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
FAM21C	253725	broad.mit.edu	36	10	45585064	45585064	+	Silent	SNP	C	T	T			TCGA-06-0192-01	TCGA-06-0192-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:45585064C>T	uc001jcu.1	+	c.2031C>T	c.(2029-2031)GCC>GCT	p.A677A	FAM21C_uc001jcs.1_Silent_p.A620A|FAM21C_uc001jct.1_Silent_p.A675A|FAM21C_uc001jcv.1_5'UTR	NM_015262	NP_056077	A8K5W5	A8K5W5_HUMAN	hypothetical protein LOC253725	677										ovary(1)	1														0.161074	86.093285	118.684213	48	250	CC		KEEP	---	---	---	---	capture			Silent	SNP	45585064	45585064	5757	10	C	T	T	21	21	FAM21C	T	2	2
PTEN	5728	broad.mit.edu	36	10	89710774	89710774	+	Nonsense_Mutation	SNP	T	A	A			TCGA-06-0192-01	TCGA-06-0192-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89710774T>A	uc001kfb.1	+	c.945T>A	c.(943-945)TAT>TAA	p.Y315*		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	315	C2 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.Y315fs*9(1)|p.G165_K342del(1)|p.L316fs*2(1)|p.W274_F341del(1)|p.G165_*404del(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		264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.45	113.393376	113.567099	36	44	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)	Nonsense_Mutation	SNP	89710774	89710774	13192	10	T	A	A	50	50	PTEN	A	5	4
PGR	5241	broad.mit.edu	36	11	100504664	100504664	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:100504664G>C	uc001pgh.2	-	c.348C>G	c.(346-348)GAC>GAG	p.D116E	PGR_uc001pgi.2_Missense_Mutation_p.D116E|PGR_uc009yww.1_Non-coding_Transcript|PGR_uc001pgj.2_Non-coding_Transcript|PGR_uc009ywx.1_Non-coding_Transcript	NM_000926	NP_000917	P06401	PRGR_HUMAN	progesterone receptor	116	Modulating, Pro-Rich.				cell-cell signaling|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	enzyme binding|receptor binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			lung(1)|liver(1)|central_nervous_system(1)|pancreas(1)	4		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)			Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Mifepristone(DB00834)|Norethindrone(DB00717)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)	Pancreas(124;2271 2354 21954 22882)				429				0.290323	26.76265	27.983672	9	22	GG		KEEP	---	---	---	---	capture		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Missense_Mutation	SNP	100504664	100504664	12228	11	G	C	C	48	48	PGR	C	3	3
DDI1	414301	broad.mit.edu	36	11	103413266	103413266	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0192-01	TCGA-06-0192-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:103413266A>C	uc001phr.2	+	c.506A>C	c.(505-507)GAA>GCA	p.E169A	PDGFD_uc001php.1_Intron|PDGFD_uc001phq.1_Intron	NM_001001711	NP_001001711	Q8WTU0	DDI1_HUMAN	DDI1, DNA-damage inducible 1, homolog 1	169					proteolysis		aspartic-type endopeptidase activity			large_intestine(3)|pancreas(1)	4		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)												0.202312	90.944023	105.171824	35	138	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)	Missense_Mutation	SNP	103413266	103413266	4499	11	A	C	C	9	9	DDI1	C	4	4
SPATA19	219938	broad.mit.edu	36	11	133217202	133217202	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0192-01	TCGA-06-0192-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:133217202C>T	uc001qgv.1	-	c.446G>A	c.(445-447)CGT>CAT	p.R149H		NM_174927	NP_777587	Q7Z5L4	SPT19_HUMAN	spermatogenesis associated 19	149					cell differentiation|multicellular organismal development|spermatogenesis	mitochondrial outer membrane					0	all_hematologic(175;0.127)	all_cancers(12;5.59e-17)|all_epithelial(12;2.65e-12)|all_lung(97;0.00045)|Lung NSC(97;0.000861)|Breast(109;0.000873)|Medulloblastoma(222;0.0425)|Esophageal squamous(93;0.0844)|all_neural(223;0.117)												0.092593	6.60801	33.664952	15	147	CC		KEEP	---	---	---	---	capture		Epithelial(10;4.36e-10)|all cancers(11;7.1e-09)|BRCA - Breast invasive adenocarcinoma(10;8.45e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00286)|Lung(977;0.207)	Missense_Mutation	SNP	133217202	133217202	15512	11	C	T	T	19	19	SPATA19	T	1	1
LUZP2	338645	broad.mit.edu	36	11	24892639	24892639	+	Silent	SNP	G	C	C			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:24892639G>C	uc001mqs.1	+	c.501G>C	c.(499-501)GGG>GGC	p.G167G	LUZP2_uc009yif.1_Silent_p.G81G|LUZP2_uc009yig.1_Intron	NM_001009909	NP_001009909	Q86TE4	LUZP2_HUMAN	leucine zipper protein 2	167	Potential.|Leucine-zipper.					extracellular region				ovary(1)	1														0.409091	32.071609	32.230327	9	13	GG		KEEP	---	---	---	---	capture			Silent	SNP	24892639	24892639	9463	11	G	C	C	41	41	LUZP2	C	3	3
C11orf41	25758	broad.mit.edu	36	11	33639117	33639117	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0192-01	TCGA-06-0192-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:33639117C>G	uc001mup.2	+	c.5267C>G	c.(5266-5268)CCG>CGG	p.P1756R		NM_012194	NP_036326	Q6ZVL6	CK041_HUMAN	hypothetical protein LOC25758	1750						integral to membrane				ovary(2)	2														0.208333	6.892535	8.785354	5	19	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33639117	33639117	1679	11	C	G	G	23	23	C11orf41	G	3	3
LRP4	4038	broad.mit.edu	36	11	46837290	46837290	+	Silent	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:46837290G>A	uc001ndn.2	-	c.5538C>T	c.(5536-5538)GAC>GAT	p.D1846D	LRP4_uc001ndm.2_Silent_p.D88D	NM_002334	NP_002325	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein	1846	Cytoplasmic (Potential).				endocytosis|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane	calcium ion binding|receptor activity			ovary(1)	1														0.101449	7.846265	29.718929	14	124	GG		KEEP	---	---	---	---	capture		Lung(87;0.159)	Silent	SNP	46837290	46837290	9332	11	G	A	A	48	48	LRP4	A	2	2
OR5F1	338674	broad.mit.edu	36	11	55517743	55517743	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55517743G>A	uc001nie.1	-	c.935C>T	c.(934-936)TCC>TTC	p.S312F		NM_003697	NP_003688	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F,	312	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2	Esophageal squamous(21;0.00448)													0.272727	47.12481	50.195181	18	48	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55517743	55517743	11568	11	G	A	A	41	41	OR5F1	A	2	2
OR9G1	390174	broad.mit.edu	36	11	56224873	56224873	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0192-01	TCGA-06-0192-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:56224873C>A	uc001njd.1	+	c.434C>A	c.(433-435)GCA>GAA	p.A145E		NM_001013358	NP_001013376	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G,	145	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.12234	55.363724	107.895029	46	330	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56224873	56224873	11661	11	C	A	A	25	25	OR9G1	A	3	3
TPP1	1200	broad.mit.edu	36	11	6594128	6594128	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0192-01	TCGA-06-0192-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:6594128C>T	uc001mel.1	-	c.1069G>A	c.(1069-1071)GCC>ACC	p.A357T	TPP1_uc001mek.1_Missense_Mutation_p.A114T	NM_000391	NP_000382	O14773	TPP1_HUMAN	tripeptidyl-peptidase I preproprotein	357					bone resorption|cell death|lipid metabolic process|lysosome organization|nervous system development|neuromuscular process controlling balance|peptide catabolic process|protein catabolic process|proteolysis	lysosome|melanosome|soluble fraction	metal ion binding|peptide binding|protein binding|serine-type endopeptidase activity|tripeptidyl-peptidase activity				0		Medulloblastoma(188;0.00263)|all_neural(188;0.026)												0.197044	77.511	94.856171	40	163	CC		KEEP	---	---	---	---	capture		Epithelial(150;3.45e-09)|BRCA - Breast invasive adenocarcinoma(625;0.131)	Missense_Mutation	SNP	6594128	6594128	16955	11	C	T	T	27	27	TPP1	T	1	1
DHCR7	1717	broad.mit.edu	36	11	70832826	70832826	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0192-01	TCGA-06-0192-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:70832826C>A	uc001oqk.1	-	c.182G>T	c.(181-183)TGT>TTT	p.C61F	DHCR7_uc001oql.1_Missense_Mutation_p.C61F	NM_001360	NP_001351	Q9UBM7	DHCR7_HUMAN	7-dehydrocholesterol reductase	61					cholesterol biosynthetic process|oxidation-reduction process	endoplasmic reticulum membrane|integral to membrane|nuclear outer membrane	7-dehydrocholesterol reductase activity|protein binding			ovary(1)|liver(1)	2					NADH(DB00157)									0.2	6.691656	8.364906	4	16	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70832826	70832826	4656	11	C	A	A	17	17	DHCR7	A	3	3
CLEC1A	51267	broad.mit.edu	36	12	10133053	10133053	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0192-01	TCGA-06-0192-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:10133053C>T	uc001qxb.1	-	c.151G>A	c.(151-153)GCC>ACC	p.A51T	CLEC1A_uc009zhf.1_5'UTR|CLEC1A_uc001qxc.1_5'UTR|CLEC1A_uc001qxd.1_Intron	NM_016511	NP_057595	Q8NC01	CLC1A_HUMAN	C-type lectin-like receptor-1	51	Cytoplasmic (Potential).				cell surface receptor linked signaling pathway|defense response	integral to plasma membrane|intracellular	sugar binding|transmembrane receptor activity			ovary(1)|central_nervous_system(1)	2														0.34	94.717697	96.981415	34	66	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10133053	10133053	3642	12	C	T	T	26	26	CLEC1A	T	2	2
ABCC9	10060	broad.mit.edu	36	12	21896666	21896666	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0192-01	TCGA-06-0192-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:21896666T>C	uc001rfh.1	-	c.2546A>G	c.(2545-2547)CAT>CGT	p.H849R	ABCC9_uc001rfi.1_Missense_Mutation_p.H849R|ABCC9_uc001rfj.1_Missense_Mutation_p.H813R	NM_020297	NP_064693	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	849	Cytoplasmic (Potential).|ABC transporter 1.				defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)	4					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)									0.369369	120.446601	122.111049	41	70	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21896666	21896666	60	12	T	C	C	51	51	ABCC9	C	4	4
ARNTL2	56938	broad.mit.edu	36	12	27412578	27412578	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0192-01	TCGA-06-0192-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:27412578C>T	uc001rht.1	+	c.148C>T	c.(148-150)CGA>TGA	p.R50*	ARNTL2_uc001rhu.1_Nonsense_Mutation_p.R50*|ARNTL2_uc009zji.1_Nonsense_Mutation_p.R50*|ARNTL2_uc001rhv.1_Nonsense_Mutation_p.R50*|ARNTL2_uc001rhw.1_Nonsense_Mutation_p.R61*	NM_020183	NP_064568	Q8WYA1	BMAL2_HUMAN	aryl hydrocarbon receptor nuclear	50					circadian rhythm|entrainment of circadian clock|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription regulator activity			ovary(1)	1	Colorectal(261;0.0847)|Lung SC(9;0.184)													0.33945	102.650209	105.129931	37	72	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	27412578	27412578	986	12	C	T	T	19	19	ARNTL2	T	5	1
ASB8	140461	broad.mit.edu	36	12	46829896	46829896	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:46829896G>T	uc001rrh.1	-	c.387C>A	c.(385-387)AAC>AAA	p.N129K	ASB8_uc001rri.1_Missense_Mutation_p.N129K	NM_024095	NP_077000	Q9H765	ASB8_HUMAN	ankyrin repeat and SOCS box-containing 8	129	ANK 3.				intracellular signal transduction	cytoplasm|nucleus				kidney(1)	1														0.328767	134.605613	138.424891	48	98	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46829896	46829896	1047	12	G	T	T	48	48	ASB8	T	3	3
FGD6	55785	broad.mit.edu	36	12	94127513	94127513	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:94127513G>A	uc001tdp.2	-	c.1678C>T	c.(1678-1680)CGG>TGG	p.R560W	FGD6_uc009zsx.1_Intron	NM_018351	NP_060821	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	560					actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|breast(1)	3														0.266055	142.049123	152.831788	58	160	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	94127513	94127513	6074	12	G	A	A	40	40	FGD6	A	1	1
CDK17	5128	broad.mit.edu	36	12	95213032	95213032	+	Splice_Site_SNP	SNP	C	G	G			TCGA-06-0192-01	TCGA-06-0192-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:95213032C>G	uc001tep.1	-	c.874_splice	c.e10-1	p.L292_splice	CDK17_uc009ztk.1_Splice_Site_SNP_p.L292_splice	NM_002595	NP_002586			PCTAIRE protein kinase 2						protein phosphorylation		ATP binding|cyclin-dependent protein kinase activity			ovary(3)|lung(2)|kidney(1)|central_nervous_system(1)	7										253				0.215909	49.2748	55.830209	19	69	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	95213032	95213032	3262	12	C	G	G	28	28	CDK17	G	5	3
ZIC2	7546	broad.mit.edu	36	13	99432943	99432943	+	Silent	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:99432943G>A	uc001von.1	+	c.624G>A	c.(622-624)GCG>GCA	p.A208A		NM_007129	NP_009060	O95409	ZIC2_HUMAN	zinc finger protein of the cerebellum 2	208	Necessary for interaction with MDFIC and transcriptional activation or repression (By similarity).				brain development|positive regulation of sequence-specific DNA binding transcription factor activity|visual perception	cytoplasm|nucleus	chromatin DNA binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription repressor activity|zinc ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					Pancreas(97;119 1522 31925 44771 48764)								0.244444	24.710479	27.383466	11	34	GG		KEEP	---	---	---	---	capture			Silent	SNP	99432943	99432943	18270	13	G	A	A	38	38	ZIC2	A	1	1
OR4N4	283694	broad.mit.edu	36	15	19883877	19883877	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0192-01	TCGA-06-0192-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:19883877T>A	uc001yuc.1	+	c.41T>A	c.(40-42)CTC>CAC	p.L14H	LOC727924_uc001yub.1_Non-coding_Transcript|OR4N4_uc001yue.2_Missense_Mutation_p.L14H	NM_001005241	NP_001005241	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N,	14	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(4)	4		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)												0.375	233.810269	236.77721	81	135	TT		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)	Missense_Mutation	SNP	19883877	19883877	11488	15	T	A	A	54	54	OR4N4	A	4	4
GABRB3	2562	broad.mit.edu	36	15	24363947	24363947	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0192-01	TCGA-06-0192-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:24363947A>G	uc001zbb.1	-	c.877T>C	c.(877-879)TTT>CTT	p.F293L	GABRB3_uc001zaz.1_Missense_Mutation_p.F237L|GABRB3_uc001zba.1_Missense_Mutation_p.F237L	NM_021912	NP_068712	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta	237	Extracellular (Probable).				synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	4		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)			Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)									0.268657	55.521187	58.756744	18	49	AA		KEEP	---	---	---	---	capture		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Missense_Mutation	SNP	24363947	24363947	6419	15	A	G	G	3	3	GABRB3	G	4	4
TTBK2	146057	broad.mit.edu	36	15	40825729	40825729	+	Silent	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:40825729G>A	uc001zqo.1	-	c.3291C>T	c.(3289-3291)GTC>GTT	p.V1097V	TTBK2_uc010bcy.1_Silent_p.V1028V	NM_173500	NP_775771	Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2	1097					cell death		ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|stomach(1)|pancreas(1)	6		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)								253				0.327869	53.377332	54.981008	20	41	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(94;3.23e-07)	Silent	SNP	40825729	40825729	17231	15	G	A	A	41	41	TTBK2	A	2	2
DUOX1	53905	broad.mit.edu	36	15	43219045	43219045	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0192-01	TCGA-06-0192-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:43219045C>T	uc001zus.1	+	c.1345C>T	c.(1345-1347)CGC>TGC	p.R449C	DUOX1_uc001zut.1_Missense_Mutation_p.R449C|DUOX1_uc010bee.1_Intron	NM_017434	NP_787954	Q9NRD9	DUOX1_HUMAN	dual oxidase 1 precursor	449	Peroxidase-like; mediates peroxidase activity.|Extracellular (Potential).				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide biosynthetic process|hydrogen peroxide catabolic process|oxidation-reduction process|response to cAMP|superoxide anion generation	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|NADP binding|peroxidase activity			ovary(5)|breast(1)	6		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)												0.270833	66.811418	71.356298	26	70	CC		KEEP	---	---	---	---	capture		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)	Missense_Mutation	SNP	43219045	43219045	4985	15	C	T	T	23	23	DUOX1	T	1	1
USP50	373509	broad.mit.edu	36	15	48626000	48626000	+	Silent	SNP	C	T	T			TCGA-06-0192-01	TCGA-06-0192-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:48626000C>T	uc001zyq.2	-	c.15G>A	c.(13-15)CCG>CCA	p.P5P		NM_203494	NP_987090	E9PP86	E9PP86_HUMAN	ubiquitin specific protease 50	5					ubiquitin-dependent protein catabolic process		ubiquitin thiolesterase activity				0														0.148936	20.985487	32.110606	14	80	CC		KEEP	---	---	---	---	capture		all cancers(107;0.000519)|GBM - Glioblastoma multiforme(94;0.00288)	Silent	SNP	48626000	48626000	17646	15	C	T	T	19	19	USP50	T	1	1
SPNS1	83985	broad.mit.edu	36	16	28894164	28894164	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0192-01	TCGA-06-0192-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:28894164T>G	uc002drw.1	+	c.326T>G	c.(325-327)GTG>GGG	p.V109G	SPNS1_uc002drx.1_5'UTR|SPNS1_uc002dry.1_Missense_Mutation_p.V64G|SPNS1_uc002dsa.1_Missense_Mutation_p.V64G|SPNS1_uc002drz.1_Missense_Mutation_p.V64G|SPNS1_uc010byp.1_Missense_Mutation_p.V64G|SPNS1_uc010byq.1_5'UTR	NM_032038	NP_114427	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 isoform 1	64	Helical; (Potential).				lipid transport|transmembrane transport	integral to membrane|mitochondrial inner membrane	protein binding				0														0.333333	6.318008	6.541413	3	6	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	28894164	28894164	15587	16	T	G	G	59	59	SPNS1	G	4	4
GRIN2A	2903	broad.mit.edu	36	16	9765711	9765711	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:9765711G>A	uc002czp.1	-	c.3191C>T	c.(3190-3192)ACG>ATG	p.T1064M	GRIN2A_uc002czq.1_Missense_Mutation_p.T1064M|GRIN2A_uc002czr.2_Missense_Mutation_p.T1064M	NM_000833	NP_000824	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	1064	Cytoplasmic (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			ovary(4)|lung(1)|breast(1)|kidney(1)|skin(1)	8					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)				p.T1064K(MEC1-Tumor)	324				0.241573	202.168822	223.864379	86	270	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	9765711	9765711	7058	16	G	A	A	40	40	GRIN2A	A	1	1
HOXB13	10481	broad.mit.edu	36	17	44159365	44159365	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0192-01	TCGA-06-0192-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:44159365C>T	uc002ioa.1	-	c.641G>A	c.(640-642)CGT>CAT	p.R214H		NM_006361	NP_006352	Q92826	HXB13_HUMAN	homeobox B13	214					angiogenesis|epidermis development|regulation of transcription, DNA-dependent|response to wounding		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0														0.241071	61.592758	68.429526	27	85	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44159365	44159365	7592	17	C	T	T	19	19	HOXB13	T	1	1
LPHN1	22859	broad.mit.edu	36	19	14122968	14122968	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0192-01	TCGA-06-0192-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:14122968C>T	uc002myg.1	-	c.4142G>A	c.(4141-4143)CGG>CAG	p.R1381Q	LPHN1_uc002myh.1_Missense_Mutation_p.R1376Q	NM_001008701	NP_001008701	O94910	LPHN1_HUMAN	latrophilin 1 isoform 1 precursor	1381	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(1)|central_nervous_system(1)	2														0.285714	21.241551	22.364081	8	20	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	14122968	14122968	9288	19	C	T	T	23	23	LPHN1	T	1	1
CYP4F3	4051	broad.mit.edu	36	19	15631048	15631048	+	Silent	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:15631048G>A	uc002nbj.1	+	c.1416G>A	c.(1414-1416)GCG>GCA	p.A472A	CYP4F3_uc002nbk.1_Silent_p.A472A	NM_000896	NP_000887	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F,	472					leukotriene metabolic process|oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	electron carrier activity|heme binding|leukotriene-B4 20-monooxygenase activity|oxygen binding			ovary(3)	3														0.131313	17.310259	30.389798	13	86	GG		KEEP	---	---	---	---	capture			Silent	SNP	15631048	15631048	4355	19	G	A	A	40	40	CYP4F3	A	1	1
CPAMD8	27151	broad.mit.edu	36	19	16868126	16868126	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:16868126G>C	uc002nfb.1	-	c.5428C>G	c.(5428-5430)CCG>GCG	p.P1810A	CPAMD8_uc002nfd.1_Missense_Mutation_p.P275A	NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain	1763						extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)	12										1067				0.25	8.724157	10.104163	6	18	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16868126	16868126	3933	19	G	C	C	42	42	CPAMD8	C	3	3
ZNF430	80264	broad.mit.edu	36	19	21031532	21031532	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0192-01	TCGA-06-0192-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:21031532A>G	uc002npj.1	+	c.578A>G	c.(577-579)AAT>AGT	p.N193S	ZNF430_uc002npk.1_Missense_Mutation_p.N192S	NM_025189	NP_079465	Q9H8G1	ZN430_HUMAN	zinc finger protein 430	193					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.186441	27.691462	33.124565	11	48	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21031532	21031532	18497	19	A	G	G	4	4	ZNF430	G	4	4
MEGF8	1954	broad.mit.edu	36	19	47564588	47564588	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0192-01	TCGA-06-0192-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:47564588T>G	uc002otl.2	+	c.6214T>G	c.(6214-6216)TGT>GGT	p.C2072G	MEGF8_uc002otm.2_Missense_Mutation_p.C1680G|MEGF8_uc002otn.2_5'Flank	NM_001410	NP_001401	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	2139	Extracellular (Potential).|PSI 7.					integral to membrane	calcium ion binding|structural molecule activity			ovary(1)	1		Prostate(69;0.00682)												0.285714	8.003324	8.575276	4	10	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47564588	47564588	9852	19	T	G	G	59	59	MEGF8	G	4	4
TOMM40L	84134	broad.mit.edu	36	1	159464883	159464883	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:159464883G>A	uc001fzd.1	+	c.649G>A	c.(649-651)GCC>ACC	p.A217T	TOMM40L_uc009wue.1_Missense_Mutation_p.A99T|TOMM40L_uc009wuf.1_Non-coding_Transcript|TOMM40L_uc001fze.1_Missense_Mutation_p.A217T	NM_032174	NP_115550	Q969M1	TM40L_HUMAN	translocase of outer mitochondrial membrane 40	217					protein transport	mitochondrial outer membrane|pore complex	porin activity|voltage-gated anion channel activity			large_intestine(1)	1	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)													0.162791	23.612516	32.901499	14	72	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(70;0.00376)		Missense_Mutation	SNP	159464883	159464883	16900	1	G	A	A	42	42	TOMM40L	A	2	2
C1orf107	27042	broad.mit.edu	36	1	208075077	208075077	+	Silent	SNP	A	G	G			TCGA-06-0192-01	TCGA-06-0192-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:208075077A>G	uc001hhr.1	+	c.597A>G	c.(595-597)AAA>AAG	p.K199K	C1orf107_uc009xcu.1_5'UTR	NM_014388	NP_055203	Q68CQ4	DIEXF_HUMAN	digestive-organ expansion factor homolog	199					multicellular organismal development	nucleus					0														0.235955	63.531521	69.202593	21	68	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(81;0.0367)	Silent	SNP	208075077	208075077	2048	1	A	G	G	3	3	C1orf107	G	4	4
CHRM3	1131	broad.mit.edu	36	1	238137899	238137899	+	Silent	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:238137899G>A	uc001hyp.1	+	c.525G>A	c.(523-525)ACG>ACA	p.T175T	CHRM3_uc009xgk.1_Silent_p.T175T	NM_000740	NP_000731	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	175	Cytoplasmic (By similarity).				cell proliferation|energy reserve metabolic process|nervous system development|protein modification process|regulation of insulin secretion	basolateral plasma membrane|cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)	4	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)			Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Cevimeline(DB00185)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Darifenacin(DB00496)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Solifenacin(DB01591)|Thiethylperazine(DB00372)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tridihexethyl(DB00505)									0.305755	232.416763	241.746469	85	193	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Silent	SNP	238137899	238137899	3512	1	G	A	A	40	40	CHRM3	A	1	1
MECR	51102	broad.mit.edu	36	1	29429959	29429959	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0192-01	TCGA-06-0192-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:29429959T>G	uc001brq.1	-	c.47A>C	c.(46-48)CAG>CCG	p.Q16P	MECR_uc001brp.1_5'UTR|MECR_uc001brr.1_5'UTR|MECR_uc001brs.1_Non-coding_Transcript|MECR_uc001brt.1_5'UTR	NM_016011	NP_001019903	Q9BV79	MECR_HUMAN	trans-2-enoyl-CoA reductase, mitochondrial	16					fatty acid biosynthetic process|oxidation-reduction process	mitochondrion	trans-2-enoyl-CoA reductase (NADPH) activity|zinc ion binding			ovary(1)	1		Colorectal(325;0.000389)|Breast(348;0.00765)|Lung NSC(340;0.0081)|all_lung(284;0.00914)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)												0.466667	40.255946	40.283765	14	16	TT		KEEP	---	---	---	---	capture		Colorectal(126;3.39e-07)|COAD - Colon adenocarcinoma(152;2.04e-05)|STAD - Stomach adenocarcinoma(196;0.0195)|BRCA - Breast invasive adenocarcinoma(304;0.053)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.137)	Missense_Mutation	SNP	29429959	29429959	9813	1	T	G	G	55	55	MECR	G	4	4
FOXJ3	22887	broad.mit.edu	36	1	42429738	42429738	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:42429738G>A	uc001che.1	-	c.1174C>T	c.(1174-1176)CAG>TAG	p.Q392*	FOXJ3_uc001chf.1_Nonsense_Mutation_p.Q392*|FOXJ3_uc001chg.1_Nonsense_Mutation_p.Q392*|FOXJ3_uc001chh.1_Nonsense_Mutation_p.Q358*	NM_014947	NP_055762	Q9UPW0	FOXJ3_HUMAN	forkhead box J3	392					embryo development|negative regulation of gene-specific transcription from RNA polymerase II promoter|organ development|pattern specification process|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific 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			ovary(2)	2	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)												0.282828	126.618285	135.008575	56	142	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	42429738	42429738	6259	1	G	A	A	46	46	FOXJ3	A	5	2
ELTD1	64123	broad.mit.edu	36	1	79176097	79176097	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:79176097G>T	uc001diq.2	-	c.743C>A	c.(742-744)ACA>AAA	p.T248K		NM_022159	NP_071442	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain	248	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(1)	1														0.272727	168.616867	179.375311	63	168	GG		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)	Missense_Mutation	SNP	79176097	79176097	5276	1	G	T	T	48	48	ELTD1	T	3	3
OVOL2	58495	broad.mit.edu	36	20	17953451	17953451	+	Silent	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:17953451G>A	uc002wqi.1	-	c.657C>T	c.(655-657)TGC>TGT	p.C219C		NM_021220	NP_067043	Q9BRP0	OVOL2_HUMAN	zinc finger protein 339	219	C2H2-type 4.				negative regulation of keratinocyte differentiation|negative regulation of Notch signaling pathway|negative regulation of transcription by competitive promoter binding|regulation of cell cycle|regulation of keratinocyte proliferation|transcription, DNA-dependent	nucleus|nucleus	DNA binding|promoter binding|zinc ion binding			central_nervous_system(1)	1														0.309091	90.717996	94.285743	34	76	GG		KEEP	---	---	---	---	capture			Silent	SNP	17953451	17953451	11740	20	G	A	A	38	38	OVOL2	A	1	1
PLCG1	5335	broad.mit.edu	36	20	39234583	39234583	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:39234583G>A	uc002xjo.1	+	c.3014G>A	c.(3013-3015)CGA>CAA	p.R1005Q	PLCG1_uc002xjp.1_Missense_Mutation_p.R1005Q	NM_002660	NP_002651	P19174	PLCG1_HUMAN	phospholipase C gamma 1 isoform a	1005	PI-PLC Y-box.				activation of phospholipase C activity|axon guidance|blood coagulation|cellular response to epidermal growth factor stimulus|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|interspecies interaction between organisms|intracellular signal transduction|leukocyte migration|nerve growth factor receptor signaling pathway|phospholipid catabolic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of epithelial cell migration|T cell receptor signaling pathway	cytosol|lamellipodium|plasma membrane|ruffle	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|receptor signaling protein activity			breast(3)|lung(2)|skin(1)	6		Myeloproliferative disorder(115;0.00878)								429				0.205882	46.019231	54.200609	21	81	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	39234583	39234583	12461	20	G	A	A	37	37	PLCG1	A	1	1
TMPRSS15	5651	broad.mit.edu	36	21	18569431	18569431	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0192-01	TCGA-06-0192-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr21:18569431T>A	uc002ykw.1	-	c.2858A>T	c.(2857-2859)AAT>ATT	p.N953I		NM_002772	NP_002763	P98073	ENTK_HUMAN	enterokinase precursor	953	Extracellular (Potential).|Peptidase S1.				proteolysis	brush border|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(5)|breast(1)	6														0.234177	87.408835	97.617505	37	121	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18569431	18569431	16787	21	T	A	A	52	52	TMPRSS15	A	4	4
MX2	4600	broad.mit.edu	36	21	41700562	41700562	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:41700562G>A	uc002yzf.1	+	c.1672G>A	c.(1672-1674)GTG>ATG	p.V558M	MX2_uc002yzg.1_Missense_Mutation_p.V281M|MX2_uc010gop.1_Missense_Mutation_p.V40M	NM_002463	NP_002454	P20592	MX2_HUMAN	myxovirus resistance protein 2	558					response to virus|type I interferon-mediated signaling pathway	cytoplasm|nucleus	GTP binding|GTPase activity			ovary(2)	2		Prostate(19;1.57e-07)|all_epithelial(19;0.0222)												0.111111	12.547661	27.355141	11	88	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41700562	41700562	10392	21	G	A	A	36	36	MX2	A	2	2
GAL3ST1	9514	broad.mit.edu	36	22	29281019	29281019	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0192-01	TCGA-06-0192-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr22:29281019A>C	uc003aig.1	-	c.1193T>G	c.(1192-1194)ATC>AGC	p.I398S	GAL3ST1_uc003aih.1_Missense_Mutation_p.I398S|GAL3ST1_uc003aii.1_Missense_Mutation_p.I398S|GAL3ST1_uc010gvz.1_Missense_Mutation_p.I398S	NM_004861	NP_004852	Q99999	G3ST1_HUMAN	galactose-3-O-sulfotransferase 1	398	Lumenal (Potential).				protein N-linked glycosylation	Golgi membrane|integral to plasma membrane|membrane fraction	galactosylceramide sulfotransferase activity				0														0.303448	133.133985	138.141058	44	101	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29281019	29281019	6461	22	A	C	C	12	12	GAL3ST1	C	4	4
TRIOBP	11078	broad.mit.edu	36	22	36483973	36483973	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0192-01	TCGA-06-0192-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr22:36483973A>G	uc003att.1	+	c.6095A>G	c.(6094-6096)GAG>GGG	p.E2032G	TRIOBP_uc003atu.1_Missense_Mutation_p.E1860G|TRIOBP_uc003atv.1_Missense_Mutation_p.E319G|TRIOBP_uc003atw.1_Missense_Mutation_p.E319G|TRIOBP_uc003atx.1_5'UTR|TRIOBP_uc010gxh.1_5'UTR	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6	2032					actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)													0.304348	7.357223	8.249269	7	16	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36483973	36483973	17103	22	A	G	G	11	11	TRIOBP	G	4	4
SMCR7L	54471	broad.mit.edu	36	22	38239698	38239698	+	Silent	SNP	C	G	G			TCGA-06-0192-01	TCGA-06-0192-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:38239698C>G	uc003axw.2	+	c.816C>G	c.(814-816)GGC>GGG	p.G272G	SMCR7L_uc010gxz.1_Silent_p.G94G|SMCR7L_uc003axx.1_Silent_p.G272G|SMCR7L_uc003axy.1_Silent_p.G94G	NM_019008	NP_061881	Q9NQG6	SMC7L_HUMAN	hypothetical protein LOC54471	272						integral to membrane|mitochondrion				central_nervous_system(1)	1	Melanoma(58;0.04)											OREG0026577	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.322581	22.335927	23.20427	10	21	CC		KEEP	---	---	---	---	capture			Silent	SNP	38239698	38239698	15289	22	C	G	G	28	28	SMCR7L	G	3	3
CYP2D6	1565	broad.mit.edu	36	22	40855782	40855782	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:40855782G>C	uc003bce.1	-	c.254C>G	c.(253-255)GCG>GGG	p.A85G	CYP2D6_uc010gyu.1_5'UTR|CYP2D6_uc003bcf.1_Missense_Mutation_p.A85G	NM_000106	NP_000097	Q6NWU0	Q6NWU0_HUMAN	cytochrome P450, family 2, subfamily D,	85					oxidation-reduction process		electron carrier activity|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen			breast(1)	1														0.275862	9.842165	11.198188	8	21	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40855782	40855782	4334	22	G	C	C	38	38	CYP2D6	C	3	3
FAM123C	205147	broad.mit.edu	36	2	131237640	131237640	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:131237640G>A	uc002trw.2	+	c.1525G>A	c.(1525-1527)GTC>ATC	p.V509I	FAM123C_uc010fms.1_Missense_Mutation_p.V509I|FAM123C_uc010fmt.1_Missense_Mutation_p.V509I|FAM123C_uc010fmu.1_Missense_Mutation_p.V509I|FAM123C_uc010fmv.1_Missense_Mutation_p.V509I	NM_152698	NP_689911	Q8N944	F123C_HUMAN	hypothetical protein LOC205147	509										pancreas(2)|ovary(1)	3	Colorectal(110;0.1)													0.388889	37.738886	38.129078	14	22	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.13)	Missense_Mutation	SNP	131237640	131237640	5621	2	G	A	A	40	40	FAM123C	A	1	1
HECW2	57520	broad.mit.edu	36	2	196892122	196892122	+	Silent	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:196892122G>A	uc002utm.1	-	c.1737C>T	c.(1735-1737)GGC>GGT	p.G579G	HECW2_uc002utl.1_Silent_p.G223G	NM_020760	NP_065811	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin	579					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			ovary(5)|pancreas(1)|kidney(1)|central_nervous_system(1)|skin(1)	9														0.285714	73.510074	77.835141	30	75	GG		KEEP	---	---	---	---	capture			Silent	SNP	196892122	196892122	7326	2	G	A	A	38	38	HECW2	A	1	1
ALS2CR12	130540	broad.mit.edu	36	2	201862452	201862452	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0192-01	TCGA-06-0192-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:201862452A>C	uc010ftg.1	-	c.1184T>G	c.(1183-1185)ATC>AGC	p.I395S	ALS2CR12_uc002uya.2_Missense_Mutation_p.I372S|ALS2CR12_uc010fth.1_Non-coding_Transcript	NM_139163	NP_631902	Q96Q35	AL2SB_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	395	Potential.				regulation of GTPase activity		protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3														0.22807	144.295536	159.753497	52	176	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	201862452	201862452	556	2	A	C	C	12	12	ALS2CR12	C	4	4
TRPM8	79054	broad.mit.edu	36	2	234534359	234534359	+	Silent	SNP	C	A	A			TCGA-06-0192-01	TCGA-06-0192-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:234534359C>A	uc002vvh.1	+	c.1563C>A	c.(1561-1563)CTC>CTA	p.L521L	TRPM8_uc010fyj.1_Silent_p.L209L	NM_024080	NP_076985	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel,	521	Cytoplasmic (Potential).					integral to membrane					0		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)			Menthol(DB00825)					505				0.333333	100.43347	103.166404	37	74	CC		KEEP	---	---	---	---	capture		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Silent	SNP	234534359	234534359	17143	2	C	A	A	29	29	TRPM8	A	3	3
GOLGA4	2803	broad.mit.edu	36	3	37344041	37344041	+	Nonsense_Mutation	SNP	T	G	G			TCGA-06-0192-01	TCGA-06-0192-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:37344041T>G	uc003cgw.1	+	c.5726T>G	c.(5725-5727)TTA>TGA	p.L1909*	GOLGA4_uc003cgv.1_Nonsense_Mutation_p.L1887*|GOLGA4_uc010hgs.1_Intron|GOLGA4_uc003cgx.1_Nonsense_Mutation_p.L1768*|GOLGA4_uc010hgr.1_Nonsense_Mutation_p.L1448*	NM_002078	NP_002069	Q13439	GOGA4_HUMAN	golgi autoantigen, golgin subfamily a, 4	1887	Potential.|Glu-rich.				vesicle-mediated transport	Golgi membrane|trans-Golgi network				ovary(2)|breast(1)|central_nervous_system(1)	4														0.162791	10.578481	15.267975	7	36	TT		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	37344041	37344041	6824	3	T	G	G	61	61	GOLGA4	G	5	4
PCDHGB4	8641	broad.mit.edu	36	5	140749174	140749174	+	Silent	SNP	C	T	T			TCGA-06-0192-01	TCGA-06-0192-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140749174C>T	uc003lkc.1	+	c.1539C>T	c.(1537-1539)TTC>TTT	p.F513F	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGA8_uc003lkd.1_5'Flank|PCDHGB4_uc010jfy.1_Silent_p.F513F|PCDHGA8_uc003lkb.2_5'Flank	NM_003736	NP_003727	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4 isoform 1	513	Cadherin 5.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.230769	104.803433	118.628173	48	160	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Silent	SNP	140749174	140749174	11985	5	C	T	T	31	31	PCDHGB4	T	1	1
STK32A	202374	broad.mit.edu	36	5	146599407	146599407	+	Nonsense_Mutation	SNP	C	A	A			TCGA-06-0192-01	TCGA-06-0192-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:146599407C>A	uc010jgn.1	+	c.17C>A	c.(16-18)TCA>TAA	p.S6*	STK32A_uc003lol.2_Nonsense_Mutation_p.S6*|STK32A_uc003lom.2_Nonsense_Mutation_p.S6*	NM_001112724	NP_001106195	Q8WU08	ST32A_HUMAN	serine/threonine kinase 32A isoform 1	6					protein phosphorylation		ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|skin(1)	3										651				0.230769	6.817437	7.681678	3	10	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Nonsense_Mutation	SNP	146599407	146599407	15817	5	C	A	A	29	29	STK32A	A	5	3
WWC1	23286	broad.mit.edu	36	5	167801324	167801324	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:167801324G>A	uc003lzu.1	+	c.2340G>A	c.(2338-2340)TGG>TGA	p.W780*	WWC1_uc003lzv.1_Nonsense_Mutation_p.W686*|WWC1_uc003lzw.1_Nonsense_Mutation_p.W579*|WWC1_uc010jjf.1_Nonsense_Mutation_p.W47*	NM_015238	NP_056053	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	780	C2.				cell migration|positive regulation of MAPKKK cascade|regulation of hippo signaling cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|ruffle membrane	protein binding|transcription coactivator activity			ovary(2)|breast(1)	3	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)												0.222222	59.320253	68.281596	28	98	GG		KEEP	---	---	---	---	capture	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)	Nonsense_Mutation	SNP	167801324	167801324	17985	5	G	A	A	44	44	WWC1	A	5	2
TMEM174	134288	broad.mit.edu	36	5	72505744	72505744	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:72505744G>A	uc003kco.1	+	c.728G>A	c.(727-729)CGC>CAC	p.R243H	TMEM174_uc010izc.1_Missense_Mutation_p.R243H	NM_153217	NP_694949	Q8WUU8	TM174_HUMAN	transmembrane protein 174	243						integral to membrane				ovary(1)	1		Lung NSC(167;0.0378)|Ovarian(174;0.0908)|Prostate(461;0.165)												0.372263	133.947558	135.926089	51	86	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(47;1.46e-54)	Missense_Mutation	SNP	72505744	72505744	16624	5	G	A	A	38	38	TMEM174	A	1	1
SNX9	51429	broad.mit.edu	36	6	158251004	158251004	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0192-01	TCGA-06-0192-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:158251004C>T	uc003qqv.1	+	c.908C>T	c.(907-909)TCA>TTA	p.S303L		NM_016224	NP_057308	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	303	PX.				cell communication|intracellular protein transport|lipid tube assembly|positive regulation of GTPase activity|positive regulation of protein oligomerization|receptor-mediated endocytosis	clathrin-coated vesicle|cytoplasmic vesicle membrane|extrinsic to internal side of plasma membrane|ruffle|trans-Golgi network	1-phosphatidylinositol binding|protein homodimerization activity|ubiquitin protein ligase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)												0.195804	54.807752	67.152616	28	115	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)	Missense_Mutation	SNP	158251004	158251004	15409	6	C	T	T	29	29	SNX9	T	2	2
HLA-F	3134	broad.mit.edu	36	6	29799627	29799627	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0192-01	TCGA-06-0192-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:29799627A>G	uc003nno.2	+	c.278A>G	c.(277-279)CAG>CGG	p.Q93R	HLA-F_uc010jrl.1_Missense_Mutation_p.Q93R|HLA-F_uc003nnm.2_Missense_Mutation_p.Q93R	NM_001098479	NP_001091949	P30511	HLAF_HUMAN	major histocompatibility complex, class I, F	93	Alpha-1.|Extracellular (Potential).				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity				0														0.3	16.442681	17.157173	6	14	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29799627	29799627	7502	6	A	G	G	7	7	HLA-F	G	4	4
AGPAT1	10554	broad.mit.edu	36	6	32247071	32247071	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:32247071G>A	uc003oae.1	-	c.181C>T	c.(181-183)CGC>TGC	p.R61C	PPT2_uc003nzy.1_Non-coding_Transcript|AGPAT1_uc003oaf.1_Missense_Mutation_p.R61C|AGPAT1_uc003oag.1_Missense_Mutation_p.T54M|AGPAT1_uc003oah.1_Missense_Mutation_p.R61C|AGPAT1_uc003oai.1_Missense_Mutation_p.R61C	NM_006411	NP_116130	Q99943	PLCA_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 1	61					energy reserve metabolic process|phosphatidic acid biosynthetic process|positive regulation of cellular metabolic process|positive regulation of cytokine production|positive regulation of cytokine-mediated signaling pathway|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity			central_nervous_system(1)	1														0.319328	204.256102	211.138896	76	162	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32247071	32247071	389	6	G	A	A	40	40	AGPAT1	A	1	1
MAPK13	5603	broad.mit.edu	36	6	36207102	36207102	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:36207102G>A	uc003ols.1	+	c.196G>A	c.(196-198)GCC>ACC	p.A66T	MAPK13_uc003olt.1_Non-coding_Transcript	NM_002754	NP_002745	O15264	MK13_HUMAN	mitogen-activated protein kinase 13	66	Protein kinase.				cell cycle|intracellular protein kinase cascade|nerve growth factor receptor signaling pathway|Ras protein signal transduction|response to stress		ATP binding|MAP kinase activity|protein binding			breast(2)|central_nervous_system(1)	3										208				0.278912	97.582854	104.070953	41	106	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36207102	36207102	9658	6	G	A	A	38	38	MAPK13	A	1	1
TDRD6	221400	broad.mit.edu	36	6	46766962	46766962	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0192-01	TCGA-06-0192-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:46766962T>A	uc003oyj.1	+	c.3138T>A	c.(3136-3138)GAT>GAA	p.D1046E	TDRD6_uc010jze.1_Missense_Mutation_p.D1040E	NM_001010870	NP_001010870	O60522	TDRD6_HUMAN	tudor domain containing 6	1046	Tudor 5.				cell differentiation|multicellular organismal development|spermatogenesis	chromatoid body	nucleic acid binding			breast(3)|ovary(2)	5														0.413043	120.433463	121.040822	38	54	TT		KEEP	---	---	---	---	capture	Lung(136;0.192)		Missense_Mutation	SNP	46766962	46766962	16261	6	T	A	A	51	51	TDRD6	A	4	4
HIPK2	28996	broad.mit.edu	36	7	138966567	138966567	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:138966567G>A	uc003vvf.2	-	c.1231C>T	c.(1231-1233)CGG>TGG	p.R411W	HIPK2_uc003vvd.2_Missense_Mutation_p.R411W	NM_022740	NP_073577	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2 isoform	411	Protein kinase.|Interaction with DAXX.				apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation of BMP signaling pathway|positive regulation of JNK cascade|positive regulation of transforming growth factor beta receptor signaling pathway|SMAD protein signal transduction|transcription, DNA-dependent|virus-host interaction	centrosome|nuclear membrane|PML body	ATP binding|protein serine/threonine kinase activity|SMAD binding|transcription corepressor activity|virion binding			ovary(3)|central_nervous_system(3)|skin(1)	7	Melanoma(164;0.205)									363				0.2	13.131935	15.643912	6	24	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	138966567	138966567	7402	7	G	A	A	37	37	HIPK2	A	1	1
KEL	3792	broad.mit.edu	36	7	142368568	142368568	+	Splice_Site_SNP	SNP	C	T	T			TCGA-06-0192-01	TCGA-06-0192-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:142368568C>T	uc003wcb.1	-	c.223_splice	c.e3+1	p.R75_splice		NM_000420	NP_000411			Kell blood group, metallo-endopeptidase						proteolysis|vasoconstriction	integral to membrane|plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(3)|central_nervous_system(1)	4	Melanoma(164;0.059)													0.226277	72.560583	81.980974	31	106	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	142368568	142368568	8448	7	C	T	T	19	19	KEL	T	5	1
GPR141	353345	broad.mit.edu	36	7	37747318	37747318	+	Silent	SNP	C	T	T			TCGA-06-0192-01	TCGA-06-0192-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:37747318C>T	uc003tfm.1	+	c.798C>T	c.(796-798)AAC>AAT	p.N266N		NM_181791	NP_861456	Q7Z602	GP141_HUMAN	G protein-coupled receptor 141	266	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)	3									p.N266N(RPMI8226-Tumor)|p.N266N(COLO775-Tumor)	74				0.192857	114.890043	139.550098	54	226	CC		KEEP	---	---	---	---	capture			Silent	SNP	37747318	37747318	6923	7	C	T	T	19	19	GPR141	T	1	1
LAMC3	10319	broad.mit.edu	36	9	132917834	132917834	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0192-01	TCGA-06-0192-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:132917834C>T	uc004caa.1	+	c.1766C>T	c.(1765-1767)TCT>TTT	p.S589F		NM_006059	NP_006050	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3 precursor	589	Laminin IV type A.				cell adhesion	basement membrane|membrane	structural molecule activity			ovary(2)|pancreas(1)	3	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)										OREG0019556	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.17284	9.269093	17.593837	14	67	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)	Missense_Mutation	SNP	132917834	132917834	8939	9	C	T	T	32	32	LAMC3	T	2	2
PRUNE2	158471	broad.mit.edu	36	9	78512750	78512750	+	Silent	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:78512750G>A	uc010mpk.1	-	c.4260C>T	c.(4258-4260)TCC>TCT	p.S1420S		NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	1420					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0														0.164474	50.593193	66.827682	25	127	GG		KEEP	---	---	---	---	capture			Silent	SNP	78512750	78512750	13092	9	G	A	A	39	39	PRUNE2	A	1	1
NKAP	79576	broad.mit.edu	36	X	118961582	118961582	+	Silent	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:118961582G>A	uc004esh.1	-	c.15C>T	c.(13-15)TCC>TCT	p.S5S		NM_024528	NP_078804	Q8N5F7	NKAP_HUMAN	NFKB activating protein	5	Ser-rich.				Notch signaling pathway|positive regulation of alpha-beta T cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	chromatin binding|protein binding|transcription repressor activity			ovary(2)	2														0.318182	34.631184	35.926087	14	30	GG		KEEP	---	---	---	---	capture			Silent	SNP	118961582	118961582	10840	23	G	A	A	39	39	NKAP	A	1	1
CYBB	1536	broad.mit.edu	36	X	37548316	37548316	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:37548316G>A	uc004ddr.2	+	c.1140G>A	c.(1138-1140)TGG>TGA	p.W380*		NM_000397	NP_000388	P04839	CY24B_HUMAN	cytochrome b-245 beta polypeptide	380	Cytoplasmic (Potential).|FAD-binding FR-type.				electron transport chain|inflammatory response|innate immune response|respiratory burst|superoxide anion generation	NADPH oxidase complex	electron carrier activity|flavin adenine dinucleotide binding|heme binding|protein heterodimerization activity|superoxide-generating NADPH oxidase activity|voltage-gated ion channel activity			central_nervous_system(1)|skin(1)	2														0.42	61.565548	61.845017	21	29	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	37548316	37548316	4298	23	G	A	A	41	41	CYBB	A	5	2
ZCCHC5	203430	broad.mit.edu	36	X	77800519	77800519	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0192-01	TCGA-06-0192-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:77800519G>A	uc004edc.1	-	c.55C>T	c.(55-57)CGG>TGG	p.R19W	ZCCHC5_uc010nmd.1_Missense_Mutation_p.R19W	NM_152694	NP_689907	Q8N8U3	ZCHC5_HUMAN	zinc finger, CCHC domain containing 5	19							nucleic acid binding|zinc ion binding			ovary(1)	1														0.533333	48.399075	48.427843	16	14	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	77800519	77800519	18179	23	G	A	A	37	37	ZCCHC5	A	1	1
NF1	4763	broad.mit.edu	36	17	26701334	26701335	+	Frame_Shift_Ins	INS	-	A	A			TCGA-06-0192-01	TCGA-06-0192-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:26701334_26701335insA	uc002hgg.1	+	c.7329_7330insA	c.(7327-7332)CTTACAfs	p.L2443fs	NF1_uc002hgh.1_Frame_Shift_Ins_p.L2422fs|NF1_uc010cso.1_Frame_Shift_Ins_p.L631fs	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	2443_2444					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(1)		soft_tissue(155)|central_nervous_system(56)|large_intestine(27)|lung(19)|haematopoietic_and_lymphoid_tissue(13)|ovary(12)|autonomic_ganglia(7)|skin(3)|stomach(2)|breast(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	300		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)						847	TCGA GBM(6;<1E-8)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			0.38			23	37				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	26701334	26701335	10756	17	-	A	A	61	61	NF1	A	5	5
IRF5	3663	broad.mit.edu	36	7	128374603	128374617	+	Splice_Site_Del	DEL	ACTCTGCGGCCGCCT	-	-			TCGA-06-0192-01	TCGA-06-0192-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:128374603_128374617delACTCTGCGGCCGCCT	uc003vog.1	+	c.e7_splice_site			IRF5_uc010llr.1_In_Frame_Del_p.LCGRL162del|IRF5_uc010lls.1_In_Frame_Del_p.LCGRL162del|IRF5_uc003voh.1_Splice_Site_Del|IRF5_uc010llt.1_Intron|IRF5_uc003voi.1_Splice_Site_Del|IRF5_uc003vok.2_3'UTR|IRF5_uc010llu.1_In_Frame_Del_p.LCGRL162del|IRF5_uc003voj.2_Splice_Site_Del|IRF5_uc010llv.1_3'UTR|IRF5_uc010llw.1_In_Frame_Del_p.LCGRL162del	NM_002200	NP_002191			interferon regulatory factor 5 isoform a						interferon-gamma-mediated signaling pathway|regulation of transcription, DNA-dependent|type I interferon-mediated signaling pathway	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0														0.35			17	31				---	---	---	---	capture_indel			Splice_Site_Del	DEL	128374603	128374617	8136	7	ACTCTGCGGCCGCCT	-	-	6	6	IRF5	-	5	5
PCM1	5108	broad.mit.edu	36	8	17916505	17916506	+	Frame_Shift_Ins	INS	-	A	A			TCGA-06-0192-01	TCGA-06-0192-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:17916505_17916506insA	uc003wyi.2	+	c.5717_5718insA	c.(5716-5718)TTAfs	p.L1906fs	PCM1_uc003wyj.2_Intron|PCM1_uc003wyk.2_Frame_Shift_Ins_p.L588fs	NM_006197	NP_006188	Q15154	PCM1_HUMAN	pericentriolar material 1	1906					centrosome organization|cilium assembly|G2/M transition of mitotic cell cycle|interkinetic nuclear migration|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome	centriolar satellite|cytosol|nuclear membrane|pericentriolar material	identical protein binding		PCM1/JAK2(30)	haematopoietic_and_lymphoid_tissue(30)|ovary(2)|breast(1)	33				Colorectal(111;0.0789)						797				0.42			14	19				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	17916505	17916506	12004	8	-	A	A	61	61	PCM1	A	5	5
