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
ACADSB	36	broad.mit.edu	36	10	124800694	124800694	+	Splice_Site_SNP	SNP	T	A	A			TCGA-06-0119-01	TCGA-06-0119-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:124800694T>A	uc001lhb.1	+	c.1128_splice	c.e9+2	p.E376_splice		NM_001609	NP_001600			acyl-Coenzyme A dehydrogenase, short/branched						branched chain family amino acid catabolic process|fatty acid metabolic process|oxidation-reduction process	mitochondrial matrix	flavin adenine dinucleotide binding			ovary(1)|central_nervous_system(1)	2		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)			L-Isoleucine(DB00167)									0.2	6.517576	7.772368	3	12	TT		KEEP	---	---	---	---	capture		Colorectal(40;0.0811)|COAD - Colon adenocarcinoma(40;0.0835)	Splice_Site_SNP	SNP	124800694	124800694	116	10	T	A	A	57	57	ACADSB	A	5	4
NAV2	89797	broad.mit.edu	36	11	19858100	19858100	+	Silent	SNP	G	C	C			TCGA-06-0119-01	TCGA-06-0119-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:19858100G>C	uc009yhw.1	+	c.621G>C	c.(619-621)CCG>CCC	p.P207P	NAV2_uc001mpp.1_Silent_p.P143P|NAV2_uc001mpr.2_Silent_p.P207P	NM_182964	NP_892009	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 1	207	Gln-rich.					nucleus	ATP binding|helicase activity			ovary(1)|pancreas(1)	2														0.275862	8.416853	9.872213	8	21	GG		KEEP	---	---	---	---	capture			Silent	SNP	19858100	19858100	10580	11	G	C	C	38	38	NAV2	C	3	3
NAT10	55226	broad.mit.edu	36	11	34086440	34086440	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0119-01	TCGA-06-0119-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:34086440A>C	uc001mvk.1	+	c.92A>C	c.(91-93)GAT>GCT	p.D31A		NM_024662	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 isoform a	31						nucleolus	ATP binding|N-acetyltransferase activity|protein binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)												0.090452	15.106291	48.758782	18	181	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	34086440	34086440	10570	11	A	C	C	12	12	NAT10	C	4	4
OR8K3	219473	broad.mit.edu	36	11	55842682	55842682	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0119-01	TCGA-06-0119-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55842682T>G	uc001niq.1	+	c.324T>G	c.(322-324)ATT>ATG	p.I108M		NM_001005202	NP_001005202	Q8NH51	OR8K3_HUMAN	olfactory receptor, family 8, subfamily K,	108	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|large_intestine(1)|central_nervous_system(1)	4	Esophageal squamous(21;0.00448)													0.084337	9.822098	38.931775	14	152	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55842682	55842682	11655	11	T	G	G	63	63	OR8K3	G	4	4
OR56A4	120793	broad.mit.edu	36	11	5980236	5980236	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0119-01	TCGA-06-0119-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:5980236G>A	uc001mce.1	-	c.719C>T	c.(718-720)TCC>TTC	p.S240F		NM_001005179	NP_001005179	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, subfamily A,	188	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)												0.139241	17.06677	27.005453	11	68	GG		KEEP	---	---	---	---	capture		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	Missense_Mutation	SNP	5980236	5980236	11545	11	G	A	A	41	41	OR56A4	A	2	2
SLCO1A2	6579	broad.mit.edu	36	12	21348714	21348714	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0119-01	TCGA-06-0119-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:21348714C>T	uc001rer.1	-	c.503G>A	c.(502-504)CGT>CAT	p.R168H	SLCO1A2_uc001res.1_Missense_Mutation_p.R168H|SLCO1A2_uc001ret.1_Missense_Mutation_p.R166H|SLCO1A2_uc001reu.1_Missense_Mutation_p.R148H	NM_021094	NP_602307	P46721	SO1A2_HUMAN	organic anion transporting polypeptide A	168	Helical; Name=4; (Potential).				bile acid metabolic process|sodium-independent organic anion transport	integral to membrane|plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(1)|ovary(1)|pancreas(1)	3														0.108696	12.122214	33.064202	15	123	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21348714	21348714	15219	12	C	T	T	19	19	SLCO1A2	T	1	1
DDX11	1663	broad.mit.edu	36	12	31146627	31146627	+	Splice_Site_SNP	SNP	G	T	T			TCGA-06-0119-01	TCGA-06-0119-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:31146627G>T	uc001rjt.1	+	c.2272_splice	c.e23-1	p.A758_splice	DDX11_uc001rjr.1_Splice_Site_SNP_p.A758_splice|DDX11_uc001rjs.1_Splice_Site_SNP_p.A708_splice|DDX11_uc001rju.1_Splice_Site_SNP_p.A430_splice|DDX11_uc001rjv.1_Splice_Site_SNP_p.A758_splice|DDX11_uc001rjw.1_Splice_Site_SNP_p.A732_splice|DDX11_uc009zjn.1_Splice_Site_SNP|DDX11_uc009zjo.1_5'Flank	NM_152438	NP_689651			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11						G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitotic sister chromatid segregation|positive regulation of cell proliferation|S phase of mitotic cell cycle|sister chromatid cohesion	midbody|nuclear chromatin|nucleolus|spindle pole	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|RNA binding			breast(3)	3	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)										Multiple Myeloma(12;0.14)			0.113333	15.560244	37.699884	17	133	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	31146627	31146627	4514	12	G	T	T	35	35	DDX11	T	5	3
NUP107	57122	broad.mit.edu	36	12	67411188	67411188	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0119-01	TCGA-06-0119-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:67411188T>C	uc001suf.1	+	c.1766T>C	c.(1765-1767)ATA>ACA	p.I589T	NUP107_uc001sug.1_Intron	NM_020401	NP_065134	P57740	NU107_HUMAN	nucleoporin 107kDa	589					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding				0	Breast(13;6.25e-06)													0.1	9.542384	22.324742	8	72	TT		KEEP	---	---	---	---	capture	Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)		Missense_Mutation	SNP	67411188	67411188	11158	12	T	C	C	49	49	NUP107	C	4	4
TRHDE	29953	broad.mit.edu	36	12	71301216	71301216	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0119-01	TCGA-06-0119-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:71301216T>A	uc001sxa.1	+	c.2396T>A	c.(2395-2397)TTT>TAT	p.F799Y		NM_013381	NP_037513	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	799	Extracellular (Potential).				cell-cell signaling|proteolysis|signal transduction	integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(2)	2														0.125984	18.70702	36.057265	16	111	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71301216	71301216	17023	12	T	A	A	64	64	TRHDE	A	4	4
FLT3	2322	broad.mit.edu	36	13	27490705	27490705	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0119-01	TCGA-06-0119-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:27490705C>T	uc001urw.1	-	c.2440G>A	c.(2440-2442)GCC>ACC	p.A814T	FLT3_uc010aao.1_Non-coding_Transcript	NM_004119	NP_004110	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	814	Protein kinase.|Cytoplasmic (Potential).				positive regulation of cell proliferation	integral to plasma membrane	ATP binding|vascular endothelial growth factor receptor activity			haematopoietic_and_lymphoid_tissue(8072)|ovary(2)|lung(1)|central_nervous_system(1)	8076	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)			Sorafenib(DB00398)|Sunitinib(DB01268)					630				0.110236	13.255001	32.348071	14	113	CC		KEEP	---	---	---	---	capture	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Missense_Mutation	SNP	27490705	27490705	6184	13	C	T	T	27	27	FLT3	T	1	1
JAG2	3714	broad.mit.edu	36	14	104685721	104685721	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0119-01	TCGA-06-0119-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:104685721C>G	uc001yqg.1	-	c.2121G>C	c.(2119-2121)AAG>AAC	p.K707N	JAG2_uc010axf.1_5'Flank|JAG2_uc001yqf.1_Missense_Mutation_p.K111N|JAG2_uc001yqh.1_Missense_Mutation_p.K669N	NM_002226	NP_002217	Q9Y219	JAG2_HUMAN	jagged 2 isoform a precursor	707	Extracellular (Potential).|EGF-like 12; calcium-binding (Potential).				auditory receptor cell fate commitment|cell communication|cell cycle|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation|spermatogenesis|thymic T cell selection	integral to plasma membrane	calcium ion binding|growth factor activity|Notch binding			lung(3)	3		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)								501				0.333333	6.420121	6.642467	3	6	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)	Missense_Mutation	SNP	104685721	104685721	8239	14	C	G	G	32	32	JAG2	G	3	3
YLPM1	56252	broad.mit.edu	36	14	74334508	74334508	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0119-01	TCGA-06-0119-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:74334508G>A	uc001xqj.2	+	c.2755G>A	c.(2755-2757)GTA>ATA	p.V919I	YLPM1_uc001xql.2_Non-coding_Transcript	NM_019589	NP_062535	P49750	YLPM1_HUMAN	YLP motif containing 1	724					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3														0.147059	7.799062	11.830216	5	29	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)	Missense_Mutation	SNP	74334508	74334508	18069	14	G	A	A	40	40	YLPM1	A	1	1
SETD3	84193	broad.mit.edu	36	14	98936244	98936244	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0119-01	TCGA-06-0119-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:98936244G>A	uc001ygc.1	-	c.1283C>T	c.(1282-1284)ACA>ATA	p.T428I		NM_032233	NP_115609	Q86TU7	SETD3_HUMAN	SET domain containing 3 isoform a	428					peptidyl-lysine dimethylation|peptidyl-lysine monomethylation|peptidyl-lysine trimethylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone methyltransferase activity (H3-K36 specific)|transcription coactivator activity				0		all_cancers(154;0.224)|all_epithelial(191;0.0644)|Melanoma(154;0.0866)												0.142857	15.633187	25.97776	12	72	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	98936244	98936244	14621	14	G	A	A	48	48	SETD3	A	2	2
CHD9	80205	broad.mit.edu	36	16	51884416	51884416	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0119-01	TCGA-06-0119-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:51884416G>A	uc002ehb.1	+	c.5461G>A	c.(5461-5463)GAA>AAA	p.E1821K	CHD9_uc002egy.1_Missense_Mutation_p.E1821K|CHD9_uc002ehc.1_Missense_Mutation_p.E1821K|CHD9_uc002ehf.1_Missense_Mutation_p.E935K|CHD9_uc010cbw.1_Missense_Mutation_p.E189K	NM_025134	NP_079410	Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	1821					cellular lipid metabolic process|chromatin assembly or disassembly|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|cytoplasm|nucleoplasm	ATP binding|chromatin binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)								1157				0.333333	10.24098	10.797292	7	14	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51884416	51884416	3466	16	G	A	A	41	41	CHD9	A	2	2
PRR25	388199	broad.mit.edu	36	16	795855	795855	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0119-01	TCGA-06-0119-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:795855T>G	uc002cki.1	+	c.412T>G	c.(412-414)TGG>GGG	p.W138G		NM_001013638	NP_001013660	Q96S07	PRR25_HUMAN	hypothetical protein LOC388199	138	Pro-rich.									large_intestine(1)	1														0.3125	6.485517	7.037589	5	11	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	795855	795855	13046	16	T	G	G	55	55	PRR25	G	4	4
NUFIP2	57532	broad.mit.edu	36	17	24638124	24638124	+	Silent	SNP	T	C	C			TCGA-06-0119-01	TCGA-06-0119-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:24638124T>C	uc002hdy.2	-	c.1014A>G	c.(1012-1014)AAA>AAG	p.K338K	NUFIP2_uc002hdx.2_Intron	NM_020772	NP_065823	Q7Z417	NUFP2_HUMAN	nuclear fragile X mental retardation protein	338						nucleus|polysomal ribosome	protein binding|RNA binding			ovary(1)|breast(1)	2														0.125984	54.124279	88.811555	32	222	TT		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(11;0.000457)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)		Silent	SNP	24638124	24638124	11154	17	T	C	C	60	60	NUFIP2	C	4	4
NF1	4763	broad.mit.edu	36	17	26580289	26580289	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0119-01	TCGA-06-0119-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:26580289C>T	uc002hgg.1	+	c.2530C>T	c.(2530-2532)CTT>TTT	p.L844F	NF1_uc002hgh.1_Missense_Mutation_p.L844F|NF1_uc002hgi.1_5'UTR|NF1_uc010csn.1_Missense_Mutation_p.L704F	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	844			L -> F (in NF1).|L -> P (in NF1).|L -> R (in NF1; sporadic).		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.?(3)		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)								847	TCGA GBM(6;<1E-8)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			0.189873	31.370531	38.487085	15	64	CC		KEEP	---	---	---	---	capture		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)	Missense_Mutation	SNP	26580289	26580289	10756	17	C	T	T	24	24	NF1	T	2	2
GAS2L2	246176	broad.mit.edu	36	17	31097294	31097294	+	Silent	SNP	G	A	A			TCGA-06-0119-01	TCGA-06-0119-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:31097294G>A	uc002hjv.1	-	c.1335C>T	c.(1333-1335)GCC>GCT	p.A445A		NM_139285	NP_644814	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	445					cell cycle arrest	cytoplasm|cytoskeleton				ovary(1)|skin(1)	2		Ovarian(249;0.17)												0.100386	18.910629	60.171344	26	233	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)	Silent	SNP	31097294	31097294	6511	17	G	A	A	47	47	GAS2L2	A	2	2
KRT28	162605	broad.mit.edu	36	17	36206768	36206768	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0119-01	TCGA-06-0119-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36206768C>T	uc002hvh.1	-	c.904G>A	c.(904-906)GCC>ACC	p.A302T		NM_181535	NP_853513	Q7Z3Y7	K1C28_HUMAN	keratin 25D	302	Rod.|Coil 2.					cytoplasm|intermediate filament	structural molecule activity			ovary(1)	1		Breast(137;0.000301)				Melanoma(19;789 869 15380 26882 39836)								0.125	15.906414	30.19295	13	91	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36206768	36206768	8780	17	C	T	T	27	27	KRT28	T	1	1
MTMR4	9110	broad.mit.edu	36	17	53936410	53936410	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0119-01	TCGA-06-0119-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:53936410C>A	uc002iwj.1	-	c.1656G>T	c.(1654-1656)ATG>ATT	p.M552I		NM_004687	NP_004678	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	552	Myotubularin phosphatase.					cytoplasm|membrane	protein tyrosine phosphatase activity|zinc ion binding			skin(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)													0.169643	36.551891	48.12442	19	93	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53936410	53936410	10339	17	C	A	A	21	21	MTMR4	A	3	3
MTMR4	9110	broad.mit.edu	36	17	53940837	53940837	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0119-01	TCGA-06-0119-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:53940837C>T	uc002iwj.1	-	c.542G>A	c.(541-543)AGC>AAC	p.S181N		NM_004687	NP_004678	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	181	Myotubularin phosphatase.					cytoplasm|membrane	protein tyrosine phosphatase activity|zinc ion binding			skin(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)													0.119048	11.284958	23.260661	10	74	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53940837	53940837	10339	17	C	T	T	28	28	MTMR4	T	2	2
GH1	2688	broad.mit.edu	36	17	59348884	59348884	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0119-01	TCGA-06-0119-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:59348884C>T	uc002jdj.1	-	c.424G>A	c.(424-426)GAC>AAC	p.D142N	GH1_uc002jdi.1_Missense_Mutation_p.D127N|GH1_uc002jdk.1_Missense_Mutation_p.D102N|GH1_uc002jdl.1_Intron|GH1_uc002jdm.1_Intron|GH1_uc002jdn.2_Intron	NM_000515	NP_000506	P01241	SOMA_HUMAN	growth hormone 1 isoform 1	142					glucose transport|growth hormone receptor signaling pathway|JAK-STAT cascade|positive regulation of activation of JAK2 kinase activity|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of MAP kinase activity|positive regulation of multicellular organism growth|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|response to estradiol stimulus	extracellular space	growth factor activity|growth hormone receptor binding|hormone activity|metal ion binding|prolactin receptor binding				0										99				0.104478	9.821554	30.7617	14	120	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59348884	59348884	6635	17	C	T	T	30	30	GH1	T	2	2
FADS6	283985	broad.mit.edu	36	17	70390340	70390340	+	Silent	SNP	C	T	T			TCGA-06-0119-01	TCGA-06-0119-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:70390340C>T	uc002jmd.1	-	c.453G>A	c.(451-453)ACG>ACA	p.T151T		NM_178128	NP_835229	Q8N9I5	FADS6_HUMAN	fatty acid desaturase domain family, member 6	157					fatty acid biosynthetic process|oxidation-reduction process	integral to membrane	oxidoreductase activity				0	all_lung(278;0.172)|Lung NSC(278;0.207)													0.25	10.39282	11.30144	4	12	CC		KEEP	---	---	---	---	capture			Silent	SNP	70390340	70390340	5565	17	C	T	T	19	19	FADS6	T	1	1
SLC26A11	284129	broad.mit.edu	36	17	75810090	75810090	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0119-01	TCGA-06-0119-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:75810090C>T	uc002jyb.1	+	c.136C>T	c.(136-138)CAG>TAG	p.Q46*	SGSH_uc002jxz.2_5'Flank|SGSH_uc002jya.2_5'Flank|SGSH_uc002jxy.2_5'Flank|SLC26A11_uc002jyc.1_Nonsense_Mutation_p.Q46*|SLC26A11_uc002jyd.1_Nonsense_Mutation_p.Q46*|SLC26A11_uc010dhv.1_Nonsense_Mutation_p.Q46*	NM_173626	NP_775897	Q86WA9	S2611_HUMAN	solute carrier family 26, member 11	46	Extracellular (Potential).					endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosomal membrane|plasma membrane	anion:anion antiporter activity|secondary active sulfate transmembrane transporter activity				0	all_neural(118;0.0538)													0.25	19.35769	21.403655	9	27	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(97;0.0344)|BRCA - Breast invasive adenocarcinoma(99;0.0908)		Nonsense_Mutation	SNP	75810090	75810090	15013	17	C	T	T	25	25	SLC26A11	T	5	2
ANO8	57719	broad.mit.edu	36	19	17297028	17297028	+	Silent	SNP	G	A	A			TCGA-06-0119-01	TCGA-06-0119-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:17297028G>A	uc002ngf.1	-	c.2829C>T	c.(2827-2829)TCC>TCT	p.S943S	ANO8_uc010eap.1_Non-coding_Transcript	NM_020959	NP_066010	Q9HCE9	ANO8_HUMAN	anoctamin 8	943	Extracellular (Potential).					chloride channel complex	chloride channel activity			ovary(3)	3														0.122222	14.698087	27.244044	11	79	GG		KEEP	---	---	---	---	capture			Silent	SNP	17297028	17297028	711	19	G	A	A	39	39	ANO8	A	1	1
NTF4	4909	broad.mit.edu	36	19	54256786	54256786	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0119-01	TCGA-06-0119-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:54256786A>C	uc002pmf.2	-	c.281T>G	c.(280-282)CTG>CGG	p.L94R	NTF4_uc010emr.1_Missense_Mutation_p.L94R	NM_006179	NP_006170	P34130	NTF4_HUMAN	neurotrophin 5 preproprotein	94					adult locomotory behavior|epidermis development|ganglion mother cell fate determination|long-term memory|sensory organ boundary specification	endoplasmic reticulum lumen|extracellular region	growth factor activity				0		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_epithelial(76;3.83e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)												0.15	7.41677	12.130128	6	34	AA		KEEP	---	---	---	---	capture		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)	Missense_Mutation	SNP	54256786	54256786	11102	19	A	C	C	7	7	NTF4	C	4	4
KLK6	5653	broad.mit.edu	36	19	56158483	56158483	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0119-01	TCGA-06-0119-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:56158483C>T	uc002puh.1	-	c.359G>A	c.(358-360)CGC>CAC	p.R120H	KLK6_uc010eoj.1_Intron|KLK6_uc002puj.1_Missense_Mutation_p.R4H|KLK6_uc002puk.1_Missense_Mutation_p.A14T|KLK6_uc002pul.1_Missense_Mutation_p.R111H|KLK6_uc002pum.1_Missense_Mutation_p.R4H|KLK6_uc002pui.1_Missense_Mutation_p.R111H	NM_001012965	NP_001012983	Q92876	KLK6_HUMAN	kallikrein-related peptidase 6 isoform B	111	Peptidase S1.				amyloid precursor protein metabolic process|central nervous system development|collagen catabolic process|hormone metabolic process|myelination|positive regulation of G-protein coupled receptor protein signaling pathway|protein autoprocessing|proteolysis|regulation of cell differentiation|tissue regeneration	endoplasmic reticulum|extracellular region|microsome|mitochondrion|nucleolus	protein binding|serine-type endopeptidase activity				0		all_neural(266;0.026)												0.176471	20.509466	27.18269	12	56	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00372)|GBM - Glioblastoma multiforme(134;0.00871)	Missense_Mutation	SNP	56158483	56158483	8722	19	C	T	T	27	27	KLK6	T	1	1
SPAG17	200162	broad.mit.edu	36	1	118425686	118425686	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0119-01	TCGA-06-0119-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:118425686C>G	uc001ehk.1	-	c.1865G>C	c.(1864-1866)GGG>GCG	p.G622A		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	622						cilium|flagellar axoneme|microtubule				ovary(2)|large_intestine(1)	3	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)												0.125561	35.832881	66.386218	28	195	CC		KEEP	---	---	---	---	capture		Lung(183;0.0858)	Missense_Mutation	SNP	118425686	118425686	15482	1	C	G	G	22	22	SPAG17	G	3	3
ADAM30	11085	broad.mit.edu	36	1	120239867	120239867	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0119-01	TCGA-06-0119-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:120239867C>G	uc001eij.1	-	c.616G>C	c.(616-618)GAA>CAA	p.E206Q		NM_021794	NP_068566	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30 preproprotein	206	Peptidase M12B.|Extracellular (Potential).				proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			ovary(2)|lung(1)	3	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138)												0.119403	25.600484	44.659133	16	118	CC		KEEP	---	---	---	---	capture		Lung(183;0.0204)|LUSC - Lung squamous cell carcinoma(189;0.117)	Missense_Mutation	SNP	120239867	120239867	249	1	C	G	G	30	30	ADAM30	G	3	3
HMCN1	83872	broad.mit.edu	36	1	184322978	184322978	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0119-01	TCGA-06-0119-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:184322978G>A	uc001grq.1	+	c.9053G>A	c.(9052-9054)CGA>CAA	p.R3018Q		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1	3018	Ig-like C2-type 28.				bioluminescence|protein-chromophore linkage|response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)	22														0.119048	19.088136	36.995908	15	111	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	184322978	184322978	7511	1	G	A	A	37	37	HMCN1	A	1	1
COG2	22796	broad.mit.edu	36	1	228873935	228873935	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0119-01	TCGA-06-0119-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:228873935G>C	uc001htw.1	+	c.825G>C	c.(823-825)ATG>ATC	p.M275I	COG2_uc001htx.1_Missense_Mutation_p.M275I	NM_007357	NP_031383	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2 isoform	275					Golgi organization|intra-Golgi vesicle-mediated transport|intracellular protein transport|oligosaccharide biosynthetic process|protein glycosylation	Golgi membrane|Golgi stack|Golgi transport complex	protein binding|protein transporter activity				0	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)												0.148148	58.569425	81.031423	28	161	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	228873935	228873935	3796	1	G	C	C	48	48	COG2	C	3	3
TEKT2	27285	broad.mit.edu	36	1	36326363	36326363	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0119-01	TCGA-06-0119-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:36326363G>C	uc001bzr.1	+	c.1282G>C	c.(1282-1284)GAG>CAG	p.E428Q	TEKT2_uc001bzs.1_Missense_Mutation_p.E334Q|ADPRHL2_uc001bzt.1_5'Flank|ADPRHL2_uc001bzu.1_5'Flank	NM_014466	NP_055281	Q9UIF3	TEKT2_HUMAN	tektin 2	428					cell projection organization|microtubule cytoskeleton organization	actin cytoskeleton|cilium axoneme|flagellar axoneme|focal adhesion|microtubule|nucleolus					0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)												0.153846	7.682049	10.66156	4	22	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36326363	36326363	16280	1	G	C	C	41	41	TEKT2	C	3	3
SLC35C2	51006	broad.mit.edu	36	20	44412522	44412522	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0119-01	TCGA-06-0119-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:44412522A>G	uc002xro.1	-	c.1016T>C	c.(1015-1017)CTG>CCG	p.L339P	SLC35C2_uc002xrp.1_Missense_Mutation_p.L318P|SLC35C2_uc002xrq.1_Missense_Mutation_p.L339P|SLC35C2_uc002xrr.1_Missense_Mutation_p.L339P	NM_173179	NP_775271	Q9NQQ7	S35C2_HUMAN	solute carrier family 35, member C2 isoform a	339					transport	integral to membrane				ovary(1)	1		Myeloproliferative disorder(115;0.0122)												0.096774	7.436473	22.560928	9	84	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44412522	44412522	15077	20	A	G	G	7	7	SLC35C2	G	4	4
PKDREJ	10343	broad.mit.edu	36	22	45035670	45035670	+	Silent	SNP	G	A	A			TCGA-06-0119-01	TCGA-06-0119-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:45035670G>A	uc003bhh.1	-	c.2214C>T	c.(2212-2214)ATC>ATT	p.I738I		NM_006071	NP_006062	Q9NTG1	PKDRE_HUMAN	receptor for egg jelly-like protein precursor	738	Extracellular (Potential).|REJ.				acrosome reaction|neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity			breast(3)|ovary(2)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)												0.145455	39.408752	59.342811	24	141	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)	Silent	SNP	45035670	45035670	12395	22	G	A	A	37	37	PKDREJ	A	1	1
TTN	7273	broad.mit.edu	36	2	179171771	179171771	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0119-01	TCGA-06-0119-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179171771C>T	uc002umr.1	-	c.49207G>A	c.(49207-49209)GTG>ATG	p.V16403M	TTN_uc002ums.1_Missense_Mutation_p.V10098M|TTN_uc010frc.1_Missense_Mutation_p.V10031M|TTN_uc010frd.1_Missense_Mutation_p.V9906M	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	17330										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153										8722				0.161417	74.747596	102.423507	41	213	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179171771	179171771	17290	2	C	T	T	19	19	TTN	T	1	1
COL6A3	1293	broad.mit.edu	36	2	237950265	237950265	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0119-01	TCGA-06-0119-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:237950265C>T	uc002vwl.2	-	c.2959G>A	c.(2959-2961)GTG>ATG	p.V987M	COL6A3_uc002vwk.2_Missense_Mutation_p.V987M|COL6A3_uc002vwm.2_Missense_Mutation_p.V786M|COL6A3_uc002vwn.2_Missense_Mutation_p.V787M|COL6A3_uc002vwo.2_Missense_Mutation_p.V781M|COL6A3_uc002vwq.2_Missense_Mutation_p.V781M|COL6A3_uc002vwr.2_Missense_Mutation_p.V580M	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	987	Nonhelical region.|VWFA 5.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|pancreas(1)	15		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)												0.128788	44.310322	79.713156	34	230	CC		KEEP	---	---	---	---	capture		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)	Missense_Mutation	SNP	237950265	237950265	3839	2	C	T	T	19	19	COL6A3	T	1	1
C2orf16	84226	broad.mit.edu	36	2	27654877	27654877	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0119-01	TCGA-06-0119-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:27654877T>C	uc002rkz.2	+	c.1934T>C	c.(1933-1935)GTA>GCA	p.V645A		NM_032266	NP_115642	Q68DN1	CB016_HUMAN	hypothetical protein LOC84226	645										large_intestine(1)	1	Acute lymphoblastic leukemia(172;0.155)													0.137615	30.056689	43.896249	15	94	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27654877	27654877	2243	2	T	C	C	57	57	C2orf16	C	4	4
KIAA1109	84162	broad.mit.edu	36	4	123420436	123420436	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0119-01	TCGA-06-0119-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:123420436G>T	uc003ieh.1	+	c.8648G>T	c.(8647-8649)GGG>GTG	p.G2883V	KIAA1109_uc003iel.1_Missense_Mutation_p.G818V	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	hypothetical protein LOC84162	2883					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(7)|central_nervous_system(1)|pancreas(1)	9														0.151786	22.988874	36.016477	17	95	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	123420436	123420436	8516	4	G	T	T	43	43	KIAA1109	T	3	3
KCTD16	57528	broad.mit.edu	36	5	143566763	143566763	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0119-01	TCGA-06-0119-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:143566763A>T	uc003lnm.1	+	c.293A>T	c.(292-294)GAT>GTT	p.D98V	KCTD16_uc003lnn.1_Missense_Mutation_p.D98V	NM_020768	NP_065819	Q68DU8	KCD16_HUMAN	potassium channel tetramerisation domain	98	BTB.					cell junction|postsynaptic membrane|presynaptic membrane|voltage-gated potassium channel complex	voltage-gated potassium channel activity			large_intestine(2)|ovary(1)	3		all_hematologic(541;0.118)												0.21875	31.134365	35.786942	14	50	AA		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Missense_Mutation	SNP	143566763	143566763	8409	5	A	T	T	12	12	KCTD16	T	4	4
ADAMTS16	170690	broad.mit.edu	36	5	5315847	5315847	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0119-01	TCGA-06-0119-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:5315847C>T	uc003jdl.1	+	c.2740C>T	c.(2740-2742)CGA>TGA	p.R914*	ADAMTS16_uc003jdk.1_Nonsense_Mutation_p.R914*	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1	914	TSP type-1 2.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8														0.104651	7.232071	20.583239	9	77	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	5315847	5315847	262	5	C	T	T	19	19	ADAMTS16	T	5	1
THEMIS	387357	broad.mit.edu	36	6	128176582	128176582	+	Silent	SNP	G	A	A			TCGA-06-0119-01	TCGA-06-0119-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:128176582G>A	uc003qbi.1	-	c.897C>T	c.(895-897)AGC>AGT	p.S299S	THEMIS_uc010kfa.1_Silent_p.S202S|THEMIS_uc010kfb.1_Silent_p.S264S	NM_001010923	NP_001010923	Q8N1K5	THMS1_HUMAN	hypothetical protein LOC387357	299	CABIT 2.				negative T cell selection|positive T cell selection|T cell receptor signaling pathway	cytoplasm|nucleus				ovary(2)	2														0.128713	29.085299	56.264668	26	176	GG		KEEP	---	---	---	---	capture			Silent	SNP	128176582	128176582	16388	6	G	A	A	46	46	THEMIS	A	2	2
OR12D2	26529	broad.mit.edu	36	6	29472535	29472535	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0119-01	TCGA-06-0119-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:29472535T>C	uc003nmf.2	+	c.80T>C	c.(79-81)GTG>GCG	p.V27A		NM_013936	NP_039224	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D,	27	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.117391	27.06149	60.174156	27	203	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29472535	29472535	11337	6	T	C	C	59	59	OR12D2	C	4	4
OR2A12	346525	broad.mit.edu	36	7	143423515	143423515	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0119-01	TCGA-06-0119-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:143423515C>A	uc003wdw.1	+	c.382C>A	c.(382-384)CCC>ACC	p.P128T		NM_001004135	NP_001004135	Q8NGT7	O2A12_HUMAN	olfactory receptor, family 2, subfamily A,	128	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3	Melanoma(164;0.0783)													0.12	33.345893	68.7047	30	220	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	143423515	143423515	11381	7	C	A	A	22	22	OR2A12	A	3	3
PKD1L1	168507	broad.mit.edu	36	7	47833581	47833581	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0119-01	TCGA-06-0119-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:47833581G>C	uc003tny.1	-	c.6746C>G	c.(6745-6747)GCC>GGC	p.A2249G	C7orf69_uc003toa.1_Intron|PKD1L1_uc003tob.2_5'UTR	NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1	2249	Cytoplasmic (Potential).				cell-cell adhesion	integral to membrane				ovary(7)|breast(1)	8														0.230769	10.953023	12.670507	6	20	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47833581	47833581	12388	7	G	C	C	42	42	PKD1L1	C	3	3
FAM164A	51101	broad.mit.edu	36	8	79753470	79753470	+	Splice_Site_SNP	SNP	G	A	A			TCGA-06-0119-01	TCGA-06-0119-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:79753470G>A	uc003ybd.1	+	c.210_splice	c.e3+1	p.R70_splice		NM_016010	NP_057094			hypothetical protein LOC51101											ovary(1)	1														0.137255	30.265488	49.752472	21	132	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	79753470	79753470	5682	8	G	A	A	44	44	FAM164A	A	5	2
RAD54B	25788	broad.mit.edu	36	8	95473069	95473069	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0119-01	TCGA-06-0119-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:95473069T>A	uc003ygk.1	-	c.1753A>T	c.(1753-1755)ATA>TTA	p.I585L	RAD54B_uc003ygl.1_Non-coding_Transcript|RAD54B_uc010may.1_Missense_Mutation_p.I392L	NM_012415	NP_036547	Q9Y620	RA54B_HUMAN	RAD54 homolog B	585					mitotic recombination|reciprocal meiotic recombination	nucleus	ATP binding|DNA binding|DNA helicase activity|RNA helicase activity			kidney(2)|lung(1)	3	Breast(36;4.5e-05)													0.110294	31.556755	72.437453	30	242	TT		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(8;0.00217)		Missense_Mutation	SNP	95473069	95473069	13452	8	T	A	A	49	49	RAD54B	A	4	4
MEGF9	1955	broad.mit.edu	36	9	122424762	122424762	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0119-01	TCGA-06-0119-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:122424762A>G	uc004bkj.1	-	c.1007T>C	c.(1006-1008)TTG>TCG	p.L336S		NM_001080497	NP_001073966	Q9H1U4	MEGF9_HUMAN	multiple EGF-like-domains 9	299	Laminin EGF-like 2.|Extracellular (Potential).					integral to membrane	calcium ion binding|receptor activity				0														0.173913	7.221029	9.50399	4	19	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	122424762	122424762	9853	9	A	G	G	5	5	MEGF9	G	4	4
LHX3	8022	broad.mit.edu	36	9	138232348	138232348	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0119-01	TCGA-06-0119-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:138232348C>A	uc004cgz.1	-	c.167G>T	c.(166-168)TGG>TTG	p.W56L	LHX3_uc004cha.1_Missense_Mutation_p.W51L	NM_014564	NP_055379	Q9UBR4	LHX3_HUMAN	LIM homeobox protein 3 isoform b	51	LIM zinc-binding 1.				inner ear development|organ morphogenesis|regulation of transcription, DNA-dependent	nucleus	RNA polymerase II transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1		Myeloproliferative disorder(178;0.0511)												0.171875	19.683619	26.198507	11	53	CC		KEEP	---	---	---	---	capture		Epithelial(140;8.43e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.26e-07)	Missense_Mutation	SNP	138232348	138232348	9098	9	C	A	A	21	21	LHX3	A	3	3
ABCA2	20	broad.mit.edu	36	9	139030953	139030953	+	Silent	SNP	G	C	C			TCGA-06-0119-01	TCGA-06-0119-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:139030953G>C	uc004ckm.1	-	c.2907C>G	c.(2905-2907)GGC>GGG	p.G969G	ABCA2_uc010nby.1_Silent_p.G869G|ABCA2_uc010nbz.1_Silent_p.G939G|ABCA2_uc004ckl.1_Silent_p.G869G|ABCA2_uc004ckn.1_Non-coding_Transcript	NM_212533	NP_997698	Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A, member 2	938					cholesterol homeostasis|lipid metabolic process|regulation of intracellular cholesterol transport|regulation of transcription from RNA polymerase II promoter|response to drug|response to steroid hormone stimulus	ATP-binding cassette (ABC) transporter complex|cytoplasmic membrane-bounded vesicle|endosome|integral to membrane|lysosomal membrane|microtubule organizing center	ATP binding|ATPase activity, coupled to transmembrane movement of substances				0	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)												0.227273	8.27038	9.772652	5	17	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)	Silent	SNP	139030953	139030953	33	9	G	C	C	46	46	ABCA2	C	3	3
ARL13A	392509	broad.mit.edu	36	X	100127464	100127464	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0119-01	TCGA-06-0119-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:100127464G>A	uc004ego.1	+	c.283G>A	c.(283-285)GTC>ATC	p.V95I	ARL13A_uc010nng.1_Missense_Mutation_p.V95I	NM_001012990	NP_001013008	Q5H913	AR13A_HUMAN	ADP-ribosylation factor-like 13	95							GTP binding			ovary(1)	1														0.193182	36.835854	44.559733	17	71	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100127464	100127464	943	23	G	A	A	40	40	ARL13A	A	1	1
SLC6A14	11254	broad.mit.edu	36	X	115500644	115500644	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0119-01	TCGA-06-0119-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:115500644C>T	uc004eqi.1	+	c.1598C>T	c.(1597-1599)ACG>ATG	p.T533M		NM_007231	NP_009162	Q9UN76	S6A14_HUMAN	solute carrier family 6 (amino acid	533	Helical; Name=11; (Potential).				cellular amino acid metabolic process|response to toxin	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity			ovary(2)|pancreas(1)	3					L-Proline(DB00172)									0.147287	32.242904	47.655717	19	110	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	115500644	115500644	15174	23	C	T	T	19	19	SLC6A14	T	1	1
RHOXF1	158800	broad.mit.edu	36	X	119133428	119133428	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0119-01	TCGA-06-0119-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:119133428T>A	uc004esk.1	-	c.373A>T	c.(373-375)ACT>TCT	p.T125S		NM_139282	NP_644811	Q8NHV9	RHXF1_HUMAN	Rhox homeobox family, member 1	125	Homeobox.				gamete generation|multicellular organismal development|regulation of transcription, DNA-dependent|steroid hormone receptor signaling pathway	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0														0.131579	19.636093	34.726089	15	99	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	119133428	119133428	13822	23	T	A	A	59	59	RHOXF1	A	4	4
IRAK1	3654	broad.mit.edu	36	X	152936680	152936680	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0119-01	TCGA-06-0119-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:152936680C>T	uc004fjs.1	-	c.880G>A	c.(880-882)GGC>AGC	p.G294S	IRAK1_uc004fjr.1_Missense_Mutation_p.G294S|IRAK1_uc004fjt.1_Missense_Mutation_p.G294S|IRAK1_uc010nur.1_Intron|IRAK1_uc004fju.1_Missense_Mutation_p.G320S	NM_001569	NP_001560	P51617	IRAK1_HUMAN	interleukin-1 receptor-associated kinase 1	294	Protein kinase.				activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|anti-apoptosis|innate immune response|interleukin-1-mediated signaling pathway|JNK cascade|lipopolysaccharide-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of NF-kappaB transcription factor activity|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|protein autophosphorylation|protein oligomerization|regulation of cytokine-mediated signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transmembrane receptor protein serine/threonine kinase signaling pathway	cytosol|endosome membrane|interleukin-1 receptor complex	ATP binding|NF-kappaB-inducing kinase activity|protein binding|protein heterodimerization activity|protein homodimerization activity|transcription activator activity|ubiquitin-protein ligase activity			lung(4)|ovary(2)|breast(1)|central_nervous_system(1)	8	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)									83				0.103093	8.68509	23.898892	10	87	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152936680	152936680	8124	23	C	T	T	23	23	IRAK1	T	1	1
MAGEB1	4112	broad.mit.edu	36	X	30179154	30179154	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0119-01	TCGA-06-0119-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:30179154T>C	uc004dcc.1	+	c.623T>C	c.(622-624)ATC>ACC	p.I208T	MAGEB1_uc004dcd.1_Missense_Mutation_p.I208T|MAGEB1_uc004dce.1_Missense_Mutation_p.I208T|MAGEB1_uc010ngh.1_Missense_Mutation_p.I208T	NM_002363	NP_803134	P43366	MAGB1_HUMAN	melanoma antigen family B, 1	208	MAGE.										0														0.1875	14.031789	16.957185	6	26	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30179154	30179154	9553	23	T	C	C	50	50	MAGEB1	C	4	4
MXRA5	25878	broad.mit.edu	36	X	3245366	3245366	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0119-01	TCGA-06-0119-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:3245366C>T	uc004crg.2	-	c.6356G>A	c.(6355-6357)CGC>CAC	p.R2119H		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican	2119	Ig-like C2-type 5.					extracellular region				ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(23;0.00031)|Lung NSC(23;0.000946)												0.190476	16.477661	20.237995	8	34	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3245366	3245366	10397	23	C	T	T	27	27	MXRA5	T	1	1
FAM47A	158724	broad.mit.edu	36	X	34058799	34058799	+	Silent	SNP	C	T	T			TCGA-06-0119-01	TCGA-06-0119-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:34058799C>T	uc004ddg.1	-	c.1518G>A	c.(1516-1518)TCG>TCA	p.S506S		NM_203408	NP_981953	Q5JRC9	FA47A_HUMAN	hypothetical protein LOC158724	506			Missing.							ovary(4)|central_nervous_system(1)	5														0.2	37.117913	44.64135	18	72	CC		KEEP	---	---	---	---	capture			Silent	SNP	34058799	34058799	5790	23	C	T	T	23	23	FAM47A	T	1	1
PHF16	9767	broad.mit.edu	36	X	46769095	46769095	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0119-01	TCGA-06-0119-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:46769095G>A	uc004dgx.1	+	c.310G>A	c.(310-312)GTT>ATT	p.V104I	PHF16_uc004dgy.1_Missense_Mutation_p.V104I	NM_001077445	NP_055550	Q92613	JADE3_HUMAN	PHD finger protein 16	104					histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0														0.131579	14.500835	24.523815	10	66	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46769095	46769095	12250	23	G	A	A	40	40	PHF16	A	1	1
RBM10	8241	broad.mit.edu	36	X	46926305	46926305	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0119-01	TCGA-06-0119-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:46926305G>A	uc004dhi.1	+	c.1900G>A	c.(1900-1902)GTC>ATC	p.V634I	RBM10_uc004dhf.1_Missense_Mutation_p.V569I|RBM10_uc004dhg.1_Missense_Mutation_p.V491I|RBM10_uc004dhh.1_Missense_Mutation_p.V568I|RBM10_uc010nhq.1_Missense_Mutation_p.V492I	NM_005676	NP_005667	P98175	RBM10_HUMAN	RNA binding motif protein 10 isoform 1	569	Tyr-rich.				mRNA processing|RNA splicing	chromatin remodeling complex	nucleotide binding|RNA binding|zinc ion binding			large_intestine(1)|ovary(1)|pancreas(1)	3						Melanoma(171;120 2705 19495 39241)								0.191176	21.32511	27.41071	13	55	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46926305	46926305	13572	23	G	A	A	40	40	RBM10	A	1	1
MICALCL	84953	broad.mit.edu	36	11	12272960	12272965	+	In_Frame_Del	DEL	CTCCTA	-	-			TCGA-06-0119-01	TCGA-06-0119-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:12272960_12272965delCTCCTA	uc001mkg.1	+	c.1406_1411delCTCCTA	c.(1405-1413)CCTCCTACA>CCA	p.PT470del		NM_032867	NP_116256	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	470_471					cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm	mitogen-activated protein kinase binding				0				Epithelial(150;0.00177)										0.47			8	9				---	---	---	---	capture_indel			In_Frame_Del	DEL	12272960	12272965	9962	11	CTCCTA	-	-	24	24	MICALCL	-	5	5
PRR25	388199	broad.mit.edu	36	16	795519	795524	+	In_Frame_Del	DEL	GCAGCT	-	-			TCGA-06-0119-01	TCGA-06-0119-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:795519_795524delGCAGCT	uc002cki.1	+	c.76_81delGCAGCT	c.(76-81)GCAGCTdel	p.AA26del		NM_001013638	NP_001013660	Q96S07	PRR25_HUMAN	hypothetical protein LOC388199	26_27										large_intestine(1)	1														0.31			4	9				---	---	---	---	capture_indel			In_Frame_Del	DEL	795519	795524	13046	16	GCAGCT	-	-	42	42	PRR25	-	5	5
