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	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	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
PNLIPRP1	5407	broad.mit.edu	36	10	118341353	118341353	+	Missense_Mutation	SNP	A	G	G			TCGA-28-1755-01	TCGA-28-1755-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:118341353A>G	uc001lco.1	+	c.130A>G	c.(130-132)ATT>GTT	p.I44V	PNLIPRP1_uc001lcp.2_Missense_Mutation_p.I44V|PNLIPRP1_uc001lcn.2_Missense_Mutation_p.I44V|PNLIPRP1_uc009xys.1_Non-coding_Transcript	NM_006229	NP_006220	P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1	44					lipid metabolic process		calcium ion binding|triglyceride lipase activity			ovary(1)|breast(1)	2				all cancers(201;0.0161)										0.793103	74.935731	77.242443	23	6	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	118341353	118341353	12576	10	A	G	G	4	4	PNLIPRP1	G	4	4
ABI1	10006	broad.mit.edu	36	10	27088058	27088058	+	Silent	SNP	C	A	A			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:27088058C>A	uc001isx.1	-	c.1017G>T	c.(1015-1017)GTG>GTT	p.V339V	ABI1_uc001isy.1_Silent_p.V312V|ABI1_uc001isz.1_Silent_p.V307V|ABI1_uc001ita.1_Silent_p.V312V|ABI1_uc001itb.1_Silent_p.V356V|ABI1_uc001itc.1_Silent_p.V311V|ABI1_uc001itd.1_Silent_p.V311V|ABI1_uc001ite.1_Silent_p.V306V	NM_005470	NP_005461	Q8IZP0	ABI1_HUMAN	abl-interactor 1 isoform a	339	Pro-rich.				actin polymerization or depolymerization|cellular component movement|negative regulation of cell proliferation|peptidyl-tyrosine phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	cell junction|cytoskeleton|cytosol|endoplasmic reticulum|filopodium|growth cone|lamellipodium|nucleus|soluble fraction|synapse|synaptosome	cytoskeletal protein binding			central_nervous_system(1)	1										359				0.444444	101.690185	101.88378	32	40	CC		KEEP	---	---	---	---	capture			Silent	SNP	27088058	27088058	89	10	C	A	A	29	29	ABI1	A	3	3
AKR1C1	1645	broad.mit.edu	36	10	5001128	5001128	+	Missense_Mutation	SNP	T	C	C			TCGA-28-1755-01	TCGA-28-1755-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:5001128T>C	uc001iho.1	+	c.562T>C	c.(562-564)TGC>CGC	p.C188R	AKR1E2_uc001ihl.1_Intron|AKR1C3_uc001ihr.1_Intron|AKR1C1_uc001ihq.1_Missense_Mutation_p.C188R	NM_001353	NP_001344	Q04828	AK1C1_HUMAN	aldo-keto reductase family 1, member C1	188					bile acid and bile salt transport|bile acid metabolic process|cholesterol homeostasis|intestinal cholesterol absorption|oxidation-reduction process|protein homooligomerization|response to organophosphorus|xenobiotic metabolic process	cytosol	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity|aldo-keto reductase (NADP) activity|androsterone dehydrogenase (B-specific) activity|bile acid binding|indanol dehydrogenase activity|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity			ovary(2)	2					NADH(DB00157)	Colon(130;2054 2316 13360 15380)								0.453608	399.792725	400.345926	132	159	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5001128	5001128	472	10	T	C	C	55	55	AKR1C1	C	4	4
MRGPRX1	259249	broad.mit.edu	36	11	18912562	18912562	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:18912562C>T	uc001mpg.1	-	c.346G>A	c.(346-348)GTG>ATG	p.V116M		NM_147199	NP_671732	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	116	Helical; Name=3; (Potential).				acute-phase response	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(2)|central_nervous_system(1)	3														0.409091	158.785268	159.746553	54	78	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18912562	18912562	10159	11	C	T	T	19	19	MRGPRX1	T	1	1
OR52M1	119772	broad.mit.edu	36	11	4523394	4523394	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:4523394G>A	uc001lzb.1	+	c.398G>A	c.(397-399)CGT>CAT	p.R133H		NM_001004137	NP_001004137	Q8NGK5	O52M1_HUMAN	olfactory receptor, family 52, subfamily M,	133	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)										0.395122	242.99867	244.94891	81	124	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	4523394	4523394	11536	11	G	A	A	40	40	OR52M1	A	1	1
OR10W1	81341	broad.mit.edu	36	11	57791307	57791307	+	Silent	SNP	C	T	T			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:57791307C>T	uc001nmq.1	-	c.600G>A	c.(598-600)GTG>GTA	p.V200V		NM_207374	NP_997257	Q8NGF6	O10W1_HUMAN	olfactory receptor, family 10, subfamily W,	200	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(21;0.0589)												0.528302	81.893987	81.930416	28	25	CC		KEEP	---	---	---	---	capture			Silent	SNP	57791307	57791307	11327	11	C	T	T	25	25	OR10W1	T	2	2
RNF10	9921	broad.mit.edu	36	12	119457045	119457046	+	Missense_Mutation	DNP	CA	AG	AG			TCGA-28-1755-01	TCGA-28-1755-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:119457045_119457046CA>AG	uc001typ.2	+	c.48_49CA>AG	c.(46-51)GACAAG>GAAGAG	p.16_17DK>EE		NM_014868	NP_055683	Q8N5U6	RNF10_HUMAN	ring finger protein 10	16_17					negative regulation of Schwann cell proliferation|positive regulation of myelination|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	promoter binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)													0.263158	8.663514	9.630583	5	14	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	119457045	119457046	13899	12	CA	AG	AG	17	17	RNF10	AG	3	3
TMEM132D	121256	broad.mit.edu	36	12	128132451	128132451	+	Missense_Mutation	SNP	C	A	A			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:128132451C>A	uc009zyl.1	-	c.1729G>T	c.(1729-1731)GTG>TTG	p.V577L	TMEM132D_uc001uia.2_Missense_Mutation_p.V115L	NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D	577	Extracellular (Potential).					integral to membrane				ovary(10)|pancreas(2)	12	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)										0.289474	26.501503	27.95818	11	27	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	128132451	128132451	16579	12	C	A	A	18	18	TMEM132D	A	3	3
DCAF11	80344	broad.mit.edu	36	14	23658866	23658866	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:23658866G>A	uc001wlv.1	+	c.1013G>A	c.(1012-1014)CGC>CAC	p.R338H	DCAF11_uc001wlw.1_Missense_Mutation_p.R338H|DCAF11_uc001wlx.1_Missense_Mutation_p.R312H|DCAF11_uc001wly.1_Missense_Mutation_p.R294H|DCAF11_uc001wlz.1_Missense_Mutation_p.R238H|DCAF11_uc001wma.2_Missense_Mutation_p.R338H|DCAF11_uc001wmb.2_Missense_Mutation_p.R312H|DCAF11_uc001wmd.1_Missense_Mutation_p.R338H|DCAF11_uc001wme.1_Missense_Mutation_p.R298H|DCAF11_uc001wmc.1_Missense_Mutation_p.R238H	NM_025230	NP_079506	Q8TEB1	DCA11_HUMAN	WD repeat domain 23 isoform 1	338	WD 4.				protein ubiquitination	CUL4 RING ubiquitin ligase complex	protein binding				0														0.428571	43.220074	43.375517	15	20	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	23658866	23658866	4433	14	G	A	A	38	38	DCAF11	A	1	1
GZMB	3002	broad.mit.edu	36	14	24170939	24170939	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:24170939C>T	uc001wps.1	-	c.565G>A	c.(565-567)GTG>ATG	p.V189M	GZMB_uc010ama.1_Missense_Mutation_p.V177M|GZMB_uc010amb.1_Non-coding_Transcript	NM_004131	NP_004122	P10144	GRAB_HUMAN	granzyme B precursor	189	Peptidase S1.				activation of pro-apoptotic gene products|cleavage of lamin|cytolysis|induction of apoptosis by intracellular signals	cytosol|immunological synapse|nucleus	protein binding|serine-type endopeptidase activity				0				GBM - Glioblastoma multiforme(265;0.028)										0.573171	316.774363	317.540914	94	70	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	24170939	24170939	7196	14	C	T	T	19	19	GZMB	T	1	1
NEK9	91754	broad.mit.edu	36	14	74643054	74643054	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:74643054G>A	uc001xrl.1	-	c.1432C>T	c.(1432-1434)CTC>TTC	p.L478F	NEK9_uc001xrk.1_5'UTR	NM_033116	NP_149107	Q8TD19	NEK9_HUMAN	NIMA-related kinase 9	478	RCC1 2.				cell division|mitosis|protein phosphorylation	mitochondrion|nucleus	ATP binding|metal ion binding|protein kinase binding|protein serine/threonine kinase activity			lung(2)|ovary(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.00718)						359				0.101299	33.242779	94.324104	39	346	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74643054	74643054	10730	14	G	A	A	35	35	NEK9	A	2	2
THBS1	7057	broad.mit.edu	36	15	37663859	37663859	+	Nonsense_Mutation	SNP	C	T	T			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:37663859C>T	uc001zkh.1	+	c.970C>T	c.(970-972)CAG>TAG	p.Q324*		NM_003246	NP_003237	P07996	TSP1_HUMAN	thrombospondin 1 precursor	324	VWFC.				activation of MAPK activity|anti-apoptosis|apoptosis|cell adhesion|cell cycle arrest|cell migration|cellular response to heat|chronic inflammatory response|engulfment of apoptotic cell|immune response|induction of apoptosis|negative regulation of angiogenesis|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|negative regulation of blood vessel endothelial cell migration|negative regulation of caspase activity|negative regulation of cGMP-mediated signaling|negative regulation of dendritic cell antigen processing and presentation|negative regulation of endothelial cell proliferation|negative regulation of fibrinolysis|negative regulation of fibroblast growth factor receptor signaling pathway|negative regulation of focal adhesion assembly|negative regulation of interleukin-12 production|negative regulation of nitric oxide mediated signal transduction|negative regulation of plasma membrane long-chain fatty acid transport|negative regulation of plasminogen activation|peptide cross-linking|platelet activation|platelet degranulation|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of fibroblast migration|positive regulation of macrophage activation|positive regulation of macrophage chemotaxis|positive regulation of oxygen and reactive oxygen species metabolic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transforming growth factor-beta1 production|positive regulation of translation|positive regulation of tumor necrosis factor biosynthetic process|response to calcium ion|response to drug|response to glucose stimulus|response to hypoxia|response to magnesium ion|response to progesterone stimulus|sprouting angiogenesis	external side of plasma membrane|extracellular matrix|fibrinogen complex|platelet alpha granule lumen	calcium ion binding|collagen V binding|eukaryotic cell surface binding|fibrinogen binding|fibroblast growth factor 2 binding|fibronectin binding|heparin binding|identical protein binding|integrin binding|laminin binding|low-density lipoprotein particle binding|phosphatidylserine binding|proteoglycan binding|structural molecule activity|transforming growth factor beta binding			central_nervous_system(3)|ovary(2)	5		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)	Becaplermin(DB00102)									0.147059	36.412303	52.68599	20	116	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	37663859	37663859	16381	15	C	T	T	29	29	THBS1	T	5	2
BUB1B	701	broad.mit.edu	36	15	38297162	38297162	+	Splice_Site_SNP	SNP	T	C	C			TCGA-28-1755-01	TCGA-28-1755-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:38297162T>C	uc001zkx.2	+	c.e21_splice_site			PAK6_uc010bbl.1_Splice_Site_SNP|PAK6_uc010bbm.1_Splice_Site_SNP	NM_001211	NP_001202			budding uninhibited by benzimidazoles 1 beta						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell division|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|phosphatidylinositol-mediated signaling|protein localization to kinetochore|protein phosphorylation|spindle organization	anaphase-promoting complex|condensed chromosome outer kinetochore|cytosol|microtubule organizing center|perinuclear region of cytoplasm|spindle midzone	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)|kidney(1)	2		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)						298				0.411765	71.167329	71.513706	21	30	TT		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	38297162	38297162	1605	15	T	C	C	57	57	BUB1B	C	5	4
PPIP5K1	9677	broad.mit.edu	36	15	41660760	41660760	+	Missense_Mutation	SNP	G	T	T			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:41660760G>T	uc001zrw.1	-	c.896C>A	c.(895-897)GCC>GAC	p.A299D	PPIP5K1_uc001zsa.2_Missense_Mutation_p.A299D|PPIP5K1_uc001zru.1_Missense_Mutation_p.A299D|PPIP5K1_uc001zrv.1_Missense_Mutation_p.A299D|PPIP5K1_uc001zrx.1_Missense_Mutation_p.A299D|PPIP5K1_uc001zry.2_Missense_Mutation_p.A299D|PPIP5K1_uc001zrz.1_Missense_Mutation_p.A299D|PPIP5K1_uc001zsb.2_Missense_Mutation_p.A299D	NM_014659	NP_055474	Q6PFW1	VIP1_HUMAN	histidine acid phosphatase domain containing 2A	299					inositol metabolic process	cytosol	acid phosphatase activity|ATP binding|diphosphoinositol-pentakisphosphate kinase activity|inositol 1,3,4,5,6-pentakisphosphate kinase activity|inositol hexakisphosphate 5-kinase activity				0														0.376771	395.539777	400.22327	133	220	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41660760	41660760	12767	15	G	T	T	42	42	PPIP5K1	T	3	3
SGK269	79834	broad.mit.edu	36	15	75194419	75194419	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:75194419C>T	uc002bcm.2	-	c.4375G>A	c.(4375-4377)GTT>ATT	p.V1459I		NM_024776	NP_079052	Q9H792	PEAK1_HUMAN	NKF3 kinase family member	1459	Protein kinase.				cell migration|protein autophosphorylation|substrate adhesion-dependent cell spreading	actin cytoskeleton|cytoplasm|focal adhesion	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding				0				STAD - Stomach adenocarcinoma(199;0.124)						217				0.141176	140.636652	214.528626	84	511	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	75194419	75194419	14702	15	C	T	T	19	19	SGK269	T	1	1
RASGRF1	5923	broad.mit.edu	36	15	77041555	77041555	+	Missense_Mutation	SNP	T	G	G			TCGA-28-1755-01	TCGA-28-1755-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:77041555T>G	uc002beq.1	-	c.3808A>C	c.(3808-3810)AAA>CAA	p.K1270Q	RASGRF1_uc002beo.1_Missense_Mutation_p.K486Q|RASGRF1_uc002bep.1_Missense_Mutation_p.K1115Q	NM_002891	NP_002882	Q13972	RGRF1_HUMAN	Ras protein-specific guanine	1272	Ras-GEF.				activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|growth cone|plasma membrane|synaptosome	Rho guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)|central_nervous_system(1)	4										694				0.210526	7.888382	9.362764	4	15	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	77041555	77041555	13533	15	T	G	G	64	64	RASGRF1	G	4	4
LRRK1	79705	broad.mit.edu	36	15	99386862	99386863	+	Missense_Mutation	DNP	GA	TC	TC			TCGA-28-1755-01	TCGA-28-1755-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:99386862_99386863GA>TC	uc002bwr.1	+	c.2865_2866GA>TC	c.(2863-2868)AGGATG>AGTCTG	p.955_956RM>SL		NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	leucine-rich repeat kinase 1	955_956					protein phosphorylation|small GTPase mediated signal transduction	mitochondrion	ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1)	12	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)							1100				0.2	15.566553	20.602912	12	48	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	99386862	99386863	9408	15	GA	TC	TC	41	41	LRRK1	TC	3	3
ITGAD	3681	broad.mit.edu	36	16	31335366	31335366	+	Silent	SNP	C	T	T			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:31335366C>T	uc010cap.1	+	c.2400C>T	c.(2398-2400)AAC>AAT	p.N800N	ITGAD_uc002ebv.1_Silent_p.N799N	NM_005353	NP_005344	Q13349	ITAD_HUMAN	integrin, alpha D precursor	799	Extracellular (Potential).				cell-cell adhesion|cell-matrix adhesion|immune response|integrin-mediated signaling pathway	integrin complex	receptor activity			skin(1)	1														0.5	134.84474	134.84474	43	43	CC		KEEP	---	---	---	---	capture			Silent	SNP	31335366	31335366	8188	16	C	T	T	19	19	ITGAD	T	1	1
B4GALNT2	124872	broad.mit.edu	36	17	44574488	44574488	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:44574488C>T	uc002ion.1	+	c.488C>T	c.(487-489)GCG>GTG	p.A163V		NM_153446	NP_703147	Q8NHY0	B4GN2_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 2	163	Lumenal (Potential).				lipid glycosylation|negative regulation of cell-cell adhesion|UDP-N-acetylgalactosamine metabolic process	integral to Golgi membrane	acetylgalactosaminyltransferase activity			large_intestine(1)|ovary(1)	2			all cancers(6;0.000316)			GBM(124;244 1635 8663 18097 33175)								0.367347	54.748437	55.501688	18	31	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44574488	44574488	1288	17	C	T	T	27	27	B4GALNT2	T	1	1
RABEP1	9135	broad.mit.edu	36	17	5194521	5194521	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:5194521C>T	uc002gbm.2	+	c.836C>T	c.(835-837)ACG>ATG	p.T279M	RABEP1_uc010clc.1_Missense_Mutation_p.T272M|RABEP1_uc010cld.1_Missense_Mutation_p.T236M|RABEP1_uc002gbl.2_Missense_Mutation_p.T279M	NM_004703	NP_004694	Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	279	Potential.				apoptosis|cellular membrane fusion|endocytosis|protein transport	centrosome|cytoplasmic membrane-bounded vesicle|early endosome|recycling endosome	growth factor activity|GTPase activator activity|protein homodimerization activity			large_intestine(1)|ovary(1)	2										903				0.292683	172.03187	179.913062	60	145	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5194521	5194521	13420	17	C	T	T	19	19	RABEP1	T	1	1
ELAVL3	1995	broad.mit.edu	36	19	11438456	11438456	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:11438456C>T	uc002mry.1	-	c.196G>A	c.(196-198)GAG>AAG	p.E66K	ELAVL3_uc002mrx.1_Missense_Mutation_p.E66K	NM_001420	NP_001411	Q14576	ELAV3_HUMAN	ELAV-like protein 3 isoform 1	66	RRM 1.				cell differentiation|nervous system development		AU-rich element binding|nucleotide binding			ovary(1)|breast(1)	2														0.390335	321.911689	324.740975	105	164	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11438456	11438456	5242	19	C	T	T	31	31	ELAVL3	T	1	1
EMR3	84658	broad.mit.edu	36	19	14609975	14609975	+	Missense_Mutation	SNP	C	T	T	rs35094696	unknown	TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:14609975C>T	uc002mzi.2	-	c.1426G>A	c.(1426-1428)GCT>ACT	p.A476T	EMR3_uc010dzp.1_Missense_Mutation_p.A424T	NM_032571	NP_115960	Q9BY15	EMR3_HUMAN	egf-like module-containing mucin-like receptor	476	Helical; Name=4; (Potential).				neuropeptide signaling pathway	extracellular space|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(5)	5														0.520635	494.945303	495.061992	164	151	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	14609975	14609975	5299	19	C	T	T	27	27	EMR3	T	1	1
CEACAM8	1088	broad.mit.edu	36	19	47785525	47785525	+	Silent	SNP	G	A	A			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:47785525G>A	uc002oud.1	-	c.627C>T	c.(625-627)GAC>GAT	p.D209D		NM_001816	NP_001807	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion	209	Ig-like C2-type 1.				immune response	anchored to membrane|extracellular space|integral to plasma membrane				ovary(1)	1		Prostate(69;0.00899)												0.428064	734.868364	737.408174	241	322	GG		KEEP	---	---	---	---	capture			Silent	SNP	47785525	47785525	3331	19	G	A	A	40	40	CEACAM8	A	1	1
HCN2	610	broad.mit.edu	36	19	566887	566887	+	Missense_Mutation	SNP	G	T	T			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:566887G>T	uc002lpe.1	+	c.2083G>T	c.(2083-2085)GTC>TTC	p.V695F		NM_001194	NP_001185	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic	695	Cytoplasmic (Potential).				cell-cell signaling|muscle contraction	voltage-gated potassium channel complex	cAMP binding|protein binding|sodium channel activity|voltage-gated potassium channel activity				0		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;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)		Melanoma(145;1175 2427 8056 36306)								0.210526	10.789907	12.262208	4	15	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	566887	566887	7279	19	G	T	T	40	40	HCN2	T	3	3
LILRB2	10288	broad.mit.edu	36	19	59475598	59475598	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:59475598C>T	uc002qfb.1	-	c.215G>A	c.(214-216)CGG>CAG	p.R72Q	LILRA6_uc002qew.1_Intron|LILRB2_uc010eri.1_Missense_Mutation_p.R72Q|LILRB2_uc010erj.1_Non-coding_Transcript|LILRB2_uc002qfc.1_Missense_Mutation_p.R72Q	NM_005874	NP_005865	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor,	72	Extracellular (Potential).|Ig-like C2-type 1.				cell surface receptor linked signaling pathway|cell-cell signaling|cellular defense response|immune response|regulation of immune response	integral to plasma membrane|membrane fraction	receptor activity				0	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)										0.636364	73.309775	73.868542	21	12	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59475598	59475598	9117	19	C	T	T	23	23	LILRB2	T	1	1
OTUD7B	56957	broad.mit.edu	36	1	148185815	148185815	+	Silent	SNP	G	A	A			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:148185815G>A	uc001etn.1	-	c.1284C>T	c.(1282-1284)TAC>TAT	p.Y428Y		NM_020205	NP_064590	Q6GQQ9	OTU7B_HUMAN	zinc finger protein Cezanne	428	Catalytic.				negative regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|microtubule cytoskeleton|nucleus	cysteine-type peptidase activity|DNA binding|protein binding|zinc ion binding				0	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)											0.416107	197.026066	197.940813	62	87	GG		KEEP	---	---	---	---	capture			Silent	SNP	148185815	148185815	11732	1	G	A	A	48	48	OTUD7B	A	2	2
C1orf107	27042	broad.mit.edu	36	1	208078942	208078942	+	Silent	SNP	C	T	T			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:208078942C>T	uc001hhr.1	+	c.1128C>T	c.(1126-1128)CTC>CTT	p.L376L	C1orf107_uc009xcu.1_Silent_p.L91L	NM_014388	NP_055203	Q68CQ4	DIEXF_HUMAN	digestive-organ expansion factor homolog	376					multicellular organismal development	nucleus					0				OV - Ovarian serous cystadenocarcinoma(81;0.0367)										0.229508	35.01852	39.11123	14	47	CC		KEEP	---	---	---	---	capture			Silent	SNP	208078942	208078942	2048	1	C	T	T	31	31	C1orf107	T	1	1
PTPN14	5784	broad.mit.edu	36	1	212624570	212624570	+	Silent	SNP	C	T	T			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:212624570C>T	uc001hkk.1	-	c.1251G>A	c.(1249-1251)GGG>GGA	p.G417G		NM_005401	NP_005392	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type	417						cytoplasm|cytoskeleton	binding|protein tyrosine phosphatase activity			breast(2)|ovary(1)|kidney(1)|skin(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		Colon(92;557 1424 24372 34121 40073)								0.661417	517.209118	523.060234	168	86	CC		KEEP	---	---	---	---	capture			Silent	SNP	212624570	212624570	13238	1	C	T	T	30	30	PTPN14	T	2	2
C1orf198	84886	broad.mit.edu	36	1	229070732	229070732	+	Missense_Mutation	SNP	G	C	C			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:229070732G>C	uc001hub.1	-	c.150C>G	c.(148-150)ATC>ATG	p.I50M	C1orf198_uc001huc.1_Intron|C1orf198_uc001hud.1_Missense_Mutation_p.I12M	NM_032800	NP_116189	Q9H425	CA198_HUMAN	hypothetical protein LOC84886 isoform 1	50											0	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)												0.285714	8.091423	8.670395	4	10	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	229070732	229070732	2094	1	G	C	C	41	41	C1orf198	C	3	3
OR2T12	127064	broad.mit.edu	36	1	246525061	246525061	+	Missense_Mutation	SNP	A	G	G			TCGA-28-1755-01	TCGA-28-1755-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246525061A>G	uc001iee.1	-	c.443T>C	c.(442-444)CTC>CCC	p.L148P		NM_001004692	NP_001004692	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T,	148	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	p.L148H(1)		ovary(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)											0.38961	82.935453	83.785911	30	47	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	246525061	246525061	11425	1	A	G	G	11	11	OR2T12	G	4	4
OR2G6	391211	broad.mit.edu	36	1	246751996	246751996	+	Silent	SNP	G	A	A			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246751996G>A	uc001ien.1	+	c.426G>A	c.(424-426)GCG>GCA	p.A142A		NM_001013355	NP_001013373	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G,	142	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)											0.289474	56.942254	59.94799	22	54	GG		KEEP	---	---	---	---	capture			Silent	SNP	246751996	246751996	11406	1	G	A	A	40	40	OR2G6	A	1	1
EPHA10	284656	broad.mit.edu	36	1	37999926	37999926	+	Silent	SNP	G	A	A			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:37999926G>A	uc009vvi.1	-	c.588C>T	c.(586-588)GGC>GGT	p.G196G	EPHA10_uc001cbw.2_Silent_p.G196G	NM_001099439	NP_001092909	Q5JZY3	EPHAA_HUMAN	EPH receptor A10 isofom 3	196	Extracellular (Potential).				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular region|integral to membrane|integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding|transmembrane-ephrin receptor activity			breast(3)|stomach(1)	4	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)								328				0.529412	29.67924	29.692462	9	8	GG		KEEP	---	---	---	---	capture			Silent	SNP	37999926	37999926	5359	1	G	A	A	38	38	EPHA10	A	1	1
PTPRT	11122	broad.mit.edu	36	20	40146877	40146877	+	Missense_Mutation	SNP	A	T	T			TCGA-28-1755-01	TCGA-28-1755-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:40146877A>T	uc010ggj.1	-	c.4052T>A	c.(4051-4053)GTC>GAC	p.V1351D	PTPRT_uc002xkg.1_Missense_Mutation_p.V1332D|PTPRT_uc010ggi.1_Missense_Mutation_p.V535D	NM_133170	NP_573400	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1332	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 2.				homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			ovary(7)|lung(5)|skin(2)	14		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)								646				0.211268	29.404833	34.881656	15	56	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40146877	40146877	13270	20	A	T	T	10	10	PTPRT	T	4	4
ZNF831	128611	broad.mit.edu	36	20	57215408	57215408	+	Missense_Mutation	SNP	G	T	T			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:57215408G>T	uc002yan.1	+	c.3929G>T	c.(3928-3930)CGC>CTC	p.R1310L		NM_178457	NP_848552	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1310						intracellular	nucleic acid binding|zinc ion binding			ovary(1)|skin(1)	2	all_lung(29;0.0085)													0.526316	33.353519	33.36529	10	9	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	57215408	57215408	18784	20	G	T	T	38	38	ZNF831	T	3	3
C20orf54	113278	broad.mit.edu	36	20	693995	693995	+	Missense_Mutation	SNP	A	C	C			TCGA-28-1755-01	TCGA-28-1755-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:693995A>C	uc002wed.2	-	c.424T>G	c.(424-426)TTT>GTT	p.F142V	C20orf54_uc002wee.2_Missense_Mutation_p.F142V	NM_033409	NP_212134	Q9NQ40	RFT2_HUMAN	hypothetical protein LOC113278	142	Helical; (Potential).				sensory perception of sound	integral to plasma membrane	riboflavin transporter activity			ovary(2)	2														0.2	12.172982	15.528699	8	32	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	693995	693995	2194	20	A	C	C	3	3	C20orf54	C	4	4
RRP1	8568	broad.mit.edu	36	21	44035681	44035681	+	Silent	SNP	G	A	A			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:44035681G>A	uc002zds.2	+	c.156G>A	c.(154-156)CTG>CTA	p.L52L	RRP1_uc010gpk.1_5'UTR|RRP1_uc010gpl.1_5'Flank	NM_003683	NP_003674	P56182	RRP1_HUMAN	ribosomal RNA processing 1 homolog	52					rRNA processing	nucleolus|preribosome, small subunit precursor					0				COAD - Colon adenocarcinoma(84;0.00753)|Colorectal(79;0.0157)|STAD - Stomach adenocarcinoma(101;0.171)										0.2	15.704579	18.634636	7	28	GG		KEEP	---	---	---	---	capture			Silent	SNP	44035681	44035681	14165	21	G	A	A	46	46	RRP1	A	2	2
COL18A1	80781	broad.mit.edu	36	21	45721809	45721809	+	Missense_Mutation	SNP	C	G	G			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:45721809C>G	uc002zhi.1	+	c.1525C>G	c.(1525-1527)CCT>GCT	p.P509A	COL18A1_uc002zhg.1_Missense_Mutation_p.P329A	NM_030582	NP_085059	P39060	COIA1_HUMAN	alpha 1 type XVIII collagen isoform 1 precursor	744	Nonhelical region 1 (NC1).				cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)						1836				0.666667	31.272774	31.660566	10	5	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45721809	45721809	3813	21	C	G	G	22	22	COL18A1	G	3	3
PICK1	9463	broad.mit.edu	36	22	36798514	36798515	+	Missense_Mutation	DNP	AC	CT	CT			TCGA-28-1755-01	TCGA-28-1755-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:36798514_36798515AC>CT	uc003auq.1	+	c.641_642AC>CT	c.(640-642)CAC>CCT	p.H214P	PICK1_uc003aur.1_Missense_Mutation_p.H214P|PICK1_uc003aus.1_Missense_Mutation_p.H214P|PICK1_uc003aut.1_Missense_Mutation_p.H214P	NM_012407	NP_036539	Q9NRD5	PICK1_HUMAN	protein interacting with C kinase 1	214	AH.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|DNA methylation involved in embryo development|DNA methylation involved in gamete generation|monoamine transport|neuronal ion channel clustering|protein phosphorylation|receptor clustering|retrograde vesicle-mediated transport, Golgi to ER|synaptic transmission	cell junction|endocytic vesicle membrane|Golgi apparatus|perinuclear region of cytoplasm|presynaptic membrane	ATPase activity|metal ion binding|protein C-terminus binding|protein kinase C binding|receptor binding				0	Melanoma(58;0.045)													0.333333	16.987737	17.580287	8	16	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	36798514	36798515	12305	22	AC	CT	CT	6	6	PICK1	CT	4	4
IL1F9	56300	broad.mit.edu	36	2	113454095	113454095	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:113454095C>T	uc002tio.1	+	c.199C>T	c.(199-201)CTT>TTT	p.L67F	IL1F9_uc010fkr.1_Missense_Mutation_p.L32F	NM_019618	NP_062564	Q9NZH8	IL1F9_HUMAN	interleukin 1 family, member 9	67					cell-cell signaling	extracellular space	cytokine activity|interleukin-1 receptor antagonist activity			ovary(1)|central_nervous_system(1)	2						Esophageal Squamous(44;715 981 6239 42838 46707)								0.146341	49.288944	74.027873	30	175	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	113454095	113454095	7958	2	C	T	T	32	32	IL1F9	T	2	2
FAM126B	285172	broad.mit.edu	36	2	201554687	201554687	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:201554687G>A	uc002uwt.1	-	c.1144C>T	c.(1144-1146)CGT>TGT	p.R382C	FAM126B_uc002uwu.1_Missense_Mutation_p.R356C|FAM126B_uc002uwv.1_Missense_Mutation_p.R382C	NM_173822	NP_776183	Q8IXS8	F126B_HUMAN	hypothetical protein LOC285172	382						intracellular				ovary(1)	1														0.567742	274.494086	275.114275	88	67	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	201554687	201554687	5627	2	G	A	A	38	38	FAM126B	A	1	1
DYSF	8291	broad.mit.edu	36	2	71562593	71562593	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:71562593C>T	uc010fen.1	+	c.224C>T	c.(223-225)ACG>ATG	p.T75M	DYSF_uc002sie.1_Missense_Mutation_p.T74M|DYSF_uc002sig.2_Missense_Mutation_p.T74M|DYSF_uc010fee.1_Missense_Mutation_p.T74M|DYSF_uc010fef.1_Missense_Mutation_p.T74M|DYSF_uc010feg.1_Missense_Mutation_p.T74M|DYSF_uc010feh.1_Missense_Mutation_p.T74M|DYSF_uc010fei.1_Missense_Mutation_p.T74M|DYSF_uc010fej.1_Missense_Mutation_p.T75M|DYSF_uc002sif.1_Missense_Mutation_p.T75M|DYSF_uc010fek.1_Missense_Mutation_p.T75M|DYSF_uc010fel.1_Missense_Mutation_p.T75M|DYSF_uc010fem.1_Missense_Mutation_p.T75M|DYSF_uc010feo.1_Missense_Mutation_p.T75M	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8	74	Cytoplasmic (Potential).|C2 1.					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)	6														0.337838	72.961261	74.677771	25	49	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71562593	71562593	5045	2	C	T	T	19	19	DYSF	T	1	1
ADAMTS9	56999	broad.mit.edu	36	3	64583022	64583022	+	Missense_Mutation	SNP	A	T	T			TCGA-28-1755-01	TCGA-28-1755-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:64583022A>T	uc003dmg.1	-	c.2578T>A	c.(2578-2580)TAC>AAC	p.Y860N	ADAMTS9_uc003dmh.1_Missense_Mutation_p.Y689N|ADAMTS9_uc003dmk.1_Missense_Mutation_p.Y860N	NM_182920	NP_891550	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1	860	Spacer.				glycoprotein catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)	3		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)										0.403101	150.570856	151.630148	52	77	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	64583022	64583022	274	3	A	T	T	14	14	ADAMTS9	T	4	4
NDST3	9348	broad.mit.edu	36	4	119194673	119194673	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:119194673G>A	uc003ibx.1	+	c.160G>A	c.(160-162)GAC>AAC	p.D54N	NDST3_uc003ibw.2_Missense_Mutation_p.D54N	NM_004784	NP_004775	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan	54	Lumenal (Potential).|Heparan sulfate N-deacetylase 3.					Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			large_intestine(1)	1														0.305882	147.091606	152.774261	52	118	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	119194673	119194673	10656	4	G	A	A	37	37	NDST3	A	1	1
OTOP1	133060	broad.mit.edu	36	4	4250501	4250501	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:4250501C>T	uc003ghp.1	-	c.961G>A	c.(961-963)GTG>ATG	p.V321M		NM_177998	NP_819056	Q7RTM1	OTOP1_HUMAN	otopetrin 1	321	Helical; (Potential).				biomineral tissue development	extracellular space|integral to membrane				ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)										0.552448	214.777478	215.117204	79	64	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	4250501	4250501	11717	4	C	T	T	19	19	OTOP1	T	1	1
C5orf32	84418	broad.mit.edu	36	5	139603152	139603152	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:139603152G>A	uc003lfd.1	+	c.266G>A	c.(265-267)TGC>TAC	p.C89Y	C5orf32_uc010jfi.1_Non-coding_Transcript	NM_032412	NP_115788	Q9H1C7	CE032_HUMAN	hypothetical protein LOC84418	89	Poly-Cys.										0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.123656	23.291229	48.994446	23	163	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	139603152	139603152	2389	5	G	A	A	46	46	C5orf32	A	2	2
ITK	3702	broad.mit.edu	36	5	156603851	156603851	+	Missense_Mutation	SNP	A	G	G			TCGA-28-1755-01	TCGA-28-1755-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:156603851A>G	uc003lwo.1	+	c.1234A>G	c.(1234-1236)AAA>GAA	p.K412E		NM_005546	NP_005537	Q08881	ITK_HUMAN	IL2-inducible T-cell kinase	412	Protein kinase.				cellular defense response|intracellular signal transduction|protein phosphorylation|T cell receptor signaling pathway	cytosol|plasma membrane	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			ovary(8)|lung(4)|skin(3)|stomach(1)|central_nervous_system(1)	17	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.1)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			Esophageal Squamous(70;1378 1469 8785 19883)				330				0.123711	6.647346	20.089845	12	85	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	156603851	156603851	8213	5	A	G	G	9	9	ITK	G	4	4
ENC1	8507	broad.mit.edu	36	5	73967862	73967863	+	Missense_Mutation	DNP	GA	TT	TT			TCGA-28-1755-01	TCGA-28-1755-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:73967862_73967863GA>TT	uc003kdc.2	-	c.204_205TC>AA	c.(202-207)AGTCGC>AGAAGC	p.68_69SR>RS	ENC1_uc010izg.1_Missense_Mutation_p.68_69SR>RS	NM_003633	NP_003624	O14682	ENC1_HUMAN	ectodermal-neural cortex (with BTB-like domain)	68_69	BTB.				nervous system development	cytoplasm|cytoskeleton|nuclear matrix	actin binding			ovary(1)|pancreas(1)|skin(1)	3		all_lung(232;0.0154)|Lung NSC(167;0.0331)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.45e-59)										0.195876	33.278142	41.639735	19	78	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	73967862	73967863	5306	5	GA	TT	TT	37	37	ENC1	TT	3	3
LAMA4	3910	broad.mit.edu	36	6	112537426	112537426	+	Missense_Mutation	SNP	T	C	C			TCGA-28-1755-01	TCGA-28-1755-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:112537426T>C	uc003pvu.2	-	c.5379A>G	c.(5377-5379)ATA>ATG	p.I1793M	LAMA4_uc003pvv.2_Missense_Mutation_p.I1786M|LAMA4_uc003pvt.2_Missense_Mutation_p.I1786M	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor	1793	Laminin G-like 5.				cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)										0.373418	175.288765	177.509386	59	99	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	112537426	112537426	8931	6	T	C	C	57	57	LAMA4	C	4	4
HIVEP2	3097	broad.mit.edu	36	6	143116537	143116537	+	Missense_Mutation	SNP	T	A	A			TCGA-28-1755-01	TCGA-28-1755-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:143116537T>A	uc003qjd.1	-	c.6741A>T	c.(6739-6741)TTA>TTT	p.L2247F		NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer	2247					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		Esophageal Squamous(107;843 1510 13293 16805 42198)								0.146341	17.486626	27.317623	12	70	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	143116537	143116537	7478	6	T	A	A	57	57	HIVEP2	A	4	4
HLA-DRB5	3127	broad.mit.edu	36	6	32595329	32595329	+	Missense_Mutation	SNP	C	A	A			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:32595329C>A	uc003obj.1	-	c.448G>T	c.(448-450)GGT>TGT	p.G150C	HLA-DRB5_uc003obk.2_Missense_Mutation_p.G150C	NM_002125	NP_002116	Q30154	DRB5_HUMAN	major histocompatibility complex, class II, DR	150	Ig-like C1-type.|Beta-2.|Extracellular (Potential).				antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0														0.5	6.821687	6.821687	3	3	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32595329	32595329	7500	6	C	A	A	21	21	HLA-DRB5	A	3	3
ABP1	26	broad.mit.edu	36	7	150189196	150189196	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:150189196C>T	uc003wia.1	+	c.2279C>T	c.(2278-2280)CCT>CTT	p.P760L	ABP1_uc003why.1_Missense_Mutation_p.P741L|ABP1_uc003whz.1_Missense_Mutation_p.P741L	NM_001091	NP_001082	P19801	ABP1_HUMAN	amiloride binding protein 1 precursor	741					amine metabolic process|oxidation-reduction process	extracellular space|peroxisome	copper ion binding|diamine oxidase activity|heparin binding|histamine oxidase activity|methylputrescine oxidase activity|primary amine oxidase activity|propane-1,3-diamine oxidase activity|quinone binding			ovary(2)|breast(2)	4	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Amiloride(DB00594)|Spermine(DB00127)	Pancreas(195;1227 3054 24912 28503)								0.2875	57.896541	61.135167	23	57	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	150189196	150189196	99	7	C	T	T	24	24	ABP1	T	2	2
HTR5A	3361	broad.mit.edu	36	7	154506933	154506933	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:154506933G>A	uc003wlu.1	+	c.877G>A	c.(877-879)GTG>ATG	p.V293M		NM_024012	NP_076917	P47898	5HT5A_HUMAN	5-hydroxytryptamine receptor 5A	293	Helical; Name=6; (By similarity).					integral to plasma membrane	serotonin receptor activity			ovary(2)|large_intestine(1)	3	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0238)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)										0.112121	44.372487	93.385434	37	293	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	154506933	154506933	7750	7	G	A	A	40	40	HTR5A	A	1	1
PTPRN2	5799	broad.mit.edu	36	7	157080715	157080715	+	Silent	SNP	G	A	A			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:157080715G>A	uc003wno.1	-	c.2472C>T	c.(2470-2472)CCC>CCT	p.P824P	PTPRN2_uc003wnp.1_Silent_p.P807P|PTPRN2_uc003wnq.1_Silent_p.P795P|PTPRN2_uc003wnr.1_Silent_p.P786P	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N	824	Cytoplasmic (Potential).|Tyrosine-protein phosphatase.					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)	6	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)										0.265625	46.39131	49.539586	17	47	GG		KEEP	---	---	---	---	capture			Silent	SNP	157080715	157080715	13265	7	G	A	A	39	39	PTPRN2	A	1	1
AHR	196	broad.mit.edu	36	7	17345167	17345167	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:17345167G>A	uc003stu.1	+	c.1193G>A	c.(1192-1194)CGA>CAA	p.R398Q	AHR_uc003stt.2_Non-coding_Transcript	NM_001621	NP_001612	P35869	AHR_HUMAN	aryl hydrocarbon receptor	398					apoptosis|blood vessel development|cell cycle|regulation of B cell proliferation|response to stress|transcription from RNA polymerase II promoter|xenobiotic metabolic process	cytosolic aryl hydrocarbon receptor complex|transcription factor complex	Hsp90 protein binding|ligand-dependent nuclear receptor activity|promoter binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulator activity			urinary_tract(1)|kidney(1)|pancreas(1)	3	Lung NSC(10;0.0392)|all_lung(11;0.0754)													0.544304	147.528805	147.663568	43	36	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17345167	17345167	419	7	G	A	A	37	37	AHR	A	1	1
HOXA7	3204	broad.mit.edu	36	7	27161162	27161162	+	Missense_Mutation	SNP	G	T	T			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:27161162G>T	uc003sys.1	-	c.584C>A	c.(583-585)ACT>AAT	p.T195N	HOXA6_uc003syq.1_5'Flank	NM_006896	NP_008827	P31268	HXA7_HUMAN	homeobox A7	195				PT -> RL (in Ref. 4; CAA59270).|T -> I (in Ref. 9; no nucleotide entry).	angiogenesis|negative regulation of cell-matrix adhesion|negative regulation of keratinocyte differentiation|negative regulation of leukocyte migration|negative regulation of monocyte differentiation|negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|transcription factor binding|transcription repressor activity				0														0.263158	8.769531	9.73271	5	14	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27161162	27161162	7589	7	G	T	T	36	36	HOXA7	T	3	3
ST18	9705	broad.mit.edu	36	8	53247665	53247665	+	Missense_Mutation	SNP	A	T	T			TCGA-28-1755-01	TCGA-28-1755-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:53247665A>T	uc003xqz.1	-	c.309T>A	c.(307-309)AGT>AGA	p.S103R	ST18_uc003xra.1_Missense_Mutation_p.S103R|ST18_uc003xrb.1_Missense_Mutation_p.S103R	NM_014682	NP_055497	O60284	ST18_HUMAN	suppression of tumorigenicity 18	103						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)												0.571429	53.303025	53.427485	16	12	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53247665	53247665	15730	8	A	T	T	10	10	ST18	T	4	4
GCNT1	2650	broad.mit.edu	36	9	78307987	78307987	+	Silent	SNP	G	A	A			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:78307987G>A	uc010mpf.1	+	c.870G>A	c.(868-870)GTG>GTA	p.V290V	GCNT1_uc010mpg.1_Silent_p.V290V|GCNT1_uc010mph.1_Silent_p.V290V|GCNT1_uc004akf.2_Silent_p.V290V|GCNT1_uc010mpi.1_Silent_p.V290V|GCNT1_uc004akh.2_Silent_p.V290V|GCNT1_uc010mpj.1_Silent_p.V290V	NM_001490	NP_001481	Q02742	GCNT1_HUMAN	beta-1,3-galactosyl-O-glycosyl-glycoprotein	290	Lumenal (Potential).|Catalytic (By similarity).				protein O-linked glycosylation	Golgi membrane|integral to membrane	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity				0														0.236842	24.859183	27.261853	9	29	GG		KEEP	---	---	---	---	capture			Silent	SNP	78307987	78307987	6566	9	G	A	A	47	47	GCNT1	A	2	2
HTR2C	3358	broad.mit.edu	36	X	114047712	114047712	+	Silent	SNP	C	T	T			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:114047712C>T	uc004epu.1	+	c.855C>T	c.(853-855)AAC>AAT	p.N285N	HTR2C_uc010nqc.1_Silent_p.N285N|HTR2C_uc004epv.1_3'UTR	NM_000868	NP_000859	P28335	5HT2C_HUMAN	5-hydroxytryptamine (serotonin) receptor 2C	285	Cytoplasmic (By similarity).				cGMP biosynthetic process|ERK1 and ERK2 cascade|feeding behavior|phosphatidylinositol biosynthetic process|release of sequestered calcium ion into cytosol|response to drug|serotonin receptor signaling pathway|synaptic transmission	cytoplasm|integral to membrane|nucleus|plasma membrane	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding|drug binding|phosphatidylinositol phospholipase C activity|protein binding|serotonin binding|serotonin receptor activity			ovary(3)	3					Chlorprothixene(DB01239)|Clozapine(DB00363)|Dexfenfluramine(DB01191)|Fenfluramine(DB00574)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Thiethylperazine(DB00372)|Tramadol(DB00193)|Ziprasidone(DB00246)									0.368932	105.060886	106.638376	38	65	CC		KEEP	---	---	---	---	capture			Silent	SNP	114047712	114047712	7743	23	C	T	T	19	19	HTR2C	T	1	1
FRMPD4	9758	broad.mit.edu	36	X	12646191	12646191	+	Missense_Mutation	SNP	G	T	T			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:12646191G>T	uc004cuz.1	+	c.3325G>T	c.(3325-3327)GCA>TCA	p.A1109S		NM_014728	NP_055543	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	1109					positive regulation of synapse structural plasticity	cytoskeleton|dendritic spine	phosphatidylinositol-4,5-bisphosphate binding|protein binding			central_nervous_system(5)|ovary(3)|skin(2)|large_intestine(1)|lung(1)|pancreas(1)	13														0.325	75.236841	77.403439	26	54	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12646191	12646191	6309	23	G	T	T	34	34	FRMPD4	T	3	3
PNMA3	29944	broad.mit.edu	36	X	151977340	151977340	+	Missense_Mutation	SNP	G	T	T			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:151977340G>T	uc004fhc.2	+	c.1272G>T	c.(1270-1272)AGG>AGT	p.R424S	PNMA5_uc004fha.2_5'Flank|PNMA3_uc010ntz.1_Missense_Mutation_p.R424S|PNMA3_uc004fhd.2_5'Flank	NM_013364	NP_037496	Q9UL41	PNMA3_HUMAN	paraneoplastic cancer-testis-brain antigen	424	CCHC-type.				apoptosis	nucleolus	nucleic acid binding|zinc ion binding			skin(2)|large_intestine(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.4375	19.708659	19.76513	7	9	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	151977340	151977340	12581	23	G	T	T	43	43	PNMA3	T	3	3
OTUD5	55593	broad.mit.edu	36	X	48676742	48676742	+	Missense_Mutation	SNP	A	G	G			TCGA-28-1755-01	TCGA-28-1755-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:48676742A>G	uc004dlu.1	-	c.1013T>C	c.(1012-1014)GTG>GCG	p.V338A	OTUD5_uc004dlt.2_Missense_Mutation_p.V333A|OTUD5_uc004dlv.1_Missense_Mutation_p.V333A	NM_017602	NP_060072	Q96G74	OTUD5_HUMAN	OTU domain containing 5 isoform a	338	OTU.				negative regulation of type I interferon production		cysteine-type peptidase activity			pancreas(1)	1														0.381132	286.824626	290.102134	101	164	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48676742	48676742	11728	23	A	G	G	6	6	OTUD5	G	4	4
CLCN5	1184	broad.mit.edu	36	X	49742210	49742210	+	Missense_Mutation	SNP	C	G	G			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:49742210C>G	uc004dor.1	+	c.2287C>G	c.(2287-2289)CTT>GTT	p.L763V	CLCN5_uc004doq.1_Missense_Mutation_p.L763V|CLCN5_uc004dos.1_Missense_Mutation_p.L693V|CLCN5_uc004dot.1_Missense_Mutation_p.L693V	NM_001127899	NP_001121371	P51795	CLCN5_HUMAN	chloride channel 5 isoform a	693	CBS 2.|Cytoplasmic (By similarity).				excretion	apical part of cell|endosome membrane|Golgi membrane|integral to plasma membrane	antiporter activity|ATP binding			ovary(2)|lung(1)|central_nervous_system(1)	4	Ovarian(276;0.236)													0.425	197.357957	198.145922	68	92	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49742210	49742210	3602	23	C	G	G	24	24	CLCN5	G	3	3
ITIH5L	347365	broad.mit.edu	36	X	54801913	54801913	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1755-01	TCGA-28-1755-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:54801913C>T	uc004dtj.1	-	c.1319G>A	c.(1318-1320)CGC>CAC	p.R440H		NM_198510	NP_940912	Q6UXX5	ITH5L_HUMAN	inter-alpha (globulin) inhibitor H5-like	440	VWFA.				hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			lung(2)|ovary(1)|breast(1)|skin(1)	5										249				0.446602	129.011663	129.269696	46	57	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54801913	54801913	8212	23	C	T	T	27	27	ITIH5L	T	1	1
SNX12	29934	broad.mit.edu	36	X	70204752	70204752	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1755-01	TCGA-28-1755-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:70204752G>A	uc004dyr.1	-	c.130C>T	c.(130-132)CGC>TGC	p.R44C	SNX12_uc004dyp.1_Non-coding_Transcript	NM_013346	NP_037478	Q9UMY4	SNX12_HUMAN	sorting nexin 12	44	PX.				cell communication|protein transport	membrane	phosphatidylinositol binding|protein binding				0	Renal(35;0.156)													0.411765	62.263163	62.610267	21	30	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70204752	70204752	15383	23	G	A	A	40	40	SNX12	A	1	1
FANCA	2175	broad.mit.edu	36	16	88332614	88332615	+	Frame_Shift_Del	DEL	GC	-	-			TCGA-28-1755-01	TCGA-28-1755-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:88332614_88332615delGC	uc002fou.1	-	c.4263_4264delGC	c.(4261-4266)CTGCTGfs	p.L1421fs	ZNF276_uc010ciq.1_3'UTR|ZNF276_uc002foq.2_3'UTR|ZNF276_uc010cir.1_Non-coding_Transcript|ZNF276_uc002for.2_3'UTR|ZNF276_uc010cis.1_3'UTR|ZNF276_uc002fos.2_3'UTR|ZNF276_uc002fot.2_Non-coding_Transcript	NM_000135	NP_000126	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A isoform	1421_1422					DNA repair|protein complex assembly	cytoplasm|nucleoplasm	protein binding			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)						1099				0.62			8	5				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	88332614	88332615	5898	16	GC	-	-	34	34	FANCA	-	5	5
ZMYND15	84225	broad.mit.edu	36	17	4592058	4592058	+	Frame_Shift_Del	DEL	T	-	-			TCGA-28-1755-01	TCGA-28-1755-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:4592058_4592058delT	uc002fyu.1	+	c.927_927delT	c.(925-927)CGTfs	p.R309fs	CXCL16_uc002fyr.2_5'Flank|CXCL16_uc002fys.2_5'Flank|ZMYND15_uc002fyt.1_Frame_Shift_Del_p.R309fs|ZMYND15_uc002fyv.1_Frame_Shift_Del_p.R309fs	NM_032265	NP_115641	Q9H091	ZMY15_HUMAN	zinc finger, MYND-type containing 15 isoform 2	309							zinc ion binding				0														0.50			79	79				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	4592058	4592058	18299	17	T	-	-	59	59	ZMYND15	-	5	5
PRAME	23532	broad.mit.edu	36	22	21222325	21222326	+	Frame_Shift_Ins	INS	-	T	T			TCGA-28-1755-01	TCGA-28-1755-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:21222325_21222326insT	uc002zwf.1	-	c.775_776insA	c.(775-777)ATGfs	p.M259fs	PRAME_uc010gtr.1_Frame_Shift_Ins_p.M259fs|PRAME_uc002zwg.1_Frame_Shift_Ins_p.M259fs|PRAME_uc002zwh.1_Frame_Shift_Ins_p.M259fs|PRAME_uc002zwi.1_Frame_Shift_Ins_p.M259fs|PRAME_uc002zwj.1_Frame_Shift_Ins_p.M259fs|PRAME_uc002zwk.1_Frame_Shift_Ins_p.M259fs	NM_206956	NP_996839	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	259					apoptosis|cell differentiation|negative regulation of apoptosis|negative regulation of cell differentiation|negative regulation of retinoic acid receptor signaling pathway|positive regulation of cell proliferation|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|plasma membrane	retinoic acid receptor binding|transcription repressor activity			central_nervous_system(2)	2	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		Melanoma(73;1707 1838 15168 27201)				1184				0.35			168	311				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	21222325	21222326	12860	22	-	T	T	8	8	PRAME	T	5	5
SH3D19	152503	broad.mit.edu	36	4	152273654	152273654	+	Frame_Shift_Del	DEL	A	-	-			TCGA-28-1755-01	TCGA-28-1755-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:152273654_152273654delA	uc010ipl.1	-	c.1891_1891delT	c.(1891-1893)TCTfs	p.S631fs	SH3D19_uc003imb.2_Frame_Shift_Del_p.S389fs|SH3D19_uc003imc.2_Frame_Shift_Del_p.S575fs|SH3D19_uc003ime.2_Frame_Shift_Del_p.S611fs	NM_001009555	NP_001009555	Q5HYK7	SH319_HUMAN	SH3 domain containing 19 isoform a	634					cellular membrane organization|positive regulation of membrane protein ectodomain proteolysis|post-Golgi vesicle-mediated transport	cytosol|Golgi apparatus|nucleus|plasma membrane	proline-rich region binding			ovary(1)	1	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)												0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	152273654	152273654	14740	4	A	-	-	11	11	SH3D19	-	5	5
SMC1A	8243	broad.mit.edu	36	X	53456734	53456736	+	In_Frame_Del	DEL	TCA	-	-			TCGA-28-1755-01	TCGA-28-1755-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:53456734_53456736delTCA	uc004dsg.1	-	c.693_695delTGA	c.(691-696)AATGAA>AAA	p.231_232NE>K	SMC1A_uc004dsh.1_In_Frame_Del_p.209_210NE>K|SMC1A_uc004dsi.1_In_Frame_Del_p.97_98NE>K	NM_006306	NP_006297	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	231_232	Potential.				cell cycle checkpoint|cell division|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic sister chromatid cohesion|mitotic spindle organization|negative regulation of DNA endoreduplication|nuclear mRNA splicing, via spliceosome|response to radiation|signal transduction in response to DNA damage	cohesin core heterodimer|condensed chromosome kinetochore|condensed nuclear chromosome|cytoplasm|meiotic cohesin complex|nucleoplasm	ATP binding|chromatin binding|microtubule motor activity|protein heterodimerization activity			ovary(5)	5														0.41			54	79				---	---	---	---	capture_indel			In_Frame_Del	DEL	53456734	53456736	15279	23	TCA	-	-	62	62	SMC1A	-	5	5
