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
ANKRD30A	91074	broad.mit.edu	36	10	37548371	37548371	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:37548371C>T	uc001iza.1	+	c.3557C>T	c.(3556-3558)ACG>ATG	p.T1186M		NM_052997	NP_443723	Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1242					regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(7)|breast(1)	8														0.705882	110.087241	112.013786	36	15	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37548371	37548371	663	10	C	T	T	19	19	ANKRD30A	T	1	1
CHAT	1103	broad.mit.edu	36	10	50543015	50543015	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0876-01	TCGA-06-0876-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:50543015T>C	uc001jhz.2	+	c.2164T>C	c.(2164-2166)TGC>CGC	p.C722R	CHAT_uc001jhv.1_Missense_Mutation_p.C604R|CHAT_uc001jhx.1_Missense_Mutation_p.C604R|CHAT_uc001jhy.1_Missense_Mutation_p.C604R|CHAT_uc001jia.2_Missense_Mutation_p.C640R	NM_020549	NP_066266	P28329	CLAT_HUMAN	choline acetyltransferase isoform 2	722					neurotransmitter biosynthetic process|neurotransmitter secretion	cytosol|nucleus	choline O-acetyltransferase activity			central_nervous_system(3)	3		all_neural(218;0.107)			Choline(DB00122)									0.686747	360.13841	365.277861	114	52	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;0.000585)	Missense_Mutation	SNP	50543015	50543015	3447	10	T	C	C	55	55	CHAT	C	4	4
PTEN	5728	broad.mit.edu	36	10	89643818	89643818	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0876-01	TCGA-06-0876-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89643818T>C	uc001kfb.1	+	c.136T>C	c.(136-138)TAC>CAC	p.Y46H		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	46	Phosphatase tensin-type.				apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of focal adhesion assembly|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of cyclin-dependent protein kinase activity|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.0?(12)|p.Y27_N212>Y(2)|p.G44fs*11(1)|p.G44fs*8(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)						31	p.Y46H(HEC59-Tumor)	264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.691176	170.453446	172.670269	47	21	TT		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)	Missense_Mutation	SNP	89643818	89643818	13192	10	T	C	C	49	49	PTEN	C	4	4
MUC2	4583	broad.mit.edu	36	11	1069701	1069701	+	Silent	SNP	G	C	C			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:1069701G>C	uc001lsx.1	+	c.918G>C	c.(916-918)TCG>TCC	p.S306S		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	306	TIL.					inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)			Pranlukast(DB01411)									0.375	6.919801	7.030609	3	5	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Silent	SNP	1069701	1069701	10369	11	G	C	C	38	38	MUC2	C	3	3
FOXRED1	55572	broad.mit.edu	36	11	125651501	125651501	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0876-01	TCGA-06-0876-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:125651501A>G	uc001qdi.1	+	c.974A>G	c.(973-975)TAT>TGT	p.Y325C	FOXRED1_uc001qdj.1_Missense_Mutation_p.Y114C|FOXRED1_uc001qdk.1_Missense_Mutation_p.Y114C	NM_017547	NP_060017	Q96CU9	FXRD1_HUMAN	FAD-dependent oxidoreductase domain containing	325					oxidation-reduction process	integral to membrane|mitochondrion	oxidoreductase activity|protein binding				0	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.224)												0.203125	20.927659	26.186136	13	51	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0729)	Missense_Mutation	SNP	125651501	125651501	6279	11	A	G	G	16	16	FOXRED1	G	4	4
ABCC8	6833	broad.mit.edu	36	11	17454822	17454822	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:17454822G>C	uc001mnc.1	-	c.78C>G	c.(76-78)TGC>TGG	p.C26W		NM_000352	NP_000343	Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C, member 8	26	Extracellular (By similarity).				carbohydrate metabolic process|energy reserve metabolic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium ion transmembrane transporter activity|sulfonylurea receptor activity			ovary(1)	1					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)									0.3125	8.228584	8.754133	5	11	GG		KEEP	---	---	---	---	capture		READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Missense_Mutation	SNP	17454822	17454822	59	11	G	C	C	34	34	ABCC8	C	3	3
OR4X2	119764	broad.mit.edu	36	11	48223432	48223432	+	Silent	SNP	C	T	T			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:48223432C>T	uc001ngs.1	+	c.201C>T	c.(199-201)TCC>TCT	p.S67S		NM_001004727	NP_001004727	Q8NGF9	OR4X2_HUMAN	olfactory receptor, family 4, subfamily X,	67	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.350575	176.473861	179.878351	61	113	CC		KEEP	---	---	---	---	capture			Silent	SNP	48223432	48223432	11495	11	C	T	T	23	23	OR4X2	T	1	1
CTSW	1521	broad.mit.edu	36	11	65404330	65404330	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:65404330G>A	uc001ogc.1	+	c.169G>A	c.(169-171)GAA>AAA	p.E57K	CTSW_uc001ogb.1_Missense_Mutation_p.E57K	NM_001335	NP_001326	P56202	CATW_HUMAN	cathepsin W preproprotein	57					immune response|proteolysis		cysteine-type endopeptidase activity			central_nervous_system(1)	1														0.4	63.838267	64.319438	22	33	GG		KEEP	---	---	---	---	capture		READ - Rectum adenocarcinoma(159;0.168)	Missense_Mutation	SNP	65404330	65404330	4201	11	G	A	A	33	33	CTSW	A	2	2
PXN	5829	broad.mit.edu	36	12	119136072	119136072	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0876-01	TCGA-06-0876-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:119136072A>C	uc001txt.2	-	c.1465T>G	c.(1465-1467)TCA>GCA	p.S489A	PXN_uc001txv.2_Missense_Mutation_p.S370A|PXN_uc001txx.2_Missense_Mutation_p.S322A|PXN_uc001txy.2_Missense_Mutation_p.S455A|PXN_uc001txz.2_Non-coding_Transcript|PXN_uc001txu.2_Missense_Mutation_p.S301A	NM_001080855	NP_001074324	P49023	PAXI_HUMAN	paxillin isoform 1	489	LIM zinc-binding 3.				cell junction assembly|cell-matrix adhesion|cellular response to reactive oxygen species|epidermal growth factor receptor signaling pathway|growth hormone receptor signaling pathway|muscle contraction|signal complex assembly	cytoplasm|focal adhesion|lamellipodium|microtubule associated complex	beta-catenin binding|vinculin binding|zinc ion binding			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)									115				0.3	9.021273	9.378528	3	7	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	119136072	119136072	13310	12	A	C	C	11	11	PXN	C	4	4
OR6C70	390327	broad.mit.edu	36	12	54149970	54149970	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:54149970C>A	uc001sha.1	-	c.220G>T	c.(220-222)GCT>TCT	p.A74S		NM_001005499	NP_001005499	A6NIJ9	O6C70_HUMAN	olfactory receptor, family 6, subfamily C,	74	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.409091	106.081871	106.717703	36	52	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54149970	54149970	11607	12	C	A	A	25	25	OR6C70	A	3	3
IFNG	3458	broad.mit.edu	36	12	66837992	66837992	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:66837992G>A	uc001stw.1	-	c.334C>T	c.(334-336)CGA>TGA	p.R112*		NM_000619	NP_000610	P01579	IFNG_HUMAN	interferon, gamma	112					cell cycle arrest|interferon-gamma-mediated signaling pathway|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of interleukin-17 production|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of metanephric nephron tubule epithelial cell differentiation|negative regulation of smooth muscle cell proliferation|positive regulation of calcidiol 1-monooxygenase activity|positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity|positive regulation of fructose 1,6-bisphosphate metabolic process|positive regulation of interleukin-12 production|positive regulation of interleukin-23 production|positive regulation of killing of cells of other organism|positive regulation of membrane protein ectodomain proteolysis|positive regulation of mesenchymal cell proliferation|positive regulation of nitric oxide biosynthetic process|positive regulation of osteoclast differentiation|positive regulation of peptidyl-serine phosphorylation of STAT protein|positive regulation of smooth muscle cell apoptosis|positive regulation of tumor necrosis factor (ligand) superfamily member 11 production|positive regulation of tyrosine phosphorylation of Stat1 protein|positive regulation of vitamin D biosynthetic process|protein import into nucleus, translocation|regulation of insulin secretion|regulation of interferon-gamma-mediated signaling pathway|response to virus	extracellular space	cytokine activity|interferon-gamma receptor binding				0					Glucosamine(DB01296)|Interferon gamma-1b(DB00033)|Simvastatin(DB00641)					63				0.36019	209.039893	212.671318	76	135	GG		KEEP	---	---	---	---	capture	Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000829)	Nonsense_Mutation	SNP	66837992	66837992	7849	12	G	A	A	40	40	IFNG	A	5	1
IRS2	8660	broad.mit.edu	36	13	109232607	109232607	+	Silent	SNP	T	G	G			TCGA-06-0876-01	TCGA-06-0876-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr13:109232607T>G	uc001vqv.1	-	c.3795A>C	c.(3793-3795)CCA>CCC	p.P1265P		NM_003749	NP_003740	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2	1265	Poly-Pro.				fibroblast growth factor receptor signaling pathway|glucose metabolic process|insulin receptor signaling pathway|lipid homeostasis|negative regulation of B cell apoptosis|negative regulation of kinase activity|negative regulation of plasma membrane long-chain fatty acid transport|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of B cell proliferation|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|response to glucose stimulus	cytosol|plasma membrane	insulin receptor binding|signal transducer activity			large_intestine(2)|upper_aerodigestive_tract(1)|kidney(1)|skin(1)	5	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)				Melanoma(100;613 2409 40847)				156				0.444444	9.095388	9.119972	4	5	TT		KEEP	---	---	---	---	capture	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)		Silent	SNP	109232607	109232607	8145	13	T	G	G	59	59	IRS2	G	4	4
COL4A1	1282	broad.mit.edu	36	13	109615227	109615227	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:109615227C>T	uc001vqw.2	-	c.4133G>A	c.(4132-4134)GGC>GAC	p.G1378D	COL4A1_uc010agl.1_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein	1378	Triple-helical region.				angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)												0.433333	38.070421	38.18664	13	17	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)		Missense_Mutation	SNP	109615227	109615227	3827	13	C	T	T	26	26	COL4A1	T	2	2
N4BP2L2	10443	broad.mit.edu	36	13	31915656	31915656	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:31915656G>A	uc010abe.1	-	c.1018C>T	c.(1018-1020)CAA>TAA	p.Q340*	N4BP2L2_uc001uuj.2_Intron|N4BP2L2_uc001uug.2_Nonsense_Mutation_p.Q223*|N4BP2L2_uc010abd.1_Nonsense_Mutation_p.Q253*|N4BP2L2_uc001uuh.2_Nonsense_Mutation_p.Q171*	NM_033111	NP_149102	Q92802	N42L2_HUMAN	phosphonoformate immuno-associated protein 5	Error:Variant_position_missing_in_Q92802_after_alignment					cell killing		ATP binding				0		Lung SC(185;0.0262)												0.282609	30.653862	32.608164	13	33	GG		KEEP	---	---	---	---	capture		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)	Nonsense_Mutation	SNP	31915656	31915656	10507	13	G	A	A	45	45	N4BP2L2	A	5	2
ANKDD1A	348094	broad.mit.edu	36	15	62996735	62996735	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:62996735C>T	uc002aoa.1	+	c.236C>T	c.(235-237)GCG>GTG	p.A79V	ANKDD1A_uc002anx.1_Missense_Mutation_p.A79V|ANKDD1A_uc002any.2_5'UTR|ANKDD1A_uc002anz.2_Intron|ANKDD1A_uc002aob.2_Missense_Mutation_p.A49V	NM_182703	NP_874362	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A	79					signal transduction						0														0.266667	19.688661	21.162733	8	22	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	62996735	62996735	627	15	C	T	T	27	27	ANKDD1A	T	1	1
VPS4A	27183	broad.mit.edu	36	16	67911550	67911550	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0876-01	TCGA-06-0876-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:67911550T>G	uc002eww.1	+	c.626T>G	c.(625-627)GTC>GGC	p.V209G		NM_013245	NP_037377	Q9UN37	VPS4A_HUMAN	vacuolar protein sorting factor 4A	209					cell cycle|cellular membrane organization|cytokinesis|endosome transport|protein transport	cytosol|late endosome membrane|midbody|perinuclear region of cytoplasm	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein domain specific binding				0		Ovarian(137;0.101)												0.277778	9.12879	9.959843	5	13	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	67911550	67911550	17779	16	T	G	G	58	58	VPS4A	G	4	4
ADAD2	161931	broad.mit.edu	36	16	82785269	82785269	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:82785269G>C	uc002fhq.1	+	c.575G>C	c.(574-576)CGC>CCC	p.R192P	ADAD2_uc002fhr.1_Intron	NM_139174	NP_631913	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2 isoform	Error:Variant_position_missing_in_Q8NCV1_after_alignment					RNA processing	intracellular	adenosine deaminase activity|double-stranded RNA binding				0														0.3	6.852798	7.629524	6	14	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	82785269	82785269	233	16	G	C	C	38	38	ADAD2	C	3	3
SPIRE2	84501	broad.mit.edu	36	16	88464080	88464080	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0876-01	TCGA-06-0876-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:88464080T>C	uc002foz.1	+	c.2044T>C	c.(2044-2046)TCC>CCC	p.S682P	SPIRE2_uc010ciw.1_Missense_Mutation_p.S634P|SPIRE2_uc002fpa.1_Missense_Mutation_p.S634P|SPIRE2_uc010cix.1_Missense_Mutation_p.S549P	NM_032451	NP_115827	Q8WWL2	SPIR2_HUMAN	spire homolog 2	682					transport	cytoplasm|cytoskeleton	actin binding|zinc ion binding			central_nervous_system(1)	1		Lung NSC(15;5.15e-06)|all_lung(18;8.38e-06)|all_hematologic(23;0.0194)												0.333333	6.983749	7.397731	5	10	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(80;0.0286)	Missense_Mutation	SNP	88464080	88464080	15585	16	T	C	C	62	62	SPIRE2	C	4	4
AIPL1	23746	broad.mit.edu	36	17	6279062	6279062	+	Silent	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:6279062G>A	uc002gcp.1	-	c.87C>T	c.(85-87)ACC>ACT	p.T29T	AIPL1_uc002gcq.1_Silent_p.T29T|AIPL1_uc002gcr.1_Silent_p.T29T|AIPL1_uc010clk.1_Silent_p.T29T|AIPL1_uc010cll.1_Silent_p.T29T|AIPL1_uc002gcs.1_Silent_p.T29T	NM_014336	NP_055151	Q9NZN9	AIPL1_HUMAN	aryl hydrocarbon receptor interacting	29					protein farnesylation|protein folding|visual perception	cytoplasm|nucleus	farnesylated protein binding|unfolded protein binding				0														0.342466	68.28727	69.87168	25	48	GG		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(228;0.141)	Silent	SNP	6279062	6279062	439	17	G	A	A	39	39	AIPL1	A	1	1
TP53	7157	broad.mit.edu	36	17	7518264	7518264	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7518264G>A	uc002gim.2	-	c.742C>T	c.(742-744)CGG>TGG	p.R248W	TP53_uc002gig.1_Missense_Mutation_p.R248W|TP53_uc002gih.1_Missense_Mutation_p.R248W|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R116W|TP53_uc010cng.1_Missense_Mutation_p.R116W|TP53_uc002gii.1_Missense_Mutation_p.R116W|TP53_uc010cnh.1_Missense_Mutation_p.R248W|TP53_uc010cni.1_Missense_Mutation_p.R248W|TP53_uc002gij.2_Missense_Mutation_p.R248W|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.R155W|TP53_uc002gio.2_Missense_Mutation_p.R116W	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	248	|Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain.|Interaction with AXIN1 (By similarity).		R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|NR -> IP (in a sporadic cancer; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.R248W(438)|p.R248G(11)|p.0?(6)|p.R248Q(4)|p.R248R(2)|p.N247_R248delNR(2)|p.N247_R248>KW(2)|p.M246_P250delMNRRP(2)|p.R248fs*97(2)|p.R248_P250delRRP(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)				Pancreas(47;798 1329 9957 10801)	R248W(CAS1_CENTRAL_NERVOUS_SYSTEM)|R248W(COLO680N_OESOPHAGUS)|R248W(SW837_LARGE_INTESTINE)|R248W(KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(RD_SOFT_TISSUE)|R248W(VCAP_PROSTATE)|R248W(JIMT1_BREAST)|R248W(GCT_SOFT_TISSUE)|R248W(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(786O_KIDNEY)|R248W(COLO320_LARGE_INTESTINE)|R248W(LXF289_LUNG)|R248W(LUDLU1_LUNG)|R248W(MIAPACA2_PANCREAS)|R248W(HCC2157_BREAST)	111	p.R248W(SW837-Tumor)|p.R248W(786O-Tumor)|p.R248W(LUDLU1-Tumor)|p.R248W(VCAP-Tumor)|p.R248*(DB-Tumor)|p.R248W(MIAPACA2-Tumor)|p.R248W(HCC2157-Tumor)|p.R248W(LXF289-Tumor)|p.R248G(8505C-Tumor)|p.R248A(SF126-Tumor)|p.R248W(SET2-Tumor)|p.R248W(KO52-Tumor)|p.R248W(SNU1040-Tumor)|p.R248W(GCT-Tumor)|p.R248W(JIMT1-Tumor)|p.R248W(COLO320-Tumor)|p.R248W(CAS1-Tumor)|p.R248W(NCIH2106-Tumor)|p.R248W(SNUC5-Tumor)|p.R248W(COLO680N-Tumor)|p.R248W(RD-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.375	76.515767	77.49969	27	45	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Missense_Mutation	SNP	7518264	7518264	16923	17	G	A	A	39	39	TP53	A	1	1
C18orf26	284254	broad.mit.edu	36	18	50416155	50416155	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:50416155C>A	uc002lfq.1	+	c.414C>A	c.(412-414)AAC>AAA	p.N138K	C18orf26_uc002lfp.1_Missense_Mutation_p.N86K	NM_173629	NP_775900	Q8N1N2	CR026_HUMAN	hypothetical protein LOC284254	138						integral to membrane					0														0.370968	132.82049	134.633276	46	78	CC		KEEP	---	---	---	---	capture		Colorectal(16;0.0193)|READ - Rectum adenocarcinoma(59;0.178)	Missense_Mutation	SNP	50416155	50416155	1961	18	C	A	A	17	17	C18orf26	A	3	3
SERPINB12	89777	broad.mit.edu	36	18	59374443	59374443	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:59374443G>A	uc002ljb.1	+	c.71G>A	c.(70-72)CGT>CAT	p.R24H	SERPINB12_uc002lja.1_Missense_Mutation_p.R24H	NM_080474	NP_536722	Q96P63	SPB12_HUMAN	serine (or cysteine) proteinase inhibitor, clade	24					negative regulation of protein catabolic process|regulation of proteolysis	cytoplasm	enzyme binding|serine-type endopeptidase inhibitor activity				0														0.372796	408.702241	414.34202	148	249	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59374443	59374443	14587	18	G	A	A	40	40	SERPINB12	A	1	1
KLF1	10661	broad.mit.edu	36	19	12857209	12857209	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:12857209G>A	uc002mvo.1	-	c.835C>T	c.(835-837)CAC>TAC	p.H279Y		NM_006563	NP_006554	Q13351	KLF1_HUMAN	Kruppel-like factor 1 (erythroid)	279	C2H2-type 1.				erythrocyte differentiation|positive regulation of gene-specific transcription	nucleus	promoter binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Hepatocellular(1079;0.137)												0.261905	23.502615	25.659987	11	31	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(1328;0.00016)|Lung(535;0.171)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	12857209	12857209	8649	19	G	A	A	46	46	KLF1	A	2	2
GDF1	2657	broad.mit.edu	36	19	18841883	18841883	+	Silent	SNP	C	G	G			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:18841883C>G	uc002nki.1	-	c.234G>C	c.(232-234)TCG>TCC	p.S78S		NM_001492	NP_001483	P27539	GDF1_HUMAN	growth differentiation factor 1	78					growth	extracellular space	cytokine activity|growth factor activity				0														0.363636	6.394222	6.614603	4	7	CC		KEEP	---	---	---	---	capture			Silent	SNP	18841883	18841883	6578	19	C	G	G	27	27	GDF1	G	3	3
ZNF208	7757	broad.mit.edu	36	19	21947450	21947450	+	Silent	SNP	A	G	G			TCGA-06-0876-01	TCGA-06-0876-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:21947450A>G	uc002nqp.1	-	c.1926T>C	c.(1924-1926)ATT>ATC	p.I642I	ZNF208_uc002nqo.1_Intron	NM_007153	NP_009084			zinc finger protein 208											ovary(5)	5		all_lung(12;0.0961)|Lung NSC(12;0.103)												0.242424	87.123436	95.120963	32	100	AA		KEEP	---	---	---	---	capture			Silent	SNP	21947450	21947450	18357	19	A	G	G	9	9	ZNF208	G	4	4
SIGLEC9	27180	broad.mit.edu	36	19	56321190	56321190	+	Silent	SNP	C	T	T			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:56321190C>T	uc002pvu.1	+	c.741C>T	c.(739-741)GAC>GAT	p.D247D		NM_014441	NP_055256	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	247	Extracellular (Potential).|Ig-like C2-type 2.				cell adhesion|cell surface receptor linked signaling pathway	integral to plasma membrane	sugar binding				0		all_neural(266;0.0529)												0.366412	129.354824	131.413964	48	83	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)	Silent	SNP	56321190	56321190	14810	19	C	T	T	19	19	SIGLEC9	T	1	1
CD33	945	broad.mit.edu	36	19	56420569	56420569	+	Silent	SNP	C	T	T			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:56420569C>T	uc002pwa.2	+	c.321C>T	c.(319-321)GAC>GAT	p.D107D	CD33_uc010eos.1_Silent_p.D107D|CD33_uc010eot.1_Intron|CD33_uc010eou.1_5'Flank	NM_001772	NP_001763	P20138	CD33_HUMAN	CD33 antigen isoform 1 precursor	107	Extracellular (Potential).|Ig-like V-type.				cell adhesion|cell-cell signaling|negative regulation of cell proliferation	integral to plasma membrane	receptor activity|sugar binding				0		all_neural(266;0.0199)			Gemtuzumab ozogamicin(DB00056)									0.451613	164.988714	165.24083	56	68	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Silent	SNP	56420569	56420569	3133	19	C	T	T	19	19	CD33	T	1	1
EPS8L3	79574	broad.mit.edu	36	1	110105890	110105890	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:110105890G>A	uc001dyq.1	-	c.5C>T	c.(4-6)TCA>TTA	p.S2L	EPS8L3_uc001dys.1_Missense_Mutation_p.S2L|EPS8L3_uc001dyr.1_Missense_Mutation_p.S2L|EPS8L3_uc009wfm.1_Intron|EPS8L3_uc009wfn.1_5'UTR|EPS8L3_uc009wfo.1_Missense_Mutation_p.S2L	NM_139053	NP_620641	Q8TE67	ES8L3_HUMAN	epidermal growth factor receptor pathway	2						cytoplasm	protein binding			ovary(2)|skin(1)	3		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)												0.313725	39.673971	41.253229	16	35	GG		KEEP	---	---	---	---	capture		Lung(183;0.0245)|Colorectal(144;0.0365)|all cancers(265;0.103)|Epithelial(280;0.109)|LUSC - Lung squamous cell carcinoma(189;0.137)|COAD - Colon adenocarcinoma(174;0.141)	Missense_Mutation	SNP	110105890	110105890	5390	1	G	A	A	45	45	EPS8L3	A	2	2
SH2D2A	9047	broad.mit.edu	36	1	155050694	155050694	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:155050694G>C	uc009wsh.1	-	c.355C>G	c.(355-357)CTG>GTG	p.L119V	NTRK1_uc001fqf.1_5'Flank|NTRK1_uc009wsi.1_5'Flank|SH2D2A_uc001fqc.1_Missense_Mutation_p.L81V|SH2D2A_uc001fqd.1_Missense_Mutation_p.L109V|SH2D2A_uc001fqe.1_Missense_Mutation_p.L91V	NM_003975	NP_003966	Q9NP31	SH22A_HUMAN	SH2 domain protein 2A	109	SH2.				angiogenesis|cell differentiation|signal transduction	cytoplasm|soluble fraction	SH3 domain binding|SH3/SH2 adaptor activity				0	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)									2				0.333333	10.066582	10.43731	5	10	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	155050694	155050694	14723	1	G	C	C	34	34	SH2D2A	C	3	3
DPT	1805	broad.mit.edu	36	1	166936880	166936880	+	Missense_Mutation	SNP	T	A	A	rs71662134	unknown	TCGA-06-0876-01	TCGA-06-0876-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:166936880T>A	uc001gfp.1	-	c.538A>T	c.(538-540)AGG>TGG	p.R180W		NM_001937	NP_001928	Q07507	DERM_HUMAN	dermatopontin precursor	180	2 X 53-55 AA tandem repeats.|3 X 6 AA repeats of D-R-[EQ]-W-[NQK]- [FY].				cell adhesion	extracellular space|proteinaceous extracellular matrix				ovary(1)	1	all_hematologic(923;0.208)													0.365482	200.131359	203.27246	72	125	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	166936880	166936880	4923	1	T	A	A	56	56	DPT	A	4	4
HHAT	55733	broad.mit.edu	36	1	208704578	208704578	+	Silent	SNP	C	T	T			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:208704578C>T	uc009xcx.1	+	c.963C>T	c.(961-963)CTC>CTT	p.L321L	HHAT_uc001hhz.2_Silent_p.L321L|HHAT_uc009xcy.1_Silent_p.L193L|HHAT_uc001hia.2_Silent_p.L11L	NM_001122834	NP_001116306	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase	321					multicellular organismal development	endoplasmic reticulum membrane|integral to membrane	GTP binding			ovary(2)	2														0.335526	138.086035	141.7202	51	101	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)	Silent	SNP	208704578	208704578	7373	1	C	T	T	30	30	HHAT	T	2	2
CENPF	1063	broad.mit.edu	36	1	212886602	212886602	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:212886602G>A	uc001hkm.1	+	c.7066G>A	c.(7066-7068)GCT>ACT	p.A2356T		NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F	2452	2-2.|Potential.|2 X 177 AA tandem repeats.				cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding			ovary(6)|central_nervous_system(4)|large_intestine(2)	12						Colon(80;575 1284 11000 14801 43496)								0.314286	58.821431	60.971507	22	48	GG		KEEP	---	---	---	---	capture		all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)	Missense_Mutation	SNP	212886602	212886602	3364	1	G	A	A	34	34	CENPF	A	2	2
CSMD2	114784	broad.mit.edu	36	1	33843468	33843468	+	Splice_Site_SNP	SNP	C	T	T			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:33843468C>T	uc001bxm.1	-	c.6532_splice	c.e42+1	p.V2178_splice	CSMD2_uc001bxn.1_Splice_Site_SNP_p.V2180_splice|CSMD2_uc001bxo.1_Splice_Site_SNP_p.V1051_splice	NM_052896	NP_443128			CUB and Sushi multiple domains 2							integral to membrane|plasma membrane	protein binding			ovary(5)|pancreas(1)	6		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)												0.282609	31.45687	33.409482	13	33	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	33843468	33843468	4086	1	C	T	T	18	18	CSMD2	T	5	2
EIF2C3	192669	broad.mit.edu	36	1	36247218	36247218	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0876-01	TCGA-06-0876-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:36247218T>C	uc001bzp.1	+	c.1015T>C	c.(1015-1017)TAC>CAC	p.Y339H	EIF2C3_uc001bzq.1_Missense_Mutation_p.Y105H	NM_024852	NP_803171	Q9H9G7	AGO3_HUMAN	eukaryotic translation initiation factor 2C, 3	339	PAZ.				mRNA catabolic process|negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				Colon(144;60 2363 31043 40539)								0.34375	15.553576	16.368571	11	21	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36247218	36247218	5196	1	T	C	C	53	53	EIF2C3	C	4	4
LRRC8B	23507	broad.mit.edu	36	1	89822631	89822631	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:89822631G>A	uc001dnh.1	+	c.1834G>A	c.(1834-1836)GAG>AAG	p.E612K	LRRC8B_uc001dni.1_Missense_Mutation_p.E612K|LRRC8B_uc001dnj.1_Missense_Mutation_p.E612K	NM_015350	NP_056165	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member	612	LRR 7.					integral to membrane				ovary(2)	2		all_lung(203;0.17)												0.322368	128.516758	132.77822	49	103	GG		KEEP	---	---	---	---	capture		all cancers(265;0.00515)|Epithelial(280;0.0241)	Missense_Mutation	SNP	89822631	89822631	9398	1	G	A	A	45	45	LRRC8B	A	2	2
LPIN3	64900	broad.mit.edu	36	20	39410908	39410908	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:39410908C>T	uc010ggh.1	+	c.524C>T	c.(523-525)TCC>TTC	p.S175F	LPIN3_uc002xjx.1_Missense_Mutation_p.S175F	NM_022896	NP_075047	Q9BQK8	LPIN3_HUMAN	lipin 3	175					fatty acid metabolic process	nucleus	phosphatidate phosphatase activity			ovary(3)|central_nervous_system(1)	4		Myeloproliferative disorder(115;0.000739)												0.333333	15.191346	15.721411	7	14	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	39410908	39410908	9293	20	C	T	T	30	30	LPIN3	T	2	2
SEMG1	6406	broad.mit.edu	36	20	43270466	43270466	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:43270466C>T	uc002xni.1	+	c.1114C>T	c.(1114-1116)CGC>TGC	p.R372C	SEMG1_uc002xnh.1_Intron|SEMG1_uc002xnj.1_Missense_Mutation_p.R312C|SEMG2_uc010ggz.1_Intron	NM_003007	NP_002998	P04279	SEMG1_HUMAN	semenogelin I isoform a preproprotein	372	58 AA repeat 2.				insemination|sexual reproduction	extracellular space|stored secretory granule	structural molecule activity				0		Myeloproliferative disorder(115;0.0122)												0.38961	83.124132	83.948352	30	47	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43270466	43270466	14530	20	C	T	T	19	19	SEMG1	T	1	1
ZNFX1	57169	broad.mit.edu	36	20	47299193	47299193	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0876-01	TCGA-06-0876-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr20:47299193T>G	uc002xui.1	-	c.3775A>C	c.(3775-3777)ATG>CTG	p.M1259L		NM_021035	NP_066363	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	1259							metal ion binding			ovary(2)	2														0.329114	152.097842	156.214022	52	106	TT		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Missense_Mutation	SNP	47299193	47299193	18809	20	T	G	G	51	51	ZNFX1	G	4	4
LAMA5	3911	broad.mit.edu	36	20	60321577	60321577	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:60321577C>G	uc002ycq.1	-	c.8917G>C	c.(8917-8919)GTG>CTG	p.V2973L		NM_005560	NP_005551	O15230	LAMA5_HUMAN	laminin alpha 5	2973	Laminin G-like 2.				angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding|receptor activity|structural molecule activity			pancreas(1)	1	Breast(26;1.57e-08)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)									0.235294	8.295905	9.382637	4	13	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		Missense_Mutation	SNP	60321577	60321577	8932	20	C	G	G	19	19	LAMA5	G	3	3
PI4KA	5297	broad.mit.edu	36	22	19504060	19504060	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:19504060G>C	uc002zsz.2	-	c.484C>G	c.(484-486)CTG>GTG	p.L162V	PI4KA_uc010gsq.1_Missense_Mutation_p.L220V	NM_058004	NP_477352	P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase type 3 alpha	162					phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission	Golgi-associated vesicle	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			lung(2)|salivary_gland(1)	3	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)				GBM(136;1332 1831 3115 23601 50806)				873				0.31203	219.311865	227.689016	83	183	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)		Missense_Mutation	SNP	19504060	19504060	12297	22	G	C	C	35	35	PI4KA	C	3	3
LIMS2	55679	broad.mit.edu	36	2	128116193	128116193	+	Silent	SNP	C	G	G			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:128116193C>G	uc002tox.1	-	c.633G>C	c.(631-633)CTG>CTC	p.L211L	LIMS2_uc002tou.1_5'UTR|LIMS2_uc002tov.1_Silent_p.L35L|LIMS2_uc002tow.1_Silent_p.L35L|LIMS2_uc010fmb.1_Silent_p.L97L|LIMS2_uc002toy.1_Silent_p.L182L|LIMS2_uc002toz.1_Silent_p.L182L|LIMS2_uc002tpa.1_Silent_p.L187L|LIMS2_uc002tpb.1_Silent_p.L182L	NM_017980	NP_060450	Q7Z4I7	LIMS2_HUMAN	LIM and senescent cell antigen-like domains 2	187	LIM zinc-binding 3.				cell junction assembly	cytosol|focal adhesion|nucleus	zinc ion binding				0	Colorectal(110;0.1)													0.2	7.186652	8.863217	4	16	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.0681)	Silent	SNP	128116193	128116193	9130	2	C	G	G	25	25	LIMS2	G	3	3
AMMECR1L	83607	broad.mit.edu	36	2	128348024	128348024	+	Silent	SNP	C	A	A			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:128348024C>A	uc002tpl.1	-	c.255G>T	c.(253-255)GCG>GCT	p.A85A	AMMECR1L_uc002tpm.1_Silent_p.A85A	NM_031445	NP_113633	Q6DCA0	AMERL_HUMAN	AMME chromosomal region gene 1-like	85										central_nervous_system(1)	1	Colorectal(110;0.1)													0.282297	156.271623	165.150466	59	150	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.07)	Silent	SNP	128348024	128348024	582	2	C	A	A	27	27	AMMECR1L	A	3	3
FBLN2	2199	broad.mit.edu	36	3	13652993	13652993	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0876-01	TCGA-06-0876-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:13652993A>C	uc003bya.1	+	c.3262A>C	c.(3262-3264)ACC>CCC	p.T1088P	FBLN2_uc003byb.1_Missense_Mutation_p.T1041P	NM_001004019	NP_001004019	P98095	FBLN2_HUMAN	fibulin 2 isoform a precursor	1042	EGF-like 10; calcium-binding.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(1)	1														0.210526	6.366666	7.871361	4	15	AA		KEEP	---	---	---	---	capture	UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)		Missense_Mutation	SNP	13652993	13652993	5935	3	A	C	C	10	10	FBLN2	C	4	4
NT5DC2	64943	broad.mit.edu	36	3	52534051	52534051	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:52534051G>C	uc003deo.1	-	c.1204C>G	c.(1204-1206)CAG>GAG	p.Q402E	NT5DC2_uc003dem.1_Missense_Mutation_p.Q272E|NT5DC2_uc003den.1_Missense_Mutation_p.Q368E|NT5DC2_uc010hmi.1_Missense_Mutation_p.Q343E|NT5DC2_uc010hmj.1_Missense_Mutation_p.Q218E	NM_022908	NP_075059	Q9H857	NT5D2_HUMAN	5'-nucleotidase domain containing 2 isoform 2	402							hydrolase activity|metal ion binding				0														0.3	12.539648	13.256204	6	14	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;1.7e-05)|Kidney(197;0.00177)|KIRC - Kidney renal clear cell carcinoma(197;0.002)|OV - Ovarian serous cystadenocarcinoma(275;0.0476)	Missense_Mutation	SNP	52534051	52534051	11096	3	G	C	C	46	46	NT5DC2	C	3	3
POU4F2	5458	broad.mit.edu	36	4	147780839	147780839	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:147780839C>T	uc003ikv.1	+	c.659C>T	c.(658-660)CCG>CTG	p.P220L		NM_004575	NP_004566	Q12837	PO4F2_HUMAN	Brn3b POU domain transcription factor	220					negative regulation of transcription from RNA polymerase II promoter	nuclear speck	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			breast(1)	1	all_hematologic(180;0.151)													0.321429	23.764695	24.558014	9	19	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	147780839	147780839	12709	4	C	T	T	23	23	POU4F2	T	1	1
NR3C2	4306	broad.mit.edu	36	4	149576723	149576723	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:149576723C>T	uc003ilj.2	-	c.740G>A	c.(739-741)AGG>AAG	p.R247K	NR3C2_uc003ilk.2_Missense_Mutation_p.R247K|NR3C2_uc010iph.1_Non-coding_Transcript	NM_000901	NP_000892	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	247	Modulating.				regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	endoplasmic reticulum membrane|nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			large_intestine(1)	1	all_hematologic(180;0.151)				Desoxycorticosterone Pivalate(DB01134)|Eplerenone(DB00700)|Fludrocortisone(DB00687)|Spironolactone(DB00421)	Melanoma(27;428 957 40335 51025 51111)								0.38843	143.902535	145.220489	47	74	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(119;0.0614)	Missense_Mutation	SNP	149576723	149576723	11036	4	C	T	T	24	24	NR3C2	T	2	2
FHDC1	85462	broad.mit.edu	36	4	154101183	154101183	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:154101183C>T	uc003inf.2	+	c.680C>T	c.(679-681)GCG>GTG	p.A227V		NM_033393	NP_203751	Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	227	FH2.				actin cytoskeleton organization		actin binding			large_intestine(1)|ovary(1)	2	all_hematologic(180;0.093)													0.4375	137.955048	138.33683	49	63	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	154101183	154101183	6114	4	C	T	T	27	27	FHDC1	T	1	1
FRAS1	80144	broad.mit.edu	36	4	79604671	79604671	+	Silent	SNP	C	T	T			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:79604671C>T	uc003hkx.2	+	c.6936C>T	c.(6934-6936)CCC>CCT	p.P2312P	FRAS1_uc003hlb.1_Silent_p.P534P	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	2312	CSPG 11.|Extracellular (Potential).				cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5														0.394958	139.325011	140.465481	47	72	CC		KEEP	---	---	---	---	capture			Silent	SNP	79604671	79604671	6288	4	C	T	T	23	23	FRAS1	T	1	1
FTMT	94033	broad.mit.edu	36	5	121215637	121215637	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:121215637C>T	uc003kss.1	+	c.80C>T	c.(79-81)GCG>GTG	p.A27V		NM_177478	NP_803431	Q8N4E7	FTMT_HUMAN	mitochondrial ferritin	27					cellular iron ion homeostasis|iron ion transport|oxidation-reduction process|positive regulation of cell proliferation|positive regulation of lyase activity|positive regulation of oxidoreductase activity|positive regulation of transferase activity	mitochondrion	ferric iron binding|ferroxidase activity			ovary(1)	1		all_cancers(142;0.0124)|Prostate(80;0.0322)												0.381818	59.065652	59.737836	21	34	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;0.000171)|OV - Ovarian serous cystadenocarcinoma(64;0.000188)|all cancers(49;0.0027)	Missense_Mutation	SNP	121215637	121215637	6336	5	C	T	T	27	27	FTMT	T	1	1
PCDHA2	56146	broad.mit.edu	36	5	140156087	140156087	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140156087G>A	uc003lhd.1	+	c.1354G>A	c.(1354-1356)GCG>ACG	p.A452T	PCDHA1_uc003lha.1_Intron|PCDHA1_uc003lhb.1_Intron|PCDHA2_uc003lhc.1_Missense_Mutation_p.A452T	NM_018905	NP_061728	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2 isoform 1 precursor	452	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(4)	4														0.372881	237.246916	240.592879	88	148	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140156087	140156087	11944	5	G	A	A	38	38	PCDHA2	A	1	1
ADRA1B	147	broad.mit.edu	36	5	159276604	159276604	+	Silent	SNP	C	T	T			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:159276604C>T	uc003lxt.1	+	c.114C>T	c.(112-114)CCC>CCT	p.P38P		NM_000679	NP_000670	P35368	ADA1B_HUMAN	alpha-1B-adrenergic receptor	38	Extracellular (By similarity).				cell proliferation|cell-cell signaling|G-protein signaling, coupled to cAMP nucleotide second messenger|intracellular protein kinase cascade	integral to plasma membrane	alpha1-adrenergic receptor activity				0	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)			Alfuzosin(DB00346)|Bethanidine(DB00217)|Dapiprazole(DB00298)|Debrisoquin(DB04840)|Dextroamphetamine(DB01576)|Doxazosin(DB00590)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Guanfacine(DB01018)|Labetalol(DB00598)|Lisdexamfetamine(DB01255)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Midodrine(DB00211)|Modafinil(DB00745)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Olanzapine(DB00334)|Phendimetrazine(DB01579)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propericiazine(DB01608)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Sertindole(DB06144)|Tamsulosin(DB00706)|Terazosin(DB01162)|Trazodone(DB00656)									0.413953	269.337092	270.726839	89	126	CC		KEEP	---	---	---	---	capture	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Silent	SNP	159276604	159276604	336	5	C	T	T	22	22	ADRA1B	T	2	2
RGS14	10636	broad.mit.edu	36	5	176728340	176728340	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0876-01	TCGA-06-0876-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:176728340T>C	uc003mgf.1	+	c.866T>C	c.(865-867)CTT>CCT	p.L289P	RGS14_uc003mgg.1_Missense_Mutation_p.L136P|RGS14_uc003mgh.1_Missense_Mutation_p.L136P|RGS14_uc003mgi.1_Missense_Mutation_p.L59P|RGS14_uc003mgj.1_5'Flank	NM_006480	NP_006471	O43566	RGS14_HUMAN	regulator of G-protein signalling 14	289					chromosome segregation|long-term memory|long-term synaptic potentiation|negative regulation of ERK1 and ERK2 cascade|negative regulation of MAP kinase activity|negative regulation of synaptic plasticity|nucleocytoplasmic transport|platelet-derived growth factor receptor signaling pathway|positive regulation of neurogenesis|regulation of G-protein coupled receptor protein signaling pathway|regulation of transcription in response to stress|response to oxidative stress|spindle organization|visual learning|zygote asymmetric cell division	centrosome|dendritic spine|nuclear body|plasma membrane|postsynaptic density|spindle pole	GDP-dissociation inhibitor activity|GTPase activator activity|microtubule binding|receptor signaling complex scaffold activity|receptor signaling protein activity			lung(1)	1	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)				NSCLC(47;353 1896 28036)						OREG0017086	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.337349	87.777521	89.718103	28	55	TT		KEEP	---	---	---	---	capture	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Missense_Mutation	SNP	176728340	176728340	13771	5	T	C	C	56	56	RGS14	C	4	4
SYNE1	23345	broad.mit.edu	36	6	152502833	152502833	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:152502833C>T	uc010kiw.1	-	c.25403G>A	c.(25402-25404)CGT>CAT	p.R8468H	SYNE1_uc003qor.2_Missense_Mutation_p.R1391H|SYNE1_uc010kiv.1_Missense_Mutation_p.R2992H|SYNE1_uc003qos.2_Missense_Mutation_p.R2992H|SYNE1_uc003qot.2_Missense_Mutation_p.R8420H|SYNE1_uc003qou.2_Missense_Mutation_p.R8468H|SYNE1_uc003qop.2_Missense_Mutation_p.R653H|SYNE1_uc003qoq.2_Missense_Mutation_p.R670H	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8468	Cytoplasmic (Potential).|Spectrin 31.		R -> H (in a colorectal cancer sample; somatic mutation).		cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding	p.R8468H(1)		central_nervous_system(15)|ovary(8)|large_intestine(5)|pancreas(2)	30		Ovarian(120;0.0955)												0.34375	115.252838	118.016856	44	84	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)	Missense_Mutation	SNP	152502833	152502833	15966	6	C	T	T	19	19	SYNE1	T	1	1
ZKSCAN4	387032	broad.mit.edu	36	6	28321003	28321003	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0876-01	TCGA-06-0876-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:28321003A>G	uc003nks.1	-	c.1508T>C	c.(1507-1509)ATT>ACT	p.I503T		NM_019110	NP_061983	Q969J2	ZKSC4_HUMAN	zinc finger with KRAB and SCAN domains 4	503	C2H2-type 6.				regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1														0.408284	226.252035	227.491832	69	100	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	28321003	28321003	18280	6	A	G	G	4	4	ZKSCAN4	G	4	4
PGC	5225	broad.mit.edu	36	6	41812709	41812709	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:41812709G>T	uc003ora.1	-	c.1026C>A	c.(1024-1026)TAC>TAA	p.Y342*	TFEB_uc003oqu.1_5'Flank	NM_002630	NP_002621	P20142	PEPC_HUMAN	progastricsin (pepsinogen C)	342					digestion|proteolysis	extracellular space	aspartic-type endopeptidase activity				0	Ovarian(28;0.0355)|Colorectal(47;0.121)													0.178571	6.678373	9.41551	5	23	GG		KEEP	---	---	---	---	capture	Epithelial(12;0.000132)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)		Nonsense_Mutation	SNP	41812709	41812709	12208	6	G	T	T	36	36	PGC	T	5	3
DOCK4	9732	broad.mit.edu	36	7	111182886	111182886	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:111182886C>T	uc003vfy.1	-	c.4445G>A	c.(4444-4446)TGG>TAG	p.W1482*	DOCK4_uc003vfw.1_Nonsense_Mutation_p.W887*|DOCK4_uc003vfx.1_Nonsense_Mutation_p.W1437*	NM_014705	NP_055520	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1437	DHR-2.				cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|guanyl-nucleotide exchange factor activity|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|receptor tyrosine kinase binding|SH3 domain binding			ovary(2)|central_nervous_system(1)	3		Acute lymphoblastic leukemia(1;0.0441)												0.156627	20.316547	29.662499	13	70	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	111182886	111182886	4873	7	C	T	T	21	21	DOCK4	T	5	2
WNT2	7472	broad.mit.edu	36	7	116747860	116747860	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:116747860G>A	uc003viz.1	-	c.307C>T	c.(307-309)CGA>TGA	p.R103*	WNT2_uc003vja.1_Missense_Mutation_p.P28L	NM_003391	NP_003382	P09544	WNT2_HUMAN	wingless-type MMTV integration site family	103					atrial cardiac muscle tissue morphogenesis|canonical Wnt receptor signaling pathway|cardiac epithelial to mesenchymal transition|cellular response to retinoic acid|cellular response to transforming growth factor beta stimulus|dorsal/ventral axis specification|iris morphogenesis|labyrinthine layer blood vessel development|lens development in camera-type eye|lung induction|mammary gland epithelium development|negative regulation of gene-specific transcription from RNA polymerase II promoter|neuron differentiation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of fibroblast proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, calcium modulating pathway	cytoplasm|extracellular space|proteinaceous extracellular matrix	cytokine activity|frizzled binding|frizzled-2 binding|signal transducer activity			central_nervous_system(2)|ovary(1)|breast(1)	4	all_epithelial(6;2.24e-06)|Lung NSC(10;0.000936)|all_lung(10;0.00109)													0.15625	17.313834	24.529296	10	54	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)	Nonsense_Mutation	SNP	116747860	116747860	17960	7	G	A	A	39	39	WNT2	A	5	1
RAPGEF5	9771	broad.mit.edu	36	7	22131793	22131793	+	Silent	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:22131793G>A	uc003svg.1	-	c.2031C>T	c.(2029-2031)ATC>ATT	p.I677I		NM_012294	NP_036426	Q92565	RPGF5_HUMAN	Rap guanine nucleotide exchange factor (GEF) 5	527	Ras-GEF.				nervous system development|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	nucleus	GTP-dependent protein binding|Rap guanyl-nucleotide exchange factor activity			ovary(1)	1														0.302817	108.653711	113.593412	43	99	GG		KEEP	---	---	---	---	capture			Silent	SNP	22131793	22131793	13507	7	G	A	A	37	37	RAPGEF5	A	1	1
TBX20	57057	broad.mit.edu	36	7	35254833	35254833	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:35254833C>G	uc003ter.1	-	c.526G>C	c.(526-528)GAC>CAC	p.D176H	TBX20_uc010kxa.1_Missense_Mutation_p.D176H	NM_001077653	NP_001071121	Q9UMR3	TBX20_HUMAN	T-box transcription factor TBX20 isoform A	176	T-box.					nucleus	DNA binding			central_nervous_system(1)	1														0.266667	7.679214	9.347843	8	22	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35254833	35254833	16182	7	C	G	G	31	31	TBX20	G	3	3
EGFR	1956	broad.mit.edu	36	7	55178574	55178574	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55178574G>A	uc003tqk.1	+	c.323G>A	c.(322-324)AGA>AAA	p.R108K	EGFR_uc003tqh.1_Missense_Mutation_p.R108K|EGFR_uc003tqi.1_Missense_Mutation_p.R108K|EGFR_uc003tqj.1_Missense_Mutation_p.R108K|EGFR_uc010kzg.1_Missense_Mutation_p.R108K	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	108	Approximate.|Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.R108K(7)|p.V30_R297>G(5)		lung(8200)|central_nervous_system(103)|upper_aerodigestive_tract(37)|prostate(32)|ovary(31)|thyroid(23)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|stomach(6)|urinary_tract(6)|skin(5)|adrenal_gland(5)|kidney(4)|soft_tissue(4)|bone(3)|NS(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)|pancreas(1)	8515	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)				Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8		608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.31218	831.371149	862.083109	305	672	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Missense_Mutation	SNP	55178574	55178574	5156	7	G	A	A	33	33	EGFR	A	2	2
EGFR	1956	broad.mit.edu	36	7	55189316	55189316	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55189316C>A	uc003tqk.1	+	c.866C>A	c.(865-867)GCC>GAC	p.A289D	EGFR_uc003tqh.1_Missense_Mutation_p.A289D|EGFR_uc003tqi.1_Missense_Mutation_p.A289D|EGFR_uc003tqj.1_Missense_Mutation_p.A289D|EGFR_uc010kzg.1_Missense_Mutation_p.A244D	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	289	Approximate.|Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.A289V(20)|p.V30_R297>G(10)|p.A289D(3)		lung(8200)|central_nervous_system(103)|upper_aerodigestive_tract(37)|prostate(32)|ovary(31)|thyroid(23)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|stomach(6)|urinary_tract(6)|skin(5)|adrenal_gland(5)|kidney(4)|soft_tissue(4)|bone(3)|NS(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)|pancreas(1)	8515	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)				Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8	p.A289V(HEC6-Tumor)|p.A289D(HS683-Tumor)|p.A289V(RL952-Tumor)	608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.088266	10.270472	175.140089	85	878	CC		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Missense_Mutation	SNP	55189316	55189316	5156	7	C	A	A	26	26	EGFR	A	3	3
EGFR	1956	broad.mit.edu	36	7	55200537	55200537	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55200537G>T	uc003tqk.1	+	c.1793G>T	c.(1792-1794)GGA>GTA	p.G598V	EGFR_uc003tqi.1_Missense_Mutation_p.G598V|EGFR_uc003tqj.1_Missense_Mutation_p.G598V|EGFR_uc010kzg.1_Missense_Mutation_p.G553V|EGFR_uc003tqn.1_Non-coding_Transcript	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	598	Approximate.|Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.G598V(16)		lung(8200)|central_nervous_system(103)|upper_aerodigestive_tract(37)|prostate(32)|ovary(31)|thyroid(23)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|stomach(6)|urinary_tract(6)|skin(5)|adrenal_gland(5)|kidney(4)|soft_tissue(4)|bone(3)|NS(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)|pancreas(1)	8515	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)				Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8		608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.304392	703.594175	737.077485	298	681	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Missense_Mutation	SNP	55200537	55200537	5156	7	G	T	T	41	41	EGFR	T	3	3
ZKSCAN1	7586	broad.mit.edu	36	7	99459752	99459752	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:99459752G>A	uc003usk.1	+	c.466G>A	c.(466-468)GGG>AGG	p.G156R	ZKSCAN1_uc003usj.2_Missense_Mutation_p.G155R|ZKSCAN1_uc003usl.1_Missense_Mutation_p.G120R|ZKSCAN1_uc003usm.1_Intron	NM_003439	NP_003430	P17029	ZKSC1_HUMAN	zinc finger protein 36	156					regulation of transcription, DNA-dependent|viral reproduction	mitochondrion|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)													0.165	64.449859	85.752285	33	167	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.129)		Missense_Mutation	SNP	99459752	99459752	18277	7	G	A	A	43	43	ZKSCAN1	A	2	2
DLGAP2	9228	broad.mit.edu	36	8	1484313	1484313	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:1484313G>A	uc003wpl.1	+	c.47G>A	c.(46-48)GGG>GAG	p.G16E	DLGAP2_uc003wpm.1_Missense_Mutation_p.G16E	NM_004745	NP_004736	Q9P1A6	DLGP2_HUMAN	discs large-associated protein 2	95					nerve-nerve synaptic transmission	cell junction|neurofilament|postsynaptic density|postsynaptic membrane	protein binding				0		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)												0.472222	48.866708	48.891191	17	19	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)	Missense_Mutation	SNP	1484313	1484313	4740	8	G	A	A	43	43	DLGAP2	A	2	2
ADAMDEC1	27299	broad.mit.edu	36	8	24310866	24310866	+	Silent	SNP	C	T	T			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:24310866C>T	uc003xdz.1	+	c.579C>T	c.(577-579)GAC>GAT	p.D193D	ADAMDEC1_uc010lub.1_Silent_p.D114D	NM_014479	NP_055294	O15204	ADEC1_HUMAN	ADAM-like, decysin 1 isoform 1	193					integrin-mediated signaling pathway|negative regulation of cell adhesion|proteolysis	extracellular region|integral to membrane	integrin binding|metalloendopeptidase activity|zinc ion binding				0		Prostate(55;0.0181)				Ovarian(147;687 1849 3699 25981 31337)								0.252788	164.181654	179.103914	68	201	CC		KEEP	---	---	---	---	capture		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)	Silent	SNP	24310866	24310866	255	8	C	T	T	19	19	ADAMDEC1	T	1	1
SDCBP	6386	broad.mit.edu	36	8	59654907	59654907	+	Silent	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:59654907G>A	uc003xts.1	+	c.768G>A	c.(766-768)AAG>AAA	p.K256K	SDCBP_uc003xtn.1_Silent_p.K250K|SDCBP_uc003xto.1_Silent_p.K249K|SDCBP_uc003xtq.1_Silent_p.K250K|SDCBP_uc003xtr.1_Silent_p.K249K|SDCBP_uc003xtp.1_Silent_p.K244K	NM_001007070	NP_001007071	O00560	SDCB1_HUMAN	syntenin isoform 3	250	PDZ 2.				actin cytoskeleton organization|axon guidance|positive regulation of JNK cascade|positive regulation of phosphorylation|protein targeting to membrane|substrate-dependent cell migration, cell extension|synaptic transmission	cytoskeleton|cytosol|endoplasmic reticulum membrane|focal adhesion|interleukin-5 receptor complex|melanosome|nucleus	cytoskeletal adaptor activity|frizzled binding|interleukin-5 receptor binding|protein heterodimerization activity|protein N-terminus binding|syndecan binding				0		all_lung(136;0.0271)|Lung NSC(129;0.0351)|all_epithelial(80;0.0554)												0.355828	174.118458	177.097252	58	105	GG		KEEP	---	---	---	---	capture			Silent	SNP	59654907	59654907	14440	8	G	A	A	35	35	SDCBP	A	2	2
OR2K2	26248	broad.mit.edu	36	9	113130327	113130327	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:113130327C>T	uc004bfd.1	-	c.208G>A	c.(208-210)GAT>AAT	p.D70N		NM_205859	NP_995581	Q8NGT1	OR2K2_HUMAN	olfactory receptor, family 2, subfamily K,	99	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.423077	129.058038	129.599112	44	60	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	113130327	113130327	11411	9	C	T	T	30	30	OR2K2	T	2	2
COL27A1	85301	broad.mit.edu	36	9	116060657	116060657	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:116060657C>T	uc004bih.1	+	c.3157C>T	c.(3157-3159)CGA>TGA	p.R1053*	COL27A1_uc004bii.1_Non-coding_Transcript	NM_032888	NP_116277	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1053	Pro-rich.|Collagen-like 7.|Triple-helical region.				cell adhesion		extracellular matrix structural constituent			ovary(3)	3														0.327586	50.297675	51.830641	19	39	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	116060657	116060657	3823	9	C	T	T	31	31	COL27A1	T	5	1
C9orf171	389799	broad.mit.edu	36	9	134364580	134364580	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:134364580C>T	uc004cbn.1	+	c.404C>T	c.(403-405)GCC>GTC	p.A135V	C9orf171_uc004cbo.1_Missense_Mutation_p.A99V	NM_207417	NP_997300	Q6ZQR2	CI171_HUMAN	hypothetical protein LOC389799	135										ovary(4)|large_intestine(1)	5														0.386139	105.309372	106.453721	39	62	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	134364580	134364580	2585	9	C	T	T	26	26	C9orf171	T	2	2
COL5A1	1289	broad.mit.edu	36	9	136782526	136782526	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:136782526C>A	uc004cfe.1	+	c.1639C>A	c.(1639-1641)CAA>AAA	p.Q547K		NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein	547	Interrupted collagenous region.				axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)|skin(1)	8		Myeloproliferative disorder(178;0.0341)												0.26087	7.983895	9.227383	6	17	CC		KEEP	---	---	---	---	capture		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)	Missense_Mutation	SNP	136782526	136782526	3834	9	C	A	A	25	25	COL5A1	A	3	3
DOCK8	81704	broad.mit.edu	36	9	386909	386909	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:386909C>G	uc003zgf.1	+	c.3095C>G	c.(3094-3096)GCA>GGA	p.A1032G	DOCK8_uc003zgi.1_Missense_Mutation_p.A964G|DOCK8_uc010mgu.1_Missense_Mutation_p.A334G|DOCK8_uc010mgv.1_Missense_Mutation_p.A932G|DOCK8_uc010mgw.1_Missense_Mutation_p.A334G|DOCK8_uc003zgk.1_Missense_Mutation_p.A490G	NM_203447	NP_982272	Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1032					blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)	6		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)												0.266667	94.046291	99.946714	32	88	CC		KEEP	---	---	---	---	capture		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)	Missense_Mutation	SNP	386909	386909	4877	9	C	G	G	25	25	DOCK8	G	3	3
DOCK8	81704	broad.mit.edu	36	9	389200	389200	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0876-01	TCGA-06-0876-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:389200C>G	uc003zgf.1	+	c.3175C>G	c.(3175-3177)CTT>GTT	p.L1059V	DOCK8_uc003zgi.1_Missense_Mutation_p.L991V|DOCK8_uc010mgu.1_Missense_Mutation_p.L361V|DOCK8_uc010mgv.1_Missense_Mutation_p.L959V|DOCK8_uc010mgw.1_Missense_Mutation_p.L361V|DOCK8_uc003zgk.1_Missense_Mutation_p.L517V	NM_203447	NP_982272	Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1059					blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)	6		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)												0.310606	101.214216	105.438873	41	91	CC		KEEP	---	---	---	---	capture		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)	Missense_Mutation	SNP	389200	389200	4877	9	C	G	G	24	24	DOCK8	G	3	3
DOCK8	81704	broad.mit.edu	36	9	429373	429373	+	Silent	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:429373G>A	uc003zgf.1	+	c.5208G>A	c.(5206-5208)GCG>GCA	p.A1736A	DOCK8_uc003zgi.1_Silent_p.A1668A|DOCK8_uc010mgu.1_Silent_p.A1038A|DOCK8_uc010mgv.1_Silent_p.A1636A|DOCK8_uc003zgk.1_Silent_p.A1194A	NM_203447	NP_982272	Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1736	DHR-2.				blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)	6		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)												0.294118	109.550591	114.707183	40	96	GG		KEEP	---	---	---	---	capture		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)	Silent	SNP	429373	429373	4877	9	G	A	A	39	39	DOCK8	A	1	1
FOXB2	442425	broad.mit.edu	36	9	78825378	78825378	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:78825378G>C	uc004ako.1	+	c.988G>C	c.(988-990)GCA>CCA	p.A330P		NM_001013735	NP_001013757	Q5VYV0	FOXB2_HUMAN	forkhead box B2	330	Poly-Ala.				brain development|embryo development|negative regulation of gene-specific transcription from RNA polymerase II promoter|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0														0.384615	7.290633	7.466782	5	8	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	78825378	78825378	6235	9	G	C	C	38	38	FOXB2	C	3	3
ARMCX2	9823	broad.mit.edu	36	X	100798455	100798455	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:100798455G>A	uc004eid.1	-	c.776C>T	c.(775-777)GCA>GTA	p.A259V	ARMCX2_uc004eie.2_Missense_Mutation_p.A259V|ARMCX2_uc004eif.2_Missense_Mutation_p.A259V|ARMCX2_uc004eig.2_Missense_Mutation_p.A259V|ARMCX2_uc010nnt.1_Missense_Mutation_p.A259V|ARMCX2_uc010nnu.1_Missense_Mutation_p.A259V	NM_177949	NP_808818	Q7L311	ARMX2_HUMAN	ALEX2 protein	259	Ala-rich.					integral to membrane	binding			ovary(6)	6														0.38796	298.64983	301.929058	116	183	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100798455	100798455	978	23	G	A	A	46	46	ARMCX2	A	2	2
NRK	203447	broad.mit.edu	36	X	105039765	105039765	+	Silent	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:105039765G>A	uc004emd.1	+	c.1476G>A	c.(1474-1476)CAG>CAA	p.Q492Q	NRK_uc010npc.1_Silent_p.Q160Q	NM_198465	NP_940867	Q7Z2Y5	NRK_HUMAN	Nik related kinase	492	Gln-rich.				protein phosphorylation		ATP binding|protein serine/threonine kinase activity|small GTPase regulator activity			breast(7)|ovary(3)|lung(2)|large_intestine(1)|central_nervous_system(1)	14										430				0.301205	67.234988	70.169866	25	58	GG		KEEP	---	---	---	---	capture			Silent	SNP	105039765	105039765	11060	23	G	A	A	35	35	NRK	A	2	2
DCX	1641	broad.mit.edu	36	X	110531023	110531023	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:110531023G>A	uc004epd.1	-	c.799C>T	c.(799-801)CGC>TGC	p.R267C	DCX_uc004epe.1_Missense_Mutation_p.R186C|DCX_uc004epf.1_Missense_Mutation_p.R186C|DCX_uc004epg.1_Missense_Mutation_p.R186C	NM_000555	NP_835366	O43602	DCX_HUMAN	doublecortin isoform a	267	Doublecortin 2.		R -> C (in SBHX).		axon guidance|central nervous system development|intracellular signal transduction	cytosol|microtubule associated complex	microtubule binding			central_nervous_system(2)|lung(1)|skin(1)	4														0.39779	212.171866	213.822856	72	109	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	110531023	110531023	4489	23	G	A	A	39	39	DCX	A	1	1
ANKRD58	347454	broad.mit.edu	36	X	118777516	118777516	+	Silent	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:118777516G>A	uc010nql.1	+	c.858G>A	c.(856-858)TCG>TCA	p.S286S		NM_001105576	NP_001099046	A6NJG2	ANR58_HUMAN	ankyrin repeat domain 58	286											0														0.439024	47.946346	48.078334	18	23	GG		KEEP	---	---	---	---	capture			Silent	SNP	118777516	118777516	692	23	G	A	A	38	38	ANKRD58	A	1	1
CNGA2	1260	broad.mit.edu	36	X	150663143	150663143	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0876-01	TCGA-06-0876-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:150663143T>A	uc004fey.1	+	c.1512T>A	c.(1510-1512)GAT>GAA	p.D504E		NM_005140	NP_005131	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	504	cAMP (By similarity).|Cytoplasmic (Potential).				response to stimulus|sensory perception of smell	intracellular cyclic nucleotide activated cation channel complex	cAMP binding|intracellular cAMP activated cation channel activity			breast(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.313725	88.469222	91.615633	32	70	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	150663143	150663143	3735	23	T	A	A	51	51	CNGA2	A	4	4
ARSF	416	broad.mit.edu	36	X	3031960	3031960	+	Silent	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:3031960G>A	uc004cre.1	+	c.1260G>A	c.(1258-1260)CAG>CAA	p.Q420Q	ARSF_uc004crf.1_Silent_p.Q420Q	NM_004042	NP_004033	P54793	ARSF_HUMAN	arylsulfatase F precursor	420						extracellular region	arylsulfatase activity|metal ion binding			ovary(2)	2		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)												0.439655	161.212477	161.579988	51	65	GG		KEEP	---	---	---	---	capture			Silent	SNP	3031960	3031960	1009	23	G	A	A	35	35	ARSF	A	2	2
SLC38A5	92745	broad.mit.edu	36	X	48204339	48204339	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:48204339G>T	uc010nid.1	-	c.929C>A	c.(928-930)ACC>AAC	p.T310N	SLC38A5_uc004djk.2_Missense_Mutation_p.T259N	NM_033518	NP_277053	Q8WUX1	S38A5_HUMAN	solute carrier family 38, member 5	310	Helical; (Potential).				cellular nitrogen compound metabolic process|ion transport	integral to membrane|plasma membrane				ovary(3)	3														0.222222	17.28335	19.837376	8	28	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48204339	48204339	15104	23	G	T	T	44	44	SLC38A5	T	3	3
HUWE1	10075	broad.mit.edu	36	X	53590156	53590156	+	Silent	SNP	G	A	A			TCGA-06-0876-01	TCGA-06-0876-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:53590156G>A	uc004dso.1	-	c.10881C>T	c.(10879-10881)GCC>GCT	p.A3627A	HUWE1_uc004dsn.1_Silent_p.A2435A|HUWE1_uc004dsp.1_Silent_p.A3627A|HUWE1_uc004dsq.1_5'Flank	NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1	3627					base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17														0.211538	26.096775	30.097252	11	41	GG		KEEP	---	---	---	---	capture			Silent	SNP	53590156	53590156	7761	23	G	A	A	43	43	HUWE1	A	2	2
DLG5	9231	broad.mit.edu	36	10	79247588	79247588	+	Frame_Shift_Del	DEL	A	-	-			TCGA-06-0876-01	TCGA-06-0876-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:79247588_79247588delA	uc001jzk.1	-	c.3737_3737delT	c.(3736-3738)ATGfs	p.M1246fs	DLG5_uc009xru.1_Non-coding_Transcript|DLG5_uc001jzi.1_Frame_Shift_Del_p.M1fs|DLG5_uc001jzj.1_Frame_Shift_Del_p.M661fs|DLG5_uc001jzl.2_Frame_Shift_Del_p.M850fs	NM_004747	NP_004738	Q8TDM6	DLG5_HUMAN	discs large homolog 5	1246					cell-cell adhesion|intracellular signal transduction|negative regulation of cell proliferation|regulation of apoptosis	cell junction|cytoplasm	beta-catenin binding|cytoskeletal protein binding|receptor signaling complex scaffold activity			ovary(5)|breast(3)	8	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)											0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	79247588	79247588	4738	10	A	-	-	8	8	DLG5	-	5	5
FA2H	79152	broad.mit.edu	36	16	73305642	73305642	+	Frame_Shift_Del	DEL	C	-	-			TCGA-06-0876-01	TCGA-06-0876-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:73305642_73305642delC	uc002fde.1	-	c.1066_1066delG	c.(1066-1068)GGTfs	p.G356fs	FA2H_uc002fdd.1_Frame_Shift_Del_p.D129fs	NM_024306	NP_077282	Q7L5A8	FA2H_HUMAN	fatty acid 2-hydroxylase	356				D -> G (in Ref. 1; BAB71632).	cell death|electron transport chain|fatty acid biosynthetic process|sphingolipid metabolic process|transport	endoplasmic reticulum membrane|integral to membrane|microsome	heme binding|oxidoreductase activity				0														0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	73305642	73305642	5549	16	C	-	-	30	30	FA2H	-	5	5
TTC13	79573	broad.mit.edu	36	1	229126223	229126223	+	Frame_Shift_Del	DEL	T	-	-			TCGA-06-0876-01	TCGA-06-0876-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:229126223_229126223delT	uc001huf.2	-	c.1801_1801delA	c.(1801-1803)ATTfs	p.I601fs	TTC13_uc009xfi.1_Frame_Shift_Del_p.I548fs|TTC13_uc009xfj.1_Non-coding_Transcript|TTC13_uc001hug.2_Frame_Shift_Del_p.I548fs|TTC13_uc009xfk.1_Frame_Shift_Del_p.I491fs	NM_024525	NP_078801	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13 isoform a	601							binding			ovary(1)|skin(1)	2	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)										0.40			69	104				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	229126223	229126223	17234	1	T	-	-	51	51	TTC13	-	5	5
