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	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	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
GRHL3	57822	broad.mit.edu	37	1	24676595	24676595	+	Nonsense_Mutation	SNP	C	G	G			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr1:24676595C>G	uc001biy.2	+	15	1738	c.1692C>G	c.(1690-1692)TAC>TAG	p.Y564*	GRHL3_uc001bix.2_Nonsense_Mutation_p.Y559*|GRHL3_uc001biz.2_Nonsense_Mutation_p.Y466*	NM_021180	NP_067003	Q8TE85	GRHL3_HUMAN	sister-of-mammalian grainyhead protein isoform	559					regulation of actin cytoskeleton organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00171)|all_lung(284;0.00226)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;8.72e-25)|Colorectal(126;4.38e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00377)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.143)		ACAAAGTCTACAAGAAATGCA	0.498													3	51	---	---	---	---	PASS
RUNX3	864	broad.mit.edu	37	1	25229113	25229113	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr1:25229113G>A	uc001bjq.2	-	5	1159	c.748C>T	c.(748-750)CGC>TGC	p.R250C	RUNX3_uc010oen.1_Missense_Mutation_p.R197C|RUNX3_uc009vrj.2_Missense_Mutation_p.R264C|RUNX3_uc001bjr.2_Missense_Mutation_p.R264C|RUNX3_uc001bjs.2_RNA	NM_004350	NP_004341	Q13761	RUNX3_HUMAN	runt-related transcription factor 3 isoform 2	250	Pro/Ser/Thr-rich.				cell proliferation|induction of apoptosis|negative regulation of cell cycle|negative regulation of epithelial cell proliferation|protein phosphorylation|transcription from RNA polymerase II promoter	cytoplasm|nucleus	ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00131)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;2.85e-26)|Colorectal(126;4.35e-08)|COAD - Colon adenocarcinoma(152;1.92e-06)|GBM - Glioblastoma multiforme(114;0.000102)|STAD - Stomach adenocarcinoma(196;0.000766)|KIRC - Kidney renal clear cell carcinoma(1967;0.00148)|BRCA - Breast invasive adenocarcinoma(304;0.00173)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.136)		GGGAAGGAGCGGTCAAACTGG	0.637													5	202	---	---	---	---	PASS
CC2D1B	200014	broad.mit.edu	37	1	52827241	52827241	+	Missense_Mutation	SNP	G	A	A	rs149044360		TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr1:52827241G>A	uc001ctq.1	-	4	400	c.262C>T	c.(262-264)CGG>TGG	p.R88W	CC2D1B_uc001cts.2_5'Flank	NM_032449	NP_115825	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	88										ovary(2)	2						tccACATCCCGCATACAGTCT	0.473													4	93	---	---	---	---	PASS
ARNT	405	broad.mit.edu	37	1	150801579	150801579	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr1:150801579T>G	uc001evr.1	-	12	1300	c.1157A>C	c.(1156-1158)TAC>TCC	p.Y386S	ARNT_uc001evs.1_Missense_Mutation_p.Y371S|ARNT_uc009wmb.1_Missense_Mutation_p.Y372S|ARNT_uc009wmc.1_Missense_Mutation_p.Y386S|ARNT_uc009wmd.1_Missense_Mutation_p.Y371S|ARNT_uc009wme.1_Missense_Mutation_p.Y386S|ARNT_uc010pcl.1_Missense_Mutation_p.Y370S	NM_001668	NP_001659	P27540	ARNT_HUMAN	aryl hydrocarbon receptor nuclear translocator	386	PAS 2.				positive regulation of hormone biosynthetic process|positive regulation vascular endothelial growth factor production|regulation of transcription from RNA polymerase II promoter in response to oxidative stress|response to hypoxia		aryl hydrocarbon receptor binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity			skin(4)|lung(3)|central_nervous_system(1)|kidney(1)	9	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			CTGTGGCTGGTAGCCAACAGT	0.453			T	ETV6	AML								9	29	---	---	---	---	PASS
MIR555	693140	broad.mit.edu	37	1	155316142	155316142	+	RNA	SNP	T	C	C			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr1:155316142T>C	hsa-mir-555|MI0003561	-			c.95T>C			RAG1AP1_uc010pey.1_Intron|ASH1L_uc001fkt.2_Intron|ASH1L_uc009wqq.2_Intron																	0						CTCCTACTTATAGATCAGAGT	0.378													6	179	---	---	---	---	PASS
NTRK1	4914	broad.mit.edu	37	1	156849827	156849827	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr1:156849827C>T	uc001fqh.1	+	16	2139	c.2083C>T	c.(2083-2085)CCG>TCG	p.P695S	NTRK1_uc001fqf.1_Missense_Mutation_p.P659S|NTRK1_uc009wsi.1_Missense_Mutation_p.P394S|NTRK1_uc001fqi.1_Missense_Mutation_p.P689S|NTRK1_uc009wsk.1_Missense_Mutation_p.P692S	NM_002529	NP_002520	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	695	Cytoplasmic (Potential).|Protein kinase.		P -> L (in CIPA).		activation of adenylate cyclase activity|activation of MAPKK activity|activation of phospholipase C activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development|phosphatidylinositol-mediated signaling|Ras protein signal transduction	endosome|integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein serine/threonine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(9)|ovary(6)|stomach(1)|central_nervous_system(1)	17	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Imatinib(DB00619)	TCGCTGGATGCCGCCCGAGAG	0.647			T	TPM3|TPR|TFG	papillary thyroid					TSP Lung(10;0.080)			4	96	---	---	---	---	PASS
CACNA1S	779	broad.mit.edu	37	1	201061108	201061108	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr1:201061108C>A	uc001gvv.2	-	4	760	c.533G>T	c.(532-534)GGG>GTG	p.G178V		NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,	178	Helical; Name=S4 of repeat I; (Potential).|I.				axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	ACTAGGCACCCCCGACACCAG	0.612													3	69	---	---	---	---	PASS
EML4	27436	broad.mit.edu	37	2	42513409	42513409	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr2:42513409C>T	uc002rsi.2	+	10	1274	c.1012C>T	c.(1012-1014)CCT>TCT	p.P338S	EML4_uc010fap.2_Missense_Mutation_p.P280S|EML4_uc002rsj.2_Missense_Mutation_p.P27S	NM_019063	NP_061936	Q9HC35	EMAL4_HUMAN	echinoderm microtubule associated protein like 4	338	WD 1.				microtubule-based process|mitosis	cytoplasm|microtubule	protein binding		EML4/ALK(246)	lung(246)|ovary(2)|central_nervous_system(1)|skin(1)	250						GTTTTTGCAGCCTCTACAACC	0.443			T	ALK	NSCLC								73	116	---	---	---	---	PASS
WASH2P	375260	broad.mit.edu	37	2	114355998	114355998	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr2:114355998C>G	uc002tkh.2	+	5	674	c.616C>G	c.(616-618)CAC>GAC	p.H206D	WASH2P_uc002tka.2_RNA|WASH2P_uc002tkb.2_RNA|WASH2P_uc002tkd.2_RNA	NM_182905	NP_878908			WAS protein family homolog 1												0						CCAAGGTGGGCACTTGATGTC	0.612													3	11	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179659235	179659235	+	Missense_Mutation	SNP	A	T	T			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr2:179659235A>T	uc010zfg.1	-	8	1513	c.1289T>A	c.(1288-1290)GTT>GAT	p.V430D	TTN_uc010zfh.1_Missense_Mutation_p.V430D|TTN_uc010zfi.1_Missense_Mutation_p.V430D|TTN_uc010zfj.1_Missense_Mutation_p.V430D|TTN_uc002unb.2_Missense_Mutation_p.V430D|TTN_uc010frg.1_Missense_Mutation_p.V104D	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	430							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)			AACGGCAGCAACAACAGTCGC	0.458													9	151	---	---	---	---	PASS
COL3A1	1281	broad.mit.edu	37	2	189856917	189856917	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr2:189856917G>A	uc002uqj.1	+	14	1076	c.959G>A	c.(958-960)CGG>CAG	p.R320Q	COL3A1_uc010frw.1_RNA	NM_000090	NP_000081	P02461	CO3A1_HUMAN	collagen type III alpha 1 preproprotein	320	Triple-helical region.				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)	TAGGGTGCTCGGGGTAATGAC	0.378													30	190	---	---	---	---	PASS
PPARG	5468	broad.mit.edu	37	3	12475528	12475528	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr3:12475528A>G	uc003bwx.2	+	7	1493	c.1402A>G	c.(1402-1404)ACA>GCA	p.T468A	PPARG_uc003bwr.2_Missense_Mutation_p.T440A|PPARG_uc003bws.2_Missense_Mutation_p.T440A|PPARG_uc003bwu.2_Missense_Mutation_p.T440A|PPARG_uc003bwv.2_3'UTR	NM_015869	NP_056953	P37231	PPARG_HUMAN	peroxisome proliferative activated receptor	468	Ligand-binding.				activation of caspase activity|cell fate commitment|cell maturation|cellular response to insulin stimulus|epithelial cell differentiation|glucose homeostasis|induction of apoptosis|innate immune response|lipid homeostasis|lipoprotein transport|long-chain fatty acid transport|low-density lipoprotein particle receptor biosynthetic process|monocyte differentiation|negative regulation of cholesterol storage|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|placenta development|positive regulation of fat cell differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to lipid|response to low-density lipoprotein particle stimulus|white fat cell differentiation	cytosol|nucleoplasm	activating transcription factor binding|arachidonic acid binding|drug binding|enzyme binding|prostaglandin receptor activity|retinoid X receptor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|kidney(1)	2					Atorvastatin(DB01076)|Icosapent(DB00159)|Pioglitazone(DB01132)|Rosiglitazone(DB00412)|Troglitazone(DB00197)	CCAGAAAATGACAGACCTCAG	0.522			T	PAX8	follicular thyroid		Insulin resistance ; lipodystrophy|familial partial L;diabetes mellitus|insulin-resistantI|with acanthosis nigricans and hypertension						3	101	---	---	---	---	PASS
XIRP1	165904	broad.mit.edu	37	3	39230128	39230128	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr3:39230128C>T	uc003cjk.1	-	2	1030	c.809G>A	c.(808-810)CGC>CAC	p.R270H	XIRP1_uc003cji.2_Missense_Mutation_p.R270H|XIRP1_uc003cjj.2_Intron	NM_194293	NP_919269	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	270	Xin 6.						actin binding			ovary(4)|breast(2)|central_nervous_system(1)|pancreas(1)	8				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		AAAGAGCCAGCGGGCAGACCT	0.677													42	73	---	---	---	---	PASS
KCNIP4	80333	broad.mit.edu	37	4	20751288	20751288	+	Silent	SNP	G	A	A			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr4:20751288G>A	uc003gqe.2	-	4	459	c.375C>T	c.(373-375)TTC>TTT	p.F125F	KCNIP4_uc003gqf.1_Silent_p.F121F|KCNIP4_uc003gqg.1_Silent_p.F80F|KCNIP4_uc003gqh.1_Silent_p.F117F|KCNIP4_uc003gqi.1_Silent_p.F80F|PACRGL_uc003gpu.2_Intron|PACRGL_uc003gpx.3_Intron|PACRGL_uc003gpw.2_Intron|KCNIP4_uc010iel.2_Silent_p.F122F|KCNIP4_uc003gqd.3_Silent_p.F105F	NM_147182	NP_671711	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4 isoform 3	142	EF-hand 2.|1 (Potential).					plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)				AGCTTACCTCGAAACTCACAG	0.358													22	85	---	---	---	---	PASS
FRG1	2483	broad.mit.edu	37	4	190883030	190883030	+	Missense_Mutation	SNP	G	T	T	rs112946446		TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr4:190883030G>T	uc003izs.2	+	8	874	c.683G>T	c.(682-684)AGT>ATT	p.S228I		NM_004477	NP_004468	Q14331	FRG1_HUMAN	FSHD region gene 1	228					rRNA processing	Cajal body|catalytic step 2 spliceosome|nuclear speck|nucleolus					0		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		AAAGAAGACAGTAAAATTCTT	0.318													14	323	---	---	---	---	PASS
HOMER1	9456	broad.mit.edu	37	5	78697840	78697840	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr5:78697840G>T	uc003kfy.2	-	6	1669	c.566C>A	c.(565-567)ACC>AAC	p.T189N	HOMER1_uc010jab.2_Intron|HOMER1_uc010jac.2_Intron|HOMER1_uc010jad.2_Missense_Mutation_p.T15N	NM_004272	NP_004263	Q86YM7	HOME1_HUMAN	homer 1	189	Potential.				activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic density|postsynaptic membrane					0		Lung NSC(167;0.00131)|all_lung(232;0.00151)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.87e-44)|Epithelial(54;7.07e-41)|all cancers(79;5.5e-36)		TCCTTTGAGGGTAGCCAGTTC	0.428													10	162	---	---	---	---	PASS
ATG12	9140	broad.mit.edu	37	5	115177236	115177236	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr5:115177236G>A	uc003krh.2	-	1	264	c.155C>T	c.(154-156)CCG>CTG	p.P52L	AP3S1_uc003krl.2_5'Flank|AP3S1_uc003krk.2_5'Flank|AP3S1_uc003krm.2_5'Flank|ATG12_uc003kri.2_Missense_Mutation_p.P52L|ATG12_uc003krj.2_RNA	NM_004707	NP_004698	O94817	ATG12_HUMAN	APG12 autophagy 12-like	5					autophagic vacuole assembly|negative regulation of type I interferon production	pre-autophagosomal structure membrane	protein binding				0		all_cancers(142;0.00377)|all_epithelial(76;0.000129)|Prostate(80;0.0132)|Ovarian(225;0.0776)|Lung NSC(810;0.245)		OV - Ovarian serous cystadenocarcinoma(64;7.59e-08)|Epithelial(69;7.05e-07)|all cancers(49;3.11e-05)		CACAGACTGCGGCTCCTCCGC	0.607													81	92	---	---	---	---	PASS
PCDHA5	56143	broad.mit.edu	37	5	140202486	140202486	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr5:140202486C>T	uc003lhl.2	+	1	1126	c.1126C>T	c.(1126-1128)CGT>TGT	p.R376C	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Missense_Mutation_p.R376C|PCDHA5_uc003lhj.1_Missense_Mutation_p.R376C	NM_018908	NP_061731	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5 isoform 1 precursor	376	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(1)|breast(1)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGTGTCTGACCGTGACTCAGG	0.542													14	186	---	---	---	---	PASS
PTK7	5754	broad.mit.edu	37	6	43111336	43111336	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr6:43111336G>T	uc003oub.1	+	14	2427	c.2229G>T	c.(2227-2229)GAG>GAT	p.E743D	PTK7_uc003ouc.1_Missense_Mutation_p.E687D|PTK7_uc003oud.1_Missense_Mutation_p.E703D|PTK7_uc003oue.1_Missense_Mutation_p.E613D|PTK7_uc003ouf.1_RNA|PTK7_uc003oug.1_RNA|PTK7_uc011dve.1_Missense_Mutation_p.E751D|PTK7_uc010jyj.1_Intron	NM_002821	NP_002812	Q13308	PTK7_HUMAN	PTK7 protein tyrosine kinase 7 isoform a	743	Cytoplasmic (Potential).				actin cytoskeleton reorganization|canonical Wnt receptor signaling pathway|cell adhesion|cell migration	cell-cell junction|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			ovary(2)|large_intestine(1)	3			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			AGGGCGAGGAGCCAGAGATGG	0.677											OREG0017450	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	34	---	---	---	---	PASS
DLX5	1749	broad.mit.edu	37	7	96653697	96653697	+	Missense_Mutation	SNP	A	T	T	rs149635296	byFrequency	TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr7:96653697A>T	uc003uon.2	-	1	447	c.239T>A	c.(238-240)GTG>GAG	p.V80E	DLX5_uc011kim.1_Missense_Mutation_p.V80E	NM_005221	NP_005212	P56178	DLX5_HUMAN	distal-less homeobox 5	80					cell proliferation|endochondral ossification|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(1)	1	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					GGAGCCGTTCACGCCGTGATA	0.612													22	58	---	---	---	---	PASS
RGS20	8601	broad.mit.edu	37	8	54791832	54791832	+	Silent	SNP	A	T	T			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr8:54791832A>T	uc003xrp.2	+	2	272	c.180A>T	c.(178-180)GCA>GCT	p.A60A	RGS20_uc003xrq.2_Intron|RGS20_uc010lye.2_Intron|RGS20_uc010lyf.2_Intron|RGS20_uc003xrr.2_5'Flank|RGS20_uc003xrs.2_5'Flank|RGS20_uc003xrt.2_5'Flank	NM_170587	NP_733466	O76081	RGS20_HUMAN	regulator of G-protein signaling 20 isoform a	60					negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|nucleus|plasma membrane	GTPase activator activity|protein binding|signal transducer activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(7;1.37e-06)|Epithelial(17;0.000126)|all cancers(17;0.0009)			TCCCGCCTGCACAGCTCCCAG	0.597													88	166	---	---	---	---	PASS
SULF1	23213	broad.mit.edu	37	8	70498706	70498706	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr8:70498706A>G	uc010lza.1	+	7	1244	c.527A>G	c.(526-528)AAT>AGT	p.N176S	SULF1_uc003xyd.2_Missense_Mutation_p.N176S|SULF1_uc003xye.2_Missense_Mutation_p.N176S|SULF1_uc003xyf.2_Missense_Mutation_p.N176S|SULF1_uc003xyg.2_Missense_Mutation_p.N176S	NM_015170	NP_055985	Q8IWU6	SULF1_HUMAN	sulfatase 1 precursor	176					apoptosis|bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			central_nervous_system(3)|ovary(2)|pancreas(1)|skin(1)	7	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			GTTTGTCGCAATGGCATCAAA	0.388													16	293	---	---	---	---	PASS
RBM12B	389677	broad.mit.edu	37	8	94746488	94746488	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr8:94746488C>G	uc003yfz.2	-	3	2344	c.2151G>C	c.(2149-2151)CAG>CAC	p.Q717H		NM_203390	NP_976324	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	717							nucleotide binding|RNA binding				0	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			CCTGGGGTGACTGCCTGAAGT	0.627													145	235	---	---	---	---	PASS
ANXA13	312	broad.mit.edu	37	8	124705463	124705463	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr8:124705463G>A	uc003yqu.2	-	8	689	c.616C>T	c.(616-618)CGA>TGA	p.R206*	ANXA13_uc003yqt.2_Nonsense_Mutation_p.R247*	NM_004306	NP_004297	P27216	ANX13_HUMAN	annexin A13 isoform a	206	Annexin 3.				cell differentiation	plasma membrane	calcium ion binding|calcium-dependent phospholipid binding			ovary(1)|pancreas(1)|skin(1)	3	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)			AAGGTGGCTCGTAACTGCTTG	0.448													9	404	---	---	---	---	PASS
CYC1	1537	broad.mit.edu	37	8	145150822	145150822	+	Silent	SNP	G	A	A			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr8:145150822G>A	uc003zaz.3	+	2	259	c.216G>A	c.(214-216)GCG>GCA	p.A72A	CYC1_uc003zay.2_Silent_p.A13A	NM_001916	NP_001907	P08574	CY1_HUMAN	cytochrome c-1	72					respiratory electron transport chain|transport	cell junction|integral to membrane|mitochondrial inner membrane|respiratory chain	electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity|heme binding				0	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;8.71e-40)|all cancers(56;3e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CAGGGGGTGCGGGGCTGGCCA	0.652											OREG0019052	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	67	---	---	---	---	PASS
KIAA2026	158358	broad.mit.edu	37	9	5968943	5968943	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr9:5968943G>T	uc003zjq.3	-	3	1504	c.1288C>A	c.(1288-1290)CTT>ATT	p.L430I		NM_001017969	NP_001017969	Q5HYC2	K2026_HUMAN	hypothetical protein LOC158358	430										ovary(2)|central_nervous_system(1)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		AGACCCTTAAGTAGCCACACT	0.383													5	32	---	---	---	---	PASS
ATP8B5P	158381	broad.mit.edu	37	9	35450217	35450217	+	RNA	SNP	C	T	T			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr9:35450217C>T	uc010mkn.1	+	10		c.3067C>T			ATP8B5P_uc010mko.2_RNA|ATP8B5P_uc010mkp.2_RNA|ATP8B5P_uc003zwu.2_Intron					Homo sapiens cDNA, FLJ17320.												0						GGTTTGAATGCGGTGTAGAAA	0.373													3	63	---	---	---	---	PASS
HSPA12A	259217	broad.mit.edu	37	10	118441315	118441315	+	Silent	SNP	G	T	T			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr10:118441315G>T	uc001lct.2	-	8	1014	c.909C>A	c.(907-909)TCC>TCA	p.S303S	HSPA12A_uc001lcu.2_Silent_p.S220S	NM_025015	NP_079291	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A	303							ATP binding			ovary(1)	1				all cancers(201;0.0158)		CCTCCAGCTCGGACCAGATTT	0.478											OREG0020558	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	73	---	---	---	---	PASS
OR52E4	390081	broad.mit.edu	37	11	5905957	5905957	+	Silent	SNP	C	T	T			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr11:5905957C>T	uc010qzs.1	+	1	435	c.435C>T	c.(433-435)ATC>ATT	p.I145I	TRIM5_uc001mbq.1_Intron	NM_001005165	NP_001005165	Q8NGH9	O52E4_HUMAN	olfactory receptor, family 52, subfamily E,	145	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.24e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCATCAGTATCCTAGCTTCTG	0.453													6	256	---	---	---	---	PASS
DNAJC4	3338	broad.mit.edu	37	11	64000258	64000258	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr11:64000258C>A	uc001nys.2	+	5	910	c.448C>A	c.(448-450)CAC>AAC	p.H150N	uc001nyr.1_5'Flank|DNAJC4_uc001nyt.2_Missense_Mutation_p.H151N|DNAJC4_uc001nyu.2_Missense_Mutation_p.H150N|VEGFB_uc001nyw.2_5'Flank|VEGFB_uc001nyx.2_5'Flank	NM_005528	NP_005519	Q9NNZ3	DNJC4_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 4	150					protein folding|response to unfolded protein	integral to membrane|membrane fraction	heat shock protein binding|unfolded protein binding				0						GCAGCAGCAACACAAACAAAA	0.607													3	107	---	---	---	---	PASS
GRM5	2915	broad.mit.edu	37	11	88781128	88781128	+	Translation_Start_Site	SNP	G	A	A			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr11:88781128G>A	uc001pcq.2	-	1	113	c.-87C>T	c.(-89--85)AACGT>AATGT		GRM5_uc009yvm.2_Translation_Start_Site|GRM5_uc009yvn.1_Translation_Start_Site	NM_001143831	NP_001137303	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5 isoform a						activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(2)|lung(2)|breast(1)	9		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)	GATGTCCTACGTTGAGTCGCA	0.408													14	21	---	---	---	---	PASS
CNTN5	53942	broad.mit.edu	37	11	99690380	99690380	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr11:99690380A>C	uc001pga.2	+	4	500	c.161A>C	c.(160-162)TAC>TCC	p.Y54S	CNTN5_uc009ywv.1_Missense_Mutation_p.Y54S|CNTN5_uc001pfz.2_Missense_Mutation_p.Y54S|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long	54					cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		AGACCACGATACAGCAGCCCT	0.428													5	188	---	---	---	---	PASS
C11orf70	85016	broad.mit.edu	37	11	101946634	101946634	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr11:101946634G>T	uc001pgp.2	+	5	494	c.466G>T	c.(466-468)GAA>TAA	p.E156*	C11orf70_uc001pgo.2_Nonstop_Mutation_p.*100L|C11orf70_uc001pgq.2_Nonsense_Mutation_p.E118*	NM_032930	NP_116319	Q9BRQ4	CK070_HUMAN	hypothetical protein LOC85016	156										skin(1)	1	all_epithelial(12;0.0137)	Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.0137)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0335)		AGAAAAATATGAAATATTCAG	0.343													17	191	---	---	---	---	PASS
MIP	4284	broad.mit.edu	37	12	56848144	56848144	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr12:56848144C>T	uc001slh.2	-	1	286	c.254G>A	c.(253-255)CGT>CAT	p.R85H		NM_012064	NP_036196	P30301	MIP_HUMAN	major intrinsic protein of lens fiber	85	Helical; (By similarity).				response to stimulus|visual perception	gap junction|integral to plasma membrane	structural constituent of eye lens			skin(1)	1						GCAGAAGGCACGGAGCAGGGA	0.597													34	46	---	---	---	---	PASS
HELB	92797	broad.mit.edu	37	12	66725033	66725033	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr12:66725033T>C	uc001sti.2	+	12	2798	c.2770T>C	c.(2770-2772)TAT>CAT	p.Y924H	HELB_uc010ssz.1_RNA|HELB_uc009zqt.1_RNA	NM_033647	NP_387467	Q8NG08	HELB_HUMAN	helicase (DNA) B	924					DNA replication, synthesis of RNA primer		ATP binding|ATP-dependent 5'-3' DNA helicase activity|single-stranded DNA-dependent ATP-dependent DNA helicase activity			central_nervous_system(1)|pancreas(1)	2			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		CTGCCGAGTGTATGTGATTGC	0.532													43	99	---	---	---	---	PASS
TPTE2	93492	broad.mit.edu	37	13	20000609	20000609	+	Missense_Mutation	SNP	C	T	T	rs141691551	by1000genomes	TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr13:20000609C>T	uc001umd.2	-	19	1562	c.1351G>A	c.(1351-1353)GGT>AGT	p.G451S	TPTE2_uc009zzk.2_Intron|TPTE2_uc009zzl.2_Missense_Mutation_p.G340S|TPTE2_uc001ume.2_Missense_Mutation_p.G374S|TPTE2_uc009zzm.2_Missense_Mutation_p.G122S|TPTE2_uc010tcm.1_RNA|TPTE2_uc010tcl.1_Missense_Mutation_p.G122S	NM_199254	NP_954863	Q6XPS3	TPTE2_HUMAN	TPTE and PTEN homologous inositol lipid	451	C2 tensin-type.					endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		AGAGGTGGACCGTCATATACA	0.338													7	206	---	---	---	---	PASS
C14orf101	54916	broad.mit.edu	37	14	57114085	57114085	+	Missense_Mutation	SNP	C	T	T	rs147042249		TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr14:57114085C>T	uc001xcm.2	+	16	2116	c.1994C>T	c.(1993-1995)TCG>TTG	p.S665L	C14orf101_uc001xcj.2_RNA|C14orf101_uc001xcn.2_RNA|C14orf101_uc010trf.1_Missense_Mutation_p.S198L|C14orf101_uc001xco.2_Missense_Mutation_p.S198L	NM_017799	NP_060269	Q9NX78	CN101_HUMAN	hypothetical protein LOC54916	665						integral to membrane				breast(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(311;0.226)		GTGCTGTTATCGGAAACCATC	0.478													10	126	---	---	---	---	PASS
DYNC1H1	1778	broad.mit.edu	37	14	102474613	102474613	+	Silent	SNP	C	A	A			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr14:102474613C>A	uc001yks.2	+	29	6080	c.5916C>A	c.(5914-5916)TCC>TCA	p.S1972S		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	1972	AAA 1 (By similarity).				cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10						CGGCTGTGTCCCAGCAGGTGC	0.537													38	51	---	---	---	---	PASS
ADAMTS7	11173	broad.mit.edu	37	15	79051880	79051880	+	Silent	SNP	C	T	T	rs1045121	by1000genomes	TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr15:79051880C>T	uc002bej.3	-	24	5155	c.4944G>A	c.(4942-4944)ACG>ACA	p.T1648T		NM_014272	NP_055087	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1648	PLAC.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0						GTAGGCGCAGCGTCTCGCAGA	0.697													4	16	---	---	---	---	PASS
CCNF	899	broad.mit.edu	37	16	2503242	2503242	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr16:2503242C>A	uc002cqd.1	+	14	1607	c.1519C>A	c.(1519-1521)CAA>AAA	p.Q507K	CCNF_uc002cqe.1_Missense_Mutation_p.Q199K	NM_001761	NP_001752	P41002	CCNF_HUMAN	cyclin F	507					cell division|mitosis|negative regulation of centrosome duplication|protein ubiquitination|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	centriole|nucleus|SCF ubiquitin ligase complex	protein binding			central_nervous_system(1)|kidney(1)	2		Ovarian(90;0.17)				GGACTACAGGCAAGTCTCTCT	0.572													6	99	---	---	---	---	PASS
PDXDC1	23042	broad.mit.edu	37	16	15122751	15122751	+	Silent	SNP	C	T	T	rs117411702	by1000genomes	TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr16:15122751C>T	uc002dda.3	+	15	1445	c.1221C>T	c.(1219-1221)GCC>GCT	p.A407A	PDXDC1_uc010uzl.1_Silent_p.A392A|PDXDC1_uc010uzm.1_Silent_p.A316A|PDXDC1_uc002dcz.2_Silent_p.A384A|PDXDC1_uc002ddb.3_Silent_p.A380A|PDXDC1_uc010uzn.1_Silent_p.A379A|PDXDC1_uc002ddc.2_Silent_p.A407A	NM_015027	NP_055842	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain	407					carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding	p.A407A(1)		skin(1)	1					Pyridoxal Phosphate(DB00114)	TGTTTAAAGCCGTCCCAGTGC	0.552													3	81	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	18441762	18441762	+	Silent	SNP	A	G	G	rs149995059		TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr16:18441762A>G	uc010bvw.2	-	7	1139	c.483T>C	c.(481-483)CCT>CCC	p.P161P						SubName: Full=cDNA FLJ59085, highly similar to Polycystin-1;																		CCTGGGGACCAGGGTGGCCGG	0.706													5	5	---	---	---	---	PASS
TIMM22	29928	broad.mit.edu	37	17	900589	900589	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr17:900589C>A	uc002fsc.2	+	1	233	c.207C>A	c.(205-207)TGC>TGA	p.C69*		NM_013337	NP_037469	Q9Y584	TIM22_HUMAN	translocase of inner mitochondrial membrane 22	69					transmembrane transport	integral to membrane|mitochondrial inner membrane	protein transporter activity				0				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		TGGAAAGCTGCGCTTTCAAGG	0.662													3	47	---	---	---	---	PASS
NLRP1	22861	broad.mit.edu	37	17	5418327	5418327	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr17:5418327A>G	uc002gci.2	-	17	4724	c.4169T>C	c.(4168-4170)ATA>ACA	p.I1390T	NLRP1_uc002gcg.1_Intron|NLRP1_uc002gck.2_Missense_Mutation_p.I1346T|NLRP1_uc002gcj.2_Missense_Mutation_p.I1360T|NLRP1_uc002gcl.2_Missense_Mutation_p.I1316T|NLRP1_uc002gch.3_Missense_Mutation_p.I1346T	NM_033004	NP_127497	Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1 isoform 1	1390	CARD.				defense response to bacterium|induction of apoptosis|neuron apoptosis|positive regulation of interleukin-1 beta secretion|response to muramyl dipeptide	cytoplasm|NALP1 inflammasome complex|nucleus	ATP binding|caspase activator activity|enzyme binding|protein domain specific binding			lung(4)|breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	9		Colorectal(1115;3.48e-05)				CACTCGGGCTATCAGCTGCTC	0.582													3	93	---	---	---	---	PASS
KRT25	147183	broad.mit.edu	37	17	38911399	38911399	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr17:38911399C>A	uc002hve.2	-	1	186	c.125G>T	c.(124-126)GGA>GTA	p.G42V		NM_181534	NP_853512	Q7Z3Z0	K1C25_HUMAN	keratin 25	42	Head.|Gly-rich.					cytoplasm|intermediate filament	structural molecule activity			ovary(2)	2		Breast(137;0.00526)				GAAGCCACTTCCAATCCCTGA	0.557													5	67	---	---	---	---	PASS
C17orf28	283987	broad.mit.edu	37	17	72949181	72949181	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr17:72949181C>A	uc002jmj.3	-	16	2121	c.1972G>T	c.(1972-1974)GAG>TAG	p.E658*	C17orf28_uc002jmi.2_Nonsense_Mutation_p.E60*|C17orf28_uc010wrs.1_Nonsense_Mutation_p.E457*	NM_030630	NP_085133	Q8IV36	CQ028_HUMAN	hypothetical protein LOC283987	658						integral to membrane|plasma membrane	protein binding				0	all_lung(278;0.151)|Lung NSC(278;0.185)					TGGCTGGGCTCCTGGCCCCCA	0.672													3	13	---	---	---	---	PASS
ANKRD30B	374860	broad.mit.edu	37	18	14757889	14757889	+	Silent	SNP	C	G	G			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr18:14757889C>G	uc010dlo.2	+	5	873	c.693C>G	c.(691-693)GTC>GTG	p.V231V	ANKRD30B_uc010xak.1_RNA	NM_001145029	NP_001138501	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	231	ANK 5.									ovary(1)|skin(1)	2						ATGTTGACGTCTTTGCTGAAG	0.378													3	65	---	---	---	---	PASS
TTC39C	125488	broad.mit.edu	37	18	21663014	21663014	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr18:21663014T>C	uc002kuw.2	+	6	1405	c.953T>C	c.(952-954)ATG>ACG	p.M318T	TTC39C_uc002kuu.2_Missense_Mutation_p.M257T	NM_001135993	NP_001129465	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C isoform 1	318	TPR 1.						binding			ovary(1)	1						TCCCTCTTTATGTTTTTCAAG	0.398													71	47	---	---	---	---	PASS
ASXL3	80816	broad.mit.edu	37	18	31326361	31326361	+	Silent	SNP	T	C	C			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr18:31326361T>C	uc010dmg.1	+	12	6604	c.6549T>C	c.(6547-6549)AAT>AAC	p.N2183N	ASXL3_uc002kxq.2_Silent_p.N1890N	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	2183					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3						GTGGCTCCAATCCTGCCACAG	0.478													12	99	---	---	---	---	PASS
ABCA7	10347	broad.mit.edu	37	19	1041420	1041420	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr19:1041420A>C	uc002lqw.3	+	2	291	c.60A>C	c.(58-60)AGA>AGC	p.R20S	ABCA7_uc010dsb.1_5'Flank|ABCA7_uc010dsa.2_Missense_Mutation_p.R20S	NM_019112	NP_061985	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A, member 7	20					phagocytosis|transmembrane transport	ATP-binding cassette (ABC) transporter complex|endosome membrane|Golgi membrane|integral to membrane|plasma membrane	ATP binding|ATPase activity|transporter activity			pancreas(7)|ovary(1)|central_nervous_system(1)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ATCGCCGGAGACAGCCGGTAA	0.632													9	72	---	---	---	---	PASS
TBXA2R	6915	broad.mit.edu	37	19	3600348	3600348	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr19:3600348C>T	uc002lyg.1	-	2	499	c.285G>A	c.(283-285)TGG>TGA	p.W95*	TBXA2R_uc002lye.1_Nonsense_Mutation_p.W95*	NM_001060	NP_001051	P21731	TA2R_HUMAN	thromboxane A2 receptor isoform alpha	95	Extracellular (Potential).				platelet activation	integral to plasma membrane	guanyl-nucleotide exchange factor activity|protein binding|thromboxane A2 receptor activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)	Ridogrel(DB01207)	CCACGGCGTGCCACTCGAAGA	0.672													3	50	---	---	---	---	PASS
ZNF844	284391	broad.mit.edu	37	19	12187394	12187394	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr19:12187394T>C	uc002mtb.2	+	4	1602	c.1459T>C	c.(1459-1461)TTT>CTT	p.F487L	ZNF844_uc010dym.1_Missense_Mutation_p.F330L	NM_001136501	NP_001129973	Q08AG5	ZN844_HUMAN	zinc finger protein 844	487					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GCCTTCATTTTTTCCACTTCC	0.448													3	127	---	---	---	---	PASS
ZNF98	148198	broad.mit.edu	37	19	22585603	22585603	+	Missense_Mutation	SNP	T	C	C	rs2957812	by1000genomes	TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr19:22585603T>C	uc002nqt.2	-	3	363	c.241A>G	c.(241-243)ACT>GCT	p.T81A		NM_001098626	NP_001092096	A6NK75	ZNF98_HUMAN	zinc finger protein 98	81	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				GGGGGTTCAGTTACCATCTCA	0.403													4	213	---	---	---	---	PASS
LILRB5	10990	broad.mit.edu	37	19	54760066	54760066	+	Silent	SNP	G	T	T			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr19:54760066G>T	uc002qex.2	-	4	606	c.495C>A	c.(493-495)ACC>ACA	p.T165T	LILRA6_uc002qew.1_Intron|LILRB5_uc010yer.1_Silent_p.T156T|LILRB5_uc002qey.2_Silent_p.T165T|LILRB5_uc002qez.2_Intron|LILRB5_uc002qfa.1_Intron|LILRB5_uc010yes.1_Intron	NM_006840	NP_006831	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor,	165	Extracellular (Potential).|Ig-like C2-type 2.				cell surface receptor linked signaling pathway|defense response	integral to membrane	transmembrane receptor activity			ovary(1)|pancreas(1)	2	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GTGAGTACAGGGTCCTGGGGA	0.557													57	105	---	---	---	---	PASS
ZNF814	730051	broad.mit.edu	37	19	58385546	58385546	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr19:58385546G>T	uc002qqo.2	-	3	1484	c.1212C>A	c.(1210-1212)GAC>GAA	p.D404E	ZNF814_uc002qqk.2_Intron|ZNF814_uc010yhl.1_Intron	NM_001144989	NP_001138461	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	404					regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0						AATGTTTTTTGTCAGTGTGAA	0.393													7	29	---	---	---	---	PASS
TCF15	6939	broad.mit.edu	37	20	585299	585299	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr20:585299C>A	uc002wdz.2	-	2	565	c.536G>T	c.(535-537)CGT>CTT	p.R179L		NM_004609	NP_004600	Q12870	TCF15_HUMAN	basic helix-loop-helix transcription factor 15	179					regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0		Breast(17;0.231)				CCCCAGGTCACGACGGCCACC	0.507													2	3	---	---	---	---	PASS
SNAP25	6616	broad.mit.edu	37	20	10277647	10277647	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr20:10277647G>A	uc002wnq.1	+	6	568	c.356G>A	c.(355-357)CGT>CAT	p.R119H	SNAP25_uc002wnr.1_Missense_Mutation_p.R119H|SNAP25_uc002wns.1_Missense_Mutation_p.R56H|SNAP25_uc010gca.1_Missense_Mutation_p.R119H|SNAP25_uc010gcb.1_Missense_Mutation_p.R56H|SNAP25_uc010gcc.1_Intron	NM_130811	NP_570824	P60880	SNP25_HUMAN	synaptosomal-associated protein 25 isoform	119					energy reserve metabolic process|glutamate secretion|neurotransmitter uptake|synaptic vesicle docking involved in exocytosis	cell junction|growth cone|perinuclear region of cytoplasm|synapse|synaptosome				skin(2)	2					Botulinum Toxin Type A(DB00083)	CAGCCTGCTCGTGTAGTGGAC	0.478													34	49	---	---	---	---	PASS
PLUNC	51297	broad.mit.edu	37	20	31825550	31825550	+	Silent	SNP	C	T	T	rs6120177	byFrequency	TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr20:31825550C>T	uc002wyv.2	+	2	103	c.33C>T	c.(31-33)TAC>TAT	p.Y11Y	PLUNC_uc002wyt.3_Silent_p.Y11Y|PLUNC_uc002wyu.3_Silent_p.Y11Y	NM_130852	NP_570913	Q9NP55	PLUNC_HUMAN	palate, lung and nasal epithelium associated	11					innate immune response	extracellular region	lipid binding				0						TTGTCTTCTACGGGCTGTTAG	0.537													51	71	---	---	---	---	PASS
MMP24	10893	broad.mit.edu	37	20	33839802	33839802	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr20:33839802A>G	uc002xbu.2	+	3	493	c.490A>G	c.(490-492)AGG>GGG	p.R164G	EDEM2_uc010zuv.1_Intron	NM_006690	NP_006681	Q9Y5R2	MMP24_HUMAN	matrix metalloproteinase 24 preproprotein	164	Extracellular (Potential).				proteolysis	integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding				0			BRCA - Breast invasive adenocarcinoma(18;0.00252)			ACAGAAGTGGAGGCAAAAACA	0.552													4	121	---	---	---	---	PASS
C21orf99	149992	broad.mit.edu	37	21	14439357	14439357	+	RNA	SNP	C	G	G			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr21:14439357C>G	uc002yja.3	+	10		c.2875C>G				NR_026916				Homo sapiens C21orf99 protein (C21orf99) mRNA, complete cds.												0						TGAATCAGCTCAATCAATCGC	0.274													2	3	---	---	---	---	PASS
SHROOM2	357	broad.mit.edu	37	X	9912815	9912815	+	Silent	SNP	C	T	T			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chrX:9912815C>T	uc004csu.1	+	9	4536	c.4446C>T	c.(4444-4446)CCC>CCT	p.P1482P	SHROOM2_uc004csv.2_Silent_p.P316P|SHROOM2_uc011mic.1_Silent_p.P317P|SHROOM2_uc004csw.1_Silent_p.P317P	NM_001649	NP_001640	Q13796	SHRM2_HUMAN	apical protein of Xenopus-like	1482	ASD2.				apical protein localization|brain development|cell migration|cell morphogenesis|cellular pigment accumulation|ear development|establishment of melanosome localization|eye pigment granule organization|lens morphogenesis in camera-type eye|melanosome organization	apical plasma membrane|cell-cell adherens junction|microtubule|tight junction	actin filament binding|beta-catenin binding|ligand-gated sodium channel activity			ovary(3)|skin(3)|upper_aerodigestive_tract(1)|breast(1)	8		Hepatocellular(5;0.000888)				TCTGCAAGCCCAGCGAGTTTG	0.647													3	42	---	---	---	---	PASS
ZMYM3	9203	broad.mit.edu	37	X	70471027	70471027	+	Splice_Site	SNP	C	A	A			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chrX:70471027C>A	uc004dzh.1	-	4	865	c.778_splice	c.e4+1	p.I260_splice	BCYRN1_uc011mpt.1_Intron|ZMYM3_uc004dzi.1_Splice_Site_p.I260_splice|ZMYM3_uc004dzj.1_Splice_Site_p.I260_splice|ZMYM3_uc011mpu.1_Splice_Site|ZMYM3_uc004dzk.3_Splice_Site_p.I260_splice|ZMYM3_uc004dzl.3_Splice_Site_p.I260_splice|ZMYM3_uc004dzm.3_Splice_Site_p.I260_splice	NM_201599	NP_963893	Q14202	ZMYM3_HUMAN	zinc finger protein 261						multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Renal(35;0.156)					ATCCTACTTACTGCTCTCAGT	0.532													65	15	---	---	---	---	PASS
OGT	8473	broad.mit.edu	37	X	70767813	70767813	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chrX:70767813T>G	uc004eaa.1	+	5	805	c.588T>G	c.(586-588)AAT>AAG	p.N196K	BCYRN1_uc011mpt.1_Intron|OGT_uc004eab.1_Missense_Mutation_p.N186K|OGT_uc004eac.2_Missense_Mutation_p.N57K|OGT_uc004ead.2_5'UTR	NM_181672	NP_858058	O15294	OGT1_HUMAN	O-linked GlcNAc transferase isoform 1	196	TPR 5.				cellular response to retinoic acid|positive regulation of granulocyte differentiation|positive regulation of histone H3-K4 methylation|positive regulation of proteolysis|protein O-linked glycosylation|signal transduction	cytosol|MLL5-L complex	enzyme activator activity|protein binding|protein N-acetylglucosaminyltransferase activity			ovary(3)|kidney(1)|pancreas(1)	5	Renal(35;0.156)					CTTGGAGTAATCTTGGCTGTG	0.378													9	189	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	12957	12957	+	RNA	SNP	T	C	C			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chrM:12957T>C	uc004cox.3	+	1		c.621T>C			uc004coy.2_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		CTAAACGCTAATCCAAGCCTC	0.522													12	1	---	---	---	---	PASS
LASS6	253782	broad.mit.edu	37	2	169417720	169417720	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chr2:169417720delT	uc002ueb.1	+	3	419	c.295delT	c.(295-297)TTGfs	p.L99fs	LASS6_uc002uec.1_Frame_Shift_Del_p.L99fs	NM_203463	NP_982288	Q6ZMG9	CERS6_HUMAN	longevity assurance homolog 6	99	Cytoplasmic (Potential).|Homeobox.					endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			skin(1)	1						TGAAAAGAGATTGGAAGGCCT	0.428													250	14	---	---	---	---	
GPR64	10149	broad.mit.edu	37	X	19026198	19026199	+	Frame_Shift_Ins	INS	-	T	T			TCGA-CH-5741-01A-11D-1576-08	TCGA-CH-5741-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3c1be2ab-1f84-46dc-b166-4d703d0e8ffa	3b14c841-4ca0-49a9-b938-de2ebbea8bdf	g.chrX:19026198_19026199insT	uc004cyx.2	-	19	1629_1630	c.1465_1466insA	c.(1465-1467)ATTfs	p.I489fs	GPR64_uc004cyy.2_Frame_Shift_Ins_p.I486fs|GPR64_uc004cyz.2_Frame_Shift_Ins_p.I475fs|GPR64_uc004czb.2_Frame_Shift_Ins_p.I489fs|GPR64_uc004czc.2_Frame_Shift_Ins_p.I473fs|GPR64_uc004czd.2_Frame_Shift_Ins_p.I465fs|GPR64_uc004cze.2_Frame_Shift_Ins_p.I459fs|GPR64_uc004czf.2_Frame_Shift_Ins_p.I451fs|GPR64_uc004cza.2_Frame_Shift_Ins_p.I467fs|GPR64_uc004cyw.2_Frame_Shift_Ins_p.I473fs|GPR64_uc010nfj.2_Intron	NM_001079858	NP_001073327	Q8IZP9	GPR64_HUMAN	G protein-coupled receptor 64 isoform 1	489	Extracellular (Potential).				neuropeptide signaling pathway|spermatogenesis	cytoplasm|integral to plasma membrane	G-protein coupled receptor activity				0	Hepatocellular(33;0.183)					AGGAAGAGTAATTGTGCCAATA	0.391													23	91	---	---	---	---	
