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
DYNC2H1	79659	broad.mit.edu	36	11	102844538	102844538	+	Missense_Mutation	SNP	G	T	T			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:102844538G>T	uc001phn.1	+	c.12681G>T	c.(12679-12681)TTG>TTT	p.L4227F	DYNC2H1_uc001pho.2_Missense_Mutation_p.L4220F|DYNC2H1_uc009yxe.1_Missense_Mutation_p.L833F	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	4220					cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)												0.275862	8.36697	9.782194	8	21	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)	Missense_Mutation	SNP	102844538	102844538	5032	11	G	T	T	48	48	DYNC2H1	T	3	3
OR6M1	390261	broad.mit.edu	36	11	123181980	123181980	+	Missense_Mutation	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:123181980C>T	uc001pzh.1	-	c.288G>A	c.(286-288)ATG>ATA	p.M96I		NM_001005325	NP_001005325	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M,	96	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)												0.3	57.545517	60.048389	21	49	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)	Missense_Mutation	SNP	123181980	123181980	11615	11	C	T	T	29	29	OR6M1	T	2	2
ANO9	338440	broad.mit.edu	36	11	423453	423453	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:423453G>A	uc001lpi.2	-	c.211C>T	c.(211-213)CGG>TGG	p.R71W		NM_001012302	NP_001012302	A1A5B4	ANO9_HUMAN	tumor protein p53 inducible protein 5	71	Cytoplasmic (Potential).					chloride channel complex	chloride channel activity			central_nervous_system(2)|ovary(1)|skin(1)	4														0.160494	26.823481	35.709789	13	68	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	423453	423453	712	11	G	A	A	39	39	ANO9	A	1	1
TTC17	55761	broad.mit.edu	36	11	43421456	43421456	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:43421456G>A	uc001mxi.1	+	c.2257G>A	c.(2257-2259)GTG>ATG	p.V753M	TTC17_uc001mxh.2_Missense_Mutation_p.V810M|TTC17_uc001mxj.2_Missense_Mutation_p.V580M|TTC17_uc001mxk.1_De_novo_Start_InFrame	NM_018259	NP_060729	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	753							binding			ovary(5)	5														0.318182	78.06819	80.654334	28	60	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43421456	43421456	17238	11	G	A	A	44	44	TTC17	A	2	2
OR4X1	390113	broad.mit.edu	36	11	48242315	48242315	+	Silent	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:48242315G>A	uc001ngt.1	+	c.327G>A	c.(325-327)GAG>GAA	p.E109E		NM_001004726	NP_001004726	Q8NH49	OR4X1_HUMAN	olfactory receptor, family 4, subfamily X,	109	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2														0.402778	93.360799	93.955948	29	43	GG		KEEP	---	---	---	---	capture			Silent	SNP	48242315	48242315	11494	11	G	A	A	35	35	OR4X1	A	2	2
ACY3	91703	broad.mit.edu	36	11	67169749	67169749	+	Missense_Mutation	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:67169749C>T	uc001omq.1	-	c.422G>A	c.(421-423)CGC>CAC	p.R141H		NM_080658	NP_542389	Q96HD9	ACY3_HUMAN	aspartoacylase (aminocyclase) 3	141					interspecies interaction between organisms	apical plasma membrane|cytoplasm	hydrolase activity, acting on ester bonds|metal ion binding				0					L-Aspartic Acid(DB00128)	GBM(56;346 1011 27014 29495 46841)								0.315789	64.684041	66.971849	24	52	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	67169749	67169749	228	11	C	T	T	27	27	ACY3	T	1	1
RELT	84957	broad.mit.edu	36	11	72779852	72779852	+	Missense_Mutation	SNP	G	C	C			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:72779852G>C	uc001otv.1	+	c.303G>C	c.(301-303)TGG>TGC	p.W101C	RELT_uc001otw.1_Missense_Mutation_p.W101C|RELT_uc009yto.1_Missense_Mutation_p.W19C|RELT_uc001otx.1_5'Flank	NM_152222	NP_689408	Q969Z4	TR19L_HUMAN	RELT tumor necrosis factor receptor precursor	101	Extracellular (Potential).					cytoplasm|integral to membrane|plasma membrane	receptor activity				0														0.361842	173.081329	175.63567	55	97	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	72779852	72779852	13690	11	G	C	C	43	43	RELT	C	3	3
ZNF385A	25946	broad.mit.edu	36	12	53064574	53064574	+	Missense_Mutation	SNP	G	C	C			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:53064574G>C	uc001sfy.2	-	c.52C>G	c.(52-54)CCC>GCC	p.P18A	ZNF385A_uc009zno.1_Non-coding_Transcript|ZNF385A_uc001sfw.1_5'UTR|ZNF385A_uc001sfx.1_5'UTR|ZNF385A_uc001sfz.2_Missense_Mutation_p.P18A	NM_015481	NP_056296	Q96PM9	Z385A_HUMAN	zinc finger protein 385A isoform c	340					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding|zinc ion binding			ovary(1)	1														0.833333	8.761277	9.322526	5	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53064574	53064574	18468	12	G	C	C	42	42	ZNF385A	C	3	3
TRHDE	29953	broad.mit.edu	36	12	71058045	71058045	+	Nonsense_Mutation	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:71058045C>T	uc001sxa.1	+	c.1057C>T	c.(1057-1059)CGA>TGA	p.R353*		NM_013381	NP_037513	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	353	Extracellular (Potential).				cell-cell signaling|proteolysis|signal transduction	integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(2)	2														0.274194	42.444745	45.294885	17	45	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	71058045	71058045	17023	12	C	T	T	19	19	TRHDE	T	5	1
ATP11A	23250	broad.mit.edu	36	13	112533797	112533797	+	Silent	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:112533797C>T	uc001vsj.2	+	c.1329C>T	c.(1327-1329)AAC>AAT	p.N443N	ATP11A_uc001vsi.2_Silent_p.N443N|ATP11A_uc001vsm.1_Silent_p.N319N	NM_032189	NP_115565	P98196	AT11A_HUMAN	ATPase, class VI, type 11A isoform b	443	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			large_intestine(2)|ovary(2)	4	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)							p.N443N(HS698.T-Tumor)	1064				0.285714	37.531393	39.549487	14	35	CC		KEEP	---	---	---	---	capture			Silent	SNP	112533797	112533797	1138	13	C	T	T	19	19	ATP11A	T	1	1
CLYBL	171425	broad.mit.edu	36	13	99223235	99223235	+	Missense_Mutation	SNP	C	G	G			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:99223235C>G	uc001vok.1	+	c.219C>G	c.(217-219)GAC>GAG	p.D73E		NM_206808	NP_996531	Q8N0X4	CLYBL_HUMAN	citrate lyase beta like	73					cellular aromatic compound metabolic process	citrate lyase complex|mitochondrion	citrate (pro-3S)-lyase activity|metal ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)													0.113208	18.61778	34.269162	12	94	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99223235	99223235	3711	13	C	G	G	20	20	CLYBL	G	3	3
TDRD9	122402	broad.mit.edu	36	14	103550881	103550881	+	Nonsense_Mutation	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:103550881C>T	uc001yom.2	+	c.2173C>T	c.(2173-2175)CGA>TGA	p.R725*	TDRD9_uc001yon.2_Nonsense_Mutation_p.R463*|TDRD9_uc010awx.1_Nonsense_Mutation_p.R440*	NM_153046	NP_694591	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	725					cell differentiation|DNA methylation involved in gamete generation|fertilization|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	nucleus|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(2)|central_nervous_system(1)	3		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)												0.31401	178.997008	185.370816	65	142	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	103550881	103550881	16263	14	C	T	T	27	27	TDRD9	T	5	1
MYH7	4625	broad.mit.edu	36	14	22952869	22952869	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:22952869G>A	uc001wjw.1	-	c.5729C>T	c.(5728-5730)GCG>GTG	p.A1910V	MYH7_uc001wjx.1_Missense_Mutation_p.A1910V	NM_000257	NP_000248	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1910	Potential.				adult heart development|muscle filament sliding|regulation of heart rate|ventricular cardiac muscle tissue morphogenesis	focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(3)	3	all_cancers(95;2.54e-05)													0.224	59.523131	68.220155	28	97	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(265;0.00725)	Missense_Mutation	SNP	22952869	22952869	10434	14	G	A	A	38	38	MYH7	A	1	1
LTBP2	4053	broad.mit.edu	36	14	74062566	74062566	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:74062566G>A	uc001xqa.1	-	c.2393C>T	c.(2392-2394)ACG>ATG	p.T798M		NM_000428	NP_000419	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding	798					protein secretion|protein targeting|transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|growth factor binding			liver(1)	1														0.26087	15.539333	16.729896	6	17	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)	Missense_Mutation	SNP	74062566	74062566	9450	14	G	A	A	40	40	LTBP2	A	1	1
NRXN3	9369	broad.mit.edu	36	14	78251217	78251217	+	Missense_Mutation	SNP	G	C	C			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:78251217G>C	uc001xun.1	+	c.907G>C	c.(907-909)GGA>CGA	p.G303R	NRXN3_uc001xum.1_Non-coding_Transcript|NRXN3_uc010asv.1_Missense_Mutation_p.G437R	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor	676	EGF-like 2.|Extracellular (Potential).				axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|pancreas(2)|breast(1)|central_nervous_system(1)	7		Renal(4;0.00876)												0.261905	48.679477	53.017279	22	62	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)	Missense_Mutation	SNP	78251217	78251217	11072	14	G	C	C	43	43	NRXN3	C	3	3
NDN	4692	broad.mit.edu	36	15	21482851	21482851	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:21482851G>A	uc001ywk.1	-	c.607C>T	c.(607-609)CGC>TGC	p.R203C		NM_002487	NP_002478	Q99608	NECD_HUMAN	necdin	203	MAGE.				negative regulation of cell proliferation|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perikaryon	DNA binding				0		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)												0.272727	33.080846	35.12919	12	32	GG		KEEP	---	---	---	---	capture		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00179)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)	Missense_Mutation	SNP	21482851	21482851	10646	15	G	A	A	39	39	NDN	A	1	1
AQP9	366	broad.mit.edu	36	15	56246269	56246269	+	Missense_Mutation	SNP	T	A	A			TCGA-32-2632-01	TCGA-32-2632-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:56246269T>A	uc002aez.2	+	c.217T>A	c.(217-219)TAT>AAT	p.Y73N		NM_020980	NP_066190	O43315	AQP9_HUMAN	aquaporin 9	73	Helical; (Potential).				cellular response to cAMP|excretion|immune response|metabolic process|response to mercury ion|response to osmotic stress|water homeostasis	integral to plasma membrane|intracellular membrane-bounded organelle	amine transmembrane transporter activity|carboxylic acid transmembrane transporter activity|glycerol channel activity|porin activity|purine base transmembrane transporter activity|pyrimidine base transmembrane transporter activity|water channel activity			ovary(1)	1														0.163366	62.172154	83.901927	33	169	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(80;0.16)	Missense_Mutation	SNP	56246269	56246269	844	15	T	A	A	61	61	AQP9	A	4	4
RABEP2	79874	broad.mit.edu	36	16	28829999	28829999	+	Silent	SNP	G	C	C			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:28829999G>C	uc002drq.1	-	c.897C>G	c.(895-897)GGC>GGG	p.G299G	RABEP2_uc010byn.1_Intron|RABEP2_uc002drr.2_Silent_p.G299G	NM_024816	NP_079092	Q9H5N1	RABE2_HUMAN	rabaptin, RAB GTPase binding effector protein 2	299	Potential.				endocytosis|protein transport	early endosome	growth factor activity|GTPase activator activity			ovary(1)|breast(1)	2						Pancreas(66;639 1284 10093 31061 49099)								0.25	9.405556	10.306301	4	12	GG		KEEP	---	---	---	---	capture			Silent	SNP	28829999	28829999	13421	16	G	C	C	42	42	RABEP2	C	3	3
HYDIN	54768	broad.mit.edu	36	16	69424359	69424359	+	Missense_Mutation	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:69424359C>T	uc002ezr.1	-	c.13789G>A	c.(13789-13791)GTG>ATG	p.V4597M	HYDIN_uc010cfy.1_Non-coding_Transcript	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	4598										ovary(1)	1		Ovarian(137;0.0654)												0.146853	32.673896	49.81871	21	122	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69424359	69424359	7767	16	C	T	T	18	18	HYDIN	T	2	2
GRIN2A	2903	broad.mit.edu	36	16	9851240	9851240	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:9851240G>A	uc002czp.1	-	c.1202C>T	c.(1201-1203)CCG>CTG	p.P401L	GRIN2A_uc002czq.1_Missense_Mutation_p.P401L|GRIN2A_uc002czr.2_Missense_Mutation_p.P401L	NM_000833	NP_000824	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	401	Extracellular (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)					324				0.353846	135.816508	138.262353	46	84	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	9851240	9851240	7058	16	G	A	A	39	39	GRIN2A	A	1	1
CCL15	6359	broad.mit.edu	36	17	31335545	31335545	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:31335545G>A	uc002hko.1	-	c.184C>T	c.(184-186)CGT>TGT	p.R62C	CCL16_uc002hkl.1_5'Flank|CCL16_uc002hkm.1_5'Flank|CCL14_uc002hkn.1_Non-coding_Transcript|CCL14_uc002hkp.1_Missense_Mutation_p.R46C	NM_032962	NP_116738	Q16663	CCL15_HUMAN	chemokine (C-C motif) ligand 14 isoform 2	64					cell-cell signaling|cellular calcium ion homeostasis|immune response	extracellular space	chemoattractant activity|chemokine activity|heparin binding|signal transducer activity			ovary(1)	1		Ovarian(249;0.17)												0.282353	60.965454	64.582266	24	61	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)	Missense_Mutation	SNP	31335545	31335545	3011	17	G	A	A	38	38	CCL15	A	1	1
KRT38	8687	broad.mit.edu	36	17	36850556	36850556	+	Silent	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36850556G>A	uc002hwq.1	-	c.144C>T	c.(142-144)AAC>AAT	p.N48N		NM_006771	NP_006762	O76015	KRT38_HUMAN	keratin 38	48	Head.					intermediate filament	structural molecule activity				0		Breast(137;0.000496)												0.411111	105.055699	105.677189	37	53	GG		KEEP	---	---	---	---	capture			Silent	SNP	36850556	36850556	8790	17	G	A	A	40	40	KRT38	A	1	1
ABCA9	10350	broad.mit.edu	36	17	64553046	64553046	+	Missense_Mutation	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:64553046C>T	uc002jhu.1	-	c.331G>A	c.(331-333)GAA>AAA	p.E111K	ABCA9_uc010dez.1_Missense_Mutation_p.E111K|ABCA9_uc002jhv.1_Missense_Mutation_p.E111K	NM_080283	NP_525022	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A, member 9	111					transport	integral to membrane	ATP binding|ATPase activity			ovary(4)|central_nervous_system(1)	5	Breast(10;1.47e-12)													0.142857	35.977612	56.638575	24	144	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	64553046	64553046	40	17	C	T	T	29	29	ABCA9	T	2	2
CABYR	26256	broad.mit.edu	36	18	19989679	19989679	+	Missense_Mutation	SNP	A	T	T			TCGA-32-2632-01	TCGA-32-2632-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr18:19989679A>T	uc002kux.1	+	c.216A>T	c.(214-216)GAA>GAT	p.E72D	CABYR_uc002kuy.1_Missense_Mutation_p.E72D|CABYR_uc002kuz.1_Missense_Mutation_p.E72D|CABYR_uc002kva.1_Missense_Mutation_p.E54D|CABYR_uc002kvb.1_De_novo_Start_OutOfFrame|CABYR_uc002kvc.1_Missense_Mutation_p.E72D|CABYR_uc010dlw.1_Non-coding_Transcript	NM_012189	NP_036321	O75952	CABYR_HUMAN	calcium-binding tyrosine	72					ciliary or flagellar motility|signal transduction|sperm capacitation	cytoplasm|cytoskeleton|flagellum|motile cilium|nucleus	calcium ion binding|cAMP-dependent protein kinase regulator activity|enzyme binding|protein heterodimerization activity|SH3 domain binding				0	all_cancers(21;9.13e-05)|all_epithelial(16;5.49e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0305)|Ovarian(20;0.17)													0.378947	105.074556	106.296894	36	59	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19989679	19989679	2652	18	A	T	T	3	3	CABYR	T	4	4
TNFRSF11A	8792	broad.mit.edu	36	18	58168086	58168086	+	Silent	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:58168086G>A	uc002lin.1	+	c.219G>A	c.(217-219)CCG>CCA	p.P73P	TNFRSF11A_uc010dpv.1_Silent_p.P73P	NM_003839	NP_003830	Q9Y6Q6	TNR11_HUMAN	tumor necrosis factor receptor superfamily,	73	TNFR-Cys 2.|Extracellular (Potential).				adaptive immune response|cell-cell signaling|circadian temperature homeostasis|monocyte chemotaxis|osteoclast differentiation|positive regulation of cell proliferation|positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling|positive regulation of fever generation by positive regulation of prostaglandin secretion|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|response to interleukin-1|response to lipopolysaccharide	external side of plasma membrane|integral to membrane	metal ion binding|tumor necrosis factor receptor activity				0		Colorectal(73;0.188)												0.295775	239.003168	249.589954	84	200	GG		KEEP	---	---	---	---	capture			Silent	SNP	58168086	58168086	16825	18	G	A	A	39	39	TNFRSF11A	A	1	1
HMHA1	23526	broad.mit.edu	36	19	1031969	1031969	+	Missense_Mutation	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:1031969C>T	uc002lqz.1	+	c.2096C>T	c.(2095-2097)GCG>GTG	p.A699V	HMHA1_uc002lra.1_Missense_Mutation_p.A539V|HMHA1_uc002lrb.1_Missense_Mutation_p.A582V|HMHA1_uc002lrc.1_Missense_Mutation_p.A334V|HMHA1_uc002lrd.1_5'Flank|HMHA1_uc010dsd.1_5'Flank	NM_012292	NP_036424	Q92619	HMHA1_HUMAN	minor histocompatibility antigen HA-1	699					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding			lung(1)	1		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)												0.3	14.84291	15.557359	6	14	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	1031969	1031969	7532	19	C	T	T	27	27	HMHA1	T	1	1
CYP4F22	126410	broad.mit.edu	36	19	15512449	15512449	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:15512449G>A	uc002nbh.2	+	c.860G>A	c.(859-861)CGT>CAT	p.R287H		NM_173483	NP_775754	Q6NT55	CP4FN_HUMAN	cytochrome P450, family 4, subfamily F,	287					oxidation-reduction process	endoplasmic reticulum membrane|microsome	electron carrier activity|heme binding|monooxygenase activity			pancreas(1)	1														0.357143	118.117457	120.391252	45	81	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15512449	15512449	4354	19	G	A	A	40	40	CYP4F22	A	1	1
GTPBP3	84705	broad.mit.edu	36	19	17313117	17313117	+	Silent	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:17313117G>A	uc002ngg.2	+	c.1335G>A	c.(1333-1335)AAG>AAA	p.K445K	GTPBP3_uc002ngh.2_Silent_p.K392K|GTPBP3_uc010eas.1_Silent_p.K413K|GTPBP3_uc002ngi.2_Silent_p.K79K	NM_133644	NP_598399	Q969Y2	GTPB3_HUMAN	GTP binding protein 3 (mitochondrial) isoform	413					tRNA modification	mitochondrion	GTP binding|GTPase activity				0														0.295455	34.955384	36.603737	13	31	GG		KEEP	---	---	---	---	capture			Silent	SNP	17313117	17313117	7161	19	G	A	A	35	35	GTPBP3	A	2	2
ZNF599	148103	broad.mit.edu	36	19	39942617	39942617	+	Missense_Mutation	SNP	G	T	T			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:39942617G>T	uc010edn.1	-	c.929C>A	c.(928-930)CCC>CAC	p.P310H	ZNF599_uc010edm.1_Missense_Mutation_p.P273H	NM_001007248	NP_001007249	Q96NL3	ZN599_HUMAN	zinc finger protein 599	310					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)													0.293478	133.269003	140.299532	54	130	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(66;0.138)		Missense_Mutation	SNP	39942617	39942617	18624	19	G	T	T	43	43	ZNF599	T	3	3
CCDC8	83987	broad.mit.edu	36	19	51606498	51606498	+	Silent	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:51606498C>T	uc002pep.1	-	c.1410G>A	c.(1408-1410)AGG>AGA	p.R470R		NM_032040	NP_114429	Q9H0W5	CCDC8_HUMAN	coiled-coil domain containing 8	470						plasma membrane				ovary(3)	3														0.367521	129.208064	131.007579	43	74	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;4.66e-05)|all cancers(93;0.000582)|Epithelial(262;0.00428)|GBM - Glioblastoma multiforme(486;0.0421)	Silent	SNP	51606498	51606498	2977	19	C	T	T	22	22	CCDC8	T	2	2
HAS1	3036	broad.mit.edu	36	19	56908762	56908762	+	Silent	SNP	G	C	C			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:56908762G>C	uc002pxn.1	-	c.1488C>G	c.(1486-1488)GGC>GGG	p.G496G	HAS1_uc010epc.1_Silent_p.G89G|HAS1_uc010epd.1_3'UTR|HAS1_uc002pxo.1_Silent_p.G489G|HAS1_uc002pxp.1_Silent_p.G488G	NM_001523	NP_001514	Q92839	HAS1_HUMAN	hyaluronan synthase 1	489	Extracellular (Potential).				cell adhesion	integral to plasma membrane	hyaluronan synthase activity|protein binding			ovary(1)|pancreas(1)	2		all_neural(266;0.0189)|Medulloblastoma(540;0.146)				NSCLC(132;636 2450 45807 47979)								0.3	6.820443	7.178281	3	7	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)	Silent	SNP	56908762	56908762	7243	19	G	C	C	46	46	HAS1	C	3	3
LILRB1	10859	broad.mit.edu	36	19	59839781	59839781	+	Missense_Mutation	SNP	C	A	A			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:59839781C>A	uc002qgm.1	+	c.1678C>A	c.(1678-1680)CAG>AAG	p.Q560K	LILRB1_uc010erp.1_3'UTR|LILRB1_uc002qgj.1_Missense_Mutation_p.Q558K|LILRB1_uc002qgk.1_Missense_Mutation_p.Q559K|LILRB1_uc002qgl.1_Missense_Mutation_p.Q559K|LILRB1_uc010erq.1_Missense_Mutation_p.Q542K|LILRB1_uc010err.1_Non-coding_Transcript	NM_001081637	NP_001075106	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor,	558	Cytoplasmic (Potential).				regulation of immune response|response to virus	integral to membrane|plasma membrane	protein phosphatase 1 binding|receptor activity			large_intestine(1)|ovary(1)	2														0.144928	17.402099	25.773417	10	59	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.0188)	Missense_Mutation	SNP	59839781	59839781	9116	19	C	A	A	21	21	LILRB1	A	3	3
NLRP7	199713	broad.mit.edu	36	19	60142812	60142812	+	Missense_Mutation	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:60142812C>T	uc010esl.1	-	c.1271G>A	c.(1270-1272)CGT>CAT	p.R424H	NLRP7_uc002qig.2_Missense_Mutation_p.R396H|NLRP7_uc002qii.2_Missense_Mutation_p.R396H|NLRP7_uc002qih.2_Missense_Mutation_p.R396H|NLRP7_uc010esk.1_Missense_Mutation_p.R396H	NM_001127255	NP_001120727	Q8WX94	NALP7_HUMAN	NACHT, leucine rich repeat and PYD containing 7	396	NACHT.						ATP binding			large_intestine(1)|breast(1)|central_nervous_system(1)	3														0.37931	27.303555	27.677756	11	18	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.0325)	Missense_Mutation	SNP	60142812	60142812	10885	19	C	T	T	19	19	NLRP7	T	1	1
RDH8	50700	broad.mit.edu	36	19	9992987	9992987	+	Missense_Mutation	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:9992987C>T	uc002mmr.1	+	c.593C>T	c.(592-594)GCG>GTG	p.A198V		NM_015725	NP_056540	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	198					estrogen biosynthetic process|oxidation-reduction process|response to stimulus|visual perception	cytoplasm|integral to plasma membrane	binding|estradiol 17-beta-dehydrogenase activity|NADP-retinol dehydrogenase activity|retinol dehydrogenase activity			ovary(3)|pancreas(1)	4					Vitamin A(DB00162)									0.361963	160.179033	162.912554	59	104	CC		KEEP	---	---	---	---	capture	Epithelial(33;4.24e-05)		Missense_Mutation	SNP	9992987	9992987	13665	19	C	T	T	27	27	RDH8	T	1	1
NOTCH2	4853	broad.mit.edu	36	1	120266472	120266472	+	Missense_Mutation	SNP	G	C	C			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:120266472G>C	uc001eik.1	-	c.5123C>G	c.(5122-5124)TCT>TGT	p.S1708C		NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein	1708	Cytoplasmic (Potential).				anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			haematopoietic_and_lymphoid_tissue(7)|ovary(4)|lung(3)|central_nervous_system(2)|kidney(2)|breast(1)	19	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)								581				0.293333	70.836534	73.694332	22	53	GG		KEEP	---	---	---	---	capture		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)	Missense_Mutation	SNP	120266472	120266472	10951	1	G	C	C	33	33	NOTCH2	C	3	3
FLG	2312	broad.mit.edu	36	1	150545439	150545439	+	Silent	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150545439G>A	uc001ezu.1	-	c.8547C>T	c.(8545-8547)GAC>GAT	p.D2849D		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	2849	Ser-rich.|Filaggrin 17.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.154267	235.449406	339.846822	141	773	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Silent	SNP	150545439	150545439	6160	1	G	A	A	40	40	FLG	A	1	1
FLG	2312	broad.mit.edu	36	1	150547516	150547516	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150547516G>A	uc001ezu.1	-	c.6470C>T	c.(6469-6471)TCG>TTG	p.S2157L		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	2157	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.3575	808.013413	822.324898	286	514	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150547516	150547516	6160	1	G	A	A	37	37	FLG	A	1	1
SPTA1	6708	broad.mit.edu	36	1	156880804	156880804	+	Missense_Mutation	SNP	G	C	C			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:156880804G>C	uc001fst.1	-	c.4201C>G	c.(4201-4203)CAG>GAG	p.Q1401E		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1401	Spectrin 14.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.252252	70.341334	76.533099	28	83	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	156880804	156880804	15630	1	G	C	C	47	47	SPTA1	C	3	3
SPEN	23013	broad.mit.edu	36	1	16075659	16075659	+	Missense_Mutation	SNP	C	A	A			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:16075659C>A	uc001axk.1	+	c.780C>A	c.(778-780)AGC>AGA	p.S260R		NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	260	Ser-rich.|Arg-rich.|By similarity.				interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	14		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)								551				0.125	7.116499	13.712247	6	42	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)	Missense_Mutation	SNP	16075659	16075659	15550	1	C	A	A	26	26	SPEN	A	3	3
ASPM	259266	broad.mit.edu	36	1	195379197	195379197	+	Missense_Mutation	SNP	A	G	G			TCGA-32-2632-01	TCGA-32-2632-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:195379197A>G	uc001gtu.1	-	c.808T>C	c.(808-810)TCT>CCT	p.S270P	ASPM_uc001gtv.1_Missense_Mutation_p.S270P|ASPM_uc001gtw.2_Intron	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	270					mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6														0.426396	288.462187	289.39258	84	113	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	195379197	195379197	1075	1	A	G	G	9	9	ASPM	G	4	4
ABCD3	5825	broad.mit.edu	36	1	94726061	94726061	+	Missense_Mutation	SNP	T	C	C			TCGA-32-2632-01	TCGA-32-2632-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:94726061T>C	uc001dqn.2	+	c.1091T>C	c.(1090-1092)CTT>CCT	p.L364P	ABCD3_uc009wdr.1_Intron|ABCD3_uc001dqo.2_Missense_Mutation_p.L52P	NM_002858	NP_002849	P28288	ABCD3_HUMAN	ATP-binding cassette, sub-family D, member 3	364	ABC transmembrane type-1.				peroxisomal long-chain fatty acid import|peroxisome organization	cytosol|integral to peroxisomal membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances				0		all_lung(203;0.000434)|Lung NSC(277;0.0019)												0.10101	12.373025	28.101533	10	89	TT		KEEP	---	---	---	---	capture		all cancers(265;0.0261)|Epithelial(280;0.165)	Missense_Mutation	SNP	94726061	94726061	63	1	T	C	C	56	56	ABCD3	C	4	4
PHF20	51230	broad.mit.edu	36	20	33990291	33990291	+	Silent	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:33990291G>A	uc002xek.1	+	c.2559G>A	c.(2557-2559)CAG>CAA	p.Q853Q		NM_016436	NP_057520	Q9BVI0	PHF20_HUMAN	PHD finger protein 20	853					regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)													0.235955	50.502038	56.205034	21	68	GG		KEEP	---	---	---	---	capture			Silent	SNP	33990291	33990291	12254	20	G	A	A	33	33	PHF20	A	2	2
SEMG1	6406	broad.mit.edu	36	20	43269974	43269974	+	Missense_Mutation	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:43269974C>T	uc002xni.1	+	c.622C>T	c.(622-624)CGT>TGT	p.R208C	SEMG1_uc002xnh.1_Missense_Mutation_p.R208C|SEMG1_uc002xnj.1_Missense_Mutation_p.R208C|SEMG2_uc010ggz.1_Intron	NM_003007	NP_002998	P04279	SEMG1_HUMAN	semenogelin I isoform a preproprotein	208	42 AA repeat 1.				insemination|sexual reproduction	extracellular space|stored secretory granule	structural molecule activity				0		Myeloproliferative disorder(115;0.0122)												0.358491	108.520149	110.389506	38	68	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43269974	43269974	14530	20	C	T	T	19	19	SEMG1	T	1	1
ADAMTS1	9510	broad.mit.edu	36	21	27139078	27139078	+	Silent	SNP	G	T	T			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:27139078G>T	uc002ymf.1	-	c.67C>A	c.(67-69)CGG>AGG	p.R23R		NM_006988	NP_008919	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1	23					integrin-mediated signaling pathway|negative regulation of cell proliferation|proteolysis		heparin binding|zinc ion binding			lung(3)|large_intestine(2)|central_nervous_system(1)	6		Breast(209;0.000962)										OREG0026151	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.375	37.303147	37.737737	12	20	GG		KEEP	---	---	---	---	capture		Lung(58;0.215)	Silent	SNP	27139078	27139078	256	21	G	T	T	38	38	ADAMTS1	T	3	3
EFCAB6	64800	broad.mit.edu	36	22	42264721	42264721	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:42264721G>A	uc003bdy.1	-	c.3917C>T	c.(3916-3918)CCC>CTC	p.P1306L	EFCAB6_uc003bdz.1_Missense_Mutation_p.P1154L|EFCAB6_uc010gzi.1_Missense_Mutation_p.P1154L	NM_022785	NP_942153	Q5THR3	EFCB6_HUMAN	CAP-binding protein complex interacting protein	1306	Interaction with PARK7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding			ovary(3)|pancreas(1)	4		Ovarian(80;0.0247)|all_neural(38;0.025)												0.314286	95.735906	98.958834	33	72	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42264721	42264721	5126	22	G	A	A	43	43	EFCAB6	A	2	2
PNPLA5	150379	broad.mit.edu	36	22	42618380	42618380	+	Missense_Mutation	SNP	G	T	T			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:42618380G>T	uc003beg.1	-	c.321C>A	c.(319-321)GAC>GAA	p.D107E	PNPLA5_uc010gzl.1_Missense_Mutation_p.D107E|PNPLA5_uc003beh.1_Intron	NM_138814	NP_620169	Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	107	Patatin.				lipid catabolic process		hydrolase activity				0		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)												0.208333	9.863445	11.754868	5	19	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42618380	42618380	12595	22	G	T	T	40	40	PNPLA5	T	3	3
SLC5A7	60482	broad.mit.edu	36	2	107980819	107980819	+	Missense_Mutation	SNP	T	A	A			TCGA-32-2632-01	TCGA-32-2632-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:107980819T>A	uc002tdv.1	+	c.542T>A	c.(541-543)CTC>CAC	p.L181H	SLC5A7_uc010fjj.1_Missense_Mutation_p.L181H|SLC5A7_uc010fjk.1_Non-coding_Transcript	NM_021815	NP_068587	Q9GZV3	SC5A7_HUMAN	solute carrier family 5 (choline transporter),	181	Helical; (Potential).				acetylcholine biosynthetic process|neurotransmitter secretion	integral to membrane|plasma membrane	choline:sodium symporter activity			ovary(2)|central_nervous_system(1)	3					Choline(DB00122)									0.398625	327.544112	330.15799	116	175	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	107980819	107980819	15167	2	T	A	A	54	54	SLC5A7	A	4	4
CNTNAP5	129684	broad.mit.edu	36	2	125246855	125246855	+	Missense_Mutation	SNP	A	G	G			TCGA-32-2632-01	TCGA-32-2632-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:125246855A>G	uc002tno.1	+	c.2540A>G	c.(2539-2541)GAG>GGG	p.E847G	CNTNAP5_uc010flu.1_Missense_Mutation_p.E848G	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	847	Laminin G-like 3.|Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10														0.224	80.336974	89.086039	28	97	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.248)	Missense_Mutation	SNP	125246855	125246855	3788	2	A	G	G	11	11	CNTNAP5	G	4	4
SCN7A	6332	broad.mit.edu	36	2	166981610	166981610	+	Silent	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:166981610G>A	uc002udu.1	-	c.3267C>T	c.(3265-3267)GAC>GAT	p.D1089D	SCN7A_uc010fpm.1_Non-coding_Transcript	NM_002976	NP_002967	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha	1089					muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			large_intestine(1)	1														0.452381	57.121332	57.204039	19	23	GG		KEEP	---	---	---	---	capture			Silent	SNP	166981610	166981610	14405	2	G	A	A	44	44	SCN7A	A	2	2
MYO3B	140469	broad.mit.edu	36	2	170969058	170969058	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:170969058G>A	uc002ufy.1	+	c.2333G>A	c.(2332-2334)CGC>CAC	p.R778H	MYO3B_uc002ufv.2_Missense_Mutation_p.R778H|MYO3B_uc010fqb.1_Missense_Mutation_p.R778H|MYO3B_uc002ufz.1_Missense_Mutation_p.R778H|MYO3B_uc002ufw.1_Non-coding_Transcript|MYO3B_uc002ufx.1_Non-coding_Transcript|MYO3B_uc002ugb.1_Non-coding_Transcript	NM_138995	NP_620482	Q8WXR4	MYO3B_HUMAN	myosin IIIB isoform 2	778	Myosin head-like.				protein phosphorylation|response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(5)|skin(2)|central_nervous_system(1)	16										1118				0.328571	56.3921	58.220741	23	47	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	170969058	170969058	10472	2	G	A	A	38	38	MYO3B	A	1	1
TTN	7273	broad.mit.edu	36	2	179161765	179161765	+	Missense_Mutation	SNP	T	C	C			TCGA-32-2632-01	TCGA-32-2632-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179161765T>C	uc002umr.1	-	c.55229A>G	c.(55228-55230)GAA>GGA	p.E18410G	TTN_uc002ums.1_Missense_Mutation_p.E12105G|TTN_uc010frc.1_Missense_Mutation_p.E12038G|TTN_uc010frd.1_Missense_Mutation_p.E11913G	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	19337										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				0.455357	180.61804	180.811734	51	61	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179161765	179161765	17290	2	T	C	C	62	62	TTN	C	4	4
SPHKAP	80309	broad.mit.edu	36	2	228592112	228592112	+	Missense_Mutation	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:228592112C>T	uc002vpq.1	-	c.1702G>A	c.(1702-1704)GTG>ATG	p.V568M	SPHKAP_uc002vpp.1_Missense_Mutation_p.V568M	NM_030623	NP_085126	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	568						cytoplasm	protein binding			ovary(4)|lung(1)	5		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)												0.174129	66.087983	86.253812	35	166	CC		KEEP	---	---	---	---	capture		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)	Missense_Mutation	SNP	228592112	228592112	15560	2	C	T	T	19	19	SPHKAP	T	1	1
QPCT	25797	broad.mit.edu	36	2	37453035	37453035	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:37453035G>A	uc002rqg.1	+	c.856G>A	c.(856-858)GAT>AAT	p.D286N	QPCT_uc002rqh.1_Missense_Mutation_p.D237N	NM_012413	NP_036545	Q16769	QPCT_HUMAN	glutaminyl-peptide cyclotransferase precursor	286					peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase|proteolysis	extracellular region	acyltransferase activity|glutaminyl-peptide cyclotransferase activity|peptidase activity|zinc ion binding			central_nervous_system(1)	1		Ovarian(717;0.051)|all_hematologic(82;0.21)												0.250996	162.760396	176.86526	63	188	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37453035	37453035	13332	2	G	A	A	41	41	QPCT	A	2	2
KIAA1524	57650	broad.mit.edu	36	3	109762185	109762185	+	Splice_Site_SNP	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:109762185C>T	uc003dxb.2	-	c.1827_splice	c.e14+1	p.V609_splice		NM_020890	NP_065941			p90 autoantigen							cytoplasm|integral to membrane	protein binding			ovary(2)|central_nervous_system(1)	3														0.298387	198.44899	207.461957	74	174	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	109762185	109762185	8548	3	C	T	T	18	18	KIAA1524	T	5	2
COL6A5	256076	broad.mit.edu	36	3	131657119	131657119	+	Missense_Mutation	SNP	A	T	T			TCGA-32-2632-01	TCGA-32-2632-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:131657119A>T	uc010htj.1	+	c.6709A>T	c.(6709-6711)AGC>TGC	p.S2237C	COL6A5_uc010hti.1_Non-coding_Transcript|COL6A5_uc010htk.1_Missense_Mutation_p.S276C	NM_153264	NP_694996	A8TX70	CO6A5_HUMAN	collagen, type XXIX, alpha 1	2237	Nonhelical region.				axon guidance|cell adhesion	collagen					0														0.202532	36.453588	42.947966	16	63	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	131657119	131657119	3840	3	A	T	T	3	3	COL6A5	T	4	4
LEKR1	389170	broad.mit.edu	36	3	158246065	158246065	+	Silent	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:158246065C>T	uc003fba.1	+	c.999C>T	c.(997-999)CGC>CGT	p.R333R		NM_001004316	NP_001004316	D3DNK7	D3DNK7_HUMAN	leucine, glutamate and lysine rich 1	Error:Variant_position_missing_in_D3DNK7_after_alignment											0														0.331429	156.606522	161.005348	58	117	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)		Silent	SNP	158246065	158246065	9041	3	C	T	T	27	27	LEKR1	T	1	1
C3orf45	132228	broad.mit.edu	36	3	50299242	50299242	+	Silent	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:50299242C>T	uc003cyz.1	+	c.306C>T	c.(304-306)CTC>CTT	p.L102L		NM_153215	NP_694947	Q8N112	CC045_HUMAN	hypothetical protein LOC132228	102	Helical; (Potential).					integral to membrane				ovary(1)	1														0.338983	57.382326	58.734576	20	39	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)	Silent	SNP	50299242	50299242	2324	3	C	T	T	31	31	C3orf45	T	1	1
STAB1	23166	broad.mit.edu	36	3	52515883	52515883	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:52515883G>A	uc003dej.1	+	c.1966G>A	c.(1966-1968)GAG>AAG	p.E656K	STAB1_uc003dei.1_Missense_Mutation_p.E656K	NM_015136	NP_055951	Q9NY15	STAB1_HUMAN	stabilin 1 precursor	656	Extracellular (Potential).				cell adhesion|cell-cell signaling|defense response to bacterium|inflammatory response|negative regulation of angiogenesis|receptor-mediated endocytosis	integral to plasma membrane	bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			large_intestine(3)|pancreas(1)|breast(1)|central_nervous_system(1)|skin(1)	7														0.336957	88.669081	90.797837	31	61	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)	Missense_Mutation	SNP	52515883	52515883	15755	3	G	A	A	37	37	STAB1	A	1	1
C3orf67	200844	broad.mit.edu	36	3	58831043	58831043	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:58831043G>A	uc003dkt.1	-	c.373C>T	c.(373-375)CGG>TGG	p.R125W	C3orf67_uc003dks.1_5'Flank|C3orf67_uc003dkv.1_De_novo_Start_InFrame|C3orf67_uc003dkw.2_Missense_Mutation_p.R33W	NM_198463	NP_940865	Q6ZVT6	CC067_HUMAN	hypothetical protein LOC200844	125											0		all_cancers(2;0.000156)|all_epithelial(2;0.000493)|Breast(2;0.00446)|all_lung(2;0.074)|Lung NSC(2;0.248)												0.107143	15.324021	36.761388	15	125	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(55;5.93e-06)|Kidney(10;0.00155)|KIRC - Kidney renal clear cell carcinoma(10;0.00172)|OV - Ovarian serous cystadenocarcinoma(275;0.23)	Missense_Mutation	SNP	58831043	58831043	2334	3	G	A	A	40	40	C3orf67	A	1	1
CENPE	1062	broad.mit.edu	36	4	104263590	104263590	+	Missense_Mutation	SNP	T	C	C			TCGA-32-2632-01	TCGA-32-2632-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:104263590T>C	uc003hxb.1	-	c.7030A>G	c.(7030-7032)AAA>GAA	p.K2344E	CENPE_uc003hxc.1_Missense_Mutation_p.K2223E	NM_001813	NP_001804	Q02224	CENPE_HUMAN	centromere protein E	2344	Kinetochore-binding domain.|Potential.				blood coagulation|cell division|kinetochore assembly|microtubule-based movement|mitotic chromosome movement towards spindle pole|mitotic metaphase|mitotic metaphase plate congression|mitotic prometaphase|multicellular organismal development|positive regulation of protein kinase activity	condensed chromosome kinetochore|cytosol|microtubule|nucleus|spindle	ATP binding|kinetochore binding|microtubule motor activity			ovary(5)|breast(4)	9														0.306878	186.705275	192.975437	58	131	TT		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)	Missense_Mutation	SNP	104263590	104263590	3363	4	T	C	C	61	61	CENPE	C	4	4
LDB2	9079	broad.mit.edu	36	4	16206585	16206585	+	Missense_Mutation	SNP	T	C	C			TCGA-32-2632-01	TCGA-32-2632-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:16206585T>C	uc003goz.1	-	c.247A>G	c.(247-249)ACC>GCC	p.T83A	LDB2_uc003goy.1_5'UTR|LDB2_uc003gpa.1_Missense_Mutation_p.T83A|LDB2_uc003gpb.1_Missense_Mutation_p.T83A|LDB2_uc010iee.1_Missense_Mutation_p.T83A	NM_001290	NP_001281	O43679	LDB2_HUMAN	LIM domain binding 2 isoform a	83							LIM domain binding|transcription cofactor activity				0														0.296296	11.007999	12.068507	8	19	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16206585	16206585	9020	4	T	C	C	58	58	LDB2	C	4	4
ING2	3622	broad.mit.edu	36	4	184668458	184668458	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:184668458G>A	uc003ivs.1	+	c.202G>A	c.(202-204)GAA>AAA	p.E68K		NM_001564	NP_001555	Q9H160	ING2_HUMAN	inhibitor of growth family, member 2	68	Potential.				chromatin modification|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of growth|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	CCAAT-binding factor complex|Sin3 complex	chromatin binding|DNA binding|protein complex binding|transcription activator activity|zinc ion binding			ovary(1)	1		all_lung(41;5.16e-14)|Lung NSC(41;1.33e-13)|Colorectal(36;0.00139)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|all_hematologic(60;0.0207)|Prostate(90;0.0235)|all_neural(102;0.202)												0.325301	157.102675	161.592818	54	112	GG		KEEP	---	---	---	---	capture		all cancers(43;1.15e-26)|Epithelial(43;2.98e-22)|OV - Ovarian serous cystadenocarcinoma(60;7.64e-10)|GBM - Glioblastoma multiforme(59;4.22e-06)|Colorectal(24;5.87e-06)|STAD - Stomach adenocarcinoma(60;2.09e-05)|COAD - Colon adenocarcinoma(29;5.15e-05)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)	Missense_Mutation	SNP	184668458	184668458	8037	4	G	A	A	37	37	ING2	A	1	1
SLC6A18	348932	broad.mit.edu	36	5	1297741	1297741	+	Silent	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:1297741G>A	uc003jby.1	+	c.1515G>A	c.(1513-1515)GCG>GCA	p.A505A		NM_182632	NP_872438	Q96N87	S6A18_HUMAN	solute carrier family 6, member 18	505	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity			ovary(1)	1	all_cancers(3;2.99e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.76e-10)													0.264706	67.982417	73.084883	27	75	GG		KEEP	---	---	---	---	capture	Epithelial(17;0.000356)|all cancers(22;0.00124)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Silent	SNP	1297741	1297741	15178	5	G	A	A	40	40	SLC6A18	A	1	1
RAPGEF6	51735	broad.mit.edu	36	5	130968278	130968278	+	Missense_Mutation	SNP	T	A	A			TCGA-32-2632-01	TCGA-32-2632-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:130968278T>A	uc003kvp.1	-	c.227A>T	c.(226-228)AAT>ATT	p.N76I	RAPGEF6_uc003kvn.1_Missense_Mutation_p.N26I|RAPGEF6_uc003kvo.1_Missense_Mutation_p.N26I|RAPGEF6_uc010jdi.1_Missense_Mutation_p.N26I|RAPGEF6_uc010jdj.1_Missense_Mutation_p.N26I|RAPGEF6_uc003kvr.1_Missense_Mutation_p.N26I|RAPGEF6_uc010jdk.1_Missense_Mutation_p.N26I	NM_016340	NP_057424	Q8TEU7	RPGF6_HUMAN	PDZ domain-containing guanine nucleotide	26					Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3						Melanoma(168;435 1955 13113 13877 23213)								0.131579	13.394641	23.424963	10	66	TT		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)	Missense_Mutation	SNP	130968278	130968278	13508	5	T	A	A	52	52	RAPGEF6	A	4	4
FBXO38	81545	broad.mit.edu	36	5	147776749	147776749	+	Splice_Site_SNP	SNP	G	C	C			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:147776749G>C	uc003lpf.1	+	c.1408_splice	c.e12-1	p.G470_splice	FBXO38_uc003lpg.1_Splice_Site_SNP_p.G470_splice|FBXO38_uc003lph.2_Splice_Site_SNP_p.G470_splice	NM_205836	NP_995308			F-box protein 38 isoform b							cytoplasm|nucleus				ovary(4)|skin(1)	5														0.11236	14.382006	27.590198	10	79	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Splice_Site_SNP	SNP	147776749	147776749	5983	5	G	C	C	35	35	FBXO38	C	5	3
FBXO38	81545	broad.mit.edu	36	5	147776831	147776831	+	Missense_Mutation	SNP	G	C	C			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:147776831G>C	uc003lpf.1	+	c.1489G>C	c.(1489-1491)GAC>CAC	p.D497H	FBXO38_uc003lpg.1_Missense_Mutation_p.D497H|FBXO38_uc003lph.2_Missense_Mutation_p.D497H	NM_205836	NP_995308	Q6PIJ6	FBX38_HUMAN	F-box protein 38 isoform b	497						cytoplasm|nucleus				ovary(4)|skin(1)	5														0.093023	7.330521	21.660438	8	78	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	147776831	147776831	5983	5	G	C	C	45	45	FBXO38	C	3	3
NIPAL4	348938	broad.mit.edu	36	5	156822820	156822820	+	Missense_Mutation	SNP	C	G	G			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:156822820C>G	uc003lwx.2	+	c.364C>G	c.(364-366)CTG>GTG	p.L122V	ADAM19_uc003lww.1_Intron|NIPAL4_uc010jin.1_Silent_p.A56A	NM_001099287	NP_001092757	Q0D2K0	NIPA4_HUMAN	ichthyin protein	122	Helical; (Potential).					integral to membrane	receptor activity				0														0.26087	59.42137	64.216152	24	68	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	156822820	156822820	10828	5	C	G	G	24	24	NIPAL4	G	3	3
GABRA1	2554	broad.mit.edu	36	5	161256896	161256896	+	Nonsense_Mutation	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:161256896C>T	uc010jiw.1	+	c.1261C>T	c.(1261-1263)CGA>TGA	p.R421*	GABRA1_uc010jix.1_Nonsense_Mutation_p.R421*|GABRA1_uc010jiy.1_Nonsense_Mutation_p.R421*|GABRA1_uc003lyx.2_Nonsense_Mutation_p.R421*|GABRA1_uc010jiz.1_Nonsense_Mutation_p.R421*|GABRA1_uc010jja.1_Nonsense_Mutation_p.R421*|GABRA1_uc010jjb.1_Nonsense_Mutation_p.R421*	NM_000806	NP_001121120	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha	421	Cytoplasmic (Probable).				gamma-aminobutyric acid signaling pathway|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(2)|pancreas(1)	3	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)			Alprazolam(DB00404)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Halazepam(DB00801)|Halothane(DB01159)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Metharbital(DB00463)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Picrotoxin(DB00466)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Zaleplon(DB00962)|Zolpidem(DB00425)									0.397059	335.841044	338.363307	108	164	CC		KEEP	---	---	---	---	capture	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.228)	Nonsense_Mutation	SNP	161256896	161256896	6411	5	C	T	T	23	23	GABRA1	T	5	1
BASP1	10409	broad.mit.edu	36	5	17328800	17328800	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:17328800G>A	uc003jfx.1	+	c.475G>A	c.(475-477)GCC>ACC	p.A159T	BASP1_uc010ity.1_Missense_Mutation_p.A159T	NM_006317	NP_006308	P80723	BASP1_HUMAN	brain abundant, membrane attached signal protein	159					glomerular visceral epithelial cell differentiation|negative regulation of gene-specific transcription	cytoplasm|cytoskeleton|growth cone|nuclear speck|plasma membrane	promoter binding|protein domain specific binding|specific transcriptional repressor activity|transcription corepressor activity				0														0.583333	22.827035	22.899859	7	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17328800	17328800	1338	5	G	A	A	38	38	BASP1	A	1	1
DDX4	54514	broad.mit.edu	36	5	55119433	55119433	+	Silent	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:55119433G>A	uc003jqg.2	+	c.1020G>A	c.(1018-1020)GCG>GCA	p.A340A	DDX4_uc010ivz.1_Silent_p.A320A|DDX4_uc003jqh.2_Silent_p.A306A|DDX4_uc003jqi.1_Silent_p.A340A|DDX4_uc003jqj.1_Silent_p.A191A	NM_024415	NP_077726	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 isoform	340	Helicase ATP-binding.				multicellular organismal development|sperm motility	pi-body|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(1)|skin(1)	2		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)												0.269036	145.193367	154.673249	53	144	GG		KEEP	---	---	---	---	capture			Silent	SNP	55119433	55119433	4531	5	G	A	A	39	39	DDX4	A	1	1
FAM81B	153643	broad.mit.edu	36	5	94775573	94775573	+	Missense_Mutation	SNP	T	A	A			TCGA-32-2632-01	TCGA-32-2632-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:94775573T>A	uc003kla.1	+	c.460T>A	c.(460-462)TCG>ACG	p.S154T	FAM81B_uc010jbe.1_5'UTR	NM_152548	NP_689761	Q96LP2	FA81B_HUMAN	hypothetical protein LOC153643	154										ovary(1)	1		all_cancers(142;1.1e-06)|all_epithelial(76;1.48e-09)|all_lung(232;0.000696)|Lung NSC(167;0.000947)|Ovarian(225;0.00473)												0.3	114.113175	119.106461	42	98	TT		KEEP	---	---	---	---	capture		all cancers(79;1.04e-16)	Missense_Mutation	SNP	94775573	94775573	5855	5	T	A	A	50	50	FAM81B	A	4	4
MCHR2	84539	broad.mit.edu	36	6	100502447	100502447	+	Missense_Mutation	SNP	C	A	A			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:100502447C>A	uc003pqh.1	-	c.304G>T	c.(304-306)GGG>TGG	p.G102W	MCHR2_uc003pqi.1_Missense_Mutation_p.G102W	NM_001040179	NP_115892	Q969V1	MCHR2_HUMAN	melanin-concentrating hormone receptor 2	102	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(2)|central_nervous_system(1)	3		all_cancers(76;4.87e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0309)|Colorectal(196;0.069)												0.288136	174.727879	184.213113	68	168	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(108;0.0429)	Missense_Mutation	SNP	100502447	100502447	9772	6	C	A	A	21	21	MCHR2	A	3	3
HDAC2	3066	broad.mit.edu	36	6	114372188	114372188	+	Missense_Mutation	SNP	G	C	C			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:114372188G>C	uc003pwd.1	-	c.1453C>G	c.(1453-1455)CAT>GAT	p.H485D	HDAC2_uc003pwc.1_Missense_Mutation_p.H361D|HDAC2_uc003pwe.1_Missense_Mutation_p.H361D	NM_001527	NP_001518	Q92769	HDAC2_HUMAN	histone deacetylase 2	391					blood coagulation|chromatin remodeling|dendrite development|embryonic digit morphogenesis|epidermal cell differentiation|eyelid development in camera-type eye|fungiform papilla formation|hair follicle placode formation|maintenance of chromatin silencing|negative regulation of apoptosis|negative regulation of cell cycle|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of MHC class II biosynthetic process|negative regulation of neuron projection development|negative regulation of sequence-specific DNA binding transcription factor activity|nerve growth factor receptor signaling pathway|odontogenesis of dentine-containing tooth|positive regulation of cell proliferation|positive regulation of collagen biosynthetic process|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of proteolysis|positive regulation of receptor biosynthetic process	cytoplasm|ESC/E(Z) complex|NuRD complex|Sin3 complex	chromatin binding|enzyme binding|histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|sequence-specific DNA binding|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(2)|central_nervous_system(1)	3		all_cancers(87;0.000629)|all_epithelial(87;0.00274)|Colorectal(196;0.0317)|all_lung(197;0.24)			Vorinostat(DB02546)					302				0.421488	175.507013	176.157626	51	70	GG		KEEP	---	---	---	---	capture		all cancers(137;0.00318)|OV - Ovarian serous cystadenocarcinoma(136;0.00569)|Epithelial(106;0.0112)|GBM - Glioblastoma multiforme(226;0.0832)	Missense_Mutation	SNP	114372188	114372188	7290	6	G	C	C	45	45	HDAC2	C	3	3
MAP7	9053	broad.mit.edu	36	6	136723950	136723950	+	Silent	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:136723950C>T	uc003qgz.1	-	c.1587G>A	c.(1585-1587)GAG>GAA	p.E529E	MAP7_uc003qha.1_Silent_p.E492E|MAP7_uc010kgq.1_Silent_p.E435E	NM_003980	NP_003971	Q14244	MAP7_HUMAN	microtubule-associated protein 7	529	Potential.				establishment or maintenance of cell polarity|microtubule cytoskeleton organization|protein localization in plasma membrane|response to osmotic stress	basolateral plasma membrane|microtubule|microtubule associated complex|nucleus|perinuclear region of cytoplasm	receptor binding|structural molecule activity				0	Colorectal(23;0.24)													0.125	9.219166	15.81069	6	42	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(68;0.00199)|OV - Ovarian serous cystadenocarcinoma(155;0.00643)	Silent	SNP	136723950	136723950	9649	6	C	T	T	24	24	MAP7	T	2	2
PIK3CG	5294	broad.mit.edu	36	7	106296588	106296588	+	Missense_Mutation	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:106296588C>T	uc003vdv.2	+	c.1346C>T	c.(1345-1347)TCC>TTC	p.S449F	PIK3CG_uc003vdu.1_Missense_Mutation_p.S449F|PIK3CG_uc003vdw.1_Missense_Mutation_p.S449F	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	449					G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			central_nervous_system(8)|lung(7)|pancreas(3)|ovary(2)|skin(1)	21										292				0.155914	49.054891	70.087952	29	157	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	106296588	106296588	12340	7	C	T	T	30	30	PIK3CG	T	2	2
GCC1	79571	broad.mit.edu	36	7	127009405	127009405	+	Missense_Mutation	SNP	G	C	C			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:127009405G>C	uc003vma.1	-	c.2227C>G	c.(2227-2229)CTC>GTC	p.L743V		NM_024523	NP_078799	Q96CN9	GCC1_HUMAN	Golgi coiled-coil protein 1	743	Potential.|GRIP.					Golgi membrane|plasma membrane	protein binding			ovary(2)	2														0.11399	31.207223	59.569139	22	171	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	127009405	127009405	6551	7	G	C	C	33	33	GCC1	C	3	3
MGAM	8972	broad.mit.edu	36	7	141383097	141383097	+	Missense_Mutation	SNP	G	T	T			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:141383097G>T	uc003vwy.1	+	c.2082G>T	c.(2080-2082)CAG>CAT	p.Q694H		NM_004668	NP_004659	O43451	MGA_HUMAN	maltase-glucoamylase	694	Lumenal (Potential).|Maltase.				polysaccharide digestion|starch catabolic process	apical plasma membrane|integral to membrane	carbohydrate binding|glucan 1,4-alpha-glucosidase activity|maltose alpha-glucosidase activity			ovary(2)	2	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)									0.228963	274.007794	308.442414	117	394	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	141383097	141383097	9931	7	G	T	T	35	35	MGAM	T	3	3
CNTNAP2	26047	broad.mit.edu	36	7	146456811	146456811	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:146456811G>A	uc003weu.1	+	c.1033G>A	c.(1033-1035)GTC>ATC	p.V345I		NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor	345	Laminin G-like 1.|Extracellular (Potential).				behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)												0.205521	151.549511	177.763321	67	259	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.0319)		Missense_Mutation	SNP	146456811	146456811	3785	7	G	A	A	40	40	CNTNAP2	A	1	1
SSPO	23145	broad.mit.edu	36	7	149148924	149148924	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:149148924G>A	uc010lpk.1	+	c.12334G>A	c.(12334-12336)GTG>ATG	p.V4112M	SSPO_uc003wgh.2_5'Flank|SSPO_uc010lpm.1_5'Flank|SSPO_uc003wgg.2_5'Flank|SSPO_uc003wgi.1_5'Flank	NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin	4112					cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)													0.19403	26.438747	32.289824	13	54	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.00625)		Missense_Mutation	SNP	149148924	149148924	15705	7	G	A	A	40	40	SSPO	A	1	1
ABCB5	340273	broad.mit.edu	36	7	20710911	20710911	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:20710911G>A	uc010kuh.1	+	c.2377G>A	c.(2377-2379)GGC>AGC	p.G793S	ABCB5_uc003suw.2_Missense_Mutation_p.G348S|ABCB5_uc010kui.1_Missense_Mutation_p.G348S	NM_178559	NP_848654	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B, member 5	348	Extracellular (Potential).|ABC transmembrane type-1.				regulation of membrane potential	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus	ATP binding|ATPase activity, coupled to transmembrane movement of substances|efflux transmembrane transporter activity			large_intestine(1)|ovary(1)|pancreas(1)	3														0.225	70.457569	78.79762	27	93	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	20710911	20710911	45	7	G	A	A	35	35	ABCB5	A	2	2
CHN2	1124	broad.mit.edu	36	7	29506125	29506125	+	Missense_Mutation	SNP	A	C	C			TCGA-32-2632-01	TCGA-32-2632-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:29506125A>C	uc003szz.1	+	c.857A>C	c.(856-858)CAC>CCC	p.H286P	CHN2_uc010kva.1_Missense_Mutation_p.H56P|CHN2_uc010kvb.1_Intron|CHN2_uc010kvc.1_Missense_Mutation_p.H251P|CHN2_uc010kvd.1_Missense_Mutation_p.H142P|CHN2_uc010kve.1_Missense_Mutation_p.H150P|CHN2_uc003taa.1_Missense_Mutation_p.H150P|CHN2_uc010kvf.1_Intron|CHN2_uc010kvg.1_Missense_Mutation_p.H150P|CHN2_uc010kvh.1_Intron|CHN2_uc010kvi.1_Missense_Mutation_p.H150P|CHN2_uc010kvj.1_Missense_Mutation_p.H105P|CHN2_uc010kvk.1_Intron|CHN2_uc010kvl.1_Non-coding_Transcript|CHN2_uc010kvm.1_Missense_Mutation_p.H105P	NM_004067	NP_004058	P52757	CHIO_HUMAN	beta chimerin isoform 2	286	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|membrane	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)	2						Ovarian(1;44 48 13232 18918 31480)								0.260417	71.132583	76.121674	25	71	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29506125	29506125	3497	7	A	C	C	6	6	CHN2	C	4	4
CCDC129	223075	broad.mit.edu	36	7	31648925	31648925	+	Silent	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:31648925G>A	uc003tcj.1	+	c.1416G>A	c.(1414-1416)TCG>TCA	p.S472S	CCDC129_uc003tci.1_Silent_p.S323S|CCDC129_uc003tck.1_Silent_p.S380S	NM_194300	NP_919276	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	472											0														0.243781	123.385959	135.404684	49	152	GG		KEEP	---	---	---	---	capture			Silent	SNP	31648925	31648925	2884	7	G	A	A	39	39	CCDC129	A	1	1
SDK1	221935	broad.mit.edu	36	7	4214346	4214346	+	Silent	SNP	G	C	C			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:4214346G>C	uc003smx.1	+	c.5304G>C	c.(5302-5304)CTG>CTC	p.L1768L	SDK1_uc010kso.1_Silent_p.L1024L|SDK1_uc003smy.1_Silent_p.L255L	NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 isoform 1	1768	Fibronectin type-III 11.				cell adhesion	integral to membrane				large_intestine(3)|ovary(2)	5		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)												0.125	8.79903	19.800853	10	70	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)	Silent	SNP	4214346	4214346	14454	7	G	C	C	45	45	SDK1	C	3	3
KIAA0415	9907	broad.mit.edu	36	7	4787434	4787434	+	Silent	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:4787434C>T	uc003sne.1	+	c.144C>T	c.(142-144)CTC>CTT	p.L48L	KIAA0415_uc010ksp.1_Non-coding_Transcript	NM_014855	NP_055670	O43299	K0415_HUMAN	hypothetical protein LOC9907	48					cell death|double-strand break repair via homologous recombination	cytoplasm|nucleus	protein binding			central_nervous_system(1)	1		Ovarian(82;0.0175)												0.236364	65.000912	71.98846	26	84	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (126;0.091)|OV - Ovarian serous cystadenocarcinoma(56;8.35e-15)	Silent	SNP	4787434	4787434	8482	7	C	T	T	32	32	KIAA0415	T	2	2
EGFR	1956	broad.mit.edu	36	7	55177569	55177569	+	Missense_Mutation	SNP	T	G	G			TCGA-32-2632-01	TCGA-32-2632-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55177569T>G	uc003tqk.1	+	c.185T>G	c.(184-186)CTT>CGT	p.L62R	EGFR_uc003tqh.1_Missense_Mutation_p.L62R|EGFR_uc003tqi.1_Missense_Mutation_p.L62R|EGFR_uc003tqj.1_Missense_Mutation_p.L62R|EGFR_uc010kzg.1_Missense_Mutation_p.L62R	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	62	Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.V30_R297>G(5)|p.L62R(1)		lung(8200)|central_nervous_system(103)|upper_aerodigestive_tract(37)|prostate(32)|ovary(31)|thyroid(23)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|stomach(6)|urinary_tract(6)|skin(5)|adrenal_gland(5)|kidney(4)|soft_tissue(4)|bone(3)|NS(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)|pancreas(1)	8515	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)				Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8		608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.957317	3433.33648	3523.751211	942	42	TT		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Missense_Mutation	SNP	55177569	55177569	5156	7	T	G	G	56	56	EGFR	G	4	4
CALN1	83698	broad.mit.edu	36	7	70913286	70913286	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:70913286G>A	uc003twb.2	-	c.629C>T	c.(628-630)TCG>TTG	p.S210L	CALN1_uc003twa.2_Missense_Mutation_p.S168L|CALN1_uc003twc.2_Missense_Mutation_p.S168L	NM_031468	NP_113656	Q9BXU9	CABP8_HUMAN	calneuron 1 isoform 1	168	Cytoplasmic (Potential).					Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding				0		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)												0.156863	88.311215	122.684691	48	258	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70913286	70913286	2708	7	G	A	A	37	37	CALN1	A	1	1
TM7SF4	81501	broad.mit.edu	36	8	105430494	105430494	+	Missense_Mutation	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:105430494C>T	uc003ylx.1	+	c.538C>T	c.(538-540)CAT>TAT	p.H180Y		NM_030788	NP_110415	Q9H295	TM7S4_HUMAN	dendritic cell-specific transmembrane protein	180					osteoclast differentiation	cell surface|integral to membrane|plasma membrane				pancreas(2)|large_intestine(1)|ovary(1)	4														0.352381	213.180254	217.219143	74	136	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)		Missense_Mutation	SNP	105430494	105430494	16506	8	C	T	T	21	21	TM7SF4	T	2	2
DOCK5	80005	broad.mit.edu	36	8	25215816	25215816	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:25215816G>A	uc003xeg.1	+	c.905G>A	c.(904-906)CGC>CAC	p.R302H	DOCK5_uc003xef.2_Missense_Mutation_p.R302H|DOCK5_uc010luf.1_Non-coding_Transcript|DOCK5_uc003xeh.1_Missense_Mutation_p.R16H	NM_024940	NP_079216	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	302						cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)				Pancreas(145;34 1887 3271 10937 30165)								0.533333	24.400077	24.414497	8	7	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)	Missense_Mutation	SNP	25215816	25215816	4874	8	G	A	A	38	38	DOCK5	A	1	1
DOCK5	80005	broad.mit.edu	36	8	25245719	25245719	+	Missense_Mutation	SNP	T	A	A			TCGA-32-2632-01	TCGA-32-2632-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:25245719T>A	uc003xeg.1	+	c.1939T>A	c.(1939-1941)TCC>ACC	p.S647T	DOCK5_uc010luf.1_Non-coding_Transcript|DOCK5_uc003xei.1_Missense_Mutation_p.S217T|DOCK5_uc003xej.1_Non-coding_Transcript|DOCK5_uc003xeh.1_Missense_Mutation_p.S361T	NM_024940	NP_079216	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	647	DHR-1.					cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)				Pancreas(145;34 1887 3271 10937 30165)								0.309735	95.381236	99.026867	35	78	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)	Missense_Mutation	SNP	25245719	25245719	4874	8	T	A	A	54	54	DOCK5	A	4	4
DOCK5	80005	broad.mit.edu	36	8	25321497	25321497	+	Silent	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:25321497C>T	uc003xeg.1	+	c.5175C>T	c.(5173-5175)AGC>AGT	p.S1725S	PPP2R2A_uc003xek.1_Intron|DOCK5_uc003xej.1_Non-coding_Transcript	NM_024940	NP_079216	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1725						cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)				Pancreas(145;34 1887 3271 10937 30165)								0.190476	8.487977	10.368627	4	17	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)	Silent	SNP	25321497	25321497	4874	8	C	T	T	27	27	DOCK5	T	1	1
PTK2B	2185	broad.mit.edu	36	8	27364317	27364317	+	Silent	SNP	G	A	A			TCGA-32-2632-01	TCGA-32-2632-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:27364317G>A	uc003xfn.1	+	c.2475G>A	c.(2473-2475)GAG>GAA	p.E825E	PTK2B_uc003xfo.1_Silent_p.E825E|PTK2B_uc003xfp.1_Silent_p.E825E|PTK2B_uc003xfq.1_Silent_p.E783E|PTK2B_uc003xfs.1_Silent_p.E22E	NM_173174	NP_775268	Q14289	FAK2_HUMAN	PTK2B protein tyrosine kinase 2 beta isoform a	825	Interaction with TGFB1I1 (By similarity).				apoptosis|bone resorption|positive regulation of cell proliferation|signal complex assembly	cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity|signal transducer activity			ovary(1)|skin(1)	2		Ovarian(32;2.72e-05)								347				0.206349	33.239033	38.275013	13	50	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)	Silent	SNP	27364317	27364317	13218	8	G	A	A	35	35	PTK2B	A	2	2
JPH1	56704	broad.mit.edu	36	8	75390022	75390022	+	Silent	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:75390022C>T	uc003yae.1	-	c.768G>A	c.(766-768)ACG>ACA	p.T256T	JPH1_uc003yaf.2_Silent_p.T256T|JPH1_uc003yag.1_Silent_p.T120T	NM_020647	NP_065698	Q9HDC5	JPH1_HUMAN	junctophilin 1	256	Cytoplasmic (Potential).|Ser-rich.				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional membrane complex|junctional sarcoplasmic reticulum membrane|plasma membrane				ovary(1)	1	Breast(64;0.00576)													0.388889	166.47679	168.030771	56	88	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)		Silent	SNP	75390022	75390022	8264	8	C	T	T	31	31	JPH1	T	1	1
NUP214	8021	broad.mit.edu	36	9	133005879	133005879	+	Nonsense_Mutation	SNP	C	T	T			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:133005879C>T	uc004cag.1	+	c.1255C>T	c.(1255-1257)CGA>TGA	p.R419*	NUP214_uc004caf.1_Nonsense_Mutation_p.R419*|NUP214_uc004cah.1_Nonsense_Mutation_p.R419*	NM_005085	NP_005076	P35658	NU214_HUMAN	nucleoporin 214kDa	419					carbohydrate metabolic process|glucose transport|mRNA metabolic process|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore|nucleoplasm	protein binding			breast(3)|ovary(2)|lung(1)|central_nervous_system(1)	7	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)				Pancreas(4;24 48 25510 30394 32571)				1058				0.419048	134.283707	134.883795	44	61	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)	Nonsense_Mutation	SNP	133005879	133005879	11167	9	C	T	T	27	27	NUP214	T	5	1
CNTNAP3	79937	broad.mit.edu	36	9	39134249	39134249	+	Missense_Mutation	SNP	T	G	G			TCGA-32-2632-01	TCGA-32-2632-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:39134249T>G	uc004abi.1	-	c.1744A>C	c.(1744-1746)ACC>CCC	p.T582P	CNTNAP3_uc004abj.1_Missense_Mutation_p.T582P|CNTNAP3_uc004abk.1_Missense_Mutation_p.T582P|CNTNAP3_uc010mmf.1_Intron|CNTNAP3_uc004abl.1_Intron	NM_033655	NP_387504	Q9BZ76	CNTP3_HUMAN	cell recognition molecule CASPR3	582	EGF-like 1.|Extracellular (Potential).				cell adhesion|cell recognition|signal transduction	extracellular region|integral to membrane|plasma membrane	receptor binding			ovary(1)	1														1	8.752057	8.685319	4	0	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)	Missense_Mutation	SNP	39134249	39134249	3786	9	T	G	G	58	58	CNTNAP3	G	4	4
IL1RAPL2	26280	broad.mit.edu	36	X	104898247	104898247	+	Missense_Mutation	SNP	C	A	A			TCGA-32-2632-01	TCGA-32-2632-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:104898247C>A	uc004elz.1	+	c.1998C>A	c.(1996-1998)CAC>CAA	p.H666Q		NM_017416	NP_059112	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	666	Cytoplasmic (Potential).				central nervous system development|innate immune response	integral to membrane	interleukin-1, Type II, blocking receptor activity			breast(2)|ovary(1)	3														0.72	306.989444	312.423565	90	35	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	104898247	104898247	7963	23	C	A	A	17	17	IL1RAPL2	A	3	3
DMD	1756	broad.mit.edu	36	X	32396734	32396734	+	Silent	SNP	A	G	G			TCGA-32-2632-01	TCGA-32-2632-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:32396734A>G	uc004dda.1	-	c.2964T>C	c.(2962-2964)TCT>TCC	p.S988S	DMD_uc004dcz.2_Silent_p.S865S|DMD_uc004dcy.1_Silent_p.S984S|DMD_uc004ddb.1_Silent_p.S980S|DMD_uc010ngo.1_Intron	NM_004006	NP_004001	P11532	DMD_HUMAN	dystrophin Dp427m isoform	988	Spectrin 6.				muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)												0.12766	10.116124	16.468587	6	41	AA		KEEP	---	---	---	---	capture			Silent	SNP	32396734	32396734	4760	23	A	G	G	11	11	DMD	G	4	4
RB1	5925	broad.mit.edu	36	13	47839712	47839712	+	Frame_Shift_Del	DEL	A	-	-			TCGA-32-2632-01	TCGA-32-2632-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:47839712_47839712delA	uc001vcb.1	+	c.1021_1021delA	c.(1021-1023)AAAfs	p.K341fs	RB1_uc010act.1_Frame_Shift_Del_p.K42fs	NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1	341					androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|transcription repressor activity|ubiquitin protein ligase binding	p.0?(13)|p.D340fs*5(1)		lung(93)|eye(89)|central_nervous_system(47)|bone(22)|breast(20)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|soft_tissue(8)|prostate(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	355		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)			6	p.K341fs(42MGBA-Tumor)	568	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			0.31			28	62				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	47839712	47839712	13559	13	A	-	-	13	13	RB1	-	5	5
TBC1D23	55773	broad.mit.edu	36	3	101485337	101485338	+	Frame_Shift_Ins	INS	-	A	A			TCGA-32-2632-01	TCGA-32-2632-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:101485337_101485338insA	uc003dtt.1	+	c.468_469insA	c.(466-471)TACATTfs	p.Y156fs	TBC1D23_uc003dts.1_Frame_Shift_Ins_p.Y156fs	NM_018309	NP_060779	Q9NUY8	TBC23_HUMAN	TBC1 domain family, member 23	156_157	Rab-GAP TBC.					intracellular	Rab GTPase activator activity			ovary(1)|liver(1)	2														0.35			43	81				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	101485337	101485338	16135	3	-	A	A	17	17	TBC1D23	A	5	5
BHLHB9	80823	broad.mit.edu	36	X	101891198	101891199	+	Frame_Shift_Ins	INS	-	A	A			TCGA-32-2632-01	TCGA-32-2632-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:101891198_101891199insA	uc004ejo.1	+	c.619_620insA	c.(619-621)GAAfs	p.E207fs	BHLHB9_uc004ejp.1_Frame_Shift_Ins_p.E207fs|BHLHB9_uc010nog.1_Frame_Shift_Ins_p.E207fs	NM_030639	NP_085142	Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class	207						cytoplasm|nucleus	binding			ovary(2)	2														0.69			140	64				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	101891198	101891199	1445	23	-	A	A	45	45	BHLHB9	A	5	5
