processing body|dendrite|postsynaptic density|postsynaptic membrane	nucleotide binding|RNA binding			ovary(1)|breast(1)	2			BRCA - Breast invasive adenocarcinoma(143;0.229)			TCAAGCCTCTGAGATGGGCTC	0.552													26	31	---	---	---	---	PASS
ACAN	176	broad.mit.edu	37	15	89400176	89400176	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89400176G>A	uc010upo.1	+	12	4734	c.4360G>A	c.(4360-4362)GGA>AGA	p.G1454R	ACAN_uc010upp.1_Missense_Mutation_p.G1454R|ACAN_uc002bna.2_RNA	NM_013227	NP_037359	E7EX88	E7EX88_HUMAN	aggrecan isoform 2 precursor	1454					cell adhesion		hyaluronic acid binding|sugar binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			GCTTCCTTCTGGAGAAGTTCT	0.517													60	102	---	---	---	---	PASS
CRTC3	64784	broad.mit.edu	37	15	91157683	91157683	+	Splice_Site	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91157683A>G	uc002bpp.2	+	7	684	c.578_splice	c.e7-2	p.G193_splice	CRTC3_uc002bpo.2_Splice_Site_p.G193_splice	NM_022769	NP_073606	Q6UUV7	CRTC3_HUMAN	transducer of regulated CREB protein 3 isoform						interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus			CRTC3/MAML2(26)	salivary_gland(26)|ovary(1)	27	Melanoma(11;0.00551)|Lung NSC(78;0.0931)|all_lung(78;0.163)		BRCA - Breast invasive adenocarcinoma(143;0.0745)			CTTTCCCGCTAGGTTTCTGTG	0.333			T	MAML2	salivary gland mucoepidermoid								19	32	---	---	---	---	PASS
VPS33B	26276	broad.mit.edu	37	15	91550170	91550170	+	Intron	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91550170C>A	uc002bqp.1	-						VPS33B_uc002bqq.1_Intron|VPS33B_uc010uqu.1_Intron	NM_018668	NP_061138	Q9H267	VP33B_HUMAN	vacuolar protein sorting 33B (yeast homolog))						cellular membrane fusion|lysosome localization|melanosome localization|platelet alpha granule organization|protein transport|vesicle docking involved in exocytosis	late endosome membrane|lysosomal membrane|perinuclear region of cytoplasm|platelet alpha granule	protein binding			ovary(2)	2	Lung NSC(78;0.0987)|all_lung(78;0.175)					GAACGCTGGGCATAATTTACC	0.488													6	63	---	---	---	---	PASS
ARRDC4	91947	broad.mit.edu	37	15	98512595	98512595	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98512595G>T	uc010bom.2	+	5	1027	c.868G>T	c.(868-870)GAC>TAC	p.D290Y	ARRDC4_uc002bui.3_Missense_Mutation_p.D203Y	NM_183376	NP_899232	Q8NCT1	ARRD4_HUMAN	arrestin domain containing 4	290					signal transduction						0	Melanoma(26;0.00539)|Lung NSC(78;0.0125)|all_lung(78;0.0222)		OV - Ovarian serous cystadenocarcinoma(32;0.0417)			TATCAGAGTGGACTATTCCTT	0.403													6	39	---	---	---	---	PASS
LRRK1	79705	broad.mit.edu	37	15	101598339	101598339	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101598339G>A	uc002bwr.2	+	29	4991	c.4672G>A	c.(4672-4674)GAG>AAG	p.E1558K	LRRK1_uc010usb.1_RNA|LRRK1_uc010usc.1_RNA|LRRK1_uc002bws.2_RNA	NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	leucine-rich repeat kinase 1	1558					small GTPase mediated signal transduction	mitochondrion	ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1)	12	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TGGAAAAGAGGAGTCCAGGTA	0.448													5	21	---	---	---	---	PASS
PKD1	5310	broad.mit.edu	37	16	2156207	2156207	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2156207C>A	uc002cos.1	-	19	7797	c.7588G>T	c.(7588-7590)GGC>TGC	p.G2530C	PKD1_uc002cot.1_Missense_Mutation_p.G2530C|PKD1_uc010bse.1_5'Flank	NM_001009944	NP_001009944	P98161	PKD1_HUMAN	polycystin 1 isoform 1 precursor	2530	Extracellular (Potential).|REJ.				calcium-independent cell-matrix adhesion|homophilic cell adhesion|neuropeptide signaling pathway	basolateral plasma membrane|integral to plasma membrane	protein domain specific binding|sugar binding			central_nervous_system(2)|skin(1)	3						GAGAGGCTGCCCTTGTAGACA	0.692													4	1	---	---	---	---	PASS
USP7	7874	broad.mit.edu	37	16	8993508	8993508	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8993508C>A	uc002czl.2	-	22	2615	c.2416G>T	c.(2416-2418)GAT>TAT	p.D806Y	USP7_uc010uyk.1_Missense_Mutation_p.D707Y|USP7_uc002czj.2_RNA|USP7_uc010uyj.1_Missense_Mutation_p.D707Y|USP7_uc002czk.2_Missense_Mutation_p.D790Y	NM_003470	NP_003461	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7	806					interspecies interaction between organisms|multicellular organismal development|protein deubiquitination|regulation of sequence-specific DNA binding transcription factor activity|ubiquitin-dependent protein catabolic process	cytoplasm|PML body	cysteine-type endopeptidase activity|p53 binding|protein C-terminus binding|transcription factor binding|ubiquitin protein ligase binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)	3						AATCCAGGATCATTAGGGATT	0.373													13	34	---	---	---	---	PASS
GRIN2A	2903	broad.mit.edu	37	16	9862768	9862768	+	Silent	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9862768C>A	uc002czo.3	-	12	3083	c.2535G>T	c.(2533-2535)CTG>CTT	p.L845L	GRIN2A_uc010uym.1_Silent_p.L845L|GRIN2A_uc010uyn.1_Silent_p.L688L|GRIN2A_uc002czr.3_Silent_p.L845L	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	845	Cytoplasmic (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	AACAGAAGCGCAGCTTCCAGT	0.577													9	37	---	---	---	---	PASS
SMG1	23049	broad.mit.edu	37	16	18826808	18826808	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18826808G>T	uc002dfm.2	-	59	10831	c.10468C>A	c.(10468-10470)CAG>AAG	p.Q3490K	SMG1_uc010bwb.2_Missense_Mutation_p.Q3350K|SMG1_uc010bwa.2_Missense_Mutation_p.Q2221K	NM_015092	NP_055907	Q96Q15	SMG1_HUMAN	PI-3-kinase-related kinase SMG-1	3490					DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16						GTGATTTCCTGGAGCATTTCA	0.383													5	61	---	---	---	---	PASS
SMG1	23049	broad.mit.edu	37	16	18856853	18856853	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18856853C>A	uc002dfm.2	-	39	6480	c.6117G>T	c.(6115-6117)TGG>TGT	p.W2039C	SMG1_uc010bwb.2_Missense_Mutation_p.W1899C|SMG1_uc010bwa.2_Missense_Mutation_p.W770C|SMG1_uc002dfo.3_Missense_Mutation_p.W337C	NM_015092	NP_055907	Q96Q15	SMG1_HUMAN	PI-3-kinase-related kinase SMG-1	2039					DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16						TATCCTGAAACCATTTTTCAT	0.458													23	40	---	---	---	---	PASS
GPR139	124274	broad.mit.edu	37	16	20043574	20043574	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20043574A>G	uc002dgu.1	-	2	707	c.545T>C	c.(544-546)GTC>GCC	p.V182A	GPR139_uc010vaw.1_Missense_Mutation_p.V89A	NM_001002911	NP_001002911	Q6DWJ6	GP139_HUMAN	G protein-coupled receptor 139	182	Helical; Name=5; (Potential).					integral to membrane|plasma membrane				ovary(2)	2						CCAGATGAGGACGTGATGCAC	0.488													11	21	---	---	---	---	PASS
CHP2	63928	broad.mit.edu	37	16	23768853	23768853	+	Silent	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23768853C>G	uc002dmb.1	+	7	963	c.540C>G	c.(538-540)TCC>TCG	p.S180S		NM_022097	NP_071380	O43745	CHP2_HUMAN	hepatocellular carcinoma antigen gene 520	180	EF-hand 4.						calcium ion binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(48;0.0144)		TCCCTCAGTCCTTAGAGAAGA	0.522													49	113	---	---	---	---	PASS
SEZ6L2	26470	broad.mit.edu	37	16	29906726	29906726	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29906726C>G	uc002duq.3	-	5	947	c.707G>C	c.(706-708)GGA>GCA	p.G236A	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|SEZ6L2_uc002dup.3_Missense_Mutation_p.G166A|SEZ6L2_uc002dur.3_Missense_Mutation_p.G166A|SEZ6L2_uc002dus.3_Intron|SEZ6L2_uc010vec.1_Missense_Mutation_p.G236A|SEZ6L2_uc010ved.1_Missense_Mutation_p.G192A	NM_201575	NP_963869	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2 isoform	236	CUB 1.|Extracellular (Potential).					endoplasmic reticulum membrane|integral to membrane|plasma membrane				ovary(1)|skin(1)	2						GCCTGGGGATCCCCCACCAGC	0.627													7	12	---	---	---	---	PASS
ITGAL	3683	broad.mit.edu	37	16	30522395	30522395	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30522395G>T	uc002dyi.3	+	24	2900	c.2724G>T	c.(2722-2724)CTG>CTT	p.L908L	ITGAL_uc002dyj.3_Silent_p.L824L|ITGAL_uc010vev.1_Silent_p.L142L	NM_002209	NP_002200	P20701	ITAL_HUMAN	integrin alpha L isoform a precursor	908	Extracellular (Potential).				blood coagulation|heterophilic cell-cell adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell	integrin complex	cell adhesion molecule binding|receptor activity			ovary(3)|lung(3)|central_nervous_system(3)|breast(1)	10					Efalizumab(DB00095)	CAGACCTCCTGGAGGACAACT	0.562													26	39	---	---	---	---	PASS
FBXL19	54620	broad.mit.edu	37	16	30941629	30941629	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30941629G>T	uc002eab.2	+	7	1243	c.1085G>T	c.(1084-1086)GGC>GTC	p.G362V	FBXL19_uc002dzz.1_Missense_Mutation_p.G50V|FBXL19_uc002eaa.1_Missense_Mutation_p.G261V	NM_001099784	NP_001093254	Q6PCT2	FXL19_HUMAN	F-box and leucine-rich repeat protein 19	362							DNA binding|zinc ion binding			ovary(2)|lung(1)|breast(1)	4						GGCAGCTCTGGCGAGAAGGAG	0.736													6	7	---	---	---	---	PASS
ARMC5	79798	broad.mit.edu	37	16	31473358	31473358	+	Intron	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31473358G>T	uc002ecc.2	+						ARMC5_uc010vfn.1_Intron|ARMC5_uc010vfo.1_Intron|ARMC5_uc002eca.3_Intron|ARMC5_uc010vfp.1_Intron|ARMC5_uc002ecb.2_Intron	NM_001105247	NP_001098717	Q96C12	ARMC5_HUMAN	armadillo repeat containing 5 isoform a								binding			pancreas(1)	1						CTGGTAAGAGGCTGTGAGGTT	0.582													14	23	---	---	---	---	PASS
MMP2	4313	broad.mit.edu	37	16	55530863	55530863	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55530863C>A	uc002ehz.3	+	10	1809	c.1498C>A	c.(1498-1500)CGT>AGT	p.R500S	MMP2_uc010vhd.1_Missense_Mutation_p.R424S|MMP2_uc010ccc.2_Missense_Mutation_p.R450S|MMP2_uc002eia.3_5'UTR	NM_004530	NP_004521	P08253	MMP2_HUMAN	matrix metalloproteinase 2 isoform a	500	Required for inhibitor TIMP2 binding.|Hemopexin-like 1.				angiogenesis|collagen catabolic process|proteolysis	extracellular space|membrane|nucleus|proteinaceous extracellular matrix	metalloendopeptidase activity|protein binding|zinc ion binding			large_intestine(3)|ovary(3)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	11		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Marimastat(DB00786)|Sulindac(DB00605)	TGTGACGCCACGTGACAAGCC	0.602													11	21	---	---	---	---	PASS
SETD6	79918	broad.mit.edu	37	16	58552942	58552942	+	3'UTR	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58552942C>A	uc002ens.2	+	8					SETD6_uc002enr.2_3'UTR|SETD6_uc010cdm.2_RNA	NM_001160305	NP_001153777	Q8TBK2	SETD6_HUMAN	SET domain containing 6 isoform a						negative regulation of NF-kappaB transcription factor activity|peptidyl-lysine monomethylation|regulation of inflammatory response	nucleus	NF-kappaB binding|protein-lysine N-methyltransferase activity			ovary(1)	1						AGCAGTTTCCCTGTTCCCTGA	0.393													4	19	---	---	---	---	PASS
TMCO7	79613	broad.mit.edu	37	16	69074319	69074319	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69074319A>T	uc002ewi.3	+	17	3115	c.3103A>T	c.(3103-3105)ACT>TCT	p.T1035S		NM_024562	NP_078838	Q9C0B7	TMCO7_HUMAN	transmembrane and coiled-coil domains 7	1035						integral to membrane	binding				0		Ovarian(137;0.0568)		OV - Ovarian serous cystadenocarcinoma(108;0.0446)|Epithelial(162;0.198)		CCAGAAAGCTACTGAGGTCAG	0.483													9	4	---	---	---	---	PASS
ZNF23	7571	broad.mit.edu	37	16	71483409	71483409	+	Silent	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71483409T>C	uc002faf.2	-	6	1333	c.519A>G	c.(517-519)TTA>TTG	p.L173L	ZNF23_uc002fad.2_Silent_p.L115L|ZNF23_uc002fae.2_Silent_p.L115L|ZNF23_uc010vmf.1_Silent_p.L115L|ZNF23_uc002fag.2_Silent_p.L115L|ZNF23_uc002fah.2_Silent_p.L173L|ZNF23_uc002fai.2_Silent_p.L212L	NM_145911	NP_666016	P17027	ZNF23_HUMAN	zinc finger protein 23	173	C2H2-type 1; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Ovarian(137;0.00768)		BRCA - Breast invasive adenocarcinoma(221;0.0686)		AGGGCTCTACTAATTCTTCAC	0.403													15	25	---	---	---	---	PASS
ZFHX3	463	broad.mit.edu	37	16	72821528	72821528	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72821528C>A	uc002fck.2	-	10	11320	c.10647G>T	c.(10645-10647)GAG>GAT	p.E3549D	uc002fcj.1_Intron|ZFHX3_uc002fcl.2_Missense_Mutation_p.E2635D	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	3549	C2H2-type 22.				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)				GCAAGGCCGACTCGAGATGTT	0.458													43	78	---	---	---	---	PASS
LDHD	197257	broad.mit.edu	37	16	75149456	75149456	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75149456A>T	uc002fdm.2	-	2	222	c.175T>A	c.(175-177)TCG>ACG	p.S59T	LDHD_uc002fdn.2_Missense_Mutation_p.S59T	NM_153486	NP_705690	Q86WU2	LDHD_HUMAN	D-lactate dehydrogenase isoform 1 precursor	59							D-lactate dehydrogenase (cytochrome) activity|flavin adenine dinucleotide binding|protein binding				0						CTGTGCACCGACTCATCGCGC	0.647													3	4	---	---	---	---	PASS
WWOX	51741	broad.mit.edu	37	16	78198080	78198080	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78198080G>T	uc002ffk.2	+	5	535	c.410G>T	c.(409-411)GGG>GTG	p.G137V	WWOX_uc010vnk.1_Missense_Mutation_p.G24V|WWOX_uc002ffl.2_Missense_Mutation_p.G137V|WWOX_uc010che.2_Intron|WWOX_uc002ffj.1_Missense_Mutation_p.G137V	NM_016373	NP_057457	Q9NZC7	WWOX_HUMAN	WW domain-containing oxidoreductase isoform 1	137	NADP (By similarity).|Interaction with MAPT (By similarity).				apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		TAAACCATAGGGTTCGAAACC	0.448													10	16	---	---	---	---	PASS
ATP2C2	9914	broad.mit.edu	37	16	84486818	84486818	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84486818G>T	uc002fhx.2	+	19	1995	c.1906G>T	c.(1906-1908)GAG>TAG	p.E636*	ATP2C2_uc010chj.2_Nonsense_Mutation_p.E636*|ATP2C2_uc002fhy.2_Nonsense_Mutation_p.E653*|ATP2C2_uc002fhz.2_Nonsense_Mutation_p.E485*	NM_014861	NP_055676	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	636	Extracellular (Potential).				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						GGAGAAGGGCGAGCTGGCCGA	0.622													3	15	---	---	---	---	PASS
OR1G1	8390	broad.mit.edu	37	17	3030761	3030761	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3030761C>T	uc002fvc.1	-	1	85	c.85G>A	c.(85-87)GGG>AGG	p.G29R		NM_003555	NP_003546	P47890	OR1G1_HUMAN	olfactory receptor, family 1, subfamily G,	29	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						AGGAAGGACCCAAAGAGGGGC	0.493													48	49	---	---	---	---	PASS
DNAH2	146754	broad.mit.edu	37	17	7644287	7644287	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7644287C>G	uc002giu.1	+	10	1680	c.1666C>G	c.(1666-1668)CGT>GGT	p.R556G	DNAH2_uc002git.2_Missense_Mutation_p.R638G|DNAH2_uc010vuk.1_Missense_Mutation_p.R556G	NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	556	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(6)|central_nervous_system(1)	13		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CATCCTCCGGCGTCGCATCGA	0.607													26	33	---	---	---	---	PASS
GAS7	8522	broad.mit.edu	37	17	9923211	9923211	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9923211G>T	uc002gmg.1	-	2	348	c.187C>A	c.(187-189)CCT>ACT	p.P63T	GAS7_uc010vvd.1_Missense_Mutation_p.P15T|GAS7_uc002gmi.2_5'UTR|GAS7_uc002gmj.1_Missense_Mutation_p.P3T|GAS7_uc010coh.1_Missense_Mutation_p.P3T	NM_201433	NP_958839	O60861	GAS7_HUMAN	growth arrest-specific 7 isoform c	63					cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			lung(1)|pancreas(1)	2						ACCATTCCAGGCTTCTGTTGG	0.532			T	MLL	AML*								8	21	---	---	---	---	PASS
MYH8	4626	broad.mit.edu	37	17	10303705	10303705	+	Splice_Site	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10303705A>G	uc002gmm.2	-	27	3830	c.3735_splice	c.e27+1	p.K1245_splice	uc002gml.1_Intron	NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,						muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			skin(6)|ovary(3)|breast(2)	11						AGTATTGGGTACCTTGGCTTT	0.433									Trismus-Pseudocamptodactyly_Syndrome_with_Cardiac_Myxoma_and_Freckling				5	119	---	---	---	---	PASS
MYH4	4622	broad.mit.edu	37	17	10360881	10360881	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10360881A>C	uc002gmn.2	-	16	1864	c.1753T>G	c.(1753-1755)TAT>GAT	p.Y585D	uc002gml.1_Intron	NM_017533	NP_060003	Q9Y623	MYH4_HUMAN	myosin, heavy polypeptide 4, skeletal muscle	585	Myosin head-like.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(10)|skin(2)|central_nervous_system(1)	13						GTGCCGGCATAGTGCACCAGT	0.522													52	21	---	---	---	---	PASS
MYH2	4620	broad.mit.edu	37	17	10432170	10432170	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10432170G>T	uc010coi.2	-	27	3709	c.3581C>A	c.(3580-3582)ACA>AAA	p.T1194K	uc002gml.1_Intron|MYH2_uc002gmp.3_Missense_Mutation_p.T1194K|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	1194	Potential.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14						GGTGGCCGCTGTGGCTTCATG	0.577													15	71	---	---	---	---	PASS
DNAH9	1770	broad.mit.edu	37	17	11572467	11572467	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11572467G>A	uc002gne.2	+	16	2886	c.2818G>A	c.(2818-2820)GGA>AGA	p.G940R	DNAH9_uc010coo.2_Missense_Mutation_p.G234R	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	940	Stem (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TCTGGAGTCTGGAGTGAAGGG	0.483													8	120	---	---	---	---	PASS
ZNF18	7566	broad.mit.edu	37	17	11896038	11896038	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11896038G>A	uc002gng.1	-	4	714	c.109C>T	c.(109-111)CCT>TCT	p.P37S	ZNF18_uc002gnh.1_Missense_Mutation_p.P37S|ZNF18_uc002gni.1_Missense_Mutation_p.P37S	NM_144680	NP_653281	P17022	ZNF18_HUMAN	zinc finger protein 18	37					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(1)	1				Colorectal(4;3.33e-05)|COAD - Colon adenocarcinoma(4;0.000494)|READ - Rectum adenocarcinoma(10;0.233)		GCGGTCTCAGGGCTGGAGAGT	0.582													38	23	---	---	---	---	PASS
MAP2K4	6416	broad.mit.edu	37	17	11984822	11984822	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11984822C>A	uc002gnj.2	+	3	437	c.368C>A	c.(367-369)CCA>CAA	p.P123Q	MAP2K4_uc002gnk.2_Missense_Mutation_p.P134Q|MAP2K4_uc010vvi.1_Missense_Mutation_p.P5Q|MAP2K4_uc010vvj.1_Intron|MIR744_hsa-mir-744|MI0005559_5'Flank	NM_003010	NP_003001	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4	123	Protein kinase.				cellular response to mechanical stimulus|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|JUN kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	p.?(1)		large_intestine(14)|breast(12)|lung(8)|ovary(8)|pancreas(8)|stomach(2)|central_nervous_system(1)|biliary_tract(1)|testis(1)|endometrium(1)|urinary_tract(1)|skin(1)	58		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)		GTCCACAAACCAAGTGGGCAA	0.413			D|Mis|N		pancreatic|breast|colorectal								5	48	---	---	---	---	PASS
MYOCD	93649	broad.mit.edu	37	17	12664015	12664015	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12664015G>T	uc002gnn.2	+	12	2535	c.2236G>T	c.(2236-2238)GAA>TAA	p.E746*	MYOCD_uc002gno.2_Nonsense_Mutation_p.E794*|MYOCD_uc002gnq.2_Nonsense_Mutation_p.E470*	NM_153604	NP_705832	Q8IZQ8	MYCD_HUMAN	myocardin isoform 2	746					cardiac muscle cell differentiation|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|positive regulation of smooth muscle cell differentiation|positive regulation of smooth muscle contraction|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation|regulation of histone acetylation|smooth muscle cell differentiation	nucleus	nucleic acid binding|RNA polymerase II transcription factor binding transcription factor activity|transcription factor binding			central_nervous_system(2)|skin(2)|ovary(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		CGTGCTTATTGAAAGCGGAGG	0.458													5	7	---	---	---	---	PASS
NOS2	4843	broad.mit.edu	37	17	26084309	26084309	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26084309G>A	uc002gzu.2	-	27	3689	c.3425C>T	c.(3424-3426)GCG>GTG	p.A1142V		NM_000625	NP_000616	P35228	NOS2_HUMAN	nitric oxide synthase 2A	1142					arginine catabolic process|defense response to Gram-negative bacterium|innate immune response in mucosa|nitric oxide biosynthetic process|peptidyl-cysteine S-nitrosylation|platelet activation|positive regulation of killing of cells of other organism|positive regulation of leukocyte mediated cytotoxicity|regulation of cellular respiration|regulation of insulin secretion|superoxide metabolic process	cytosol|nucleus	arginine binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|protein homodimerization activity|tetrahydrobiopterin binding			skin(2)|ovary(1)|breast(1)	4					Dexamethasone(DB01234)|Hydrocortisone(DB00741)|L-Arginine(DB00125)|L-Citrulline(DB00155)	GGGCTGCACCGCCACCCTGTC	0.532											OREG0024267	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	13	31	---	---	---	---	PASS
PIGS	94005	broad.mit.edu	37	17	26885500	26885500	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26885500G>T	uc002hbo.2	-	8	1301	c.928C>A	c.(928-930)CGG>AGG	p.R310R	PIGS_uc002hbn.2_Silent_p.R302R|PIGS_uc010wap.1_Silent_p.R249R	NM_033198	NP_149975	Q96S52	PIGS_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	310	Lumenal (Potential).				attachment of GPI anchor to protein|C-terminal protein lipidation	GPI-anchor transamidase complex	protein binding			breast(2)|urinary_tract(1)|kidney(1)	4	Lung NSC(42;0.00431)					TCACCCAGCCGGGACTCCACT	0.572													3	16	---	---	---	---	PASS
TRAF4	9618	broad.mit.edu	37	17	27075299	27075299	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27075299C>T	uc002hcs.2	+	5	590	c.482C>T	c.(481-483)CCC>CTC	p.P161L	TRAF4_uc002hcq.1_Intron	NM_004295	NP_004286	Q9BUZ4	TRAF4_HUMAN	TNF receptor-associated factor 4	161	TRAF-type 2.				apoptosis|positive regulation of JNK cascade|positive regulation of protein homodimerization activity|positive regulation of protein kinase activity|regulation of apoptosis|signal transduction	cytoskeleton|nucleus|perinuclear region of cytoplasm|tight junction	DNA binding|ubiquitin-protein ligase activity|WW domain binding|zinc ion binding			upper_aerodigestive_tract(1)|lung(1)	2	Lung NSC(42;0.01)		Epithelial(11;3.26e-05)|all cancers(11;0.000272)|OV - Ovarian serous cystadenocarcinoma(11;0.235)			GGTATGTGCCCCCAGGAGAGT	0.602													11	26	---	---	---	---	PASS
UNC45B	146862	broad.mit.edu	37	17	33498366	33498366	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33498366C>A	uc002hja.2	+	13	1818	c.1721C>A	c.(1720-1722)TCG>TAG	p.S574*	UNC45B_uc002hjb.2_Nonsense_Mutation_p.S572*|UNC45B_uc002hjc.2_Nonsense_Mutation_p.S572*|UNC45B_uc010cto.2_Nonsense_Mutation_p.S493*	NM_173167	NP_775259	Q8IWX7	UN45B_HUMAN	cardiomyopathy associated 4 isoform 1	574					cell differentiation|muscle organ development	cytosol	binding			ovary(3)|central_nervous_system(2)|breast(1)	6		Ovarian(249;0.17)				ATCCTGTACTCGGTGGCCACC	0.557											OREG0024327	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	51	---	---	---	---	PASS
UNC45B	146862	broad.mit.edu	37	17	33501267	33501267	+	Nonsense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33501267A>T	uc002hja.2	+	14	1940	c.1843A>T	c.(1843-1845)AAG>TAG	p.K615*	UNC45B_uc002hjb.2_Nonsense_Mutation_p.K613*|UNC45B_uc002hjc.2_Nonsense_Mutation_p.K613*|UNC45B_uc010cto.2_Nonsense_Mutation_p.K534*	NM_173167	NP_775259	Q8IWX7	UN45B_HUMAN	cardiomyopathy associated 4 isoform 1	615					cell differentiation|muscle organ development	cytosol	binding			ovary(3)|central_nervous_system(2)|breast(1)	6		Ovarian(249;0.17)				TCAGGACAAGAAGGACTTTAT	0.502													25	86	---	---	---	---	PASS
CWC25	54883	broad.mit.edu	37	17	36959000	36959000	+	Silent	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36959000C>A	uc002hqu.2	-	9	1269	c.1116G>T	c.(1114-1116)CGG>CGT	p.R372R	CWC25_uc010wdv.1_Silent_p.R309R|CWC25_uc010wdw.1_RNA|PIP4K2B_uc002hqs.2_5'Flank|PIP4K2B_uc010wdt.1_5'Flank	NM_017748	NP_060218	Q9NXE8	CWC25_HUMAN	coiled-coil domain containing 49	372	Potential.										0						GCCTCTGCTCCCGTTCCTCAT	0.522													24	74	---	---	---	---	PASS
WIPF2	147179	broad.mit.edu	37	17	38421393	38421393	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38421393G>T	uc002hug.1	+	5	1205	c.965G>T	c.(964-966)GGA>GTA	p.G322V	WIPF2_uc002huh.1_Missense_Mutation_p.G172V|WIPF2_uc010cww.1_Missense_Mutation_p.G172V|WIPF2_uc002hui.1_Missense_Mutation_p.G322V|WIPF2_uc010cwx.1_Intron|WIPF2_uc010cwy.1_Missense_Mutation_p.G322V	NM_133264	NP_573571	Q8TF74	WIPF2_HUMAN	WIRE protein	322						cytoplasm|cytoskeleton	actin binding			upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	3						CCCAGTCGGGGAGCAGGTAAG	0.522										HNSCC(43;0.11)			9	37	---	---	---	---	PASS
KRT33B	3884	broad.mit.edu	37	17	39521219	39521219	+	Silent	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39521219G>A	uc002hwl.2	-	6	954	c.909C>T	c.(907-909)AGC>AGT	p.S303S		NM_002279	NP_002270	Q14525	KT33B_HUMAN	type I hair keratin 3B	303	Coil 2.|Rod.					intermediate filament	protein binding|structural molecule activity				0		Breast(137;0.000496)				AGCGGGCCTCGCTCTCTGTCA	0.582													12	38	---	---	---	---	PASS
PTRF	284119	broad.mit.edu	37	17	40574766	40574766	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40574766A>T	uc002hzo.2	-	1	509	c.350T>A	c.(349-351)GTC>GAC	p.V117D	PTRF_uc010wgi.1_Missense_Mutation_p.V99D	NM_012232	NP_036364	Q6NZI2	PTRF_HUMAN	polymerase I and transcript release factor	117					regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription|transcription initiation from RNA polymerase I promoter	caveola|cytosol|endoplasmic reticulum|microsome|mitochondrion|nucleoplasm	protein binding|rRNA primary transcript binding			breast(1)	1		all_cancers(22;0.00146)|Breast(137;0.00116)|all_epithelial(22;0.0134)		BRCA - Breast invasive adenocarcinoma(366;0.193)		GTTGACGCTGACCTTGCGCAC	0.667													3	5	---	---	---	---	PASS
IGF2BP1	10642	broad.mit.edu	37	17	47120878	47120878	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47120878G>T	uc002iom.2	+	10	1500	c.1166G>T	c.(1165-1167)AGC>ATC	p.S389I	IGF2BP1_uc010dbj.2_Missense_Mutation_p.S250I	NM_006546	NP_006537	Q9NZI8	IF2B1_HUMAN	insulin-like growth factor 2 mRNA binding	389	Necessary for interaction with ELAVL4 and binding to TAU mRNA (By similarity).				CRD-mediated mRNA stabilization|negative regulation of translation|regulation of mRNA stability involved in response to stress	CRD-mediated mRNA stability complex|cytosol|dendritic spine|lamellipodium|nucleus|plasma membrane|stress granule	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity			kidney(1)	1						CCTCCCAGCAGCGTTACTGGG	0.577													10	35	---	---	---	---	PASS
PPP1R9B	84687	broad.mit.edu	37	17	48216853	48216853	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48216853C>A	uc002iqh.3	-	8	1963	c.1960G>T	c.(1960-1962)GAG>TAG	p.E654*		NM_032595	NP_115984	Q96SB3	NEB2_HUMAN	protein phosphatase 1, regulatory subunit 9B	652	Interacts with TGN38 (By similarity).				cell cycle arrest|cell differentiation|cell migration|filopodium assembly|negative regulation of cell growth|nervous system development|regulation of cell growth by extracellular stimulus|regulation of cell proliferation|regulation of exit from mitosis|RNA splicing	adherens junction|cytoskeleton|dendritic spine|filopodium|lamellipodium|nucleoplasm|protein phosphatase type 1 complex|ruffle membrane|synapse	actin binding|protein phosphatase 1 binding|protein phosphatase inhibitor activity				0						AGTGCATCCTCGTTCTCCGCT	0.612													5	157	---	---	---	---	PASS
TMEM100	55273	broad.mit.edu	37	17	53798268	53798268	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53798268C>A	uc002iuj.3	-	2	475	c.164G>T	c.(163-165)CGC>CTC	p.R55L	TMEM100_uc002iuk.3_Missense_Mutation_p.R55L	NM_018286	NP_060756	Q9NV29	TM100_HUMAN	transmembrane protein 100	55						integral to membrane					0						GATGATGCAGCGGTAGCAGGA	0.537													35	66	---	---	---	---	PASS
ANKFN1	162282	broad.mit.edu	37	17	54520245	54520245	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54520245A>T	uc002iun.1	+	9	1094	c.1059A>T	c.(1057-1059)AAA>AAT	p.K353N		NM_153228	NP_694960	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain	353	Fibronectin type-III.									large_intestine(1)|ovary(1)	2						ACAATATGAAAGGATGGGGAC	0.458													13	54	---	---	---	---	PASS
HELZ	9931	broad.mit.edu	37	17	65162609	65162609	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65162609G>T	uc010wqk.1	-	15	2067	c.1880C>A	c.(1879-1881)CCA>CAA	p.P627Q	HELZ_uc002jfv.3_RNA|HELZ_uc002jfx.3_Missense_Mutation_p.P627Q	NM_014877	NP_055692			helicase with zinc finger domain											ovary(1)|pancreas(1)	2	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					AGGACTCCATGGTATGGTGGG	0.358													5	84	---	---	---	---	PASS
PITPNC1	26207	broad.mit.edu	37	17	65688927	65688927	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65688927G>T	uc002jgc.2	+	9	1269	c.922G>T	c.(922-924)GAC>TAC	p.D308Y	PITPNC1_uc002jgb.2_3'UTR	NM_012417	NP_036549	Q9UKF7	PITC1_HUMAN	phosphatidylinositol transfer protein,	308					signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding	p.D308D(1)		skin(1)	1	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)			CACACTTCCAGACCCTGAGAA	0.502													35	122	---	---	---	---	PASS
BPTF	2186	broad.mit.edu	37	17	65955663	65955663	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65955663C>A	uc002jgf.2	+	24	7994	c.7933C>A	c.(7933-7935)CTG>ATG	p.L2645M	BPTF_uc002jge.2_Missense_Mutation_p.L2628M|BPTF_uc002jgg.2_Missense_Mutation_p.L302M|BPTF_uc002jgh.2_Missense_Mutation_p.L104M	NM_182641	NP_872579	Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2771					brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NURF complex	sequence-specific DNA binding|transcription factor binding|zinc ion binding			ovary(2)|skin(2)	4	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			ACAGGAAGAGCTGAAGAGAGA	0.418													32	89	---	---	---	---	PASS
C17orf80	55028	broad.mit.edu	37	17	71232591	71232591	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71232591G>A	uc002jjm.3	+	3	1164	c.970G>A	c.(970-972)GAA>AAA	p.E324K	C17orf80_uc010wqu.1_Missense_Mutation_p.E324K|C17orf80_uc010dfj.2_Missense_Mutation_p.E324K|C17orf80_uc002jjk.1_Missense_Mutation_p.E324K|C17orf80_uc002jjl.3_Missense_Mutation_p.E324K	NM_017941	NP_060411	Q9BSJ5	CQ080_HUMAN	lung cancer-related protein 8 isoform a	324	Extracellular (Potential).					integral to membrane				skin(1)	1			LUSC - Lung squamous cell carcinoma(166;0.197)			AGAAAAGCAGGAACGGACTGT	0.463													4	35	---	---	---	---	PASS
BTBD17	388419	broad.mit.edu	37	17	72352885	72352885	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72352885G>T	uc002jkn.2	-	3	1348	c.1348C>A	c.(1348-1350)CGC>AGC	p.R450S		NM_001080466	NP_001073935	A6NE02	BTBDH_HUMAN	BTB (POZ) domain containing 17 precursor	450						extracellular region					0						TCGGAGTTGCGCCGCTGCAGG	0.677													4	10	---	---	---	---	PASS
UNK	85451	broad.mit.edu	37	17	73780809	73780809	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73780809C>G	uc002jpm.2	+	2	76	c.76C>G	c.(76-78)CCG>GCG	p.P26A	UNK_uc002jpn.2_RNA|UNK_uc002jpo.2_RNA	NM_001080419	NP_001073888	Q9C0B0	UNK_HUMAN	zinc finger CCCH-type domain containing 5	Error:Variant_position_missing_in_Q9C0B0_after_alignment							nucleic acid binding|zinc ion binding				0			all cancers(21;2.61e-06)|Epithelial(20;7.39e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|LUSC - Lung squamous cell carcinoma(166;0.154)			AAAATTCCAGCCGGACATAGA	0.642													10	13	---	---	---	---	PASS
ACOX1	51	broad.mit.edu	37	17	73945424	73945424	+	Silent	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73945424C>A	uc002jqf.2	-	12	1892	c.1602G>T	c.(1600-1602)GTG>GTT	p.V534V	ACOX1_uc010wsq.1_Silent_p.V496V|ACOX1_uc002jqe.2_Silent_p.V534V|ACOX1_uc010wsr.1_Silent_p.V466V	NM_007292	NP_009223	Q15067	ACOX1_HUMAN	acyl-Coenzyme A oxidase 1 isoform b	534				VV -> GL (in Ref. 1; AAA19113 and 2; AAA18595).	fatty acid beta-oxidation using acyl-CoA oxidase|generation of precursor metabolites and energy|prostaglandin metabolic process|very long-chain fatty acid metabolic process	peroxisomal matrix	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity|flavin adenine dinucleotide binding|protein N-terminus binding			ovary(1)	1						GCTTAACTACCACATAGTGGC	0.358													5	105	---	---	---	---	PASS
ACOX1	51	broad.mit.edu	37	17	73969781	73969781	+	Nonsense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73969781G>A	uc002jqf.2	-	3	645	c.355C>T	c.(355-357)CAG>TAG	p.Q119*	ACOX1_uc010wsq.1_Intron|ACOX1_uc002jqe.2_Intron|ACOX1_uc010wsr.1_5'UTR	NM_007292	NP_009223	Q15067	ACOX1_HUMAN	acyl-Coenzyme A oxidase 1 isoform b	119				Q -> E (in Ref. 4; AAB30019).	fatty acid beta-oxidation using acyl-CoA oxidase|generation of precursor metabolites and energy|prostaglandin metabolic process|very long-chain fatty acid metabolic process	peroxisomal matrix	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity|flavin adenine dinucleotide binding|protein N-terminus binding			ovary(1)	1						TTCTCTTTCTGAGCAGTGGTG	0.483													22	48	---	---	---	---	PASS
HGS	9146	broad.mit.edu	37	17	79667556	79667556	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79667556C>T	uc002kbg.2	+	19	2019	c.1942C>T	c.(1942-1944)CCC>TCC	p.P648S	MRPL12_uc002kbh.1_5'Flank|SLC25A10_uc010wut.1_5'Flank	NM_004712	NP_004703	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine	648	Interaction with NF2.|Gln-rich.				cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of JAK-STAT cascade|regulation of protein catabolic process	cytosol|early endosome membrane|multivesicular body membrane	metal ion binding|protein domain specific binding			ovary(1)	1	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			GCAGGCGGCCCCCCAGGCCCA	0.652													7	20	---	---	---	---	PASS
COLEC12	81035	broad.mit.edu	37	18	335079	335079	+	Silent	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:335079G>A	uc002kkm.2	-	6	1694	c.1479C>T	c.(1477-1479)CCC>CCT	p.P493P		NM_130386	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	493	Collagen-like 2.|Extracellular (Potential).				carbohydrate mediated signaling|innate immune response|phagocytosis, recognition|protein homooligomerization	collagen|integral to membrane	galactose binding|low-density lipoprotein particle binding|metal ion binding|pattern recognition receptor activity|scavenger receptor activity			ovary(1)|pancreas(1)	2		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				CACGCTCTCCGGGGGGACCAG	0.672													4	17	---	---	---	---	PASS
EPB41L3	23136	broad.mit.edu	37	18	5433490	5433490	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5433490C>A	uc002kmt.1	-	8	976	c.890G>T	c.(889-891)GGG>GTG	p.G297V	EPB41L3_uc010wzh.1_Missense_Mutation_p.G297V|EPB41L3_uc002kmu.1_Missense_Mutation_p.G297V|EPB41L3_uc010dkq.1_Missense_Mutation_p.G188V|EPB41L3_uc010dks.1_Missense_Mutation_p.G319V	NM_012307	NP_036439	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	297	FERM.				cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity			ovary(5)	5						TAAATCTACCCCATACATTGA	0.323													4	20	---	---	---	---	PASS
ARHGAP28	79822	broad.mit.edu	37	18	6851023	6851023	+	Intron	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6851023C>T	uc010wzi.1	+						ARHGAP28_uc002knc.2_Intron|ARHGAP28_uc002knd.2_Intron|ARHGAP28_uc002kne.2_Intron|ARHGAP28_uc002knf.2_Intron			B4DXL2	B4DXL2_HUMAN	SubName: Full=Putative uncharacterized protein ARHGAP28;						signal transduction	intracellular				pancreas(1)	1		Colorectal(10;0.168)				GCTTTCATTTCTTCCGTTAGC	0.428													9	57	---	---	---	---	PASS
CHST9	83539	broad.mit.edu	37	18	24496619	24496619	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24496619T>A	uc002kwd.2	-	5	1134	c.936A>T	c.(934-936)AAA>AAT	p.K312N	C18orf16_uc002kwb.2_Intron|C18orf16_uc010xbm.1_Intron|CHST9_uc002kwc.2_Missense_Mutation_p.K227N|CHST9_uc002kwe.2_Missense_Mutation_p.K312N	NM_031422	NP_113610	Q7L1S5	CHST9_HUMAN	GalNAc-4-sulfotransferase 2	312	Lumenal (Potential).				carbohydrate biosynthetic process|glycosaminoglycan metabolic process|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	extracellular region|Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			ovary(2)|skin(1)	3	all_lung(6;0.0145)|Ovarian(20;0.124)					TTGGTCGATATTTCTTGATAA	0.398													31	72	---	---	---	---	PASS
DTNA	1837	broad.mit.edu	37	18	32398154	32398154	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32398154T>A	uc010dmn.1	+	7	737	c.736T>A	c.(736-738)TGC>AGC	p.C246S	DTNA_uc002kxu.2_Missense_Mutation_p.C246S|DTNA_uc010xbx.1_Intron|DTNA_uc002kxv.3_Missense_Mutation_p.C246S|DTNA_uc002kxw.2_Missense_Mutation_p.C246S|DTNA_uc002kxx.2_Missense_Mutation_p.C246S|DTNA_uc010dmj.2_Missense_Mutation_p.C246S|DTNA_uc002kxz.2_Missense_Mutation_p.C246S|DTNA_uc002kxy.2_Missense_Mutation_p.C246S|DTNA_uc010dmk.1_RNA|DTNA_uc010dml.2_Missense_Mutation_p.C246S|DTNA_uc002kyb.3_Missense_Mutation_p.C246S|DTNA_uc010dmm.2_Missense_Mutation_p.C246S|DTNA_uc010xby.1_5'UTR|DTNA_uc010dmo.2_5'Flank|DTNA_uc002kyd.3_5'Flank|DTNA_uc010xbz.1_5'Flank|DTNA_uc010xca.1_5'Flank|DTNA_uc002kye.2_5'Flank	NM_001390	NP_001381	Q9Y4J8	DTNA_HUMAN	dystrobrevin alpha isoform 1	246	Interaction with MAGEE1 (By similarity).|ZZ-type.				neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0						GTGTTCCTACTGCCACAGTGA	0.468													21	61	---	---	---	---	PASS
ELP2	55250	broad.mit.edu	37	18	33726217	33726217	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33726217G>T	uc002kzk.1	+	11	1008	c.998G>T	c.(997-999)CGA>CTA	p.R333L	ELP2_uc010xcg.1_Missense_Mutation_p.R398L|ELP2_uc002kzl.1_RNA|ELP2_uc002kzm.1_Missense_Mutation_p.R307L|ELP2_uc010xch.1_Intron|ELP2_uc002kzn.1_Intron|ELP2_uc002kzo.1_Missense_Mutation_p.R263L	NM_018255	NP_060725	Q6IA86	ELP2_HUMAN	elongator protein 2	333					regulation of transcription from RNA polymerase II promoter	Golgi apparatus|transcription elongation factor complex				breast(2)|ovary(1)|skin(1)	4						GTACAGGTTCGAGTAGGTGAA	0.398													5	120	---	---	---	---	PASS
C18orf10	25941	broad.mit.edu	37	18	34380196	34380196	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34380196C>A	uc002kzw.1	-	5	889	c.461G>T	c.(460-462)GGG>GTG	p.G154V	C18orf10_uc002kzv.1_Missense_Mutation_p.G154V|C18orf10_uc010xci.1_Missense_Mutation_p.G119V|C18orf10_uc002kzx.1_Missense_Mutation_p.G111V|C18orf10_uc002kzy.3_Missense_Mutation_p.G154V	NM_015476	NP_056291	Q68CL5	TPGS2_HUMAN	tubulin polyglutamylase complex subunit 2	154						cytoplasm|microtubule				skin(1)	1						GCAAACTTTCCCACTGCCATT	0.478													7	158	---	---	---	---	PASS
ATP5A1	498	broad.mit.edu	37	18	43664494	43664494	+	Missense_Mutation	SNP	T	A	A	rs146748835		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43664494T>A	uc002lbr.1	-	11	1646	c.1556A>T	c.(1555-1557)CAC>CTC	p.H519L	ATP5A1_uc010dnl.1_Missense_Mutation_p.H469L|ATP5A1_uc002lbs.1_Missense_Mutation_p.H469L|ATP5A1_uc002lbt.1_Missense_Mutation_p.H519L	NM_004046	NP_004037	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1	519					ATP hydrolysis coupled proton transport|embryo development|lipid metabolic process|negative regulation of endothelial cell proliferation|respiratory electron transport chain	mitochondrial matrix|plasma membrane	ATP binding|eukaryotic cell surface binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|MHC class I protein binding|proton-transporting ATPase activity, rotational mechanism				0						CAAGGCTTGGTGCTGGCTGAC	0.373													6	34	---	---	---	---	PASS
NETO1	81832	broad.mit.edu	37	18	70526196	70526196	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70526196G>T	uc002lkw.2	-	4	618	c.334C>A	c.(334-336)CCA>ACA	p.P112T	NETO1_uc002lkx.1_Missense_Mutation_p.P111T|NETO1_uc002lky.1_Missense_Mutation_p.P112T|NETO1_uc002lkz.2_Missense_Mutation_p.P111T	NM_138966	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin- and tolloid-like protein 1 isoform 3	112	CUB 1.|Extracellular (Potential).				memory|regulation of long-term neuronal synaptic plasticity|visual learning	cell junction|excitatory synapse|extracellular region|integral to membrane|postsynaptic density|postsynaptic membrane	receptor activity			ovary(2)|skin(2)	4		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		CCAATTATTGGAGAAAAGCCA	0.373													5	75	---	---	---	---	PASS
TSHZ1	10194	broad.mit.edu	37	18	73000059	73000059	+	Silent	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73000059C>A	uc002lly.2	+	2	3125	c.2562C>A	c.(2560-2562)ATC>ATA	p.I854I		NM_005786	NP_005777	Q6ZSZ6	TSH1_HUMAN	teashirt family zinc finger 1	899	Homeobox; atypical.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		ACCTTCTCATCCTGCAGGCCC	0.602													6	17	---	---	---	---	PASS
ARRDC5	645432	broad.mit.edu	37	19	4902594	4902594	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4902594G>T	uc002mbm.2	-	1	286	c.286C>A	c.(286-288)CCA>ACA	p.P96T		NM_001080523	NP_001073992	A6NEK1	ARRD5_HUMAN	arrestin domain containing 5	96					signal transduction						0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0257)		CCCTCCACTGGGAATGTCTTT	0.473													5	66	---	---	---	---	PASS
INSR	3643	broad.mit.edu	37	19	7152890	7152890	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7152890T>C	uc002mgd.1	-	10	2187	c.2078A>G	c.(2077-2079)GAT>GGT	p.D693G	INSR_uc002mge.1_Missense_Mutation_p.D693G|INSR_uc002mgf.2_Missense_Mutation_p.D693G	NM_000208	NP_000199	P06213	INSR_HUMAN	insulin receptor isoform Long precursor	693	Fibronectin type-III 1.				activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	CTTCTGAGAATCTTCAGACTC	0.532													21	77	---	---	---	---	PASS
FBN3	84467	broad.mit.edu	37	19	8155142	8155142	+	Intron	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8155142G>T	uc002mjf.2	-						FBN3_uc002mje.2_5'Flank	NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor							proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11						GTGTCTGTGGGGTGGGGGCTC	0.607													6	16	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9027212	9027212	+	Intron	SNP	T	A	A	rs7256403	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9027212T>A	uc002mkp.2	-							NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16						cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						TGACTGGTACTTACTCGTGGG	0.483													6	17	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9071136	9071136	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9071136T>G	uc002mkp.2	-	3	16514	c.16310A>C	c.(16309-16311)CAA>CCA	p.Q5437P		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	5439	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GACAGAGGATTGTGATTTATG	0.507													14	214	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9074850	9074850	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9074850C>T	uc002mkp.2	-	3	12800	c.12596G>A	c.(12595-12597)GGC>GAC	p.G4199D		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	4201	Thr-rich.|Extracellular (Potential).|Ser-rich.				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						CTTCCCCAGGCCAGAGGTCTC	0.498													5	69	---	---	---	---	PASS
FARSA	2193	broad.mit.edu	37	19	13041110	13041110	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13041110G>T	uc002mvs.2	-	4	478	c.430C>A	c.(430-432)CGG>AGG	p.R144R	FARSA_uc002mvt.2_RNA|FARSA_uc010xmv.1_Silent_p.R144R|FARSA_uc010dyy.1_Silent_p.R65R	NM_004461	NP_004452	Q9Y285	SYFA_HUMAN	phenylalanyl-tRNA synthetase, alpha subunit	144					phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|phenylalanine-tRNA ligase activity|protein binding|tRNA binding			ovary(1)	1					L-Phenylalanine(DB00120)	TGTCCCCCCCGGACCAGCTGG	0.652													3	13	---	---	---	---	PASS
LPHN1	22859	broad.mit.edu	37	19	14288365	14288365	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14288365C>A	uc010xnn.1	-	3	558	c.262G>T	c.(262-264)GCC>TCC	p.A88S	LPHN1_uc010xno.1_Missense_Mutation_p.A88S	NM_001008701	NP_001008701	O94910	LPHN1_HUMAN	latrophilin 1 isoform 1 precursor	88	SUEL-type lectin.|Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(2)|lung(2)|central_nervous_system(1)	5						ATCTTGAAGGCGTCCGGCAGG	0.567													27	91	---	---	---	---	PASS
SLC1A6	6511	broad.mit.edu	37	19	15083565	15083565	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15083565A>T	uc002naa.1	-	1	166	c.158T>A	c.(157-159)CTG>CAG	p.L53Q	SLC1A6_uc010dzu.1_Missense_Mutation_p.L53Q|SLC1A6_uc010xod.1_Silent_p.P57P|SLC1A6_uc002nab.2_Missense_Mutation_p.L53Q|SLC1A6_uc002nac.2_Missense_Mutation_p.L53Q|SLC1A6_uc002nad.1_Missense_Mutation_p.L53Q	NM_005071	NP_005062	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity	53	Cytoplasmic (Potential).				synaptic transmission	integral to plasma membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|L-aspartate transmembrane transporter activity|sodium:dicarboxylate symporter activity			pancreas(3)|ovary(2)|skin(1)	6					L-Glutamic Acid(DB00142)	GTTTCGGCGCAGGAAGCGCAG	0.657													4	20	---	---	---	---	PASS
C19orf44	84167	broad.mit.edu	37	19	16611672	16611672	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16611672G>T	uc002neh.1	+	2	142	c.69G>T	c.(67-69)TTG>TTT	p.L23F	MED26_uc002nee.2_Intron|C19orf44_uc002nef.1_Missense_Mutation_p.L23F|C19orf44_uc002neg.2_Missense_Mutation_p.L23F|C19orf44_uc010eai.1_RNA	NM_032207	NP_115583	Q9H6X5	CS044_HUMAN	hypothetical protein LOC84167	23											0						ATGTTTCCTTGGAAGATTCAA	0.413													5	84	---	---	---	---	PASS
ZNF682	91120	broad.mit.edu	37	19	20117806	20117806	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20117806T>C	uc002noq.2	-	4	628	c.505A>G	c.(505-507)ACA>GCA	p.T169A	ZNF682_uc002noo.2_Missense_Mutation_p.T137A|ZNF682_uc002nop.2_Missense_Mutation_p.T137A|ZNF682_uc010eck.2_Missense_Mutation_p.T93A	NM_033196	NP_149973	O95780	ZN682_HUMAN	zinc finger protein 682 isoform 1	169					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2						AGTTTCTCTGTAGTATGTCTT	0.308													7	10	---	---	---	---	PASS
ZNF714	148206	broad.mit.edu	37	19	21300743	21300743	+	Nonsense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21300743A>T	uc002npo.3	+	6	1636	c.1276A>T	c.(1276-1278)AAA>TAA	p.K426*	ZNF714_uc002npl.2_Nonsense_Mutation_p.K271*|ZNF714_uc010ecp.1_Nonsense_Mutation_p.K377*|ZNF714_uc002npn.2_RNA	NM_182515	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	426	C2H2-type 12.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GAAACTCTACAAATGTGAAGA	0.373													19	47	---	---	---	---	PASS
ZNF99	7652	broad.mit.edu	37	19	22939151	22939151	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22939151G>T	uc010xrh.1	-	8	2967	c.2967C>A	c.(2965-2967)GCC>GCA	p.A989A		NM_001080409	NP_001073878			zinc finger protein 99											ovary(1)|skin(1)	2		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				ACTGGTTAAAGGCTTTGCCAC	0.373													5	68	---	---	---	---	PASS
ZNF675	171392	broad.mit.edu	37	19	23836363	23836363	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23836363C>A	uc002nri.2	-	4	1554	c.1372G>T	c.(1372-1374)GGC>TGC	p.G458C		NM_138330	NP_612203	Q8TD23	ZN675_HUMAN	zinc finger protein 675	458	C2H2-type 12.				bone resorption|cytokine-mediated signaling pathway|hemopoiesis|I-kappaB kinase/NF-kappaB cascade|negative regulation of JNK cascade|negative regulation of osteoclast differentiation|negative regulation of protein kinase activity|negative regulation of transcription, DNA-dependent|regulation of ossification|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)|kidney(1)	2		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				AAAGCTTTGCCACATTCTTCA	0.353													6	40	---	---	---	---	PASS
PLEKHF1	79156	broad.mit.edu	37	19	30164785	30164785	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30164785G>C	uc002nsh.3	+	2	141	c.39G>C	c.(37-39)CAG>CAC	p.Q13H	PLEKHF1_uc002nsi.3_Missense_Mutation_p.Q98H	NM_024310	NP_077286	Q96S99	PKHF1_HUMAN	apoptosis-inducing protein D	13					apoptosis	lysosome|nucleus|perinuclear region of cytoplasm	metal ion binding				0	Ovarian(5;0.000567)|Breast(6;0.0602)|Esophageal squamous(110;0.239)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|STAD - Stomach adenocarcinoma(5;1.7e-06)|Lung(7;0.0623)|LUAD - Lung adenocarcinoma(5;0.0989)|BRCA - Breast invasive adenocarcinoma(6;0.225)			TCAACAGCCAGCGCATCGCGG	0.667													12	32	---	---	---	---	PASS
ZNF420	147923	broad.mit.edu	37	19	37618677	37618677	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37618677C>G	uc002ofl.2	+	5	999	c.784C>G	c.(784-786)CAG>GAG	p.Q262E		NM_144689	NP_653290	Q8TAQ5	ZN420_HUMAN	zinc finger protein 420	262	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GGCCTTTACTCAGAATTCACA	0.388													24	62	---	---	---	---	PASS
ZNF383	163087	broad.mit.edu	37	19	37726441	37726441	+	Intron	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37726441A>G	uc002oft.1	+						ZNF383_uc002ofs.1_Intron|ZNF383_uc002ofu.1_Intron	NM_152604	NP_689817	Q8NA42	ZN383_HUMAN	zinc finger protein 383						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ACGTATGTTTATTGTTTCAGG	0.398													6	49	---	---	---	---	PASS
RASGRP4	115727	broad.mit.edu	37	19	38911579	38911579	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38911579G>T	uc002oir.2	-	4	560	c.346C>A	c.(346-348)CTG>ATG	p.L116M	RASGRP4_uc010efz.1_RNA|RASGRP4_uc010ega.1_RNA|RASGRP4_uc010xua.1_Missense_Mutation_p.L116M|RASGRP4_uc010xub.1_Missense_Mutation_p.L116M|RASGRP4_uc010xuc.1_Missense_Mutation_p.L116M|RASGRP4_uc010xud.1_Missense_Mutation_p.L116M|RASGRP4_uc010xue.1_Missense_Mutation_p.L116M|RASGRP4_uc010egb.2_Missense_Mutation_p.L116M	NM_170604	NP_733749	Q8TDF6	GRP4_HUMAN	RAS guanyl releasing protein 4 isoform a	116	N-terminal Ras-GEF.				activation of phospholipase C activity|cell growth|cell proliferation|myeloid cell differentiation|positive regulation of Ras protein signal transduction|regulation of G-protein coupled receptor protein signaling pathway|response to extracellular stimulus|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine kinase signaling pathway	cytoplasm|membrane fraction|plasma membrane|soluble fraction	diacylglycerol binding|GTP-dependent protein binding|metal ion binding|Ras guanyl-nucleotide exchange factor activity			pancreas(1)|lung(1)|skin(1)	3	all_cancers(60;4.21e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			AGCCGTCTCAGCTCCTGGGTG	0.577													17	44	---	---	---	---	PASS
RYR1	6261	broad.mit.edu	37	19	38993342	38993342	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38993342G>A	uc002oit.2	+	48	7940	c.7810G>A	c.(7810-7812)GAG>AAG	p.E2604K	RYR1_uc002oiu.2_Missense_Mutation_p.E2604K|RYR1_uc002oiv.1_5'UTR	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	2604	Cytoplasmic.|6 X approximate repeats.				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)	TGACGTCATCGAGGACTGCCT	0.458													6	12	---	---	---	---	PASS
MAP4K1	11184	broad.mit.edu	37	19	39100635	39100635	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39100635G>T	uc002oix.1	-	12	949	c.841C>A	c.(841-843)CGA>AGA	p.R281R	MAP4K1_uc002oiw.1_5'Flank|MAP4K1_uc002oiy.1_Silent_p.R281R|MAP4K1_uc010xug.1_5'UTR	NM_007181	NP_009112	Q92918	M4K1_HUMAN	mitogen-activated protein kinase kinase kinase	281					activation of JUN kinase activity|peptidyl-serine phosphorylation		ATP binding|MAP kinase kinase kinase kinase activity|protein binding|small GTPase regulator activity			skin(4)|lung(3)|ovary(1)	8	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			ATCAGGCCTCGATTCAGCCCA	0.577													16	30	---	---	---	---	PASS
FCGBP	8857	broad.mit.edu	37	19	40368472	40368472	+	Silent	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40368472G>A	uc002omp.3	-	28	12884	c.12876C>T	c.(12874-12876)ACC>ACT	p.T4292T		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor	4292	VWFD 10.					extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CATGGCAGGTGGTGAAGGGGC	0.627													13	61	---	---	---	---	PASS
FCGBP	8857	broad.mit.edu	37	19	40433521	40433521	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40433521T>A	uc002omp.3	-	2	756	c.748A>T	c.(748-750)ACC>TCC	p.T250S		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor	250	IgGFc-binding.					extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			ACATAGTGGGTGCCCCAGGCA	0.582													13	23	---	---	---	---	PASS
ATP1A3	478	broad.mit.edu	37	19	42486229	42486229	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42486229C>A	uc002osg.2	-	9	1177	c.1023G>T	c.(1021-1023)ATG>ATT	p.M341I	ATP1A3_uc010xwf.1_Missense_Mutation_p.M352I|ATP1A3_uc010xwg.1_Missense_Mutation_p.M311I|ATP1A3_uc010xwh.1_Missense_Mutation_p.M354I|ATP1A3_uc002osh.2_Missense_Mutation_p.M341I	NM_152296	NP_689509	P13637	AT1A3_HUMAN	Na+/K+ -ATPase alpha 3 subunit	341	Cytoplasmic (Potential).				ATP biosynthetic process	endoplasmic reticulum|Golgi apparatus	ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			ovary(1)|pancreas(1)	2						tcttccGGGCCATGCGCTTGG	0.478													18	59	---	---	---	---	PASS
PSG1	5669	broad.mit.edu	37	19	43375969	43375969	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43375969C>T	uc002ovb.2	-	3	797	c.659G>A	c.(658-660)CGG>CAG	p.R220Q	PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Missense_Mutation_p.R220Q|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG1_uc002oun.2_RNA|PSG1_uc002our.1_Missense_Mutation_p.R220Q|PSG1_uc010eio.1_Missense_Mutation_p.R220Q|PSG1_uc002oux.1_Missense_Mutation_p.R149Q|PSG1_uc002ouy.1_Missense_Mutation_p.R220Q|PSG1_uc002ouz.1_Missense_Mutation_p.R220Q|PSG1_uc002ova.1_Intron|PSG1_uc002ovc.2_Intron|PSG1_uc002ovd.1_Missense_Mutation_p.R220Q	NM_006905	NP_008836	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	220	Ig-like C2-type 1.				female pregnancy	extracellular region				ovary(2)	2		Prostate(69;0.00682)				CACTGGGTTCCGTATTTCACA	0.517													8	294	---	---	---	---	PASS
PSG7	5676	broad.mit.edu	37	19	43430142	43430142	+	Silent	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43430142G>A	uc002ovl.3	-	6	1128	c.1026C>T	c.(1024-1026)ACC>ACT	p.T342T	PSG3_uc002ouf.2_Intron|PSG11_uc002ouw.2_Silent_p.T255T|PSG7_uc002ous.1_RNA|PSG7_uc002out.1_Silent_p.T68T|PSG10_uc002ouv.1_Intron|PSG6_uc002ovh.1_Intron|PSG6_uc002ovi.2_Intron|PSG6_uc010xwk.1_Intron|PSG11_uc002ovk.1_Silent_p.T255T|PSG7_uc010xwl.1_Silent_p.T220T	NM_002783	NP_002774	Q13046	PSG7_HUMAN	pregnancy specific beta-1-glycoprotein 7	342	Ig-like C2-type 3.				female pregnancy	extracellular region					0		Prostate(69;0.00682)				AATGGTAATAGGTGAATGAAG	0.478													44	150	---	---	---	---	PASS
BCAM	4059	broad.mit.edu	37	19	45317915	45317915	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45317915G>T	uc002ozu.2	+	8	1020	c.976G>T	c.(976-978)GGA>TGA	p.G326*	BCAM_uc002ozt.1_Nonsense_Mutation_p.G326*	NM_005581	NP_005572	P50895	BCAM_HUMAN	basal cell adhesion molecule isoform 1	326	Extracellular (Potential).|Ig-like C2-type 1.				cell-matrix adhesion	integral to plasma membrane	laminin binding|laminin receptor activity			skin(1)	1	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				GACCCTGGAGGGAGTGACCCG	0.632													12	27	---	---	---	---	PASS
RSPH6A	81492	broad.mit.edu	37	19	46313920	46313920	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46313920C>G	uc002pdm.2	-	2	972	c.829G>C	c.(829-831)GCG>CCG	p.A277P	RSPH6A_uc002pdl.2_Missense_Mutation_p.A13P	NM_030785	NP_110412	Q9H0K4	RSH6A_HUMAN	radial spokehead-like 1	277						intracellular				ovary(1)|central_nervous_system(1)	2						GTGAACAGCGCCTTCTGTTTC	0.632													22	62	---	---	---	---	PASS
HRC	3270	broad.mit.edu	37	19	49658431	49658431	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49658431G>A	uc002pmv.2	-	1	251	c.64C>T	c.(64-66)CTC>TTC	p.L22F	TRPM4_uc002pmw.2_5'Flank|TRPM4_uc010emu.2_5'Flank|TRPM4_uc010yak.1_5'Flank|TRPM4_uc002pmx.2_5'Flank|TRPM4_uc010emv.2_5'Flank|TRPM4_uc010yal.1_5'Flank	NM_002152	NP_002143	P23327	SRCH_HUMAN	histidine rich calcium binding protein	22					muscle contraction	sarcoplasmic reticulum lumen	calcium ion binding			ovary(1)	1		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		GCCGGGGGGAGGAGCAGGCTG	0.667													11	15	---	---	---	---	PASS
KLK15	55554	broad.mit.edu	37	19	51329879	51329879	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51329879C>T	uc002ptl.2	-	4	647	c.616G>A	c.(616-618)GAG>AAG	p.E206K	KLK1_uc002ptk.1_5'Flank|KLK1_uc010ycg.1_5'Flank|KLK15_uc002ptm.2_Intron|KLK15_uc002ptn.2_Intron|KLK15_uc002pto.2_Missense_Mutation_p.E205K|KLK15_uc010ych.1_RNA|KLK15_uc010yci.1_Intron|KLK15_uc010eod.2_Intron	NM_017509	NP_059979	Q9H2R5	KLK15_HUMAN	kallikrein-related peptidase 15 isoform 4	206	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			lung(1)|breast(1)	2		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00758)|GBM - Glioblastoma multiforme(134;0.0143)		GCTCTGACCTCACAGGATTCT	0.582													11	56	---	---	---	---	PASS
KLK5	25818	broad.mit.edu	37	19	51452188	51452188	+	Silent	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51452188G>A	uc002pue.2	-	5	737	c.519C>T	c.(517-519)AAC>AAT	p.N173N	KLK5_uc002puf.2_Silent_p.N173N|KLK5_uc002pug.2_Silent_p.N173N	NM_001077491	NP_001070959	Q9Y337	KLK5_HUMAN	kallikrein-related peptidase 5 preproprotein	173	Peptidase S1.				epidermis development|positive regulation of G-protein coupled receptor protein signaling pathway|proteolysis	extracellular space	protein binding|serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00379)|GBM - Glioblastoma multiforme(134;0.00888)		GAGAGGAGACGTTGATGGGTC	0.537													8	30	---	---	---	---	PASS
ZNF613	79898	broad.mit.edu	37	19	52448633	52448633	+	Silent	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52448633C>T	uc002pxz.1	+	6	1920	c.1497C>T	c.(1495-1497)CTC>CTT	p.L499L	ZNF613_uc002pya.1_Silent_p.L463L	NM_001031721	NP_001026891	Q6PF04	ZN613_HUMAN	zinc finger protein 613 isoform 1	499	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.0183)		AATCATGTCTCAACAGACATC	0.448													15	33	---	---	---	---	PASS
PPP2R1A	5518	broad.mit.edu	37	19	52725505	52725505	+	Intron	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52725505G>A	uc002pyp.2	+						PPP2R1A_uc010ydk.1_Intron|PPP2R1A_uc002pyq.2_Intron	NM_014225	NP_055040	P30153	2AAA_HUMAN	alpha isoform of regulatory subunit A, protein						ceramide metabolic process|chromosome segregation|G2/M transition of mitotic cell cycle|inactivation of MAPK activity|induction of apoptosis|negative regulation of cell growth|negative regulation of tyrosine phosphorylation of Stat3 protein|protein complex assembly|protein dephosphorylation|regulation of cell adhesion|regulation of cell differentiation|regulation of DNA replication|regulation of transcription, DNA-dependent|regulation of Wnt receptor signaling pathway|response to organic substance|RNA splicing|second-messenger-mediated signaling	chromosome, centromeric region|cytosol|membrane|microtubule cytoskeleton|mitochondrion|nucleus|protein phosphatase type 2A complex|soluble fraction	antigen binding|protein heterodimerization activity|protein phosphatase type 2A regulator activity			endometrium(31)|ovary(28)|lung(2)|breast(2)|skin(1)|kidney(1)|pancreas(1)	66				GBM - Glioblastoma multiforme(134;0.00456)|OV - Ovarian serous cystadenocarcinoma(262;0.015)		GTGAGGTCTGGATACTCCCCC	0.443			Mis		clear cell ovarian carcinoma								4	33	---	---	---	---	PASS
ZNF677	342926	broad.mit.edu	37	19	53741317	53741317	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53741317G>T	uc002qbf.1	-	5	848	c.663C>A	c.(661-663)ATC>ATA	p.I221I	ZNF677_uc002qbg.1_Silent_p.I221I	NM_182609	NP_872415	Q86XU0	ZN677_HUMAN	zinc finger protein 677	221					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(134;0.00352)		AGGAACTATTGATAGACTTCT	0.343													8	32	---	---	---	---	PASS
NLRP12	91662	broad.mit.edu	37	19	54314451	54314451	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54314451G>T	uc002qch.3	-	3	682	c.462C>A	c.(460-462)AGC>AGA	p.S154R	NLRP12_uc010eqw.2_5'Flank|NLRP12_uc002qci.3_Missense_Mutation_p.S154R|NLRP12_uc002qcj.3_Missense_Mutation_p.S154R|NLRP12_uc002qck.3_RNA|NLRP12_uc010eqx.2_Missense_Mutation_p.S154R	NM_144687	NP_653288	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12 isoform	154					negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interleukin-1 secretion|negative regulation of interleukin-6 biosynthetic process|negative regulation of protein autophosphorylation|negative regulation of Toll signaling pathway|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|regulation of interleukin-18 biosynthetic process|release of cytoplasmic sequestered NF-kappaB	cytoplasm	ATP binding|caspase activator activity|protein binding			ovary(4)|upper_aerodigestive_tract(2)|lung(1)	7	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		TGTACCGGTGGCTGAGGTTGA	0.617													25	62	---	---	---	---	PASS
ZNF667	63934	broad.mit.edu	37	19	56953379	56953379	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56953379G>T	uc002qnd.2	-	5	1147	c.985C>A	c.(985-987)CCT>ACT	p.P329T	ZNF667_uc010etl.2_Missense_Mutation_p.P111T|ZNF667_uc002qne.2_Missense_Mutation_p.P329T|ZNF667_uc010etm.2_Missense_Mutation_p.P272T	NM_022103	NP_071386	Q5HYK9	ZN667_HUMAN	zinc finger protein 667	329					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		CATTTAAAAGGATTCTCTAAA	0.368													15	66	---	---	---	---	PASS
ZNF835	90485	broad.mit.edu	37	19	57175029	57175029	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57175029G>T	uc010ygo.1	-	2	1604	c.1604C>A	c.(1603-1605)CCT>CAT	p.P535H	ZNF835_uc010ygn.1_Missense_Mutation_p.P513H	NM_001005850	NP_001005850			zinc finger protein 835											pancreas(3)|skin(1)	4						TGAGAGCCCAGGTGTTGAGTC	0.602													5	77	---	---	---	---	PASS
PEG3	5178	broad.mit.edu	37	19	57326183	57326183	+	Silent	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57326183C>A	uc002qnu.2	-	7	3978	c.3627G>T	c.(3625-3627)CGG>CGT	p.R1209R	ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnt.2_Silent_p.R1180R|PEG3_uc002qnv.2_Silent_p.R1209R|PEG3_uc002qnw.2_Silent_p.R1085R|PEG3_uc002qnx.2_Silent_p.R1083R|PEG3_uc010etr.2_Silent_p.R1209R	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	1209					apoptosis|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		CACGATTCCTCCGTGGCTTCA	0.493													28	70	---	---	---	---	PASS
PEG3	5178	broad.mit.edu	37	19	57327459	57327459	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57327459G>T	uc002qnu.2	-	7	2702	c.2351C>A	c.(2350-2352)TCT>TAT	p.S784Y	ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnt.2_Missense_Mutation_p.S755Y|PEG3_uc002qnv.2_Missense_Mutation_p.S784Y|PEG3_uc002qnw.2_Missense_Mutation_p.S660Y|PEG3_uc002qnx.2_Missense_Mutation_p.S658Y|PEG3_uc010etr.2_Missense_Mutation_p.S784Y	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	784					apoptosis|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		AGCTTCCACAGAGGCTAAGCT	0.428													6	142	---	---	---	---	PASS
ZIM3	114026	broad.mit.edu	37	19	57646983	57646983	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57646983T>G	uc002qnz.1	-	5	1108	c.722A>C	c.(721-723)CAT>CCT	p.H241P		NM_052882	NP_443114	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	241	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CATTTTCTGATGTTGAAAGAG	0.373													13	58	---	---	---	---	PASS
ZSCAN4	201516	broad.mit.edu	37	19	58187877	58187877	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58187877C>A	uc002qpu.2	+	3	1061	c.364C>A	c.(364-366)CTG>ATG	p.L122M		NM_152677	NP_689890	Q8NAM6	ZSCA4_HUMAN	zinc finger and SCAN domain containing 4	122	SCAN box.				telomere maintenance via telomere lengthening|viral reproduction	nuclear chromosome, telomeric region	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CATAGAAGACCTGACTGATGA	0.423													15	39	---	---	---	---	PASS
PANK2	80025	broad.mit.edu	37	20	3888926	3888926	+	Splice_Site	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3888926G>A	uc002wkc.2	+	2	987	c.981_splice	c.e2+1	p.T327_splice	PANK2_uc002wkb.2_Splice_Site_p.T36_splice|PANK2_uc010gbd.1_Splice_Site|PANK2_uc002wkd.2_Intron|PANK2_uc002wke.2_Splice_Site_p.T36_splice|PANK2_uc002wkf.2_Intron	NM_153638	NP_705902	Q9BZ23	PANK2_HUMAN	pantothenate kinase 2 isoform 1 preproprotein						cell death|coenzyme A biosynthetic process|pantothenate metabolic process	mitochondrial intermembrane space|nucleus	ATP binding|pantothenate kinase activity|protein binding				0						TTTTCTCACAGTATGCATTTT	0.348													6	16	---	---	---	---	PASS
ASXL1	171023	broad.mit.edu	37	20	31022723	31022723	+	Silent	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31022723A>T	uc002wxs.2	+	12	2634	c.2208A>T	c.(2206-2208)ACA>ACT	p.T736T	ASXL1_uc010geb.2_Silent_p.T627T	NM_015338	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like 1 isoform 1	736					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	PR-DUB complex	metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(239)|large_intestine(6)|central_nervous_system(2)|ovary(1)	248						AGAGGGCTACAGTTGGACTCA	0.592			F|N|Mis		MDS|CMML								6	25	---	---	---	---	PASS
DNMT3B	1789	broad.mit.edu	37	20	31381363	31381363	+	Missense_Mutation	SNP	G	A	A	rs138596278		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31381363G>A	uc002wyc.2	+	10	1409	c.1088G>A	c.(1087-1089)CGT>CAT	p.R363H	DNMT3B_uc010ztx.1_Intron|DNMT3B_uc010zty.1_Intron|DNMT3B_uc002wyd.2_Intron|DNMT3B_uc002wye.2_Intron|DNMT3B_uc010gee.2_Intron|DNMT3B_uc010gef.2_Intron|DNMT3B_uc010ztz.1_Intron|DNMT3B_uc010zua.1_Intron|DNMT3B_uc002wyf.2_Intron|DNMT3B_uc002wyg.2_Missense_Mutation_p.R62H	NM_006892	NP_008823	Q9UBC3	DNM3B_HUMAN	DNA cytosine-5 methyltransferase 3 beta isoform	363					negative regulation of histone H3-K9 methylation|positive regulation of gene expression|positive regulation of histone H3-K4 methylation		metal ion binding|protein binding|transcription corepressor activity			lung(3)|ovary(2)	5						tcgaaggtgcgtcgtgcaggc	0.134													6	19	---	---	---	---	PASS
CTNNBL1	56259	broad.mit.edu	37	20	36375010	36375010	+	Splice_Site	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36375010A>T	uc010zvw.1	+	4	556	c.465_splice	c.e4+2	p.T155_splice	CTNNBL1_uc002xhh.2_5'UTR|CTNNBL1_uc010zvv.1_Missense_Mutation_p.D129V	NM_030877	NP_110517	Q8WYA6	CTBL1_HUMAN	beta catenin-like 1						apoptosis|positive regulation of apoptosis|somatic diversification of immunoglobulins	nucleus	enzyme binding			ovary(2)	2		Myeloproliferative disorder(115;0.00878)				GATAATACAGATATCCTTTCA	0.498													5	54	---	---	---	---	PASS
CTNNBL1	56259	broad.mit.edu	37	20	36375019	36375019	+	Intron	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36375019C>G	uc010zvw.1	+						CTNNBL1_uc002xhh.2_5'UTR|CTNNBL1_uc010zvv.1_Nonsense_Mutation_p.S132*	NM_030877	NP_110517	Q8WYA6	CTBL1_HUMAN	beta catenin-like 1						apoptosis|positive regulation of apoptosis|somatic diversification of immunoglobulins	nucleus	enzyme binding			ovary(2)	2		Myeloproliferative disorder(115;0.00878)				GATATCCTTTCAGATCTGACC	0.488													6	58	---	---	---	---	PASS
CHD6	84181	broad.mit.edu	37	20	40068760	40068760	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40068760C>T	uc002xka.1	-	26	4065	c.3887G>A	c.(3886-3888)AGG>AAG	p.R1296K	CHD6_uc002xkb.1_Missense_Mutation_p.R62K	NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1296					chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)				GGCATTGTACCTTTCATAACC	0.443													10	42	---	---	---	---	PASS
PLTP	5360	broad.mit.edu	37	20	44533578	44533578	+	Intron	SNP	T	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44533578T>A	uc002xqn.1	-						PLTP_uc002xql.1_Intron|PLTP_uc002xqm.1_Intron|PLTP_uc002xqo.1_Intron|PLTP_uc002xqp.1_Intron|PLTP_uc002xqq.1_Intron|PLTP_uc010zxj.1_Intron|PLTP_uc010ghj.1_Intron	NM_006227	NP_006218	P55058	PLTP_HUMAN	phospholipid transfer protein isoform a						cellular lipid metabolic process|lipid transport	extracellular region	lipid binding			ovary(1)	1		Myeloproliferative disorder(115;0.0122)				GGCCATGACATACCTTGTCCC	0.582													11	18	---	---	---	---	PASS
SLC12A5	57468	broad.mit.edu	37	20	44675020	44675020	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44675020G>T	uc010zxl.1	+	14	1877	c.1801G>T	c.(1801-1803)GTG>TTG	p.V601L	SLC12A5_uc010zxm.1_RNA|SLC12A5_uc002xrb.2_Missense_Mutation_p.V578L	NM_001134771	NP_001128243	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium-chloride	601	Cytoplasmic (Potential).				potassium ion transport|sodium ion transport	integral to membrane	potassium:chloride symporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	GGCCTGTGCAGTGCAGACGCT	0.552													7	35	---	---	---	---	PASS
CASS4	57091	broad.mit.edu	37	20	55027876	55027876	+	Silent	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55027876G>A	uc002xxp.2	+	6	1869	c.1644G>A	c.(1642-1644)GTG>GTA	p.V548V	CASS4_uc002xxq.3_Silent_p.V548V|CASS4_uc002xxr.2_Silent_p.V548V|CASS4_uc010zze.1_Silent_p.V494V|CASS4_uc010gio.2_Intron	NM_001164116	NP_001157588	Q9NQ75	CASS4_HUMAN	HEF-like protein isoform a	548					cell adhesion	cytoplasm|cytoskeleton|focal adhesion	two-component sensor activity			ovary(2)|skin(1)	3						AAGTTCTTGTGACTGACAGTG	0.493													6	35	---	---	---	---	PASS
EDN3	1908	broad.mit.edu	37	20	57896155	57896155	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57896155A>T	uc002yap.2	+	3	818	c.449A>T	c.(448-450)CAG>CTG	p.Q150L	EDN3_uc002yao.1_Missense_Mutation_p.Q150L|EDN3_uc002yaq.2_Missense_Mutation_p.Q150L|EDN3_uc002yar.2_Missense_Mutation_p.Q150L|EDN3_uc002yas.2_Missense_Mutation_p.Q150L	NM_000114	NP_000105	P14138	EDN3_HUMAN	endothelin 3 isoform 1 preproprotein	150					cell surface receptor linked signaling pathway|inositol phosphate-mediated signaling|neutrophil chemotaxis|peptide hormone secretion|positive regulation of heart rate|positive regulation of hormone secretion|positive regulation of leukocyte chemotaxis|positive regulation of MAP kinase activity|positive regulation of mitosis|regulation of systemic arterial blood pressure by endothelin|regulation of vasoconstriction|vein smooth muscle contraction	extracellular space|soluble fraction	endothelin B receptor binding|hormone activity			skin(1)	1	all_lung(29;0.0115)					GGGAATCTGCAGCTCTCACAT	0.577													11	37	---	---	---	---	PASS
RTEL1	51750	broad.mit.edu	37	20	62319501	62319501	+	Silent	SNP	G	A	A	rs114292675	byFrequency	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62319501G>A	uc002yfu.1	+	19	1948	c.1605G>A	c.(1603-1605)GAG>GAA	p.E535E	RTEL1_uc011abc.1_RNA|RTEL1_uc002yft.1_Silent_p.E535E|RTEL1_uc011abd.1_Silent_p.E559E|RTEL1_uc011abe.1_Silent_p.E312E|RTEL1_uc002yfw.2_RNA|RTEL1_uc002yfx.1_5'Flank	NM_016434	NP_057518	Q9NZ71	RTEL1_HUMAN	regulator of telomere elongation helicase 1	535					DNA repair|regulation of double-strand break repair via homologous recombination|telomere maintenance	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|iron-sulfur cluster binding|metal ion binding				0	all_cancers(38;6.47e-12)|all_epithelial(29;3.75e-13)		Epithelial(9;1.25e-09)|all cancers(9;5.13e-09)|BRCA - Breast invasive adenocarcinoma(10;7.26e-05)|OV - Ovarian serous cystadenocarcinoma(5;0.00223)|Colorectal(105;0.107)			GGTTTTCCGAGGAGTGCTTAT	0.657													8	34	---	---	---	---	PASS
UMODL1	89766	broad.mit.edu	37	21	43510517	43510517	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43510517G>T	uc002zaf.1	+	6	900	c.900G>T	c.(898-900)ACG>ACT	p.T300T	UMODL1_uc002zad.1_Silent_p.T228T|UMODL1_uc002zae.1_Silent_p.T228T|UMODL1_uc002zag.1_Silent_p.T300T|UMODL1_uc010gow.1_Silent_p.T92T|UMODL1_uc002zai.1_5'UTR|UMODL1_uc010gox.1_RNA|UMODL1_uc010goy.1_5'UTR|UMODL1_uc002zaj.1_RNA|UMODL1_uc010goz.1_Intron	NM_001004416	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1 isoform 1 precursor	300	Extracellular (Potential).|EGF-like 1; calcium-binding (Potential).					cytoplasm|extracellular region|integral to membrane|plasma membrane	calcium ion binding|peptidase inhibitor activity			ovary(2)|skin(1)	3						CTCCAGCCACGTCTCCACGGA	0.478													19	25	---	---	---	---	PASS
DIP2A	23181	broad.mit.edu	37	21	47931501	47931501	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47931501G>T	uc002zjo.2	+	8	1259	c.1076G>T	c.(1075-1077)GGG>GTG	p.G359V	DIP2A_uc011afy.1_Missense_Mutation_p.G295V|DIP2A_uc011afz.1_Missense_Mutation_p.G355V|DIP2A_uc002zjl.2_Missense_Mutation_p.G359V|DIP2A_uc002zjm.2_Missense_Mutation_p.G359V|DIP2A_uc010gql.2_Missense_Mutation_p.G316V|DIP2A_uc002zjn.2_Missense_Mutation_p.G359V|DIP2A_uc002zjp.1_Missense_Mutation_p.G104V	NM_015151	NP_055966	Q14689	DIP2A_HUMAN	disco-interacting protein 2A isoform a	359					multicellular organismal development	nucleus	catalytic activity|transcription factor binding			ovary(2)	2	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		GATACAACTGGGAAAGCCGTC	0.537													5	20	---	---	---	---	PASS
CCT8L2	150160	broad.mit.edu	37	22	17073266	17073266	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17073266A>G	uc002zlp.1	-	1	435	c.175T>C	c.(175-177)TTC>CTC	p.F59L		NM_014406	NP_055221	Q96SF2	TCPQM_HUMAN	T-complex protein 1	59					cellular protein metabolic process	cytoplasm	anion channel activity|ATP binding|calcium-activated potassium channel activity			ovary(1)	1	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				GTCACCAGGAACTTCTGCCGG	0.642													6	31	---	---	---	---	PASS
CECR1	51816	broad.mit.edu	37	22	17680460	17680460	+	Intron	SNP	G	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17680460G>C	uc002zmk.1	-						CECR1_uc010gqu.1_Intron|CECR1_uc011agi.1_Intron|CECR1_uc011agj.1_Intron|CECR1_uc002zmj.1_Silent_p.S3S	NM_017424	NP_059120	Q9NZK5	CECR1_HUMAN	cat eye syndrome critical region protein 1						adenosine catabolic process|hypoxanthine salvage|inosine biosynthetic process|multicellular organismal development|purine ribonucleoside monophosphate biosynthetic process	extracellular space|Golgi apparatus	adenosine deaminase activity|adenosine receptor binding|growth factor activity|heparin binding|protein homodimerization activity|proteoglycan binding|zinc ion binding			ovary(1)	1		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)				TCCATTCCAGGGAATCCATCT	0.512													8	23	---	---	---	---	PASS
CRYBB2	1415	broad.mit.edu	37	22	25627687	25627687	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25627687G>T	uc003abp.1	+	6	614	c.566G>T	c.(565-567)CGT>CTT	p.R189L		NM_000496	NP_000487	P43320	CRBB2_HUMAN	crystallin, beta B2	189	Beta/gamma crystallin 'Greek key' 4.				response to stimulus|visual perception		structural constituent of eye lens				0						TCCGTGCGCCGTATCCGCGAC	0.652													19	53	---	---	---	---	PASS
MYO18B	84700	broad.mit.edu	37	22	26231332	26231332	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26231332C>A	uc003abz.1	+	17	3380	c.3130C>A	c.(3130-3132)CAT>AAT	p.H1044N	MYO18B_uc003aca.1_Missense_Mutation_p.H925N|MYO18B_uc010guy.1_Missense_Mutation_p.H926N|MYO18B_uc010guz.1_Missense_Mutation_p.H925N|MYO18B_uc011aka.1_Missense_Mutation_p.H198N|MYO18B_uc011akb.1_Missense_Mutation_p.H557N	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1044	Myosin head-like.					nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						TGAGGAAGTCCATGTAGAGGG	0.582													7	38	---	---	---	---	PASS
KREMEN1	83999	broad.mit.edu	37	22	29534767	29534767	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29534767C>G	uc011akm.1	+	7	1133	c.1120C>G	c.(1120-1122)CCA>GCA	p.P374A	KREMEN1_uc003ael.2_Missense_Mutation_p.P374A|KREMEN1_uc011akn.1_Missense_Mutation_p.P257A	NM_032045	NP_114434	Q96MU8	KREM1_HUMAN	kringle-containing transmembrane protein 1	372	Extracellular (Potential).				cell communication|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane|membrane fraction	protein binding			ovary(3)|lung(2)	5						TCAGACTGTCCCAGGTAGCAA	0.572													5	35	---	---	---	---	PASS
FBXO7	25793	broad.mit.edu	37	22	32889094	32889094	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32889094C>G	uc003amq.2	+	7	1253	c.970C>G	c.(970-972)CTG>GTG	p.L324V	FBXO7_uc003amr.2_Missense_Mutation_p.L210V|FBXO7_uc003ams.2_Missense_Mutation_p.L168V|FBXO7_uc003amt.2_Missense_Mutation_p.L245V|FBXO7_uc003amu.2_Missense_Mutation_p.L210V|FBXO7_uc003amv.2_Missense_Mutation_p.L23V	NM_012179	NP_036311	Q9Y3I1	FBX7_HUMAN	F-box only protein 7 isoform 1	324					cell death|regulation of protein stability|ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(1)	1						CCTTTTAGCACTGAACCTACC	0.423													23	42	---	---	---	---	PASS
LARGE	9215	broad.mit.edu	37	22	33712090	33712090	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33712090C>T	uc003and.3	-	12	2011	c.1432G>A	c.(1432-1434)GCT>ACT	p.A478T	LARGE_uc011amd.1_Missense_Mutation_p.A277T|LARGE_uc003ane.3_Missense_Mutation_p.A478T|LARGE_uc010gwp.2_Missense_Mutation_p.A426T|LARGE_uc011ame.1_Missense_Mutation_p.A410T|LARGE_uc011amf.1_Missense_Mutation_p.A478T|LARGE_uc010gwq.1_RNA	NM_004737	NP_004728	O95461	LARGE_HUMAN	like-glycosyltransferase	478	Lumenal (Potential).				glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)				GACAGCTGAGCGACCAGGGTG	0.602													4	17	---	---	---	---	PASS
LARGE	9215	broad.mit.edu	37	22	34046621	34046621	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34046621G>A	uc003and.3	-	4	719	c.140C>T	c.(139-141)TCC>TTC	p.S47F	LARGE_uc003ane.3_Missense_Mutation_p.S47F|LARGE_uc010gwp.2_Missense_Mutation_p.S47F|LARGE_uc011ame.1_5'UTR|LARGE_uc011amf.1_Missense_Mutation_p.S47F	NM_004737	NP_004728	O95461	LARGE_HUMAN	like-glycosyltransferase	47	Lumenal (Potential).				glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)				GTGTGCCTGGGACTCCAGCGG	0.647													5	19	---	---	---	---	PASS
MGAT3	4248	broad.mit.edu	37	22	39884066	39884066	+	Nonsense_Mutation	SNP	C	A	A	rs5995740		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39884066C>A	uc003axv.3	+	2	953	c.714C>A	c.(712-714)TGC>TGA	p.C238*	MGAT3_uc010gxy.2_Nonsense_Mutation_p.C238*	NM_002409	NP_002400	Q09327	MGAT3_HUMAN	mannosyl (beta-1,4-)-glycoprotein	238	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	beta-1,4-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity				0	Melanoma(58;0.04)					TTGTGGTGTGCGAGTCCAACT	0.617													6	13	---	---	---	---	PASS
EFCAB6	64800	broad.mit.edu	37	22	44068001	44068001	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44068001C>T	uc003bdy.1	-	15	1707	c.1492G>A	c.(1492-1494)GTT>ATT	p.V498I	EFCAB6_uc003bdz.1_Missense_Mutation_p.V346I|EFCAB6_uc010gzi.1_Missense_Mutation_p.V346I|EFCAB6_uc010gzk.1_RNA	NM_022785	NP_073622	Q5THR3	EFCB6_HUMAN	CAP-binding protein complex interacting protein	498					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	7		Ovarian(80;0.0247)|all_neural(38;0.025)				GTATCATGAACAATTTCTTCC	0.373													13	29	---	---	---	---	PASS
SMC1B	27127	broad.mit.edu	37	22	45779397	45779397	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45779397C>A	uc003bgc.2	-	12	2060	c.2008G>T	c.(2008-2010)GAG>TAG	p.E670*	SMC1B_uc003bgd.2_Nonsense_Mutation_p.E670*|SMC1B_uc003bge.1_Nonsense_Mutation_p.E453*	NM_148674	NP_683515	Q8NDV3	SMC1B_HUMAN	SMC1 structural maintenance of chromosomes	670	Potential.				chromosome organization|meiosis	chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nucleus	ATP binding			ovary(2)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		TTCTTTAACTCTTTCTCATCC	0.353													5	55	---	---	---	---	PASS
CELSR1	9620	broad.mit.edu	37	22	46793652	46793652	+	Missense_Mutation	SNP	C	A	A	rs141922879		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46793652C>A	uc003bhw.1	-	12	5620	c.5620G>T	c.(5620-5622)GAC>TAC	p.D1874Y	CELSR1_uc011arc.1_Missense_Mutation_p.D195Y	NM_014246	NP_055061	Q9NYQ6	CELR1_HUMAN	cadherin EGF LAG seven-pass G-type receptor 1	1874	Extracellular (Potential).|EGF-like 5; calcium-binding.				central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			lung(4)|breast(4)|pancreas(2)|skin(1)	11		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		GTACAGGGGTCGTCCACATCA	0.642													5	7	---	---	---	---	PASS
CERK	64781	broad.mit.edu	37	22	47095313	47095313	+	Silent	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47095313G>T	uc003bia.2	-	8	947	c.840C>A	c.(838-840)CTC>CTA	p.L280L	CERK_uc010hae.2_Silent_p.L82L	NM_022766	NP_073603	Q8TCT0	CERK1_HUMAN	ceramide kinase	280					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|ceramide metabolic process	integral to membrane of membrane fraction|membrane|nucleus	ATP binding|ceramide kinase activity|diacylglycerol kinase activity|magnesium ion binding			skin(1)	1		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)|BRCA - Breast invasive adenocarcinoma(115;0.171)		AGTAGCGAAGGAGTGTGCTGT	0.607													5	53	---	---	---	---	PASS
MAGEB4	4115	broad.mit.edu	37	X	30261064	30261064	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30261064T>C	uc004dcb.2	+	1	896	c.812T>C	c.(811-813)CTG>CCG	p.L271P	MAGEB1_uc004dcc.2_5'Flank|MAGEB1_uc004dcd.2_5'Flank	NM_002367	NP_002358	O15481	MAGB4_HUMAN	melanoma antigen family B, 4	271	MAGE.									ovary(1)	1						TATCAATTCCTGTGGGGTCCA	0.493													24	24	---	---	---	---	PASS
GK	2710	broad.mit.edu	37	X	30719001	30719001	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30719001A>G	uc004dch.3	+	11	1009	c.830A>G	c.(829-831)CAG>CGG	p.Q277R	GK_uc010ngj.2_Missense_Mutation_p.Q271R|GK_uc004dci.3_Missense_Mutation_p.Q271R|GK_uc011mjz.1_Missense_Mutation_p.Q72R|GK_uc011mka.1_Missense_Mutation_p.Q114R|GK_uc010ngk.2_Missense_Mutation_p.Q66R	NM_203391	NP_976325	P32189	GLPK_HUMAN	glycerol kinase isoform a	277					glycerol-3-phosphate metabolic process|triglyceride biosynthetic process	cytosol|mitochondrial outer membrane	ATP binding|glycerol kinase activity			central_nervous_system(1)	1						ATGTGCTTCCAGATTGGACAA	0.348													10	7	---	---	---	---	PASS
FTHL17	53940	broad.mit.edu	37	X	31089888	31089888	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31089888G>T	uc004dcl.1	-	1	286	c.183C>A	c.(181-183)GAC>GAA	p.D61E		NM_031894	NP_114100	Q9BXU8	FHL17_HUMAN	ferritin, heavy polypeptide-like 17	61	Ferritin-like diiron.				cellular iron ion homeostasis|iron ion transport		ferric iron binding|oxidoreductase activity				0						CCATTTTGTCGTCCGACAGGC	0.577													9	13	---	---	---	---	PASS
CYBB	1536	broad.mit.edu	37	X	37663381	37663381	+	Silent	SNP	T	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37663381T>G	uc004ddr.2	+	9	1210	c.1149T>G	c.(1147-1149)CCT>CCG	p.P383P	CYBB_uc011mke.1_RNA|CYBB_uc011mkf.1_Silent_p.P351P|CYBB_uc011mkg.1_Silent_p.P116P	NM_000397	NP_000388	P04839	CY24B_HUMAN	cytochrome b-245 beta polypeptide	383	Cytoplasmic (Potential).|FAD-binding FR-type.				electron transport chain|inflammatory response|innate immune response|respiratory burst|superoxide anion generation	NADPH oxidase complex	electron carrier activity|flavin adenine dinucleotide binding|heme binding|protein heterodimerization activity|superoxide-generating NADPH oxidase activity|voltage-gated ion channel activity			central_nervous_system(1)|skin(1)	2						GGAAACTACCTAAGTGAGTAA	0.418													13	12	---	---	---	---	PASS
USP9X	8239	broad.mit.edu	37	X	41026799	41026799	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41026799C>T	uc004dfb.2	+	17	3026	c.2393C>T	c.(2392-2394)ACG>ATG	p.T798M	USP9X_uc004dfc.2_Missense_Mutation_p.T798M	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform	798					BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6						GAGATATACACGAACCTTGGT	0.373													12	9	---	---	---	---	PASS
HEPH	9843	broad.mit.edu	37	X	65474970	65474970	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65474970T>G	uc011moz.1	+	16	2726	c.2666T>G	c.(2665-2667)GTG>GGG	p.V889G	HEPH_uc004dwn.2_Missense_Mutation_p.V889G|HEPH_uc004dwo.2_Missense_Mutation_p.V619G|HEPH_uc010nkr.2_Missense_Mutation_p.V697G|HEPH_uc011mpa.1_Missense_Mutation_p.V889G|HEPH_uc010nks.2_Missense_Mutation_p.V178G	NM_138737	NP_620074	Q9BQS7	HEPH_HUMAN	hephaestin isoform a	886	Extracellular (Potential).|Plastocyanin-like 5.				cellular iron ion homeostasis|copper ion transport|transmembrane transport	integral to membrane|plasma membrane	copper ion binding|oxidoreductase activity			lung(5)|ovary(4)	9						TATTCTGCAGTGGATCCCATC	0.478													8	3	---	---	---	---	PASS
TSIX	9383	broad.mit.edu	37	X	73046973	73046973	+	RNA	SNP	T	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73046973T>C	uc004ebn.2	+	1		c.34934T>C			XIST_uc004ebm.1_RNA	NR_003255				Homo sapiens XIST antisense RNA (non-protein coding) (TSIX), non-coding RNA.												0						CTACTTGAGTTCTGGGTTTTA	0.493													33	44	---	---	---	---	PASS
GPRASP1	9737	broad.mit.edu	37	X	101911570	101911570	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101911570G>T	uc004ejj.3	+	5	3530	c.2729G>T	c.(2728-2730)TGG>TTG	p.W910L	GPRASP1_uc004eji.3_Missense_Mutation_p.W910L|GPRASP1_uc010nod.2_Missense_Mutation_p.W910L	NM_014710	NP_055525	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting	910	Glu-rich.|OPRD1-binding.					cytoplasm	protein binding			ovary(1)|lung(1)	2						TTTGGGTCCTGGTTCTGGGAT	0.483													5	57	---	---	---	---	PASS
TMSB15B	286527	broad.mit.edu	37	X	103219092	103219092	+	5'UTR	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103219092C>G	uc010noz.2	+	2					TMSB15B_uc004elo.3_RNA|TMSB15B_uc004elq.3_RNA	NM_194324	NP_919305	P0CG34	TB15A_HUMAN	thymosin beta15b						actin cytoskeleton organization|sequestering of actin monomers	cytoplasm|cytoskeleton	actin binding			skin(1)	1						TTCTTCTAGTCAAGATGAGTG	0.234													9	20	---	---	---	---	PASS
ALG13	79868	broad.mit.edu	37	X	111003210	111003210	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:111003210G>T	uc011msy.1	+	27	3431	c.3397G>T	c.(3397-3399)GTA>TTA	p.V1133L	ALG13_uc011msx.1_Missense_Mutation_p.V950L|ALG13_uc011msz.1_Missense_Mutation_p.V1055L|ALG13_uc011mta.1_Missense_Mutation_p.V950L|ALG13_uc011mtb.1_Missense_Mutation_p.V950L			Q9NP73	ALG13_HUMAN	SubName: Full=Asparagine-linked glycosylation 13 homolog (S. cerevisiae);	1133					dolichol-linked oligosaccharide biosynthetic process|lipid glycosylation|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane	carbohydrate binding|N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity			lung(1)	1						TTCTCATTATGTACCTCAGGG	0.388													9	15	---	---	---	---	PASS
SLC6A14	11254	broad.mit.edu	37	X	115590127	115590127	+	3'UTR	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115590127C>G	uc004eqi.2	+	14						NM_007231	NP_009162	Q9UN76	S6A14_HUMAN	solute carrier family 6 (amino acid						cellular amino acid metabolic process|response to toxin	integral to membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity			ovary(2)|pancreas(1)	3					L-Proline(DB00172)	AATGAGATCTCATTGAAAAAA	0.328													30	23	---	---	---	---	PASS
ENOX2	10495	broad.mit.edu	37	X	129759346	129759346	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129759346C>A	uc004evw.2	-	16	2193	c.1775G>T	c.(1774-1776)GGA>GTA	p.G592V	ENOX2_uc004evx.2_Missense_Mutation_p.G563V|ENOX2_uc004evy.2_Missense_Mutation_p.G563V|ENOX2_uc004evv.2_Missense_Mutation_p.G417V	NM_182314	NP_872114	Q16206	ENOX2_HUMAN	ecto-NOX disulfide-thiol exchanger 2 isoform b	592				G->V: Loss of activity.	cell growth|electron transport chain|regulation of growth|transport|ultradian rhythm	cytosol|external side of plasma membrane|extracellular space	nucleic acid binding|nucleotide binding|protein disulfide oxidoreductase activity			ovary(1)	1						CAGGCTGGCTCCAACTCCAGT	0.473													12	17	---	---	---	---	PASS
MAGEC2	51438	broad.mit.edu	37	X	141291581	141291581	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:141291581C>G	uc004fbu.1	-	3	541	c.193G>C	c.(193-195)GGT>CGT	p.G65R		NM_016249	NP_057333	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2	65						cytoplasm|nucleus				breast(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)					TCCTCAGGACCACCAAGAATC	0.413										HNSCC(46;0.14)			14	32	---	---	---	---	PASS
PRDM16	63976	broad.mit.edu	37	1	3098089	3098090	+	Intron	DEL	AG	-	-	rs36223313		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3098089_3098090delAG	uc001akf.2	+						PRDM16_uc001akc.2_Intron|PRDM16_uc001akd.2_Intron|PRDM16_uc001ake.2_Intron|PRDM16_uc009vlh.2_Intron	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1						brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		gtcttacacaagcggtcttaca	0.000			T	EVI1	MDS|AML								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	10958077	10958078	+	IGR	DEL	GT	-	-	rs35259916		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10958077_10958078delGT								CASZ1 (101370 upstream) : C1orf127 (48455 downstream)																							ATCCTGGCGAgtgtgtgtgtgt	0.450													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	13180769	13180770	+	IGR	INS	-	T	T	rs142704943	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13180769_13180770insT								PRAMEF5 (63018 upstream) : LOC440563 (2191 downstream)																							CTCTCTTTCTCTCCTTTTTTGG	0.297													3	3	---	---	---	---	
CROCCL1	84809	broad.mit.edu	37	1	16945182	16945184	+	RNA	DEL	AAT	-	-	rs71803374		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16945182_16945184delAAT	uc010ocf.1	-	4		c.973_975delATT			CROCCL1_uc009vov.1_RNA|CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						TACTGATGAAAATAATAACAGAT	0.246													7	6	---	---	---	---	
CROCCL1	84809	broad.mit.edu	37	1	16961933	16961934	+	Intron	DEL	AA	-	-	rs3050680		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16961933_16961934delAA	uc001azg.1	-						CROCCL1_uc001azf.2_5'Flank|CROCCL1_uc001azi.1_Intron|uc001azj.1_Intron					Homo sapiens mRNA for FLJ00313 protein.												0						accctgtctcaaaaaaaaaaaa	0.089													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	19362935	19362938	+	IGR	DEL	GAGA	-	-	rs146617941		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19362935_19362938delGAGA								IFFO2 (80109 upstream) : UBR4 (35666 downstream)																							CAAAGCCAGGGAGAGAGAGAGAGA	0.490													4	2	---	---	---	---	
EIF4G3	8672	broad.mit.edu	37	1	21237345	21237345	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21237345delA	uc001bec.2	-						EIF4G3_uc010odi.1_Intron|EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.2_Intron	NM_003760	NP_003751	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4						interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		ATAATCATGTAAAATATTTAT	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	22489246	22489247	+	IGR	INS	-	G	G	rs144102922	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22489246_22489247insG								WNT4 (18861 upstream) : ZBTB40 (289097 downstream)																							GTGTCTTCTCAGAAGGGGATGG	0.589													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	25380784	25380787	+	IGR	DEL	CCTT	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25380784_25380787delCCTT								RUNX3 (89172 upstream) : SYF2 (167980 downstream)																							tccctccctcccttcctccctccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	29780321	29780323	+	IGR	DEL	CTC	-	-	rs12753181		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29780321_29780323delCTC								PTPRU (127006 upstream) : None (None downstream)																							ccccctccttctcctcctcctcc	0.227													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	30196697	30196702	+	IGR	DEL	CAGCAT	-	-	rs72368977	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30196697_30196702delCAGCAT								PTPRU (543382 upstream) : MATN1 (987424 downstream)																							tcaccactaccagcatcaccaacatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	33446130	33446130	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33446130delA								RNF19B (15844 upstream) : AK2 (27456 downstream)																							CCTGGTGGGGAAAAAAaaaag	0.294													4	2	---	---	---	---	
HIVEP3	59269	broad.mit.edu	37	1	42184446	42184447	+	Intron	DEL	CA	-	-	rs71816719		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42184446_42184447delCA	uc001cgz.3	-						HIVEP3_uc001cha.3_Intron	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				ctTTcacacccacacacacaca	0.322													5	4	---	---	---	---	
MAGOH	4116	broad.mit.edu	37	1	53694870	53694870	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53694870delT	uc001cvf.1	-						MAGOH_uc010ont.1_Intron	NM_002370	NP_002361	P61326	MGN_HUMAN	mago-nashi homolog						mRNA 3'-end processing|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translation|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|exon-exon junction complex|nuclear speck	protein binding|RNA binding				0						TCTATGTAGGttttttttttt	0.189													6	3	---	---	---	---	
GLIS1	148979	broad.mit.edu	37	1	53980254	53980254	+	Intron	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53980254delC	uc001cvr.1	-							NM_147193	NP_671726	Q8NBF1	GLIS1_HUMAN	GLIS family zinc finger 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			skin(1)	1						CCCCCGAGATCCCCCCTTGTT	0.577													13	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	54586175	54586175	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54586175delG								C1orf83 (7983 upstream) : CDCP2 (18493 downstream)																							GCAGCAGGGCGGGTGCAGGCA	0.602													4	2	---	---	---	---	
SSBP3	23648	broad.mit.edu	37	1	54738025	54738025	+	Intron	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54738025delC	uc001cxe.2	-						SSBP3_uc001cxf.2_Intron|SSBP3_uc001cxg.2_Intron	NM_145716	NP_663768	Q9BWW4	SSBP3_HUMAN	single stranded DNA binding protein 3 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	single-stranded DNA binding				0						GGAGGTTCCTCCCACTGTGGC	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	59441645	59441646	+	IGR	DEL	GT	-	-	rs113592069		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59441645_59441646delGT								JUN (191860 upstream) : LOC729467 (155964 downstream)																							ataaaGAGCAgtgtgtgtgtgt	0.084													6	3	---	---	---	---	
TCTEX1D1	200132	broad.mit.edu	37	1	67242229	67242234	+	Intron	DEL	TATGTG	-	-	rs35979624		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67242229_67242234delTATGTG	uc001dcv.2	+						TCTEX1D1_uc009wau.2_Intron|TCTEX1D1_uc009wav.2_Intron	NM_152665	NP_689878	Q8N7M0	TC1D1_HUMAN	Tctex1 domain containing 1												0						ATTCTACATATAtgtgtgtgtgtggg	0.252													3	4	---	---	---	---	
PTGER3	5733	broad.mit.edu	37	1	71467059	71467059	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71467059delT	uc001dfg.1	-						PTGER3_uc001dfh.1_Intron|PTGER3_uc001dfi.1_Intron|PTGER3_uc001dfj.1_Intron|PTGER3_uc001dfk.1_Intron|PTGER3_uc001dfl.1_Intron|PTGER3_uc009wbm.1_Intron|PTGER3_uc001dfm.1_Intron|PTGER3_uc001dfn.2_Intron|PTGER3_uc009wbn.1_Intron|PTGER3_uc009wbo.2_Intron|PTGER3_uc001dfo.2_Intron|PTGER3_uc001dfp.1_Intron	NM_198714	NP_942007	P43115	PE2R3_HUMAN	prostaglandin E receptor 3, subtype EP3 isoform						cell death|positive regulation of fever generation|transcription, DNA-dependent	integral to plasma membrane|nuclear envelope	ligand-dependent nuclear receptor activity|prostaglandin E receptor activity			pancreas(1)|lung(1)|skin(1)	3					Bimatoprost(DB00905)	GATTTAGCAGTTAGGATGAAG	0.234													4	2	---	---	---	---	
SLC44A5	204962	broad.mit.edu	37	1	76010189	76010190	+	Intron	DEL	CA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76010189_76010190delCA	uc001dgu.2	-						SLC44A5_uc001dgt.2_Intron|SLC44A5_uc001dgs.2_Intron|SLC44A5_uc001dgr.2_Intron|SLC44A5_uc010oqz.1_Intron|SLC44A5_uc010ora.1_Intron|SLC44A5_uc010orb.1_Intron	NM_152697	NP_689910	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5 isoform A							integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4						tgtgcatgtgcacacacacaca	0.000													4	2	---	---	---	---	
NEXN	91624	broad.mit.edu	37	1	78394991	78394992	+	Intron	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78394991_78394992insT	uc001dic.3	+						NEXN_uc001dia.3_Intron|NEXN_uc009wcb.1_Intron|NEXN_uc001dib.3_Intron|NEXN_uc001did.1_Intron|NEXN_uc001dif.1_Intron	NM_144573	NP_653174	Q0ZGT2	NEXN_HUMAN	nexilin (F actin binding protein)						regulation of cell migration|regulation of cytoskeleton organization	cytoskeleton|Z disc	actin filament binding|structural constituent of muscle			ovary(2)	2				Colorectal(170;0.114)		TGAATTGTTTATTTGGTTAGGT	0.322													23	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	88034086	88034087	+	IGR	DEL	TG	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88034086_88034087delTG								LMO4 (219483 upstream) : None (None downstream)																							tgtgtgtgtatgtgtgtgtgtg	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	89768046	89768046	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89768046delG								GBP5 (29502 upstream) : GBP6 (61390 downstream)																							ggtgctgattggtgcatttac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	100088781	100088781	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100088781delA								LPPR4 (313645 upstream) : PALMD (22650 downstream)																							accctgttgcaaaaaaaaaaa	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	101117879	101117880	+	IGR	INS	-	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101117879_101117880insA								GPR88 (110297 upstream) : VCAM1 (67417 downstream)																							ATGTTAAAAAGAAAAAAAAAAA	0.134													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	102570687	102570692	+	IGR	DEL	ACACAC	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102570687_102570692delACACAC								OLFM3 (107897 upstream) : COL11A1 (771332 downstream)																							accaaaaaatacacacacacacacac	0.000													4	2	---	---	---	---	
KCND3	3752	broad.mit.edu	37	1	112434603	112434604	+	Intron	DEL	TG	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112434603_112434604delTG	uc001ebu.1	-						KCND3_uc001ebv.1_Intron	NM_004980	NP_004971	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related							sarcolemma|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|metal ion binding			ovary(2)|large_intestine(1)	3		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)		tgtgtgtgtctgtgtgtgtgtg	0.000													5	3	---	---	---	---	
MAGI3	260425	broad.mit.edu	37	1	114150873	114150873	+	Intron	DEL	A	-	-	rs35374478		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114150873delA	uc001edk.2	+						MAGI3_uc001edh.3_Intron|MAGI3_uc001edi.3_Intron|MAGI3_uc010owm.1_Intron|MAGI3_uc001edj.2_Intron	NM_001142782	NP_001136254	Q5TCQ9	MAGI3_HUMAN	membrane-associated guanylate kinase-related  3						apoptosis|interspecies interaction between organisms|intracellular signal transduction	nucleus|tight junction	ATP binding|guanylate kinase activity|protein binding			lung(3)|ovary(2)|central_nervous_system(1)	6	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-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)		ggaagaagggaAAAGGAAGAG	0.249													4	2	---	---	---	---	
NOTCH2	4853	broad.mit.edu	37	1	120560007	120560008	+	Intron	INS	-	A	A	rs138352700	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120560007_120560008insA	uc001eik.2	-						NOTCH2_uc001eil.2_Intron|NOTCH2_uc001eim.3_Intron	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein						anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		cctctgttcttataaccctgag	0.035			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142551474	142551475	+	IGR	DEL	TA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142551474_142551475delTA								None (None upstream) : None (None downstream)																							tgaaaaattttatgtcagcgta	0.010													4	3	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	144530876	144530877	+	Intron	INS	-	CC	CC	rs72257362		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144530876_144530877insCC	uc010oxr.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818							cytoplasm					0						cttaactgaggcctctctctct	0.000													5	3	---	---	---	---	
LOC200030	200030	broad.mit.edu	37	1	148001178	148001180	+	Intron	DEL	AGG	-	-	rs35235086		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148001178_148001180delAGG	uc001eqf.2	-						LOC200030_uc010ozz.1_Intron|LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqg.2_Intron|FLJ39739_uc001eqo.1_Intron	NM_017940	NP_060410	Q86T75	NBPFB_HUMAN	hypothetical protein LOC55672							cytoplasm					0						TTTTAATAATAGGAGGTCAGTAA	0.374													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148683455	148683456	+	IGR	INS	-	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148683455_148683456insA								PPIAL4E (38662 upstream) : NBPF16 (55986 downstream)																							ctccgtgtcagaaaaaaaaacc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148847577	148847578	+	IGR	DEL	AT	-	-	rs142173842		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148847577_148847578delAT								NBPF16 (89266 upstream) : LOC645166 (80708 downstream)																							cacatatttaatatgttatatg	0.000													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148849797	148849797	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148849797delT								NBPF16 (91486 upstream) : LOC645166 (78489 downstream)																							tctcatttcatttgatcattt	0.000													4	3	---	---	---	---	
LOC645166	645166	broad.mit.edu	37	1	148941572	148941574	+	Intron	DEL	CTT	-	-	rs139120496		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148941572_148941574delCTT	uc010pbc.1	+						LOC645166_uc010pbd.1_Intron|LOC645166_uc009wkw.1_Intron	NR_027355				Homo sapiens cDNA, FLJ18771.												0						TTTCCCTCTCCTTCTTTCATTCA	0.217													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149028755	149028756	+	IGR	DEL	AT	-	-	rs141540912		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149028755_149028756delAT								LOC645166 (75701 upstream) : LOC388692 (250720 downstream)																							tacAGCAGACATAATCTATTTA	0.134													3	3	---	---	---	---	
OTUD7B	56957	broad.mit.edu	37	1	149923390	149923390	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149923390delG	uc001etn.2	-							NM_020205	NP_064590	Q6GQQ9	OTU7B_HUMAN	zinc finger protein Cezanne						negative regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|microtubule cytoskeleton|nucleus	cysteine-type peptidase activity|DNA binding|protein binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)			GCCCTTTCCTGGATTACTACA	0.393													4	2	---	---	---	---	
SPRR2D	6703	broad.mit.edu	37	1	153065195	153065197	+	Intron	DEL	TGA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153065195_153065197delTGA	uc009wnz.2	-						SPRR2A_uc001fbf.2_Intron|SPRR2A_uc009woa.2_Intron			P22532	SPR2D_HUMAN	Homo sapiens cDNA FLJ76407 complete cds, highly similar to Homo sapiens small proline-rich protein 2D (SPRR2D), mRNA.						keratinization	cornified envelope|cytoplasm					0	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			TCATGGGGAgtgatgatgatgat	0.236													4	2	---	---	---	---	
ATF6	22926	broad.mit.edu	37	1	161781577	161781578	+	Intron	INS	-	CATA	CATA	rs139290620	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161781577_161781578insCATA	uc001gbr.2	+						ATF6_uc001gbq.1_Intron	NM_007348	NP_031374	P18850	ATF6A_HUMAN	activating transcription factor 6						positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response|protein folding	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleoplasm	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|skin(1)	3	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)			atccatccatccatatacacac	0.000													3	3	---	---	---	---	
DDR2	4921	broad.mit.edu	37	1	162644789	162644790	+	Intron	INS	-	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162644789_162644790insA	uc001gcf.2	+						DDR2_uc001gcg.2_Intron	NM_001014796	NP_001014796	Q16832	DDR2_HUMAN	discoidin domain receptor family, member 2						cell adhesion	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(2)|central_nervous_system(2)|ovary(1)|kidney(1)	6	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)			actaaaagtacaaaaaaaaact	0.000													4	2	---	---	---	---	
MAEL	84944	broad.mit.edu	37	1	166973638	166973638	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166973638delA	uc001gdy.1	+						MAEL_uc001gdz.1_Intron|MAEL_uc009wvf.1_Intron	NM_032858	NP_116247	Q96JY0	MAEL_HUMAN	maelstrom homolog						cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|multicellular organismal development|piRNA metabolic process|spermatogenesis	piP-body	DNA binding			skin(1)	1						TTGTCTGTATATTGTGTGTCT	0.289													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	168744012	168744012	+	IGR	DEL	C	-	-	rs75933899		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168744012delC								DPT (45584 upstream) : MGC4473 (12167 downstream)																							CTGGCCCACACTTTTCTCATC	0.433													4	2	---	---	---	---	
SLC9A11	284525	broad.mit.edu	37	1	173571886	173571886	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173571886delT	uc001giz.2	-						SLC9A11_uc010pmq.1_Intron	NM_178527	NP_848622	Q5TAH2	S9A11_HUMAN	solute carrier family 9, member 11						sodium ion transport	integral to membrane	ion channel activity|solute:hydrogen antiporter activity			ovary(2)	2						TATTTAAGGCTTACCTTTGGT	0.358													4	2	---	---	---	---	
CACYBP	27101	broad.mit.edu	37	1	174966747	174966747	+	5'Flank	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174966747delG	uc001gkj.1	+						CACYBP_uc001gki.1_5'Flank|CACYBP_uc010pmw.1_5'Flank	NM_014412	NP_055227	Q9HB71	CYBP_HUMAN	calcyclin binding protein isoform 1							beta-catenin destruction complex	protein homodimerization activity				0						aaggcacaatggggaagcaga	0.000													4	2	---	---	---	---	
ASTN1	460	broad.mit.edu	37	1	176869589	176869590	+	Intron	DEL	TC	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176869589_176869590delTC	uc001glc.2	-						ASTN1_uc001glb.1_Intron|ASTN1_uc001gld.1_Intron	NM_004319	NP_004310	O14525	ASTN1_HUMAN	astrotactin isoform 1						cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1)	15						ctggtgtgtttctctctctctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	177398527	177398528	+	IGR	INS	-	AC	AC	rs145362071	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177398527_177398528insAC								FAM5B (146970 upstream) : SEC16B (498961 downstream)																							TGTCTCTGAGTacacacacaca	0.267													3	3	---	---	---	---	
C1orf220	400798	broad.mit.edu	37	1	178514136	178514136	+	Intron	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178514136delC	uc001glx.1	+						C1orf49_uc001glv.1_Intron	NM_207467	NP_997350			hypothetical protein LOC400798												0						AATATTCTCTCAACTCTGTGA	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	178903997	178903997	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178903997delT								RALGPS2 (14762 upstream) : FAM20B (91077 downstream)																							ctgaagctccttatttcctgc	0.144													4	2	---	---	---	---	
FAM20B	9917	broad.mit.edu	37	1	178999437	178999438	+	Intron	INS	-	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178999437_178999438insA	uc001gmc.2	+							NM_014864	NP_055679	O75063	XYLK_HUMAN	hypothetical protein LOC9917 precursor							Golgi membrane|integral to membrane	ATP binding|kinase activity|phosphotransferase activity, alcohol group as acceptor			ovary(3)	3						TAGTTTTCTGTAAAAAAAAAAA	0.366													4	2	---	---	---	---	
TDRD5	163589	broad.mit.edu	37	1	179606858	179606859	+	Intron	INS	-	G	G	rs78212582		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179606858_179606859insG	uc001gnf.1	+						TDRD5_uc010pnp.1_Intron|TDRD5_uc001gnh.1_Intron	NM_173533	NP_775804	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5						DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|skin(2)|central_nervous_system(1)	5						tgggggaaaaaaaaaaaaTACT	0.104													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	182988322	182988322	+	IGR	DEL	A	-	-	rs34679748		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182988322delA								C1orf14 (65769 upstream) : LAMC1 (4273 downstream)																							CAATTCTGTTAAAAAAAAAAA	0.294													4	3	---	---	---	---	
NCF2	4688	broad.mit.edu	37	1	183533451	183533451	+	Intron	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183533451delC	uc001gqj.3	-						NCF2_uc010pod.1_Intron|NCF2_uc010poe.1_Intron|NCF2_uc001gqk.3_Intron	NM_000433	NP_000424	P19878	NCF2_HUMAN	neutrophil cytosolic factor 2						cellular defense response|innate immune response|respiratory burst|superoxide anion generation	NADPH oxidase complex|nucleolus	electron carrier activity|protein C-terminus binding			ovary(3)	3						TAGCAGGGATCCCAAAGGTCA	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	185475684	185475687	+	IGR	DEL	TTTA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185475684_185475687delTTTA								IVNS1ABP (189223 upstream) : HMCN1 (227996 downstream)																							aagtgtttcgtttatttatttatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	186965456	186965457	+	IGR	INS	-	ACAC	ACAC			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186965456_186965457insACAC								PLA2G4A (7351 upstream) : None (None downstream)																							ATGACCAGcacacacacacaca	0.342													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	192223095	192223096	+	IGR	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192223095_192223096insT								RGS18 (68152 upstream) : RGS21 (63026 downstream)																							ctctttagttgttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	193536040	193536041	+	IGR	DEL	TA	-	-	rs74133807		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193536040_193536041delTA								CDC73 (312100 upstream) : None (None downstream)																							AGAGAGAgtgtatgtgtgtgtg	0.292													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	193650105	193650108	+	IGR	DEL	CACA	-	-	rs34809009		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193650105_193650108delCACA								CDC73 (426165 upstream) : None (None downstream)																							tatgcacttgcacacacacacaca	0.039													4	2	---	---	---	---	
CFH	3075	broad.mit.edu	37	1	196662006	196662007	+	Intron	INS	-	ACCTACCTACCT	ACCTACCTACCT	rs72199042		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196662006_196662007insACCTACCTACCT	uc001gtj.3	+						CFH_uc001gti.3_Intron|CFH_uc009wyw.2_Intron|CFH_uc009wyx.2_Intron	NM_000186	NP_000177	P08603	CFAH_HUMAN	complement factor H isoform a precursor						complement activation, alternative pathway	extracellular space				skin(4)|ovary(1)|breast(1)	6						ctccctctgtcacctccctccc	0.069													3	3	---	---	---	---	
MFSD4	148808	broad.mit.edu	37	1	205539553	205539554	+	Intron	INS	-	CCGGC	CCGGC	rs149123536	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205539553_205539554insCCGGC	uc001hcv.3	+						MFSD4_uc010prk.1_Intron|MFSD4_uc010prl.1_Intron	NM_181644	NP_857595	Q8N468	MFSD4_HUMAN	major facilitator superfamily domain containing						transmembrane transport	integral to membrane				skin(2)|central_nervous_system(1)	3	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)			CTCTGGAGGGGCCGTTCTGGGC	0.574													5	3	---	---	---	---	
LGTN	1939	broad.mit.edu	37	1	206766826	206766827	+	Intron	DEL	GA	-	-	rs113332386		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206766826_206766827delGA	uc001heh.2	-						LGTN_uc009xbw.2_Intron	NM_006893	NP_008824	P41214	EIF2D_HUMAN	ligatin						intracellular protein transport	cytoplasm	protein binding|receptor activity|translation initiation factor activity				0	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			gagagagcgcgagagagagaga	0.213													5	3	---	---	---	---	
FAIM3	9214	broad.mit.edu	37	1	207097789	207097792	+	5'Flank	DEL	TGAA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207097789_207097792delTGAA	uc001hey.2	-						FAIM3_uc010prz.1_5'Flank|FAIM3_uc010psa.1_5'Flank|FAIM3_uc010psb.1_5'Flank	NM_005449	NP_005440	O60667	FAIM3_HUMAN	Fas apoptotic inhibitory molecule 3 isoform a						anti-apoptosis|cellular defense response	integral to membrane				central_nervous_system(1)	1	Breast(84;0.201)					gtggagtgtgtgaatgtgtggtgt	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	208919394	208919395	+	IGR	DEL	AT	-	-	rs113449378		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208919394_208919395delAT								PLXNA2 (501729 upstream) : LOC642587 (682773 downstream)																							gctaattaacatataaatttgc	0.000													0	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	209338019	209338019	+	IGR	DEL	T	-	-	rs143032641		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209338019delT								PLXNA2 (920354 upstream) : LOC642587 (264149 downstream)																							aaaatacagattttgatttac	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	215448869	215448871	+	IGR	DEL	ATG	-	-	rs61548931		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215448869_215448871delATG								KCNK2 (38434 upstream) : KCTD3 (291864 downstream)																							CTCCACGTCTATGGTATCTTCAC	0.369													2	4	---	---	---	---	
ESRRG	2104	broad.mit.edu	37	1	216924998	216924998	+	Intron	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216924998delC	uc001hky.1	-						ESRRG_uc009xdp.1_Intron|ESRRG_uc001hkz.1_Intron|ESRRG_uc010puc.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron	NM_206595	NP_996318	P62508	ERR3_HUMAN	estrogen-related receptor gamma isoform 2						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	CACAAGATGGCTAGAATAGTT	0.463													4	2	---	---	---	---	
SPATA17	128153	broad.mit.edu	37	1	217982921	217982927	+	Intron	DEL	TATAATA	-	-	rs2377704	byFrequency	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217982921_217982927delTATAATA	uc001hlh.1	+						SPATA17_uc001hli.2_Intron	NM_138796	NP_620151	Q96L03	SPT17_HUMAN	spermatogenesis associated 17							cytoplasm	calmodulin binding			pancreas(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)		gcattggatttataataacaaaccctt	0.000													3	4	---	---	---	---	
EPRS	2058	broad.mit.edu	37	1	220219832	220219834	+	5'UTR	DEL	CGC	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220219832_220219834delCGC	uc001hly.1	-	1					EPRS_uc010puf.1_5'UTR|EPRS_uc001hlz.1_5'UTR|EPRS_uc009xdt.1_5'UTR	NM_004446	NP_004437	P07814	SYEP_HUMAN	glutamyl-prolyl tRNA synthetase						glutamyl-tRNA aminoacylation|prolyl-tRNA aminoacylation|protein complex assembly	cytosol|soluble fraction	ATP binding|glutamate-tRNA ligase activity|proline-tRNA ligase activity|protein binding|RNA binding			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(131;0.0735)	L-Glutamic Acid(DB00142)|L-Proline(DB00172)	GCGTACccgacgccgccgcagcc	0.315													4	5	---	---	---	---	
MOSC2	54996	broad.mit.edu	37	1	220947414	220947414	+	Intron	DEL	T	-	-	rs5781185		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220947414delT	uc001hmq.2	+						MOSC2_uc001hmr.2_Intron|MOSC2_uc009xdx.2_Intron	NM_017898	NP_060368	Q969Z3	MOSC2_HUMAN	MOCO sulphurase C-terminal domain containing 2							mitochondrial outer membrane|peroxisome	molybdenum ion binding|oxidoreductase activity|pyridoxal phosphate binding				0				GBM - Glioblastoma multiforme(131;0.00499)|all cancers(67;0.204)		CACATCCTCGttttttttttt	0.144													5	3	---	---	---	---	
CDC42BPA	8476	broad.mit.edu	37	1	227489064	227489064	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227489064delT	uc001hqr.2	-						CDC42BPA_uc001hqs.2_Intron|CDC42BPA_uc009xes.2_Intron|CDC42BPA_uc010pvs.1_Intron	NM_003607	NP_003598	Q5VT25	MRCKA_HUMAN	CDC42-binding protein kinase alpha isoform B						actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)				GATGTAGACAttttttttttt	0.174													4	2	---	---	---	---	
RGS7	6000	broad.mit.edu	37	1	241029811	241029811	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241029811delA	uc001hyv.2	-						RGS7_uc010pyh.1_Intron|RGS7_uc010pyj.1_Intron|RGS7_uc001hyu.2_Intron|RGS7_uc009xgn.1_Intron|RGS7_uc001hyw.2_Intron|RGS7_uc001hyt.2_Intron	NM_002924	NP_002915	P49802	RGS7_HUMAN	regulator of G-protein signaling 7						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			actccgtctcaaaaaaaaaaa	0.224													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	242995203	242995204	+	IGR	INS	-	GAAA	GAAA	rs10926878	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242995203_242995204insGAAA								PLD5 (307205 upstream) : CEP170 (292527 downstream)																							aaggaaggaaggaaggaaggag	0.000													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	243111605	243111607	+	IGR	DEL	TAT	-	-	rs56272209		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243111605_243111607delTAT								PLD5 (423607 upstream) : CEP170 (176124 downstream)																							aatccacacatatcaacactaac	0.000													2	5	---	---	---	---	
SNTG2	54221	broad.mit.edu	37	2	1101453	1101453	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1101453delG	uc002qwq.2	+						SNTG2_uc002qwp.2_Intron|SNTG2_uc010ewi.2_Intron	NM_018968	NP_061841	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2						central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		GGTGCAGGCTGGGCTTTCCAG	0.577													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	4594698	4594699	+	IGR	INS	-	A	A	rs141791260	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4594698_4594699insA								ALLC (844440 upstream) : None (None downstream)																							cctgaaatgtcaaaagttcaag	0.000													3	3	---	---	---	---	
GREB1	9687	broad.mit.edu	37	2	11693698	11693698	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11693698delT	uc002rbk.1	+						GREB1_uc002rbl.2_Intron|GREB1_uc002rbm.2_Intron|GREB1_uc002rbn.1_Intron	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1							integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		CCCCATTCTATTTTTTTTTTT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	23171793	23171794	+	IGR	INS	-	A	A	rs144020506	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23171793_23171794insA								None (None upstream) : KLHL29 (583661 downstream)																							TGTGGGTACTGAAAACTGAGAA	0.411													4	4	---	---	---	---	
KIF3C	3797	broad.mit.edu	37	2	26152778	26152778	+	Intron	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26152778delC	uc002rgu.2	-						KIF3C_uc010eyj.1_Intron|KIF3C_uc010ykr.1_Intron	NM_002254	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C						blood coagulation|microtubule-based movement	cytosol|kinesin complex|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					agacacctcgcccggccTCCC	0.279													17	12	---	---	---	---	
CIB4	130106	broad.mit.edu	37	2	26839988	26839989	+	Intron	INS	-	TG	TG	rs146713738	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26839988_26839989insTG	uc002rhm.2	-							NM_001029881	NP_001025052	A0PJX0	CIB4_HUMAN	calcium and integrin binding family member 4								calcium ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					agAGCATGGAAtgtgtgtgtgt	0.317													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	37682050	37682051	+	IGR	INS	-	A	A	rs144588775	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37682050_37682051insA								QPCT (81586 upstream) : CDC42EP3 (188692 downstream)																							AAGGCTTGGAGAGTGGTTGCAT	0.436													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	44319877	44319878	+	IGR	DEL	TT	-	-	rs57372472		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44319877_44319878delTT								LRPPRC (96733 upstream) : PPM1B (76122 downstream)																							ctttcctttctttctttccttt	0.020													2	4	---	---	---	---	
MSH6	2956	broad.mit.edu	37	2	48013202	48013203	+	Intron	INS	-	C	C	rs138450616	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48013202_48013203insC	uc002rwd.3	+						MSH6_uc002rwc.2_Intron|MSH6_uc010fbj.2_Intron|MSH6_uc010yoi.1_Intron|MSH6_uc010yoj.1_Intron	NM_000179	NP_000170	P52701	MSH6_HUMAN	mutS homolog 6						determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes	MutSalpha complex	ATP binding|DNA-dependent ATPase activity|protein binding			large_intestine(53)|central_nervous_system(28)|endometrium(28)|stomach(22)|haematopoietic_and_lymphoid_tissue(9)|lung(7)|skin(6)|urinary_tract(5)|breast(5)|ovary(3)|thyroid(1)|upper_aerodigestive_tract(1)	168		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AATTGTAGACTCCAAGTGGAAA	0.475			Mis|N|F|S		colorectal	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	54236887	54236888	+	IGR	INS	-	CAGG	CAGG			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54236887_54236888insCAGG								PSME4 (38910 upstream) : ACYP2 (105522 downstream)																							AGCACAGTAACCAGGCTACAAG	0.381													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	55737461	55737461	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55737461delT								CCDC88A (90404 upstream) : CCDC104 (9279 downstream)																							ttcttttgtcttttttttttt	0.050													4	3	---	---	---	---	
VRK2	7444	broad.mit.edu	37	2	58363368	58363369	+	Intron	INS	-	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58363368_58363369insC	uc002rzo.2	+						VRK2_uc010fcb.2_Intron|VRK2_uc002rzs.2_Intron|VRK2_uc002rzr.2_Intron|VRK2_uc010fcc.2_Intron|VRK2_uc002rzv.2_Intron|VRK2_uc010fcd.2_Intron|VRK2_uc002rzp.2_Intron|VRK2_uc010ypg.1_Intron|VRK2_uc002rzq.2_Intron|VRK2_uc002rzu.2_Intron|VRK2_uc002rzt.2_Intron	NM_001130482	NP_001123954	Q86Y07	VRK2_HUMAN	vaccinia related kinase 2 isoform 2							integral to membrane	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1						TCTTTTGTTTTCCCCTTTCTCT	0.401													4	2	---	---	---	---	
C2orf74	339804	broad.mit.edu	37	2	61379058	61379058	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61379058delA	uc010ypl.1	+						C2orf74_uc002sba.2_Intron	NM_001143960	NP_001137432	A8MZ97	CB074_HUMAN	hypothetical protein LOC339804 isoform 2							integral to membrane					0						ACATTGTGGCAAAGGCCACCC	0.363													4	2	---	---	---	---	
USP34	9736	broad.mit.edu	37	2	61588757	61588758	+	Intron	INS	-	G	G	rs143596050	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61588757_61588758insG	uc002sbe.2	-							NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			agaatgaaactggatccttatc	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	67570771	67570772	+	IGR	INS	-	A	A	rs147580516	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67570771_67570772insA								MEIS1 (770881 upstream) : ETAA1 (53670 downstream)																							ccaccaccatcaaaaaaaaaag	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	67571975	67571975	+	IGR	DEL	T	-	-	rs72393557		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67571975delT								MEIS1 (772085 upstream) : ETAA1 (52467 downstream)																							ACCATGGACCttttttttttt	0.159													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	72087009	72087012	+	IGR	DEL	GTGT	-	-	rs144814313		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72087009_72087012delGTGT								DYSF (173117 upstream) : CYP26B1 (269355 downstream)																							atgtatgtgagtgtgtgtgcatga	0.162													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	73851205	73851207	+	IGR	DEL	TCC	-	-	rs112833082		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73851205_73851207delTCC								ALMS1 (14159 upstream) : NAT8 (16643 downstream)																							CAGCTTCTGGtcctcctcctcct	0.340													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	76344170	76344171	+	IGR	DEL	TG	-	-	rs72419432		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76344170_76344171delTG								C2orf3 (406059 upstream) : LRRTM4 (630687 downstream)																							TGTCATGATAtgtgtgtgtgtg	0.292													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	85544589	85544590	+	IGR	INS	-	CAACA	CAACA	rs140958510	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85544589_85544590insCAACA								TCF7L1 (7085 upstream) : TGOLN2 (557 downstream)																							GCTACTGAAAGCAGGCAGCCAG	0.559													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90408415	90408416	+	Intron	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90408415_90408416insT	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		TTTTTTCCCTCTTTCTGATTTG	0.342													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91932789	91932789	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91932789delA								LOC654342 (84814 upstream) : GGT8P (30579 downstream)																							GAGGAAGGATAGTGGGAATGT	0.453													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92275723	92275723	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92275723delG								FKSG73 (145229 upstream) : None (None downstream)																							ggcctatggtgaaaaaaggga	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96615737	96615737	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96615737delG	uc010yug.1	-											Homo sapiens cDNA FLJ54441 complete cds, highly similar to Homo sapiens ankyrin repeat domain 36 (ANKRD36), mRNA.																		AAGGAAAAAAGAAGAATCCAG	0.308													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	109128817	109128818	+	Intron	INS	-	AAAC	AAAC	rs141375092	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109128817_109128818insAAAC	uc002tee.3	-											Homo sapiens cDNA FLJ38668 fis, clone HLUNG2008439.																		cgccatctcaaaaacaaacaaa	0.124													4	2	---	---	---	---	
MERTK	10461	broad.mit.edu	37	2	112697687	112697687	+	Intron	DEL	T	-	-	rs34805317		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112697687delT	uc002thk.1	+						MERTK_uc002thl.1_Intron	NM_006343	NP_006334	Q12866	MERTK_HUMAN	MER receptor tyrosine kinase precursor						cell surface receptor linked signaling pathway|cell-cell signaling|leukocyte migration	integral to plasma membrane|soluble fraction	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(6)|upper_aerodigestive_tract(1)|stomach(1)|kidney(1)	9						gcttctactctttttttttTC	0.164													3	3	---	---	---	---	
ZC3H8	84524	broad.mit.edu	37	2	112977227	112977228	+	Intron	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112977227_112977228insT	uc002thp.2	-							NM_032494	NP_115883	Q8N5P1	ZC3H8_HUMAN	zinc finger CCCH-type containing 8						apoptosis|negative regulation of T cell differentiation in thymus|negative regulation of transcription, DNA-dependent|positive regulation of thymocyte apoptosis|response to antibiotic|T cell homeostasis	nucleus	RNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						gagtggggtgattttttttttt	0.000													4	2	---	---	---	---	
DPP10	57628	broad.mit.edu	37	2	115530240	115530240	+	Intron	DEL	T	-	-	rs142960201		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115530240delT	uc002tla.1	+						DPP10_uc002tlb.1_Intron	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10						ACCTCATACCTTTTTTTTTTT	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	120489328	120489329	+	IGR	DEL	GA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120489328_120489329delGA								TMEM177 (8137 upstream) : PTPN4 (27878 downstream)																							ctcatggtctgagagagagaga	0.000													4	2	---	---	---	---	
NCRNA00164	554226	broad.mit.edu	37	2	132984602	132984602	+	Intron	DEL	A	-	-	rs62166094		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132984602delA	uc002ttj.3	-							NR_027020				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0						gtgggaaaggaaatatcttca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133022246	133022247	+	IGR	INS	-	T	T	rs146127817		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133022246_133022247insT								NCRNA00164 (6704 upstream) : GPR39 (151900 downstream)																							GATAGCCTTTCTTTGTTTTCAC	0.307													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133024006	133024007	+	IGR	DEL	AG	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133024006_133024007delAG								NCRNA00164 (8464 upstream) : GPR39 (150140 downstream)																							aaagacagaaagagagagacag	0.050													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133052507	133052508	+	IGR	INS	-	G	G	rs139970457	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133052507_133052508insG								NCRNA00164 (36965 upstream) : GPR39 (121639 downstream)																							ttaacatggcattttccctctg	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	135551065	135551065	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135551065delA								TMEM163 (25731 upstream) : ACMSD (45121 downstream)																							aagagatggcaaaaacaacag	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	140258730	140258731	+	IGR	DEL	CA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140258730_140258731delCA								NXPH2 (720919 upstream) : LRP1B (730265 downstream)																							gacacacatgcacacacacaca	0.000													4	3	---	---	---	---	
MBD5	55777	broad.mit.edu	37	2	149213327	149213328	+	Intron	INS	-	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149213327_149213328insA	uc002twm.3	+						MBD5_uc010zbs.1_5'Flank|MBD5_uc010fns.2_5'Flank	NM_018328	NP_060798	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5							chromosome|nucleus	chromatin binding|DNA binding			skin(3)|ovary(2)	5				BRCA - Breast invasive adenocarcinoma(221;0.0569)		AGAGCAGGCAGAAAAAAAAAAA	0.401													4	2	---	---	---	---	
PKP4	8502	broad.mit.edu	37	2	159499793	159499794	+	Intron	DEL	GG	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159499793_159499794delGG	uc002tzv.2	+						PKP4_uc002tzt.1_Intron|PKP4_uc002tzu.2_Intron|PKP4_uc002tzw.2_Intron|PKP4_uc002tzx.2_Intron|PKP4_uc002tzy.1_Intron|PKP4_uc002tzz.1_Intron|PKP4_uc002uaa.2_Intron	NM_003628	NP_003619	Q99569	PKP4_HUMAN	plakophilin 4 isoform a						cell adhesion	desmosome	protein binding			ovary(5)|skin(2)	7						GAAGTTCCCTGGGTGACATGAA	0.455										HNSCC(62;0.18)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	168285187	168285187	+	IGR	DEL	A	-	-	rs79691421		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168285187delA								XIRP2 (168928 upstream) : B3GALT1 (389995 downstream)																							gactccatttaaaaaaaaaGT	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	179688789	179688790	+	IGR	DEL	AC	-	-	rs67882082		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179688789_179688790delAC								TTN (16639 upstream) : CCDC141 (8557 downstream)																							ACAGAGAAAAacacacacacac	0.297													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	184853402	184853403	+	IGR	INS	-	T	T	rs71401959		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184853402_184853403insT								NUP35 (826995 upstream) : ZNF804A (609690 downstream)																							tcggtggatagttttttttttt	0.000													3	5	---	---	---	---	
ZC3H15	55854	broad.mit.edu	37	2	187366254	187366255	+	Intron	DEL	TG	-	-	rs149066234		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187366254_187366255delTG	uc002upo.2	+							NM_018471	NP_060941	Q8WU90	ZC3HF_HUMAN	erythropoietin 4 immediate early response							cytoplasm|nucleolus|plasma membrane	nucleic acid binding|zinc ion binding			skin(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Epithelial(96;0.0922)|all cancers(119;0.233)			CTTAATAGACTGtttataaaaa	0.183													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	193363498	193363499	+	IGR	DEL	CA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193363498_193363499delCA								TMEFF2 (303854 upstream) : PCGEM1 (251072 downstream)																							cctgcgCATGcacacacacaca	0.025													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	194426362	194426363	+	IGR	DEL	AC	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:194426362_194426363delAC								PCGEM1 (784741 upstream) : None (None downstream)																							TTTCTCTcatacacacacacac	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	197485181	197485181	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197485181delC								HECW2 (27846 upstream) : CCDC150 (19175 downstream)																							CTCTTTTCTACCCACTCCCTC	0.318													4	2	---	---	---	---	
CASP8	841	broad.mit.edu	37	2	202145287	202145287	+	Intron	DEL	T	-	-	rs67287666		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202145287delT	uc002uxr.1	+						CASP8_uc002uxo.1_Intron|CASP8_uc002uxp.1_Intron|CASP8_uc002uxq.1_Intron|CASP8_uc002uxt.1_Intron|CASP8_uc002uxu.1_Intron|CASP8_uc002uxw.1_Intron|CASP8_uc002uxy.1_Intron|CASP8_uc002uxx.1_Intron|CASP8_uc010ftf.2_Intron|CASP8_uc010fte.1_Intron	NM_033355	NP_203519	Q14790	CASP8_HUMAN	caspase 8 isoform B precursor						activation of caspase activity|activation of pro-apoptotic gene products|cellular component disassembly involved in apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis involved in cellular protein catabolic process|response to tumor necrosis factor	centrosome|cytosol|mitochondrial outer membrane	cysteine-type endopeptidase activity|protein binding|protein binding			upper_aerodigestive_tract(2)|ovary(1)|breast(1)|skin(1)	5						ggaaaaatgcttttggaaata	0.000										HNSCC(4;0.00038)			4	2	---	---	---	---	
CDK15	65061	broad.mit.edu	37	2	202730282	202730282	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202730282delT	uc002uyt.2	+						CDK15_uc010ftm.2_Intron|CDK15_uc002uys.2_Intron|CDK15_uc010ftn.1_Intron|CDK15_uc002uyu.1_Intron	NM_139158	NP_631897	Q96Q40	CDK15_HUMAN	PFTAIRE protein kinase 2								ATP binding|cyclin-dependent protein kinase activity|metal ion binding|protein binding			breast(2)|ovary(1)|lung(1)|kidney(1)	5					Adenosine triphosphate(DB00171)	GGACACTGGCTTTTAGAGCAT	0.328													4	2	---	---	---	---	
ICA1L	130026	broad.mit.edu	37	2	203697808	203697808	+	Intron	DEL	A	-	-	rs147146988		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203697808delA	uc002uzh.1	-						ICA1L_uc002uzi.1_Intron|ICA1L_uc002uzk.1_Intron	NM_138468	NP_612477	Q8NDH6	ICA1L_HUMAN	islet cell autoantigen 1,69kDa-like isoform 1												0						ctatatagggaaaaaaaaaga	0.000													3	3	---	---	---	---	
CPS1	1373	broad.mit.edu	37	2	211476693	211476693	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211476693delA	uc002vee.3	+						CPS1_uc010fur.2_Intron|CPS1_uc010fus.2_Intron	NM_001875	NP_001866	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform b						carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)|skin(1)	13				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)		AAAAAGGAACACCTTTTTTTT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	226029438	226029439	+	IGR	INS	-	TGC	TGC	rs141409551	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226029438_226029439insTGC								DOCK10 (122108 upstream) : KIAA1486 (236163 downstream)																							GATTCTGCCCTtgctgctgctg	0.490													4	3	---	---	---	---	
COPS7B	64708	broad.mit.edu	37	2	232651907	232651907	+	Intron	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232651907delC	uc002vsg.1	+						COPS7B_uc010fxy.1_Intron|COPS7B_uc002vsh.1_Intron|COPS7B_uc002vsi.1_Intron	NM_022730	NP_073567	Q9H9Q2	CSN7B_HUMAN	COP9 constitutive photomorphogenic homolog						cullin deneddylation	cytoplasm|signalosome				ovary(1)|liver(1)|skin(1)	3		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Renal(207;0.025)		Epithelial(121;1.36e-12)|BRCA - Breast invasive adenocarcinoma(100;0.00136)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		ACTCGTTGTTCCCCAGCACTT	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	236367701	236367702	+	IGR	INS	-	A	A	rs35426244		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236367701_236367702insA								SH3BP4 (403345 upstream) : AGAP1 (35034 downstream)																							gatcctgtctcaaaaaaaaaag	0.163													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	237553269	237553269	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237553269delA								CXCR7 (62277 upstream) : COPS8 (440815 downstream)																							TGATGCCCTCATCATTTCCAT	0.582													4	2	---	---	---	---	
CNTN6	27255	broad.mit.edu	37	3	1217246	1217247	+	Intron	INS	-	CTTT	CTTT	rs144671311	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1217246_1217247insCTTT	uc003boz.2	+						CNTN6_uc010hbo.2_Intron|CNTN6_uc011asj.1_Intron|CNTN6_uc003bpa.2_Intron	NM_014461	NP_055276	Q9UQ52	CNTN6_HUMAN	contactin 6 precursor						axon guidance|cell adhesion|central nervous system development|Notch signaling pathway	anchored to membrane|plasma membrane				skin(3)|lung(2)|breast(2)|pancreas(1)	8		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		tccttttacaaattactaagga	0.000													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	3559909	3559909	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3559909delT								CRBN (338519 upstream) : SUMF1 (263127 downstream)																							GTGGTACACCTTTTAAATGGA	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	23726569	23726569	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23726569delT								UBE2E2 (94273 upstream) : UBE2E1 (120870 downstream)																							agaaaaatgattttttttttt	0.090													4	2	---	---	---	---	
SCN10A	6336	broad.mit.edu	37	3	38835085	38835086	+	Intron	DEL	AT	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38835085_38835086delAT	uc003ciq.2	-							NM_006514	NP_006505	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha						sensory perception	voltage-gated sodium channel complex				ovary(5)|skin(3)|large_intestine(1)|kidney(1)	10				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dibucaine(DB00527)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)	TAAGTTAGAGatatatatatat	0.381													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	40409494	40409494	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40409494delC								EIF1B (55581 upstream) : ENTPD3 (19179 downstream)																							acttattggacctaatggata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	45224914	45224921	+	IGR	DEL	CAGGCAGG	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45224914_45224921delCAGGCAGG								CDCP1 (37000 upstream) : TMEM158 (41036 downstream)																							ATTCTGATCCcaggcaggcaggcaggca	0.457													4	2	---	---	---	---	
DAG1	1605	broad.mit.edu	37	3	49516745	49516746	+	Intron	INS	-	T	T	rs35759587		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49516745_49516746insT	uc003cxc.3	+							NM_004393	NP_004384	Q14118	DAG1_HUMAN	dystroglycan 1 preproprotein						cytoskeletal anchoring at plasma membrane|interspecies interaction between organisms|microtubule anchoring|negative regulation of cell migration|negative regulation of MAPKKK cascade|negative regulation of protein kinase B signaling cascade	basement membrane|contractile ring|cytoplasm|cytoskeleton|dystrophin-associated glycoprotein complex|extracellular space|filopodium|integral to membrane|integral to membrane of membrane fraction|lamellipodium|nucleoplasm	actin binding|alpha-actinin binding|calcium ion binding|laminin-1 binding|receptor activity|structural constituent of muscle|tubulin binding|vinculin binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		TTGAGTATAGAttttttttttt	0.252													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	59629502	59629502	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59629502delA								C3orf67 (593744 upstream) : FHIT (105536 downstream)																							ccctgtctccaaaaaaacaaa	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	64230280	64230281	+	IGR	DEL	GT	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64230280_64230281delGT								PRICKLE2 (19149 upstream) : ADAMTS9 (271052 downstream)																							TGAATGACTGgtgtgtgtgtgt	0.218													3	3	---	---	---	---	
EIF4E3	317649	broad.mit.edu	37	3	71754946	71754947	+	Intron	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71754946_71754947insT	uc003dov.3	-						EIF4E3_uc011bgc.1_Intron|EIF4E3_uc003dox.2_Intron|EIF4E3_uc011bgd.1_Intron|EIF4E3_uc010hoc.2_Intron	NM_001134651	NP_001128123	Q8N5X7	IF4E3_HUMAN	eukaryotic translation initiation factor 4E						regulation of translation	cytoplasm|mRNA cap binding complex	translation initiation factor activity				0		Prostate(10;0.0166)		BRCA - Breast invasive adenocarcinoma(55;2.56e-05)|Epithelial(33;2.9e-05)|Lung(16;9.28e-05)|LUSC - Lung squamous cell carcinoma(21;0.00227)		GCCGTGTTCTAtttttttttct	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	75875801	75875802	+	IGR	INS	-	T	T	rs144617957		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75875801_75875802insT								ZNF717 (41131 upstream) : None (None downstream)																							cttaaagtataaaaaaaaaaaT	0.158													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	83564318	83564318	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:83564318delC								None (None upstream) : None (None downstream)																							cattggggtgctaccctcttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	94527116	94527116	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:94527116delA								NSUN3 (681486 upstream) : LOC255025 (129991 downstream)																							atatgtctataagagcaattg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	96117472	96117472	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96117472delT								None (None upstream) : EPHA6 (415953 downstream)																							ttttttattctttttgtttat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	102224486	102224486	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102224486delA								ZPLD1 (25801 upstream) : None (None downstream)																							aacaatggggaaaatgtctcc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	104483567	104483567	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104483567delT								None (None upstream) : ALCAM (602146 downstream)																							CAAATGAGAATTTTTTTTTTT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	106415615	106415616	+	IGR	INS	-	TT	TT	rs80204896		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106415615_106415616insTT								CBLB (827349 upstream) : LOC100302640 (140044 downstream)																							TTTCTCAATTAttttttttttt	0.173													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	108455325	108455326	+	IGR	DEL	TT	-	-	rs72364422		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108455325_108455326delTT								DZIP3 (41633 upstream) : RETNLB (19160 downstream)																							ctgttcagaatttgcctttggt	0.000													2	6	---	---	---	---	
PVRL3	25945	broad.mit.edu	37	3	110804548	110804548	+	Intron	DEL	T	-	-	rs74799279		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110804548delT	uc003dxt.1	+						PVRL3_uc003dxu.1_Intron	NM_015480	NP_056295	Q9NQS3	PVRL3_HUMAN	poliovirus receptor-related 3 precursor						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane	cell adhesion molecule binding|protein homodimerization activity			upper_aerodigestive_tract(2)	2						tgtagcagtattttttttttt	0.030													4	2	---	---	---	---	
PHLDB2	90102	broad.mit.edu	37	3	111692836	111692837	+	Intron	INS	-	A	A	rs137973833	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111692836_111692837insA	uc010hqa.2	+						PHLDB2_uc003dyc.2_Intron|PHLDB2_uc003dyd.2_Intron|PHLDB2_uc003dyg.2_Intron|PHLDB2_uc003dyh.2_Intron|PHLDB2_uc003dyi.2_Intron|PHLDB2_uc003dyj.2_Intron	NM_001134438	NP_001127910	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B,							cytoplasm|intermediate filament cytoskeleton|plasma membrane				ovary(4)|skin(2)	6						TCTCTTTGAGGAAAAAAAATAT	0.371													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	112904401	112904401	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112904401delC								C3orf17 (165846 upstream) : BOC (26011 downstream)																							gagactgactcccaaaagaca	0.005													4	2	---	---	---	---	
ZBTB20	26137	broad.mit.edu	37	3	114214300	114214301	+	Intron	DEL	AC	-	-	rs63080863		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114214300_114214301delAC	uc003ebj.2	-						ZBTB20_uc010hqp.2_Intron|ZBTB20_uc003ebk.2_Intron|ZBTB20_uc003ebl.2_Intron|ZBTB20_uc003ebm.2_Intron|ZBTB20_uc003ebn.2_Intron	NM_015642	NP_056457	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		GTCTGTGTATacacacacacac	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	116989268	116989268	+	IGR	DEL	A	-	-	rs67776733		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116989268delA								LOC285194 (553383 upstream) : None (None downstream)																							GAGCTCTGATAAAATCCTTAC	0.378													3	3	---	---	---	---	
GSK3B	2932	broad.mit.edu	37	3	119711993	119711993	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119711993delA	uc003edo.2	-						GSK3B_uc003edn.2_Intron	NM_001146156	NP_001139628	P49841	GSK3B_HUMAN	glycogen synthase kinase 3 beta isoform 2						axon guidance|epithelial to mesenchymal transition|ER overload response|glycogen metabolic process|hippocampus development|negative regulation of apoptosis|negative regulation of protein binding|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|positive regulation of cell-matrix adhesion|positive regulation of protein complex assembly|positive regulation of protein export from nucleus|positive regulation of Rac GTPase activity|regulation of microtubule-based process|superior temporal gyrus development	Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|nucleus|plasma membrane	ATP binding|beta-catenin binding|NF-kappaB binding|p53 binding|protein kinase A catalytic subunit binding|protein serine/threonine kinase activity|RNA polymerase II transcription factor binding|tau-protein kinase activity|ubiquitin protein ligase binding			lung(2)	2				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)	tgtaaggaagaaaaaaaaaaa	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	119849899	119849899	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119849899delT	uc003edp.2	+											Homo sapiens cDNA clone IMAGE:4827879.																		TGTGGGTGGGTTTTTTTTTTC	0.433													4	2	---	---	---	---	
GPR156	165829	broad.mit.edu	37	3	119910104	119910104	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119910104delA	uc011bjf.1	-						GPR156_uc011bjg.1_Intron	NM_153002	NP_694547	Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156							integral to membrane|plasma membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(114;0.19)		tctgtctcagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	122071796	122071797	+	IGR	INS	-	A	A	rs146513043	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122071796_122071797insA								CSTA (10983 upstream) : CCDC58 (6640 downstream)																							ACTTATTCTCCAGAATTATTGG	0.327													6	3	---	---	---	---	
PDIA5	10954	broad.mit.edu	37	3	122879295	122879296	+	Intron	INS	-	G	G	rs147231201	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122879295_122879296insG	uc003egc.1	+						PDIA5_uc003egd.1_Intron	NM_006810	NP_006801	Q14554	PDIA5_HUMAN	protein disulfide isomerase A5 precursor						cell redox homeostasis|glycerol ether metabolic process|protein folding|response to stress	endoplasmic reticulum lumen	electron carrier activity|protein disulfide isomerase activity|protein disulfide oxidoreductase activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.0427)		TTTACTCATGCGGGGCTCCTCC	0.530													1	9	---	---	---	---	
SLC41A3	54946	broad.mit.edu	37	3	125760706	125760707	+	Intron	INS	-	T	T	rs141184101	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125760706_125760707insT	uc003eij.2	-						SLC41A3_uc003eii.2_Intron|SLC41A3_uc003eil.2_Intron|SLC41A3_uc003eik.2_Intron|SLC41A3_uc011bkh.1_Intron|SLC41A3_uc010hsd.1_Intron	NM_001008485	NP_001008485	Q96GZ6	S41A3_HUMAN	solute carrier family 41, member 3 isoform 1							integral to membrane|plasma membrane	cation transmembrane transporter activity				0				GBM - Glioblastoma multiforme(114;0.167)		tcagaaaccagttaagatctgc	0.000													2	6	---	---	---	---	
MGLL	11343	broad.mit.edu	37	3	127432936	127432936	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127432936delA	uc003ejx.2	-						MGLL_uc003ejw.2_Intron|MGLL_uc011bko.1_Intron|MGLL_uc003ejv.2_Intron	NM_001003794	NP_001003794	Q99685	MGLL_HUMAN	monoglyceride lipase isoform 2						arachidonic acid metabolic process|fatty acid biosynthetic process|inflammatory response|platelet activation|regulation of endocannabinoid signaling pathway|regulation of inflammatory response|regulation of sensory perception of pain|triglyceride catabolic process	plasma membrane	acylglycerol lipase activity|carboxylesterase activity|lysophospholipase activity|protein homodimerization activity				0						GCTTCGTAGGAAAAAAAAAAA	0.428													4	2	---	---	---	---	
COL29A1	256076	broad.mit.edu	37	3	130088918	130088919	+	Intron	DEL	AA	-	-	rs143001290	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130088918_130088919delAA	uc010htj.1	+						COL29A1_uc010hti.1_Intron	NM_153264	NP_694996	A8TX70	CO6A5_HUMAN	collagen, type XXIX, alpha 1						axon guidance|cell adhesion	collagen					0						TTAATTCCTTAAAGTATCACTC	0.327													4	2	---	---	---	---	
NCRNA00119	348808	broad.mit.edu	37	3	132511269	132511270	+	Intron	INS	-	T	T	rs67784360		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132511269_132511270insT	uc003epg.1	+							NR_002811				Homo sapiens cDNA clone IMAGE:4826885.												0						AACGCACACTATTTTTTTTTTT	0.426													4	2	---	---	---	---	
EPHB1	2047	broad.mit.edu	37	3	134526337	134526338	+	Intron	DEL	GT	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134526337_134526338delGT	uc003eqt.2	+						EPHB1_uc010htz.1_Intron|EPHB1_uc011bly.1_Intron	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30						tggggaaggAgtgtgtgtgtgt	0.109													5	3	---	---	---	---	
CLSTN2	64084	broad.mit.edu	37	3	140123134	140123134	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140123134delA	uc003etn.2	+						CLSTN2_uc003etm.2_Intron	NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor						homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7						GGGAGGAATGAACAGTAAACC	0.453										HNSCC(16;0.037)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	140751372	140751372	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140751372delT								SLC25A36 (52587 upstream) : SPSB4 (19371 downstream)																							ttatagcaaatttttttctag	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	144750665	144750665	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144750665delT								None (None upstream) : None (None downstream)																							attatgtgtcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	145976948	145976948	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145976948delC								PLSCR4 (7982 upstream) : PLSCR2 (174134 downstream)																							GAGAAAGGCTCTTTCTAGCAC	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	149424601	149424601	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149424601delA								WWTR1 (3486 upstream) : COMMD2 (31659 downstream)																							ACCTTTTAAGAAAAGGAAGGT	0.328													4	2	---	---	---	---	
RNF13	11342	broad.mit.edu	37	3	149651064	149651065	+	Intron	DEL	TA	-	-	rs6781658		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149651064_149651065delTA	uc003exn.3	+						RNF13_uc003exp.3_Intron|RNF13_uc010hvh.2_Intron	NM_007282	NP_009213	O43567	RNF13_HUMAN	ring finger protein 13						protein autoubiquitination	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane|nuclear inner membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		all_neural(597;0.0138)|Myeloproliferative disorder(1037;0.0255)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			tttttttttttaaattgtcttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	149997676	149997676	+	IGR	DEL	T	-	-	rs4681601	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149997676delT								PFN2 (308935 upstream) : TSC22D2 (129112 downstream)																							taaaaaaaaattttttgtaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	150374329	150374329	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150374329delA								SELT (26097 upstream) : FAM194A (3348 downstream)																							aagaggaaggaaaaaaagggg	0.025													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	151349486	151349489	+	IGR	DEL	AAAC	-	-	rs79673196		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151349486_151349489delAAAC								IGSF10 (172989 upstream) : AADACL2 (102215 downstream)																							tgttggagataaacagatagctct	0.029													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	151558227	151558228	+	IGR	DEL	CA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151558227_151558228delCA								AADAC (11951 upstream) : SUCNR1 (33209 downstream)																							CGCATGTGTGcacacacacaca	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	151642956	151642957	+	IGR	INS	-	ATGG	ATGG	rs149307868	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151642956_151642957insATGG								SUCNR1 (43306 upstream) : LOC401093 (337456 downstream)																							GCTAGCTCCTCGTGAATTCTTT	0.475													3	3	---	---	---	---	
SSR3	6747	broad.mit.edu	37	3	156270093	156270093	+	Intron	DEL	A	-	-	rs67759255		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156270093delA	uc003fau.2	-						SSR3_uc011bop.1_Intron	NM_007107	NP_009038	Q9UNL2	SSRG_HUMAN	signal sequence receptor gamma subunit						cotranslational protein targeting to membrane	integral to endoplasmic reticulum membrane|microsome|Sec61 translocon complex	protein binding|signal sequence binding				0			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			agtctgtctcaaaaaaaaaaa	0.104													4	2	---	---	---	---	
IFT80	57560	broad.mit.edu	37	3	160076112	160076112	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160076112delT	uc011boy.1	-						IFT80_uc003fda.2_Intron|IFT80_uc003fdb.1_Intron|IFT80_uc003fdd.1_Intron|IFT80_uc003fde.1_Intron	NM_020800	NP_065851	Q9P2H3	IFT80_HUMAN	WD repeat domain 56							cilium axoneme|microtubule basal body				ovary(1)	1			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			CCCTCAACCATTTTTTTTTTA	0.184													5	3	---	---	---	---	
KPNA4	3840	broad.mit.edu	37	3	160219811	160219812	+	3'UTR	DEL	TA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160219811_160219812delTA	uc003fdn.2	-	17						NM_002268	NP_002259	O00629	IMA4_HUMAN	karyopherin alpha 4						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding				0			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			tatatatatgtatatatatata	0.302													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	161170280	161170281	+	IGR	DEL	TG	-	-	rs112222201		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161170280_161170281delTG								C3orf57 (80409 upstream) : OTOL1 (44315 downstream)																							tgtatgtgtttgtgtgtgtgtg	0.119													6	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	161294527	161294528	+	IGR	DEL	TC	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161294527_161294528delTC								OTOL1 (72799 upstream) : None (None downstream)																							tctctctctttctctctctctc	0.267													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	163677396	163677397	+	IGR	INS	-	A	A	rs146811553	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163677396_163677397insA								None (None upstream) : MIR1263 (211862 downstream)																							ggttaagtcacaaaaaaaaagc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	163934322	163934322	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163934322delT								MIR1263 (44978 upstream) : MIR720 (124807 downstream)																							tcagtgcatcttgctgctccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	164002158	164002159	+	IGR	DEL	AC	-	-	rs146431453		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164002158_164002159delAC								MIR1263 (112814 upstream) : MIR720 (56970 downstream)																							gtatgtgtgtacacacacacac	0.000													4	3	---	---	---	---	
PRKCI	5584	broad.mit.edu	37	3	169957530	169957530	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169957530delT	uc003fgs.2	+							NM_002740	NP_002731	P41743	KPCI_HUMAN	protein kinase C, iota						anti-apoptosis|cellular membrane organization|cellular response to insulin stimulus|establishment or maintenance of epithelial cell apical/basal polarity|intracellular signal transduction|nerve growth factor receptor signaling pathway|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|protein targeting to membrane|secretion|tight junction assembly|vesicle-mediated transport	cytosol|endosome|nucleus|polarisome	ATP binding|phospholipid binding|protein binding|protein kinase C activity|zinc ion binding			lung(2)|ovary(1)|breast(1)|skin(1)	5	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			tggtagagtgttttttttttt	0.000													4	2	---	---	---	---	
SLC2A2	6514	broad.mit.edu	37	3	170719712	170719712	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170719712delT	uc003fhe.1	-						SLC2A2_uc003fhf.1_Intron|SLC2A2_uc011bpu.1_Intron	NM_000340	NP_000331	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose						carbohydrate metabolic process|cellular lipid metabolic process|endocrine pancreas development|energy reserve metabolic process|regulation of insulin secretion	integral to plasma membrane|membrane fraction	D-glucose transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)			AGTATATGACTTTTTTTTTTG	0.299													4	2	---	---	---	---	
TNIK	23043	broad.mit.edu	37	3	170921971	170921971	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170921971delA	uc003fhh.2	-						TNIK_uc003fhi.2_Intron|TNIK_uc003fhj.2_Intron|TNIK_uc003fhk.2_Intron|TNIK_uc003fhl.2_Intron|TNIK_uc003fhm.2_Intron|TNIK_uc003fhn.2_Intron|TNIK_uc003fho.2_Intron	NM_015028	NP_055843	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase isoform 1						actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			GAGAGATCAGAATCTTTATTG	0.433													4	2	---	---	---	---	
NCEH1	57552	broad.mit.edu	37	3	172411249	172411250	+	Intron	INS	-	A	A	rs72265455		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172411249_172411250insA	uc011bpx.1	-						NCEH1_uc003fig.2_Intron|NCEH1_uc011bpw.1_Intron|NCEH1_uc011bpy.1_Intron	NM_001146276	NP_001139748	Q6PIU2	NCEH1_HUMAN	arylacetamide deacetylase-like 1 isoform a						lipid catabolic process	endoplasmic reticulum|integral to membrane|microsome	carboxylesterase activity				0						GCCTGAATATGAAAAAAAAAAA	0.361													4	2	---	---	---	---	
NAALADL2	254827	broad.mit.edu	37	3	174598445	174598445	+	Intron	DEL	C	-	-	rs76089421		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174598445delC	uc003fit.2	+						NAALADL2_uc003fiu.1_Intron	NM_207015	NP_996898	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	peptidase activity			pancreas(1)	1	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		cctagattatccttctcatag	0.000													3	5	---	---	---	---	
NAALADL2	254827	broad.mit.edu	37	3	175175473	175175474	+	Intron	INS	-	T	T	rs139834344		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175175473_175175474insT	uc003fit.2	+						NAALADL2_uc003fiu.1_Intron|NAALADL2_uc010hwy.1_Intron|NAALADL2_uc010hwz.1_Intron	NM_207015	NP_996898	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	peptidase activity			pancreas(1)	1	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		tgtctggctaattttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	176481219	176481219	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176481219delA								NAALADL2 (957793 upstream) : TBL1XR1 (257324 downstream)																							cagagtctctaagaagataaa	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	177620660	177620660	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177620660delA								TBL1XR1 (705612 upstream) : KCNMB2 (633564 downstream)																							TTCTGACAGCAAAAAAGAACA	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	180303889	180303889	+	IGR	DEL	T	-	-	rs11367394		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180303889delT								PEX5L (549372 upstream) : TTC14 (16029 downstream)																							ccattcctacttttttttttt	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	182262503	182262504	+	IGR	DEL	TG	-	-	rs140900910		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182262503_182262504delTG								SOX2OT (803500 upstream) : ATP11B (248787 downstream)																							cagaacaaactgttttttagag	0.000													4	2	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	188531907	188531908	+	Intron	DEL	AC	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188531907_188531908delAC	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc011bsj.1_Intron	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		acacatacagacacacacacac	0.183			T	HMGA2|MLL|C12orf9	lipoma|leukemia								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	189635931	189635932	+	IGR	INS	-	ACACAT	ACACAT	rs139407973	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189635931_189635932insACACAT								TP63 (20863 upstream) : LEPREL1 (38587 downstream)																							cacacacacacacacacacaca	0.000													5	4	---	---	---	---	
TM4SF19	116211	broad.mit.edu	37	3	196061999	196062000	+	Intron	INS	-	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196061999_196062000insA	uc003fwl.1	-						TM4SF19_uc003fwj.2_Intron|TM4SF19_uc010iad.1_Intron|TM4SF19_uc011btv.1_Intron	NM_138461	NP_612470	Q96DZ7	T4S19_HUMAN	transmembrane 4 L six family member 19							integral to membrane					0	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;3.94e-24)|all cancers(36;4.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.53e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		AGGTGGGGGTTggagaggggag	0.064													3	3	---	---	---	---	
MAEA	10296	broad.mit.edu	37	4	1327129	1327130	+	Intron	INS	-	A	A	rs113840820		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1327129_1327130insA	uc003gda.2	+						MAEA_uc003gdb.2_Intron|MAEA_uc011bvb.1_Intron|MAEA_uc003gdc.2_Intron|MAEA_uc003gdd.2_Intron|MAEA_uc011bvc.1_Intron|MAEA_uc011bvd.1_Intron|MAEA_uc010ibt.2_Intron|MAEA_uc010ibu.2_Intron	NM_001017405	NP_001017405	Q7L5Y9	MAEA_HUMAN	macrophage erythroblast attacher isoform 1						cell adhesion|cell cycle|cell division|erythrocyte maturation|negative regulation of myeloid cell apoptosis|regulation of mitotic cell cycle	actomyosin contractile ring|integral to plasma membrane|membrane fraction|nuclear matrix|spindle	actin binding			ovary(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(23;0.0201)			accttgtctccaaaaaaaaaaa	0.257													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	2580597	2580599	+	IGR	DEL	GAG	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2580597_2580599delGAG								RNF4 (63016 upstream) : FAM193A (17229 downstream)																							taggctgagagaggaggaggagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3583593	3583594	+	Intron	INS	-	GGCAGGG	GGCAGGG	rs111262590		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3583593_3583594insGGCAGGG	uc003ghj.1	+						uc003ghk.1_Intron					Homo sapiens cDNA FLJ35424 fis, clone SMINT2001461.																		GGCCGGGCACAGGCAGGGGGCA	0.619													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3583719	3583725	+	Intron	DEL	GGAAGGA	-	-	rs66844729		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3583719_3583725delGGAAGGA	uc003ghj.1	+						uc003ghk.1_Intron					Homo sapiens cDNA FLJ35424 fis, clone SMINT2001461.																		AAAGGGGGCTGGAAGGAGGGGCGGGCG	0.589													4	2	---	---	---	---	
EVC2	132884	broad.mit.edu	37	4	5710988	5710990	+	5'Flank	DEL	AGG	-	-	rs67550450		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5710988_5710990delAGG	uc003gij.2	-						EVC2_uc011bwb.1_5'UTR|EVC2_uc003gik.2_5'UTR|EVC_uc003gil.1_5'Flank|EVC_uc003gim.1_5'Flank	NM_147127	NP_667338	Q86UK5	LBN_HUMAN	limbin							integral to membrane				large_intestine(3)|ovary(2)	5						CAAGGGACGCAGGAGGAGGAGGA	0.571													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	5933475	5933476	+	IGR	DEL	CC	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5933475_5933476delCC								CRMP1 (38690 upstream) : C4orf50 (25369 downstream)																							TTCTGAGGAGCCTAAGGTTTGC	0.594													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	11337474	11337474	+	IGR	DEL	T	-	-	rs138135314		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11337474delT								CLNK (651088 upstream) : MIR572 (32977 downstream)																							tctttctttcttttttttttt	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	12630203	12630204	+	IGR	DEL	AC	-	-	rs35399420		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12630203_12630204delAC								None (None upstream) : HSP90AB2P (704833 downstream)																							CATTTATCCGacacacacacac	0.252													4	2	---	---	---	---	
FLJ39653	202020	broad.mit.edu	37	4	16254129	16254130	+	Intron	DEL	AG	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16254129_16254130delAG	uc011bxf.1	+						FLJ39653_uc011bxg.1_Intron	NR_027696				RecName: Full=Uncharacterized protein FLJ39653;												0						cattttccttaggaaggcttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	27691952	27691952	+	IGR	DEL	T	-	-	rs34539567		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27691952delT								STIM2 (666144 upstream) : None (None downstream)																							gtgatttcacttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	35391982	35391983	+	IGR	INS	-	AA	AA	rs113123561		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35391982_35391983insAA								None (None upstream) : ARAP2 (557861 downstream)																							tctacaaaaagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	37157463	37157465	+	IGR	DEL	AAC	-	-	rs142885027	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37157463_37157465delAAC								MIR1255B-1 (729413 upstream) : KIAA1239 (89225 downstream)																							ATTTAGATAAaacaacaacaaca	0.197													4	2	---	---	---	---	
PDS5A	23244	broad.mit.edu	37	4	39907478	39907479	+	Intron	INS	-	A	A	rs148467423	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39907478_39907479insA	uc003guv.3	-						PDS5A_uc010ifo.2_Intron|PDS5A_uc003guw.3_Intron	NM_001100399	NP_001093869	Q29RF7	PDS5A_HUMAN	PDS5, regulator of cohesion maintenance, homolog						cell division|mitosis|negative regulation of DNA replication	chromatin|nucleus	identical protein binding				0						aaggagggaagaaaaaaaggaa	0.084													5	3	---	---	---	---	
ATP8A1	10396	broad.mit.edu	37	4	42644007	42644007	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42644007delT	uc003gwr.2	-						ATP8A1_uc003gws.2_Intron|ATP8A1_uc011byz.1_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)	CTCACCTTTGTTTTTTTTTTT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	44584978	44584978	+	IGR	DEL	A	-	-	rs71648791		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44584978delA								KCTD8 (134154 upstream) : YIPF7 (39376 downstream)																							ggacaaaaagaaaaaaaaaat	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	48961314	48961314	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48961314delG								OCIAD2 (52499 upstream) : CWH43 (26951 downstream)																							agaagagaatggggtgggaaa	0.000													4	4	---	---	---	---	
DCUN1D4	23142	broad.mit.edu	37	4	52754070	52754071	+	Intron	INS	-	TT	TT			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:52754070_52754071insTT	uc003gze.2	+						DCUN1D4_uc003gzf.2_Intron|DCUN1D4_uc011bzn.1_Intron|DCUN1D4_uc003gzg.2_Intron|DCUN1D4_uc003gzh.2_Intron|DCUN1D4_uc011bzo.1_Intron	NM_001040402	NP_001035492	Q92564	DCNL4_HUMAN	DCN1, defective in cullin neddylation 1, domain											ovary(2)	2			GBM - Glioblastoma multiforme(4;1.93e-11)|LUSC - Lung squamous cell carcinoma(32;0.00654)			tttttttttggttttttttttt	0.312													4	2	---	---	---	---	
FTLP10	100130017	broad.mit.edu	37	4	69047814	69047814	+	5'Flank	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69047814delC	uc010iho.1	+							NR_015446				Homo sapiens ferritin light chain-like pseudogene mRNA, partial sequence.												0						TTGTGTCACACAAAAAACCCA	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	71421930	71421930	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71421930delG								AMTN (23471 upstream) : AMBN (36071 downstream)																							gacacaaggaggggaacatca	0.000													4	2	---	---	---	---	
AFF1	4299	broad.mit.edu	37	4	87875758	87875758	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87875758delG	uc011ccz.1	+						AFF1_uc011ccx.1_Intron|AFF1_uc003hqh.1_Intron|AFF1_uc011ccy.1_Intron	NM_005935	NP_005926	P51825	AFF1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia							nucleus	sequence-specific DNA binding transcription factor activity			breast(1)	1		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		gctactgacaggggtccaggt	0.000													4	2	---	---	---	---	
DKK2	27123	broad.mit.edu	37	4	108029355	108029355	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108029355delA	uc010ilw.1	-									Q9UBU2	DKK2_HUMAN	Homo sapiens dickkopf-2 mRNA, complete cds.						multicellular organismal development|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	extracellular space				ovary(3)|lung(1)|skin(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)		cagtgttaagagagaatttat	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	111255368	111255369	+	IGR	INS	-	A	A	rs144053050	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111255368_111255369insA								ELOVL6 (135548 upstream) : ENPEP (141860 downstream)																							ccactaaaaataaaaaaattag	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	116610933	116610933	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:116610933delA								NDST4 (575901 upstream) : MIR1973 (609948 downstream)																							AGCTTGTCTTAAAAAAAAAAG	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	118902535	118902535	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118902535delC								TRAM1L1 (895799 upstream) : NDST3 (52238 downstream)																							acacccacagccatctgatct	0.000													4	2	---	---	---	---	
MAD2L1	4085	broad.mit.edu	37	4	120988472	120988473	+	5'Flank	INS	-	C	C	rs146373922	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120988472_120988473insC	uc003idl.2	-						MAD2L1_uc003idm.2_5'Flank	NM_002358	NP_002349	Q13257	MD2L1_HUMAN	MAD2-like 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of apoptosis|negative regulation of mitotic anaphase-promoting complex activity|positive regulation of mitotic cell cycle spindle assembly checkpoint	condensed chromosome kinetochore|cytosol|nucleus|perinuclear region of cytoplasm	protein homodimerization activity				0						ACGCAGCTTTTCCCGAGAAATT	0.530											OREG0016309	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1	5	---	---	---	---	
LOC285419	285419	broad.mit.edu	37	4	124623782	124623784	+	Intron	DEL	TTC	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124623782_124623784delTTC	uc011cgn.1	+							NR_027105				Homo sapiens mRNA; cDNA DKFZp686P12109 (from clone DKFZp686P12109).												0						tgtggaagtattcttctagtatt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	127770884	127770884	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:127770884delA								None (None upstream) : INTU (783236 downstream)																							aggcatccagaaaaaaaaaaa	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	130293674	130293675	+	IGR	DEL	CA	-	-	rs4975179		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130293674_130293675delCA								C4orf33 (259832 upstream) : None (None downstream)																							cacacgcgcgcacacacacaca	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	130505380	130505380	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130505380delC								C4orf33 (471538 upstream) : None (None downstream)																							TCCCTTACATCCAGCACTGCT	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	134991143	134991144	+	IGR	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134991143_134991144insT								PCDH10 (878412 upstream) : PABPC4L (126347 downstream)																							cctttggagggttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	135315370	135315370	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:135315370delC								PABPC4L (192467 upstream) : None (None downstream)																							TTGGTTTGATCCCCCAGAACA	0.323													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	136518024	136518024	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:136518024delC								None (None upstream) : None (None downstream)																							gctacttgggcaagcatgact	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	141407427	141407428	+	Intron	INS	-	CA	CA	rs57402037		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141407427_141407428insCA	uc003iij.1	-											Homo sapiens similar to RIKEN cDNA 4933434I20, mRNA (cDNA clone IMAGE:5267198).																		ctaatttcattgttttctgcta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	143883184	143883184	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143883184delT								INPP4B (115580 upstream) : USP38 (222886 downstream)																							agggaattgcttttcttccat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	166759223	166759223	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166759223delT								CPE (339742 upstream) : TLL1 (35187 downstream)																							tttattttcctttttttttta	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	177355866	177355881	+	IGR	DEL	TTCCTTCCTTCTTTCA	-	-	rs61644129		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177355866_177355881delTTCCTTCCTTCTTTCA								SPCS3 (102472 upstream) : VEGFC (248810 downstream)																							ctttcattccttccttccttctttcattccttcctt	0.139													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190637625	190637625	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190637625delA								None (None upstream) : FRG1 (224349 downstream)																							CTGCACTCCTAACCCTGGATT	0.413													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190838721	190838733	+	Intron	DEL	ACTGAAGGCACTA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190838721_190838733delACTGAAGGCACTA	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		TAAGGCACCCACTGAAGGCACTAACTGAAGGCC	0.601													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	8650869	8650870	+	IGR	INS	-	TT	TT	rs111996773		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8650869_8650870insTT								MTRR (749636 upstream) : SEMA5A (384268 downstream)																							tattgttttccttttttttttt	0.000													3	3	---	---	---	---	
CTNND2	1501	broad.mit.edu	37	5	11312112	11312113	+	Intron	DEL	CA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11312112_11312113delCA	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron|CTNND2_uc011cmx.1_Intron	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8						atatgcaccccacacacacact	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	15315402	15315402	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15315402delA								ANKH (443515 upstream) : FBXL7 (184903 downstream)																							tcaaaaaaacaaaaaaaaaga	0.000													4	2	---	---	---	---	
BASP1	10409	broad.mit.edu	37	5	17248928	17248928	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17248928delA	uc003jfx.2	+							NM_006317	NP_006308	P80723	BASP1_HUMAN	brain abundant, membrane attached signal protein						glomerular visceral epithelial cell differentiation|negative regulation of transcription, DNA-dependent	cytoplasm|cytoskeleton|growth cone|nuclear speck|plasma membrane	protein domain specific binding|transcription corepressor activity|transcription regulatory region DNA binding				0						GCTTGTTGATAATTTAAAAAG	0.398													4	2	---	---	---	---	
CDH12	1010	broad.mit.edu	37	5	22224514	22224514	+	Intron	DEL	C	-	-	rs112551589		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22224514delC	uc003jgk.2	-							NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						TCAGGTGCATCCTGCATGAGG	0.229										HNSCC(59;0.17)			2	4	---	---	---	---	
CDH9	1007	broad.mit.edu	37	5	26886265	26886265	+	Intron	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26886265delC	uc003jgs.1	-						CDH9_uc011cnv.1_Intron	NM_016279	NP_057363	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|skin(2)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)	9						TATCTTAAATCCATGTATTTG	0.269													11	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	29450614	29450615	+	IGR	DEL	TT	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29450614_29450615delTT								None (None upstream) : None (None downstream)																							tctctctctcttgctcctgctt	0.000													4	2	---	---	---	---	
PDZD2	23037	broad.mit.edu	37	5	32000586	32000597	+	Intron	DEL	TTTGTTTTTGTT	-	-	rs71863988		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32000586_32000597delTTTGTTTTTGTT	uc003jhl.2	+						PDZD2_uc003jhm.2_Intron|PDZD2_uc011cnx.1_Intron	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9						CCTTAAGAAGtttgtttttgtttttgtttttg	0.222													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	41685978	41685978	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41685978delG								PLCXD3 (175248 upstream) : OXCT1 (44190 downstream)																							ccagcctgaaggcttttatga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	41712150	41712150	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41712150delT								PLCXD3 (201420 upstream) : OXCT1 (18018 downstream)																							tgtattacacttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	43584713	43584713	+	Intron	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43584713delC	uc003jod.1	-											Homo sapiens cDNA FLJ39349 fis, clone PEBLM1000071, moderately similar to Leptin receptor.																		tgttggctcacccttgaattc	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	46349465	46349466	+	IGR	INS	-	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:46349465_46349466insC								HCN1 (653245 upstream) : None (None downstream)																							agttgaatgtacacatcacaaa	0.000													6	3	---	---	---	---	
PARP8	79668	broad.mit.edu	37	5	50129699	50129700	+	Intron	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50129699_50129700insT	uc003jon.3	+						PARP8_uc011cpz.1_Intron|PARP8_uc003joo.2_Intron|PARP8_uc003jop.2_Intron	NM_024615	NP_078891	Q8N3A8	PARP8_HUMAN	poly (ADP-ribose) polymerase family, member 8							intracellular	NAD+ ADP-ribosyltransferase activity			lung(3)|large_intestine(1)|ovary(1)	5		Lung NSC(810;0.0305)|Breast(144;0.222)				TCTAGATAGGCTTTTTTTTTTT	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	72402951	72402951	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72402951delT								FCHO2 (16603 upstream) : TMEM171 (13437 downstream)																							ggttgtttggtttttttgttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	84455637	84455638	+	IGR	DEL	GT	-	-	rs35800868		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84455637_84455638delGT								EDIL3 (775026 upstream) : None (None downstream)																							gactggtaAAgtgtgtgtgtgt	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	92066193	92066193	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92066193delA								None (None upstream) : FLJ42709 (678872 downstream)																							CTTTCTATAGAAAAAAAAAAA	0.308													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	120603516	120603516	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:120603516delC								PRR16 (580554 upstream) : FTMT (584134 downstream)																							GATTCTCTGTCCCAGTAGTCA	0.428													4	2	---	---	---	---	
FSTL4	23105	broad.mit.edu	37	5	132805635	132805636	+	Intron	INS	-	A	A	rs145777254	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132805635_132805636insA	uc003kyn.1	-							NM_015082	NP_055897	Q6MZW2	FSTL4_HUMAN	follistatin-like 4 precursor							extracellular region	calcium ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTCTTATGCAGAAAAAAAAAAC	0.450													4	2	---	---	---	---	
CDKL3	51265	broad.mit.edu	37	5	133677378	133677378	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133677378delA	uc003kzf.3	-						CDKL3_uc011cxm.1_Intron|CDKL3_uc011cxn.1_Intron|CDKL3_uc010jdw.2_Intron|CDKL3_uc011cxo.1_Intron|CDKL3_uc011cxp.1_Intron|CDKL3_uc011cxq.1_Intron|CDKL3_uc003kzg.3_Intron|CDKL3_uc011cxr.1_Intron	NM_001113575	NP_001107047	Q8IVW4	CDKL3_HUMAN	cyclin-dependent kinase-like 3 isoform 1							cytoplasm	ATP binding|cyclin-dependent protein kinase activity			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			tgccaacaggaaaaggctacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	157602271	157602276	+	IGR	DEL	GTGGTA	-	-	rs3078259		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157602271_157602276delGTGGTA								CLINT1 (316103 upstream) : EBF1 (520648 downstream)																							ATCTCCTTCTGTGGTAGTGGCTCTTG	0.442											OREG0016985	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	3	---	---	---	---	
GABRB2	2561	broad.mit.edu	37	5	160899463	160899464	+	Intron	DEL	CA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160899463_160899464delCA	uc003lys.1	-						GABRB2_uc011deh.1_Intron|GABRB2_uc003lyr.1_Intron|GABRB2_uc003lyt.1_Intron|GABRB2_uc010jiu.1_Intron|GABRB2_uc011dei.1_Intron	NM_021911	NP_068711	P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|GABA-A receptor activity				0	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	cgcacacatgcacacacacaca	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	166505490	166505498	+	IGR	DEL	AACAACAAC	-	-	rs61688020		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166505490_166505498delAACAACAAC								None (None upstream) : ODZ2 (206345 downstream)																							ctctgtctcaaacaacaacaacaacaaca	0.086													4	2	---	---	---	---	
ERGIC1	57222	broad.mit.edu	37	5	172364948	172364948	+	Intron	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172364948delC	uc003mbw.3	+						ERGIC1_uc003mby.3_Intron|ERGIC1_uc011dfa.1_Intron|ERGIC1_uc003mca.3_Intron	NM_001031711	NP_001026881	Q969X5	ERGI1_HUMAN	endoplasmic reticulum-golgi intermediate						ER to Golgi vesicle-mediated transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	protein binding			skin(2)|ovary(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			ttgcggtgagccaggatcact	0.000													4	2	---	---	---	---	
C5orf41	153222	broad.mit.edu	37	5	172538284	172538285	+	Intron	INS	-	TT	TT			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172538284_172538285insTT	uc003mch.2	+						C5orf41_uc011dfd.1_Intron	NM_153607	NP_705835	Q8IUR6	CE041_HUMAN	luman-recruiting factor								protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Renal(175;0.000159)|Lung NSC(126;0.00223)|all_lung(126;0.00391)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			acctgtcttccttttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	174087414	174087415	+	IGR	INS	-	CCT	CCT			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174087414_174087415insCCT								HMP19 (551233 upstream) : MSX2 (64160 downstream)																							CCCTGCCCCCACCTCCTTCCCA	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	174357183	174357184	+	IGR	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174357183_174357184insT								MSX2 (199282 upstream) : DRD1 (510492 downstream)																							ttccttccttcttttttttgat	0.000													4	2	---	---	---	---	
UIMC1	51720	broad.mit.edu	37	5	176352031	176352032	+	Intron	INS	-	A	A	rs79686597		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176352031_176352032insA	uc011dfp.1	-						UIMC1_uc003mfc.1_Intron|UIMC1_uc003mfd.1_Intron|UIMC1_uc003mfe.1_Intron|UIMC1_uc003mff.1_Intron	NM_016290	NP_057374	Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1						double-strand break repair|G2/M transition DNA damage checkpoint|histone H2A K63-linked deubiquitination|negative regulation of transcription, DNA-dependent|positive regulation of DNA repair|response to ionizing radiation|transcription, DNA-dependent	BRCA1-A complex	histone binding|K63-linked polyubiquitin binding			ovary(3)|skin(1)	4	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			gactctgcctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
MYLK4	340156	broad.mit.edu	37	6	2690213	2690214	+	Intron	INS	-	T	T	rs150721339	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2690213_2690214insT	uc003mty.3	-							NM_001012418	NP_001012418	Q86YV6	MYLK4_HUMAN	myosin light chain kinase family, member 4								ATP binding|protein serine/threonine kinase activity			breast(3)|ovary(1)	4	Ovarian(93;0.0412)	all_hematologic(90;0.0897)				AAGCATCTTGATAACATTCACT	0.361													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	3570708	3570709	+	IGR	INS	-	G	G	rs140431602	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3570708_3570709insG								SLC22A23 (113915 upstream) : C6orf145 (152127 downstream)																							GGTTACGTTGTGGCAGATTCTG	0.480													3	3	---	---	---	---	
CDYL	9425	broad.mit.edu	37	6	4946453	4946453	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4946453delG	uc003mwi.2	+						CDYL_uc003mwj.2_Intron|CDYL_uc003mwk.2_Intron|CDYL_uc011dhx.1_Intron|CDYL_uc011dhy.1_Intron	NM_001143971	NP_001137443	Q9Y232	CDYL1_HUMAN	chromodomain protein, Y chromosome-like isoform						regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	histone acetyltransferase activity				0	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		cctccatggcggatgctctca	0.373													4	2	---	---	---	---	
FARS2	10667	broad.mit.edu	37	6	5640373	5640374	+	Intron	DEL	GT	-	-	rs71540875		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5640373_5640374delGT	uc010jnv.1	+						FARS2_uc003mwr.2_Intron	NM_006567	NP_006558	O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2 precursor						phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)	CTTTTGTCAGgtgtgtgtgtgt	0.376													4	2	---	---	---	---	
GFOD1	54438	broad.mit.edu	37	6	13382183	13382186	+	Intron	DEL	ACAA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13382183_13382186delACAA	uc003nat.1	-						GFOD1_uc003nas.1_Intron	NM_018988	NP_061861	Q9NXC2	GFOD1_HUMAN	glucose-fructose oxidoreductase domain							extracellular region	binding|oxidoreductase activity			ovary(2)	2	Breast(50;0.0296)|Ovarian(93;0.0454)	all_hematologic(90;0.135)	Epithelial(50;0.0348)|BRCA - Breast invasive adenocarcinoma(129;0.1)|all cancers(50;0.108)			acacacacacacaAACTTGCTGAC	0.123													4	2	---	---	---	---	
ATXN1	6310	broad.mit.edu	37	6	16586275	16586276	+	Intron	DEL	CA	-	-	rs61649104	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16586275_16586276delCA	uc003nbt.2	-						ATXN1_uc010jpi.2_Intron|ATXN1_uc010jpj.1_Intron|ATXN1_uc003nbu.1_Intron	NM_000332	NP_000323	P54253	ATX1_HUMAN	ataxin 1						cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing	cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm	identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association			skin(3)|central_nervous_system(1)	4	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				caagcatgcgcacacacacaca	0.327													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	18566163	18566164	+	Intron	INS	-	CCTT	CCTT	rs140064438	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18566163_18566164insCCTT	uc003nct.1	+											Homo sapiens cDNA FLJ25799 fis, clone TST07088.																		ttccctccctcccttccttcct	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	18764008	18764008	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18764008delT								MIR548A1 (191897 upstream) : None (None downstream)																							ccatcacgcctggataatttt	0.000													4	2	---	---	---	---	
LRRC16A	55604	broad.mit.edu	37	6	25397769	25397769	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25397769delA	uc011djw.1	+						LRRC16A_uc010jpx.2_Intron|LRRC16A_uc010jpy.2_Intron	NM_017640	NP_060110	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A						actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4						GCTGCCAAACAAAGGGTGTTT	0.473													4	2	---	---	---	---	
BTN2A3	54718	broad.mit.edu	37	6	26430816	26430817	+	Intron	INS	-	A	A	rs34293101		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26430816_26430817insA	uc011dkl.1	+						BTN2A3_uc011dkm.1_Intron					RecName: Full=Butyrophilin subfamily 2 member A3; Flags: Precursor;												0						agctcagtctcaaaaaaaaaaa	0.252													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	28739380	28739380	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28739380delG								SCAND3 (184268 upstream) : TRIM27 (131400 downstream)																							cattgaatatggggattaatc	0.000													4	2	---	---	---	---	
C6orf10	10665	broad.mit.edu	37	6	32303569	32303569	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32303569delG	uc011dpy.1	-							NM_006781	NP_006772	Q5SRN2	CF010_HUMAN	chromosome 6 open reading frame 10							integral to membrane				skin(1)	1						AGAAAAATAAGGGTTGAAGAA	0.398													3	8	---	---	---	---	
KIF6	221458	broad.mit.edu	37	6	39491928	39491929	+	Intron	INS	-	AG	AG	rs150825043	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39491928_39491929insAG	uc003oot.2	-						KIF6_uc010jwz.1_Intron|KIF6_uc010jxa.1_Intron|KIF6_uc011dua.1_Intron|KIF6_uc010jxb.1_Intron	NM_145027	NP_659464	Q6ZMV9	KIF6_HUMAN	kinesin family member 6						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein binding			breast(2)|central_nervous_system(1)	3						gtgtgtgtgAAagagagagaga	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	40729361	40729362	+	IGR	DEL	CT	-	-	rs68168043		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40729361_40729362delCT								LRFN2 (174235 upstream) : UNC5CL (265410 downstream)																							TCAATGctcgctctctctctct	0.203													4	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57359740	57359741	+	Intron	INS	-	A	A	rs142808209	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57359740_57359741insA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		TGTTGGATCAGAGGCTGAGGTG	0.297													4	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57388106	57388106	+	Intron	DEL	A	-	-	rs55988029		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57388106delA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		gataaacactacagacatttc	0.095													6	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57408104	57408118	+	Intron	DEL	TTTAAAAAGCTTATC	-	-	rs71839638	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57408104_57408118delTTTAAAAAGCTTATC	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		TTTAGCACTGTTTAAAAAGCTTATCTTTTCTTCCA	0.353													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57419300	57419301	+	Intron	INS	-	GTGATACA	GTGATACA	rs113964844		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57419300_57419301insGTGATACA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		aaaattagctgggtgtggtgat	0.000													5	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57511048	57511049	+	Intron	INS	-	TA	TA	rs10643529		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57511048_57511049insTA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		AGGTTTTTAAGTCTGACTTACT	0.213													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57524706	57524707	+	IGR	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57524706_57524707insT								PRIM2 (11331 upstream) : GUSBL2 (721452 downstream)																							tttaaacattatttttttttgt	0.005													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57524791	57524793	+	IGR	DEL	TTT	-	-	rs35354100		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57524791_57524793delTTT								PRIM2 (11416 upstream) : GUSBL2 (721366 downstream)																							gtaatacatcttttgtttcacac	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57534556	57534556	+	IGR	DEL	T	-	-	rs67039622		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57534556delT								PRIM2 (21181 upstream) : GUSBL2 (711603 downstream)																							cttattctgatgtagttacat	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57538773	57538773	+	IGR	DEL	G	-	-	rs10707154		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57538773delG								PRIM2 (25398 upstream) : GUSBL2 (707386 downstream)																							GATTCTCTAAGATTAATTAGC	0.358													4	6	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	64445387	64445388	+	Intron	DEL	CA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64445387_64445388delCA	uc011dxu.1	-						EYS_uc011dxt.1_Intron	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						ctgtctctgtcacacacacaca	0.000													4	2	---	---	---	---	
COL19A1	1310	broad.mit.edu	37	6	70820494	70820495	+	Intron	DEL	TG	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70820494_70820495delTG	uc003pfc.1	+						COL19A1_uc010kam.1_Intron	NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor						cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4						AGTGTCACCTTGTGTGACCACA	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	75339772	75339773	+	Intron	DEL	TC	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75339772_75339773delTC	uc003phr.2	+											Homo sapiens full length insert cDNA clone ZD50H02.																		ttccttcctttctctctctctc	0.000													4	2	---	---	---	---	
BCKDHB	594	broad.mit.edu	37	6	80907652	80907655	+	Intron	DEL	CATC	-	-	rs145203628		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80907652_80907655delCATC	uc003pjd.2	+						BCKDHB_uc003pje.2_Intron	NM_000056	NP_000047	P21953	ODBB_HUMAN	branched chain keto acid dehydrogenase E1 beta						branched chain family amino acid catabolic process	mitochondrial alpha-ketoglutarate dehydrogenase complex	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity|carboxy-lyase activity|protein binding				0		all_cancers(76;1.38e-05)|Acute lymphoblastic leukemia(125;1.15e-05)|all_hematologic(105;0.00118)|all_epithelial(107;0.0149)		BRCA - Breast invasive adenocarcinoma(397;0.0291)		tccatctgttcatccatccatcca	0.206													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	93851081	93851081	+	IGR	DEL	T	-	-	rs151336397		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93851081delT								None (None upstream) : EPHA7 (98661 downstream)																							TACCAATGTGTTTTTTTTTTC	0.338													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	104548767	104548770	+	IGR	DEL	GCTA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:104548767_104548770delGCTA								None (None upstream) : HACE1 (627198 downstream)																							atgaaaagttgctaaacatctatg	0.000													4	2	---	---	---	---	
ARMC2	84071	broad.mit.edu	37	6	109285993	109285994	+	Intron	DEL	AA	-	-	rs77214837		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109285993_109285994delAA	uc003pss.3	+						ARMC2_uc011eao.1_Intron	NM_032131	NP_115507	Q8NEN0	ARMC2_HUMAN	armadillo repeat containing 2								binding				0		all_cancers(87;1.14e-07)|Acute lymphoblastic leukemia(125;2.3e-10)|all_hematologic(75;3.3e-08)|all_epithelial(87;0.000111)|Colorectal(196;0.03)|all_lung(197;0.11)		Epithelial(106;0.000197)|BRCA - Breast invasive adenocarcinoma(108;0.000236)|all cancers(137;0.000279)|OV - Ovarian serous cystadenocarcinoma(136;0.00434)		actctgtctcaaaaaaaaaaaG	0.119													4	2	---	---	---	---	
ASF1A	25842	broad.mit.edu	37	6	119226534	119226534	+	Intron	DEL	T	-	-	rs66840336		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119226534delT	uc011ebn.1	+							NM_014034	NP_054753	Q9Y294	ASF1A_HUMAN	ASF1 anti-silencing function 1 homolog A						chromatin modification|DNA repair|loss of chromatin silencing|nucleosome assembly|transcription, DNA-dependent	chromatin remodeling complex	chromatin binding|histone binding				0		all_cancers(87;0.122)|all_epithelial(87;0.179)		GBM - Glioblastoma multiforme(226;0.0633)|OV - Ovarian serous cystadenocarcinoma(136;0.188)		TGTATAATCCTTTCATGAACC	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	120046236	120046236	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:120046236delT								MAN1A1 (375310 upstream) : None (None downstream)																							tgaggattccttttggagttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	124061918	124061927	+	IGR	DEL	TTTCTTTTTC	-	-	rs71734319		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124061918_124061927delTTTCTTTTTC								TRDN (103976 upstream) : NKAIN2 (63142 downstream)																							taataacttatttctttttctttctttctc	0.000													3	4	---	---	---	---	
NKAIN2	154215	broad.mit.edu	37	6	125134173	125134173	+	Intron	DEL	A	-	-	rs11324418		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125134173delA	uc003pzo.2	+						NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010ker.2_Intron	NM_001040214	NP_001035304	Q5VXU1	NKAI2_HUMAN	T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)		TCATAACTTTAAAAAAACATC	0.313													2	4	---	---	---	---	
HINT3	135114	broad.mit.edu	37	6	126285884	126285891	+	Intron	DEL	ACACACAC	-	-	rs3083382		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126285884_126285891delACACACAC	uc003qal.3	+						HINT3_uc010keu.2_Intron	NM_138571	NP_612638	Q9NQE9	HINT3_HUMAN	histidine triad nucleotide binding protein 3							mitochondrion|nucleolus	hydrolase activity				0				UCEC - Uterine corpus endometrioid carcinoma (4;0.153)|GBM - Glioblastoma multiforme(226;0.0321)		atagttttatacacacacacacacacac	0.053													4	2	---	---	---	---	
PTPRK	5796	broad.mit.edu	37	6	128383562	128383563	+	Intron	INS	-	A	A	rs137868779	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128383562_128383563insA	uc003qbk.2	-						PTPRK_uc003qbj.2_Intron|PTPRK_uc010kfc.2_Intron|PTPRK_uc011ebu.1_Intron|PTPRK_uc003qbl.1_Intron|PTPRK_uc011ebv.1_Intron	NM_002844	NP_002835	Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K						cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		TTCATATGTGGAAAAATGCTAA	0.208													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	134885845	134885845	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134885845delG	uc003qev.1	-											AJ606331																		CTAAATTATTGGTCTCTCTGT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	145188040	145188041	+	IGR	DEL	CA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145188040_145188041delCA								UTRN (13872 upstream) : EPM2A (758405 downstream)																							CCCCCACCGCcacacacacaca	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	153049682	153049682	+	IGR	DEL	A	-	-	rs78255359		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153049682delA								MYCT1 (3969 upstream) : VIP (22251 downstream)																							TTCTAAGTAGAAAAAAAAAAC	0.239													2	4	---	---	---	---	
SYTL3	94120	broad.mit.edu	37	6	159082239	159082239	+	5'Flank	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159082239delT	uc003qrp.2	+						SYTL3_uc011efp.1_Intron|SYTL3_uc003qro.2_Intron|SYTL3_uc003qrq.2_5'Flank|SYTL3_uc003qrr.2_5'Flank|SYTL3_uc003qrs.2_5'Flank|SYTL3_uc011efq.1_5'Flank	NM_001009991	NP_001009991	Q4VX76	SYTL3_HUMAN	synaptotagmin-like 3						intracellular protein transport	endomembrane system|membrane	Rab GTPase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)		TGATGGCTAATTTGCACCTTG	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	159540167	159540167	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159540167delG								TAGAP (73983 upstream) : FNDC1 (50262 downstream)																							ttcacatggtggtggcaagga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	166326771	166326772	+	Intron	INS	-	ACAG	ACAG			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166326771_166326772insACAG	uc003qup.1	-											Homo sapiens cDNA FLJ33369 fis, clone BRACE2005904.																		Tacacacacacacacacacaca	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	167847082	167847084	+	IGR	DEL	GGT	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167847082_167847084delGGT								TCP10 (49084 upstream) : C6orf123 (338137 downstream)																							tgtggatggaggtggtggtggta	0.187													5	3	---	---	---	---	
MLLT4	4301	broad.mit.edu	37	6	168319289	168319290	+	Intron	DEL	TG	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168319289_168319290delTG	uc003qwd.2	+						MLLT4_uc003qwb.1_Intron|MLLT4_uc003qwc.1_Intron|MLLT4_uc003qwg.1_Intron	NM_001040001	NP_001035090	P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		TGCGTCTGTCTGTGTGTGTGTG	0.500			T	MLL	AL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	517056	517057	+	IGR	INS	-	CT	CT			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:517056_517057insCT								FAM20C (216345 upstream) : PDGFA (19842 downstream)																							actgactctcactctgtcgccc	0.074													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	4527146	4527146	+	IGR	DEL	T	-	-	rs112064329		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4527146delT								SDK1 (218517 upstream) : FOXK1 (156242 downstream)																							aattctttcgttttttttttt	0.000													4	2	---	---	---	---	
RSPH10B2	728194	broad.mit.edu	37	7	6804340	6804341	+	Intron	DEL	TG	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6804340_6804341delTG	uc003sqw.1	+						RSPH10B2_uc010ktk.1_Intron|RSPH10B2_uc011jxc.1_Intron|RSPH10B2_uc010ktl.1_Intron	NM_173565	NP_775836	B2RC85	R10B2_HUMAN	radial spoke head 10 homolog B											ovary(1)|pancreas(1)|skin(1)	3						TTGTTGTTGTtgtgtgtgtgtg	0.243													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	11254427	11254427	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11254427delT								PHF14 (45186 upstream) : THSD7A (159746 downstream)																							tgttttatccttttttttcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	36781488	36781488	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36781488delA								AOAH (17335 upstream) : ELMO1 (112473 downstream)																							catggagattaagaaaatttg	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	36819735	36819736	+	IGR	DEL	AG	-	-	rs143709766		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36819735_36819736delAG								AOAH (55582 upstream) : ELMO1 (74225 downstream)																							aatgtaagacagagttttaaaa	0.000													3	3	---	---	---	---	
ELMO1	9844	broad.mit.edu	37	7	37330455	37330457	+	Intron	DEL	TGA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37330455_37330457delTGA	uc003tfk.1	-						ELMO1_uc010kxg.1_Intron	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1						actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)	6						agggtgattttgatgatgatgat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	54883208	54883208	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54883208delT								SEC61G (56269 upstream) : EGFR (203517 downstream)																							aattttaggattttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57608535	57608536	+	IGR	INS	-	T	T	rs147153132	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57608535_57608536insT								ZNF716 (75270 upstream) : None (None downstream)																							CGTTATTTGAgtaaactttgtg	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57609485	57609486	+	IGR	INS	-	G	G	rs151001824	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57609485_57609486insG								ZNF716 (76220 upstream) : None (None downstream)																							TATACTTGTGAGTTTTTTATGT	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61819627	61819627	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61819627delT								None (None upstream) : LOC643955 (932045 downstream)																							AGACAAGTCCTTTTTTTATCT	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61823842	61823843	+	IGR	INS	-	T	T	rs113647649		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61823842_61823843insT								None (None upstream) : LOC643955 (927829 downstream)																							GTAAGAATGAATAAGATTTGTG	0.223													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65309757	65309758	+	IGR	DEL	GA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65309757_65309758delGA								CCT6P1 (81096 upstream) : VKORC1L1 (28499 downstream)																							gagggagggggagagagagaga	0.005													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67347291	67347291	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67347291delG								STAG3L4 (560779 upstream) : None (None downstream)																							actccagcctgggcaacaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67619468	67619468	+	IGR	DEL	T	-	-	rs35862228		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67619468delT								STAG3L4 (832956 upstream) : None (None downstream)																							GTCAATGACATTTTTtttttt	0.060													3	4	---	---	---	---	
AUTS2	26053	broad.mit.edu	37	7	70107776	70107777	+	Intron	INS	-	GTAA	GTAA	rs140762359	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70107776_70107777insGTAA	uc003tvw.3	+						AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		CATAAACATGCGTGTCAACTCC	0.495													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	76724595	76724596	+	IGR	DEL	TA	-	-	rs66942005		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76724595_76724596delTA								LOC100132832 (42240 upstream) : CCDC146 (27338 downstream)																							tgtgtgtgtgtATATAGGAGCC	0.223													4	2	---	---	---	---	
CACNA2D1	781	broad.mit.edu	37	7	81611479	81611480	+	Intron	DEL	CT	-	-	rs150161374		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81611479_81611480delCT	uc003uhr.1	-							NM_000722	NP_000713	P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha							voltage-gated calcium channel complex	metal ion binding			ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)	tggagtctcactctgtcatgag	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	89369984	89369984	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89369984delC								ZNF804B (403640 upstream) : DPY19L2P4 (378730 downstream)																							ATACCCTTCTCCCACATACTC	0.428													4	2	---	---	---	---	
SLC25A13	10165	broad.mit.edu	37	7	95906867	95906867	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95906867delG	uc003uof.3	-						SLC25A13_uc003uog.3_Intron|SLC25A13_uc011kik.1_Intron	NM_014251	NP_055066	Q9UJS0	CMC2_HUMAN	solute carrier family 25, member 13 isoform 2						ATP biosynthetic process|gluconeogenesis|malate-aspartate shuttle|response to calcium ion	integral to plasma membrane|mitochondrial inner membrane	calcium ion binding|L-aspartate transmembrane transporter activity|L-glutamate transmembrane transporter activity			central_nervous_system(3)|skin(1)	4	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)	ttttcccacagggacacttgg	0.109													4	2	---	---	---	---	
DLX6AS	285987	broad.mit.edu	37	7	96617307	96617307	+	Intron	DEL	T	-	-	rs34869036		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96617307delT	uc003uok.2	-						DLX6AS_uc003uol.2_Intron|DLX6AS_uc010lfo.1_Intron					Homo sapiens cDNA FLJ34048 fis, clone FCBBF3000102.												0						AAAATACAACTTTTTTTTTTT	0.333													6	3	---	---	---	---	
ZAN	7455	broad.mit.edu	37	7	100364106	100364106	+	Intron	DEL	A	-	-	rs113310218		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100364106delA	uc003uwj.2	+						ZAN_uc003uwk.2_Intron|ZAN_uc003uwl.2_Intron|ZAN_uc010lhh.2_Intron|ZAN_uc010lhi.2_Intron|ZAN_uc011kkd.1_Intron	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3						binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			aaaacaaagcaaaaaaaaaca	0.463													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	101368183	101368183	+	IGR	DEL	A	-	-	rs112868375		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101368183delA								MYL10 (95607 upstream) : CUX1 (91109 downstream)																							gtcccccaccaaaaaaaaaaa	0.214													6	3	---	---	---	---	
POLR2J3	548644	broad.mit.edu	37	7	102205146	102205147	+	Intron	DEL	TC	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102205146_102205147delTC	uc011kkw.1	-						UPK3BL_uc003uzy.2_Intron|POLR2J3_uc003uzw.2_Intron	NM_001097615	NP_001091084	Q9GZM3	RPB1B_HUMAN	polymerase (RNA) II (DNA directed) polypeptide							nucleus	DNA binding|DNA-directed RNA polymerase activity|protein dimerization activity				0						ttgtcttttttctttttggggg	0.030													6	3	---	---	---	---	
RELN	5649	broad.mit.edu	37	7	103603094	103603099	+	Intron	DEL	TGTGTG	-	-	rs111928955		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103603094_103603099delTGTGTG	uc003vca.2	-						RELN_uc010liz.2_Intron	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a						axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CCAAAGTTGTtgtgtgtgtgtgtgtg	0.320													4	2	---	---	---	---	
PTPRZ1	5803	broad.mit.edu	37	7	121519910	121519910	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121519910delA	uc003vjy.2	+						PTPRZ1_uc003vjz.2_Intron	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,						central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9						tttatccttcattcctttaat	0.100													2	9	---	---	---	---	
IRF5	3663	broad.mit.edu	37	7	128582510	128582510	+	Intron	DEL	T	-	-	rs5887397		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128582510delT	uc003vog.2	+						IRF5_uc010llr.1_Intron|IRF5_uc011kot.1_Intron|IRF5_uc011kou.1_Intron|IRF5_uc010lls.1_Intron|IRF5_uc003voh.2_Intron|IRF5_uc010llt.2_Intron|IRF5_uc003voi.2_Intron|IRF5_uc010llu.1_Intron|IRF5_uc003vok.2_Intron|IRF5_uc003voj.3_Intron|IRF5_uc010llv.1_Intron|IRF5_uc010llw.1_Intron	NM_002200	NP_002191	Q13568	IRF5_HUMAN	interferon regulatory factor 5 isoform a						interferon-gamma-mediated signaling pathway|type I interferon-mediated signaling pathway	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0						ACCtttttccttttttttttt	0.303													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	130406388	130406390	+	IGR	DEL	TGT	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130406388_130406390delTGT								TSGA13 (34120 upstream) : KLF14 (11088 downstream)																							gttcctttactgtttcttgacct	0.000													4	2	---	---	---	---	
EXOC4	60412	broad.mit.edu	37	7	133137754	133137754	+	Intron	DEL	T	-	-	rs34597258		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133137754delT	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron|EXOC4_uc003vri.2_Intron|EXOC4_uc003vrj.2_Intron	NM_021807	NP_068579	Q96A65	EXOC4_HUMAN	SEC8 protein isoform a						vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)				AGTCTGTAAGTTTTATCATGA	0.368													2	6	---	---	---	---	
EXOC4	60412	broad.mit.edu	37	7	133436284	133436284	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133436284delG	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron|EXOC4_uc003vrl.2_Intron|EXOC4_uc011kpp.1_Intron	NM_021807	NP_068579	Q96A65	EXOC4_HUMAN	SEC8 protein isoform a						vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)				AAGTTTAATTGGTTTTCATGG	0.393													4	2	---	---	---	---	
SLC13A4	26266	broad.mit.edu	37	7	135404550	135404551	+	Intron	DEL	TA	-	-	rs58887893		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135404550_135404551delTA	uc003vta.2	-						SLC13A4_uc003vtb.2_Intron|SLC13A4_uc003vtc.1_Intron	NM_012450	NP_036582	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate							integral to plasma membrane	sodium:sulfate symporter activity				0						tgtgtgtgtgtatgtgtgtgtg	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	137858113	137858113	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137858113delT								AKR1D1 (55063 upstream) : TRIM24 (286966 downstream)																							aggcctgaacttgcaactggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	138497236	138497237	+	IGR	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138497236_138497237insT								TMEM213 (6469 upstream) : KIAA1549 (18892 downstream)																							cctcatttcacttttttttttt	0.050													4	2	---	---	---	---	
ZC3HAV1	56829	broad.mit.edu	37	7	138787475	138787478	+	Intron	DEL	ACAC	-	-	rs113108708		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138787475_138787478delACAC	uc003vun.2	-						ZC3HAV1_uc003vup.2_Intron	NM_020119	NP_064504	Q7Z2W4	ZCCHV_HUMAN	zinc finger antiviral protein isoform 1						response to virus	cytoplasm|nucleus	NAD+ ADP-ribosyltransferase activity|RNA binding|zinc ion binding			ovary(1)	1						ctgtctctatacacacacacacac	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	141036953	141036958	+	IGR	DEL	CACCAT	-	-	rs62638832		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141036953_141036958delCACCAT								MRPS33 (322172 upstream) : AGK (214120 downstream)																							tcatcaccaccaccatcaccaccacc	0.000													3	3	---	---	---	---	
KEL	3792	broad.mit.edu	37	7	142660835	142660835	+	5'Flank	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142660835delC	uc003wcb.2	-							NM_000420	NP_000411	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase						proteolysis|vasoconstriction	integral to membrane|plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(3)|central_nervous_system(1)	4	Melanoma(164;0.059)					AGCCATTGTGCCCCCTGGGGC	0.488													4	2	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	147269678	147269678	+	Intron	DEL	C	-	-	rs5888271		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147269678delC	uc003weu.1	+							NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			TGCTCAAAATCCGAGAAAGAC	0.378										HNSCC(39;0.1)			2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	150144801	150144802	+	RNA	INS	-	TC	TC	rs142971191	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150144801_150144802insTC	uc003whi.1	+	4		c.1616_1617insTC			uc010lps.1_RNA					Homo sapiens cDNA FLJ39839 fis, clone SPLEN2014136.																		taacaaagatgtctgcagtgaa	0.074													3	3	---	---	---	---	
ABP1	26	broad.mit.edu	37	7	150533290	150533290	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150533290delA	uc003why.1	+							NM_001091	NP_001082	P19801	ABP1_HUMAN	amiloride binding protein 1 precursor						amine metabolic process	extracellular space|peroxisome	copper ion binding|diamine oxidase activity|heparin binding|histamine oxidase activity|methylputrescine oxidase activity|primary amine oxidase activity|propane-1,3-diamine oxidase activity|quinone binding			ovary(2)|breast(2)|skin(2)	6	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Amiloride(DB00594)|Spermine(DB00127)	AGAGCAACAGAAAAGCCCAGG	0.532													4	2	---	---	---	---	
PRKAG2	51422	broad.mit.edu	37	7	151500850	151500850	+	Intron	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151500850delC	uc003wkk.2	-						PRKAG2_uc003wkj.2_Intron|PRKAG2_uc010lqe.1_Intron|PRKAG2_uc003wkm.1_Intron|uc003wkn.2_5'Flank	NM_016203	NP_057287	Q9UGJ0	AAKG2_HUMAN	AMP-activated protein kinase gamma2 subunit						ATP biosynthetic process|carnitine shuttle|cell cycle arrest|fatty acid biosynthetic process|glycogen metabolic process|insulin receptor signaling pathway|intracellular protein kinase cascade|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein kinase activity|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation|regulation of glucose import|regulation of glycolysis|sterol biosynthetic process	AMP-activated protein kinase complex|cytosol|nucleoplasm	ADP binding|ATP binding|cAMP-dependent protein kinase inhibitor activity|cAMP-dependent protein kinase regulator activity|phosphorylase kinase regulator activity|protein kinase activator activity|protein kinase binding			breast(1)|kidney(1)	2	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)		atggtgaaatcccatctctac	0.119													3	3	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151958099	151958103	+	Intron	DEL	GAATT	-	-	rs75454419		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151958099_151958103delGAATT	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)		AAGTAGAAAGGAATTATAAGAACAA	0.259			N		medulloblastoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	153556420	153556420	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153556420delT								None (None upstream) : DPP6 (27999 downstream)																							ACATTCTAACTTTCTCTCAAG	0.468													4	2	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	153832831	153832831	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153832831delA	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			CTGAGCACACACTTCCTATCT	0.493													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157959046	157959046	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157959046delT	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		GATCATCTCCTCCTCCCACTG	0.677													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	2567394	2567395	+	Intron	DEL	AC	-	-	rs139348237		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2567394_2567395delAC	uc003wqb.1	-											Homo sapiens cDNA FLJ46912 fis, clone SKNMC2000583.																		taaaacacgtacacacacacca	0.074													4	2	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	4226532	4226532	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4226532delT	uc011kwk.1	-							NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		tttgctctggtttttctagtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	5204049	5204052	+	IGR	DEL	CACA	-	-	rs34340907		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5204049_5204052delCACA								CSMD1 (351721 upstream) : None (None downstream)																							GTACATATTTcacacacacacaca	0.123													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	12448061	12448061	+	Intron	DEL	T	-	-	rs147215813		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12448061delT	uc003wvy.3	-											Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																		cattattgcatttttaCTTTT	0.124													4	4	---	---	---	---	
MTMR7	9108	broad.mit.edu	37	8	17259950	17259950	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17259950delT	uc003wxm.2	-							NM_004686	NP_004677	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7								protein tyrosine phosphatase activity			skin(1)	1				Colorectal(111;0.112)		ataaccatccttctaccctct	0.000													4	2	---	---	---	---	
DOCK5	80005	broad.mit.edu	37	8	25123737	25123738	+	Intron	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25123737_25123738insT	uc003xeg.2	+						DOCK5_uc010luf.1_Intron|DOCK5_uc003xef.2_Intron	NM_024940	NP_079216	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5							cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		ATTATGCCttcttttttttttt	0.228													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	31468268	31468268	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31468268delA								WRN (436992 upstream) : NRG1 (29000 downstream)																							caggagtcctacgaagtattt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	36162628	36162629	+	IGR	DEL	AC	-	-	rs72327226		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36162628_36162629delAC								UNC5D (510448 upstream) : KCNU1 (479213 downstream)																							CTGATGCAAGacacacacacac	0.243													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	37257099	37257100	+	IGR	DEL	TC	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37257099_37257100delTC								KCNU1 (463458 upstream) : ZNF703 (296201 downstream)																							tgtctttgtttctctctctctc	0.109													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	46899565	46899565	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:46899565delT								None (None upstream) : BEYLA (852943 downstream)																							ggaaacactctttttgtagaa	0.000													8	4	---	---	---	---	
KIAA0146	23514	broad.mit.edu	37	8	48241007	48241007	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48241007delT	uc003xqd.2	+						KIAA0146_uc011lcz.1_Intron|KIAA0146_uc011lda.1_Intron|KIAA0146_uc011ldb.1_Intron|KIAA0146_uc010lxs.2_Intron|KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc011lde.1_Intron	NM_001080394	NP_001073863	Q14159	K0146_HUMAN	hypothetical protein LOC23514												0		Lung NSC(58;0.175)				tggctaattattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	70961588	70961589	+	IGR	DEL	TC	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70961588_70961589delTC								SLCO5A1 (214289 upstream) : PRDM14 (2436 downstream)																							CTGCACTATATCTCTCTCTCAA	0.485													4	2	---	---	---	---	
ZNF704	619279	broad.mit.edu	37	8	81654050	81654050	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81654050delA	uc003yby.1	-							NM_001033723	NP_001028895	Q6ZNC4	ZN704_HUMAN	zinc finger protein 704							intracellular	zinc ion binding				0	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)			ttcctttgtgaaaaaaggact	0.000													4	2	---	---	---	---	
LRRC69	100130742	broad.mit.edu	37	8	92124684	92124684	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92124684delT	uc010mal.1	+						LRRC69_uc003yev.1_Intron	NM_001129890	NP_001123362	Q6ZNQ3	LRC69_HUMAN	leucine rich repeat containing 69												0						atcaatgtgatataacacatt	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	94941893	94941893	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94941893delC								PDP1 (3599 upstream) : CDH17 (197501 downstream)																							tctgtaatctcagcactttgg	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	97088040	97088040	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97088040delG								C8orf37 (806603 upstream) : GDF6 (66520 downstream)																							catcatcactggccatcagag	0.000													4	2	---	---	---	---	
PTDSS1	9791	broad.mit.edu	37	8	97289208	97289209	+	Intron	INS	-	CA	CA	rs13279570	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97289208_97289209insCA	uc003yht.1	+						PTDSS1_uc003yhu.1_Intron	NM_014754	NP_055569	P48651	PTSS1_HUMAN	phosphatidylserine synthase 1						phosphatidylserine biosynthetic process	integral to membrane	transferase activity			ovary(1)	1	Breast(36;6.18e-05)				Phosphatidylserine(DB00144)	gcacgcgcgcgcacacacacac	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	101795972	101795973	+	IGR	INS	-	TCCT	TCCT			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101795972_101795973insTCCT								PABPC1 (61657 upstream) : YWHAZ (134831 downstream)																							ccctccctccctccttccttcc	0.000													4	3	---	---	---	---	
RIMS2	9699	broad.mit.edu	37	8	104773563	104773563	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104773563delA	uc003ylp.2	+							NM_001100117	NP_001093587	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2						intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			AAAGACTGtgaattagtcaag	0.164										HNSCC(12;0.0054)			4	2	---	---	---	---	
OXR1	55074	broad.mit.edu	37	8	107716542	107716547	+	Intron	DEL	GAGAGA	-	-	rs67206748		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107716542_107716547delGAGAGA	uc011lht.1	+						OXR1_uc003ymf.2_Intron|OXR1_uc011lhu.1_Intron|OXR1_uc010mcg.2_Intron|OXR1_uc010mch.2_5'Flank|OXR1_uc003ymg.1_Intron|OXR1_uc003ymi.1_Intron	NM_018002	NP_060472	Q8N573	OXR1_HUMAN	oxidation resistance 1 isoform 1						cell wall macromolecule catabolic process|response to oxidative stress	mitochondrion					0			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			TACATATATGGAGAGAGAGAGAGAGA	0.277													4	2	---	---	---	---	
SYBU	55638	broad.mit.edu	37	8	110689264	110689265	+	Intron	DEL	TG	-	-	rs35871646		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110689264_110689265delTG	uc010mct.2	-						SYBU_uc010mcs.2_Intron|SYBU_uc010mcu.2_Intron|SYBU_uc003ynp.3_Intron|SYBU_uc010mcv.2_Intron	NM_001099745	NP_001093215	Q9NX95	SYBU_HUMAN	Golgi-localized syntaphilin-related protein							cytoplasmic membrane-bounded vesicle|cytoskeleton|Golgi membrane|integral to membrane				ovary(1)	1						AGGGTGTTCAtgtgtgtgtgtg	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	120502263	120502264	+	IGR	DEL	AC	-	-	rs61424449		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120502263_120502264delAC								NOV (65585 upstream) : ENPP2 (67055 downstream)																							TTGcacatatacacacacacac	0.287													5	5	---	---	---	---	
TRIB1	10221	broad.mit.edu	37	8	126445327	126445327	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126445327delG	uc003yrx.2	+						TRIB1_uc011lis.1_Intron|TRIB1_uc010mdn.2_5'Flank	NM_025195	NP_079471	Q96RU8	TRIB1_HUMAN	G-protein-coupled receptor induced protein						JNK cascade|negative regulation of lipopolysaccharide-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell proliferation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|regulation of MAP kinase activity|response to lipopolysaccharide	cytoplasm|nucleus	ATP binding|mitogen-activated protein kinase kinase binding|protein kinase activity|protein kinase inhibitor activity|transcription factor binding|ubiquitin protein ligase binding|ubiquitin-protein ligase regulator activity			lung(1)	1	all_hematologic(1;4.97e-05)|Ovarian(258;0.00167)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)			GTGTGAAAGCGGGTAACCCTT	0.502													3	3	---	---	---	---	
PVT1	5820	broad.mit.edu	37	8	128901695	128901695	+	Intron	DEL	T	-	-	rs147217778		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128901695delT	uc010mdq.2	+						PVT1_uc003ysl.2_5'Flank|PVT1_uc010mdp.1_Intron	NR_003367				Homo sapiens Pvt1 oncogene (non-protein coding), mRNA (cDNA clone IMAGE:5517530), with apparent retained intron.												0						TTTCCTGTGattttttttttt	0.040													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	129192715	129192715	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129192715delA								MIR1208 (30281 upstream) : None (None downstream)																							ATAAGGATGGAAAAAGTTAAG	0.279													4	2	---	---	---	---	
ASAP1	50807	broad.mit.edu	37	8	131382831	131382831	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131382831delA	uc003yta.1	-						ASAP1_uc011liw.1_Intron	NM_018482	NP_060952	Q9ULH1	ASAP1_HUMAN	development and differentiation enhancing factor						cilium morphogenesis|filopodium assembly|regulation of ARF GTPase activity|signal transduction	cytoplasm|membrane	ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding			ovary(4)	4						atgtgcacataaaaccttgta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	131681357	131681358	+	IGR	INS	-	G	G	rs139169091	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131681357_131681358insG								ASAP1 (267141 upstream) : ADCY8 (111190 downstream)																							ATTTAAATCCCGCCAGAAAGCT	0.287													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	140298400	140298401	+	IGR	INS	-	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140298400_140298401insA								COL22A1 (372164 upstream) : KCNK9 (314681 downstream)																							TAATGTCTGGGAAAAGGAAGCT	0.490													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	143103988	143103988	+	IGR	DEL	G	-	-	rs67110189		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143103988delG								MIR1302-7 (236314 upstream) : NCRNA00051 (175729 downstream)																							GAGCTCAGGTGGGGAAGCTCA	0.647													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	143898434	143898435	+	IGR	INS	-	A	A	rs78586940		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143898434_143898435insA								LY6D (30426 upstream) : GML (17782 downstream)																							acacacaaaatcactcacatac	0.163													4	3	---	---	---	---	
NRBP2	340371	broad.mit.edu	37	8	144916951	144916951	+	3'UTR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144916951delC	uc011lkt.1	-	18					NRBP2_uc003yzv.2_3'UTR|NRBP2_uc003yzz.1_3'UTR|NRBP2_uc003yzw.2_3'UTR|NRBP2_uc010mfl.2_3'UTR|NRBP2_uc010mfm.2_3'UTR|NRBP2_uc011lks.1_3'UTR|NRBP2_uc003yzy.2_3'UTR	NM_178564	NP_848659	Q9NSY0	NRBP2_HUMAN	nuclear receptor binding protein 2						negative regulation of neuron apoptosis|neuron differentiation	cytoplasm	ATP binding|protein kinase activity			central_nervous_system(2)	2	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			taagactgagccaggagtgga	0.025													4	2	---	---	---	---	
UHRF2	115426	broad.mit.edu	37	9	6413833	6413833	+	Intron	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6413833delC	uc003zjy.2	+						UHRF2_uc003zjz.2_Intron	NM_152896	NP_690856	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains						cell cycle|cell differentiation|cell proliferation|protein autoubiquitination|regulation of cell cycle|ubiquitin-dependent protein catabolic process	nucleus	DNA binding|histone binding|ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0392)|Lung(218;0.129)		TGGGTCCCTGCCAGCCCCAAC	0.721													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	11472108	11472108	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:11472108delG								PTPRD (859385 upstream) : None (None downstream)																							ctgtatcacaggcaaagagct	0.000													3	4	---	---	---	---	
NFIB	4781	broad.mit.edu	37	9	14193997	14193998	+	Intron	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14193997_14193998insT	uc003zle.2	-						NFIB_uc003zlf.2_Intron|NFIB_uc011lmo.1_Intron	NM_005596	NP_005587	O00712	NFIB_HUMAN	nuclear factor I/B						anterior commissure morphogenesis|chondrocyte differentiation|Clara cell differentiation|commissural neuron axon guidance|DNA replication|glial cell differentiation|lung ciliated cell differentiation|negative regulation of DNA binding|negative regulation of epithelial cell proliferation involved in lung morphogenesis|negative regulation of mesenchymal cell proliferation involved in lung development|positive regulation of transcription from RNA polymerase II promoter|principal sensory nucleus of trigeminal nerve development|Type I pneumocyte differentiation|Type II pneumocyte differentiation	cerebellar mossy fiber|nucleolus|nucleus	RNA polymerase II transcription corepressor activity|sequence-specific DNA binding RNA polymerase II transcription factor activity				0				GBM - Glioblastoma multiforme(50;4.4e-08)|LUAD - Lung adenocarcinoma(58;0.119)|Lung(218;0.164)		TTTTATGTCTCTTTTTAAAACA	0.381			T	MYB|HGMA2	adenoid cystic carcinoma|lipoma								4	2	---	---	---	---	
KIAA1797	54914	broad.mit.edu	37	9	20973385	20973385	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20973385delT	uc003zog.1	+						KIAA1797_uc003zoh.1_Intron	NM_017794	NP_060264	Q5VW36	K1797_HUMAN	hypothetical protein LOC54914							integral to membrane	binding			ovary(8)|breast(1)|kidney(1)	10				GBM - Glioblastoma multiforme(3;2.1e-125)|Lung(42;2.76e-14)|LUSC - Lung squamous cell carcinoma(42;1.99e-11)		TTTCTGCAGCTTTTTTTTTTT	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	22715447	22715447	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22715447delT	uc003zpq.1	+											Homo sapiens cDNA FLJ35282 fis, clone PROST2007328.																		tctttgttgattttttttttc	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	26103766	26103767	+	IGR	DEL	AG	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26103766_26103767delAG								TUSC1 (424910 upstream) : C9orf82 (736917 downstream)																							aaaagcaggcagaagaacatga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	27905294	27905294	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27905294delA								C9orf72 (331452 upstream) : LINGO2 (43234 downstream)																							agtaaagcatatgattgtgta	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	37041794	37041794	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37041794delT								PAX5 (7318 upstream) : ZCCHC7 (78675 downstream)																							GTTTTTTGGATTTTTTTTTTT	0.448													4	2	---	---	---	---	
FAM75A3	727830	broad.mit.edu	37	9	40701846	40701848	+	Intron	DEL	GAA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:40701846_40701848delGAA	uc010mmj.2	+							NM_001083124	NP_001076593	Q5VYP0	F75A3_HUMAN	hypothetical protein LOC727830							integral to membrane				ovary(2)|skin(1)	3				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		GAAGTCAGTTGAAGAAGCCTGAG	0.527													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	42606607	42606607	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:42606607delC								FAM95B1 (132370 upstream) : FOXD4L2 (110627 downstream)																							ccaatcagcaccctgtcaaaa	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66463189	66463190	+	Intron	INS	-	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66463189_66463190insA	uc004aec.2	+											Homo sapiens, clone IMAGE:5213378, mRNA.																		GATATAGAAGTAAAAACCTGGG	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68429869	68429873	+	IGR	DEL	AAAGC	-	-	rs113922886		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68429869_68429873delAAAGC								FAM27B (635680 upstream) : MIR1299 (572366 downstream)																							CAAGAAAAGAAAAGCATTTAGCTCA	0.341													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69000138	69000138	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69000138delT								None (None upstream) : MIR1299 (2101 downstream)																							tgtttgtctctcacataggat	0.000													4	2	---	---	---	---	
OSTF1	26578	broad.mit.edu	37	9	77703563	77703563	+	5'UTR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77703563delG	uc004ajv.3	+	1					OSTF1_uc004ajw.3_5'UTR|OSTF1_uc004ajx.3_5'UTR|C9orf95_uc004aju.2_5'Flank|C9orf95_uc004ajs.3_5'Flank|C9orf95_uc004ajr.3_5'Flank|C9orf95_uc004ajt.3_5'Flank	NM_012383	NP_036515	Q92882	OSTF1_HUMAN	osteoclast stimulating factor 1						ossification|signal transduction	cytoplasm	identical protein binding			skin(1)	1						GGCAAGCGGTGGGCTTTTCGG	0.627													4	2	---	---	---	---	
VPS13A	23230	broad.mit.edu	37	9	79881105	79881105	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79881105delG	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						ttttgcatttgctgaagcttg	0.000													4	2	---	---	---	---	
GNA14	9630	broad.mit.edu	37	9	80182457	80182457	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80182457delA	uc004aku.2	-							NM_004297	NP_004288	O95837	GNA14_HUMAN	G alpha 14						activation of phospholipase C activity by dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(2)	2						CACAAGTTTTAAAAAAAATGC	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	81344612	81344612	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81344612delT								PSAT1 (399605 upstream) : TLE4 (842266 downstream)																							gggcttcatatccagaataca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	82892728	82892728	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82892728delA								TLE4 (551071 upstream) : None (None downstream)																							CATGACAGATAAAACAAACCT	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	84393808	84393808	+	IGR	DEL	T	-	-	rs142073124		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84393808delT								TLE1 (90212 upstream) : FLJ43950 (134544 downstream)																							CTAAAAAGCAttttttttttt	0.030													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	91589772	91589775	+	IGR	DEL	GTGT	-	-	rs112351786	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91589772_91589775delGTGT								LOC286238 (322697 upstream) : C9orf47 (16003 downstream)																							gtgcgcgcgcgtgtgtgtgtgtgt	0.382													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	92210051	92210051	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92210051delG								SEMA4D (97163 upstream) : GADD45G (9876 downstream)																							GTGGCCTCCTGGTAGGCGCTG	0.602													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	93737215	93737216	+	IGR	INS	-	GA	GA			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93737215_93737216insGA								SYK (76382 upstream) : AUH (238883 downstream)																							CACAGCCAGGGGAGAGAGAGCA	0.594													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	96681723	96681723	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96681723delT								PHF2 (239856 upstream) : BARX1 (32188 downstream)																							GCCAGTTGCCttttttttttt	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	98829882	98829883	+	Intron	INS	-	C	C	rs142288092	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98829882_98829883insC	uc004avy.3	+											Homo sapiens cDNA clone IMAGE:3638298.																		CCTGGAGGACACCCCCAGCACC	0.351													1	9	---	---	---	---	
ABCA1	19	broad.mit.edu	37	9	107629376	107629377	+	Intron	INS	-	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107629376_107629377insA	uc004bcl.2	-						ABCA1_uc004bcm.2_Intron	NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1						Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	GTGAGTTAGGGAAAAGATGAAG	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	110011239	110011239	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110011239delC								ZNF462 (237450 upstream) : RAD23B (34305 downstream)																							ctttatctttcctccaccccc	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	110871887	110871887	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110871887delT								KLF4 (619840 upstream) : ACTL7B (744984 downstream)																							GTGCAAGTCCTTTTGATGCAA	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	113856520	113856520	+	IGR	DEL	G	-	-	rs76415870	byFrequency	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113856520delG								LPAR1 (54994 upstream) : OR2K2 (233244 downstream)																							ttcatctcacgtagtgctggg	0.095													3	4	---	---	---	---	
ZNF483	158399	broad.mit.edu	37	9	114285903	114285904	+	5'Flank	DEL	TT	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114285903_114285904delTT	uc004bff.2	+						ZNF483_uc011lwq.1_5'Flank|ZNF483_uc004bfg.2_5'Flank|ZNF483_uc010mud.1_5'Flank	NM_133464	NP_597721	Q8TF39	ZN483_HUMAN	zinc finger protein 483 isoform a						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1						tttttttctctttttttttttt	0.213													4	2	---	---	---	---	
DNAJC25-GNG10	552891	broad.mit.edu	37	9	114391363	114391363	+	5'Flank	DEL	T	-	-	rs11335899		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114391363delT	uc004bfn.2	+						uc004bfk.3_Intron|DNAJC25_uc004bfl.2_5'Flank|DNAJC25_uc004bfm.2_5'Flank	NM_004125	NP_004116	Q9H1X3	DJC25_HUMAN	DNAJC25-GNG10 protein						protein folding	integral to membrane	heat shock protein binding|unfolded protein binding				0						ttacttggacttttttttttt	0.000													4	2	---	---	---	---	
DEC1	50514	broad.mit.edu	37	9	118099999	118099999	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118099999delT	uc004bjk.1	+						DEC1_uc004bjl.1_Intron	NM_017418	NP_059114	Q9P2X7	DEC1_HUMAN	deleted in esophageal cancer 1						negative regulation of cell proliferation					ovary(1)	1						ATTCAGTAACtttttttttta	0.184													4	2	---	---	---	---	
ASTN2	23245	broad.mit.edu	37	9	119477805	119477805	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119477805delT	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						tttagacatcttttcctccag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	122324462	122324465	+	IGR	DEL	GTGT	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122324462_122324465delGTGT								DBC1 (192723 upstream) : MIR147 (682792 downstream)																							ctgtgtgtacgtgtgtgtgtgtgt	0.137													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	125196843	125196843	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125196843delG								PTGS1 (38862 upstream) : OR1J2 (33997 downstream)																							tctggtggaagaaatttctaa	0.000													4	2	---	---	---	---	
SCAI	286205	broad.mit.edu	37	9	127888672	127888675	+	Intron	DEL	GTGT	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127888672_127888675delGTGT	uc004bpe.2	-						SCAI_uc004bpd.2_Intron|SCAI_uc010mwu.2_Intron	NM_001144877	NP_001138349	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion isoform 2						negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|integral to membrane|nucleus	protein binding|transcription corepressor activity			ovary(2)|breast(2)|central_nervous_system(1)	5						TGAGTTGGGGgtgtgtgtgtgtgt	0.319													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	129308908	129308908	+	IGR	DEL	A	-	-	rs34057376		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129308908delA								FAM125B (35209 upstream) : LMX1B (67840 downstream)																							ggcaatttacaaaaaaaaaag	0.000													3	3	---	---	---	---	
RALGPS1	9649	broad.mit.edu	37	9	129853724	129853725	+	Intron	INS	-	T	T	rs78757730		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129853724_129853725insT	uc004bqo.1	+						RALGPS1_uc011mab.1_Intron|RALGPS1_uc011mac.1_Intron|RALGPS1_uc004bqq.3_Intron|ANGPTL2_uc004bqr.1_Intron|ANGPTL2_uc010mxg.1_Intron	NM_014636	NP_055451	Q5JS13	RGPS1_HUMAN	Ral GEF with PH domain and SH3 binding motif 1						small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity			ovary(1)	1						GCCCCATCCCATTTTTTTTTTC	0.525													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	132332446	132332447	+	IGR	INS	-	AG	AG	rs142755175	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132332446_132332447insAG								C9orf106 (247564 upstream) : C9orf50 (42059 downstream)																							ATAAGAGGGCCAGAGAGAGAGA	0.584													3	3	---	---	---	---	
PRRX2	51450	broad.mit.edu	37	9	132463418	132463418	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132463418delT	uc004byh.2	+							NM_016307	NP_057391	Q99811	PRRX2_HUMAN	paired related homeobox 2							nuclear chromosome	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			pancreas(1)	1		Ovarian(14;0.00556)				tgtgaggccgttttggcatcc	0.169													4	2	---	---	---	---	
ADAMTS13	11093	broad.mit.edu	37	9	136306285	136306285	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136306285delG	uc004cdv.3	+						ADAMTS13_uc004cdp.3_Intron|ADAMTS13_uc004cdt.1_Intron|ADAMTS13_uc004cdu.1_Intron|ADAMTS13_uc004cdw.3_Intron|ADAMTS13_uc004cdx.3_Intron|ADAMTS13_uc004cdy.1_Intron|ADAMTS13_uc004cdz.3_Intron|ADAMTS13_uc004cds.1_Intron|ADAMTS13_uc004cdr.1_Intron	NM_139025	NP_620594	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1						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)		GGAGGGTGGAGAGACATAAGC	0.617													4	2	---	---	---	---	
NCRNA00094	266655	broad.mit.edu	37	9	136890207	136890209	+	5'Flank	DEL	TCT	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136890207_136890209delTCT	uc004ceu.2	+							NR_015427				Homo sapiens cDNA FLJ35348 fis, clone PROST2016918.												0						cctcctcctctctcagctcctcc	0.000													4	2	---	---	---	---	
COL5A1	1289	broad.mit.edu	37	9	137576961	137576972	+	Intron	DEL	CATCCATCCATC	-	-	rs141729483		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137576961_137576972delCATCCATCCATC	uc004cfe.2	+							NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein						axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		tccatccattcatccatccatccatccatcca	0.000													4	2	---	---	---	---	
EHMT1	79813	broad.mit.edu	37	9	140563846	140563846	+	Intron	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140563846delC	uc011mfc.1	+						EHMT1_uc004coa.2_Intron|EHMT1_uc004cob.1_Intron	NM_024757	NP_079033	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1						DNA methylation|embryo development|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			breast(2)|pancreas(1)	3	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		ACCCAAGACGCCCCCCACAGC	0.667													4	2	---	---	---	---	
EHMT1	79813	broad.mit.edu	37	9	140610825	140610826	+	Intron	INS	-	GG	GG			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140610825_140610826insGG	uc011mfc.1	+						EHMT1_uc004coa.2_Intron|EHMT1_uc004cob.1_Intron	NM_024757	NP_079033	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1						DNA methylation|embryo development|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			breast(2)|pancreas(1)	3	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		ggtgtcatggtgggggaggaag	0.000													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	3835144	3835145	+	IGR	INS	-	GGAA	GGAA	rs148701319	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3835144_3835145insGGAA								KLF6 (7671 upstream) : LOC100216001 (786299 downstream)																							agaaagaaaggggaaggaacaa	0.000													3	3	---	---	---	---	
UCN3	114131	broad.mit.edu	37	10	5405012	5405013	+	5'Flank	INS	-	AATG	AATG	rs148665742	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5405012_5405013insAATG	uc001ihx.1	+							NM_053049	NP_444277	Q969E3	UCN3_HUMAN	urocortin 3 preproprotein							extracellular region	hormone activity				0						aggaatgaactaatgaatgaat	0.188													4	2	---	---	---	---	
ITGA8	8516	broad.mit.edu	37	10	15581218	15581218	+	Intron	DEL	A	-	-	rs146118121		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15581218delA	uc001ioc.1	-						ITGA8_uc010qcb.1_Intron	NM_003638	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8 precursor						cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity			ovary(3)|lung(3)	6						ACctcaaacgaggcaacagaa	0.025													4	2	---	---	---	---	
STAM	8027	broad.mit.edu	37	10	17747904	17747905	+	Intron	INS	-	A	A	rs147657165		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17747904_17747905insA	uc001ipj.1	+						STAM_uc009xjw.1_Intron	NM_003473	NP_003464	Q92783	STAM1_HUMAN	signal transducing adaptor molecule 1						cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway	cytosol|early endosome membrane	SH3/SH2 adaptor activity			large_intestine(1)|ovary(1)	2						ctgtctctaccaaaaaaaaaaa	0.000													2	4	---	---	---	---	
PLXDC2	84898	broad.mit.edu	37	10	20401643	20401643	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20401643delT	uc001iqg.1	+						PLXDC2_uc001iqh.1_Intron	NM_032812	NP_116201	Q6UX71	PXDC2_HUMAN	plexin domain containing 2 precursor							integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4						ATGTTAATACTTAGGCTACCT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38961127	38961128	+	IGR	INS	-	AA	AA	rs149123449		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38961127_38961128insAA								LOC399744 (220047 upstream) : None (None downstream)																							acaacaacaacaacaacaacaa	0.010													0	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	39084440	39084449	+	IGR	DEL	CATTCCATTC	-	-	rs112061831		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:39084440_39084449delCATTCCATTC								LOC399744 (343360 upstream) : None (None downstream)																							cattccatgacattccattccattccattc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42373797	42373801	+	IGR	DEL	AATCT	-	-	rs62637360		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42373797_42373801delAATCT								None (None upstream) : LOC441666 (453514 downstream)																							attccattccaatctattccattcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42655453	42655454	+	IGR	DEL	TA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42655453_42655454delTA								None (None upstream) : LOC441666 (171861 downstream)																							aataaagttttatttcctcctg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42658919	42658919	+	IGR	DEL	T	-	-	rs143364099		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42658919delT								None (None upstream) : LOC441666 (168396 downstream)																							TATTTGTGCATTTTTTTCCTA	0.239													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	43166793	43166793	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43166793delA								ZNF33B (32801 upstream) : BMS1 (111161 downstream)																							TTTATAAAGCAAAAAAAAAAA	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	46979956	46979956	+	IGR	DEL	A	-	-	rs10707197		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46979956delA								SYT15 (9355 upstream) : GPRIN2 (13590 downstream)																							tcagaatgtgaaaaaaaAAAG	0.040													2	5	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47150847	47150848	+	Intron	INS	-	A	A	rs150565477		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47150847_47150848insA	uc001jed.3	-						uc001jef.2_Intron			P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						AAGCAACTATTAAAAAAAAAaa	0.054													4	2	---	---	---	---	
PRKG1	5592	broad.mit.edu	37	10	53180921	53180922	+	Intron	INS	-	TTGT	TTGT	rs140624432		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53180921_53180922insTTGT	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron|PRKG1_uc010qhp.1_Intron	NM_001098512	NP_001091982	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		CCTTTTATTTCttgtttgtttg	0.173													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	54351291	54351292	+	IGR	DEL	TA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54351291_54351292delTA								DKK1 (273875 upstream) : MBL2 (173849 downstream)																							ttcttctccctattaagctttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	61256947	61256947	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61256947delG								FAM13C (134286 upstream) : SLC16A9 (153575 downstream)																							cactgctggagggagtggaat	0.134													4	2	---	---	---	---	
CCAR1	55749	broad.mit.edu	37	10	70524297	70524297	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70524297delA	uc001joo.2	+						CCAR1_uc001jol.1_Intron|CCAR1_uc001jom.1_Intron|CCAR1_uc009xpx.1_Intron|CCAR1_uc001jon.1_Intron|CCAR1_uc010qiz.1_Intron|CCAR1_uc010qja.1_Intron|CCAR1_uc010qjb.1_Intron	NM_018237	NP_060707	Q8IX12	CCAR1_HUMAN	cell-cycle and apoptosis regulatory protein 1						apoptosis|cell cycle|nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm|perinuclear region of cytoplasm	calcium ion binding|nucleic acid binding|protein binding			ovary(6)|large_intestine(1)	7						gtctcaaaacaaaaaaaaaaa	0.179													4	2	---	---	---	---	
DDX21	9188	broad.mit.edu	37	10	70723858	70723859	+	Intron	DEL	AA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70723858_70723859delAA	uc001jov.1	+						DDX21_uc001jow.1_Intron	NM_004728	NP_004719	Q9NR30	DDX21_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 21							nucleolus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)	3						ccgtctcaagaaaaaaaaaaaa	0.188													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	82095804	82095804	+	IGR	DEL	A	-	-	rs72815321	byFrequency	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82095804delA								MAT1A (46370 upstream) : DYDC1 (60 downstream)																							TCCTTAGAGGAAAAAAAAAGG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	92793365	92793365	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92793365delC								ANKRD1 (112333 upstream) : NUDT9P1 (118396 downstream)																							ATAACCCCCACATCTCAAATT	0.413													4	2	---	---	---	---	
NRAP	4892	broad.mit.edu	37	10	115348616	115348616	+	3'UTR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115348616delG	uc001laj.2	-	42					HABP2_uc001lai.3_3'UTR|NRAP_uc009xyb.2_3'UTR|NRAP_uc001lak.2_3'UTR|NRAP_uc001lal.3_3'UTR	NM_198060	NP_932326	Q86VF7	NRAP_HUMAN	nebulin-related anchoring protein isoform S							fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)|upper_aerodigestive_tract(1)	10		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		TTTTAATAAAGGAAGATCTGG	0.473													15	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	115430689	115430689	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115430689delC								NRAP (6884 upstream) : CASP7 (8246 downstream)																							atgccctttacccaccaaggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	122081665	122081666	+	IGR	DEL	TT	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122081665_122081666delTT								SEC23IP (380420 upstream) : PPAPDC1A (134800 downstream)																							ATTTCTGCTCTTTGGTCTTAGT	0.337													4	2	---	---	---	---	
LHPP	64077	broad.mit.edu	37	10	126294402	126294403	+	Intron	INS	-	G	G	rs141845838	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126294402_126294403insG	uc001lhs.1	+						LHPP_uc001lht.1_Intron|LHPP_uc009yai.1_Intron|LHPP_uc009yaj.1_Intron	NM_022126	NP_071409	Q9H008	LHPP_HUMAN	phospholysine phosphohistidine inorganic						protein dephosphorylation	cytosol|nucleus	inorganic diphosphatase activity|magnesium ion binding|phosphohistidine phosphatase activity|protein homodimerization activity				0		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.163)|Colorectal(40;0.187)		GGCAGGAGGGAGAGCCAGTgga	0.530													3	3	---	---	---	---	
DHX32	55760	broad.mit.edu	37	10	127575513	127575516	+	Intron	DEL	TCTT	-	-	rs143617895		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127575513_127575516delTCTT	uc001ljg.1	-							NM_018180	NP_060650	Q7L7V1	DHX32_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32							mitochondrion|nucleus	ATP binding|helicase activity			breast(2)|ovary(1)|lung(1)	4		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				TTTCCCCATGTCTTTCTGTCTCTT	0.412													7	6	---	---	---	---	
MGMT	4255	broad.mit.edu	37	10	131459040	131459041	+	Intron	DEL	AC	-	-	rs72387327		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131459040_131459041delAC	uc001lkh.2	+							NM_002412	NP_002403	P16455	MGMT_HUMAN	O-6-methylguanine-DNA methyltransferase											ovary(1)|breast(1)	2		all_cancers(35;9.44e-09)|all_epithelial(44;6.98e-08)|Lung NSC(174;0.0157)|all_lung(145;0.0201)|all_neural(114;0.0732)|Colorectal(57;0.0792)|Breast(234;0.167)		OV - Ovarian serous cystadenocarcinoma(35;0.00291)		CCCACCCCCAacacacacacac	0.391								Direct_reversal_of_damage					2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	131822221	131822221	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131822221delG								EBF3 (60130 upstream) : GLRX3 (112442 downstream)																							AGGTGGCAGTGTTTGCCCGGC	0.592													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	135455485	135455486	+	IGR	INS	-	C	C	rs150650792	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135455485_135455486insC								FRG2B (15186 upstream) : LOC653544 (34793 downstream)																							AAAAAGTGTGGCCTCATATATG	0.411													8	6	---	---	---	---	
MUC5B	727897	broad.mit.edu	37	11	1215523	1215523	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1215523delG	uc009ycr.1	+						uc001lsz.2_RNA	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;						cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CCATCATCCTGGAGTACCACC	0.672													4	2	---	---	---	---	
ZNF195	7748	broad.mit.edu	37	11	3400201	3400202	+	Intron	INS	-	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3400201_3400202insG	uc001lxt.2	-						LOC650368_uc001lxw.3_5'Flank|LOC650368_uc010qxs.1_5'Flank|LOC650368_uc001lxx.2_5'Flank|LOC650368_uc001lxy.2_5'Flank|ZNF195_uc001lxv.2_Intron|ZNF195_uc001lxs.2_Intron|ZNF195_uc010qxr.1_Intron|ZNF195_uc009ydz.2_Intron|ZNF195_uc001lxu.2_Intron	NM_001130520	NP_001123992	O14628	ZN195_HUMAN	zinc finger protein 195 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Medulloblastoma(188;0.00106)|Breast(177;0.00328)|all_neural(188;0.00681)|Ovarian(85;0.00965)		BRCA - Breast invasive adenocarcinoma(625;0.0361)|LUSC - Lung squamous cell carcinoma(625;0.2)		CGGTTCCTCCCGAGCCGGTACC	0.599													4	2	---	---	---	---	
TRIM5	85363	broad.mit.edu	37	11	5944430	5944432	+	Intron	DEL	ACA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5944430_5944432delACA	uc001mbq.1	-							NM_033093	NP_149084	Q9C035	TRIM5_HUMAN	tripartite motif protein TRIM5 isoform delta						interspecies interaction between organisms|protein trimerization|response to virus	cytoplasm|cytoplasmic mRNA processing body	ligase activity|protein binding|protein homodimerization activity|zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)|Lung NSC(207;0.138)|all_lung(207;0.221)		Epithelial(150;7.21e-09)|BRCA - Breast invasive adenocarcinoma(625;0.139)		taactcccagacaacatttctag	0.000													4	2	---	---	---	---	
ZNF143	7702	broad.mit.edu	37	11	9485634	9485635	+	Intron	DEL	TG	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9485634_9485635delTG	uc001mhr.2	+						ZNF143_uc009yfu.2_Intron|ZNF143_uc010rby.1_Intron	NM_003442	NP_003433	P52747	ZN143_HUMAN	zinc finger protein 143						regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase III promoter|transcription from RNA polymerase II promoter|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding|zinc ion binding				0				all cancers(16;4.12e-09)|Epithelial(150;2.29e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0212)		tgtgtgtgtttgtgtgtgtgtg	0.020													4	2	---	---	---	---	
SOX6	55553	broad.mit.edu	37	11	16197617	16197620	+	Intron	DEL	GGAT	-	-	rs71826187		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16197617_16197620delGGAT	uc001mme.2	-						SOX6_uc001mmd.2_Intron|SOX6_uc001mmf.2_Intron|SOX6_uc001mmg.2_Intron	NM_001145819	NP_001139291	P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6 isoform 4						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3						acggacggacggatggatggatgg	0.152													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	22628514	22628514	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22628514delA								SLC17A6 (227470 upstream) : FANCF (15565 downstream)																							acacattctgaatatatttga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	27851974	27851974	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27851974delC								BDNF (108369 upstream) : KIF18A (190189 downstream)																							CTCATGTTGGCCAGGTCTGTT	0.592													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	28026243	28026243	+	IGR	DEL	T	-	-	rs147880978	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28026243delT								BDNF (282638 upstream) : KIF18A (15920 downstream)																							aaatgactgattatttaagaa	0.000													4	2	---	---	---	---	
RAG1	5896	broad.mit.edu	37	11	36608792	36608793	+	Intron	INS	-	TG	TG	rs146758348	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36608792_36608793insTG	uc001mwt.2	+							NM_000448		P15918	RAG1_HUMAN	recombination activating gene 1						histone monoubiquitination|immune response|pre-B cell allelic exclusion|protein autoubiquitination|T cell differentiation in thymus|V(D)J recombination	nucleus	endonuclease activity|histone binding|protein homodimerization activity|sequence-specific DNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|pancreas(1)|lung(1)|kidney(1)|skin(1)	5	all_lung(20;0.226)	all_hematologic(20;0.107)				gtatatatatatatgtgtgtgt	0.228									Familial_Hemophagocytic_Lymphohistiocytosis				4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	48765500	48765501	+	IGR	INS	-	G	G	rs61930777		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48765500_48765501insG								OR4A47 (254228 upstream) : FOLH1 (402687 downstream)																							ctgtctagtttcatgggaagat	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	48864295	48864295	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48864295delT								OR4A47 (353023 upstream) : FOLH1 (303893 downstream)																							ctttcttttgttagagcagtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	50638288	50638289	+	IGR	DEL	AC	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50638288_50638289delAC								LOC646813 (258485 upstream) : OR4A5 (773159 downstream)																							cagtttggaaacagtctttttg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	55779462	55779463	+	IGR	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55779462_55779463insT								OR5F1 (17361 upstream) : OR5AS1 (18432 downstream)																							TCTGTGTATTCTTTTTTTTTTT	0.297													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	57339277	57339278	+	IGR	DEL	CA	-	-	rs35972683		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57339277_57339278delCA								UBE2L6 (3824 upstream) : SERPING1 (25749 downstream)																							GGGTTAGTCTcacacacacaca	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	57697362	57697362	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57697362delT								CTNND1 (110711 upstream) : OR9Q1 (93991 downstream)																							gatgggtttattagtacctgc	0.010													4	2	---	---	---	---	
KDM2A	22992	broad.mit.edu	37	11	66928255	66928255	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66928255delA	uc001ojw.2	+						KDM2A_uc001ojx.2_Intron	NM_012308	NP_036440	Q9Y2K7	KDM2A_HUMAN	F-box and leucine-rich repeat protein 11						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			ovary(4)|lung(3)|breast(1)|skin(1)	9						aaaaaacaacaaaaaaaaaaT	0.055													4	2	---	---	---	---	
P4HA3	283208	broad.mit.edu	37	11	74013462	74013462	+	Frame_Shift_Del	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74013462delG	uc001ouz.2	-	3	562	c.519delC	c.(517-519)CCCfs	p.P173fs	P4HA3_uc001ouy.3_RNA|P4HA3_uc010rrj.1_Frame_Shift_Del_p.P173fs	NM_182904	NP_878907	Q7Z4N8	P4HA3_HUMAN	prolyl 4-hydroxylase, alpha III subunit	173						endoplasmic reticulum lumen	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 4-dioxygenase activity			skin(1)	1	Breast(11;2.31e-05)					AGAGCCGTTTGGGGCTGTACA	0.512													94	79	---	---	---	---	
GDPD5	81544	broad.mit.edu	37	11	75152589	75152590	+	Intron	DEL	GT	-	-	rs34643232		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75152589_75152590delGT	uc001owo.3	-						GDPD5_uc001owp.3_Intron|GDPD5_uc001own.3_Intron|GDPD5_uc009yuc.2_Intron|GDPD5_uc009yud.2_Intron	NM_030792	NP_110419	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain						glycerol metabolic process|lipid metabolic process|nervous system development	endomembrane system|growth cone|integral to membrane|perinuclear region of cytoplasm	glycerophosphodiester phosphodiesterase activity			ovary(1)	1						CTGCCCGACCgtgtgtgtgtgt	0.569													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	82224111	82224112	+	IGR	DEL	AC	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82224111_82224112delAC								None (None upstream) : FAM181B (218941 downstream)																							tatcatggaaacacacacacac	0.000													4	2	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	85155390	85155390	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85155390delA	uc001pak.2	-							NM_001142699	NP_001136171	Q15700	DLG2_HUMAN	chapsyn-110 isoform 1							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				ATAGCTGAGTAAAAAAAAAAG	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	89606091	89606091	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89606091delT								TRIM53 (21949 upstream) : TRIM49L (38490 downstream)																							tccctctgtcttttTTTTTTT	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	101688014	101688014	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101688014delC								TRPC6 (233355 upstream) : ANGPTL5 (73392 downstream)																							tcctcctggtccctcccacga	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	107113340	107113341	+	IGR	DEL	GT	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107113340_107113341delGT								GUCY1A2 (224169 upstream) : CWF19L2 (83733 downstream)																							gcgtgtgtgcgtgtgtgtgtgt	0.163													5	3	---	---	---	---	
DDX10	1662	broad.mit.edu	37	11	108586829	108586830	+	Intron	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108586829_108586830insT	uc001pkm.2	+						DDX10_uc001pkl.1_Intron	NM_004398	NP_004389	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10								ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity			breast(2)|lung(1)|prostate(1)	4		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		AGTCTAGCTTAttttttttttt	0.168			T	NUP98	AML*								4	2	---	---	---	---	
ANKK1	255239	broad.mit.edu	37	11	113265227	113265227	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113265227delG	uc001pny.2	+							NM_178510	NP_848605	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1								ATP binding|protein serine/threonine kinase activity			lung(5)|stomach(1)|ovary(1)|breast(1)	8		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		CTCAGTGGATGGGAGCAAAGG	0.274													4	2	---	---	---	---	
ZBTB16	7704	broad.mit.edu	37	11	114112921	114112921	+	Frame_Shift_Del	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114112921delG	uc001pop.2	+	5	1750	c.1486delG	c.(1486-1488)GGGfs	p.G496fs	ZBTB16_uc001poq.2_Frame_Shift_Del_p.G496fs	NM_006006	NP_005997	Q05516	ZBT16_HUMAN	promyelocytic leukemia zinc finger protein	496	C2H2-type 4.				apoptosis|central nervous system development|mesonephros development|myeloid cell differentiation|negative regulation of myeloid cell differentiation|negative regulation of transcription, DNA-dependent	nuclear speck|PML body|transcriptional repressor complex	protein homodimerization activity|zinc ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)		TCTGCTGTGTGGGAAGCGCTT	0.607													22	28	---	---	---	---	
OAF	220323	broad.mit.edu	37	11	120093632	120093638	+	Intron	DEL	AAAACAA	-	-	rs148248332	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120093632_120093638delAAAACAA	uc001pxb.2	+							NM_178507	NP_848602	Q86UD1	OAF_HUMAN	OAF homolog precursor												0		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)		aaaacaaaacaaaacaaaaaacaaaaa	0.227													2	4	---	---	---	---	
ASAM	79827	broad.mit.edu	37	11	122978511	122978512	+	Intron	INS	-	T	T	rs142071684	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122978511_122978512insT	uc001pyt.2	-							NM_024769	NP_079045	Q9H6B4	CLMP_HUMAN	adipocyte-specific adhesion molecule precursor							integral to membrane|tight junction					0		Breast(109;0.0025)|Lung NSC(97;0.0179)|all_lung(97;0.0182)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.73e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0446)		gctctctcctattttttttttg	0.109													2	4	---	---	---	---	
ST14	6768	broad.mit.edu	37	11	130061114	130061114	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130061114delG	uc001qfw.2	+						ST14_uc010sca.1_Intron	NM_021978	NP_068813	Q9Y5Y6	ST14_HUMAN	matriptase						proteolysis	integral to plasma membrane	serine-type endopeptidase activity			ovary(2)|skin(2)|central_nervous_system(1)	5	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)	ggtggcgcatgcctactcagg	0.000													4	2	---	---	---	---	
LOC100288778	100288778	broad.mit.edu	37	12	80626	80627	+	Intron	INS	-	AG	AG			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80626_80627insAG	uc010scy.1	+						uc010scx.1_Intron|LOC100288778_uc010scz.1_Intron|LOC100288778_uc010sdb.1_Intron					SubName: Full=Actin nucleation promoting factor; Flags: Fragment;												0						CCAATAGTAACAAAGTGCTGGA	0.401													4	4	---	---	---	---	
B4GALNT3	283358	broad.mit.edu	37	12	652300	652301	+	Intron	DEL	TG	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:652300_652301delTG	uc001qii.1	+						B4GALNT3_uc001qij.1_5'UTR	NM_173593	NP_775864	Q6L9W6	B4GN3_HUMAN	beta							Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			ovary(1)|skin(1)	2	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			AGGGAGAGTATGTGTGTGTGTG	0.574													4	2	---	---	---	---	
RAD52	5893	broad.mit.edu	37	12	1060892	1060896	+	5'Flank	DEL	TTCCT	-	-	rs72259033		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1060892_1060896delTTCCT	uc001qis.1	-						RAD52_uc001qit.1_5'Flank|RAD52_uc010sdt.1_5'Flank|RAD52_uc001qiu.1_Intron|RAD52_uc001qiv.1_5'Flank|RAD52_uc001qiw.1_5'Flank|RAD52_uc010sdu.1_5'Flank	NM_134424	NP_602296	P43351	RAD52_HUMAN	RAD52 homolog						DNA recombinase assembly|mitotic recombination|reciprocal meiotic recombination	nucleoplasm	DNA binding|protein binding			central_nervous_system(1)	1	all_cancers(10;0.0119)|all_epithelial(11;0.0171)|all_lung(10;0.0521)|Ovarian(42;0.0816)|Lung NSC(10;0.0987)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.0323)			tcttcatcacttcctttcttctgct	0.000								Homologous_recombination					4	2	---	---	---	---	
ERC1	23085	broad.mit.edu	37	12	1181277	1181278	+	Intron	DEL	AC	-	-	rs66465473		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1181277_1181278delAC	uc001qjb.2	+						ERC1_uc001qiz.2_Intron|ERC1_uc001qjc.2_Intron|ERC1_uc001qja.2_Intron|ERC1_uc001qjd.2_Intron|ERC1_uc001qjf.2_Intron	NM_178040	NP_829884	Q8IUD2	RB6I2_HUMAN	RAB6-interacting protein 2 isoform epsilon						I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(2)|breast(1)	5	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			aaaaaaaaaaacaaaaaaGTGT	0.173													4	2	---	---	---	---	
ERC1	23085	broad.mit.edu	37	12	1579617	1579617	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1579617delT	uc001qjb.2	+						ERC1_uc001qiz.2_Intron|ERC1_uc001qjc.2_Intron|ERC1_uc001qja.2_Intron|ERC1_uc001qjd.2_Intron|ERC1_uc001qjf.2_Intron|ERC1_uc001qje.2_Intron	NM_178040	NP_829884	Q8IUD2	RB6I2_HUMAN	RAB6-interacting protein 2 isoform epsilon						I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(2)|breast(1)	5	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			GTTTTTTTTGTTTTTTTTTTT	0.388													4	2	---	---	---	---	
C1S	716	broad.mit.edu	37	12	7125226	7125227	+	Intron	INS	-	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7125226_7125227insG	uc001qsj.2	+						LPCAT3_uc010sfw.1_Intron|LPCAT3_uc001qsi.2_Intron|LPCAT3_uc009zfp.2_Intron|LPCAT3_uc010sfx.1_Intron|LPCAT3_uc009zfq.1_Intron	NM_201442	NP_958850	P09871	C1S_HUMAN	complement component 1, s subcomponent						complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity			skin(1)	1					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	TGGTTATTAATGACAGAGCAGG	0.540													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	7690085	7690087	+	IGR	DEL	TTG	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7690085_7690087delTTG								CD163 (33671 upstream) : APOBEC1 (111910 downstream)																							gttgttgttcttgttgttgttgt	0.000													3	3	---	---	---	---	
SLCO1A2	6579	broad.mit.edu	37	12	21459958	21459958	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21459958delA	uc001rer.2	-						SLCO1A2_uc001res.2_Intron|SLCO1A2_uc010siq.1_Intron|SLCO1A2_uc010sio.1_Intron|SLCO1A2_uc010sip.1_Intron|SLCO1A2_uc001ret.2_Intron|SLCO1A2_uc001reu.2_Intron	NM_021094	NP_066580	P46721	SO1A2_HUMAN	organic anion transporting polypeptide A						bile acid metabolic process|sodium-independent organic anion transport	integral to membrane|plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(1)|pancreas(1)|ovary(1)|skin(1)	4						TTATTTTAAGAAAGTAATGAG	0.363													13	6	---	---	---	---	
ITPR2	3709	broad.mit.edu	37	12	26831345	26831346	+	Intron	INS	-	AG	AG	rs138760458	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26831345_26831346insAG	uc001rhg.2	-							NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)					AAAGGGAAGACAGAGAGAGAGA	0.371													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	28326164	28326164	+	IGR	DEL	C	-	-	rs66769304		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28326164delC								PTHLH (201248 upstream) : CCDC91 (6046 downstream)																							catgagaactcactatcacga	0.000													3	4	---	---	---	---	
TMTC1	83857	broad.mit.edu	37	12	29696554	29696554	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29696554delT	uc001rjb.2	-						TMTC1_uc001riz.2_Intron|TMTC1_uc001rja.2_Intron|TMTC1_uc001rjc.1_Intron	NM_175861	NP_787057	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat							integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					AAGATCATGGTTTTTTTTGGC	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	31296101	31296102	+	Intron	INS	-	TG	TG	rs140872427	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31296101_31296102insTG	uc010sjy.1	-											RecName: Full=Ovostatin homolog 1; Flags: Precursor;																		ggcataaactctgtgtgtgtgt	0.015													3	4	---	---	---	---	
BICD1	636	broad.mit.edu	37	12	32299743	32299744	+	Intron	INS	-	CCTC	CCTC	rs144676094	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32299743_32299744insCCTC	uc001rku.2	+						BICD1_uc001rkv.2_Intron|BICD1_uc010skd.1_Intron	NM_001714	NP_001705	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 isoform 1						anatomical structure morphogenesis|intracellular mRNA localization|microtubule anchoring at microtubule organizing center|minus-end-directed organelle transport along microtubule|positive regulation of receptor-mediated endocytosis|protein localization to organelle|RNA processing|stress granule assembly|viral reproduction	cytoplasmic vesicle|cytoskeleton|cytosol|host cell viral assembly compartment|membrane|perinuclear region of cytoplasm|trans-Golgi network	cytoskeletal adaptor activity|dynactin binding|dynein binding|proteinase activated receptor binding|Rab GTPase binding|structural constituent of cytoskeleton			large_intestine(1)|central_nervous_system(1)	2	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			cttcctcctttcctccctccct	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	33430899	33430900	+	IGR	INS	-	A	A	rs147296614	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33430899_33430900insA								PKP2 (381119 upstream) : SYT10 (97448 downstream)																							tcctaaactagaaaaaaaccaa	0.050													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	34846657	34846658	+	IGR	DEL	CT	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34846657_34846658delCT								ALG10 (665423 upstream) : None (None downstream)																							ttttgaaacactctttttgtag	0.000													7	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	37883219	37883220	+	IGR	INS	-	G	G	rs147115759	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:37883219_37883220insG								None (None upstream) : ALG10B (827337 downstream)																							gataggattatggggggggtgg	0.054													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	40895493	40895493	+	IGR	DEL	A	-	-	rs62831460		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40895493delA								LRRK2 (132409 upstream) : CNTN1 (190865 downstream)																							AGAACACTAGAAAAAAAAAAA	0.343													4	2	---	---	---	---	
FAM113B	91523	broad.mit.edu	37	12	47617221	47617221	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47617221delT	uc001rpn.2	+						FAM113B_uc010slj.1_Intron|FAM113B_uc001rpq.2_Intron	NM_138371	NP_612380	Q96HM7	F113B_HUMAN	hypothetical protein LOC91523								hydrolase activity			skin(3)|ovary(2)	5	Renal(347;0.138)|Lung SC(27;0.192)					tgcaagcaagttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	52534601	52534601	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52534601delC								C12orf44 (63323 upstream) : KRT80 (28180 downstream)																							TTCACTATTGCAGGAGCTGTC	0.453													4	2	---	---	---	---	
PCBP2	5094	broad.mit.edu	37	12	53868621	53868621	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53868621delT	uc001sdl.3	+						PCBP2_uc001sdc.3_Intron|PCBP2_uc001sdb.3_Intron|PCBP2_uc001sde.3_Intron|PCBP2_uc001sdi.3_Intron|PCBP2_uc001sdd.3_Intron|PCBP2_uc001sdf.3_Intron|PCBP2_uc009zna.2_Intron|PCBP2_uc010soi.1_Intron|PCBP2_uc001sdj.3_Intron|PCBP2_uc010soj.1_Intron|PCBP2_uc001sdk.3_Intron	NM_001128911	NP_001122383	Q15366	PCBP2_HUMAN	poly(rC) binding protein 2 isoform d						innate immune response|negative regulation of defense response to virus|negative regulation of type I interferon production|nuclear mRNA splicing, via spliceosome|proteasomal ubiquitin-dependent protein catabolic process|response to virus	cytosol|nucleoplasm|ribonucleoprotein complex	DNA binding|RNA binding|ubiquitin protein ligase binding				0						CCACCCACCCTTTTTTTTTGT	0.453													4	2	---	---	---	---	
ATF7	11016	broad.mit.edu	37	12	53955114	53955114	+	Intron	DEL	A	-	-	rs143118946		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53955114delA	uc001sdy.2	-						ATF7_uc010sok.1_Intron|ATF7_uc001sdz.2_Intron|ATF7_uc010sol.1_Intron|ATF7_uc001sea.3_Intron|ATF7_uc001seb.3_Intron	NM_001130059	NP_001123531	P17544	ATF7_HUMAN	activating transcription factor 7 isoform 1						interspecies interaction between organisms	cytoplasm|nuclear periphery|nucleoplasm	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)	2						ctgtctctttaaaaaaaaaaa	0.254													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	54329238	54329238	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54329238delC								CALCOCO1 (207931 upstream) : HOXC13 (3338 downstream)																							GCAGCCTGCACCCATCCCTAA	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	56051034	56051035	+	IGR	DEL	GT	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56051034_56051035delGT								OR10P1 (19418 upstream) : METTL7B (24295 downstream)																							GTCCgtgtgagtgtgtgtgtgt	0.391													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	68035715	68035717	+	IGR	DEL	TTC	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68035715_68035717delTTC								CAND1 (327327 upstream) : DYRK2 (6795 downstream)																							CTATCTCTCTTTCttcttcttct	0.044													4	2	---	---	---	---	
PPFIA2	8499	broad.mit.edu	37	12	81923685	81923686	+	Intron	INS	-	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81923685_81923686insA	uc001szo.1	-						PPFIA2_uc010sue.1_Intron|PPFIA2_uc010suh.1_Intron|PPFIA2_uc010sui.1_Intron|PPFIA2_uc010suj.1_Intron|PPFIA2_uc009zsi.1_Intron	NM_003625	NP_003616	B7Z663	B7Z663_HUMAN	PTPRF interacting protein alpha 2											ovary(3)|lung(2)|pancreas(1)	6						acaatctgtacaaaaaaaacca	0.000													4	2	---	---	---	---	
PLXNC1	10154	broad.mit.edu	37	12	94654286	94654286	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94654286delA	uc001tdc.2	+						PLXNC1_uc010sut.1_Intron|PLXNC1_uc009zsv.2_5'Flank	NM_005761	NP_005752	O60486	PLXC1_HUMAN	plexin C1 precursor						axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3						TCTAAACattaaaaaaaaaaa	0.438													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	95096396	95096396	+	IGR	DEL	A	-	-	rs5800168		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95096396delA								TMCC3 (52072 upstream) : MIR492 (131778 downstream)																							aggcagatacaaaATGAGGAA	0.363													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	96897018	96897019	+	Intron	DEL	TC	-	-	rs35808224		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96897018_96897019delTC	uc009ztl.1	+						uc001teq.2_Intron					RecName: Full=Uncharacterized protein C12orf55;																		ttcctttctttctctctctctc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	96931871	96931871	+	5'Flank	DEL	A	-	-	rs34150077		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96931871delA	uc001ter.1	+						uc009ztl.1_Intron|uc001teq.2_Intron					Homo sapiens cDNA FLJ31514 fis, clone NT2RI1000164.																		gccctgtttcaaaaaaaaaaG	0.005													2	4	---	---	---	---	
GNPTAB	79158	broad.mit.edu	37	12	102220580	102220580	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102220580delA	uc001tit.2	-						GNPTAB_uc001tiu.1_Intron|GNPTAB_uc001tiw.2_Intron	NM_024312	NP_077288	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase						cell differentiation	Golgi membrane|integral to membrane|nucleus	metal ion binding|transcription factor binding|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity			ovary(1)|skin(1)	2						TTTCTAAGCTAAAAAGGATCT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	102267076	102267076	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102267076delT								GNPTAB (42444 upstream) : DRAM1 (4029 downstream)																							GTTGATGCCATTTCAATAGTG	0.328													26	14	---	---	---	---	
SLC41A2	84102	broad.mit.edu	37	12	105239817	105239817	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105239817delA	uc001tla.2	-							NM_032148	NP_115524	Q96JW4	S41A2_HUMAN	solute carrier family 41, member 2							integral to membrane|plasma membrane	magnesium ion transmembrane transporter activity			ovary(1)|skin(1)	2						AAATTCAACCAAAAGCAAGCC	0.348													12	7	---	---	---	---	
WDR66	144406	broad.mit.edu	37	12	122419819	122419819	+	Intron	DEL	C	-	-	rs11331568		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122419819delC	uc009zxk.2	+							NM_144668	NP_653269	Q8TBY9	WDR66_HUMAN	WD repeat domain 66								calcium ion binding			ovary(1)|skin(1)	2	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		aatagtagtacctacctccag	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	124577491	124577492	+	IGR	INS	-	TGA	TGA			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124577491_124577492insTGA								ZNF664 (77524 upstream) : FAM101A (196218 downstream)																							gatgatgatggtgatggtgtga	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	125260215	125260215	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125260215delA								NCOR2 (208205 upstream) : SCARB1 (1960 downstream)																							ccatctctacaaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	130660353	130660353	+	IGR	DEL	A	-	-	rs77795996		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130660353delA								FZD10 (10069 upstream) : PIWIL1 (162261 downstream)																							acttcatctcaaaaaaaaaaa	0.184													4	2	---	---	---	---	
GPR133	283383	broad.mit.edu	37	12	131490244	131490244	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131490244delG	uc001uit.3	+						GPR133_uc010tbm.1_Intron	NM_198827	NP_942122	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)|skin(2)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		ACCGTGTGATGCCCTGGGTGA	0.642													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	19371520	19371520	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19371520delG								None (None upstream) : LOC284232 (37023 downstream)																							ctctgaagcagtgacacaagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	23605013	23605014	+	IGR	INS	-	A	A	rs79836101		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23605013_23605014insA								None (None upstream) : SGCG (150046 downstream)																							ccatctcaaagaaaaaaaaaaa	0.109													4	2	---	---	---	---	
B3GALTL	145173	broad.mit.edu	37	13	31821088	31821089	+	Intron	INS	-	T	T	rs71192686		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31821088_31821089insT	uc010aaz.2	+							NM_194318	NP_919299	Q6Y288	B3GLT_HUMAN	beta 1,3-galactosyltransferase-like						fucose metabolic process	endoplasmic reticulum membrane|integral to membrane	transferase activity, transferring glycosyl groups			ovary(2)	2		Lung SC(185;0.0257)		all cancers(112;0.00436)|Epithelial(112;0.0285)|OV - Ovarian serous cystadenocarcinoma(117;0.0512)|GBM - Glioblastoma multiforme(144;0.184)		cttttcttttcttttttttttt	0.302													5	3	---	---	---	---	
STARD13	90627	broad.mit.edu	37	13	34115310	34115310	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34115310delA	uc001uux.2	-							NM_052851	NP_443083	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|lipid particle|mitochondrial membrane	GTPase activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		GGGAAAGTCGAAAAAAAAAAG	0.328													4	4	---	---	---	---	
RFC3	5983	broad.mit.edu	37	13	34501879	34501879	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34501879delG	uc001uva.2	+							NM_181558	NP_853536	P40938	RFC3_HUMAN	replication factor C 3 isoform 2						cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA synthesis involved in DNA repair|nucleotide-excision repair, DNA gap filling|response to organophosphorus|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding				0		Hepatocellular(188;0.0191)|Lung SC(185;0.0548)		all cancers(112;5.09e-06)|Epithelial(112;6.52e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00107)|OV - Ovarian serous cystadenocarcinoma(117;0.0285)|GBM - Glioblastoma multiforme(144;0.123)		AAGGGGCTGAGGGTGAGCTAT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	37374579	37374590	+	IGR	DEL	AAGAAAGAAAGA	-	-	rs138573480		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37374579_37374590delAAGAAAGAAAGA								C13orf36 (102606 upstream) : RFXAP (18749 downstream)																							gtaagaaagtaagaaagaaagaaagaaagaaa	0.000													1	5	---	---	---	---	
FREM2	341640	broad.mit.edu	37	13	39430204	39430205	+	Intron	DEL	AT	-	-	rs140678969	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39430204_39430205delAT	uc001uwv.2	+						FREM2_uc001uww.2_Intron	NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2						cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		AAAAAAAAAAATAGAAAACTTC	0.163													3	3	---	---	---	---	
RCBTB2	1102	broad.mit.edu	37	13	49096544	49096545	+	Intron	DEL	AA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49096544_49096545delAA	uc001vch.2	-						RCBTB2_uc010tgg.1_Intron|RCBTB2_uc001vci.2_Intron|RCBTB2_uc010tgh.1_Intron|RCBTB2_uc001vcj.2_Intron|RCBTB2_uc010acv.1_Intron|RCBTB2_uc010tgi.1_Intron	NM_001268	NP_001259	O95199	RCBT2_HUMAN	regulator of chromosome condensation and BTB								Ran guanyl-nucleotide exchange factor activity			ovary(2)|lung(2)|skin(1)	5		all_cancers(8;4.86e-71)|all_epithelial(8;2.11e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;2.3e-10)|Lung NSC(96;1.07e-07)|Breast(56;1.53e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.00826)|Myeloproliferative disorder(33;0.0179)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(99;1.8e-09)|LUSC - Lung squamous cell carcinoma(3;0.116)		GCTAAGCTGGAAAAAAAAAAGG	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	63637291	63637291	+	IGR	DEL	T	-	-	rs75453829		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63637291delT								None (None upstream) : OR7E156P (674277 downstream)																							AGGACTCTCCTTAACAATGAG	0.358													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	76097893	76097894	+	IGR	DEL	CC	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76097893_76097894delCC								TBC1D4 (41643 upstream) : COMMD6 (1456 downstream)																							tgatcttcctcccaaaaaccca	0.000													4	2	---	---	---	---	
UCHL3	7347	broad.mit.edu	37	13	76123902	76123916	+	5'Flank	DEL	GGCGGCGGCGGCGAA	-	-	rs67763278		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76123902_76123916delGGCGGCGGCGGCGAA	uc001vjq.2	+							NM_006002	NP_005993	P15374	UCHL3_HUMAN	ubiquitin carboxyl-terminal esterase L3						ubiquitin-dependent protein catabolic process	cytoplasm	cysteine-type peptidase activity|ubiquitin binding|ubiquitin thiolesterase activity				0				GBM - Glioblastoma multiforme(99;0.0125)		GggcggaagcggcggcggcggcgaaggcggcggcT	0.581											OREG0022446	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
MYCBP2	23077	broad.mit.edu	37	13	77893245	77893246	+	Intron	DEL	GT	-	-	rs112077311		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77893245_77893246delGT	uc001vkf.2	-						MYCBP2_uc010aev.2_Intron	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		gtttgggaacgtgtgtgtgtgt	0.005													4	3	---	---	---	---	
ABCC4	10257	broad.mit.edu	37	13	95697522	95697522	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95697522delA	uc001vmd.3	-						ABCC4_uc010afj.2_Intron|ABCC4_uc010afk.2_Intron	NM_005845	NP_005836	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)	GGGAAAATTTAAAAAGAAAAT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	100148284	100148284	+	Intron	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100148284delC	uc001voi.1	-											Homo sapiens cDNA FLJ41590 fis, clone CTONG2021132.																		caccaagagtcccgagttgga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	28291707	28291708	+	IGR	INS	-	C	C			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28291707_28291708insC								None (None upstream) : FOXG1 (944579 downstream)																							taataaaaaaaacacaatgaga	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	50519464	50519465	+	IGR	DEL	AC	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50519464_50519465delAC								C14orf182 (45226 upstream) : C14orf183 (30905 downstream)																							gcacacacagacacacacacac	0.361													4	2	---	---	---	---	
FRMD6	122786	broad.mit.edu	37	14	52188463	52188466	+	Intron	DEL	AGGG	-	-	rs12878114	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52188463_52188466delAGGG	uc001wzd.2	+						FRMD6_uc001wzb.2_Intron|FRMD6_uc001wzc.2_Intron|FRMD6_uc001wze.2_Intron|FRMD6_uc001wzf.2_Intron|FRMD6_uc001wzg.2_Intron	NM_152330	NP_689543	Q96NE9	FRMD6_HUMAN	FERM domain containing 6							cytoskeleton|mitochondrion|plasma membrane	binding			ovary(1)|breast(1)|central_nervous_system(1)	3	all_epithelial(31;0.0163)|Breast(41;0.089)					ggaggaaggaagggaggaaggaag	0.186													3	3	---	---	---	---	
GNG2	54331	broad.mit.edu	37	14	52417138	52417139	+	Intron	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52417138_52417139insT	uc001wzi.2	+						GNG2_uc001wzh.2_Intron|GNG2_uc010aoc.1_Intron|GNG2_uc001wzj.2_Intron|GNG2_uc001wzk.2_Intron|GNG2_uc010aob.1_Intron	NM_053064	NP_444292	P59768	GBG2_HUMAN	guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|platelet activation|synaptic transmission	heterotrimeric G-protein complex	protein binding|signal transducer activity				0	all_epithelial(31;0.0659)|Breast(41;0.0684)				Halothane(DB01159)	TTGTGTGTGTGTTTTTTTTCTC	0.450													4	2	---	---	---	---	
CGRRF1	10668	broad.mit.edu	37	14	54989163	54989163	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54989163delT	uc001xay.2	+						CGRRF1_uc010tra.1_Intron|CGRRF1_uc001xaz.2_Intron	NM_006568	NP_006559	Q99675	CGRF1_HUMAN	cell growth regulator with ring finger domain 1						cell cycle arrest|negative regulation of cell proliferation|response to stress		zinc ion binding			ovary(1)	1						attttttaCCTTTTTTTAGGT	0.313													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	66827067	66827067	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66827067delA								FUT8 (617106 upstream) : C14orf53 (126042 downstream)																							ACAAATGAGGACAGGGACCCA	0.428													4	2	---	---	---	---	
RAD51L1	5890	broad.mit.edu	37	14	68632885	68632886	+	Intron	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68632885_68632886insT	uc001xkf.1	+						RAD51L1_uc001xkd.2_Intron|RAD51L1_uc010aqr.2_Intron|RAD51L1_uc001xke.2_Intron|RAD51L1_uc010aqs.1_Intron|RAD51L1_uc001xkg.1_Intron	NM_133509	NP_598193	O15315	RA51B_HUMAN	RAD51-like 1 isoform 3						blood coagulation|DNA repair|reciprocal meiotic recombination	nucleoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0				UCEC - Uterine corpus endometrioid carcinoma (185;0.163)|all cancers(60;3.9e-06)|OV - Ovarian serous cystadenocarcinoma(108;0.000103)|BRCA - Breast invasive adenocarcinoma(234;0.000421)		TATTTCTGCTCTTTTTTTTTTT	0.198			T	HMGA2	lipoma|uterine leiomyoma			Direct_reversal_of_damage|Homologous_recombination					3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	72394370	72394371	+	IGR	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72394370_72394371insT								SIPA1L1 (188252 upstream) : RGS6 (4785 downstream)																							ttcaagaatCCtttttttttct	0.069													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	76772966	76772966	+	IGR	DEL	T	-	-	rs36022800		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76772966delT								C14orf118 (103833 upstream) : ESRRB (64724 downstream)																							aataaatgccttttgtttaag	0.020													6	3	---	---	---	---	
NRXN3	9369	broad.mit.edu	37	14	79888568	79888568	+	Intron	DEL	T	-	-	rs11362359		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79888568delT	uc001xun.2	+						NRXN3_uc001xum.1_Intron|NRXN3_uc001xup.2_Intron|NRXN3_uc001xuq.2_Intron|NRXN3_uc010asw.2_Intron|NRXN3_uc001xur.3_Intron	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		cccccagcaattttttttttg	0.000													3	3	---	---	---	---	
CCDC88C	440193	broad.mit.edu	37	14	91764717	91764717	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91764717delA	uc010aty.2	-							NM_001080414	NP_001073883	Q9P219	DAPLE_HUMAN	DVL-binding protein DAPLE						microtubule cytoskeleton organization|protein destabilization|protein homooligomerization|regulation of protein phosphorylation|Wnt receptor signaling pathway	cytoplasm|insoluble fraction	microtubule binding|PDZ domain binding|protein self-association			ovary(3)	3		all_cancers(154;0.0468)				actccgtctcaaaaaaaaaaa	0.005													4	2	---	---	---	---	
AK7	122481	broad.mit.edu	37	14	96884805	96884806	+	Intron	INS	-	T	T	rs138335137	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96884805_96884806insT	uc001yfn.2	+							NM_152327	NP_689540	Q96M32	KAD7_HUMAN	adenylate kinase 7						cell projection organization	cytosol	adenylate kinase activity|ATP binding|cytidylate kinase activity			ovary(1)	1		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		GGCTCCAGTCATTTTCTCAGGA	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	97239988	97239989	+	IGR	DEL	TG	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97239988_97239989delTG								PAPOLA (206542 upstream) : VRK1 (23695 downstream)																							CTGTGTGGATtgtgtgtgtgtg	0.411													4	2	---	---	---	---	
EVL	51466	broad.mit.edu	37	14	100490953	100490953	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100490953delT	uc001ygt.2	+						EVL_uc001ygv.2_Intron	NM_016337	NP_057421	Q9UI08	EVL_HUMAN	Enah/Vasp-like						actin polymerization or depolymerization|axon guidance|cell surface receptor linked signaling pathway|organ morphogenesis	cytoskeleton|cytosol|focal adhesion|lamellipodium	actin binding|profilin binding|SH3 domain binding			large_intestine(2)|ovary(1)	3		Melanoma(154;0.152)				cacgtgggccttgtgctcctc	0.050													4	2	---	---	---	---	
RAGE	5891	broad.mit.edu	37	14	102741844	102741844	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102741844delT	uc001ylm.2	-						RAGE_uc010txv.1_Intron|RAGE_uc001yln.2_Intron	NM_014226	NP_055041	Q9UQ07	MOK_HUMAN	MAPK/MAK/MRK overlapping kinase						signal transduction	Golgi apparatus	ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4						gagcttgcagtgagcagagat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	104765276	104765277	+	IGR	INS	-	CCAT	CCAT	rs12880037		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104765276_104765277insCCAT								KIF26A (118042 upstream) : C14orf180 (280779 downstream)																							catccatccacccacccaccca	0.000													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106094606	106094607	+	Intron	INS	-	C	C	rs151095596	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106094606_106094607insC	uc010tyt.1	-						uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron					Parts of antibodies, mostly variable regions.												0						TGCTCCTCCTGCCCCCCCTCCC	0.703													5	4	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106236825	106236825	+	RNA	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106236825delC	uc010tyt.1	-	3613		c.57523delG			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Intron|uc001ysf.2_Intron|uc001ysh.1_RNA|uc001ysi.1_RNA					Parts of antibodies, mostly variable regions.												0						TACCTGGGCACCGTGGGCACG	0.637													85	40	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20144995	20144995	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20144995delG								None (None upstream) : GOLGA6L6 (592099 downstream)																							tattctagaaGGATAAATTAT	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20477740	20477741	+	IGR	DEL	CC	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20477740_20477741delCC								None (None upstream) : GOLGA6L6 (259353 downstream)																							CTCCTCTGCTCCCCTCAGCGGG	0.564													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21929570	21929571	+	IGR	INS	-	A	A	rs139686724		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21929570_21929571insA								NF1P1 (794945 upstream) : LOC646214 (2943 downstream)																							TTTGATAAAACAAGCCAGTCAC	0.183													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22464122	22464125	+	IGR	DEL	AATT	-	-	rs78529461		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22464122_22464125delAATT								OR4N3P (49737 upstream) : MIR1268 (49104 downstream)																							tgcttagacaaattaattgtgtca	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22556156	22556157	+	IGR	INS	-	AGT	AGT	rs147967008	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22556156_22556157insAGT								MIR1268 (42876 upstream) : GOLGA8DP (146128 downstream)																							TGAAGGTTCCCAGTAGCTCAGT	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	23409435	23409436	+	Intron	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23409435_23409436insT	uc010uab.1	-						uc002ceb.2_5'Flank	NM_001001413	NP_001001413			golgi autoantigen, golgin subfamily a, 6-like 1																		ttctttctttcttttttttttt	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	24623193	24623193	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24623193delA								PWRN2 (208098 upstream) : PWRN1 (155646 downstream)																							CTCATACTTTATTACTTGAGA	0.333													4	2	---	---	---	---	
UBE3A	7337	broad.mit.edu	37	15	25600931	25600932	+	Intron	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25600931_25600932insT	uc001zaq.2	-						uc001zae.2_Intron|UBE3A_uc001zar.2_Intron|UBE3A_uc001zas.2_Intron|UBE3A_uc001zat.2_Intron	NM_000462	NP_000453	Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A isoform 2						brain development|interspecies interaction between organisms|protein K48-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			upper_aerodigestive_tract(1)|ovary(1)|breast(1)	3		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		TTAGTTACTTGTTTTTTTTTTG	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	26244753	26244755	+	IGR	DEL	TCC	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26244753_26244755delTCC								ATP10A (134436 upstream) : GABRB3 (543940 downstream)																							ctcctcctcttcctcctcctcct	0.118													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	26448185	26448185	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26448185delT								ATP10A (337868 upstream) : GABRB3 (340510 downstream)																							AACTTTCTGCTTCATCTCTTT	0.274													4	2	---	---	---	---	
APBA2	321	broad.mit.edu	37	15	29252105	29252105	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29252105delG	uc001zck.2	+						APBA2_uc010azj.2_Intron|APBA2_uc010uat.1_Intron|APBA2_uc001zcl.2_Intron|APBA2_uc010uas.1_Intron	NM_005503	NP_005494	Q99767	APBA2_HUMAN	amyloid beta A4 precursor protein-binding,						nervous system development|protein transport		protein binding				0		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		ccagcacttcgggaggccgag	0.095													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	32784119	32784120	+	IGR	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32784119_32784120insT								CHRNA7 (322886 upstream) : ARHGAP11A (123225 downstream)																							tgctttcatgctttcttgcttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	33384290	33384290	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33384290delA								FMN1 (24205 upstream) : RYR3 (218887 downstream)																							GACCACGGTTAATACAACGTA	0.403													4	2	---	---	---	---	
SLTM	79811	broad.mit.edu	37	15	59209357	59209357	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59209357delA	uc002afp.2	-						SLTM_uc002afo.2_Intron|SLTM_uc002afq.2_Intron|SLTM_uc010bgd.2_Intron|SLTM_uc002afr.1_Intron	NM_024755	NP_079031	Q9NWH9	SLTM_HUMAN	modulator of estrogen induced transcription						apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding			ovary(1)	1						TGTCCCAAACAAAAAAAGCTT	0.418													4	2	---	---	---	---	
TLN2	83660	broad.mit.edu	37	15	62949484	62949485	+	Intron	DEL	TG	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62949484_62949485delTG	uc002alb.3	+							NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2						cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11						AGTTCTTGTCTGTGTGTGTGTG	0.436													4	2	---	---	---	---	
TLN2	83660	broad.mit.edu	37	15	63134403	63134403	+	3'UTR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63134403delT	uc002alb.3	+	56					TLN2_uc002alc.3_3'UTR|TLN2_uc010uic.1_3'UTR	NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2						cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11						CGTATTAGAATTTTTTTTTTT	0.378													6	3	---	---	---	---	
SMAD6	4091	broad.mit.edu	37	15	67070423	67070424	+	Intron	INS	-	T	T	rs72306005		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67070423_67070424insT	uc002aqf.2	+						SMAD6_uc010bhx.2_Intron|SMAD6_uc002aqg.2_Intron	NM_005585	NP_005576	O43541	SMAD6_HUMAN	SMAD family member 6 isoform 1						BMP signaling pathway|immune response|negative regulation of apoptosis|negative regulation of BMP signaling pathway|negative regulation of caspase activity|negative regulation of pathway-restricted SMAD protein phosphorylation|negative regulation of SMAD protein complex assembly|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of S phase of mitotic cell cycle|response to laminar fluid shear stress|transforming growth factor beta receptor signaling pathway|zygotic specification of dorsal/ventral axis	cytosol|transcription factor complex	co-SMAD binding|I-SMAD binding|R-SMAD binding|sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity|type I activin receptor binding|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding			skin(1)	1						ttttcttttccttttttttttt	0.238													4	2	---	---	---	---	
ADAMTS7	11173	broad.mit.edu	37	15	79056289	79056289	+	Frame_Shift_Del	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79056289delC	uc002bej.3	-	21	4783	c.4572delG	c.(4570-4572)TGGfs	p.W1524fs		NM_014272	NP_055087	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1524	TSP type-1 7.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0						AAGATGTGTACCAGCTGAGGC	0.706													4	2	---	---	---	---	
ARNT2	9915	broad.mit.edu	37	15	80880089	80880089	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80880089delG	uc002bfr.2	+						ARNT2_uc010unm.1_Intron|ARNT2_uc002bfs.2_Intron	NM_014862	NP_055677	Q9HBZ2	ARNT2_HUMAN	aryl hydrocarbon receptor nuclear translocator						central nervous system development|in utero embryonic development|response to hypoxia		aryl hydrocarbon receptor binding|DNA binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(3)|ovary(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.134)			gaattatctaggcacagagaa	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	81454778	81454779	+	IGR	DEL	TC	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81454778_81454779delTC								C15orf26 (13263 upstream) : IL16 (20314 downstream)																							gatcccacattctctctctctc	0.000													4	2	---	---	---	---	
AKAP13	11214	broad.mit.edu	37	15	86108473	86108474	+	Intron	INS	-	A	A	rs71468117		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86108473_86108474insA	uc002blv.1	+						AKAP13_uc002blt.1_Intron|AKAP13_uc002blu.1_Intron	NM_007200	NP_009131	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 2						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9						TCATTGGAATTAAAAAAAAAAA	0.351													5	4	---	---	---	---	
CRTC3	64784	broad.mit.edu	37	15	91176935	91176936	+	Intron	INS	-	TTCT	TTCT	rs143633503	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91176935_91176936insTTCT	uc002bpp.2	+						CRTC3_uc002bpo.2_Intron	NM_022769	NP_073606	Q6UUV7	CRTC3_HUMAN	transducer of regulated CREB protein 3 isoform						interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus			CRTC3/MAML2(26)	salivary_gland(26)|ovary(1)	27	Melanoma(11;0.00551)|Lung NSC(78;0.0931)|all_lung(78;0.163)		BRCA - Breast invasive adenocarcinoma(143;0.0745)			agttttctctgttctttctctc	0.000			T	MAML2	salivary gland mucoepidermoid								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	93872586	93872587	+	Intron	INS	-	A	A	rs139083106	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93872586_93872587insA	uc002bsu.1	+											Homo sapiens cDNA FLJ37033 fis, clone BRACE2011389.																		aaaacaacaacaaaaaaaacaa	0.000													4	2	---	---	---	---	
PCSK6	5046	broad.mit.edu	37	15	101914492	101914493	+	Intron	INS	-	T	T	rs144407744	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101914492_101914493insT	uc002bwy.2	-						PCSK6_uc010bpd.2_Intron|PCSK6_uc010bpe.2_Intron|PCSK6_uc002bxa.2_Intron|PCSK6_uc002bxb.2_Intron|PCSK6_uc002bxc.1_Intron|PCSK6_uc002bxd.1_Intron|PCSK6_uc002bxe.2_Intron|PCSK6_uc002bxf.1_Intron	NM_002570	NP_002561	P29122	PCSK6_HUMAN	paired basic amino acid cleaving system 4						glycoprotein metabolic process|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|regulation of BMP signaling pathway|secretion by cell	cell surface|endomembrane system|endoplasmic reticulum|extracellular matrix|extracellular space|Golgi lumen|membrane|soluble fraction	eukaryotic cell surface binding|heparin binding|nerve growth factor binding|serine-type endopeptidase activity			pancreas(2)	2	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			GCCTCCTCCTATTTTTTTTTCC	0.500													3	3	---	---	---	---	
LMF1	64788	broad.mit.edu	37	16	964678	964679	+	Intron	INS	-	C	C	rs148453221		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:964678_964679insC	uc002ckj.2	-						LMF1_uc010brh.2_Intron|LMF1_uc010bri.2_Intron|LMF1_uc002ckk.2_Intron|LMF1_uc010uuu.1_Intron|LMF1_uc010uuv.1_Intron	NM_022773	NP_073610	Q96S06	LMF1_HUMAN	lipase maturation factor 1							endoplasmic reticulum membrane|integral to membrane					0		Hepatocellular(780;0.00308)				ACTCCCTCCCTCCCATGACCAT	0.584													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	2759339	2759339	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2759339delT								KCTD5 (310 upstream) : PRSS27 (3085 downstream)																							TACAAGGGCCtttttttttcc	0.323													4	2	---	---	---	---	
CLN3	1201	broad.mit.edu	37	16	28497621	28497621	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28497621delG	uc002dpo.2	-						uc010vct.1_Intron|CLN3_uc002dpl.2_Intron|CLN3_uc010vcu.1_Intron|CLN3_uc002dpn.2_Intron|CLN3_uc002dpm.2_Intron|CLN3_uc010vcv.1_Intron|CLN3_uc010byd.2_Intron|CLN3_uc002dpp.2_Intron|CLN3_uc002dpt.1_Intron|CLN3_uc002dpq.1_Intron|CLN3_uc010bye.1_Intron|CLN3_uc002dpr.1_Intron|CLN3_uc010byf.1_Intron|CLN3_uc002dps.1_Intron|CLN3_uc002dpu.1_Intron|CLN3_uc002dpw.1_Intron|CLN3_uc010vcw.1_Intron|CLN3_uc002dqa.2_Intron|CLN3_uc010vcx.1_Intron|CLN3_uc002dpx.1_Intron|CLN3_uc002dpy.1_Intron	NM_000086	NP_000077	Q13286	CLN3_HUMAN	ceroid-lipofuscinosis, neuronal 3						amyloid precursor protein catabolic process|arginine transport|associative learning|autophagic vacuole fusion|cell death|cellular amino acid metabolic process|cytosolic calcium ion homeostasis|galactosylceramide metabolic process|globoside metabolic process|glucosylceramide metabolic process|ionotropic glutamate receptor signaling pathway|lysosomal lumen acidification|lysosomal lumen pH elevation|negative regulation of catalytic activity|negative regulation of macroautophagy|negative regulation of neuron apoptosis|negative regulation of proteolysis|neuromuscular process controlling balance|neurotransmitter metabolic process|protein catabolic process|protein folding|protein processing|receptor-mediated endocytosis|regulation of action potential|sphingomyelin metabolic process|vacuolar transport	autophagic vacuole|caveola|cytosol|early endosome|Golgi membrane|Golgi stack|integral to endoplasmic reticulum membrane|late endosome|lysosomal membrane|membrane fraction|mitochondrion|neuron projection|nucleus|synaptic vesicle|trans-Golgi network	unfolded protein binding				0						ccATGGCCAAGTTTTCTCTCC	0.348													10	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32542680	32542680	+	IGR	DEL	G	-	-	rs112657463		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32542680delG								HERC2P4 (378806 upstream) : TP53TG3B (142161 downstream)																							tggcctcaatgggcaccaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33037352	33037352	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33037352delT								SLC6A10P (140889 upstream) : MIR1826 (928156 downstream)																							TAAATGACAATGAATTTTTTT	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33393749	33393749	+	IGR	DEL	C	-	-	rs139892141	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33393749delC								SLC6A10P (497286 upstream) : MIR1826 (571759 downstream)																							taaaacaaaTCCTGAGGTTTT	0.119													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33917813	33917813	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33917813delA								None (None upstream) : MIR1826 (47695 downstream)																							tagaatctgcaaatggatatt	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33994644	33994644	+	IGR	DEL	A	-	-	rs112521650		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33994644delA								MIR1826 (29052 upstream) : UBE2MP1 (409158 downstream)																							ctgctcaatcaaaagaaaggt	0.000													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33999723	33999723	+	IGR	DEL	A	-	-	rs77214568	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33999723delA								MIR1826 (34131 upstream) : UBE2MP1 (404079 downstream)																							agatgagtagattgcgaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	35033469	35033469	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:35033469delC								LOC146481 (318502 upstream) : None (None downstream)																							AGTTGGGAGGCCAAGCCCAGT	0.607													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46496434	46496434	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46496434delA								None (None upstream) : ANKRD26P1 (6815 downstream)																							AATATTAGTTAAAATCAATTA	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	47816476	47816477	+	IGR	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47816476_47816477insT								PHKB (81043 upstream) : ABCC12 (300407 downstream)																							tgattttattcttttttttttg	0.149													3	3	---	---	---	---	
PLLP	51090	broad.mit.edu	37	16	57304349	57304349	+	Intron	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57304349delC	uc002elg.1	-							NM_015993	NP_057077	Q9Y342	PLLP_HUMAN	plasmolipin							integral to membrane	ion channel activity				0						CCTCTCTATTCCCACTGCTCC	0.627													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	62550595	62550595	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62550595delG								CDH8 (480559 upstream) : None (None downstream)																							tgtaagacttggattttcatc	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	80989228	80989230	+	IGR	DEL	GCT	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80989228_80989230delGCT								CDYL2 (151053 upstream) : C16orf61 (20471 downstream)																							accccactacgctgctgctgctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86671298	86671299	+	IGR	DEL	GA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86671298_86671299delGA								FOXL1 (55995 upstream) : FBXO31 (691645 downstream)																							TCTGGGgagggagagagagaga	0.465													4	2	---	---	---	---	
CA5A	763	broad.mit.edu	37	16	87946911	87946912	+	Intron	INS	-	T	T	rs67239544		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87946911_87946912insT	uc002fkn.1	-							NM_001739	NP_001730	P35218	CAH5A_HUMAN	carbonic anhydrase VA, mitochondrial precursor						one-carbon metabolic process	mitochondrial matrix	carbonate dehydratase activity|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0513)		ATGTTCCAGtcttttttttttt	0.050													4	2	---	---	---	---	
SCARF1	8578	broad.mit.edu	37	17	1540622	1540629	+	Intron	DEL	CTATCTAT	-	-	rs72522019		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1540622_1540629delCTATCTAT	uc002fsz.1	-						SCARF1_uc002fsy.1_Intron|SCARF1_uc002fta.1_Intron|SCARF1_uc010cjv.1_Intron	NM_003693	NP_003684	Q14162	SREC_HUMAN	scavenger receptor class F, member 1 isoform 1						cell adhesion|neuron remodeling|positive regulation of axon regeneration|receptor-mediated endocytosis	integral to membrane	low-density lipoprotein particle binding|scavenger receptor activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		aaaaCAGATCctatctatctatctatct	0.216													4	2	---	---	---	---	
SERPINF2	5345	broad.mit.edu	37	17	1645019	1645020	+	5'Flank	DEL	AC	-	-	rs113747009		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1645019_1645020delAC	uc002ftk.1	+						SERPINF2_uc010vqr.1_5'Flank	NM_000934	NP_000925	P08697	A2AP_HUMAN	alpha-2-antiplasmin isoform a precursor						acute-phase response|fibrinolysis|platelet activation|platelet degranulation|regulation of proteolysis	extracellular space|platelet alpha granule lumen	protease binding|serine-type endopeptidase inhibitor activity				0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)	Streptokinase(DB00086)	GAGGAGCCGGACAGTGAGGGTG	0.663													4	3	---	---	---	---	
SMG6	23293	broad.mit.edu	37	17	2032170	2032171	+	Intron	DEL	AC	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2032170_2032171delAC	uc002fub.1	-						SMG6_uc010vqv.1_Intron	NM_017575	NP_060045	Q86US8	EST1A_HUMAN	Smg-6 homolog, nonsense mediated mRNA decay						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation|telomere maintenance	chromosome, telomeric region|cytosol|nucleolus|telomerase holoenzyme complex	endoribonuclease activity|metal ion binding|protein binding|telomeric DNA binding			central_nervous_system(2)|lung(1)|kidney(1)	4						agacaaaaagacagaaaaagaa	0.134													4	2	---	---	---	---	
TRPV1	7442	broad.mit.edu	37	17	3496434	3496435	+	5'Flank	INS	-	TGTGTG	TGTGTG	rs3039673		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3496434_3496435insTGTGTG	uc010vrr.1	-						TRPV1_uc010vro.1_5'Flank|TRPV1_uc010vrp.1_5'Flank|TRPV1_uc010vrq.1_5'Flank|TRPV1_uc010vrs.1_Intron|TRPV1_uc010vrt.1_Intron|TRPV1_uc010vru.1_Intron	NM_080706	NP_542437	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel,						cell surface receptor linked signaling pathway|chemosensory behavior|thermoception	cell junction|dendritic spine membrane|integral to plasma membrane|postsynaptic membrane	ATP binding|calcium channel activity|calmodulin binding			ovary(1)	1				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	gtgtgtgtctgtgtgtctcact	0.094													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	4394424	4394425	+	IGR	INS	-	T	T	rs112641628		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4394424_4394425insT								SPNS3 (2926 upstream) : SPNS2 (7704 downstream)																							ATTAGTAAAGCttttttttttt	0.252													4	3	---	---	---	---	
FXR2	9513	broad.mit.edu	37	17	7516017	7516017	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7516017delA	uc002gia.1	-						FXR2_uc010vud.1_Intron|SHBG_uc010cmo.2_5'Flank|SHBG_uc010cmp.2_5'Flank|SHBG_uc010cmq.2_5'Flank|SHBG_uc010cmr.2_5'Flank|SHBG_uc010cms.2_5'Flank|SHBG_uc010cmt.2_5'Flank|SHBG_uc010cmu.2_5'Flank	NM_004860	NP_004851	P51116	FXR2_HUMAN	fragile X mental retardation syndrome related							cytosolic large ribosomal subunit	protein binding|RNA binding	p.?(1)			0				READ - Rectum adenocarcinoma(115;0.17)		AAGAGTGAGTAAAAAATGACT	0.219													4	2	---	---	---	---	
TP53	7157	broad.mit.edu	37	17	7578458	7578458	+	Frame_Shift_Del	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7578458delG	uc002gim.2	-	5	666	c.472delC	c.(472-474)CGCfs	p.R158fs	TP53_uc002gig.1_Frame_Shift_Del_p.R158fs|TP53_uc002gih.2_Frame_Shift_Del_p.R158fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.R26fs|TP53_uc010cng.1_Frame_Shift_Del_p.R26fs|TP53_uc002gii.1_Frame_Shift_Del_p.R26fs|TP53_uc010cnh.1_Frame_Shift_Del_p.R158fs|TP53_uc010cni.1_Frame_Shift_Del_p.R158fs|TP53_uc002gij.2_Frame_Shift_Del_p.R158fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Del_p.R65fs|TP53_uc002gio.2_Frame_Shift_Del_p.R26fs|TP53_uc010vug.1_Frame_Shift_Del_p.R119fs	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	158	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> F (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> C (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).|R -> Q (in a sporadic cancer; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.R158H(58)|p.R158L(53)|p.R158C(17)|p.R158G(10)|p.R158P(9)|p.0?(7)|p.R158R(6)|p.R158fs*12(5)|p.R158_A159insX(4)|p.R158_A159delRA(2)|p.R156_I162delRVRAMAI(2)|p.V157fs*9(2)|p.P153fs*22(2)|p.R158fs*11(2)|p.V157fs*22(2)|p.V157_C176del20(1)|p.R156_A161delRVRAMA(1)|p.V157_R158delVR(1)|p.P151_V173del23(1)|p.R158fs*24(1)|p.R156_R158delRVR(1)|p.R156fs*18(1)|p.R156_A161del(1)|p.R158_A159insXX(1)|p.V157_M160delVRAM(1)|p.R156fs*12(1)|p.R158F(1)|p.S149fs*72(1)|p.A159fs*21(1)|p.T155_A161delTRVRAMA(1)|p.G154fs*22(1)|p.R156fs*20(1)|p.V157_I162delVRAMAI(1)|p.V157fs*21(1)|p.R158fs*8(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		GCCATGGCGCGGACGCGGGTG	0.622		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			13	15	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	8629216	8629216	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8629216delA								MYH10 (95180 upstream) : CCDC42 (4031 downstream)																							TCTTGCTGGGAAAAACTCCAG	0.463													4	2	---	---	---	---	
GAS7	8522	broad.mit.edu	37	17	10040441	10040442	+	Intron	INS	-	AG	AG	rs142234371	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10040441_10040442insAG	uc002gmg.1	-							NM_201433	NP_958839	O60861	GAS7_HUMAN	growth arrest-specific 7 isoform c						cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			lung(1)|pancreas(1)	2						aaaagaaaaaaagagagagaga	0.000			T	MLL	AML*								4	3	---	---	---	---	
PIRT	644139	broad.mit.edu	37	17	10740888	10740889	+	Intron	INS	-	CTT	CTT	rs138825049	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10740888_10740889insCTT	uc010col.2	-							NM_001101387	NP_001094857	P0C851	PIRT_HUMAN	phosphoinositide-interacting regulator of							integral to membrane				ovary(1)	1						TGGCTTTTTTGCTTCTTCCACT	0.569													4	3	---	---	---	---	
SHISA6	388336	broad.mit.edu	37	17	11223986	11223992	+	Intron	DEL	AAGAGAG	-	-	rs79695861		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11223986_11223992delAAGAGAG	uc002gna.3	+						SHISA6_uc002gnb.3_Intron|SHISA6_uc010com.2_Intron	NM_207386	NP_997269	Q6ZSJ9	SHSA6_HUMAN	shisa homolog 6							integral to membrane				breast(1)	1						caaaaaaaaaaagagagagagagagag	0.203													3	4	---	---	---	---	
HS3ST3A1	9955	broad.mit.edu	37	17	13446734	13446735	+	Intron	INS	-	T	T	rs149309119	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13446734_13446735insT	uc002gob.1	-							NM_006042	NP_006033	Q9Y663	HS3SA_HUMAN	heparan sulfate D-glucosaminyl							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity			ovary(1)|central_nervous_system(1)	2		all_lung(20;0.114)		UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		GAGAAAAAATATTTTTTTTTCT	0.203													4	2	---	---	---	---	
MAP2K3	5606	broad.mit.edu	37	17	21210484	21210485	+	Intron	INS	-	A	A	rs143826793		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21210484_21210485insA	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron|MAP2K3_uc002gyu.2_Intron	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		cctctataatcagctgggtttt	0.000													5	3	---	---	---	---	
MAP2K3	5606	broad.mit.edu	37	17	21216528	21216528	+	Intron	DEL	G	-	-	rs5819746		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21216528delG	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron|MAP2K3_uc002gyu.2_Intron	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		GAGCATTGCAGCCCCATTTTG	0.463													2	4	---	---	---	---	
MAP2K3	5606	broad.mit.edu	37	17	21218380	21218381	+	3'UTR	INS	-	C	C	rs140342400	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21218380_21218381insC	uc002gys.2	+	12					MAP2K3_uc002gyt.2_3'UTR|MAP2K3_uc002gyu.2_3'UTR	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		CAGCTCACTCTCCCTGAGGACT	0.530													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21333424	21333424	+	IGR	DEL	C	-	-	rs111937714		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21333424delC								KCNJ12 (10245 upstream) : C17orf51 (98148 downstream)																							taaccacagaccttttcacca	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21347043	21347044	+	IGR	DEL	AG	-	-	rs111380221		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21347043_21347044delAG								KCNJ12 (23864 upstream) : C17orf51 (84528 downstream)																							aagcacaggcagagttaattta	0.000													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21548062	21548062	+	IGR	DEL	G	-	-	rs148427516		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21548062delG								C17orf51 (70331 upstream) : FAM27L (277308 downstream)																							aaaattagctgggcgtggttg	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21549031	21549032	+	IGR	INS	-	G	G	rs149320251		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21549031_21549032insG								C17orf51 (71300 upstream) : FAM27L (276338 downstream)																							CCCTGTGGCCAGGGGCACAGCT	0.114													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21563646	21563646	+	IGR	DEL	T	-	-	rs9901273	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21563646delT								C17orf51 (85915 upstream) : FAM27L (261724 downstream)																							TCCAAAAAAATAAAAGGATAG	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	22258033	22258033	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:22258033delT								FLJ36000 (344963 upstream) : None (None downstream)																							tgaaacactcttttagtagaa	0.000													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25297755	25297756	+	IGR	INS	-	GA	GA	rs74789093		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25297755_25297756insGA								None (None upstream) : WSB1 (323350 downstream)																							tgtgtgtgtgtgagagtgtgtg	0.025													4	2	---	---	---	---	
RHBDL3	162494	broad.mit.edu	37	17	30621147	30621148	+	Intron	INS	-	A	A	rs72151087		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30621147_30621148insA	uc002hhe.1	+						RHBDL3_uc010csw.1_Intron|RHBDL3_uc010csx.1_Intron|RHBDL3_uc010csy.1_Intron|RHBDL3_uc002hhf.1_Intron	NM_138328	NP_612201	P58872	RHBL3_HUMAN	rhomboid protease 3						proteolysis	integral to membrane	calcium ion binding|serine-type endopeptidase activity			ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)				aactccatctcaaaaaaaaaaa	0.223													5	3	---	---	---	---	
SLFN5	162394	broad.mit.edu	37	17	33576663	33576664	+	Intron	DEL	TT	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33576663_33576664delTT	uc002hjf.3	+						SLFN5_uc002hje.2_Intron|SLFN5_uc010wcg.1_Intron	NM_144975	NP_659412	Q08AF3	SLFN5_HUMAN	schlafen family member 5						cell differentiation		ATP binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0191)		actgtagcccttggtccctgac	0.000													4	2	---	---	---	---	
AP2B1	163	broad.mit.edu	37	17	33931783	33931783	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33931783delA	uc002hjr.2	+						AP2B1_uc002hjq.2_Intron|AP2B1_uc010wci.1_Intron|AP2B1_uc002hjs.2_Intron|AP2B1_uc002hjt.2_Intron|AP2B1_uc010ctv.2_Intron	NM_001282	NP_001273	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1						axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|vesicle-mediated transport|viral reproduction	clathrin adaptor complex|coated pit|cytosol|endocytic vesicle membrane|plasma membrane	clathrin binding|protein transporter activity			ovary(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		tctcaaaaagaaaaaaaaGGA	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	36310516	36310517	+	IGR	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36310516_36310517insT								TBC1D3 (15418 upstream) : MRPL45 (142481 downstream)																							taggtatggtatttttttttga	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	36405891	36405891	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36405891delA	uc002hpx.2	-											Homo sapiens cDNA FLJ43844 fis, clone TESTI4006308, highly  similar to Puromycin-sensitive aminopeptidase (EC 3.4.11.-).																		actctgtctcaaaaaaaaaaa	0.010													4	2	---	---	---	---	
FBXL20	84961	broad.mit.edu	37	17	37539844	37539844	+	Intron	DEL	T	-	-	rs11338157		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37539844delT	uc010wed.1	-						FBXL20_uc002hrt.2_Intron|FBXL20_uc010cvu.2_Intron	NM_032875	NP_116264	Q96IG2	FXL20_HUMAN	F-box and leucine-rich repeat protein 20							cytoplasm				ovary(1)	1			LUAD - Lung adenocarcinoma(14;0.146)			CTTTATATGCttttttttttt	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	38620745	38620748	+	IGR	DEL	AGGA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38620745_38620748delAGGA								IGFBP4 (6764 upstream) : TNS4 (11334 downstream)																							TTCATTTGGGAGGAAGGAAGGAAG	0.534													4	2	---	---	---	---	
TUBG1	7283	broad.mit.edu	37	17	40763873	40763874	+	Intron	INS	-	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40763873_40763874insA	uc002ian.2	+							NM_001070	NP_001061	P23258	TBG1_HUMAN	tubulin, gamma 1						G2/M transition of mitotic cell cycle|meiotic spindle organization|protein polymerization	condensed nuclear chromosome|cytosol|gamma-tubulin complex|polar microtubule	GTP binding|GTPase activity|protein binding|structural constituent of cytoskeleton			ovary(1)	1		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.129)		gactccatcgcaaaaaaaaata	0.050													4	2	---	---	---	---	
DHX8	1659	broad.mit.edu	37	17	41559913	41559915	+	5'Flank	DEL	TTG	-	-	rs68095178		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41559913_41559915delTTG	uc002idu.1	+						DHX8_uc010wif.1_5'Flank|DHX8_uc010wig.1_5'Flank	NM_004941	NP_004932	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8							catalytic step 2 spliceosome	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)|pancreas(1)	4		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		GGAATAAGGTTTGTTGTTGTTTT	0.261													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	43660333	43660333	+	IGR	DEL	A	-	-	rs112348572		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43660333delA								LRRC37A4 (64817 upstream) : LOC644172 (17158 downstream)																							agactcctttaaaaaaaaaaa	0.124													4	2	---	---	---	---	
SKAP1	8631	broad.mit.edu	37	17	46345855	46345856	+	Intron	INS	-	T	T	rs138700234	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46345855_46345856insT	uc002ini.1	-						SKAP1_uc002inj.1_Intron|SKAP1_uc010dbd.1_Intron|SKAP1_uc010dbe.1_Intron	NM_003726	NP_003717	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1 isoform						positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway	cytoplasm|nucleus|plasma membrane	antigen binding|protein kinase binding|SH2 domain binding				0						ATTCAAGTTAAtttttttttgt	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	46567598	46567599	+	IGR	INS	-	A	A	rs71366886		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46567598_46567599insA								SKAP1 (60004 upstream) : HOXB1 (39208 downstream)																							gactccgtctcaaaaaaaaaaa	0.183													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	48865642	48865642	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48865642delC								C17orf73 (20724 upstream) : WFIKKN2 (46369 downstream)																							ttcgtggtcgccatggtggtc	0.000													5	4	---	---	---	---	
SPAG9	9043	broad.mit.edu	37	17	49188954	49188955	+	Intron	INS	-	T	T	rs140370555	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49188954_49188955insT	uc002itc.2	-						SPAG9_uc002itb.2_Intron|SPAG9_uc002itd.2_Intron	NM_001130528	NP_001124000	O60271	JIP4_HUMAN	sperm associated antigen 9 isoform 1						positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm				lung(4)|breast(1)	5			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			CTCTTTTGTGAtttttttttgt	0.213													4	2	---	---	---	---	
UTP18	51096	broad.mit.edu	37	17	49361746	49361746	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49361746delT	uc002its.2	+							NM_016001	NP_057085	Q9Y5J1	UTP18_HUMAN	UTP18, small subunit processome component						rRNA processing	nucleolus					0			BRCA - Breast invasive adenocarcinoma(22;2.09e-07)			GTGTTTAGCCTTTTTTTTTTA	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	49659730	49659731	+	IGR	DEL	TG	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49659730_49659731delTG								UTP18 (284440 upstream) : CA10 (47944 downstream)																							tgtgtgtgtatgtgtgtgtgtg	0.020													4	2	---	---	---	---	
CA10	56934	broad.mit.edu	37	17	49997774	49997774	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49997774delA	uc002itw.3	-						CA10_uc002itv.3_Intron|CA10_uc002itx.3_Intron|CA10_uc002ity.3_Intron|CA10_uc002itz.2_Intron	NM_020178	NP_064563	Q9NS85	CAH10_HUMAN	carbonic anhydrase X						brain development					ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)			agaaaaggctaagagagtaaa	0.075													4	2	---	---	---	---	
CA10	56934	broad.mit.edu	37	17	50189551	50189552	+	Intron	INS	-	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50189551_50189552insA	uc002itw.3	-						CA10_uc002itv.3_Intron|CA10_uc002itx.3_Intron|CA10_uc002ity.3_Intron|CA10_uc002itz.2_Intron	NM_020178	NP_064563	Q9NS85	CAH10_HUMAN	carbonic anhydrase X						brain development					ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)			AGAAGAAAAAGAAAAAAAAAAA	0.317													4	2	---	---	---	---	
CA4	762	broad.mit.edu	37	17	58246612	58246612	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58246612delA	uc010wou.1	+									P22748	CAH4_HUMAN	Homo sapiens cDNA FLJ76600 complete cds, highly similar to Homo sapiens carbonic anhydrase IV (CA4), mRNA.						bicarbonate transport|one-carbon metabolic process	anchored to external side of plasma membrane|apical plasma membrane|brush border membrane|ER-Golgi intermediate compartment|membrane fraction|perinuclear region of cytoplasm|rough endoplasmic reticulum|secretory granule membrane|trans-Golgi network|transport vesicle membrane	carbonate dehydratase activity|protein binding|zinc ion binding				0	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.83e-12)|all cancers(12;6.83e-11)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Topiramate(DB00273)|Trichlormethiazide(DB01021)	cctctgtctcaaaaaaaaaaa	0.129													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	59664647	59664648	+	IGR	INS	-	A	A	rs148343360	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59664647_59664648insA								TBX4 (102178 upstream) : NACA2 (3146 downstream)																							TAAACAGGTAGAAAAATGGATT	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	60901951	60901954	+	IGR	DEL	TGTG	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60901951_60901954delTGTG								MARCH10 (16246 upstream) : MIR633 (119622 downstream)																							CACCTCTATAtgtgtgtgtgtgtg	0.147													4	2	---	---	---	---	
CACNG4	27092	broad.mit.edu	37	17	64978625	64978625	+	Intron	DEL	T	-	-	rs34429901		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64978625delT	uc002jft.1	+							NM_014405	NP_055220	Q9UBN1	CCG4_HUMAN	voltage-dependent calcium channel gamma-4						membrane depolarization|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane	voltage-gated calcium channel activity			central_nervous_system(1)	1	all_cancers(12;9.86e-11)		BRCA - Breast invasive adenocarcinoma(6;1.35e-07)			gattggcgtgttttacaatcg	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	72602056	72602056	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72602056delA								C17orf77 (11708 upstream) : CD300E (6656 downstream)																							TCAAAGAGGTAATAATAATTA	0.473													4	2	---	---	---	---	
SEPT9	10801	broad.mit.edu	37	17	75340267	75340267	+	Intron	DEL	A	-	-	rs66779838		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75340267delA	uc002jts.3	+						SEPT9_uc010wtk.1_Intron|SEPT9_uc002jtt.3_Intron|SEPT9_uc002jtu.3_Intron	NM_001113491	NP_001106963	Q9UHD8	SEPT9_HUMAN	septin 9 isoform a						cell cycle|cell division|protein heterooligomerization	microtubule|perinuclear region of cytoplasm|stress fiber	GTP binding|GTPase activity|protein binding|protein binding			breast(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(99;0.153)			gccacaaaacaaaaaaaaaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	76243689	76243690	+	IGR	INS	-	TT	TT			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76243689_76243690insTT								LOC283999 (6622 upstream) : SOCS3 (109169 downstream)																							gcctggcttcattttttttttt	0.149													4	2	---	---	---	---	
RPTOR	57521	broad.mit.edu	37	17	78565616	78565616	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78565616delG	uc002jyt.1	+						RPTOR_uc002jys.2_Intron|RPTOR_uc010wuf.1_Intron|RPTOR_uc010wug.1_Intron|RPTOR_uc002jyr.1_Intron	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor isoform 1						cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)|ovary(1)	6						tttcatgggagggggattagg	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	79505636	79505636	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79505636delT								FSCN2 (1481 upstream) : C17orf70 (1275 downstream)																							GTAGATCTCCTTTTTGTTCCA	0.607													4	2	---	---	---	---	
CCDC57	284001	broad.mit.edu	37	17	80092984	80092984	+	Intron	DEL	T	-	-	rs79085323		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80092984delT	uc002kdx.1	-						CCDC57_uc002kdy.2_Intron	NM_198082	NP_932348	Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57											ovary(2)	2	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			GAAACAGACAttttttttttt	0.169													4	2	---	---	---	---	
CCDC57	284001	broad.mit.edu	37	17	80172907	80172907	+	5'Flank	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80172907delA	uc002kdz.1	-						CCDC57_uc002kdx.1_5'Flank	NM_198082	NP_932348	Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57											ovary(2)	2	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			ccctgtctccaaaaaaaaCCC	0.045													4	2	---	---	---	---	
TBCD	6904	broad.mit.edu	37	17	80824514	80824514	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80824514delG	uc002kfz.2	+						TBCD_uc002kfx.1_Intron|TBCD_uc002kfy.1_Intron	NM_005993	NP_005984	Q9BTW9	TBCD_HUMAN	beta-tubulin cofactor D						'de novo' posttranslational protein folding|adherens junction assembly|negative regulation of cell-substrate adhesion|negative regulation of microtubule polymerization|post-chaperonin tubulin folding pathway|tight junction assembly	adherens junction|cytoplasm|lateral plasma membrane|microtubule|tight junction	beta-tubulin binding|chaperone binding|GTPase activator activity				0	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			GGCCTGGCCTGGAAGGAGGCT	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	1646695	1646696	+	IGR	INS	-	T	T	rs144529535	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1646695_1646696insT								C18orf2 (239514 upstream) : METTL4 (890829 downstream)																							tttgttcaatatatgttCAATA	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	3045759	3045759	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3045759delG								LPIN2 (33814 upstream) : MYOM1 (21047 downstream)																							CTATGTGACagggagttggaa	0.194													4	2	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	4253984	4253984	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4253984delT	uc010wyz.1	-							NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				TCCCCATTCCTTTCTGAAATT	0.413													4	2	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	4280842	4280842	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4280842delG	uc010wyz.1	-							NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				AATACTTGATGACTGATTAGC	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	7552290	7552290	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7552290delT								LRRC30 (320249 upstream) : PTPRM (15024 downstream)																							attttttgtatttttagtaga	0.000													4	2	---	---	---	---	
RALBP1	10928	broad.mit.edu	37	18	9479327	9479327	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9479327delT	uc002kob.2	+						RALBP1_uc002koc.2_Intron	NM_006788	NP_006779	Q15311	RBP1_HUMAN	ralA binding protein 1						chemotaxis|positive regulation of Cdc42 GTPase activity|small GTPase mediated signal transduction|transport	cytosol|membrane	ATPase activity, coupled to movement of substances|Rac GTPase activator activity|Rac GTPase binding|Ral GTPase binding			central_nervous_system(1)	1						ttttttggtattttttttttt	0.000													4	2	---	---	---	---	
VAPA	9218	broad.mit.edu	37	18	9924184	9924184	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9924184delA	uc002kok.2	+						VAPA_uc002koj.2_Intron	NM_194434	NP_919415	Q9P0L0	VAPA_HUMAN	vesicle-associated membrane protein-associated						cell death|cellular membrane fusion|neuron projection development|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein localization in endoplasmic reticulum|sphingolipid metabolic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane|vesicle	protein heterodimerization activity|signal transducer activity|structural molecule activity				0						TCTAAATAATAAAAAAAAAAG	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	10952870	10952870	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10952870delT								FAM38B (250891 upstream) : GNAL (736266 downstream)																							cttcccttccttccttccttc	0.000													4	2	---	---	---	---	
PTPN2	5771	broad.mit.edu	37	18	12834720	12834721	+	Intron	INS	-	A	A	rs140091439	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12834720_12834721insA	uc002krp.2	-						PTPN2_uc002krl.2_Intron|PTPN2_uc002krn.2_Intron|PTPN2_uc002kro.2_Intron|PTPN2_uc002krm.2_Intron	NM_002828	NP_002819	P17706	PTN2_HUMAN	protein tyrosine phosphatase, non-receptor type						interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway	endoplasmic reticulum|nucleoplasm	protein binding			skin(2)	2		Lung NSC(161;8.94e-06)				CAGACTGGAGGAGAAAAAAAAA	0.376													4	2	---	---	---	---	
CABLES1	91768	broad.mit.edu	37	18	20731275	20731275	+	Intron	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20731275delC	uc002kuc.2	+						CABLES1_uc002kub.2_Intron	NM_001100619	NP_001094089	Q8TDN4	CABL1_HUMAN	Cdk5 and Abl enzyme substrate 1 isoform 2						blood coagulation|cell cycle|cell division|regulation of cell cycle|regulation of cell division	cytosol|nucleus	cyclin-dependent protein kinase regulator activity|protein binding			breast(1)	1	all_cancers(21;0.000102)|all_epithelial(16;2.48e-06)|Lung NSC(20;0.00696)|all_lung(20;0.0197)|Colorectal(14;0.0202)|Ovarian(20;0.127)					agccactgtgccgggcctccc	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	21068704	21068704	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21068704delA								RIOK3 (5607 upstream) : C18orf8 (14758 downstream)																							actccatctcaaaaaaaaaaa	0.015													4	2	---	---	---	---	
TTC39C	125488	broad.mit.edu	37	18	21698619	21698619	+	Intron	DEL	T	-	-	rs67869116		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21698619delT	uc002kuw.2	+						TTC39C_uc002kuu.2_Intron	NM_001135993	NP_001129465	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C isoform 1								binding			ovary(1)	1						AGTGTGTTAAttttttttttt	0.154													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	26378976	26378976	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26378976delT								CDH2 (621531 upstream) : None (None downstream)																							agtacagacattaggggcctg	0.000													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	26889623	26889623	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26889623delG								None (None upstream) : MIR302F (989253 downstream)																							AATAGTGTCTGAAGGGCAAGG	0.423													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	28243079	28243080	+	IGR	INS	-	CTC	CTC	rs145986095	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28243079_28243080insCTC								MIR302F (364153 upstream) : DSC3 (326973 downstream)																							tcatgaatgaactcctattcac	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	31047905	31047906	+	IGR	DEL	GT	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31047905_31047906delGT								C18orf34 (27220 upstream) : ASXL3 (110635 downstream)																							gtgtttgtgcgtgtgtgtgtgt	0.223													4	2	---	---	---	---	
CELF4	56853	broad.mit.edu	37	18	35119587	35119590	+	Intron	DEL	AGTC	-	-	rs76481694		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35119587_35119590delAGTC	uc002lae.2	-						CELF4_uc010dnd.1_Intron|CELF4_uc002lag.2_Intron|CELF4_uc002laf.2_Intron|CELF4_uc002lai.2_Intron	NM_020180	NP_064565	Q9BZC1	CELF4_HUMAN	bruno-like 4, RNA binding protein isoform 1						embryo development|germ cell development|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	BRE binding|nucleotide binding|translation repressor activity, nucleic acid binding			ovary(2)	2						CACTCTTGTTAGTCAGTGCACACG	0.309													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	38102070	38102071	+	IGR	INS	-	A	A	rs145712912	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38102070_38102071insA								LOC647946 (721788 upstream) : KC6 (958167 downstream)																							aacaaaaaaacaaaacaaaaaa	0.139													1	5	---	---	---	---	
ZBTB7C	201501	broad.mit.edu	37	18	45655723	45655724	+	Intron	DEL	AA	-	-	rs71840389		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45655723_45655724delAA	uc010dnv.2	-						ZBTB7C_uc002ldb.2_Intron|ZBTB7C_uc010dnu.2_Intron|ZBTB7C_uc010dnw.2_Intron|ZBTB7C_uc010dnx.1_Intron|ZBTB7C_uc010dny.1_Intron|ZBTB7C_uc010dnz.1_Intron|ZBTB7C_uc010dob.1_Intron|ZBTB7C_uc010doc.1_Intron|ZBTB7C_uc010dod.1_Intron|ZBTB7C_uc010doe.1_Intron|ZBTB7C_uc010dof.1_Intron|ZBTB7C_uc010dog.1_Intron|ZBTB7C_uc010doh.1_Intron|ZBTB7C_uc010doi.1_Intron|ZBTB7C_uc010doj.1_Intron|ZBTB7C_uc010dok.1_Intron|ZBTB7C_uc010dol.1_Intron|ZBTB7C_uc010doa.1_Intron|ZBTB7C_uc010don.1_Intron|ZBTB7C_uc010doo.1_Intron|ZBTB7C_uc010dop.1_Intron|ZBTB7C_uc010doq.1_Intron|ZBTB7C_uc010dor.1_Intron|ZBTB7C_uc010dos.1_Intron|ZBTB7C_uc010dot.1_Intron|ZBTB7C_uc010dou.1_Intron|ZBTB7C_uc010dom.1_Intron	NM_001039360	NP_001034449	A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C							intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1						GAGAAAGTCCAAAAAAAAAAAA	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	48064380	48064380	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48064380delT								SKA1 (143846 upstream) : MAPK4 (22104 downstream)																							gatgagttggtgcacctatgc	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	49486385	49486386	+	IGR	INS	-	G	G	rs139438624	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49486385_49486386insG								MEX3C (762695 upstream) : DCC (380185 downstream)																							caatggcccttattttatttca	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	54033661	54033661	+	IGR	DEL	C	-	-	rs36075754		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54033661delC								TCF4 (730476 upstream) : TXNL1 (236394 downstream)																							ttcaacttttccccactcaat	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	56855705	56855705	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56855705delT								SEC11C (29644 upstream) : GRP (31695 downstream)																							ttgcagattattttgcagagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	64354449	64354450	+	IGR	DEL	CA	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64354449_64354450delCA								CDH19 (83233 upstream) : DSEL (819369 downstream)																							atgacacatccacagagtcttc	0.233													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	65933900	65933901	+	IGR	DEL	AC	-	-	rs34306963		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65933900_65933901delAC								DSEL (749933 upstream) : TMX3 (407026 downstream)																							CTacaaacaaacacacacacac	0.317													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	67518139	67518140	+	IGR	INS	-	A	A	rs5825975		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67518139_67518140insA								DOK6 (2314 upstream) : CD226 (12055 downstream)																							ttccCCGCCCCGGCCACCCCAC	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	68662643	68662643	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68662643delA								SOCS6 (665209 upstream) : None (None downstream)																							agctggctgcaaaaatttgca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	71224540	71224540	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71224540delT								NETO1 (689730 upstream) : FBXO15 (516048 downstream)																							ttcatctcccttacagaccca	0.000													4	2	---	---	---	---	
ZNF516	9658	broad.mit.edu	37	18	74100512	74100513	+	Intron	INS	-	C	C	rs147060824	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74100512_74100513insC	uc010dqx.1	-						ZNF516_uc002lme.2_Intron	NM_014643	NP_055458	Q92618	ZN516_HUMAN	zinc finger protein 516						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)		ccatgagccatcatgtacattg	0.000													3	3	---	---	---	---	
MBP	4155	broad.mit.edu	37	18	74805937	74805938	+	Intron	INS	-	T	T	rs74182685		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74805937_74805938insT	uc010xfd.1	-						MBP_uc002lmr.2_Intron	NM_001025101	NP_001020272	P02686	MBP_HUMAN	Golli-mbp isoform 1						central nervous system development|immune response|synaptic transmission	plasma membrane	structural constituent of myelin sheath			haematopoietic_and_lymphoid_tissue(1)	1		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.79e-06)|BRCA - Breast invasive adenocarcinoma(31;0.113)|READ - Rectum adenocarcinoma(1;0.188)		tttttttcttcttttttttttt	0.183													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	75681073	75681073	+	IGR	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75681073delC								GALR1 (698979 upstream) : None (None downstream)																							TGGATGTCTTCCCTCCCAGAG	0.617													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	2858046	2858046	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2858046delG								ZNF555 (3840 upstream) : ZNF556 (9287 downstream)																							aagtgagccaggcggggtggt	0.000													4	2	---	---	---	---	
ANKRD24	170961	broad.mit.edu	37	19	4193495	4193497	+	Intron	DEL	AAG	-	-	rs72198066		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4193495_4193497delAAG	uc010dtt.1	+						ANKRD24_uc002lzs.2_Intron	NM_133475	NP_597732	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24												0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		tttgaaggacaagaaggaggcta	0.010													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	5494756	5494756	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5494756delA								ZNRF4 (37890 upstream) : PLAC2 (63424 downstream)																							actcggacttaaaaaaaaaaa	0.189													4	2	---	---	---	---	
ACSBG2	81616	broad.mit.edu	37	19	6138686	6138688	+	Intron	DEL	CGG	-	-	rs74833622		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6138686_6138688delCGG	uc002mef.1	+						ACSBG2_uc002mee.1_Intron|ACSBG2_uc002meg.1_Intron|ACSBG2_uc002meh.1_Intron|ACSBG2_uc002mei.1_Intron|ACSBG2_uc010xiz.1_Intron	NM_030924	NP_112186	Q5FVE4	ACBG2_HUMAN	bubblegum-related acyl-CoA synthetase 2						cell differentiation|fatty acid metabolic process|multicellular organismal development|spermatogenesis	membrane|microsome|mitochondrion	acyl-CoA thioesterase activity|ATP binding|long-chain fatty acid-CoA ligase activity			ovary(1)	1						aaggcagggacggagggaggaag	0.000													4	2	---	---	---	---	
INSR	3643	broad.mit.edu	37	19	7239305	7239306	+	Intron	INS	-	C	C	rs144182683	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7239305_7239306insC	uc002mgd.1	-						INSR_uc002mge.1_Intron|INSR_uc002mgf.2_Intron	NM_000208	NP_000199	P06213	INSR_HUMAN	insulin receptor isoform Long precursor						activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	AAAAGGCCCAGCCCCCCCACCC	0.356													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	7721629	7721629	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7721629delT								STXBP2 (8871 upstream) : RETN (12343 downstream)																							GCCTGGTGACttttttttttt	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	11378356	11378357	+	IGR	DEL	AG	-	-	rs36044805		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11378356_11378357delAG								DOCK6 (5199 upstream) : TSPAN16 (28467 downstream)																							ttttggagacagggtcttgctc	0.000													3	4	---	---	---	---	
ZSWIM4	65249	broad.mit.edu	37	19	13922302	13922302	+	Intron	DEL	C	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13922302delC	uc002mxh.1	+						ZSWIM4_uc010xng.1_Intron	NM_023072	NP_075560	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4								zinc ion binding			central_nervous_system(2)	2			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			catgatcacaccactgcactc	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	14391702	14391703	+	IGR	INS	-	TC	TC	rs144657144	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14391702_14391703insTC								LPHN1 (74705 upstream) : CD97 (100510 downstream)																							ctccctccctttctctctttct	0.079													3	3	---	---	---	---	
RASAL3	64926	broad.mit.edu	37	19	15575174	15575174	+	5'UTR	DEL	G	-	-	rs76267899		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15575174delG	uc002nbe.2	-	2						NM_022904	NP_075055	Q86YV0	RASL3_HUMAN	RAS protein activator like 3						negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity				0						GTCCATGGTTGGGGGGGGGGG	0.542													6	3	---	---	---	---	
LOC126536	126536	broad.mit.edu	37	19	16133577	16133601	+	Intron	DEL	TCCCTGCATCCCCTCCTGCCCACAC	-	-	rs72075779		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16133577_16133601delTCCCTGCATCCCCTCCTGCCCACAC	uc002nbw.2	+						LOC126536_uc010xow.1_Intron|LOC126536_uc002nca.2_Intron|LOC126536_uc002ncb.1_Intron|uc010xox.1_5'Flank	NR_026828				Homo sapiens cDNA FLJ46374 fis, clone TESTI4052217.												0						TGCCCCACAGTCCCTGCATCCCCTCCTGCCCACACTCCCTGCATC	0.640													3	3	---	---	---	---	
PGPEP1	54858	broad.mit.edu	37	19	18450549	18450550	+	5'Flank	INS	-	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18450549_18450550insA	uc002nis.1	+						PGPEP1_uc002nir.1_5'Flank|PGPEP1_uc002nit.1_5'Flank|PGPEP1_uc010xqg.1_5'Flank	NM_017712	NP_060182	Q9NXJ5	PGPI_HUMAN	pyroglutamyl-peptidase I								cysteine-type peptidase activity				0						accctgtctccaaaaaaaagag	0.183													4	2	---	---	---	---	
GATAD2A	54815	broad.mit.edu	37	19	19513665	19513666	+	Intron	INS	-	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19513665_19513666insG	uc010xqt.1	+						GATAD2A_uc010xqu.1_Intron	NM_017660	NP_060130	Q86YP4	P66A_HUMAN	GATA zinc finger domain containing 2A						DNA methylation|negative regulation of transcription, DNA-dependent	nuclear speck|NuRD complex	protein binding, bridging|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						tcactgcaacctccgcctcttg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	20442507	20442507	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20442507delT								LOC284441 (72004 upstream) : ZNF826 (8571 downstream)																							GCAGCTCGtgttttttttttg	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27837754	27837754	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27837754delT								None (None upstream) : LOC148189 (443648 downstream)																							aattggaacatttagcccatt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27866551	27866551	+	IGR	DEL	T	-	-	rs111746437		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27866551delT								None (None upstream) : LOC148189 (414851 downstream)																							gtttttggtgttttagagatg	0.000													2	4	---	---	---	---	
ZFP30	22835	broad.mit.edu	37	19	38133954	38133956	+	Intron	DEL	AAA	-	-	rs72477911		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38133954_38133956delAAA	uc002ogv.1	-						ZFP30_uc002ogw.1_Intron|ZFP30_uc002ogx.1_Intron|ZFP30_uc010xtt.1_Intron	NM_014898	NP_055713	Q9Y2G7	ZFP30_HUMAN	zinc finger protein 30 homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			actccgtctcaaaaaaaaaaaaa	0.133													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	40146418	40146418	+	5'Flank	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40146418delG	uc010xvd.1	+											SubName: Full=Galectin-16;																		AGTTATGGTTGTGACTGAGTT	0.468													4	4	---	---	---	---	
SPTBN4	57731	broad.mit.edu	37	19	41055989	41055990	+	Intron	INS	-	A	A	rs75353386		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41055989_41055990insA	uc002ony.2	+						SPTBN4_uc002onx.2_Intron|SPTBN4_uc002onz.2_Intron|SPTBN4_uc010egx.2_Intron|SPTBN4_uc010egy.1_Intron|SPTBN4_uc002ooa.2_Intron	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform						actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			ccatctcaaagaaaaaaaaaaa	0.243													4	2	---	---	---	---	
PVR	5817	broad.mit.edu	37	19	45151760	45151760	+	Intron	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45151760delT	uc002ozm.2	+						PVR_uc010ejs.2_Intron|PVR_uc010xxb.1_Intron|PVR_uc010xxc.1_Intron|PVR_uc002ozn.2_Intron	NM_006505	NP_006496	P15151	PVR_HUMAN	poliovirus receptor isoform alpha						adherens junction organization|cell adhesion|cell junction assembly|interspecies interaction between organisms|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target|susceptibility to natural killer cell mediated cytotoxicity|susceptibility to T cell mediated cytotoxicity	cell junction|cell surface|cytoplasm|extracellular space|integral to membrane|nucleus	cell adhesion molecule binding|receptor activity				0	Lung NSC(12;0.00608)|all_lung(12;0.0148)	Medulloblastoma(540;0.0425)|Ovarian(192;0.0728)|Prostate(69;0.081)|all_neural(266;0.112)		Epithelial(262;0.000601)		AAACTGACCCttttttttttt	0.104													4	2	---	---	---	---	
APOC2	344	broad.mit.edu	37	19	45452269	45452270	+	Intron	INS	-	CCT	CCT	rs10622462		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45452269_45452270insCCT	uc002pah.2	+							NM_000483	NP_000474	P02655	APOC2_HUMAN	apolipoprotein C-II precursor						cholesterol efflux|chylomicron remnant clearance|high-density lipoprotein particle clearance|lipid catabolic process|lipoprotein metabolic process|negative regulation of cholesterol transport|negative regulation of lipid metabolic process|negative regulation of receptor-mediated endocytosis|negative regulation of very-low-density lipoprotein particle clearance|phospholipid efflux|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of phospholipase activity|positive regulation of phospholipid catabolic process|positive regulation of triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle remodeling	chylomicron|intermediate-density lipoprotein particle|low-density lipoprotein particle|spherical high-density lipoprotein particle|very-low-density lipoprotein particle	lipase inhibitor activity|lipid binding|lipoprotein lipase activator activity|phospholipase activator activity|phospholipase binding|protein homodimerization activity			kidney(1)	1	Lung NSC(12;0.00858)|all_lung(12;0.0197)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|Epithelial(262;0.174)		ggcccccagcccgtcctccctc	0.015													4	3	---	---	---	---	
MYPOP	339344	broad.mit.edu	37	19	46399230	46399231	+	Intron	INS	-	A	A			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46399230_46399231insA	uc002pdt.2	-							NM_001012643	NP_001012661	Q86VE0	MYPOP_HUMAN	Myb protein P42POP							nucleus	DNA binding				0						agaagatagagaaaaaaaaaat	0.252													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	49050882	49050883	+	IGR	INS	-	A	A	rs76540333		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49050882_49050883insA								LMTK3 (34436 upstream) : SULT2B1 (4546 downstream)																							gactccgtctcaaaaaaaaaaa	0.005													4	2	---	---	---	---	
NTN5	126147	broad.mit.edu	37	19	49174065	49174066	+	Frame_Shift_Ins	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49174065_49174066insT	uc002pkb.2	-	2	274_275	c.178_179insA	c.(178-180)ACCfs	p.T60fs	SEC1_uc010xzv.1_Intron|SEC1_uc002pka.2_Intron|SEC1_uc010xzw.1_Intron|SEC1_uc010ema.2_Intron|NTN5_uc002pkc.2_Frame_Shift_Ins_p.T60fs	NM_145807	NP_665806	Q8WTR8	NET5_HUMAN	netrin 5 precursor	60						extracellular region				large_intestine(1)|pancreas(1)	2						GCCATTGCAGGTTTCCCTGGCG	0.649													21	13	---	---	---	---	
CGB	1082	broad.mit.edu	37	19	49528886	49528886	+	5'Flank	DEL	C	-	-	rs36051701		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49528886delC	uc002plv.1	-						CGB_uc010yad.1_Intron|CGB_uc002plu.1_5'Flank	NM_000737	NP_000728	P01233	CGHB_HUMAN	chorionic gonadotropin beta 3 subunit precursor						apoptosis|cell-cell signaling|cellular nitrogen compound metabolic process|female gamete generation|hormone biosynthetic process|peptide hormone processing|signal transduction	extracellular region|soluble fraction	hormone activity				0		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)	Choriogonadotropin alfa(DB00097)	CCGGCGGCAGCCCCCTCCACC	0.657													7	4	---	---	---	---	
TEAD2	8463	broad.mit.edu	37	19	49851747	49851755	+	Intron	DEL	CAGCTGCAT	-	-	rs33974425		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49851747_49851755delCAGCTGCAT	uc002pnj.2	-						TEAD2_uc002png.2_Intron|TEAD2_uc002pnh.2_Intron|TEAD2_uc002pni.2_Intron|TEAD2_uc010yao.1_Intron|TEAD2_uc010emw.2_Intron	NM_003598	NP_003589	Q15562	TEAD2_HUMAN	TEA domain family member 2						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)		gtccccagaccagctgcatcaacgcacct	0.158													4	4	---	---	---	---	
CNOT3	4849	broad.mit.edu	37	19	54646150	54646151	+	Intron	DEL	AC	-	-	rs72110963		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54646150_54646151delAC	uc002qdj.1	+						CNOT3_uc010yel.1_Intron|CNOT3_uc002qdi.2_Intron|CNOT3_uc002qdk.1_5'UTR|CNOT3_uc010ere.1_5'Flank	NM_014516	NP_055331	O75175	CNOT3_HUMAN	CCR4-NOT transcription complex, subunit 3						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CCTACAGCTTacacacacacac	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	55211511	55211512	+	IGR	INS	-	GT	GT	rs147726175	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55211511_55211512insGT								LILRB4 (31667 upstream) : LILRP2 (8089 downstream)																							TCTGCACATACgtgtgtgtgtg	0.356													4	2	---	---	---	---	
U2AF2	11338	broad.mit.edu	37	19	56181818	56181818	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56181818delG	uc002qlu.2	+						U2AF2_uc002qlt.2_Intron	NM_007279	NP_009210	P26368	U2AF2_HUMAN	U2 (RNU2) small nuclear RNA auxiliary factor 2						mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	nucleoplasm|spliceosomal complex	enzyme binding|nucleotide binding|RNA binding			ovary(1)	1		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		ctgctgtcccgtgCACCCTGC	0.358													9	4	---	---	---	---	
C20orf30	29058	broad.mit.edu	37	20	5080119	5080119	+	Intron	DEL	T	-	-	rs5840075		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5080119delT	uc010gbi.2	-							NM_014145	NP_054864	Q96A57	CT030_HUMAN	hypothetical protein LOC29058 isoform 2							integral to membrane					0						acttcctgagttttttttttt	0.209													4	2	---	---	---	---	
PLCB1	23236	broad.mit.edu	37	20	8687290	8687290	+	Intron	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8687290delG	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc002wna.2_Intron|PLCB1_uc002wnc.1_Intron	NM_015192	NP_056007	Q9NQ66	PLCB1_HUMAN	phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12						GTTCTTTTGAGGGCTTTGCTC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	16705861	16705861	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16705861delA								KIF16B (151783 upstream) : SNRPB2 (4768 downstream)																							caaggacaggaaaaagggcac	0.000													4	2	---	---	---	---	
PCSK2	5126	broad.mit.edu	37	20	17334110	17334110	+	Intron	DEL	C	-	-	rs11907346		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17334110delC	uc002wpm.2	+						PCSK2_uc002wpl.2_Intron|PCSK2_uc010zrm.1_Intron	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2						enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	ctccatcacacaaaaaaaaaa	0.000													4	2	---	---	---	---	
PCSK2	5126	broad.mit.edu	37	20	17418630	17418631	+	Intron	INS	-	C	C	rs138943214	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17418630_17418631insC	uc002wpm.2	+						PCSK2_uc002wpl.2_Intron|PCSK2_uc010zrm.1_Intron	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2						enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	GGCCAGCAGTTCCCCCCCACCC	0.609													4	5	---	---	---	---	
PCSK2	5126	broad.mit.edu	37	20	17426005	17426007	+	Intron	DEL	CTT	-	-	rs149842495		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17426005_17426007delCTT	uc002wpm.2	+						PCSK2_uc002wpl.2_Intron|PCSK2_uc010zrm.1_Intron	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2						enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	TACATCCCAACTTCTTCTTAATC	0.438													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	23320160	23320161	+	IGR	INS	-	T	T	rs140357658	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23320160_23320161insT								CD93 (253183 upstream) : NXT1 (11212 downstream)																							AACAGTCTCTATCATTGATGGA	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25876583	25876583	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25876583delG								FAM182B (27797 upstream) : LOC100134868 (113852 downstream)																							TAAGGCAAAAGTAGGTATAGA	0.323													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25940580	25940581	+	Intron	INS	-	G	G			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25940580_25940581insG	uc002wvf.2	+											Homo sapiens cDNA clone IMAGE:5298175.																		acccaccaaaaactcaaattaa	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26305553	26305554	+	IGR	INS	-	C	C	rs112216336		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26305553_26305554insC								MIR663 (116639 upstream) : None (None downstream)																							agaagcattctagaaacttctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29422843	29422844	+	IGR	INS	-	C	C	rs147704708	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29422843_29422844insC								None (None upstream) : FRG1B (189035 downstream)																							accactgtactcccccaggcta	0.099													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29595962	29595963	+	IGR	DEL	TG	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29595962_29595963delTG								None (None upstream) : FRG1B (15916 downstream)																							GATGTGAAACTGTGAGTCCCAG	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29607523	29607523	+	IGR	DEL	T	-	-	rs111896705		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29607523delT								None (None upstream) : FRG1B (4356 downstream)																							acatcccccctggctcacttg	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	40588553	40588553	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40588553delT								CHD6 (341420 upstream) : PTPRT (112840 downstream)																							CCCACTCCACTTTTGGTTCTG	0.542													4	3	---	---	---	---	
WFDC9	259240	broad.mit.edu	37	20	44246694	44246694	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44246694delA	uc002xoy.2	-							NM_147198	NP_671731	Q8NEX5	WFDC9_HUMAN	protease inhibitor WAP9 precursor							extracellular region					0		Myeloproliferative disorder(115;0.0122)				tcttagctagatcttctggat	0.000													4	2	---	---	---	---	
SLC13A3	64849	broad.mit.edu	37	20	45296823	45296823	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45296823delA	uc002xsg.1	-						SLC13A3_uc010gho.1_Intron|SLC13A3_uc002xsi.3_Intron	NM_001011554	NP_001011554	Q8WWT9	S13A3_HUMAN	solute carrier family 13 member 3 isoform b							integral to membrane|plasma membrane	high affinity sodium:dicarboxylate symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	ctttaaaatcaaaagctagaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	45417978	45417979	+	IGR	DEL	GA	-	-	rs139393391	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45417978_45417979delGA								SLC2A10 (52995 upstream) : EYA2 (105284 downstream)																							tattggatgtgagcgtgtgggt	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	54553804	54553804	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54553804delT								None (None upstream) : CBLN4 (18693 downstream)																							ctgcttgcactttaggtgact	0.060													4	2	---	---	---	---	
C20orf43	51507	broad.mit.edu	37	20	55044840	55044842	+	Intron	DEL	TCT	-	-	rs146917088		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55044840_55044842delTCT	uc002xxt.2	+						C20orf43_uc010zzf.1_Intron|C20orf43_uc002xxu.2_Intron|C20orf43_uc002xxv.2_Intron|C20orf43_uc002xxs.2_Intron	NM_016407	NP_057491	Q9BY42	CT043_HUMAN	hypothetical protein LOC51507											ovary(1)	1			Colorectal(105;0.202)			tctgacctcatcttctgcccctc	0.000													3	3	---	---	---	---	
TH1L	51497	broad.mit.edu	37	20	57553502	57553511	+	5'Flank	DEL	TGGAGAAACC	-	-	rs145529733		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57553502_57553511delTGGAGAAACC	uc002yag.2	+						TH1L_uc010zzu.1_5'Flank|TH1L_uc002yaf.1_5'Flank|TH1L_uc002yah.2_5'Flank	NM_198976	NP_945327	Q8IXH7	NELFD_HUMAN	TH1-like protein						negative regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3	all_lung(29;0.00711)		Colorectal(105;0.109)			tatcatcccatggagaaacctgccctcctc	0.143													5	3	---	---	---	---	
GMEB2	26205	broad.mit.edu	37	20	62240392	62240392	+	Intron	DEL	A	-	-	rs55700463		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62240392delA	uc002yfp.1	-						GMEB2_uc002yfq.1_Intron	NM_012384	NP_036516	Q9UKD1	GMEB2_HUMAN	glucocorticoid modulatory element binding						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|metal ion binding				0	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;4.79e-09)|all cancers(9;2.76e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.0114)			CCTCTGACCCACACCTCCATT	0.512													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9834644	9834645	+	IGR	INS	-	T	T	rs149588575	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9834644_9834645insT								None (None upstream) : None (None downstream)																							ATGGATATGGATTTTTTTGAGA	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9843638	9843638	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9843638delA								None (None upstream) : None (None downstream)																							AAATGCATGCACTTTCAAATG	0.194													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9852426	9852426	+	IGR	DEL	T	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9852426delT								None (None upstream) : None (None downstream)																							GGGATGTGCATTCTGAAAAAT	0.303													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10752956	10752957	+	IGR	DEL	CT	-	-	rs111633384		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10752956_10752957delCT								None (None upstream) : TPTE (153786 downstream)																							agtttcgaaactctctttttgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10776720	10776724	+	IGR	DEL	GAATC	-	-	rs57991266		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10776720_10776724delGAATC								None (None upstream) : TPTE (130019 downstream)																							gaatggaatggaatcgaatggaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10786709	10786713	+	IGR	DEL	AATGG	-	-	rs111350469		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10786709_10786713delAATGG								None (None upstream) : TPTE (120030 downstream)																							aatggaatgcaatggaatggaatgg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10790317	10790321	+	IGR	DEL	GAATG	-	-	rs112648902		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10790317_10790321delGAATG								None (None upstream) : TPTE (116422 downstream)																							gagtggattcgaatggaatggaatg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10794577	10794577	+	IGR	DEL	A	-	-	rs112140871		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10794577delA								None (None upstream) : TPTE (112166 downstream)																							aatggaatcgaatgaaatgaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10798528	10798529	+	IGR	INS	-	G	G	rs142172968		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10798528_10798529insG								None (None upstream) : TPTE (108214 downstream)																							agtggaatggagtggaatggaa	0.000													3	3	---	---	---	---	
TPTE	7179	broad.mit.edu	37	21	10962586	10962587	+	Intron	INS	-	ATA	ATA	rs146316085	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10962586_10962587insATA	uc002yip.1	-						TPTE_uc002yis.1_Intron|TPTE_uc002yiq.1_Intron|TPTE_uc002yir.1_Intron|TPTE_uc010gkv.1_Intron	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		acaatttgactataatgtctgg	0.000													3	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11022776	11022777	+	Intron	DEL	GT	-	-	rs8131015		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11022776_11022777delGT	uc002yit.1	-						TPTE_uc002yis.1_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AGtttttttggtttttttttgt	0.124													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11099703	11099704	+	5'Flank	INS	-	A	A	rs139261899		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11099703_11099704insA	uc002yit.1	-						BAGE_uc002yix.2_5'Flank	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		agattttgagtgatggaggggg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11114232	11114232	+	IGR	DEL	T	-	-	rs71914052		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11114232delT								BAGE (15295 upstream) : None (None downstream)																							aaaaaaaaaaTATCACAGTCA	0.159													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	16771823	16771828	+	IGR	DEL	TCTCTC	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16771823_16771828delTCTCTC								NRIP1 (334697 upstream) : USP25 (330668 downstream)																							CATGAGGGCAtctctctctctctctc	0.228													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	17062962	17062962	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17062962delG								NRIP1 (625836 upstream) : USP25 (39534 downstream)																							gaacctgggaggtcaaggctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	17074727	17074727	+	IGR	DEL	G	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17074727delG								NRIP1 (637601 upstream) : USP25 (27769 downstream)																							actaaagagtgggtaaggtga	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	18515526	18515527	+	IGR	DEL	GT	-	-	rs72144314		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18515526_18515527delGT								C21orf34 (533432 upstream) : CXADR (369803 downstream)																							tcttTCATTCgtgtgtgtgtgt	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	19072654	19072654	+	IGR	DEL	T	-	-	rs77028833		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19072654delT								BTG3 (87386 upstream) : C21orf91 (77069 downstream)																							TTGGCTTCCCttttttttttt	0.244													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	19134106	19134106	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19134106delA								BTG3 (148838 upstream) : C21orf91 (15617 downstream)																							TCACGCTTTTACATATTGTCC	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	21739690	21739690	+	IGR	DEL	T	-	-	rs111670185		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21739690delT								None (None upstream) : C21orf131 (375224 downstream)																							ttcttttttctttttttttga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	25595032	25595033	+	IGR	DEL	AC	-	-	rs71893447		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:25595032_25595033delAC								None (None upstream) : None (None downstream)																							ATATACTGTAACACACACACAC	0.272													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	39394365	39394366	+	IGR	DEL	AC	-	-	rs67076231		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39394365_39394366delAC								KCNJ6 (105669 upstream) : DSCR4 (31948 downstream)																							atggctatgaacacacacacac	0.000													4	2	---	---	---	---	
BRWD1	54014	broad.mit.edu	37	21	40619002	40619003	+	Intron	INS	-	A	A	rs77516783		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40619002_40619003insA	uc002yxk.1	-						BRWD1_uc010goc.1_Intron|BRWD1_uc002yxl.2_Intron|BRWD1_uc010goe.1_Intron|BRWD1_uc010gof.1_Intron|BRWD1_uc010gog.1_Intron|BRWD1_uc010goh.1_Intron|BRWD1_uc010goi.1_Intron	NM_018963	NP_061836	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				gactccgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
ITGB2	3689	broad.mit.edu	37	21	46338912	46338912	+	Intron	DEL	A	-	-	rs140713614	by1000genomes	TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46338912delA	uc002zgf.3	-						ITGB2_uc011afl.1_Intron|ITGB2_uc010gpw.2_Intron|ITGB2_uc002zgg.2_Intron|uc002zgh.2_5'Flank	NM_000211	NP_000202	P05107	ITB2_HUMAN	integrin, beta 2 precursor						apoptosis|blood coagulation|cell-cell signaling|cell-matrix adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|multicellular organismal development|neutrophil chemotaxis|regulation of cell shape|regulation of immune response|regulation of peptidyl-tyrosine phosphorylation	integrin complex	glycoprotein binding|protein kinase binding|receptor activity			ovary(4)|central_nervous_system(3)|breast(2)	9				Colorectal(79;0.0669)	Simvastatin(DB00641)	GGAGCTGAGCATTCCCCTCTC	0.612													3	3	---	---	---	---	
C21orf57	54059	broad.mit.edu	37	21	47709946	47709947	+	Intron	DEL	TA	-	-	rs9975689		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47709946_47709947delTA	uc002ziv.2	+						C21orf57_uc002zit.1_Intron|C21orf57_uc002ziu.1_Intron|C21orf57_uc002ziw.2_Intron|C21orf57_uc002zix.2_Intron|C21orf57_uc010gqh.2_Intron|C21orf57_uc002ziy.2_Intron	NM_058181	NP_478061	P58557	YBEY_HUMAN	hypothetical protein LOC54059 isoform 1								metal ion binding|metalloendopeptidase activity				0	Breast(49;0.112)			Colorectal(79;0.236)		tgcagttttGTAtgtgtgtaag	0.035													4	2	---	---	---	---	
CECR2	27443	broad.mit.edu	37	22	17911162	17911163	+	Intron	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17911162_17911163insT	uc010gqv.1	+							NM_031413	NP_113601	Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2						chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)		Lung(27;0.146)		gcctgtatggatttgcccactc	0.045													3	5	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	22610940	22610948	+	Intron	DEL	ATGCCACGT	-	-	rs12159433		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22610940_22610948delATGCCACGT	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						CTGCCCAAGGATGCCACGTCCATTTGCTT	0.593													4	2	---	---	---	---	
GNAZ	2781	broad.mit.edu	37	22	23466507	23466508	+	3'UTR	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23466507_23466508insT	uc002zwu.1	+	3					RTDR1_uc002zwt.2_Intron	NM_002073	NP_002064	P19086	GNAZ_HUMAN	guanine nucleotide binding protein, alpha z							endoplasmic reticulum|heterotrimeric G-protein complex|nuclear envelope	G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|metabotropic serotonin receptor binding|receptor signaling protein activity			kidney(1)|skin(1)	2	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.166)		TTCAAAACATATTTTTTTTCAG	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	36855503	36855504	+	IGR	DEL	AG	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36855503_36855504delAG								MYH9 (71440 upstream) : TXN2 (7589 downstream)																							GCAGAGACAAAGAGGTGGCTGG	0.446													4	2	---	---	---	---	
PLA2G6	8398	broad.mit.edu	37	22	38529876	38529877	+	Intron	INS	-	CAT	CAT	rs35736012		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38529876_38529877insCAT	uc003auy.1	-						PLA2G6_uc003auz.1_Intron|PLA2G6_uc003ava.1_Intron|PLA2G6_uc003avb.2_Intron|PLA2G6_uc010gxk.1_Intron|PLA2G6_uc011ano.1_Intron	NM_003560	NP_003551	O60733	PA2G6_HUMAN	phospholipase A2, group VI isoform a						cardiolipin biosynthetic process|cell death|lipid catabolic process	centrosome|membrane				ovary(1)	1	Melanoma(58;0.045)				Quinacrine(DB01103)	ccatcatcatccatcatcatca	0.223													2	4	---	---	---	---	
ENTHD1	150350	broad.mit.edu	37	22	40263798	40263798	+	Intron	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40263798delA	uc003ayg.2	-							NM_152512	NP_689725	Q8IYW4	ENTD1_HUMAN	ENTH domain containing 1											ovary(2)|skin(1)	3	Melanoma(58;0.0749)					actccgtctcaaaaaaaaaaT	0.259													4	2	---	---	---	---	
EFCAB6	64800	broad.mit.edu	37	22	44191700	44191705	+	Intron	DEL	ACACAC	-	-	rs142203124		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44191700_44191705delACACAC	uc003bdy.1	-						EFCAB6_uc003bdz.1_Intron|EFCAB6_uc010gzi.1_Intron|EFCAB6_uc011aqa.1_Intron|EFCAB6_uc003bea.1_Intron	NM_022785	NP_073622	Q5THR3	EFCB6_HUMAN	CAP-binding protein complex interacting protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	7		Ovarian(80;0.0247)|all_neural(38;0.025)				TCGCCTCCCAacacacacacacacac	0.252													4	2	---	---	---	---	
PARVB	29780	broad.mit.edu	37	22	44542239	44542240	+	Intron	INS	-	CG	CG	rs149646255		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44542239_44542240insCG	uc003ben.2	+						PARVB_uc003bem.2_Intron|PARVB_uc010gzn.2_Intron|PARVB_uc003beo.2_Intron	NM_013327	NP_037459	Q9HBI1	PARVB_HUMAN	parvin, beta isoform b						cell adhesion|cell junction assembly	cytoskeleton|cytosol|focal adhesion	actin binding				0		Ovarian(80;0.0246)|all_neural(38;0.0423)				tcacacacacacatgcacacac	0.035													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	49780626	49780627	+	IGR	INS	-	TT	TT			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49780626_49780627insTT								FAM19A5 (632884 upstream) : C22orf34 (27549 downstream)																							CGTCTAAGAGATTTTCTGTGTG	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	37786873	37786873	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37786873delA								DYNLT3 (79984 upstream) : CXorf27 (63197 downstream)																							ctgaaaatacaaaaaaaaatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	10028097	10028098	+	IGR	INS	-	T	T			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10028097_10028098insT								TTTY22 (377243 upstream) : None (None downstream)																							CCCTAATAGAGTATAGGCATAA	0.361													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13462616	13462616	+	IGR	DEL	A	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13462616delA								None (None upstream) : None (None downstream)																							ACACCTTCGGACAGCACCCTC	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	58990715	58990716	+	IGR	DEL	CT	-	-			TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:58990715_58990716delCT								None (None upstream) : None (None downstream)																							ggtgaggttactcttgtctagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59032071	59032071	+	IGR	DEL	T	-	-	rs113525697		TCGA-66-2787-01	TCGA-66-2787-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59032071delT								None (None upstream) : None (None downstream)																							agcaaaactcttgtctctaaa	0.000													6	4	---	---	---	---	
