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
MXRA8	54587	broad.mit.edu	37	1	1290419	1290419	+	Missense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1290419C>T	uc001aew.2	-	5	623	c.592G>A	c.(592-594)GTG>ATG	p.V198M	MXRA8_uc001aex.3_Missense_Mutation_p.V198M|MXRA8_uc001aey.3_Missense_Mutation_p.V198M|MXRA8_uc010nyl.1_Missense_Mutation_p.V198M|MXRA8_uc001aez.2_Missense_Mutation_p.V97M|MXRA8_uc001afa.2_Missense_Mutation_p.V189M	NM_032348	NP_115724	Q9BRK3	MXRA8_HUMAN	matrix-remodelling associated 8 precursor	198	Ig-like V-type 2.|Extracellular (Potential).					integral to membrane					0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		GCCTCCTCCACGTGCCGGTCG	0.726													3	21	---	---	---	---	PASS
C1orf174	339448	broad.mit.edu	37	1	3806599	3806599	+	Silent	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3806599G>A	uc001alf.2	-	4	764	c.657C>T	c.(655-657)AGC>AGT	p.S219S	C1orf174_uc009vls.2_RNA	NM_207356	NP_997239	Q8IYL3	CA174_HUMAN	hypothetical protein LOC339448	219											0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;5.09e-25)|all_epithelial(116;9.35e-17)|all_lung(118;1.09e-06)|Lung NSC(185;0.000139)|all_neural(13;0.00287)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0219)|all_hematologic(16;0.027)|Colorectal(325;0.0276)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;1.55e-39)|OV - Ovarian serous cystadenocarcinoma(86;5.99e-23)|GBM - Glioblastoma multiforme(42;2.22e-17)|Colorectal(212;1.08e-05)|COAD - Colon adenocarcinoma(227;5.49e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.000365)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.19)		ACTCTCGTCTGCTCATTGAAG	0.373													17	107	---	---	---	---	PASS
NPHP4	261734	broad.mit.edu	37	1	6007263	6007263	+	Missense_Mutation	SNP	T	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6007263T>A	uc001alq.1	-	9	1286	c.1020A>T	c.(1018-1020)AGA>AGT	p.R340S	NPHP4_uc001als.1_RNA|NPHP4_uc009vlt.1_RNA|NPHP4_uc001alt.1_RNA	NM_015102	NP_055917	O75161	NPHP4_HUMAN	nephroretinin	340					actin cytoskeleton organization|cell-cell adhesion|signal transduction|visual behavior	cell-cell junction|centrosome|cilium|microtubule basal body	protein binding|structural molecule activity			pancreas(1)	1	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		GGAGGCGGCTTCTCAAAACCA	0.597													12	93	---	---	---	---	PASS
KIF1B	23095	broad.mit.edu	37	1	10434995	10434995	+	Missense_Mutation	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10434995G>T	uc001aqx.3	+	47	5382	c.5180G>T	c.(5179-5181)CGG>CTG	p.R1727L	KIF1B_uc001aqw.3_Missense_Mutation_p.R1681L|KIF1B_uc001aqy.2_Missense_Mutation_p.R1701L|KIF1B_uc001aqz.2_Missense_Mutation_p.R1727L|KIF1B_uc001ara.2_Missense_Mutation_p.R1687L|KIF1B_uc001arb.2_Missense_Mutation_p.R1713L	NM_015074	NP_055889	O60333	KIF1B_HUMAN	kinesin family member 1B isoform b	1727	PH.				anterograde axon cargo transport|apoptosis|neuromuscular synaptic transmission|neuron-neuron synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		GTCGTCCGTCGGCCTTATGTC	0.463													13	172	---	---	---	---	PASS
CCDC21	64793	broad.mit.edu	37	1	26595018	26595018	+	Silent	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26595018C>T	uc001bls.1	+	8	1517	c.1386C>T	c.(1384-1386)TGC>TGT	p.C462C	CCDC21_uc001blr.2_Silent_p.C462C|CCDC21_uc010ofa.1_Silent_p.C411C|CCDC21_uc001blt.1_5'Flank	NM_022778	NP_073615	Q6P2H3	CEP85_HUMAN	coiled-coil domain containing 21	462	Potential.					centrosome|nucleolus|spindle pole					0		all_cancers(24;7e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.6e-26)|Colorectal(126;1.65e-08)|COAD - Colon adenocarcinoma(152;9.48e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00155)|GBM - Glioblastoma multiforme(114;0.00917)|READ - Rectum adenocarcinoma(331;0.0649)		AAAAGAAATGCCAGAAGGAAT	0.453													4	78	---	---	---	---	PASS
GRIK3	2899	broad.mit.edu	37	1	37271748	37271748	+	Silent	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37271748C>A	uc001caz.2	-	14	2406	c.2271G>T	c.(2269-2271)GGG>GGT	p.G757G	GRIK3_uc001cba.1_Silent_p.G757G	NM_000831	NP_000822	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	757	Extracellular (Potential).				negative regulation of synaptic transmission, glutamatergic|regulation of membrane potential|synaptic transmission	cell junction|dendrite cytoplasm|integral to plasma membrane|perikaryon|postsynaptic membrane|terminal button	adenylate cyclase inhibiting metabotropic glutamate receptor activity|extracellular-glutamate-gated ion channel activity|G-protein-coupled receptor binding|kainate selective glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)|breast(1)	7		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)			L-Glutamic Acid(DB00142)	CAATGAGGCCCCCGATCTGGG	0.662													8	100	---	---	---	---	PASS
SYDE2	84144	broad.mit.edu	37	1	85648044	85648044	+	Missense_Mutation	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85648044G>A	uc009wcm.2	-	3	2330	c.2281C>T	c.(2281-2283)CAT>TAT	p.H761Y	SYDE2_uc001dku.3_Missense_Mutation_p.H761Y	NM_032184	NP_115560	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2	761	C2.				activation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	Rho GTPase activator activity			ovary(1)|central_nervous_system(1)	2				all cancers(265;0.0126)|Epithelial(280;0.0336)		ACAGTTCCATGACAACAAACT	0.373													5	87	---	---	---	---	PASS
AMY2B	280	broad.mit.edu	37	1	104114878	104114878	+	Silent	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104114878G>T	uc001duq.2	+	4	931	c.315G>T	c.(313-315)GGG>GGT	p.G105G	AMY2B_uc010ouo.1_RNA|LOC648740_uc001dur.2_Silent_p.G105G	NM_020978	NP_066188	P19961	AMY2B_HUMAN	amylase, pancreatic, alpha-2B precursor	105					carbohydrate metabolic process|digestion	extracellular region	alpha-amylase activity|metal ion binding				0		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0669)|all cancers(265;0.083)|Epithelial(280;0.094)|Lung(183;0.112)		ACAATGTTGGGGTAAGTGAAT	0.333													23	228	---	---	---	---	PASS
FNDC7	163479	broad.mit.edu	37	1	109265069	109265069	+	Silent	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109265069C>T	uc001dvx.2	+	5	711	c.711C>T	c.(709-711)AGC>AGT	p.S237S	FNDC7_uc010ova.1_Silent_p.S4S	NM_001144937	NP_001138409	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	238	Fibronectin type-III 3.					extracellular region				ovary(1)|skin(1)	2		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		TGGCTTTGAGCGACTCTTCAG	0.458													14	94	---	---	---	---	PASS
TCHHL1	126637	broad.mit.edu	37	1	152057765	152057765	+	Missense_Mutation	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152057765G>A	uc001ezo.1	-	3	2458	c.2393C>T	c.(2392-2394)TCC>TTC	p.S798F		NM_001008536	NP_001008536	Q5QJ38	TCHL1_HUMAN	trichohyalin-like 1	798							calcium ion binding			ovary(1)|skin(1)	2	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)			TAGTGGACTGGAATAGACTGC	0.488													55	299	---	---	---	---	PASS
HRNR	388697	broad.mit.edu	37	1	152187673	152187673	+	Silent	SNP	A	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152187673A>G	uc001ezt.1	-	3	6508	c.6432T>C	c.(6430-6432)TCT>TCC	p.S2144S		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	2144					keratinization		calcium ion binding|protein binding			skin(2)|ovary(1)	3	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTTCACCCCTAGATGACTGTC	0.582													9	747	---	---	---	---	PASS
NPR1	4881	broad.mit.edu	37	1	153659482	153659482	+	Intron	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153659482G>T	uc001fcs.3	+						NPR1_uc010pdz.1_Intron|NPR1_uc010pea.1_Intron	NM_000906	NP_000897	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1 precursor						body fluid secretion|intracellular signal transduction|negative regulation of angiogenesis|negative regulation of cell growth|positive regulation of renal sodium excretion|positive regulation of urine volume|receptor guanylyl cyclase signaling pathway|regulation of blood pressure|regulation of blood vessel size|regulation of vascular permeability|regulation of vasodilation		ATP binding|GTP binding|guanylate cyclase activity|natriuretic peptide receptor activity|peptide receptor activity, G-protein coupled|protein kinase activity			ovary(3)|lung(2)|stomach(1)|breast(1)	7	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Nesiritide(DB04899)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	GACTCTTATTGCCCCAGCAGG	0.522													16	59	---	---	---	---	PASS
IQGAP3	128239	broad.mit.edu	37	1	156497786	156497786	+	Missense_Mutation	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156497786C>A	uc001fpf.2	-	37	4815	c.4740G>T	c.(4738-4740)AAG>AAT	p.K1580N		NM_178229	NP_839943	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	1580					small GTPase mediated signal transduction	intracellular	calmodulin binding|Ras GTPase activator activity			ovary(5)|skin(1)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CACCCAGGAACTTGGCATTTA	0.517													10	102	---	---	---	---	PASS
PEAR1	375033	broad.mit.edu	37	1	156875138	156875138	+	Missense_Mutation	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156875138C>A	uc001fqj.1	+	4	345	c.229C>A	c.(229-231)CGT>AGT	p.R77S	PEAR1_uc009wsl.1_5'Flank|PEAR1_uc001fqk.1_5'Flank	NM_001080471	NP_001073940	Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	77	EMI.					integral to membrane				ovary(2)|central_nervous_system(1)	3	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GACCGTGTACCGTCAGGTGGT	0.657													5	38	---	---	---	---	PASS
F5	2153	broad.mit.edu	37	1	169541473	169541473	+	Missense_Mutation	SNP	C	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169541473C>G	uc001ggg.1	-	3	504	c.359G>C	c.(358-360)AGT>ACT	p.S120T	F5_uc010plr.1_RNA	NM_000130	NP_000121	P12259	FA5_HUMAN	coagulation factor V precursor	120	F5/8 type A 1.|Plastocyanin-like 1.				cell adhesion|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)	TGATAATTTACTGTACCTAAT	0.333													8	67	---	---	---	---	PASS
TOR1AIP1	26092	broad.mit.edu	37	1	179858470	179858470	+	Missense_Mutation	SNP	G	C	C	rs146164995	byFrequency	TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179858470G>C	uc001gnq.2	+	3	794	c.576G>C	c.(574-576)AGG>AGC	p.R192S	TOR1AIP1_uc001gnp.1_Missense_Mutation_p.R193S	NM_015602	NP_056417	Q5JTV8	TOIP1_HUMAN	lamina-associated polypeptide 1B	192	Nuclear (Potential).					integral to membrane|nuclear inner membrane				breast(1)|central_nervous_system(1)	2						TTGTAATCAGGTTACGTCGAC	0.308													6	253	---	---	---	---	PASS
ATP2B4	493	broad.mit.edu	37	1	203691776	203691776	+	Missense_Mutation	SNP	A	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203691776A>G	uc001gzw.2	+	18	3867	c.2983A>G	c.(2983-2985)ATT>GTT	p.I995V	ATP2B4_uc001gzv.2_Missense_Mutation_p.I995V|ATP2B4_uc009xaq.2_Missense_Mutation_p.I995V|ATP2B4_uc001gzx.2_Missense_Mutation_p.I26V|ATP2B4_uc009xar.2_Missense_Mutation_p.I26V	NM_001684	NP_001675	P23634	AT2B4_HUMAN	plasma membrane calcium ATPase 4 isoform 4b	995	Helical; (Potential).				ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|skin(1)	3	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)			CTACCGCAACATTATCTTCTG	0.463													19	123	---	---	---	---	PASS
PCNXL2	80003	broad.mit.edu	37	1	233137365	233137365	+	Missense_Mutation	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233137365C>A	uc001hvl.2	-	29	5250	c.5015G>T	c.(5014-5016)CGT>CTT	p.R1672L	PCNXL2_uc001hvk.1_Missense_Mutation_p.R324L|PCNXL2_uc001hvm.1_RNA	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2	1672						integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)				CCACTCGTCACGTGCTGTTAT	0.418													3	17	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237666632	237666632	+	Missense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237666632C>T	uc001hyl.1	+	22	2560	c.2440C>T	c.(2440-2442)CTT>TTT	p.L814F		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	814	Cytoplasmic (By similarity).				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ATTCAAATTTCTTCCTCCACC	0.413													5	49	---	---	---	---	PASS
OR2M4	26245	broad.mit.edu	37	1	248402321	248402321	+	Missense_Mutation	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248402321G>T	uc010pzh.1	+	1	91	c.91G>T	c.(91-93)GTC>TTC	p.V31F		NM_017504	NP_059974	Q96R27	OR2M4_HUMAN	olfactory receptor, family 2, subfamily M,	31	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(2)	2	all_cancers(71;0.000124)|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;0.0245)			TTTTTCTCTGGTCCTGGGCAT	0.473													32	240	---	---	---	---	PASS
NBAS	51594	broad.mit.edu	37	2	15470749	15470749	+	Missense_Mutation	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15470749C>A	uc002rcc.1	-	36	4346	c.4320G>T	c.(4318-4320)AAG>AAT	p.K1440N	NBAS_uc010exl.1_Missense_Mutation_p.K512N|NBAS_uc002rcd.1_RNA	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein	1440										ovary(2)|liver(1)|skin(1)	4						AAGTTAAAGACTTCTTCCACC	0.453													10	94	---	---	---	---	PASS
XDH	7498	broad.mit.edu	37	2	31624177	31624177	+	Missense_Mutation	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31624177G>T	uc002rnv.1	-	4	294	c.215C>A	c.(214-216)GCC>GAC	p.A72D		NM_000379	NP_000370	P47989	XDH_HUMAN	xanthine dehydrogenase	72	2Fe-2S ferredoxin-type.				purine nucleotide catabolic process|xanthine catabolic process	cytosol|extracellular region|peroxisome	2 iron, 2 sulfur cluster binding|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|molybdopterin cofactor binding|protein homodimerization activity|xanthine dehydrogenase activity|xanthine oxidase activity			skin(4)|breast(2)|ovary(1)|central_nervous_system(1)	8	Acute lymphoblastic leukemia(172;0.155)				Allopurinol(DB00437)|Carvedilol(DB01136)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Desflurane(DB01189)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|NADH(DB00157)|Nitrofurazone(DB00336)|Papaverine(DB01113)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Rasburicase(DB00049)|Spermine(DB00127)|Trifluoperazine(DB00831)|Vitamin E(DB00163)	GGCCAGGCAGGCATTGGCAGA	0.507													14	77	---	---	---	---	PASS
STON1-GTF2A1L	286749	broad.mit.edu	37	2	48808989	48808989	+	Missense_Mutation	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48808989C>A	uc010yol.1	+	1	1264	c.1217C>A	c.(1216-1218)CCA>CAA	p.P406Q	STON1_uc002rwo.3_Missense_Mutation_p.P406Q|STON1_uc010fbm.2_Missense_Mutation_p.P406Q|STON1-GTF2A1L_uc002rwp.1_Missense_Mutation_p.P406Q|STON1_uc002rwr.2_RNA|STON1_uc002rwq.2_Missense_Mutation_p.P406Q	NM_006873	NP_006864	B7ZL16	B7ZL16_HUMAN	stonin 1	406					endocytosis|intracellular protein transport|transcription initiation from RNA polymerase II promoter	clathrin adaptor complex|transcription factor TFIIA complex				ovary(3)|pancreas(1)|skin(1)	5		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GTTTCAAAACCAAAAAAGAAC	0.423													25	160	---	---	---	---	PASS
FSHR	2492	broad.mit.edu	37	2	49381457	49381457	+	Missense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49381457C>T	uc002rww.2	-	1	174	c.100G>A	c.(100-102)GAG>AAG	p.E34K	FSHR_uc002rwx.2_Missense_Mutation_p.E34K|FSHR_uc010fbn.2_Missense_Mutation_p.E34K|FSHR_uc010fbo.1_RNA	NM_000145	NP_000136	P23945	FSHR_HUMAN	follicle stimulating hormone receptor isoform 1	34	LRRNT.|Extracellular (Potential).				female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)|lung(2)|central_nervous_system(1)|skin(1)	8		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)	ACCTTGCTCTCTTGGCAGAGA	0.522									Gonadal_Dysgenesis_46_XX				6	90	---	---	---	---	PASS
TMEM131	23505	broad.mit.edu	37	2	98409416	98409416	+	Missense_Mutation	SNP	T	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98409416T>A	uc002syh.3	-	31	3806	c.3577A>T	c.(3577-3579)AGT>TGT	p.S1193C		NM_015348	NP_056163	Q92545	TM131_HUMAN	RW1 protein	1193						integral to membrane				ovary(4)|central_nervous_system(2)	6						AACCCCCTACTGTGACCGGGG	0.498													5	24	---	---	---	---	PASS
IL1R2	7850	broad.mit.edu	37	2	102626181	102626181	+	Silent	SNP	T	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102626181T>C	uc002tbm.2	+	3	454	c.225T>C	c.(223-225)GCT>GCC	p.A75A	IL1R2_uc002tbn.2_Silent_p.A75A|IL1R2_uc002tbo.1_Silent_p.A75A	NM_004633	NP_004624	P27930	IL1R2_HUMAN	interleukin 1 receptor, type II precursor	75	Extracellular (Potential).|Ig-like C2-type 1.				immune response	integral to membrane|plasma membrane	interleukin-1, Type II, blocking receptor activity			ovary(1)|breast(1)	2					Anakinra(DB00026)	ATGACTCTGCTAGGACGGTCC	0.607													55	387	---	---	---	---	PASS
GPR45	11250	broad.mit.edu	37	2	105859092	105859092	+	Silent	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105859092G>A	uc002tco.1	+	1	893	c.777G>A	c.(775-777)TTG>TTA	p.L259L		NM_007227	NP_009158	Q9Y5Y3	GPR45_HUMAN	G protein-coupled receptor 45	259	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity|protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3						GCGTGGACTTGAGCTTCAAGA	0.642													42	258	---	---	---	---	PASS
SCN7A	6332	broad.mit.edu	37	2	167322348	167322348	+	Nonsense_Mutation	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167322348G>A	uc002udu.1	-	7	941	c.814C>T	c.(814-816)CAA>TAA	p.Q272*	SCN7A_uc010fpm.1_RNA	NM_002976	NP_002967	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha	272					muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			large_intestine(1)	1						TCATTCTCTTGGGGCCATCGA	0.378													23	213	---	---	---	---	PASS
LRP2	4036	broad.mit.edu	37	2	170058365	170058365	+	Nonsense_Mutation	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170058365G>T	uc002ues.2	-	44	8438	c.8225C>A	c.(8224-8226)TCA>TAA	p.S2742*		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	2742	Extracellular (Potential).|LDL-receptor class A 17.				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)	GGCTGTCGGTGAGCAGGTGTG	0.413													13	112	---	---	---	---	PASS
ZAK	51776	broad.mit.edu	37	2	174055765	174055765	+	Intron	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174055765C>T	uc002uhz.2	+						ZAK_uc002uhx.2_Intron|ZAK_uc002uhy.2_Intron|ZAK_uc010zei.1_Intron|ZAK_uc002uia.1_Intron	NM_016653	NP_057737	Q9NYL2	MLTK_HUMAN	MLK-related kinase isoform 1						activation of JUN kinase activity|activation of MAPKK activity|cell cycle arrest|cell death|cell differentiation|cell proliferation|DNA damage checkpoint|positive regulation of apoptosis|response to radiation	cytoplasm|nucleus	ATP binding|identical protein binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding			lung(3)|stomach(1)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.176)			CCTGTTTTCTCAGATCTGTGA	0.368													34	387	---	---	---	---	PASS
NFE2L2	4780	broad.mit.edu	37	2	178098966	178098966	+	Missense_Mutation	SNP	C	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178098966C>G	uc002ulh.3	-	2	634	c.79G>C	c.(79-81)GAT>CAT	p.D27H	NFE2L2_uc002ulg.3_Missense_Mutation_p.D11H|NFE2L2_uc010zfa.1_Missense_Mutation_p.D11H|NFE2L2_uc002uli.3_Missense_Mutation_p.D11H|NFE2L2_uc010fra.2_Missense_Mutation_p.D11H|NFE2L2_uc010frb.2_Missense_Mutation_p.D11H	NM_006164	NP_006155	Q16236	NF2L2_HUMAN	nuclear factor erythroid 2-like 2 isoform 1	27					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)			AGATCTATATCTTGCCTCCAA	0.353			Mis		NSCLC|HNSCC					HNSCC(56;0.16)			10	101	---	---	---	---	PASS
NFE2L2	4780	broad.mit.edu	37	2	178098973	178098973	+	Missense_Mutation	SNP	C	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178098973C>G	uc002ulh.3	-	2	627	c.72G>C	c.(70-72)TGG>TGC	p.W24C	NFE2L2_uc002ulg.3_Missense_Mutation_p.W8C|NFE2L2_uc010zfa.1_Missense_Mutation_p.W8C|NFE2L2_uc002uli.3_Missense_Mutation_p.W8C|NFE2L2_uc010fra.2_Missense_Mutation_p.W8C|NFE2L2_uc010frb.2_Missense_Mutation_p.W8C	NM_006164	NP_006155	Q16236	NF2L2_HUMAN	nuclear factor erythroid 2-like 2 isoform 1	24					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)			TATCTTGCCTCCAAAGTATGT	0.348			Mis		NSCLC|HNSCC					HNSCC(56;0.16)			10	101	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179424877	179424877	+	Missense_Mutation	SNP	A	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179424877A>G	uc010zfg.1	-	275	78502	c.78278T>C	c.(78277-78279)GTG>GCG	p.V26093A	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.V19788A|TTN_uc010zfi.1_Missense_Mutation_p.V19721A|TTN_uc010zfj.1_Missense_Mutation_p.V19596A	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	27020							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)			GCCTGAGTCCACAATTTTGGG	0.448													21	178	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179606351	179606351	+	Missense_Mutation	SNP	A	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179606351A>G	uc010zfh.1	-	46	11320	c.11096T>C	c.(11095-11097)TTT>TCT	p.F3699S	TTN_uc010zfg.1_Intron|TTN_uc010zfi.1_Missense_Mutation_p.F3632S|TTN_uc010zfj.1_Missense_Mutation_p.F3507S|TTN_uc002umz.1_Intron	NM_133437	NP_597681	Q8WZ42	TITIN_HUMAN	titin isoform novex-2	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)			ATCACCGTCAAAAACAAATTT	0.403													29	178	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179621470	179621470	+	Missense_Mutation	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179621470G>A	uc010zfh.1	-	44	10444	c.10220C>T	c.(10219-10221)TCC>TTC	p.S3407F	TTN_uc010zfg.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron|TTN_uc002unb.2_Intron	NM_133437	NP_597681	Q8WZ42	TITIN_HUMAN	titin isoform novex-2	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)			CACTGCCTGGGACTTGGCGGA	0.383													16	118	---	---	---	---	PASS
COL3A1	1281	broad.mit.edu	37	2	189868978	189868978	+	Intron	SNP	A	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189868978A>G	uc002uqj.1	+							NM_000090	NP_000081	P02461	CO3A1_HUMAN	collagen type III alpha 1 preproprotein						axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway	collagen type III|extracellular space	extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding			central_nervous_system(7)|ovary(4)|large_intestine(2)	13			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)|Palifermin(DB00039)	CATTATCTGTATTAGGGAGCT	0.448													3	17	---	---	---	---	PASS
DNAH7	56171	broad.mit.edu	37	2	196688978	196688978	+	Splice_Site	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196688978C>T	uc002utj.3	-	49	9392	c.9291_splice	c.e49+1	p.K3097_splice		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12						TATATACTGGCCTTTACTGAT	0.358													19	145	---	---	---	---	PASS
MYL1	4632	broad.mit.edu	37	2	211163151	211163151	+	Missense_Mutation	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211163151G>T	uc002vec.2	-	3	426	c.297C>A	c.(295-297)AGC>AGA	p.S99R	MYL1_uc002veb.2_Missense_Mutation_p.S55R	NM_079420	NP_524144	P05976	MYL1_HUMAN	fast skeletal myosin alkali light chain 1	99					muscle filament sliding|muscle organ development	cytosol|muscle myosin complex|sarcomere	calcium ion binding|structural constituent of muscle			ovary(1)	1				Epithelial(149;0.00573)|Lung(261;0.0422)|LUSC - Lung squamous cell carcinoma(261;0.0444)|all cancers(144;0.057)		TACCTTCATTGCTGGGGTTTC	0.383													21	194	---	---	---	---	PASS
TRIP12	9320	broad.mit.edu	37	2	230678590	230678590	+	Missense_Mutation	SNP	T	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230678590T>C	uc002vpw.1	-	12	1947	c.1838A>G	c.(1837-1839)CAT>CGT	p.H613R	TRIP12_uc002vpx.1_Missense_Mutation_p.H661R|TRIP12_uc002vpy.1_Missense_Mutation_p.H316R|TRIP12_uc010zlz.1_Intron|TRIP12_uc010fxh.1_Missense_Mutation_p.H619R	NM_004238	NP_004229	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	613					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	proteasome complex	thyroid hormone receptor binding|ubiquitin-protein ligase activity			ovary(4)|lung(2)|breast(1)|central_nervous_system(1)|skin(1)	9		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		TTTTACCTGATGTGTTAGCCT	0.279													12	86	---	---	---	---	PASS
TTLL3	26140	broad.mit.edu	37	3	9859359	9859359	+	Missense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9859359C>T	uc003btg.2	+	5	562	c.346C>T	c.(346-348)CCG>TCG	p.P116S	ARPC4_uc003btc.1_Intron|TTLL3_uc003btd.3_Missense_Mutation_p.P116S|TTLL3_uc003btf.3_5'UTR|TTLL3_uc010hco.1_Missense_Mutation_p.P52S|TTLL3_uc003bth.3_5'UTR|TTLL3_uc011atj.1_Missense_Mutation_p.P52S|TTLL3_uc003btj.3_5'UTR|TTLL3_uc003bti.3_5'UTR	NM_001025930	NP_001021100	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	116					axoneme assembly|cilium assembly|protein polyglycylation	cilium axoneme|cytoplasm|microtubule	protein-glycine ligase activity, initiating|tubulin-tyrosine ligase activity			large_intestine(2)	2	Medulloblastoma(99;0.227)					CCGGAATTTGCCGTGGTTTGA	0.547													5	321	---	---	---	---	PASS
KCNH8	131096	broad.mit.edu	37	3	19295336	19295336	+	Silent	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19295336G>A	uc003cbk.1	+	2	462	c.267G>A	c.(265-267)GAG>GAA	p.E89E	KCNH8_uc011awe.1_Silent_p.E89E|KCNH8_uc010hex.1_5'UTR	NM_144633	NP_653234	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H,	89	Cytoplasmic (Potential).|PAS.					integral to membrane	two-component sensor activity			lung(4)|ovary(1)	5						CACTGGAGGAGAAAACAGAAT	0.418													24	224	---	---	---	---	PASS
ULK4	54986	broad.mit.edu	37	3	41973509	41973509	+	Intron	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41973509C>A	uc003ckv.3	-						ULK4_uc003ckw.2_Intron|ULK4_uc003ckx.1_Intron	NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)		CTATGAAGATCAAATAAATGT	0.323													11	64	---	---	---	---	PASS
SACM1L	22908	broad.mit.edu	37	3	45781107	45781107	+	Missense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45781107C>T	uc003cos.2	+	19	1802	c.1598C>T	c.(1597-1599)TCA>TTA	p.S533L	SACM1L_uc011bag.1_Missense_Mutation_p.S430L|SACM1L_uc011bah.1_Missense_Mutation_p.S467L|SACM1L_uc003cot.2_Missense_Mutation_p.S176L	NM_014016	NP_054735	Q9NTJ5	SAC1_HUMAN	suppressor of actin 1	533	Helical; (Potential).					Golgi apparatus				ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)		GTTGCCTTTTCAATGTGCATT	0.353													44	318	---	---	---	---	PASS
HYAL3	8372	broad.mit.edu	37	3	50332932	50332932	+	Silent	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50332932C>T	uc003czd.1	-	2	375	c.102G>A	c.(100-102)CTG>CTA	p.L34L	HYAL3_uc003czc.1_Silent_p.L34L|HYAL3_uc003cze.1_Intron|HYAL3_uc003czf.1_Intron|HYAL3_uc003czg.1_Silent_p.L34L	NM_003549	NP_003540	O43820	HYAL3_HUMAN	hyaluronoglucosaminidase 3 precursor	34					carbohydrate metabolic process	extracellular region|lysosome	hyalurononglucosaminidase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		GTACATTCCACAGCACAGAGA	0.627													20	90	---	---	---	---	PASS
FILIP1L	11259	broad.mit.edu	37	3	99648885	99648885	+	Intron	SNP	A	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99648885A>G	uc003dtm.2	-						C3orf26_uc003dtk.1_Intron|C3orf26_uc003dtl.2_Intron|FILIP1L_uc003dto.2_Intron	NM_182909	NP_878913	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like isoform 1							cytoplasm|membrane|myosin complex|nucleus				ovary(1)	1						TGTAGGAACAAAAAGTATTTC	0.403													55	153	---	---	---	---	PASS
MYH15	22989	broad.mit.edu	37	3	108147461	108147461	+	Missense_Mutation	SNP	C	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108147461C>G	uc003dxa.1	-	28	3697	c.3640G>C	c.(3640-3642)GAG>CAG	p.E1214Q		NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15	1214	Potential.					myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7						CCCTCGAGCTCAGCCAGGCTG	0.493													32	226	---	---	---	---	PASS
KIAA1524	57650	broad.mit.edu	37	3	108276190	108276190	+	Silent	SNP	C	A	A	rs62638702	byFrequency	TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108276190C>A	uc003dxb.3	-	17	2354	c.2085G>T	c.(2083-2085)GCG>GCT	p.A695A		NM_020890	NP_065941	Q8TCG1	CIP2A_HUMAN	p90 autoantigen	695	Potential.					cytoplasm|integral to membrane	protein binding			ovary(2)|central_nervous_system(1)	3						CAACTTGCTGCGCCTTCAGCA	0.388													3	162	---	---	---	---	PASS
DPPA4	55211	broad.mit.edu	37	3	109052761	109052761	+	Nonsense_Mutation	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109052761G>T	uc003dxq.3	-	2	189	c.134C>A	c.(133-135)TCA>TAA	p.S45*	DPPA4_uc011bho.1_Nonsense_Mutation_p.S45*|DPPA4_uc011bhp.1_Nonsense_Mutation_p.S45*	NM_018189	NP_060659	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	45						nucleus	protein binding			upper_aerodigestive_tract(1)	1						TCTCTTTGCTGATGTTCCTGG	0.458													36	231	---	---	---	---	PASS
KLF15	28999	broad.mit.edu	37	3	126062578	126062578	+	Missense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126062578C>T	uc011bkk.1	-	3	1425	c.1243G>A	c.(1243-1245)GTG>ATG	p.V415M		NM_014079	NP_054798	Q9UIH9	KLF15_HUMAN	Kruppel-like factor 15	415						nucleus	DNA binding|zinc ion binding			lung(1)	1				GBM - Glioblastoma multiforme(114;0.147)		TTTCAGTTCACGGAGCGCACG	0.597													9	106	---	---	---	---	PASS
RAB6B	51560	broad.mit.edu	37	3	133560150	133560150	+	Missense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133560150C>T	uc003epy.2	-	4	649	c.268G>A	c.(268-270)GTG>ATG	p.V90M	RAB6B_uc011blu.1_Missense_Mutation_p.V77M	NM_016577	NP_057661	Q9NRW1	RAB6B_HUMAN	RAB6B, member RAS oncogene family	90					protein transport|retrograde vesicle-mediated transport, Golgi to ER|small GTPase mediated signal transduction	cytoplasmic membrane-bounded vesicle|Golgi membrane	GTP binding|GTPase activity|protein binding			pancreas(1)	1						TACACCACCACAGCCACCGTG	0.637													43	122	---	---	---	---	PASS
STAG1	10274	broad.mit.edu	37	3	136221539	136221539	+	Silent	SNP	G	A	A	rs113504457	byFrequency	TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136221539G>A	uc003era.1	-	8	1051	c.759C>T	c.(757-759)GCC>GCT	p.A253A	STAG1_uc003erb.1_Silent_p.A253A|STAG1_uc003erc.1_Silent_p.A27A|STAG1_uc010hua.1_Silent_p.A116A|STAG1_uc003erd.2_Silent_p.A156A	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1	253					cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2						TATTTCTCTCGGCTTCATATT	0.383													17	264	---	---	---	---	PASS
WDR1	9948	broad.mit.edu	37	4	10080565	10080565	+	Nonsense_Mutation	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10080565C>A	uc003gmf.2	-	12	1628	c.1345G>T	c.(1345-1347)GAA>TAA	p.E449*	WDR1_uc003gmg.2_Nonsense_Mutation_p.E309*|WDR1_uc010idm.2_RNA|hsa-mir-3138|MI0014161_5'Flank	NM_017491	NP_059830	O75083	WDR1_HUMAN	WD repeat-containing protein 1 isoform 1	449	WD 8.				platelet activation|platelet degranulation|sensory perception of sound	cytoskeleton|cytosol|extracellular region	actin binding			ovary(2)|pancreas(1)	3				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)		GCCACAACTTCGGGCTCGTAG	0.612													7	79	---	---	---	---	PASS
GPR125	166647	broad.mit.edu	37	4	22414850	22414850	+	Silent	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22414850G>A	uc003gqm.1	-	14	2452	c.2187C>T	c.(2185-2187)ATC>ATT	p.I729I	GPR125_uc010ieo.1_Silent_p.I585I	NM_145290	NP_660333	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125 precursor	729	Extracellular (Potential).|GPS.				neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity			skin(1)	1		Breast(46;0.198)				GAATCGTAGTGATATTTTCAT	0.413													27	391	---	---	---	---	PASS
EPHA5	2044	broad.mit.edu	37	4	66270100	66270100	+	Silent	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66270100G>A	uc003hcy.2	-	8	1975	c.1782C>T	c.(1780-1782)CTC>CTT	p.L594L	EPHA5_uc003hcx.2_Silent_p.L526L|EPHA5_uc003hcz.2_Silent_p.L594L|EPHA5_uc011cah.1_Silent_p.L595L|EPHA5_uc011cai.1_Silent_p.L595L|EPHA5_uc003hda.2_Silent_p.L595L	NM_004439	NP_004430	P54756	EPHA5_HUMAN	ephrin receptor EphA5 isoform a precursor	594	Helical; (Potential).				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						ACCTTCCACTGAGGAGGACGC	0.488										TSP Lung(17;0.13)			18	97	---	---	---	---	PASS
UGT2B7	7364	broad.mit.edu	37	4	69974002	69974002	+	Missense_Mutation	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69974002C>A	uc003heg.3	+	5	1318	c.1272C>A	c.(1270-1272)GAC>GAA	p.D424E	UGT2B7_uc010ihq.2_Intron	NM_001074	NP_001065	P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2B7 precursor	424					lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			ovary(1)|skin(1)	2						CGAGTACAGACTTGCTGAATG	0.413													9	290	---	---	---	---	PASS
HERC5	51191	broad.mit.edu	37	4	89425483	89425483	+	Missense_Mutation	SNP	G	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89425483G>C	uc003hrt.2	+	21	2836	c.2683G>C	c.(2683-2685)GAC>CAC	p.D895H	HERC5_uc011cdm.1_Missense_Mutation_p.D533H	NM_016323	NP_057407	Q9UII4	HERC5_HUMAN	hect domain and RLD 5	895	HECT.				innate immune response|ISG15-protein conjugation|negative regulation of type I interferon production|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cyclin-dependent protein kinase activity|regulation of defense response to virus|response to virus	cytosol|perinuclear region of cytoplasm	ISG15 ligase activity|protein binding|ubiquitin-protein ligase activity			ovary(4)|lung(3)|skin(2)	9		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)		GTGCGACGAAGACATTATCAA	0.338													11	182	---	---	---	---	PASS
ARHGEF38	54848	broad.mit.edu	37	4	106510544	106510544	+	Silent	SNP	T	C	C	rs146153509		TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106510544T>C	uc003hxu.2	+	2	482	c.336T>C	c.(334-336)GAT>GAC	p.D112D		NM_017700	NP_060170	Q9NXL2	ARH38_HUMAN	hypothetical protein LOC54848	112	DH.				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|breast(1)	3						ATCTCAATGATCTAGAGCTGT	0.378													27	183	---	---	---	---	PASS
SLC25A31	83447	broad.mit.edu	37	4	128685437	128685437	+	Missense_Mutation	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128685437G>T	uc003ifl.2	+	3	546	c.400G>T	c.(400-402)GCT>TCT	p.A134S		NM_031291	NP_112581	Q9H0C2	ADT4_HUMAN	solute carrier family 25 (mitochondrial carrier;	134	Helical; Name=3; (Potential).|Solcar 2.				transmembrane transport	cilium|flagellum|integral to membrane|mitochondrial inner membrane	binding|transporter activity				0						TTCTGGTGGAGCTGCTGGGGC	0.378													4	160	---	---	---	---	PASS
PCDH10	57575	broad.mit.edu	37	4	134084389	134084389	+	Missense_Mutation	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134084389G>A	uc003iha.2	+	4	3881	c.3055G>A	c.(3055-3057)GAT>AAT	p.D1019N		NM_032961	NP_116586	Q9P2E7	PCD10_HUMAN	protocadherin 10 isoform 1 precursor	1019	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2				LUSC - Lung squamous cell carcinoma(193;0.227)		GAAGGAGCTGGATGGACTGCT	0.498													42	331	---	---	---	---	PASS
INPP4B	8821	broad.mit.edu	37	4	143350346	143350346	+	Missense_Mutation	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143350346G>T	uc003iix.3	-	6	711	c.116C>A	c.(115-117)CCG>CAG	p.P39Q	INPP4B_uc003iiw.3_Missense_Mutation_p.P39Q|INPP4B_uc011chm.1_RNA|INPP4B_uc011cho.1_RNA|INPP4B_uc003iiz.2_RNA	NM_003866	NP_003857	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II,	39	C2.				signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)					TTCCAACTGCGGTTCATTTGG	0.274													5	35	---	---	---	---	PASS
DDX60L	91351	broad.mit.edu	37	4	169300557	169300557	+	Silent	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169300557G>A	uc003irq.3	-	32	4541	c.4320C>T	c.(4318-4320)CTC>CTT	p.L1440L		NM_001012967	NP_001012985	Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1440							ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		GGCCTCTCTTGAGAAAATTTA	0.353													6	121	---	---	---	---	PASS
ZFP42	132625	broad.mit.edu	37	4	188924186	188924186	+	Nonsense_Mutation	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188924186C>A	uc003izg.1	+	3	470	c.225C>A	c.(223-225)TGC>TGA	p.C75*	ZFP42_uc003izh.1_Nonsense_Mutation_p.C75*|ZFP42_uc003izi.1_Nonsense_Mutation_p.C75*	NM_174900	NP_777560	Q96MM3	ZFP42_HUMAN	zinc finger protein 42	75					female gonad development|male gonad development|meiosis	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)		ACATAGAATGCGTCATAAGGG	0.483													10	112	---	---	---	---	PASS
ROPN1L	83853	broad.mit.edu	37	5	10465045	10465045	+	Missense_Mutation	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10465045G>T	uc003jex.3	+	5	950	c.679G>T	c.(679-681)GAT>TAT	p.D227Y		NM_031916	NP_114122	Q96C74	ROP1L_HUMAN	ropporin 1-like	227					ciliary or flagellar motility|signal transduction	cytoplasm|motile cilium	cAMP-dependent protein kinase regulator activity|protein binding			ovary(1)	1						AAACTCTGAAGATGTAGGCCA	0.363													28	176	---	---	---	---	PASS
HTR1A	3350	broad.mit.edu	37	5	63257020	63257020	+	Missense_Mutation	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63257020C>A	uc011cqt.1	-	1	527	c.527G>T	c.(526-528)CGC>CTC	p.R176L		NM_000524	NP_000515	P08908	5HT1A_HUMAN	5-hydroxytryptamine (serotonin) receptor 1A	176	Helical; Name=4; (By similarity).				behavior|positive regulation of cell proliferation	integral to plasma membrane	serotonin receptor activity			ovary(2)|pancreas(2)	4		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0575)|Colorectal(97;0.234)		Lung(70;0.105)	Alprenolol(DB00866)|Aripiprazole(DB01238)|Buspirone(DB00490)|Clozapine(DB00363)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Fluvoxamine(DB00176)|Lisuride(DB00589)|Methysergide(DB00247)|Mirtazapine(DB00370)|Pindolol(DB00960)|Propranolol(DB00571)|Quetiapine(DB01224)|Sertraline(DB01104)|Tegaserod(DB01079)|Trazodone(DB00656)|Venlafaxine(DB00285)|Ziprasidone(DB00246)	TTCCGGGGTGCGCCAGCCCAG	0.597													42	195	---	---	---	---	PASS
CAST	831	broad.mit.edu	37	5	96083050	96083050	+	Missense_Mutation	SNP	A	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96083050A>G	uc003klz.1	+	16	1199	c.1037A>G	c.(1036-1038)GAT>GGT	p.D346G	CAST_uc003klt.2_Missense_Mutation_p.D333G|CAST_uc003klu.2_Missense_Mutation_p.D429G|CAST_uc003klv.2_Missense_Mutation_p.D407G|CAST_uc003klw.2_Missense_Mutation_p.D410G|CAST_uc003klx.2_Missense_Mutation_p.D388G|CAST_uc003kly.2_Missense_Mutation_p.D394G|CAST_uc011cuo.1_Missense_Mutation_p.D392G|CAST_uc011cuq.1_Missense_Mutation_p.D194G|CAST_uc011cur.1_Missense_Mutation_p.D332G|CAST_uc011cus.1_Missense_Mutation_p.D333G|CAST_uc003kma.1_Missense_Mutation_p.D305G|CAST_uc011cut.1_Missense_Mutation_p.D274G|CAST_uc003kmb.2_Missense_Mutation_p.D292G|CAST_uc003kmc.2_Missense_Mutation_p.D346G|CAST_uc003kmd.2_Missense_Mutation_p.D324G|CAST_uc003kme.2_Missense_Mutation_p.D305G|CAST_uc003kmf.2_Missense_Mutation_p.D311G|CAST_uc003kmh.2_Missense_Mutation_p.D61G|CAST_uc010jbj.2_Missense_Mutation_p.D61G|CAST_uc010jbk.2_Missense_Mutation_p.D61G|CAST_uc010jbl.1_Missense_Mutation_p.D69G|CAST_uc003kmi.2_RNA|CAST_uc003kmj.2_Missense_Mutation_p.D69G	NM_001042443	NP_001035908	P20810	ICAL_HUMAN	calpastatin isoform i	346	Inhibitory domain 2.						calcium-dependent cysteine-type endopeptidase inhibitor activity|protein binding			central_nervous_system(3)|ovary(1)|kidney(1)	5		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)		CATTTACAGGATAAAGATGGA	0.313													18	80	---	---	---	---	PASS
PCDHA1	56147	broad.mit.edu	37	5	140167125	140167125	+	Missense_Mutation	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140167125G>A	uc003lhb.2	+	1	1250	c.1250G>A	c.(1249-1251)AGC>AAC	p.S417N	PCDHA1_uc003lha.2_Missense_Mutation_p.S417N|PCDHA1_uc003lgz.2_Missense_Mutation_p.S417N	NM_018900	NP_061723	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1 isoform 1 precursor	417	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GATCGCGAGAGCCTGTCGGTC	0.627													11	189	---	---	---	---	PASS
DOCK2	1794	broad.mit.edu	37	5	169111316	169111316	+	Silent	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169111316C>T	uc003maf.2	+	8	803	c.723C>T	c.(721-723)TTC>TTT	p.F241F	DOCK2_uc011der.1_RNA	NM_004946	NP_004937	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	241					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)			CTGAGCTCTTCATGTCTCTCT	0.483													5	243	---	---	---	---	PASS
RPL26L1	51121	broad.mit.edu	37	5	172396424	172396424	+	Silent	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172396424C>T	uc003mcc.2	+	4	360	c.318C>T	c.(316-318)ATC>ATT	p.I106I		NM_016093	NP_057177	Q9UNX3	RL26L_HUMAN	ribosomal protein L26-like 1	106					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|large ribosomal subunit	structural constituent of ribosome				0	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			AGGTGGTTATCACCAGGCTAA	0.398													25	157	---	---	---	---	PASS
F13A1	2162	broad.mit.edu	37	6	6305716	6305716	+	Missense_Mutation	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6305716C>A	uc003mwv.2	-	3	310	c.187G>T	c.(187-189)GTG>TTG	p.V63L	F13A1_uc011dib.1_Intron	NM_000129	NP_000120	P00488	F13A_HUMAN	coagulation factor XIII A1 subunit precursor	63					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)	TGGTGGTCCACCTTGTTAGTG	0.433													15	165	---	---	---	---	PASS
F13A1	2162	broad.mit.edu	37	6	6305717	6305717	+	Missense_Mutation	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6305717C>A	uc003mwv.2	-	3	309	c.186G>T	c.(184-186)AAG>AAT	p.K62N	F13A1_uc011dib.1_Intron	NM_000129	NP_000120	P00488	F13A_HUMAN	coagulation factor XIII A1 subunit precursor	62					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)	GGTGGTCCACCTTGTTAGTGT	0.428													16	165	---	---	---	---	PASS
HLA-DRA	3122	broad.mit.edu	37	6	32411252	32411252	+	Intron	SNP	C	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32411252C>G	uc003obh.2	+						HLA-DRA_uc003obi.2_Intron	NM_019111	NP_061984	P01903	DRA_HUMAN	major histocompatibility complex, class II, DR						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endoplasmic reticulum membrane|Golgi apparatus|integral to plasma membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity			ovary(1)|skin(1)	2						GGGTATGGACCAACACTCAAT	0.463									T-cell_Lymphoma_(Cutaneous)__Familial_Clustering_of|Kaposi_Sarcoma_Familial_Clustering_of				8	127	---	---	---	---	PASS
RUNX2	860	broad.mit.edu	37	6	45480107	45480107	+	Silent	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45480107G>A	uc011dvx.1	+	7	1194	c.984G>A	c.(982-984)GGG>GGA	p.G328G	RUNX2_uc011dvy.1_Silent_p.G328G|RUNX2_uc003oxt.2_Silent_p.G314G	NM_001024630	NP_001019801	Q13950	RUNX2_HUMAN	runt-related transcription factor 2 isoform a	328	Pro/Ser/Thr-rich.				negative regulation of transcription, DNA-dependent|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3						GGGGCACTGGGCTTCCTGCCA	0.597													12	135	---	---	---	---	PASS
C6orf138	442213	broad.mit.edu	37	6	47846506	47846506	+	Missense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47846506C>T	uc011dwm.1	-	3	2108	c.2023G>A	c.(2023-2025)GTC>ATC	p.V675I	C6orf138_uc011dwn.1_Missense_Mutation_p.V439I	NM_001013732	NP_001013754	Q6ZW05	CF138_HUMAN	hypothetical protein LOC442213	692	Helical; (Potential).					integral to membrane	hedgehog receptor activity			central_nervous_system(1)	1						ATTGAGGTGACGCTAAGAATT	0.453													11	63	---	---	---	---	PASS
PKHD1	5314	broad.mit.edu	37	6	51944713	51944713	+	Missense_Mutation	SNP	A	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51944713A>C	uc003pah.1	-	5	651	c.375T>G	c.(373-375)GAT>GAG	p.D125E	PKHD1_uc003pai.2_Missense_Mutation_p.D125E	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	125	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)					AAGTACAGCTATCTCGTGGTC	0.473													43	397	---	---	---	---	PASS
LGSN	51557	broad.mit.edu	37	6	63995564	63995564	+	Missense_Mutation	SNP	C	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63995564C>G	uc003peh.2	-	3	292	c.258G>C	c.(256-258)CAG>CAC	p.Q86H	LGSN_uc003pei.2_Missense_Mutation_p.Q86H|LGSN_uc003pej.1_3'UTR	NM_016571	NP_057655	Q5TDP6	LGSN_HUMAN	lengsin, lens protein with glutamine synthetase	86					glutamine biosynthetic process		glutamate-ammonia ligase activity			skin(2)	2					L-Glutamic Acid(DB00142)	ATCGTACAAACTGGAGGCGAT	0.443													14	98	---	---	---	---	PASS
COL12A1	1303	broad.mit.edu	37	6	75799856	75799856	+	Missense_Mutation	SNP	G	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75799856G>C	uc003phs.2	-	63	9077	c.8911C>G	c.(8911-8913)CCA>GCA	p.P2971A	COL12A1_uc003pht.2_Missense_Mutation_p.P1807A	NM_004370	NP_004361	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1 long isoform	2971	Triple-helical region (COL1) with 2 imperfections.				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						TGCATCCCTGGTGTGCCCGGG	0.627													35	312	---	---	---	---	PASS
FBXO30	84085	broad.mit.edu	37	6	146126628	146126628	+	Missense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146126628C>T	uc003qla.2	-	2	1113	c.914G>A	c.(913-915)GGT>GAT	p.G305D	uc003qky.1_Intron	NM_032145	NP_115521	Q8TB52	FBX30_HUMAN	F-box only protein 30	305							ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|large_intestine(1)	3		Ovarian(120;0.0776)		OV - Ovarian serous cystadenocarcinoma(155;1.95e-07)|GBM - Glioblastoma multiforme(68;0.0149)		TTTTGAATCACCATGTAAATT	0.403													13	263	---	---	---	---	PASS
NOX3	50508	broad.mit.edu	37	6	155750042	155750042	+	Missense_Mutation	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155750042G>T	uc003qqm.2	-	9	1134	c.1031C>A	c.(1030-1032)CCC>CAC	p.P344H		NM_015718	NP_056533	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	344	Extracellular (Potential).|FAD-binding FR-type.						electron carrier activity|flavin adenine dinucleotide binding|iron ion binding			ovary(1)	1		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		GTCCTCCTGGGGGGCAGAGGT	0.607													16	160	---	---	---	---	PASS
PARK2	5071	broad.mit.edu	37	6	162475185	162475185	+	Missense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162475185C>T	uc003qtx.3	-	5	690	c.556G>A	c.(556-558)GTT>ATT	p.V186I	PARK2_uc003qtv.3_RNA|PARK2_uc010kkd.2_5'UTR|PARK2_uc003qtw.3_5'UTR|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Missense_Mutation_p.V186I	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1	186					aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		GGAATTAAAACATCATCCCAG	0.398													10	132	---	---	---	---	PASS
MICALL2	79778	broad.mit.edu	37	7	1478561	1478561	+	Missense_Mutation	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1478561C>A	uc003skj.3	-	10	2184	c.2037G>T	c.(2035-2037)TGG>TGT	p.W679C	MICALL2_uc003skh.3_5'UTR|MICALL2_uc003ski.3_Missense_Mutation_p.W166C	NM_182924	NP_891554	Q8IY33	MILK2_HUMAN	MICAL-like 2 isoform 1	679						cytoplasm|cytoskeleton	zinc ion binding			central_nervous_system(1)	1		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		CCGGCCGAAGCCAGTTGTCAC	0.677													11	56	---	---	---	---	PASS
MMD2	221938	broad.mit.edu	37	7	4947058	4947058	+	Missense_Mutation	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4947058G>A	uc003sno.3	-	7	978	c.782C>T	c.(781-783)CCC>CTC	p.P261L	MMD2_uc003snl.1_Intron|MMD2_uc003snn.3_Missense_Mutation_p.P237L|MMD2_uc010ksq.2_3'UTR	NM_001100600	NP_001094070	Q8IY49	PAQRA_HUMAN	monocyte to macrophage	261	Extracellular (Potential).					integral to membrane	receptor activity			central_nervous_system(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.097)|OV - Ovarian serous cystadenocarcinoma(56;3.4e-14)		CAGGGTGCTGGGCAGATAGAG	0.537													26	174	---	---	---	---	PASS
GRB10	2887	broad.mit.edu	37	7	50660793	50660793	+	Silent	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50660793G>A	uc003tpi.2	-	16	1672	c.1641C>T	c.(1639-1641)TGC>TGT	p.C547C	GRB10_uc003tph.3_Silent_p.C489C|GRB10_uc003tpj.2_Silent_p.C501C|GRB10_uc003tpk.2_Silent_p.C547C|GRB10_uc010kzb.2_Silent_p.C489C|GRB10_uc003tpl.2_Silent_p.C541C|GRB10_uc003tpm.2_Silent_p.C489C|GRB10_uc003tpn.2_Silent_p.C489C	NM_005311	NP_005302	Q13322	GRB10_HUMAN	growth factor receptor-bound protein 10 isoform	547	SH2.				insulin receptor signaling pathway|insulin receptor signaling pathway|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway	cytosol|plasma membrane	insulin receptor binding|insulin receptor binding|SH3/SH2 adaptor activity			lung(3)|ovary(2)|upper_aerodigestive_tract(1)	6	Glioma(55;0.08)|all_neural(89;0.245)					CGTCGTCCTCGCACTGGAGAG	0.552									Russell-Silver_syndrome				13	101	---	---	---	---	PASS
MGC26647	219557	broad.mit.edu	37	7	88424009	88424009	+	Missense_Mutation	SNP	T	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88424009T>C	uc003ujv.2	-	2	430	c.248A>G	c.(247-249)GAA>GGA	p.E83G	ZNF804B_uc011khi.1_Intron	NM_152706	NP_689919	Q8TBZ9	CG062_HUMAN	hypothetical protein LOC219557	83											0	Esophageal squamous(14;0.00802)|all_hematologic(106;0.109)|Lung NSC(181;0.168)|all_lung(186;0.169)		STAD - Stomach adenocarcinoma(171;0.229)			TGTCACTGCTTCTCCTAGGTG	0.403													3	153	---	---	---	---	PASS
ALKBH4	54784	broad.mit.edu	37	7	102098423	102098423	+	Silent	SNP	A	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102098423A>G	uc003uzl.2	-	3	332	c.327T>C	c.(325-327)TAT>TAC	p.Y109Y	ALKBH4_uc003uzm.2_Silent_p.Y36Y	NM_017621	NP_060091	Q9NXW9	ALKB4_HUMAN	alkB, alkylation repair homolog 4	109						cytoplasm|nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						CTTTGGGGCCATAGTCCTGAA	0.453													7	68	---	---	---	---	PASS
ARF5	381	broad.mit.edu	37	7	127231094	127231094	+	Silent	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127231094G>T	uc003vmb.1	+	5	444	c.408G>T	c.(406-408)GTG>GTT	p.V136V	FSCN3_uc003vmc.1_5'Flank|FSCN3_uc011kog.1_5'Flank|FSCN3_uc011koh.1_5'Flank|FSCN3_uc003vmd.1_5'Flank|FSCN3_uc010llc.1_5'Flank	NM_001662	NP_001653	P84085	ARF5_HUMAN	ADP-ribosylation factor 5	136					protein transport|small GTPase mediated signal transduction|vesicle-mediated transport	Golgi apparatus|perinuclear region of cytoplasm	GTP binding|GTPase activity|protein binding			ovary(1)	1						CCATGCCCGTGAGCGAGCTGA	0.607													30	221	---	---	---	---	PASS
CALD1	800	broad.mit.edu	37	7	134617824	134617824	+	Silent	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134617824C>A	uc003vrz.2	+	5	763	c.304C>A	c.(304-306)CGG>AGG	p.R102R	CALD1_uc003vry.2_Silent_p.R102R|CALD1_uc003vsa.2_Silent_p.R102R|CALD1_uc003vsb.2_Silent_p.R102R|CALD1_uc010lmm.2_Silent_p.R102R|CALD1_uc011kpt.1_Intron|CALD1_uc003vsc.2_Silent_p.R96R|CALD1_uc003vsd.2_Silent_p.R96R|CALD1_uc011kpu.1_Silent_p.R107R|CALD1_uc011kpv.1_5'UTR|CALD1_uc003vse.2_5'UTR	NM_033138	NP_149129	Q05682	CALD1_HUMAN	caldesmon 1 isoform 1	102	Myosin and calmodulin-binding (By similarity).				cellular component movement|muscle contraction	cytosol|focal adhesion|myofibril	actin binding|calmodulin binding|myosin binding|tropomyosin binding				0						GCGCCTGGCTCGGCGTGAGGA	0.562													9	70	---	---	---	---	PASS
DPP6	1804	broad.mit.edu	37	7	154379801	154379801	+	Intron	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154379801C>A	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_3'UTR|DPP6_uc003wlm.2_Intron|DPP6_uc011kvq.1_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)			GTGAGCCTTGCAGCCTCTGCT	0.582													9	52	---	---	---	---	PASS
MYOM2	9172	broad.mit.edu	37	8	2044123	2044123	+	Missense_Mutation	SNP	A	T	T	rs62478391	byFrequency	TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2044123A>T	uc003wpx.3	+	18	2300	c.2162A>T	c.(2161-2163)AAC>ATC	p.N721I	MYOM2_uc011kwi.1_Missense_Mutation_p.N146I	NM_003970	NP_003961	P54296	MYOM2_HUMAN	myomesin 2	721	Fibronectin type-III 4.				muscle contraction	myosin filament	structural constituent of muscle			ovary(4)|central_nervous_system(1)|skin(1)	6		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		ACGCTCCTCAACTGTGACGGC	0.602													17	146	---	---	---	---	PASS
CSMD1	64478	broad.mit.edu	37	8	2820848	2820848	+	Missense_Mutation	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2820848G>T	uc011kwk.1	-	60	9743	c.9353C>A	c.(9352-9354)TCC>TAC	p.S3118Y	CSMD1_uc011kwj.1_Missense_Mutation_p.S2447Y|CSMD1_uc010lrg.2_Missense_Mutation_p.S1009Y	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	3118	Sushi 25.|Extracellular (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)		ACTTATGCTGGAGCCCCAGCG	0.552													25	244	---	---	---	---	PASS
CSGALNACT1	55790	broad.mit.edu	37	8	19315990	19315990	+	Silent	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19315990G>A	uc011kyn.1	-	5	1862	c.798C>T	c.(796-798)ATC>ATT	p.I266I	CSGALNACT1_uc011kyo.1_Silent_p.I266I|CSGALNACT1_uc003wzg.2_RNA|CSGALNACT1_uc011kyp.1_Silent_p.I265I|CSGALNACT1_uc003wzh.2_RNA	NM_001130518	NP_001123990	Q8TDX6	CGAT1_HUMAN	chondroitin sulfate	266	Lumenal (Potential).				anatomical structure morphogenesis|cell proliferation|cell recognition|chondroitin sulfate biosynthetic process|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process|extracellular matrix organization|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|heparin biosynthetic process|nervous system development|UDP-glucuronate metabolic process|UDP-N-acetylgalactosamine metabolic process	Golgi cisterna membrane|integral to Golgi membrane|soluble fraction	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|glucuronosyltransferase activity|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|peptidoglycan glycosyltransferase activity			central_nervous_system(2)|ovary(1)	3				Colorectal(111;0.182)		CTAGAGGCACGATAACATTGA	0.438													87	652	---	---	---	---	PASS
RP1	6101	broad.mit.edu	37	8	55538745	55538745	+	Missense_Mutation	SNP	C	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55538745C>G	uc003xsd.1	+	4	2451	c.2303C>G	c.(2302-2304)TCC>TGC	p.S768C	RP1_uc011ldy.1_Intron	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	768					axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			ACTCAAAATTCCAAGGTTCAA	0.289													7	87	---	---	---	---	PASS
RDH10	157506	broad.mit.edu	37	8	74209560	74209560	+	Missense_Mutation	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74209560G>A	uc003xzi.2	+	2	681	c.421G>A	c.(421-423)GTC>ATC	p.V141I	RDH10_uc003xzj.2_5'UTR	NM_172037	NP_742034	Q8IZV5	RDH10_HUMAN	retinol dehydrogenase 10	141					retinal metabolic process|retinol metabolic process|visual perception	endoplasmic reticulum membrane|integral to membrane|microsome	binding|NADP-retinol dehydrogenase activity|retinol dehydrogenase activity				0	Breast(64;0.0954)		Epithelial(68;0.0105)|all cancers(69;0.0465)|BRCA - Breast invasive adenocarcinoma(89;0.0608)			CGAAGTCTCAGTCCTGGTCAA	0.507													9	211	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113651048	113651048	+	Missense_Mutation	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113651048G>T	uc003ynu.2	-	21	3562	c.3403C>A	c.(3403-3405)CGC>AGC	p.R1135S	CSMD3_uc003yns.2_Missense_Mutation_p.R407S|CSMD3_uc003ynt.2_Missense_Mutation_p.R1095S|CSMD3_uc011lhx.1_Missense_Mutation_p.R1031S	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	1135	Extracellular (Potential).|CUB 6.					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						CCAGTCAGGCGTGCCAGTGGT	0.408										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			25	118	---	---	---	---	PASS
ASAP1	50807	broad.mit.edu	37	8	131199540	131199540	+	Intron	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131199540C>A	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						TCCTTAGAAACGAGAAAATGA	0.299													3	95	---	---	---	---	PASS
TAF1L	138474	broad.mit.edu	37	9	32635064	32635064	+	Missense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32635064C>T	uc003zrg.1	-	1	604	c.514G>A	c.(514-516)GAT>AAT	p.D172N	uc003zrh.1_Intron	NM_153809	NP_722516	Q8IZX4	TAF1L_HUMAN	TBP-associated factor RNA polymerase 1-like	172					male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	transcription factor TFIID complex	DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding			lung(8)|skin(6)|central_nervous_system(4)|large_intestine(3)|ovary(2)|stomach(1)|breast(1)|pancreas(1)	26			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		GTAATAGCATCTTGGTCCTTA	0.458													5	126	---	---	---	---	PASS
C9orf23	138716	broad.mit.edu	37	9	34610935	34610935	+	Missense_Mutation	SNP	A	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34610935A>T	uc003zuu.2	-	2	640	c.359T>A	c.(358-360)CTG>CAG	p.L120Q	C9orf23_uc003zuv.2_Missense_Mutation_p.L120Q	NM_148179	NP_680545	Q8N5L8	CI023_HUMAN	hypothetical protein LOC138716	120							nucleic acid binding				0	all_epithelial(49;0.0863)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.0385)		CCGGCTGAGCAGCACCCACAC	0.652													13	67	---	---	---	---	PASS
OR1L4	254973	broad.mit.edu	37	9	125486388	125486388	+	Silent	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125486388G>A	uc004bmu.1	+	1	120	c.120G>A	c.(118-120)GCG>GCA	p.A40A		NM_001005235	NP_001005235	Q8NGR5	OR1L4_HUMAN	olfactory receptor, family 1, subfamily L,	40	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TACTCACTGCGGTGGGGAATG	0.517													13	225	---	---	---	---	PASS
ZBTB43	23099	broad.mit.edu	37	9	129595397	129595397	+	Missense_Mutation	SNP	T	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129595397T>G	uc004bql.2	+	3	882	c.609T>G	c.(607-609)CAT>CAG	p.H203Q	ZBTB43_uc010mxf.2_Missense_Mutation_p.H203Q	NM_014007	NP_054726	O43298	ZBT43_HUMAN	zinc finger and BTB domain containing 43	203					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						CCACAGAGCATGACCGCCTGA	0.592													9	43	---	---	---	---	PASS
EXD3	54932	broad.mit.edu	37	9	140243631	140243631	+	Silent	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140243631G>A	uc004cmp.2	-	16	1957	c.1761C>T	c.(1759-1761)CAC>CAT	p.H587H	C9orf167_uc011mew.1_Intron|EXD3_uc010ncf.1_Silent_p.H267H|EXD3_uc004cmq.1_RNA	NM_017820	NP_060290	Q8N9H8	MUT7_HUMAN	exonuclease 3'-5' domain containing 3	587					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding				0						GTCTCTCTCTGTGCCTGGGCC	0.697													3	14	---	---	---	---	PASS
CUBN	8029	broad.mit.edu	37	10	17032472	17032472	+	Missense_Mutation	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17032472C>A	uc001ioo.2	-	29	4263	c.4211G>T	c.(4210-4212)AGC>ATC	p.S1404I		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	1404	CUB 9.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GAACCCGGGGCTGCTGAAGGA	0.512													13	116	---	---	---	---	PASS
GPR158	57512	broad.mit.edu	37	10	25887797	25887797	+	Missense_Mutation	SNP	T	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25887797T>C	uc001isj.2	+	11	3302	c.3242T>C	c.(3241-3243)ATT>ACT	p.I1081T	GPR158_uc001isk.2_Missense_Mutation_p.I456T	NM_020752	NP_065803	Q5T848	GP158_HUMAN	G protein-coupled receptor 158 precursor	1081	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)|large_intestine(2)|pancreas(1)|skin(1)	8						GGCCAGTCCATTTTGGAAGAT	0.502													40	247	---	---	---	---	PASS
MYO3A	53904	broad.mit.edu	37	10	26310458	26310458	+	Missense_Mutation	SNP	T	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26310458T>A	uc001isn.2	+	8	972	c.612T>A	c.(610-612)GAT>GAA	p.D204E	MYO3A_uc009xko.1_Missense_Mutation_p.D204E|MYO3A_uc009xkp.1_RNA|MYO3A_uc009xkq.1_Missense_Mutation_p.D204E|MYO3A_uc001ism.2_Missense_Mutation_p.D204E	NM_017433	NP_059129	Q8NEV4	MYO3A_HUMAN	myosin IIIA	204	Protein kinase.				protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception	cytoplasm|filamentous actin|filopodium|myosin complex	actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity			ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	18						AGCAATTGGATACCACTTATG	0.433													6	241	---	---	---	---	PASS
ZNF438	220929	broad.mit.edu	37	10	31138498	31138498	+	Missense_Mutation	SNP	T	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31138498T>C	uc010qdz.1	-	7	1271	c.836A>G	c.(835-837)AAT>AGT	p.N279S	ZNF438_uc001ivn.2_Missense_Mutation_p.N230S|ZNF438_uc010qdy.1_Missense_Mutation_p.N269S|ZNF438_uc001ivo.3_Intron|ZNF438_uc009xlg.2_Missense_Mutation_p.N279S|ZNF438_uc001ivp.3_Missense_Mutation_p.N269S|ZNF438_uc010qea.1_Missense_Mutation_p.N279S|ZNF438_uc010qeb.1_Missense_Mutation_p.N279S|ZNF438_uc010qec.1_Intron	NM_182755	NP_877432	Q7Z4V0	ZN438_HUMAN	zinc finger protein 438 isoform a	279					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)	2		Prostate(175;0.0587)				CTGAACTGCATTGCCAAGAAT	0.388													17	477	---	---	---	---	PASS
NRP1	8829	broad.mit.edu	37	10	33502318	33502318	+	Missense_Mutation	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33502318G>A	uc001iwx.3	-	9	2133	c.1610C>T	c.(1609-1611)GCG>GTG	p.A537V	NRP1_uc001iwv.3_Missense_Mutation_p.A537V|NRP1_uc009xlz.2_Missense_Mutation_p.A537V|NRP1_uc001iww.3_Missense_Mutation_p.A356V|NRP1_uc001iwy.3_Missense_Mutation_p.A537V|NRP1_uc001iwz.2_Missense_Mutation_p.A537V|NRP1_uc001ixa.2_Missense_Mutation_p.A537V|NRP1_uc001ixb.1_Missense_Mutation_p.A537V|NRP1_uc001ixc.1_Missense_Mutation_p.A537V	NM_003873	NP_003864	O14786	NRP1_HUMAN	neuropilin 1 isoform a	537	Extracellular (Potential).|F5/8 type C 2.				axon guidance|cell adhesion|cell-cell signaling|organ morphogenesis|positive regulation of cell proliferation	extracellular region|integral to membrane|plasma membrane	growth factor binding|heparin binding|metal ion binding|vascular endothelial growth factor receptor activity			central_nervous_system(2)|ovary(1)|skin(1)	4					Palifermin(DB00039)|Pegaptanib(DB04895)	CCTCACCTTCGCCTTGCGTTT	0.522													8	376	---	---	---	---	PASS
CTNNA3	29119	broad.mit.edu	37	10	68280441	68280441	+	Missense_Mutation	SNP	G	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68280441G>C	uc009xpn.1	-	11	1588	c.1465C>G	c.(1465-1467)CAT>GAT	p.H489D	CTNNA3_uc001jmw.2_Missense_Mutation_p.H489D|CTNNA3_uc001jmx.3_Missense_Mutation_p.H489D	NM_001127384	NP_001120856	Q9UI47	CTNA3_HUMAN	catenin, alpha 3	489					cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8						ACATGTATATGATTCTCCCAT	0.358													38	198	---	---	---	---	PASS
PPP1R3C	5507	broad.mit.edu	37	10	93390049	93390049	+	Missense_Mutation	SNP	T	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93390049T>C	uc001kho.2	-	2	721	c.589A>G	c.(589-591)ACT>GCT	p.T197A		NM_005398	NP_005389	Q9UQK1	PPR3C_HUMAN	protein phosphatase 1, regulatory (inhibitor)	197	Interaction with EPM2A.|CBM21.						protein serine/threonine phosphatase activity			breast(1)	1		Colorectal(252;0.235)				TCTACGTCAGTGTAGTTTTTC	0.408													30	172	---	---	---	---	PASS
CYP2C9	1559	broad.mit.edu	37	10	96702109	96702109	+	Intron	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96702109C>T	uc001kka.3	+						CYP2C9_uc009xut.2_Intron|CYP2C9_uc001kjz.2_3'UTR	NM_000771	NP_000762	P11712	CP2C9_HUMAN	cytochrome P450, family 2, subfamily C,						exogenous drug catabolic process|monocarboxylic acid metabolic process|monoterpenoid metabolic process|oxidative demethylation|steroid metabolic process|urea metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	(S)-limonene 6-monooxygenase activity|(S)-limonene 7-monooxygenase activity|4-hydroxyacetophenone monooxygenase activity|caffeine oxidase activity|drug binding|electron carrier activity|heme binding|oxygen binding|steroid hydroxylase activity			skin(4)|ovary(2)	6		Colorectal(252;0.0902)		all cancers(201;6.93e-05)	Acenocoumarol(DB01418)|Alosetron(DB00969)|Amiodarone(DB01118)|Antihemophilic Factor(DB00025)|Aprepitant(DB00673)|Bosentan(DB00559)|Carprofen(DB00821)|Carvedilol(DB01136)|Celecoxib(DB00482)|Clomipramine(DB01242)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Desogestrel(DB00304)|Diclofenac(DB00586)|Esomeprazole(DB00736)|Etodolac(DB00749)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Glibenclamide(DB01016)|Glimepiride(DB00222)|Glipizide(DB01067)|Guanfacine(DB01018)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Imipramine(DB00458)|Irbesartan(DB01029)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Losartan(DB00678)|Lumiracoxib(DB01283)|Marinol(DB00470)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mephenytoin(DB00532)|Metronidazole(DB00916)|Miconazole(DB01110)|Midazolam(DB00683)|Montelukast(DB00471)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Oxymorphone(DB01192)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pravastatin(DB00175)|Quinidine(DB00908)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Sertraline(DB01104)|Sildenafil(DB00203)|Sulfamethoxazole(DB01015)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tenoxicam(DB00469)|Terfenadine(DB00342)|Tolbutamide(DB01124)|Torasemide(DB00214)|Troleandomycin(DB01361)|Valdecoxib(DB00580)|Valsartan(DB00177)|Voriconazole(DB00582)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zileuton(DB00744)	GTGGGTGACCCTACTCCATAT	0.483													14	167	---	---	---	---	PASS
XPNPEP1	7511	broad.mit.edu	37	10	111667494	111667494	+	Silent	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111667494G>A	uc001kyp.1	-	3	212	c.72C>T	c.(70-72)ACC>ACT	p.T24T	XPNPEP1_uc009xxt.1_Silent_p.T67T|XPNPEP1_uc001kyq.1_5'UTR|XPNPEP1_uc010qrb.1_Silent_p.T67T	NM_020383	NP_065116	Q9NQW7	XPP1_HUMAN	X-prolyl aminopeptidase (aminopeptidase P) 1,	24					bradykinin catabolic process|proteolysis		manganese ion binding|metalloaminopeptidase activity|protein homodimerization activity			ovary(3)|pancreas(1)	4		Breast(234;0.174)		Epithelial(162;1.64e-05)|all cancers(201;0.000564)|BRCA - Breast invasive adenocarcinoma(275;0.0721)		GGATCGGTTCGGTCACATACT	0.522													20	211	---	---	---	---	PASS
SMPD1	6609	broad.mit.edu	37	11	6412896	6412896	+	Missense_Mutation	SNP	A	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6412896A>G	uc001mcw.2	+	2	775	c.601A>G	c.(601-603)AGC>GGC	p.S201G	SMPD1_uc001mcv.1_Intron|SMPD1_uc009yex.2_RNA|SMPD1_uc001mcx.2_Missense_Mutation_p.S201G|SMPD1_uc009yew.2_Missense_Mutation_p.S200G	NM_000543	NP_000534	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid	199					cell death|ceramide biosynthetic process|negative regulation of MAP kinase activity|nervous system development|positive regulation of protein dephosphorylation|signal transduction|sphingomyelin catabolic process|termination of signal transduction	lysosome	hydrolase activity, acting on glycosyl bonds|sphingomyelin phosphodiesterase activity				0		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Desipramine(DB01151)	TGCCCCTGTCAGCCGCATCCT	0.627													3	21	---	---	---	---	PASS
RASSF10	644943	broad.mit.edu	37	11	13032263	13032263	+	Silent	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13032263C>T	uc001mkn.1	+	2	1464	c.1464C>T	c.(1462-1464)GAC>GAT	p.D488D		NM_001080521	NP_001073990	A6NK89	RASFA_HUMAN	Ras association (RalGDS/AF-6) domain family	380					signal transduction						0				Epithelial(150;0.00399)		GTGGCCCCGACGGCGAGCTGC	0.672													2	1	---	---	---	---	PASS
RCN1	5954	broad.mit.edu	37	11	32118819	32118819	+	Silent	SNP	T	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32118819T>C	uc010reb.1	+	2	650	c.384T>C	c.(382-384)GAT>GAC	p.D128D	RCN1_uc010rea.1_Silent_p.D77D|RCN1_uc001mtk.2_5'UTR	NM_002901	NP_002892	Q15293	RCN1_HUMAN	reticulocalbin 1 precursor	128	EF-hand 2.|2; possibly ancestral (Potential).					endoplasmic reticulum lumen	calcium ion binding			large_intestine(1)	1	Lung SC(675;0.225)					AGGATTATGATAGGGACAAGG	0.458													9	46	---	---	---	---	PASS
NR1H3	10062	broad.mit.edu	37	11	47290247	47290247	+	Nonstop_Mutation	SNP	A	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47290247A>T	uc009ylm.2	+	10	1565	c.1344A>T	c.(1342-1344)TGA>TGT	p.*448C	MADD_uc001neq.2_5'Flank|MADD_uc001ner.1_5'Flank|MADD_uc001nev.1_5'Flank|MADD_uc001nes.1_5'Flank|MADD_uc001net.1_5'Flank|MADD_uc009yln.1_5'Flank|MADD_uc001neu.1_5'Flank|MADD_uc001nex.2_5'Flank|MADD_uc001nez.2_5'Flank|MADD_uc001new.2_5'Flank|NR1H3_uc010rhk.1_Nonstop_Mutation_p.*454C|NR1H3_uc001nek.2_Nonstop_Mutation_p.*403C|NR1H3_uc001nej.2_Nonstop_Mutation_p.*388C|NR1H3_uc001nel.2_Nonstop_Mutation_p.*467C|NR1H3_uc001nen.3_Nonstop_Mutation_p.*388C|NR1H3_uc001nem.2_Nonstop_Mutation_p.*448C|NR1H3_uc001nep.2_Nonstop_Mutation_p.*297C	NM_005693	NP_005684	Q13133	NR1H3_HUMAN	nuclear receptor subfamily 1, group H, member 3	448					apoptotic cell clearance|cellular response to lipopolysaccharide|cholesterol homeostasis|negative regulation of cholesterol storage|negative regulation of inflammatory response|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of lipid transport|negative regulation of macrophage activation|negative regulation of pancreatic juice secretion|negative regulation of pinocytosis|negative regulation of secretion of lysosomal enzymes|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cellular protein metabolic process|positive regulation of cholesterol efflux|positive regulation of cholesterol homeostasis|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of receptor biosynthetic process|positive regulation of toll-like receptor 4 signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of triglyceride biosynthetic process|regulation of circadian rhythm|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to progesterone stimulus|triglyceride homeostasis	nuclear chromatin|nucleoplasm	cholesterol binding|steroid hormone receptor activity|sterol response element binding|transcription coactivator activity|zinc ion binding			ovary(2)|lung(1)	3						TGCACGAATGACTGTTCTGTC	0.547													10	94	---	---	---	---	PASS
OR4A16	81327	broad.mit.edu	37	11	55111021	55111021	+	Silent	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55111021G>T	uc010rie.1	+	1	345	c.345G>T	c.(343-345)GTG>GTT	p.V115V		NM_001005274	NP_001005274	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A,	115	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(2)|pancreas(1)	3						TTTTGGTGGTGATGGCCTATG	0.458													12	481	---	---	---	---	PASS
OR4C16	219428	broad.mit.edu	37	11	55339883	55339883	+	Missense_Mutation	SNP	G	A	A	rs150706012	by1000genomes	TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55339883G>A	uc010rih.1	+	1	280	c.280G>A	c.(280-282)GAG>AAG	p.E94K		NM_001004701	NP_001004701	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C,	94	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		all_epithelial(135;0.0748)				CTCCTTCAGCGAGTGCATGAT	0.458													44	358	---	---	---	---	PASS
OR10Q1	219960	broad.mit.edu	37	11	57995510	57995510	+	Missense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57995510C>T	uc010rkd.1	-	1	838	c.838G>A	c.(838-840)GCG>ACG	p.A280T		NM_001004471	NP_001004471	Q8NGQ4	O10Q1_HUMAN	olfactory receptor, family 10, subfamily Q,	280	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Breast(21;0.0589)				TAGACCAACGCGATTTGGCTG	0.547													12	126	---	---	---	---	PASS
OR10Q1	219960	broad.mit.edu	37	11	57995829	57995829	+	Silent	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57995829G>A	uc010rkd.1	-	1	519	c.519C>T	c.(517-519)TGC>TGT	p.C173C		NM_001004471	NP_001004471	Q8NGQ4	O10Q1_HUMAN	olfactory receptor, family 10, subfamily Q,	173	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Breast(21;0.0589)				GGTGGTGGCCGCAAAAGGGCA	0.652													4	59	---	---	---	---	PASS
ZFP91	80829	broad.mit.edu	37	11	58384221	58384221	+	Missense_Mutation	SNP	C	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58384221C>G	uc001nmx.3	+	10	1303	c.1135C>G	c.(1135-1137)CGG>GGG	p.R379G	ZFP91_uc001nmy.3_Missense_Mutation_p.R378G|ZFP91-CNTF_uc010rkm.1_RNA	NM_053023	NP_444251	Q96JP5	ZFP91_HUMAN	zinc finger protein 91	379	C2H2-type 3.				activation of NF-kappaB-inducing kinase activity|protein K63-linked ubiquitination	nucleus	nucleic acid binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				ATATTGTGCTCGGGCCTTCAA	0.403													5	88	---	---	---	---	PASS
PYGM	5837	broad.mit.edu	37	11	64517934	64517934	+	Silent	SNP	A	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64517934A>G	uc001oax.3	-	17	2908	c.2091T>C	c.(2089-2091)AAT>AAC	p.N697N	PYGM_uc001oay.3_Silent_p.N609N	NM_005609	NP_005600	P11217	PYGM_HUMAN	muscle glycogen phosphorylase isoform 1	697					glucose metabolic process|glycogen catabolic process	cytosol	glycogen phosphorylase activity|protein binding			ovary(2)	2					Pyridoxal Phosphate(DB00114)	CCATCTCCACATTGGCCCCGT	0.567													36	187	---	---	---	---	PASS
CDC42BPG	55561	broad.mit.edu	37	11	64606676	64606676	+	Silent	SNP	C	T	T	rs149531322		TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64606676C>T	uc001obs.3	-	7	705	c.705G>A	c.(703-705)CCG>CCA	p.P235P		NM_017525	NP_059995	Q6DT37	MRCKG_HUMAN	CDC42 binding protein kinase gamma (DMPK-like)	235	Protein kinase.				actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|centrosome	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(3)|central_nervous_system(1)	4						AGATATAGTCCGGCGTCCCTA	0.617													12	148	---	---	---	---	PASS
NPAS4	266743	broad.mit.edu	37	11	66189957	66189957	+	Missense_Mutation	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66189957C>A	uc001ohx.1	+	3	539	c.363C>A	c.(361-363)GAC>GAA	p.D121E	NPAS4_uc010rpc.1_5'UTR	NM_178864	NP_849195	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	121	PAS 1.				transcription, DNA-dependent		DNA binding|signal transducer activity				0						GCATCTACGACATCATTGACC	0.557													22	171	---	---	---	---	PASS
CCND1	595	broad.mit.edu	37	11	69458669	69458669	+	Missense_Mutation	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69458669G>A	uc001opa.2	+	3	693	c.484G>A	c.(484-486)GAA>AAA	p.E162K		NM_053056	NP_444284	P24385	CCND1_HUMAN	cyclin D1	162					cell division|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|mitotic cell cycle G1/S transition DNA damage checkpoint|positive regulation of cyclin-dependent protein kinase activity|positive regulation of protein phosphorylation|response to drug|response to UV-A|S phase of mitotic cell cycle	cyclin-dependent protein kinase holoenzyme complex|cytosol|membrane|nucleoplasm	protein kinase binding			ovary(1)|lung(1)	2	all_cancers(3;2.01e-114)|all_epithelial(3;3.59e-122)|Breast(3;5.4e-34)|all_lung(4;1.99e-21)|Lung NSC(4;4.65e-21)|Hepatocellular(3;8.22e-16)|Melanoma(5;1.89e-05)|Ovarian(3;0.0348)		Epithelial(3;7.2e-57)|all cancers(3;7.75e-51)|BRCA - Breast invasive adenocarcinoma(2;4.9e-48)|Lung(3;1.13e-16)|LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)|LUAD - Lung adenocarcinoma(13;0.0537)		Arsenic trioxide(DB01169)	CGATTTCATTGAACACTTCCT	0.572			T	IGH@|FSTL3	CLL|B-ALL|breast					Multiple Myeloma(6;0.086)			10	72	---	---	---	---	PASS
FAT3	120114	broad.mit.edu	37	11	92614037	92614037	+	Missense_Mutation	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92614037C>A	uc001pdj.3	+	22	12285	c.12268C>A	c.(12268-12270)CTC>ATC	p.L4090I	FAT3_uc001pdi.3_Missense_Mutation_p.L530I	NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	4090	EGF-like 3.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TAAAGCTGGGCTCACTGGAGT	0.418										TCGA Ovarian(4;0.039)			61	377	---	---	---	---	PASS
APOA5	116519	broad.mit.edu	37	11	116661354	116661354	+	Silent	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116661354G>A	uc001ppr.2	-	3	599	c.591C>T	c.(589-591)AGC>AGT	p.S197S	ZNF259_uc001ppp.2_5'Flank|ZNF259_uc009yzd.2_5'Flank|ZNF259_uc001ppq.2_5'Flank|APOA5_uc009yze.2_Silent_p.S197S|APOA5_uc009yzf.2_Silent_p.S197S|APOA5_uc009yzg.2_Silent_p.S223S	NM_052968	NP_443200	Q6Q788	APOA5_HUMAN	apolipoprotein AV precursor	197					acylglycerol homeostasis|cholesterol homeostasis|lipid transport|lipoprotein metabolic process|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of receptor-mediated endocytosis|positive regulation of triglyceride catabolic process|positive regulation of very-low-density lipoprotein particle remodeling|tissue regeneration|triglyceride catabolic process|triglyceride homeostasis	chylomicron|high-density lipoprotein particle|very-low-density lipoprotein particle	enzyme binding|heparin binding|lipoprotein lipase activator activity|low-density lipoprotein particle receptor binding|phosphatidylcholine binding				0	all_hematologic(175;0.0487)	all_cancers(61;3.31e-09)|all_epithelial(67;8.03e-06)|Breast(348;0.0126)|Melanoma(852;0.0153)|Acute lymphoblastic leukemia(157;0.0257)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0433)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;4.93e-06)|all cancers(92;0.000123)|OV - Ovarian serous cystadenocarcinoma(223;0.149)		CGCTCACCAGGCTCTCGGCGT	0.711													5	28	---	---	---	---	PASS
SRPR	6734	broad.mit.edu	37	11	126134415	126134415	+	Missense_Mutation	SNP	G	T	T	rs149426729		TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126134415G>T	uc001qdh.2	-	12	1596	c.1545C>A	c.(1543-1545)GAC>GAA	p.D515E	SRPR_uc010sbm.1_Missense_Mutation_p.D487E	NM_003139	NP_003130	P08240	SRPR_HUMAN	signal recognition particle receptor	515					SRP-dependent cotranslational protein targeting to membrane	integral to membrane|signal recognition particle receptor complex	GTP binding|GTPase activity|receptor activity|signal recognition particle binding				0	all_hematologic(175;0.145)			BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0736)		CCAGCACCACGTCAAAGCCTT	0.507													3	84	---	---	---	---	PASS
CACNA2D4	93589	broad.mit.edu	37	12	1902853	1902853	+	Missense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1902853C>T	uc001qjp.2	-	38	3613	c.3382G>A	c.(3382-3384)GCC>ACC	p.A1128T	CACNA2D4_uc001qjo.2_Silent_p.V272V	NM_172364	NP_758952	Q7Z3S7	CA2D4_HUMAN	voltage-gated calcium channel alpha(2)delta-4	1128	Helical; (Potential).					integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			ovary(1)	1	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		AGCCCCCAGGCACACACAGGC	0.637													4	64	---	---	---	---	PASS
CLSTN3	9746	broad.mit.edu	37	12	7303566	7303566	+	Missense_Mutation	SNP	C	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7303566C>G	uc001qsr.2	+	16	2712	c.2434C>G	c.(2434-2436)CAC>GAC	p.H812D	CLSTN3_uc001qss.2_Missense_Mutation_p.H824D	NM_014718	NP_055533	Q9BQT9	CSTN3_HUMAN	calsyntenin 3 precursor	812	Extracellular (Potential).				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			large_intestine(1)	1						CCACCCCAGCCACGTGCTCAG	0.632													13	78	---	---	---	---	PASS
CLEC9A	283420	broad.mit.edu	37	12	10217439	10217439	+	Missense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10217439C>T	uc001qxa.2	+	8	1193	c.580C>T	c.(580-582)CCT>TCT	p.P194S		NM_207345	NP_997228	Q6UXN8	CLC9A_HUMAN	C-type lectin domain family 9, member A	194	Extracellular (Potential).|C-type lectin.				positive regulation of cytokine secretion|receptor-mediated endocytosis	cell surface|integral to membrane	receptor activity|sugar binding			ovary(1)	1						TGGCTCCTCTCCTTCTCCTGG	0.453													17	158	---	---	---	---	PASS
LRP6	4040	broad.mit.edu	37	12	12274355	12274355	+	Intron	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12274355C>A	uc001rah.3	-						BCL2L14_uc001raf.1_Intron|LRP6_uc010shl.1_Intron	NM_002336	NP_002327	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein						cellular response to cholesterol|negative regulation of protein phosphorylation|negative regulation of protein serine/threonine kinase activity|negative regulation of smooth muscle cell apoptosis|neural crest formation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell cycle|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	cell surface|cytoplasmic vesicle|endoplasmic reticulum|integral to membrane|plasma membrane	coreceptor activity|frizzled binding|kinase inhibitor activity|low-density lipoprotein receptor activity|protein homodimerization activity|toxin transporter activity|Wnt-protein binding			lung(4)|skin(4)|ovary(2)|kidney(1)|central_nervous_system(1)	12		Prostate(47;0.0865)				TGGCCTGTAGCTGGTATAGGG	0.438													7	230	---	---	---	---	PASS
NELL2	4753	broad.mit.edu	37	12	45209854	45209854	+	Missense_Mutation	SNP	T	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45209854T>C	uc001rog.2	-	3	845	c.250A>G	c.(250-252)AAA>GAA	p.K84E	NELL2_uc001rof.3_Missense_Mutation_p.K83E|NELL2_uc001roh.2_Missense_Mutation_p.K84E|NELL2_uc009zkd.2_Missense_Mutation_p.K83E|NELL2_uc010skz.1_Missense_Mutation_p.K134E|NELL2_uc010sla.1_Missense_Mutation_p.K107E|NELL2_uc001roi.1_Missense_Mutation_p.K84E|NELL2_uc010slb.1_Missense_Mutation_p.K83E|NELL2_uc001roj.2_Missense_Mutation_p.K84E	NM_001145108	NP_001138580	Q99435	NELL2_HUMAN	NEL-like protein 2 isoform b precursor	84	TSP N-terminal.				cell adhesion	extracellular region	calcium ion binding|protein binding|structural molecule activity			skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		AATTCATGTTTATTTCTCAGC	0.353													44	264	---	---	---	---	PASS
DDN	23109	broad.mit.edu	37	12	49391375	49391375	+	Silent	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49391375C>T	uc001rsv.1	-	2	1302	c.1284G>A	c.(1282-1284)GAG>GAA	p.E428E	uc001rsw.2_5'Flank	NM_015086	NP_055901	O94850	DEND_HUMAN	dendrin	428	Interaction with CD2AP and NPHS1 (By similarity).|Interaction with ACTN1.					dendritic spine membrane|endoplasmic reticulum membrane|nucleus|perikaryon				large_intestine(1)	1						CCTTCCAACCCTCCAGGGTCT	0.667													23	101	---	---	---	---	PASS
DIP2B	57609	broad.mit.edu	37	12	51069240	51069240	+	Intron	SNP	A	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51069240A>G	uc001rwv.2	+						DIP2B_uc001rwu.2_Intron|DIP2B_uc009zls.1_Intron	NM_173602	NP_775873	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B							nucleus	catalytic activity|transcription factor binding			ovary(4)|breast(1)|pancreas(1)	6						AGGTAGTAGTAAAAATACCAA	0.219													9	63	---	---	---	---	PASS
ATP2B1	490	broad.mit.edu	37	12	89992485	89992485	+	Intron	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89992485G>A	uc001tbh.2	-						ATP2B1_uc001tbg.2_Silent_p.S1129S|ATP2B1_uc009zsr.2_RNA|ATP2B1_uc001tbf.2_Intron	NM_001682	NP_001673	P20020	AT2B1_HUMAN	plasma membrane calcium ATPase 1 isoform 1b						ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3						CCCCCTGAATGGAACTTCCAC	0.473													57	355	---	---	---	---	PASS
EPYC	1833	broad.mit.edu	37	12	91366587	91366587	+	Intron	SNP	T	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91366587T>C	uc001tbk.2	-							NM_004950	NP_004941	Q99645	EPYC_HUMAN	dermatan sulfate proteoglycan 3 precursor						female pregnancy	proteinaceous extracellular matrix	glycosaminoglycan binding			skin(1)	1						CCGTTAATGCTGTCATCCATA	0.378													17	192	---	---	---	---	PASS
DCN	1634	broad.mit.edu	37	12	91546946	91546946	+	Missense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91546946C>T	uc001tbs.2	-	5	767	c.673G>A	c.(673-675)GAA>AAA	p.E225K	DCN_uc001tbo.2_Missense_Mutation_p.E116K|DCN_uc001tbp.2_Missense_Mutation_p.E78K|DCN_uc001tbq.2_Intron|DCN_uc001tbr.2_Intron|DCN_uc001tbt.2_Missense_Mutation_p.E225K|DCN_uc001tbu.2_Missense_Mutation_p.E225K	NM_133503	NP_598010	P07585	PGS2_HUMAN	decorin isoform a preproprotein	225	LRR 7.				organ morphogenesis	extracellular space				central_nervous_system(2)|ovary(1)|lung(1)	4						AGATGTAATTCCGTAAGGGAA	0.343													11	147	---	---	---	---	PASS
SLC5A8	160728	broad.mit.edu	37	12	101603402	101603402	+	Silent	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101603402G>T	uc001thz.3	-	1	615	c.225C>A	c.(223-225)CCC>CCA	p.P75P		NM_145913	NP_666018	Q8N695	SC5A8_HUMAN	solute carrier family 5 (iodide transporter),	75	Extracellular (Potential).				apoptosis|sodium ion transport	apical plasma membrane|integral to membrane	monocarboxylic acid transmembrane transporter activity|passive transmembrane transporter activity|symporter activity				0						AGACCTCGGAGGGGGTGCCCA	0.592													8	62	---	---	---	---	PASS
POLR3B	55703	broad.mit.edu	37	12	106890610	106890610	+	Silent	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106890610C>T	uc001tlp.2	+	25	3120	c.2898C>T	c.(2896-2898)GGC>GGT	p.G966G	POLR3B_uc001tlq.2_Silent_p.G908G	NM_018082	NP_060552	Q9NW08	RPC2_HUMAN	DNA-directed RNA polymerase III B isoform 1	966					innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|ribonucleoside binding			ovary(1)|central_nervous_system(1)	2						CGTTTGGAGGCAGTAAAGTGA	0.522													11	99	---	---	---	---	PASS
UBE3B	89910	broad.mit.edu	37	12	109921676	109921676	+	Missense_Mutation	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109921676G>A	uc001top.2	+	4	775	c.172G>A	c.(172-174)GAT>AAT	p.D58N	UBE3B_uc001toq.2_Missense_Mutation_p.D58N|UBE3B_uc001tol.1_Missense_Mutation_p.D58N|UBE3B_uc001tom.2_Missense_Mutation_p.D58N|UBE3B_uc001ton.2_Missense_Mutation_p.D58N|UBE3B_uc001too.1_RNA|UBE3B_uc009zvj.1_Missense_Mutation_p.D58N|UBE3B_uc001tor.2_Missense_Mutation_p.D58N	NM_130466	NP_569733	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	58	IQ.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	ubiquitin-protein ligase activity			ovary(2)|lung(2)	4						GAGAGAGATTGATGACTTTTT	0.353													26	203	---	---	---	---	PASS
C12orf51	283450	broad.mit.edu	37	12	112677676	112677676	+	Intron	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112677676C>T	uc009zwc.2	-							NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2						AAGGCCTTTCCGTACTTACCT	0.383													3	108	---	---	---	---	PASS
TMEM132D	121256	broad.mit.edu	37	12	129559349	129559349	+	Missense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129559349C>T	uc009zyl.1	-	9	2699	c.2371G>A	c.(2371-2373)GCA>ACA	p.A791T	TMEM132D_uc001uia.2_Missense_Mutation_p.A329T	NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	791	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)		TTGATGTTTGCCGTTCCAACA	0.478													5	240	---	---	---	---	PASS
PABPC3	5042	broad.mit.edu	37	13	25671432	25671432	+	Missense_Mutation	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25671432G>T	uc001upy.2	+	1	1157	c.1096G>T	c.(1096-1098)GCT>TCT	p.A366S		NM_030979	NP_112241	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	366	RRM 4.				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)		ATTGTATGTAGCTTTAGCTCA	0.483													14	119	---	---	---	---	PASS
FAM123A	219287	broad.mit.edu	37	13	25744058	25744058	+	Missense_Mutation	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25744058G>T	uc001uqb.2	-	1	1800	c.1700C>A	c.(1699-1701)GCA>GAA	p.A567E	FAM123A_uc001uqa.2_Missense_Mutation_p.A448E|FAM123A_uc001uqc.2_Missense_Mutation_p.A448E	NM_152704	NP_689917	Q8N7J2	F123A_HUMAN	hypothetical protein LOC219287 isoform 1	567										ovary(2)|large_intestine(1)|lung(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)		AGGAAGGGTTGCTGGACTTCC	0.617													8	140	---	---	---	---	PASS
FLT1	2321	broad.mit.edu	37	13	28919626	28919626	+	Missense_Mutation	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28919626G>T	uc001usb.3	-	16	2596	c.2311C>A	c.(2311-2313)CTC>ATC	p.L771I	FLT1_uc001usa.3_5'UTR	NM_002019	NP_002010	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1 isoform 1	771	Helical; (Potential).				cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)	AGCCAGAAGAGAGTCGCAGCC	0.413													5	60	---	---	---	---	PASS
C13orf36	400120	broad.mit.edu	37	13	37269448	37269448	+	Missense_Mutation	SNP	A	T	T	rs17853664		TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37269448A>T	uc001uvt.3	+	2	679	c.233A>T	c.(232-234)GAG>GTG	p.E78V		NM_203451	NP_982276	A2A2V5	CM036_HUMAN	hypothetical protein LOC400120	78				E -> G (in Ref. 3; AAH36540).		integral to membrane				skin(1)	1						TCCTACCCAGAGTATCCAAGC	0.453													12	207	---	---	---	---	PASS
ENOX1	55068	broad.mit.edu	37	13	43934113	43934113	+	Missense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43934113C>T	uc001uza.3	-	7	763	c.463G>A	c.(463-465)GAG>AAG	p.E155K	ENOX1_uc001uzb.3_Missense_Mutation_p.E155K|ENOX1_uc001uzc.3_Missense_Mutation_p.E155K|ENOX1_uc010tfm.1_5'UTR	NM_001127615	NP_001121087	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1	155	RRM.				electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)		ATAATTTCCTCAGTAGCATTT	0.403													6	160	---	---	---	---	PASS
PCDH17	27253	broad.mit.edu	37	13	58209085	58209085	+	Missense_Mutation	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58209085C>A	uc001vhq.1	+	1	3297	c.2405C>A	c.(2404-2406)ACC>AAC	p.T802N	PCDH17_uc010aec.1_Missense_Mutation_p.T802N	NM_001040429	NP_001035519	O14917	PCD17_HUMAN	protocadherin 17 precursor	802	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	7		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		GACTACCAGACCCGCCTGCCC	0.642													3	27	---	---	---	---	PASS
DIAPH3	81624	broad.mit.edu	37	13	60590068	60590068	+	Silent	SNP	T	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60590068T>C	uc001vht.2	-	7	969	c.750A>G	c.(748-750)CTA>CTG	p.L250L	DIAPH3_uc001vhu.2_5'Flank|DIAPH3_uc001vhw.1_Silent_p.L239L|DIAPH3_uc010aed.1_Silent_p.L204L|DIAPH3_uc010aee.1_Silent_p.L180L|uc001vhx.2_Intron|uc001vhy.2_Intron	NM_001042517	NP_001035982	Q9NSV4	DIAP3_HUMAN	diaphanous homolog 3 isoform a	250	GBD/FH3.				actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		TCAGGGCTTTTAGACACTGTA	0.308													4	93	---	---	---	---	PASS
NALCN	259232	broad.mit.edu	37	13	101833664	101833664	+	Intron	SNP	A	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101833664A>T	uc001vox.1	-						NALCN_uc001voy.2_Intron|NALCN_uc001voz.2_Missense_Mutation_p.C597S|NALCN_uc001vpa.2_Missense_Mutation_p.C597S	NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1							integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TGAGTGCCACAGAGGTCACGG	0.498													10	99	---	---	---	---	PASS
SLC39A2	29986	broad.mit.edu	37	14	21469520	21469520	+	Missense_Mutation	SNP	G	T	T	rs143106894		TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21469520G>T	uc001vyr.2	+	4	899	c.712G>T	c.(712-714)GGC>TGC	p.G238C	SLC39A2_uc001vys.2_Missense_Mutation_p.G139C	NM_014579	NP_055394	Q9NP94	S39A2_HUMAN	solute carrier family 39 (zinc transporter),	238	Helical; (Potential).					cytoplasmic membrane-bounded vesicle|integral to plasma membrane	zinc ion transmembrane transporter activity			ovary(2)|central_nervous_system(1)	3	all_cancers(95;0.00267)		OV - Ovarian serous cystadenocarcinoma(11;1.34e-10)|Epithelial(56;1.57e-08)|all cancers(55;7.45e-08)	GBM - Glioblastoma multiforme(265;0.0187)		GTCCCCCCTGGGCCTAGCCGT	0.567													26	144	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	22600778	22600778	+	Intron	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22600778C>A	uc001wbw.2	+						uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc010tmq.1_5'Flank					SubName: Full=Alpha-chain C region; Flags: Fragment;																		TGAAGTGCAACTATTCCTATA	0.502													3	101	---	---	---	---	PASS
FUT8	2530	broad.mit.edu	37	14	66028290	66028290	+	Silent	SNP	A	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66028290A>G	uc001xin.2	+	3	1206	c.9A>G	c.(7-9)CCA>CCG	p.P3P	FUT8_uc001xio.2_Silent_p.P3P|FUT8_uc010tsp.1_Intron|FUT8_uc001xir.3_RNA|FUT8_uc001xip.2_Silent_p.P3P|FUT8_uc001xiq.2_Intron	NM_178155	NP_835368	Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 isoform a	3	Cytoplasmic (Potential).				in utero embryonic development|L-fucose catabolic process|N-glycan processing|oligosaccharide biosynthetic process|post-translational protein modification|protein glycosylation in Golgi|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	glycoprotein 6-alpha-L-fucosyltransferase activity|SH3 domain binding			ovary(1)	1				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)		AAATGCGGCCATGGACTGGTT	0.443													31	245	---	---	---	---	PASS
ZNF410	57862	broad.mit.edu	37	14	74390097	74390097	+	Splice_Site	SNP	G	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74390097G>C	uc001xoz.1	+	11	1453	c.1271_splice	c.e11-1	p.E424_splice	ZNF410_uc001xoy.1_Splice_Site|ZNF410_uc010tuf.1_Splice_Site|ZNF410_uc010tug.1_Splice_Site_p.E155_splice|ZNF410_uc010tuh.1_Splice_Site_p.E351_splice|ZNF410_uc010tui.1_Splice_Site|ZNF410_uc010arz.1_Splice_Site_p.E441_splice|ZNF410_uc001xpa.1_Splice_Site_p.E228_splice|ZNF410_uc001xpb.1_Splice_Site_p.E377_splice|ZNF410_uc001xpc.1_Splice_Site_p.E371_splice|ZNF410_uc010tuj.1_Splice_Site_p.E228_splice	NM_021188	NP_067011	Q86VK4	ZN410_HUMAN	zinc finger protein 410						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00369)		TTGCTTCACAGAGGTGCTTGC	0.438													10	147	---	---	---	---	PASS
C14orf166B	145497	broad.mit.edu	37	14	77302627	77302627	+	Missense_Mutation	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77302627G>A	uc001xsx.2	+	4	582	c.468G>A	c.(466-468)ATG>ATA	p.M156I	C14orf166B_uc010asn.1_5'UTR|C14orf166B_uc001xsw.2_RNA|C14orf166B_uc010aso.1_RNA|C14orf166B_uc010tvg.1_RNA|C14orf166B_uc010tvh.1_RNA	NM_194287	NP_919263	Q0VAA2	CN16B_HUMAN	hypothetical protein LOC145497	156											0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0306)		TGGTGGAGATGCTACAAGAGA	0.552													10	43	---	---	---	---	PASS
MIR668	768214	broad.mit.edu	37	14	101521650	101521650	+	RNA	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101521650G>A	hsa-mir-668|MI0003761	+			c.56G>A			MIR485_hsa-mir-485|MI0002469_5'Flank|hsa-mir-323b|MI0014206_5'Flank																	0						CACTCGGCTCGGCCCACTACC	0.562													9	111	---	---	---	---	PASS
KIF26A	26153	broad.mit.edu	37	14	104641909	104641909	+	Silent	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104641909C>T	uc001yos.3	+	12	2784	c.2784C>T	c.(2782-2784)AGC>AGT	p.S928S		NM_015656	NP_056471	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	928					blood coagulation|enteric nervous system development|microtubule-based movement|negative regulation of signal transduction|regulation of cell growth by extracellular stimulus	cytosol|microtubule	ATP binding|microtubule binding|microtubule motor activity			pancreas(1)	1		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		AGGACAGCAGCGCTTGGCCTG	0.657													7	34	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	33993204	33993204	+	Missense_Mutation	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33993204C>A	uc001zhi.2	+	42	6476	c.6406C>A	c.(6406-6408)CCG>ACG	p.P2136T	RYR3_uc010bar.2_Missense_Mutation_p.P2136T	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	2136	4 X approximate repeats.|Cytoplasmic (By similarity).				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		GGGATCCACCCCGCTGGATGT	0.572											OREG0023030	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	13	---	---	---	---	PASS
SLC12A6	9990	broad.mit.edu	37	15	34531356	34531356	+	Missense_Mutation	SNP	T	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34531356T>C	uc001zhw.2	-	19	2606	c.2442A>G	c.(2440-2442)ATA>ATG	p.I814M	SLC12A6_uc001zhv.2_Missense_Mutation_p.I763M|SLC12A6_uc001zhx.2_Missense_Mutation_p.I799M|SLC12A6_uc001zhy.2_RNA|SLC12A6_uc001zhz.2_RNA|SLC12A6_uc001zia.2_Missense_Mutation_p.I755M|SLC12A6_uc001zib.2_Missense_Mutation_p.I805M|SLC12A6_uc001zic.2_Missense_Mutation_p.I814M|SLC12A6_uc010bau.2_Missense_Mutation_p.I814M|SLC12A6_uc001zid.2_Missense_Mutation_p.I755M|SLC12A6_uc001zht.2_RNA|SLC12A6_uc001zhu.2_Missense_Mutation_p.I626M	NM_133647	NP_598408	Q9UHW9	S12A6_HUMAN	solute carrier family 12, member 6 isoform a	814					angiogenesis|cellular hypotonic salinity response|potassium ion transport|sodium ion transport	basolateral plasma membrane|integral to membrane	potassium:chloride symporter activity			central_nervous_system(5)|ovary(1)|skin(1)	7		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	TTAGGTGCTTTATGGTCTGAA	0.498													38	237	---	---	---	---	PASS
MYEF2	50804	broad.mit.edu	37	15	48451802	48451802	+	Intron	SNP	G	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48451802G>C	uc001zwi.3	-						MYEF2_uc001zwj.3_Intron|MYEF2_uc001zwl.2_Intron	NM_016132	NP_057216	Q9P2K5	MYEF2_HUMAN	myelin expression factor 2						transcription, DNA-dependent	Golgi apparatus|nucleus	DNA binding|nucleotide binding|RNA binding			lung(2)|ovary(1)	3		all_lung(180;0.00217)		all cancers(107;3.73e-10)|GBM - Glioblastoma multiforme(94;7.81e-07)		ACTAAAGCTTGAACTTACATT	0.323													3	149	---	---	---	---	PASS
WDR72	256764	broad.mit.edu	37	15	53907738	53907738	+	Nonsense_Mutation	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53907738C>A	uc002acj.2	-	15	2707	c.2665G>T	c.(2665-2667)GAA>TAA	p.E889*	WDR72_uc010bfi.1_Nonsense_Mutation_p.E889*	NM_182758	NP_877435	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	889										lung(1)|skin(1)	2				all cancers(107;0.0511)		CAATTATTTTCCAATCCTCTT	0.328													12	125	---	---	---	---	PASS
TLN2	83660	broad.mit.edu	37	15	63046061	63046061	+	Missense_Mutation	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63046061G>T	uc002alb.3	+	33	4422	c.4422G>T	c.(4420-4422)CAG>CAT	p.Q1474H	TLN2_uc002alc.3_Translation_Start_Site	NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	1474					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						GGGCTAACCAGGCCATCCAGA	0.567													17	135	---	---	---	---	PASS
IREB2	3658	broad.mit.edu	37	15	78783002	78783002	+	Silent	SNP	T	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78783002T>C	uc002bdr.2	+	18	2385	c.2223T>C	c.(2221-2223)CAT>CAC	p.H741H	IREB2_uc010unb.1_Silent_p.H491H	NM_004136	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	741							4 iron, 4 sulfur cluster binding|metal ion binding|protein binding				0				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)		AAAATGCCCATGTCTTATTAT	0.383													70	359	---	---	---	---	PASS
TMC3	342125	broad.mit.edu	37	15	81637158	81637158	+	Missense_Mutation	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81637158G>T	uc002bgo.1	-	13	1467	c.1467C>A	c.(1465-1467)AGC>AGA	p.S489R	TMC3_uc010blr.1_RNA|TMC3_uc002bgp.2_Missense_Mutation_p.S489R	NM_001080532	NP_001074001	Q7Z5M5	TMC3_HUMAN	transmembrane channel-like 3	489	Cytoplasmic (Potential).					integral to membrane				ovary(1)|liver(1)	2						GAGTGTGGAGGCTAGTCTTGT	0.413													13	64	---	---	---	---	PASS
C15orf42	90381	broad.mit.edu	37	15	90168052	90168052	+	Missense_Mutation	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90168052C>A	uc002boe.2	+	20	4511	c.4511C>A	c.(4510-4512)CCT>CAT	p.P1504H	C15orf42_uc010upv.1_RNA	NM_152259	NP_689472	Q7Z2Z1	TICRR_HUMAN	leucine-rich repeat kinase 1	1504					cell cycle|DNA repair|DNA replication|formation of translation preinitiation complex|G2/M transition checkpoint|mitotic cell cycle DNA replication checkpoint|regulation of DNA-dependent DNA replication initiation|response to ionizing radiation	nucleus	chromatin binding|protein binding			ovary(4)|central_nervous_system(2)|skin(1)	7	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)			CTGTCTCACCCTGGGATTCCC	0.552													4	176	---	---	---	---	PASS
PIGQ	9091	broad.mit.edu	37	16	632882	632882	+	Splice_Site	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:632882G>T	uc002cho.2	+	10	1634	c.1532_splice	c.e10-1	p.D511_splice	PIGQ_uc010bqw.2_Splice_Site_p.I532_splice|PIGQ_uc002chn.2_Splice_Site_p.I532_splice|PIGQ_uc010uui.1_Splice_Site|PIGQ_uc002chp.2_Splice_Site_p.D81_splice|uc010uuj.1_3'UTR	NM_148920	NP_683721	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|carbohydrate metabolic process|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	phosphatidylinositol N-acetylglucosaminyltransferase activity			central_nervous_system(1)	1		Hepatocellular(780;0.00335)				TGTCCTTCCAGATAAACCCAC	0.667													35	252	---	---	---	---	PASS
PDPK1	5170	broad.mit.edu	37	16	2636802	2636802	+	Silent	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2636802C>T	uc002cqs.2	+	11	1395	c.1251C>T	c.(1249-1251)CAC>CAT	p.H417H	PDPK1_uc002cqt.2_Silent_p.H290H|PDPK1_uc010bsn.2_Silent_p.H417H|PDPK1_uc002cqu.2_Silent_p.H390H	NM_002613	NP_002604	O15530	PDPK1_HUMAN	3-phosphoinositide dependent protein kinase-1	417					actin cytoskeleton organization|activation of protein kinase B activity|insulin receptor signaling pathway|negative regulation of protein kinase activity|nerve growth factor receptor signaling pathway|peptidyl-threonine phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|synaptic transmission|T cell costimulation|T cell receptor signaling pathway	cytosol|nucleoplasm|plasma membrane	3-phosphoinositide-dependent protein kinase activity|ATP binding			central_nervous_system(2)|ovary(1)	3		Ovarian(90;0.17)			Celecoxib(DB00482)	AGTACATTCACGATCTGGACT	0.542													17	273	---	---	---	---	PASS
ANKS3	124401	broad.mit.edu	37	16	4747368	4747368	+	Silent	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4747368G>A	uc002cxj.1	-	16	2155	c.1860C>T	c.(1858-1860)CTC>CTT	p.L620L	ANKS3_uc010uxr.1_Silent_p.L143L|ANKS3_uc002cxh.1_RNA|ANKS3_uc002cxi.1_Silent_p.L547L|ANKS3_uc002cxk.2_Silent_p.L491L|ANKS3_uc002cxl.2_Silent_p.L447L|ANKS3_uc010uxs.1_Silent_p.L547L	NM_133450	NP_597707	Q6ZW76	ANKS3_HUMAN	ankyrin repeat and sterile alpha motif domain	620											0						GGGCTCCCGAGAGCTCGGGGA	0.652													15	111	---	---	---	---	PASS
A2BP1	54715	broad.mit.edu	37	16	7726840	7726840	+	Missense_Mutation	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7726840G>T	uc002cys.2	+	14	1983	c.995G>T	c.(994-996)AGT>ATT	p.S332I	A2BP1_uc002cyt.2_Missense_Mutation_p.S305I|A2BP1_uc010uxz.1_Missense_Mutation_p.S375I|A2BP1_uc010uya.1_Missense_Mutation_p.R289I|A2BP1_uc010uyb.1_Missense_Mutation_p.S332I|A2BP1_uc002cyw.2_Missense_Mutation_p.R353I|A2BP1_uc002cyy.2_Missense_Mutation_p.S353I|A2BP1_uc002cyx.2_Missense_Mutation_p.S353I|A2BP1_uc010uyc.1_Missense_Mutation_p.S326I	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4	332					mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		TACAGTGACAGGTAAGGGTCA	0.478													5	124	---	---	---	---	PASS
PAPD5	64282	broad.mit.edu	37	16	50258853	50258853	+	Missense_Mutation	SNP	T	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50258853T>A	uc010vgo.1	+	10	1550	c.1515T>A	c.(1513-1515)GAT>GAA	p.D505E	PAPD5_uc010cbi.2_RNA|PAPD5_uc002efz.2_Missense_Mutation_p.D296E|PAPD5_uc002ega.2_Missense_Mutation_p.D296E	NM_001040284	NP_001035374	Q8NDF8	PAPD5_HUMAN	PAP associated domain containing 5 isoform a	426					cell division|DNA replication|histone mRNA catabolic process|mitosis	cytoplasm|nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding				0		all_cancers(37;0.0452)		BRCA - Breast invasive adenocarcinoma(181;0.0843)|GBM - Glioblastoma multiforme(240;0.231)		CATATAGAGATTGGATATCAA	0.383													28	246	---	---	---	---	PASS
CDH8	1006	broad.mit.edu	37	16	61858915	61858915	+	Splice_Site	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61858915C>T	uc002eog.1	-	5	1087	c.835_splice	c.e5+1	p.S279_splice	CDH8_uc002eoh.2_Splice_Site_p.S48_splice	NM_001796	NP_001787	P55286	CADH8_HUMAN	cadherin 8, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		AATTAACTTACTCTGTGCAAA	0.353													8	100	---	---	---	---	PASS
FHOD1	29109	broad.mit.edu	37	16	67281231	67281231	+	Missense_Mutation	SNP	G	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67281231G>C	uc002esl.2	-	1	195	c.83C>G	c.(82-84)CCC>CGC	p.P28R	FHOD1_uc010ced.2_5'UTR|FHOD1_uc010vjh.1_5'UTR|SLC9A5_uc002esm.2_5'Flank|SLC9A5_uc010cee.2_5'Flank|SLC9A5_uc010vji.1_5'Flank	NM_013241	NP_037373	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1	28					actin cytoskeleton organization	cytoplasm|cytoskeleton|nucleus	actin binding			breast(2)|ovary(1)	3		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		ACATGCGAAGGGGTCGGTGTC	0.716													4	47	---	---	---	---	PASS
ATMIN	23300	broad.mit.edu	37	16	81077572	81077572	+	Missense_Mutation	SNP	C	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81077572C>G	uc002ffz.1	+	4	1487	c.1469C>G	c.(1468-1470)TCC>TGC	p.S490C	ATMIN_uc002fga.2_Missense_Mutation_p.S332C|ATMIN_uc010vnn.1_Missense_Mutation_p.S261C|ATMIN_uc002fgb.1_Missense_Mutation_p.S332C	NM_015251	NP_056066	O43313	ATMIN_HUMAN	ATM interactor	490					response to DNA damage stimulus	nucleus	zinc ion binding				0						GGTGGGGTCTCCAGAGAAACT	0.458													31	185	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7578457	7578457	+	Missense_Mutation	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7578457C>A	uc002gim.2	-	5	667	c.473G>T	c.(472-474)CGC>CTC	p.R158L	TP53_uc002gig.1_Missense_Mutation_p.R158L|TP53_uc002gih.2_Missense_Mutation_p.R158L|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R26L|TP53_uc010cng.1_Missense_Mutation_p.R26L|TP53_uc002gii.1_Missense_Mutation_p.R26L|TP53_uc010cnh.1_Missense_Mutation_p.R158L|TP53_uc010cni.1_Missense_Mutation_p.R158L|TP53_uc002gij.2_Missense_Mutation_p.R158L|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Missense_Mutation_p.R65L|TP53_uc002gio.2_Missense_Mutation_p.R26L|TP53_uc010vug.1_Missense_Mutation_p.R119L	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(55)|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.R158F(1)|p.P151_V173del23(1)|p.R158fs*24(1)|p.R65L(1)|p.R156_R158delRVR(1)|p.R156fs*18(1)|p.R156_A161del(1)|p.R158_A159insXX(1)|p.V157_M160delVRAM(1)|p.V157_R158delVR(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.R26L(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)		GGCCATGGCGCGGACGCGGGT	0.627		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)			12	93	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	19091451	19091451	+	IGR	SNP	T	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19091451T>G								GRAPL (29303 upstream) : EPN2 (49239 downstream)																							aagccggctttctggcgttgc	0.010													7	503	---	---	---	---	PASS
SSH2	85464	broad.mit.edu	37	17	27959688	27959688	+	Missense_Mutation	SNP	C	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27959688C>G	uc002heo.1	-	15	2443	c.2443G>C	c.(2443-2445)GAA>CAA	p.E815Q	SSH2_uc010wbh.1_Missense_Mutation_p.E842Q	NM_033389	NP_203747	Q76I76	SSH2_HUMAN	slingshot 2	815					actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(2)	2						TTGGCTAGTTCAGGCTGGGCT	0.537													34	232	---	---	---	---	PASS
LIG3	3980	broad.mit.edu	37	17	33310101	33310101	+	Missense_Mutation	SNP	A	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33310101A>G	uc002hik.1	+	2	185	c.77A>G	c.(76-78)AAA>AGA	p.K26R	LIG3_uc002hii.2_Missense_Mutation_p.K26R|LIG3_uc002hij.2_Missense_Mutation_p.K26R|LIG3_uc010cth.1_Missense_Mutation_p.K35R	NM_013975	NP_039269	P49916	DNLI3_HUMAN	ligase III, DNA, ATP-dependent isoform alpha	26					base-excision repair|cell division|DNA ligation involved in DNA repair|DNA replication|reciprocal meiotic recombination|spermatogenesis	nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|protein binding|zinc ion binding			skin(3)|lung(2)|ovary(2)|large_intestine(1)|pancreas(1)	9		Ovarian(249;0.17)			Bleomycin(DB00290)	CTATTCCGAAAACATCACTGG	0.458								Other_BER_factors					17	120	---	---	---	---	PASS
PEX12	5193	broad.mit.edu	37	17	33904306	33904306	+	Missense_Mutation	SNP	G	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33904306G>C	uc002hjp.2	-	2	1047	c.431C>G	c.(430-432)TCT>TGT	p.S144C		NM_000286	NP_000277	O00623	PEX12_HUMAN	peroxisomal biogenesis factor 12	144	Cytoplasmic (Potential).				protein import into peroxisome matrix	integral to peroxisomal membrane	protein C-terminus binding|zinc ion binding				0				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GGGATGAATAGAATATTCATC	0.453													14	249	---	---	---	---	PASS
KRT28	162605	broad.mit.edu	37	17	38953217	38953217	+	Missense_Mutation	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38953217C>A	uc002hvh.1	-	5	995	c.929G>T	c.(928-930)AGG>ATG	p.R310M		NM_181535	NP_853513	Q7Z3Y7	K1C28_HUMAN	keratin 25D	310	Rod.|Coil 2.					cytoplasm|intermediate filament	structural molecule activity			ovary(1)	1		Breast(137;0.000301)				CAGGGTGCGCCTCATCTCGGT	0.622													25	139	---	---	---	---	PASS
TTC25	83538	broad.mit.edu	37	17	40104677	40104677	+	Intron	SNP	G	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40104677G>C	uc002hyj.3	+						TTC25_uc010cxt.2_Intron	NM_031421	NP_113609	Q96NG3	TTC25_HUMAN	tetratricopeptide repeat domain 25							cytoplasm	protein binding			ovary(1)	1		all_cancers(22;8.16e-06)|Breast(137;0.000143)|all_epithelial(22;0.000236)				GAGTCCCACTGGTCTTGAAAG	0.289													6	83	---	---	---	---	PASS
TTC25	83538	broad.mit.edu	37	17	40104678	40104678	+	Intron	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40104678G>T	uc002hyj.3	+						TTC25_uc010cxt.2_Intron	NM_031421	NP_113609	Q96NG3	TTC25_HUMAN	tetratricopeptide repeat domain 25							cytoplasm	protein binding			ovary(1)	1		all_cancers(22;8.16e-06)|Breast(137;0.000143)|all_epithelial(22;0.000236)				AGTCCCACTGGTCTTGAAAGG	0.289													6	82	---	---	---	---	PASS
DHX8	1659	broad.mit.edu	37	17	41570101	41570101	+	Nonsense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41570101C>T	uc002idu.1	+	6	629	c.556C>T	c.(556-558)CGA>TGA	p.R186*	DHX8_uc010wif.1_Nonsense_Mutation_p.R95*|DHX8_uc010wig.1_Nonsense_Mutation_p.R186*	NM_004941	NP_004932	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	186	Arg/Ser-rich (RS domain).					catalytic step 2 spliceosome	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding	p.R186Q(1)		ovary(2)|kidney(1)|pancreas(1)	4		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		aaaccgagatcgagacagaga	0.209													15	117	---	---	---	---	PASS
TBX21	30009	broad.mit.edu	37	17	45822501	45822501	+	Silent	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45822501C>A	uc002ilv.1	+	6	1588	c.1377C>A	c.(1375-1377)GGC>GGA	p.G459G		NM_013351	NP_037483	Q9UL17	TBX21_HUMAN	T-box 21	459					lymphocyte migration|multicellular organismal development|positive regulation of transcription, DNA-dependent|response to virus	nucleus	sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0						TGGAACCCGGCCCTGGAGGCT	0.672													7	49	---	---	---	---	PASS
SFRS1	6426	broad.mit.edu	37	17	56083173	56083173	+	Missense_Mutation	SNP	T	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56083173T>C	uc002ivi.2	-	3	750	c.541A>G	c.(541-543)AGA>GGA	p.R181G	SFRS1_uc002ivj.2_Missense_Mutation_p.R181G	NM_006924	NP_008855	Q07955	SRSF1_HUMAN	splicing factor, arginine/serine-rich 1 isoform	181	RRM 2.				mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA 5'-splice site recognition|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytoplasm|nuclear speck	nucleotide binding|RNA binding				0		Colorectal(1115;0.0691)		LUAD - Lung adenocarcinoma(1115;0.247)		TCATGAGATCTAAACTTAGTG	0.398													20	163	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	62385991	62385991	+	IGR	SNP	C	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62385991C>G								TEX2 (45338 upstream) : PECAM1 (13873 downstream)																							CTCGGGTCACCATCTCGTTGA	0.512													5	78	---	---	---	---	PASS
FADS6	283985	broad.mit.edu	37	17	72874468	72874468	+	Missense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72874468C>T	uc002jmd.1	-	6	1057	c.1045G>A	c.(1045-1047)GGG>AGG	p.G349R	FADS6_uc010wrn.1_Missense_Mutation_p.G203R	NM_178128	NP_835229	Q8N9I5	FADS6_HUMAN	fatty acid desaturase domain family, member 6	355					fatty acid biosynthetic process	integral to membrane	oxidoreductase activity				0	all_lung(278;0.172)|Lung NSC(278;0.207)					CATTACAGCCCCACAAGCTCA	0.647													6	18	---	---	---	---	PASS
NOTUM	147111	broad.mit.edu	37	17	79911086	79911086	+	Nonsense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79911086C>T	uc010wvg.1	-	11	1514	c.1242G>A	c.(1240-1242)TGG>TGA	p.W414*		NM_178493	NP_848588	Q6P988	NOTUM_HUMAN	notum pectinacetylesterase homolog precursor	414						extracellular region	hydrolase activity				0	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			GGCTCCTGTCCCAGCAGTGCA	0.672													3	31	---	---	---	---	PASS
PTPRM	5797	broad.mit.edu	37	18	7888314	7888314	+	Missense_Mutation	SNP	C	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7888314C>G	uc002knn.3	+	3	910	c.407C>G	c.(406-408)CCA>CGA	p.P136R	PTPRM_uc010dkv.2_Missense_Mutation_p.P136R	NM_002845	NP_002836	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	136	MAM.|Extracellular (Potential).				homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)				TCTGGAGACCCAACACGTACA	0.438													11	191	---	---	---	---	PASS
DCC	1630	broad.mit.edu	37	18	50432441	50432441	+	Missense_Mutation	SNP	A	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50432441A>T	uc002lfe.1	+	3	1027	c.440A>T	c.(439-441)GAA>GTA	p.E147V	DCC_uc010xdr.1_5'UTR	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor	147	Extracellular (Potential).|Ig-like C2-type 2.				apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		TCACAGACAGAATCTGTCACA	0.423													12	117	---	---	---	---	PASS
LMAN1	3998	broad.mit.edu	37	18	57000330	57000330	+	Missense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57000330C>T	uc002lhz.2	-	11	1399	c.1367G>A	c.(1366-1368)CGA>CAA	p.R456Q		NM_005570	NP_005561	P49257	LMAN1_HUMAN	lectin, mannose-binding, 1 precursor	456	Lumenal (Potential).				blood coagulation|ER to Golgi vesicle-mediated transport|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|protein transport	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	mannose binding|metal ion binding|unfolded protein binding			skin(1)	1		Colorectal(73;0.0946)			Antihemophilic Factor(DB00025)	TACCATATTTCGCTGCACTAA	0.383													5	104	---	---	---	---	PASS
SHC2	25759	broad.mit.edu	37	19	425173	425173	+	Silent	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:425173C>T	uc002loq.3	-	10	1233	c.1233G>A	c.(1231-1233)GAG>GAA	p.E411E	SHC2_uc002lop.3_Silent_p.E152E	NM_012435	NP_036567	P98077	SHC2_HUMAN	SHC (Src homology 2 domain containing)	411	CH1.				insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol					0		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CATACAGGTGCTCCTCGTGGT	0.687													12	58	---	---	---	---	PASS
CYP4F8	11283	broad.mit.edu	37	19	15726540	15726540	+	Missense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15726540C>T	uc002nbi.2	+	2	177	c.113C>T	c.(112-114)ACC>ATC	p.T38I	CYP4F8_uc010xoi.1_Missense_Mutation_p.T38I|CYP4F8_uc010xoj.1_5'UTR	NM_007253	NP_009184	P98187	CP4F8_HUMAN	cytochrome P450, family 4, subfamily F,	38					prostaglandin metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	alkane 1-monooxygenase activity|aromatase activity|electron carrier activity|heme binding|oxygen binding|protein binding			large_intestine(1)	1						CTGGCCTGGACCTATGCCTTC	0.677													7	47	---	---	---	---	PASS
ZNF493	284443	broad.mit.edu	37	19	21606161	21606161	+	Missense_Mutation	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21606161G>A	uc002npx.2	+	2	596	c.316G>A	c.(316-318)GGA>AGA	p.G106R	ZNF493_uc002npw.2_Missense_Mutation_p.G234R|ZNF493_uc002npy.2_Missense_Mutation_p.G106R	NM_175910	NP_787106	Q6ZR52	ZN493_HUMAN	zinc finger protein 493 isoform 1	106					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						AGTTCATACTGGAGAGAAATC	0.363													6	125	---	---	---	---	PASS
ZNF676	163223	broad.mit.edu	37	19	22379425	22379425	+	Missense_Mutation	SNP	T	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22379425T>A	uc002nqs.1	-	1	329	c.11A>T	c.(10-12)AAC>ATC	p.N4I		NM_001001411	NP_001001411	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	4	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				GTTTCTGTAGTTCTCTAACAT	0.343													49	331	---	---	---	---	PASS
ZNF99	7652	broad.mit.edu	37	19	22940373	22940373	+	Missense_Mutation	SNP	T	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22940373T>C	uc010xrh.1	-	5	2065	c.2065A>G	c.(2065-2067)AAG>GAG	p.K689E		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)				TGAATTATCTTATGTTTTCTA	0.343													3	127	---	---	---	---	PASS
ZNF181	339318	broad.mit.edu	37	19	35232076	35232076	+	Missense_Mutation	SNP	C	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35232076C>G	uc002nvu.3	+	4	1253	c.790C>G	c.(790-792)CCC>GCC	p.P264A	ZNF181_uc010xsa.1_Missense_Mutation_p.P263A|ZNF181_uc010xsb.1_Missense_Mutation_p.P263A|ZNF181_uc010xsc.1_Missense_Mutation_p.P199A	NM_001029997	NP_001025168	Q2M3W8	ZN181_HUMAN	zinc finger protein 181 isoform 1	264					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			AGGAGAGAAGCCCTATGAATG	0.418													10	245	---	---	---	---	PASS
MIR518E	574487	broad.mit.edu	37	19	54233112	54233112	+	RNA	SNP	G	T	T	rs34416818		TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54233112G>T	hsa-mir-518e|MI0003169	+			c.21G>T			MIR518A1_hsa-mir-518a-1|MI0003170_5'Flank																	0						TGACCCTCTAGAGGGAAGCGC	0.428													18	192	---	---	---	---	PASS
GALP	85569	broad.mit.edu	37	19	56688488	56688488	+	Missense_Mutation	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56688488C>A	uc002qmo.1	+	2	93	c.11C>A	c.(10-12)CCC>CAC	p.P4H	GALP_uc010eti.2_Missense_Mutation_p.P4H	NM_033106	NP_149097	Q9UBC7	GALP_HUMAN	galanin-like peptide isoform 1 precursor	4					neuropeptide signaling pathway	extracellular region	hormone activity				0		Colorectal(82;0.000147)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0507)		ATGGCTCCTCCCTCCGTCCCC	0.642													4	36	---	---	---	---	PASS
STK35	140901	broad.mit.edu	37	20	2097910	2097910	+	Silent	SNP	C	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2097910C>A	uc010gak.2	+	3	1491	c.1491C>A	c.(1489-1491)TCC>TCA	p.S497S	STK35_uc010zpu.1_Intron|STK35_uc002wfw.3_Silent_p.S364S	NM_080836	NP_543026	Q8TDR2	STK35_HUMAN	serine/threonine kinase 35	497	Protein kinase.					cytoplasm|nucleolus	ATP binding|protein serine/threonine kinase activity			ovary(1)	1						GCAGGACTTCCATGTCTGAGG	0.507													37	113	---	---	---	---	PASS
TMC2	117532	broad.mit.edu	37	20	2616614	2616614	+	Silent	SNP	C	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2616614C>G	uc002wgf.1	+	18	2364	c.2349C>G	c.(2347-2349)TCC>TCG	p.S783S	TMC2_uc002wgg.1_Silent_p.S767S	NM_080751	NP_542789	Q8TDI7	TMC2_HUMAN	transmembrane cochlear-expressed protein 2	783	Cytoplasmic (Potential).					integral to membrane				ovary(3)	3						AAAGCCTTTCCCGAGCTAATG	0.458													22	76	---	---	---	---	PASS
ZNF341	84905	broad.mit.edu	37	20	32328784	32328784	+	Missense_Mutation	SNP	G	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32328784G>C	uc002wzy.2	+	2	128	c.108G>C	c.(106-108)CAG>CAC	p.Q36H	ZNF341_uc002wzx.2_Missense_Mutation_p.Q36H|ZNF341_uc010geq.2_Missense_Mutation_p.R12T|ZNF341_uc010ger.2_RNA	NM_032819	NP_116208	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	36					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						CGACAGGCCAGAGTGTCAATG	0.547													18	86	---	---	---	---	PASS
KCNG1	3755	broad.mit.edu	37	20	49626384	49626384	+	Silent	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49626384G>A	uc002xwa.3	-	2	787	c.492C>T	c.(490-492)TGC>TGT	p.C164C	KCNG1_uc002xwb.2_Silent_p.C164C	NM_002237	NP_002228	Q9UIX4	KCNG1_HUMAN	potassium voltage-gated channel, subfamily G,	164	Cytoplasmic (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|central_nervous_system(1)	2						GGCGCTTGCAGCAGCCGTCCA	0.682													10	83	---	---	---	---	PASS
CTCFL	140690	broad.mit.edu	37	20	56098952	56098952	+	Nonsense_Mutation	SNP	G	A	A			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56098952G>A	uc010gix.1	-	1	972	c.310C>T	c.(310-312)CAG>TAG	p.Q104*	CTCFL_uc010giw.1_Nonsense_Mutation_p.Q104*|CTCFL_uc002xym.2_Nonsense_Mutation_p.Q104*|CTCFL_uc010giz.1_Intron|CTCFL_uc010giy.1_Intron|CTCFL_uc010gja.1_Nonsense_Mutation_p.Q104*|CTCFL_uc010gjb.1_Nonsense_Mutation_p.Q104*|CTCFL_uc010gjc.1_Nonsense_Mutation_p.Q104*|CTCFL_uc010gjd.1_Nonsense_Mutation_p.Q104*|CTCFL_uc010gje.2_Nonsense_Mutation_p.Q104*|CTCFL_uc010gjf.2_Intron|CTCFL_uc010gjg.2_Intron|CTCFL_uc010gjh.1_Nonsense_Mutation_p.Q104*|CTCFL_uc010gji.1_Intron|CTCFL_uc010gjj.1_Nonsense_Mutation_p.Q104*|CTCFL_uc010gjk.1_Nonsense_Mutation_p.Q104*|CTCFL_uc010gjl.1_Nonsense_Mutation_p.Q104*	NM_080618	NP_542185	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor-like protein	104					cell cycle|DNA methylation involved in gamete generation|histone methylation|positive regulation of transcription, DNA-dependent|regulation of gene expression by genetic imprinting|regulation of histone H3-K4 methylation|transcription, DNA-dependent	cytoplasm|nucleus	histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|large_intestine(1)|skin(1)	4	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			CCTTCTTGCTGCTGTATGCTC	0.597													34	158	---	---	---	---	PASS
ZNF831	128611	broad.mit.edu	37	20	57829371	57829371	+	Missense_Mutation	SNP	A	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57829371A>C	uc002yan.2	+	5	4607	c.4607A>C	c.(4606-4608)GAG>GCG	p.E1536A		NM_178457	NP_848552	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1536						intracellular	nucleic acid binding|zinc ion binding			skin(13)|ovary(1)	14	all_lung(29;0.0085)					GTCACAGAAGAGGGCAGAGCA	0.493													15	45	---	---	---	---	PASS
ZNF295	49854	broad.mit.edu	37	21	43412303	43412303	+	Silent	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43412303G>T	uc002zab.3	-	3	2116	c.1902C>A	c.(1900-1902)GCC>GCA	p.A634A	ZNF295_uc002yzz.3_Intron|ZNF295_uc002yzy.3_Silent_p.A634A|ZNF295_uc002zaa.3_Silent_p.A634A	NM_001098402	NP_001091872	Q9ULJ3	ZN295_HUMAN	zinc finger protein 295 isoform L	634					negative regulation of transcription, DNA-dependent|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|nucleus	methyl-CpG binding|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3						TAATGATCAGGGCCTTCTTAA	0.453													13	173	---	---	---	---	PASS
UMODL1	89766	broad.mit.edu	37	21	43519180	43519180	+	Missense_Mutation	SNP	A	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43519180A>T	uc002zaf.1	+	7	1076	c.1076A>T	c.(1075-1077)CAG>CTG	p.Q359L	UMODL1_uc002zad.1_Missense_Mutation_p.Q287L|UMODL1_uc002zae.1_Missense_Mutation_p.Q287L|UMODL1_uc002zag.1_Missense_Mutation_p.Q359L|UMODL1_uc010gow.1_Missense_Mutation_p.Q151L|UMODL1_uc002zai.1_Missense_Mutation_p.Q10L|UMODL1_uc010gox.1_RNA|UMODL1_uc010goy.1_Missense_Mutation_p.Q10L|UMODL1_uc002zaj.1_RNA|UMODL1_uc010goz.1_Missense_Mutation_p.Q104L	NM_001004416	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1 isoform 1 precursor	359	Extracellular (Potential).|Fibronectin type-III 1.					cytoplasm|extracellular region|integral to membrane|plasma membrane	calcium ion binding|peptidase inhibitor activity			ovary(2)|skin(1)	3						GCCAGGACACAGAGCCAGGCA	0.587													13	127	---	---	---	---	PASS
UMODL1	89766	broad.mit.edu	37	21	43522280	43522280	+	Silent	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43522280C>T	uc002zaf.1	+	8	1191	c.1191C>T	c.(1189-1191)GCC>GCT	p.A397A	UMODL1_uc002zad.1_Silent_p.A325A|UMODL1_uc002zae.1_Silent_p.A325A|UMODL1_uc002zag.1_Silent_p.A397A|UMODL1_uc010gow.1_Silent_p.A189A|UMODL1_uc002zai.1_Silent_p.A48A|UMODL1_uc010gox.1_RNA|UMODL1_uc010goy.1_Silent_p.A48A|UMODL1_uc002zaj.1_RNA|UMODL1_uc010goz.1_Silent_p.A142A|C21orf128_uc002zak.2_3'UTR	NM_001004416	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1 isoform 1 precursor	397	Extracellular (Potential).|SEA 1.					cytoplasm|extracellular region|integral to membrane|plasma membrane	calcium ion binding|peptidase inhibitor activity			ovary(2)|skin(1)	3						TCTCAGATGCCCAGGTATTTG	0.428													9	93	---	---	---	---	PASS
SGSM1	129049	broad.mit.edu	37	22	25240894	25240894	+	Missense_Mutation	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25240894C>T	uc003abg.2	+	3	251	c.94C>T	c.(94-96)CGC>TGC	p.R32C	SGSM1_uc003abh.2_Missense_Mutation_p.R32C|SGSM1_uc010guu.1_Missense_Mutation_p.R32C|SGSM1_uc003abj.2_Missense_Mutation_p.R32C|SGSM1_uc003abi.1_Missense_Mutation_p.R7C|SGSM1_uc003abf.2_Missense_Mutation_p.R32C	NM_001039948	NP_001035037	Q2NKQ1	SGSM1_HUMAN	RUN and TBC1 domain containing 2 isoform 1	32						Golgi apparatus	Rab GTPase activator activity	p.R32H(1)		ovary(2)|central_nervous_system(2)|pancreas(1)	5						GGCTGTGACACGCAAGTTTGT	0.567													7	67	---	---	---	---	PASS
LIMK2	3985	broad.mit.edu	37	22	31673092	31673092	+	Intron	SNP	C	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31673092C>G	uc003akh.2	+						LIMK2_uc003akg.2_Missense_Mutation_p.A614G|LIMK2_uc003aki.2_Intron|LIMK2_uc003akj.2_Missense_Mutation_p.A676G|LIMK2_uc003akk.2_Intron|LIMK2_uc011aln.1_Intron	NM_005569	NP_005560	P53671	LIMK2_HUMAN	LIM domain kinase 2 isoform 2a							mitochondrion|nucleus	ATP binding|protein serine/threonine kinase activity|zinc ion binding			ovary(2)	2						AAGATCCGGGCCATGCAGAAG	0.602													3	121	---	---	---	---	PASS
TOM1	10043	broad.mit.edu	37	22	35741772	35741772	+	Missense_Mutation	SNP	G	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35741772G>T	uc003ann.2	+	13	1404	c.1279G>T	c.(1279-1281)GAC>TAC	p.D427Y	TOM1_uc011ami.1_Missense_Mutation_p.D394Y|TOM1_uc011amj.1_Missense_Mutation_p.D270Y|TOM1_uc003ans.2_Missense_Mutation_p.D270Y|TOM1_uc011amk.1_Missense_Mutation_p.D389Y|TOM1_uc003anp.2_Missense_Mutation_p.D427Y|TOM1_uc011aml.1_Missense_Mutation_p.D382Y|TOM1_uc003ano.2_RNA|TOM1_uc003anq.2_Missense_Mutation_p.D421Y|TOM1_uc003anr.2_Missense_Mutation_p.D270Y	NM_005488	NP_005479	O60784	TOM1_HUMAN	target of myb1 isoform 1	427					endocytosis|endosome transport|intracellular protein transport	cytosol|early endosome|membrane	protein binding			ovary(1)	1						GCTGTCCACTGACGTGGTATG	0.572													16	91	---	---	---	---	PASS
IL3RA	3563	broad.mit.edu	37	X	1464294	1464294	+	Silent	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1464294C>T	uc004cps.2	+	3	499	c.150C>T	c.(148-150)ATC>ATT	p.I50I	IL3RA_uc011mhd.1_Intron	NM_002183	NP_002174	P26951	IL3RA_HUMAN	interleukin 3 receptor, alpha precursor	50	Extracellular (Potential).					integral to membrane|plasma membrane	interleukin-3 receptor activity			skin(2)|lung(1)	3		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	TGACCGATATCGAGTGTGTTA	0.343													20	317	---	---	---	---	PASS
PHEX	5251	broad.mit.edu	37	X	22244631	22244631	+	Intron	SNP	C	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22244631C>T	uc004dah.2	+						PHEX_uc011mjr.1_Intron|PHEX_uc011mjs.1_Intron	NM_000444	NP_000435	P78562	PHEX_HUMAN	phosphate-regulating neutral endopeptidase						biomineral tissue development|cell-cell signaling|protein modification process|proteolysis|skeletal system development	integral to plasma membrane	aminopeptidase activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|lung(1)	3						TTAGGGTATGCGCTGCTACAT	0.413													4	120	---	---	---	---	PASS
KDM5C	8242	broad.mit.edu	37	X	53241055	53241055	+	Missense_Mutation	SNP	C	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53241055C>G	uc004drz.2	-	9	1689	c.1156G>C	c.(1156-1158)GAG>CAG	p.E386Q	KDM5C_uc011moc.1_RNA|KDM5C_uc011mod.1_Missense_Mutation_p.E319Q|KDM5C_uc004dsa.2_Missense_Mutation_p.E385Q	NM_004187	NP_004178	P41229	KDM5C_HUMAN	jumonji, AT rich interactive domain 1C isoform	386					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			kidney(9)|ovary(5)|salivary_gland(1)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|oesophagus(1)	18						GTAGCCTGCTCAAAGCCAAAG	0.522			N|F|S		clear cell renal carcinoma								7	23	---	---	---	---	PASS
TRPC5	7224	broad.mit.edu	37	X	111078161	111078161	+	Silent	SNP	A	G	G			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:111078161A>G	uc004epl.1	-	7	2803	c.1884T>C	c.(1882-1884)TAT>TAC	p.Y628Y	TRPC5_uc004epm.1_Silent_p.Y628Y	NM_012471	NP_036603	Q9UL62	TRPC5_HUMAN	transient receptor potential cation channel,	628	Cytoplasmic (Potential).				axon guidance	calcium channel complex|integral to plasma membrane	protein binding|store-operated calcium channel activity			urinary_tract(1)	1						CAATAAGCTGATAGGAGTTGT	0.433													71	197	---	---	---	---	PASS
ATAD3A	55210	broad.mit.edu	37	1	1458390	1458390	+	Intron	DEL	G	-	-			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1458390delG	uc001afz.1	+						ATAD3A_uc001aga.1_Intron|ATAD3A_uc001agb.1_Intron	NM_018188	NP_060658	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A								ATP binding|nucleoside-triphosphatase activity|protein binding			skin(1)	1	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.12e-36)|OV - Ovarian serous cystadenocarcinoma(86;2.18e-22)|Colorectal(212;0.000164)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00233)|BRCA - Breast invasive adenocarcinoma(365;0.00469)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0347)|Lung(427;0.147)		CCCGGATAACGGGCACCCGCA	0.647													5	3	---	---	---	---	
HECTD3	79654	broad.mit.edu	37	1	45471981	45471981	+	Intron	DEL	T	-	-	rs144329171		TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45471981delT	uc009vxk.2	-						HECTD3_uc001cmx.3_5'Flank|HECTD3_uc001cmy.3_Intron|HECTD3_uc010olh.1_Intron	NM_024602	NP_078878	Q5T447	HECD3_HUMAN	HECT domain containing 3						proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm	ubiquitin-protein ligase activity				0	Acute lymphoblastic leukemia(166;0.155)					CCTAtttctattttttttttt	0.259													5	3	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145367285	145367286	+	Intron	INS	-	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145367285_145367286insT	uc001end.3	+						NBPF9_uc010oye.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_Intron|NBPF10_uc010oyk.1_Intron|NBPF10_uc010oyl.1_Intron	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GAGAACTGTGATTTTGACTCAA	0.441													4	3	---	---	---	---	
KIF3C	3797	broad.mit.edu	37	2	26152485	26152486	+	Intron	INS	-	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26152485_26152486insT	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)					CCCATAGGCTCttttttttttt	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	26362985	26362986	+	IGR	INS	-	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26362985_26362986insT								RAB10 (2663 upstream) : HADHA (50519 downstream)																							AGAAACAGGGCTTTTTTTTTTT	0.317													4	2	---	---	---	---	
TBC1D8	11138	broad.mit.edu	37	2	101675674	101675675	+	Intron	DEL	TT	-	-			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101675674_101675675delTT	uc010fiv.2	-						TBC1D8_uc010yvw.1_Intron|TBC1D8_uc002tau.3_Intron	NM_001102426	NP_001095896	O95759	TBCD8_HUMAN	TBC1 domain family, member 8						blood circulation|positive regulation of cell proliferation	intracellular|membrane	calcium ion binding|Rab GTPase activator activity			ovary(3)	3						cagccAAGTCtttttttttttt	0.153													4	3	---	---	---	---	
PDCD6IP	10015	broad.mit.edu	37	3	33868210	33868211	+	Intron	INS	-	T	T	rs5847793		TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33868210_33868211insT	uc003cfx.2	+						PDCD6IP_uc011axv.1_3'UTR|PDCD6IP_uc003cfy.2_Intron|PDCD6IP_uc011axw.1_5'Flank	NM_013374	NP_037506	Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein						apoptosis|cell cycle|cell division|interspecies interaction between organisms|protein transport	cytosol|melanosome|microtubule organizing center	calcium-dependent protein binding			ovary(1)|skin(1)	2						AGTAGAAATAGttttttttttt	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	97926080	97926080	+	IGR	DEL	T	-	-	rs5851109		TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97926080delT								OR5H15 (37597 upstream) : OR5H6 (57049 downstream)																							AAATATATGATTTTTTTCCAT	0.308													4	2	---	---	---	---	
CCDC52	152185	broad.mit.edu	37	3	113167135	113167135	+	Intron	DEL	T	-	-			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113167135delT	uc003eag.3	-						CCDC52_uc003eaf.3_Intron	NM_144718	NP_653319	Q8N0Z3	SPICE_HUMAN	coiled-coil domain containing 52						cell division|mitosis	centriole|spindle	protein binding				0						CTTGAAAGACTTTTTTTTTTT	0.323													8	4	---	---	---	---	
NEK11	79858	broad.mit.edu	37	3	130852480	130852481	+	Intron	INS	-	CTC	CTC	rs111530704		TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130852480_130852481insCTC	uc003eny.2	+						NEK11_uc003enx.2_Intron|NEK11_uc003eoa.2_Intron|NEK11_uc003enz.2_Intron|NEK11_uc010htn.2_Intron|NEK11_uc011blk.1_Intron|NEK11_uc011bll.1_Intron|NEK11_uc003enw.1_Intron|NEK11_uc011blm.1_Intron|NEK11_uc010hto.1_Intron	NM_024800	NP_079076	Q8NG66	NEK11_HUMAN	NIMA-related kinase 11 isoform 1						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						AAGTCTTCCTTCTATAAAACTT	0.257													4	3	---	---	---	---	
GPR149	344758	broad.mit.edu	37	3	154147611	154147611	+	5'Flank	DEL	A	-	-	rs35893155		TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154147611delA	uc003faa.2	-							NM_001038705	NP_001033794	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149							integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(6)	6			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TTTCAAGCATAAAAAAAAAAA	0.348													7	4	---	---	---	---	
CCDC39	339829	broad.mit.edu	37	3	180372434	180372434	+	Intron	DEL	A	-	-			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180372434delA	uc010hxe.2	-						CCDC39_uc003fkn.2_Intron	NM_181426	NP_852091	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39						axonemal dynein complex assembly|ciliary cell motility|cilium movement involved in determination of left/right asymmetry|flagellar cell motility	cilium axoneme|cytoplasm|cytoskeleton				ovary(4)	4	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			aagaaaaaggaaaaaaaaaaa	0.303													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	12637716	12637717	+	IGR	INS	-	T	T	rs35602984		TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12637716_12637717insT								None (None upstream) : HSP90AB2P (697320 downstream)																							AATAGGCTAGCTTTTTTTTTTT	0.208													3	3	---	---	---	---	
FLJ39653	202020	broad.mit.edu	37	4	16257860	16257860	+	Intron	DEL	T	-	-	rs146274448		TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16257860delT	uc011bxf.1	+						FLJ39653_uc011bxg.1_Intron	NR_027696				RecName: Full=Uncharacterized protein FLJ39653;												0						AGGGTTTGTCTTTTTTTTTTT	0.383													5	3	---	---	---	---	
GABRB1	2560	broad.mit.edu	37	4	47427497	47427498	+	Intron	INS	-	GATAGATA	GATAGATA	rs144288589	by1000genomes	TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47427497_47427498insGATAGATA	uc003gxh.2	+						GABRB1_uc011bze.1_Intron	NM_000812	NP_000803	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)	2					Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	TGGATGATGATgatagatagat	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	1649912	1649913	+	IGR	DEL	TC	-	-			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1649912_1649913delTC								LOC728613 (15792 upstream) : MRPL36 (148587 downstream)																							tttctctctttctctctctctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	150629928	150629928	+	IGR	DEL	G	-	-			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150629928delG								PPP1R14C (58402 upstream) : IYD (60100 downstream)																							ACAACGGTGTGGAACATGagg	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	64722028	64722028	+	IGR	DEL	A	-	-			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64722028delA								INTS4L1 (27429 upstream) : ZNF92 (116740 downstream)																							gactctgtctaaaaaaaaaaa	0.179													6	3	---	---	---	---	
CA1	759	broad.mit.edu	37	8	86250862	86250889	+	Intron	DEL	TTTCTTTCTTTCTTTCTTTCTTTCTTTC	-	-	rs56255763	by1000genomes	TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86250862_86250889delTTTCTTTCTTTCTTTCTTTCTTTCTTTC	uc003ydh.2	-						CA13_uc003ydf.1_Intron|CA1_uc010mae.1_Intron|CA1_uc003ydi.2_Intron	NM_001738	NP_001729	P00915	CAH1_HUMAN	carbonic anhydrase I						one-carbon metabolic process	Golgi apparatus	carbonate dehydratase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_lung(136;4.89e-06)			Acetazolamide(DB00819)|Amlodipine(DB00381)|Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Brinzolamide(DB01194)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Dichlorphenamide(DB01144)|Ethinamate(DB01031)|Ethoxzolamide(DB00311)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Levetiracetam(DB01202)|Methazolamide(DB00703)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)|Verapamil(DB00661)|Zonisamide(DB00909)	tttccttctttttctttctttctttctttctttctttctttctttctt	0.092													6	4	---	---	---	---	
TMEM67	91147	broad.mit.edu	37	8	94794154	94794155	+	Intron	INS	-	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94794154_94794155insT	uc011lgk.1	+						TMEM67_uc010mat.1_Intron|TMEM67_uc010maw.2_Intron|TMEM67_uc003yga.3_Intron	NM_153704	NP_714915	Q5HYA8	MKS3_HUMAN	meckelin isoform 1						cilium assembly|ER-associated protein catabolic process|negative regulation of centrosome duplication	centrosome|cilium membrane|cytoplasmic vesicle membrane|endoplasmic reticulum membrane|integral to membrane|microtubule basal body	unfolded protein binding			ovary(2)	2	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)			tttgttttttcttttttttttg	0.084													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	54148810	54148810	+	IGR	DEL	T	-	-	rs78612093		TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54148810delT								DKK1 (71394 upstream) : MBL2 (376331 downstream)																							CCTTCTTGTCTTTTTTTTTTT	0.303													3	3	---	---	---	---	
ATE1	11101	broad.mit.edu	37	10	123673111	123673112	+	Intron	INS	-	AGAA	AGAA	rs143762121	by1000genomes	TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123673111_123673112insAGAA	uc001lfp.2	-						ATE1_uc001lfq.2_Intron|ATE1_uc010qtr.1_Intron|ATE1_uc010qts.1_Intron|ATE1_uc010qtt.1_Intron|ATE1_uc001lfr.2_Intron|ATE1_uc009xzu.2_Intron	NM_007041	NP_008972	O95260	ATE1_HUMAN	arginyltransferase 1 isoform 2						protein arginylation	cytoplasm|nucleus	acyltransferase activity|arginyltransferase activity				0		all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212)				ACGCTAAACTCTTCTGATATAT	0.376													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	50189137	50189138	+	IGR	INS	-	C	C	rs139000234		TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50189137_50189138insC								OR4C12 (185100 upstream) : LOC441601 (49862 downstream)																							tctctctctctttttttttttt	0.213													3	7	---	---	---	---	
SLC3A2	6520	broad.mit.edu	37	11	62655423	62655423	+	Intron	DEL	C	-	-	rs34176851		TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62655423delC	uc001nwd.2	+						SLC3A2_uc001nwb.2_Intron|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron|SLC3A2_uc001nwg.2_Intron	NM_002394	NP_002385	P08195	4F2_HUMAN	solute carrier family 3, member 2 isoform c						blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport	apical plasma membrane|cell surface|integral to membrane|melanosome	calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding				0						taacactacacccagctaatt	0.000													7	6	---	---	---	---	
PDE2A	5138	broad.mit.edu	37	11	72307501	72307508	+	Intron	DEL	ATCTCTCT	-	-	rs145397044		TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72307501_72307508delATCTCTCT	uc010rrc.1	-						PDE2A_uc001oso.2_Intron|PDE2A_uc010rra.1_Intron|PDE2A_uc001osn.2_Intron|PDE2A_uc010rrb.1_Intron|PDE2A_uc010rrd.1_Intron	NM_002599	NP_002590	O00408	PDE2A_HUMAN	phosphodiesterase 2A isoform 1						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(2)|breast(1)|skin(1)	4			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Sildenafil(DB00203)|Sulindac(DB00605)	TATGGCTCCCAtctctctctctctctct	0.447													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	40842476	40842477	+	IGR	INS	-	C	C			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40842476_40842477insC								LRRK2 (79392 upstream) : CNTN1 (243881 downstream)																							cttccttccttcttctttcctt	0.050													10	12	---	---	---	---	
EML5	161436	broad.mit.edu	37	14	89087278	89087279	+	Intron	INS	-	A	A	rs35953031		TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89087278_89087279insA	uc001xxg.2	-						EML5_uc001xxf.2_Intron|EML5_uc001xxd.2_5'Flank|EML5_uc001xxe.2_Intron	NM_183387	NP_899243	Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like							cytoplasm|microtubule				ovary(3)	3						CTTCTGCatttaaaaaaaaaaa	0.361													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	70477525	70477525	+	IGR	DEL	T	-	-			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70477525delT								TLE3 (87269 upstream) : UACA (469370 downstream)																							gggagtgggctgcagaggtga	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86742646	86742647	+	IGR	INS	-	CTTCCTCTCTTCCTTCCTTC	CTTCCTCTCTTCCTTCCTTC	rs11270969		TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86742646_86742647insCTTCCTCTCTTCCTTCCTTC								FOXL1 (127343 upstream) : FBXO31 (620297 downstream)																							TCAGGGAATTGcttcctctctt	0.262													2	4	---	---	---	---	
TTC25	83538	broad.mit.edu	37	17	40101597	40101597	+	Intron	DEL	C	-	-			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40101597delC	uc002hyj.3	+						TTC25_uc010cxt.2_Intron	NM_031421	NP_113609	Q96NG3	TTC25_HUMAN	tetratricopeptide repeat domain 25							cytoplasm	protein binding			ovary(1)	1		all_cancers(22;8.16e-06)|Breast(137;0.000143)|all_epithelial(22;0.000236)				tccctctctacaaaaaaaaaa	0.124													4	2	---	---	---	---	
AOC3	8639	broad.mit.edu	37	17	41006869	41006869	+	Intron	DEL	T	-	-			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41006869delT	uc002ibv.2	+							NM_003734	NP_003725	Q16853	AOC3_HUMAN	amine oxidase, copper containing 3 precursor						amine metabolic process|cell adhesion|inflammatory response	cell surface|integral to membrane|plasma membrane	aliphatic-amine oxidase activity|aminoacetone:oxygen oxidoreductase(deaminating) activity|copper ion binding|phenethylamine:oxygen oxidoreductase (deaminating) activity|primary amine oxidase activity|protein homodimerization activity|quinone binding|tryptamine:oxygen oxidoreductase (deaminating) activity			central_nervous_system(2)|ovary(1)|skin(1)	4		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)	Hydralazine(DB01275)|Phenelzine(DB00780)	tttcttttccttttttttttt	0.269													4	2	---	---	---	---	
SDK2	54549	broad.mit.edu	37	17	71419971	71419971	+	Intron	DEL	A	-	-	rs11287411		TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71419971delA	uc010dfm.2	-						SDK2_uc010dfn.2_Intron	NM_001144952	NP_001138424	Q58EX2	SDK2_HUMAN	sidekick 2						cell adhesion	integral to membrane				ovary(2)	2						TGGGGATCTGAAAAAAGGGAC	0.607													3	3	---	---	---	---	
FBN3	84467	broad.mit.edu	37	19	8188250	8188250	+	Intron	DEL	G	-	-	rs10419582	by1000genomes	TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8188250delG	uc002mjf.2	-							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						aaaaaaaaaagaagaagaaaa	0.239													8	5	---	---	---	---	
LRP3	4037	broad.mit.edu	37	19	33694048	33694051	+	Intron	DEL	TGAG	-	-	rs3065441		TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33694048_33694051delTGAG	uc010edh.2	+						LRP3_uc010xrp.1_Intron|LRP3_uc002nuk.3_5'Flank	NM_002333	NP_002324	O75074	LRP3_HUMAN	low density lipoprotein receptor-related protein						receptor-mediated endocytosis	coated pit|integral to membrane	receptor activity			pancreas(2)|ovary(1)	3	Esophageal squamous(110;0.137)					tgtgagcatatgagtgaggcgtgt	0.044													4	2	---	---	---	---	
PDXK	8566	broad.mit.edu	37	21	45161409	45161411	+	Intron	DEL	CTC	-	-			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45161409_45161411delCTC	uc002zdm.3	+						PDXK_uc010gpj.2_Intron|PDXK_uc002zdn.3_Intron|PDXK_uc002zdq.3_5'UTR	NM_003681	NP_003672	O00764	PDXK_HUMAN	pyridoxal kinase						cell proliferation|pyridoxal 5'-phosphate salvage	cytosol	ATP binding|lithium ion binding|magnesium ion binding|potassium ion binding|protein homodimerization activity|pyridoxal kinase activity|pyridoxal phosphate binding|sodium ion binding|zinc ion binding				0				Colorectal(79;0.109)|READ - Rectum adenocarcinoma(84;0.161)|STAD - Stomach adenocarcinoma(101;0.18)	Pyridoxal(DB00147)|Pyridoxine(DB00165)	GCCTAGTGATCTCCTTCGGGTTT	0.522													4	3	---	---	---	---	
MAP3K15	389840	broad.mit.edu	37	X	19431232	19431233	+	Intron	DEL	AC	-	-			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19431232_19431233delAC	uc004czk.1	-						MAP3K15_uc004czj.1_Intron	NM_001001671	NP_001001671	Q6ZN16	M3K15_HUMAN	mitogen-activated protein kinase kinase kinase								ATP binding|MAP kinase kinase kinase activity|metal ion binding			ovary(3)|lung(2)|stomach(1)|skin(1)	7	Hepatocellular(33;0.183)					ATGTTTTTATacacacacacac	0.144													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	28582961	28582962	+	IGR	INS	-	AT	AT	rs4008413		TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:28582961_28582962insAT								None (None upstream) : None (None downstream)																							AAGTATAAAACAAAAACCTAAA	0.322													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	M	10263	10264	+	5'Flank	INS	-	T	T			TCGA-34-2608-01	TCGA-34-2608-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:10263_10264insT	uc004cov.3	+						uc004cow.1_5'Flank|uc004cox.3_5'Flank					Homo sapiens potential LAG1 interactor mRNA, partial cds.																		TTGATCTAGAAATTGCCCTCCT	0.441													3	5	---	---	---	---	
