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
TMPRSS5	80975	broad.mit.edu	36	11	113069170	113069170	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:113069170G>C	uc001poc.2	-	c.797C>G	c.(796-798)GCC>GGC	p.A266G	TMPRSS5_uc009yys.1_Missense_Mutation_p.A257G|TMPRSS5_uc009yyt.1_Missense_Mutation_p.A222G|TMPRSS5_uc001pod.2_Missense_Mutation_p.A7G|TMPRSS5_uc009yyu.1_Missense_Mutation_p.A7G	NM_030770	NP_110397	Q9H3S3	TMPS5_HUMAN	transmembrane protease, serine 5	266	Peptidase S1.|Extracellular (Potential).				proteolysis	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(1)	1		all_cancers(61;2.71e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)												0.454545	9.071823	9.102314	5	6	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;2.75e-06)|Epithelial(105;6.34e-05)|all cancers(92;0.000502)	Missense_Mutation	SNP	113069170	113069170	16791	11	G	C	C	42	42	TMPRSS5	C	3	3
OR4D5	219875	broad.mit.edu	36	11	123316210	123316210	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:123316210G>A	uc001pzk.1	+	c.677G>A	c.(676-678)CGA>CAA	p.R226Q		NM_001001965	NP_001001965	Q8NGN0	OR4D5_HUMAN	olfactory receptor, family 4, subfamily D,	226	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)												0.296636	253.375116	265.4562	97	230	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)	Missense_Mutation	SNP	123316210	123316210	11464	11	G	A	A	37	37	OR4D5	A	1	1
STAB2	55576	broad.mit.edu	36	12	102538386	102538386	+	Silent	SNP	T	G	G			TCGA-06-0749-01	TCGA-06-0749-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:102538386T>G	uc001tjw.1	+	c.342T>G	c.(340-342)GGT>GGG	p.G114G		NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	114	Extracellular (Potential).|EGF-like 1.				angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(1)	10														0.206897	15.335549	17.643231	6	23	TT		KEEP	---	---	---	---	capture			Silent	SNP	102538386	102538386	15756	12	T	G	G	59	59	STAB2	G	4	4
GPR133	283383	broad.mit.edu	36	12	130188673	130188673	+	Silent	SNP	G	A	A			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:130188673G>A	uc001uit.2	+	c.2475G>A	c.(2473-2475)TCG>TCA	p.S825S	GPR133_uc009zyo.1_Silent_p.S107S|GPR133_uc009zyp.1_Non-coding_Transcript	NM_198827	NP_942122	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	825	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)													0.129032	9.668011	17.970018	8	54	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)	Silent	SNP	130188673	130188673	6917	12	G	A	A	38	38	GPR133	A	1	1
LRIG3	121227	broad.mit.edu	36	12	57559060	57559060	+	Silent	SNP	G	T	T			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:57559060G>T	uc001sqr.1	-	c.1896C>A	c.(1894-1896)CCC>CCA	p.P632P	LRIG3_uc009zqh.1_Silent_p.P572P	NM_153377	NP_700356	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like	632	Ig-like C2-type 2.					integral to membrane				ovary(1)|skin(1)	2														0.270677	88.867117	95.161014	36	97	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(1;1.17e-18)		Silent	SNP	57559060	57559060	9319	12	G	T	T	43	43	LRIG3	T	3	3
ACSM4	341392	broad.mit.edu	36	12	7361900	7361900	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0749-01	TCGA-06-0749-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:7361900A>G	uc001qsx.1	+	c.776A>G	c.(775-777)GAC>GGC	p.D259G		NM_001080454	NP_001073923	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member	259					fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding				0														0.305556	10.217472	11.559296	11	25	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7361900	7361900	187	12	A	G	G	10	10	ACSM4	G	4	4
PLEKHG7	440107	broad.mit.edu	36	12	91672171	91672171	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:91672171C>T	uc001tcj.1	+	c.490C>T	c.(490-492)CGG>TGG	p.R164W		NM_001004330	NP_001004330	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G	164	DH.				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1														0.276923	47.728108	50.635541	18	47	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	91672171	91672171	12501	12	C	T	T	23	23	PLEKHG7	T	1	1
FUT8	2530	broad.mit.edu	36	14	65098125	65098125	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:65098125C>T	uc001xin.1	+	c.91C>T	c.(91-93)CGA>TGA	p.R31*	FUT8_uc001xio.1_Nonsense_Mutation_p.R31*|FUT8_uc001xir.2_Non-coding_Transcript|FUT8_uc001xip.1_Nonsense_Mutation_p.R31*|FUT8_uc001xiq.1_Intron	NM_178155	NP_835369	Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 isoform a	31	Lumenal (Potential).				in utero embryonic development|L-fucose catabolic process|N-glycan processing|oligosaccharide biosynthetic process|post-translational protein modification|protein glycosylation in Golgi|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	glycoprotein 6-alpha-L-fucosyltransferase activity|SH3 domain binding			ovary(1)	1														0.28777	101.910093	107.485648	40	99	CC		KEEP	---	---	---	---	capture		all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)	Nonsense_Mutation	SNP	65098125	65098125	6361	14	C	T	T	19	19	FUT8	T	5	1
AK7	122481	broad.mit.edu	36	14	95987559	95987559	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0749-01	TCGA-06-0749-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:95987559T>C	uc001yfn.2	+	c.997T>C	c.(997-999)TTT>CTT	p.F333L		NM_152327	NP_689540	Q96M32	KAD7_HUMAN	adenylate kinase 7	333	Potential.				cell projection organization	cytosol	adenylate kinase activity|ATP binding|cytidylate kinase activity			ovary(1)	1		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)												0.293478	81.784794	85.299771	27	65	TT		KEEP	---	---	---	---	capture		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)	Missense_Mutation	SNP	95987559	95987559	447	14	T	C	C	56	56	AK7	C	4	4
PKD1	5310	broad.mit.edu	36	16	2092427	2092427	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:2092427C>G	uc002cos.1	-	c.9157G>C	c.(9157-9159)GCC>CCC	p.A3053P	PKD1_uc002cot.1_Missense_Mutation_p.A3053P|PKD1_uc010bse.1_Non-coding_Transcript	NM_001009944	NP_001009944	P98161	PKD1_HUMAN	polycystin 1 isoform 1 precursor	3053	GPS.|Extracellular (Potential).				calcium-independent cell-matrix adhesion|homophilic cell adhesion|neuropeptide signaling pathway	basolateral plasma membrane|integral to plasma membrane	protein domain specific binding|sugar binding			central_nervous_system(1)	1														0.428571	8.224031	8.255079	3	4	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2092427	2092427	12387	16	C	G	G	27	27	PKD1	G	3	3
PRKCB	5579	broad.mit.edu	36	16	24073640	24073640	+	Silent	SNP	G	A	A			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:24073640G>A	uc002dmc.1	+	c.1200G>A	c.(1198-1200)CCG>CCA	p.P400P	PRKCB_uc002dmd.1_Silent_p.P400P	NM_002738	NP_002729	P05771	KPCB_HUMAN	protein kinase C, beta isoform 2	400	Protein kinase.				apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding	p.P400P(1)		ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)				p.P400P(NCIH1869-Tumor)|p.P400P(OCIAML3-Tumor)|p.P400P(SUDHL5-Tumor)	395				0.275862	18.28762	19.599788	8	21	GG		KEEP	---	---	---	---	capture			Silent	SNP	24073640	24073640	12951	16	G	A	A	38	38	PRKCB	A	1	1
LCMT1	51451	broad.mit.edu	36	16	25051236	25051236	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:25051236G>A	uc002dnx.1	+	c.218G>A	c.(217-219)CGA>CAA	p.R73Q	LCMT1_uc002dny.1_Missense_Mutation_p.R73Q|LCMT1_uc002dnz.1_5'UTR|LCMT1_uc002doa.1_5'UTR	NM_016309	NP_057393	Q9UIC8	LCMT1_HUMAN	leucine carboxyl methyltransferase 1 isoform a	73		S-adenosyl-L-methionine (By similarity).					protein binding|protein C-terminal carboxyl O-methyltransferase activity|S-adenosylmethionine-dependent methyltransferase activity				0					L-Leucine(DB00149)	Colon(200;565 2072 24396 47922 50898)								0.448276	80.64464	80.779522	26	32	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(48;0.0336)	Missense_Mutation	SNP	25051236	25051236	9002	16	G	A	A	37	37	LCMT1	A	1	1
C16orf90	646174	broad.mit.edu	36	16	3484670	3484670	+	Silent	SNP	G	C	C			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:3484670G>C	uc002cvi.1	-	c.255C>G	c.(253-255)GGC>GGG	p.G85G		NM_001080524	NP_001073993	A8MZG2	CP090_HUMAN	hypothetical protein LOC646174	75											0														0.3125	6.313529	6.849759	5	11	GG		KEEP	---	---	---	---	capture			Silent	SNP	3484670	3484670	1896	16	G	C	C	42	42	C16orf90	C	3	3
CREBBP	1387	broad.mit.edu	36	16	3782057	3782057	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:3782057C>T	uc002cvv.1	-	c.1256G>A	c.(1255-1257)TGG>TAG	p.W419*	CREBBP_uc002cvw.1_Intron	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a	419	TAZ-type 1.				cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			ovary(6)|skin(2)|pancreas(1)|lung(1)	10		Ovarian(90;0.0266)								748				0.290541	112.221091	118.007341	43	105	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)	Nonsense_Mutation	SNP	3782057	3782057	4000	16	C	T	T	21	21	CREBBP	T	5	2
SLC12A3	6559	broad.mit.edu	36	16	55470581	55470581	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0749-01	TCGA-06-0749-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:55470581A>G	uc002ekd.2	+	c.1276A>G	c.(1276-1278)AAC>GAC	p.N426D	SLC12A3_uc010ccm.1_Missense_Mutation_p.N426D|SLC12A3_uc010ccn.1_Missense_Mutation_p.N425D	NM_000339	NP_000330	P55017	S12A3_HUMAN	solute carrier family 12, member 3 isoform 1	426					sodium ion transport	apical plasma membrane|integral to plasma membrane|membrane fraction	sodium:chloride symporter activity			ovary(2)|breast(1)	3					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)									0.333333	8.490856	8.788642	4	8	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55470581	55470581	14879	16	A	G	G	9	9	SLC12A3	G	4	4
MYH2	4620	broad.mit.edu	36	17	10368561	10368561	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:10368561C>T	uc010coi.1	-	c.5122G>A	c.(5122-5124)GCA>ACA	p.A1708T	MYH2_uc002gmp.2_Missense_Mutation_p.A1708T|MYH2_uc010coj.1_Intron	NM_001100112	NP_060004	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	1708	Potential.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|lung(1)|kidney(1)	11														0.216374	82.500444	95.177886	37	134	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10368561	10368561	10430	17	C	T	T	27	27	MYH2	T	1	1
DNAH9	1770	broad.mit.edu	36	17	11749783	11749783	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:11749783G>C	uc002gne.1	+	c.11681G>C	c.(11680-11682)GGA>GCA	p.G3894A	DNAH9_uc010coo.1_Missense_Mutation_p.G3188A|DNAH9_uc002gnf.1_Missense_Mutation_p.G206A	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	3894	AAA 6 (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	10		Breast(5;0.0122)|all_epithelial(5;0.131)												0.166667	10.960785	16.038934	8	40	GG		KEEP	---	---	---	---	capture		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)	Missense_Mutation	SNP	11749783	11749783	4791	17	G	C	C	41	41	DNAH9	C	3	3
MRM1	79922	broad.mit.edu	36	17	32032798	32032798	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0749-01	TCGA-06-0749-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:32032798T>C	uc002hne.1	+	c.446T>C	c.(445-447)GTC>GCC	p.V149A	MRM1_uc002hnf.1_Intron	NM_024864	NP_079140	Q6IN84	MRM1_HUMAN	mitochondrial rRNA methyltransferase 1 homolog	149					RNA processing	mitochondrion	RNA binding|RNA methyltransferase activity				0		Breast(25;0.00957)|Ovarian(249;0.17)												0.155556	10.296792	15.398404	7	38	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (308;0.0184)	Missense_Mutation	SNP	32032798	32032798	10164	17	T	C	C	58	58	MRM1	C	4	4
KRT16	3868	broad.mit.edu	36	17	37021167	37021167	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:37021167C>T	uc002hxg.2	-	c.727G>A	c.(727-729)GGC>AGC	p.G243S		NM_005557	NP_005548	P08779	K1C16_HUMAN	keratin 16	243	Coil 1B.|Rod.				cell proliferation|epidermis development	intermediate filament	protein binding|structural constituent of cytoskeleton				0		Breast(137;0.000307)												0.320988	148.743509	153.354533	52	110	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37021167	37021167	8768	17	C	T	T	24	24	KRT16	T	2	2
JUP	3728	broad.mit.edu	36	17	37181581	37181581	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:37181581G>C	uc002hxq.1	-	c.52C>G	c.(52-54)CAG>GAG	p.Q18E	JUP_uc002hxr.1_Missense_Mutation_p.Q18E|JUP_uc002hxs.1_Missense_Mutation_p.Q18E	NM_021991	NP_068831	P14923	PLAK_HUMAN	junction plakoglobin	18					adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|structural constituent of cell wall|transcription coactivator activity			ovary(2)|lung(2)|breast(1)	5		Breast(137;0.000162)				Colon(16;42 520 6044 17852 28530)								0.315789	10.037115	10.616075	6	13	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)	Missense_Mutation	SNP	37181581	37181581	8276	17	G	C	C	46	46	JUP	C	3	3
KIF2B	84643	broad.mit.edu	36	17	49255948	49255948	+	Silent	SNP	C	T	T			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:49255948C>T	uc002iua.2	+	c.555C>T	c.(553-555)TAC>TAT	p.Y185Y		NM_032559	NP_115948	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	185					blood coagulation|cell division|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|microtubule|microtubule organizing center|nucleolus|spindle	ATP binding|microtubule motor activity			ovary(5)	5														0.275362	94.394164	100.663247	38	100	CC		KEEP	---	---	---	---	capture			Silent	SNP	49255948	49255948	8609	17	C	T	T	19	19	KIF2B	T	1	1
ANKFN1	162282	broad.mit.edu	36	17	51807044	51807044	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:51807044G>A	uc002iun.1	+	c.889G>A	c.(889-891)GTC>ATC	p.V297I		NM_153228	NP_694960	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain	297	Fibronectin type-III.									large_intestine(1)|ovary(1)	2														0.171598	52.46626	69.700942	29	140	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51807044	51807044	628	17	G	A	A	40	40	ANKFN1	A	1	1
CCDC46	201134	broad.mit.edu	36	17	61278597	61278597	+	Silent	SNP	C	T	T			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:61278597C>T	uc002jfl.1	-	c.2181G>A	c.(2179-2181)GAG>GAA	p.E727E	CCDC46_uc010deo.1_Silent_p.E469E|CCDC46_uc010dep.1_Silent_p.E685E	NM_145036	NP_659473	Q8N8E3	CCD46_HUMAN	coiled-coil domain containing 46 isoform a	727	Potential.										0														0.280899	71.336291	75.176769	25	64	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(6;1.53e-06)		Silent	SNP	61278597	61278597	2940	17	C	T	T	24	24	CCDC46	T	2	2
FADS6	283985	broad.mit.edu	36	17	70388897	70388897	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:70388897G>C	uc002jmd.1	-	c.622C>G	c.(622-624)CTC>GTC	p.L208V		NM_178128	NP_835229	Q8N9I5	FADS6_HUMAN	fatty acid desaturase domain family, member 6	214	Helical; (Potential).				fatty acid biosynthetic process|oxidation-reduction process	integral to membrane	oxidoreductase activity				0	all_lung(278;0.172)|Lung NSC(278;0.207)													0.333333	6.720437	6.942624	3	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70388897	70388897	5565	17	G	C	C	34	34	FADS6	C	3	3
GALK1	2584	broad.mit.edu	36	17	71265970	71265970	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:71265970G>C	uc002jpk.1	-	c.1023C>G	c.(1021-1023)AGC>AGG	p.S341R		NM_000154	NP_000145	P51570	GALK1_HUMAN	galactokinase 1	341					galactose catabolic process	cytosol	ATP binding|galactokinase activity|galactose binding				0	all_cancers(13;1.5e-07)													0.5	6.66665	6.66665	4	4	GG		KEEP	---	---	---	---	capture	all cancers(21;1.03e-06)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)		Missense_Mutation	SNP	71265970	71265970	6467	17	G	C	C	42	42	GALK1	C	3	3
CYP4F2	8529	broad.mit.edu	36	19	15851424	15851424	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:15851424G>A	uc002nbs.1	-	c.1304C>T	c.(1303-1305)CCG>CTG	p.P435L		NM_001082	NP_001073	P78329	CP4F2_HUMAN	cytochrome P450, family 4, subfamily F,	435					leukotriene metabolic process|long-chain fatty acid metabolic process|oxidation-reduction process|very long-chain fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	alkane 1-monooxygenase activity|electron carrier activity|heme binding|leukotriene-B4 20-monooxygenase activity|oxygen binding|protein binding			ovary(1)|skin(1)	2														0.164502	70.956847	95.603081	38	193	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15851424	15851424	4353	19	G	A	A	39	39	CYP4F2	A	1	1
DHDH	27294	broad.mit.edu	36	19	54131219	54131219	+	Silent	SNP	C	G	G			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:54131219C>G	uc002ple.1	+	c.321C>G	c.(319-321)CGC>CGG	p.R107R		NM_014475	NP_055290	Q9UQ10	DHDH_HUMAN	dimeric dihydrodiol dehydrogenase	107					carbohydrate metabolic process|oxidation-reduction process		binding|D-xylose 1-dehydrogenase (NADP+) activity|electron carrier activity|NAD(P)+ transhydrogenase activity|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity				0		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)												0.25	6.840062	7.723461	4	12	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)	Silent	SNP	54131219	54131219	4658	19	C	G	G	27	27	DHDH	G	3	3
LASS4	79603	broad.mit.edu	36	19	8226541	8226541	+	Silent	SNP	C	G	G			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8226541C>G	uc002mjg.1	+	c.342C>G	c.(340-342)ACC>ACG	p.T114T	LASS4_uc002mjh.1_Silent_p.T63T|LASS4_uc002mji.1_5'UTR|LASS4_uc010dvz.1_Silent_p.T114T	NM_024552	NP_078828	Q9HA82	LASS4_HUMAN	LAG1 homolog, ceramide synthase 4	114	Homeobox.				regulation of transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			ovary(1)	1														0.293333	61.620709	64.488029	22	53	CC		KEEP	---	---	---	---	capture			Silent	SNP	8226541	8226541	8964	19	C	G	G	22	22	LASS4	G	3	3
ATXN7L2	127002	broad.mit.edu	36	1	109828151	109828151	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0749-01	TCGA-06-0749-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:109828151T>G	uc001dxr.1	+	c.53T>G	c.(52-54)GTG>GGG	p.V18G		NM_153340	NP_699171	Q5T6C5	AT7L2_HUMAN	ataxin 7-like 2	18										ovary(2)	2		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)												0.428571	9.316606	9.402577	6	8	TT		KEEP	---	---	---	---	capture		Colorectal(144;0.0129)|Lung(183;0.0426)|Epithelial(280;0.0675)|READ - Rectum adenocarcinoma(129;0.0693)|all cancers(265;0.071)|LUSC - Lung squamous cell carcinoma(189;0.228)	Missense_Mutation	SNP	109828151	109828151	1237	1	T	G	G	59	59	ATXN7L2	G	4	4
FLG	2312	broad.mit.edu	36	1	150543510	150543510	+	Silent	SNP	G	A	A			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150543510G>A	uc001ezu.1	-	c.10476C>T	c.(10474-10476)GAC>GAT	p.D3492D		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	3492	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)													0.28876	383.509748	404.127778	149	367	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Silent	SNP	150543510	150543510	6160	1	G	A	A	40	40	FLG	A	1	1
LCE2C	353140	broad.mit.edu	36	1	150915401	150915401	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150915401C>A	uc001fah.1	+	c.286C>A	c.(286-288)CCT>ACT	p.P96T	LCE2C_uc009wnk.1_Missense_Mutation_p.P96T	NM_178429	NP_848516	Q5TA81	LCE2C_HUMAN	late cornified envelope 2C	96	Cys-rich.				keratinization						0	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)													0.224806	63.525311	72.493224	29	100	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150915401	150915401	8990	1	C	A	A	18	18	LCE2C	A	3	3
NUP210L	91181	broad.mit.edu	36	1	152328682	152328682	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:152328682G>A	uc001fdw.1	-	c.2200C>T	c.(2200-2202)CGA>TGA	p.R734*	NUP210L_uc009woq.1_5'UTR	NM_207308	NP_997191	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	734						integral to membrane				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)													0.353741	156.05746	158.829458	52	95	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)		Nonsense_Mutation	SNP	152328682	152328682	11166	1	G	A	A	39	39	NUP210L	A	5	1
ARHGAP30	257106	broad.mit.edu	36	1	159289726	159289726	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:159289726C>T	uc001fxl.1	-	c.610G>A	c.(610-612)GTG>ATG	p.V204M	ARHGAP30_uc001fxk.1_Missense_Mutation_p.V204M|ARHGAP30_uc001fxm.1_Missense_Mutation_p.V50M|ARHGAP30_uc009wtx.1_De_novo_Start_OutOfFrame|ARHGAP30_uc001fxn.1_Missense_Mutation_p.V50M	NM_001025598	NP_001020769	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30 isoform 1	204	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(2)	2	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)													0.35	74.477706	76.064895	28	52	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(70;0.00122)		Missense_Mutation	SNP	159289726	159289726	891	1	C	T	T	19	19	ARHGAP30	T	1	1
ARHGEF10L	55160	broad.mit.edu	36	1	17863560	17863560	+	Silent	SNP	C	T	T			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:17863560C>T	uc001ban.1	+	c.2892C>T	c.(2890-2892)CCC>CCT	p.P964P	ARHGEF10L_uc009vpe.1_Silent_p.P925P|ARHGEF10L_uc001bao.1_Silent_p.P925P|ARHGEF10L_uc001bap.1_Silent_p.P920P|ARHGEF10L_uc001baq.1_Silent_p.P725P|ARHGEF10L_uc001bar.1_Silent_p.P667P|ARHGEF10L_uc009vpf.1_Non-coding_Transcript	NM_018125	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF)	964					regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)|ovary(1)|pancreas(1)	3		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)												0.242424	19.885462	21.880569	8	25	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)	Silent	SNP	17863560	17863560	909	1	C	T	T	23	23	ARHGEF10L	T	1	1
TRIM11	81559	broad.mit.edu	36	1	226649486	226649486	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:226649486G>C	uc001hss.1	-	c.950C>G	c.(949-951)GCC>GGC	p.A317G		NM_145214	NP_660215	Q96F44	TRI11_HUMAN	tripartite motif-containing 11	317	B30.2/SPRY.				response to virus	cytoplasm|nucleus	protein binding|zinc ion binding				0		Prostate(94;0.0724)												0.357143	10.884814	11.130077	5	9	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	226649486	226649486	17031	1	G	C	C	42	42	TRIM11	C	3	3
NLRP3	114548	broad.mit.edu	36	1	245673971	245673971	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:245673971C>T	uc001icr.1	+	c.2744C>T	c.(2743-2745)ACG>ATG	p.T915M	NLRP3_uc001ics.1_Missense_Mutation_p.T858M|NLRP3_uc001icu.1_Missense_Mutation_p.T915M|NLRP3_uc001icw.1_Missense_Mutation_p.T858M|NLRP3_uc001icv.1_Missense_Mutation_p.T801M	NM_001079821	NP_004886	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3 isoform a	915	LRR 7.				detection of biotic stimulus|induction of apoptosis|inflammatory response|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|positive regulation of interleukin-1 beta secretion|protein oligomerization|signal transduction	cytoplasm	ATP binding|peptidoglycan binding|protein binding			ovary(5)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	11	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)								412				0.157895	20.401292	28.843775	12	64	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0141)		Missense_Mutation	SNP	245673971	245673971	10881	1	C	T	T	19	19	NLRP3	T	1	1
LAMA5	3911	broad.mit.edu	36	20	60321209	60321209	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:60321209C>G	uc002ycq.1	-	c.9101G>C	c.(9100-9102)GGC>GCC	p.G3034A		NM_005560	NP_005551	O15230	LAMA5_HUMAN	laminin alpha 5	3034	Laminin G-like 2.				angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding|receptor activity|structural molecule activity			pancreas(1)	1	Breast(26;1.57e-08)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)									0.3125	6.57863	7.077324	5	11	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		Missense_Mutation	SNP	60321209	60321209	8932	20	C	G	G	26	26	LAMA5	G	3	3
OPRL1	4987	broad.mit.edu	36	20	62194533	62194533	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:62194533C>T	uc002yic.1	+	c.16C>T	c.(16-18)CCC>TCC	p.P6S	OPRL1_uc002yid.1_Missense_Mutation_p.P6S|OPRL1_uc002yif.2_Missense_Mutation_p.P6S	NM_182647	NP_872588	P41146	OPRX_HUMAN	opiate receptor-like 1	6	Extracellular (Potential).				elevation of cytosolic calcium ion concentration|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception	integral to plasma membrane	protein binding|X-opioid receptor activity			central_nervous_system(1)	1	all_cancers(38;4.74e-11)|all_epithelial(29;1.33e-12)|Lung NSC(23;3.27e-09)|all_lung(23;1.02e-08)													0.220339	60.88349	69.38476	26	92	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	62194533	62194533	11292	20	C	T	T	22	22	OPRL1	T	2	2
SIM2	6493	broad.mit.edu	36	21	37035984	37035984	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0749-01	TCGA-06-0749-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr21:37035984A>C	uc002yvr.1	+	c.947A>C	c.(946-948)AAC>ACC	p.N316T	SIM2_uc002yvq.1_Missense_Mutation_p.N316T	NM_005069	NP_005060	Q14190	SIM2_HUMAN	single-minded homolog 2 long isoform	316	PAC.				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(1)	1														0.444444	6.716227	6.751553	4	5	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37035984	37035984	14819	21	A	C	C	2	2	SIM2	C	4	4
KCNJ15	3772	broad.mit.edu	36	21	38593403	38593403	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:38593403C>T	uc002ywv.1	+	c.350C>T	c.(349-351)GCG>GTG	p.A117V	KCNJ15_uc002yww.1_Missense_Mutation_p.A117V|KCNJ15_uc002ywx.1_Missense_Mutation_p.A117V|KCNJ15_uc010gnu.1_Missense_Mutation_p.A117V	NM_002243	NP_733933	Q99712	IRK15_HUMAN	potassium inwardly-rectifying channel J15	117					synaptic transmission	integral to plasma membrane	inward rectifier potassium channel activity			ovary(2)|breast(1)|central_nervous_system(1)	4														0.342246	172.671097	176.769581	64	123	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38593403	38593403	8354	21	C	T	T	27	27	KCNJ15	T	1	1
UMODL1	89766	broad.mit.edu	36	21	42395385	42395385	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:42395385C>A	uc002zag.1	+	c.1227C>A	c.(1225-1227)CAC>CAA	p.H409Q	UMODL1_uc002zad.1_Missense_Mutation_p.H337Q|UMODL1_uc002zae.1_Missense_Mutation_p.H337Q|UMODL1_uc002zaf.1_Missense_Mutation_p.H409Q|UMODL1_uc010gow.1_Missense_Mutation_p.H201Q|UMODL1_uc002zai.1_Non-coding_Transcript|UMODL1_uc010gox.1_Non-coding_Transcript|UMODL1_uc010goy.1_Missense_Mutation_p.H60Q|UMODL1_uc002zaj.1_Non-coding_Transcript|UMODL1_uc010goz.1_Missense_Mutation_p.H154Q	NM_173568	NP_775839	Q5DID0	UROL1_HUMAN	uromodulin-like 1 isoform 2 precursor	409	Extracellular (Potential).|SEA 1.					cytoplasm|extracellular region|integral to membrane|plasma membrane	calcium ion binding|peptidase inhibitor activity			ovary(2)	2						Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)								0.2	49.915074	58.703585	21	84	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42395385	42395385	17538	21	C	A	A	17	17	UMODL1	A	3	3
BID	637	broad.mit.edu	36	22	16606602	16606602	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0749-01	TCGA-06-0749-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:16606602T>G	uc002znc.1	-	c.328A>C	c.(328-330)AGC>CGC	p.S110R	BID_uc002znd.1_Missense_Mutation_p.S64R|BID_uc002zne.1_5'UTR|BID_uc010gra.1_Non-coding_Transcript|BID_uc002znf.1_Intron|BID_uc010grb.1_Missense_Mutation_p.S64R|BID_uc010grc.1_Intron	NM_197966	NP_001187	P55957	BID_HUMAN	BH3 interacting domain death agonist isoform 1	64					activation of pro-apoptotic gene products|establishment of protein localization in membrane|induction of apoptosis by intracellular signals|induction of apoptosis via death domain receptors|neuron apoptosis|positive regulation of protein homooligomerization|positive regulation of release of cytochrome c from mitochondria|release of cytochrome c from mitochondria	cytosol|membrane fraction|mitochondrial outer membrane	death receptor binding				0		all_epithelial(15;0.198)								1081				0.296296	10.972635	12.056745	8	19	TT		KEEP	---	---	---	---	capture		Lung(27;0.0419)	Missense_Mutation	SNP	16606602	16606602	1455	22	T	G	G	55	55	BID	G	4	4
RRP7A	27341	broad.mit.edu	36	22	41242085	41242085	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0749-01	TCGA-06-0749-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:41242085T>C	uc003bcp.1	-	c.287A>G	c.(286-288)GAG>GGG	p.E96G	RRP7A_uc003bcq.1_Missense_Mutation_p.E73G	NM_015703	NP_056518	Q9Y3A4	RRP7A_HUMAN	ribosomal RNA processing 7 homolog A	73	RRM.						nucleotide binding|RNA binding			central_nervous_system(1)	1														0.243243	8.305572	10.694285	9	28	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41242085	41242085	14169	22	T	C	C	54	54	RRP7A	C	4	4
MYO1B	4430	broad.mit.edu	36	2	191984037	191984037	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0749-01	TCGA-06-0749-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:191984037T>C	uc010fsg.1	+	c.2767T>C	c.(2767-2769)TGT>CGT	p.C923R	MYO1B_uc002usq.1_Missense_Mutation_p.C865R|MYO1B_uc002usr.1_Missense_Mutation_p.C923R|MYO1B_uc002usu.1_Missense_Mutation_p.C168R|MYO1B_uc002usv.1_Missense_Mutation_p.C39R	NM_012223	NP_036355	O43795	MYO1B_HUMAN	myosin IB isoform 2	923						myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(5)|large_intestine(2)|ovary(1)	8														0.359223	117.353428	119.147816	37	66	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)		Missense_Mutation	SNP	191984037	191984037	10464	2	T	C	C	59	59	MYO1B	C	4	4
OTOF	9381	broad.mit.edu	36	2	26558945	26558945	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0749-01	TCGA-06-0749-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:26558945T>C	uc002rhk.1	-	c.1412A>G	c.(1411-1413)AAG>AGG	p.K471R		NM_194248	NP_919224	Q9HC10	OTOF_HUMAN	otoferlin isoform a	471	Cytoplasmic (Potential).|C2 2.				cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis	basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane	calcium ion binding			ovary(3)|breast(2)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GBM(102;732 1451 20652 24062 31372)								0.272727	115.965823	122.620401	39	104	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	26558945	26558945	11715	2	T	C	C	56	56	OTOF	C	4	4
BIRC6	57448	broad.mit.edu	36	2	32548860	32548860	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0749-01	TCGA-06-0749-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:32548860T>A	uc010ezu.1	+	c.6468T>A	c.(6466-6468)CAT>CAA	p.H2156Q		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	2156					anti-apoptosis|apoptosis|post-translational protein modification	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					Pancreas(94;175 1509 16028 18060 45422)				1555				0.25	8.119786	8.801107	3	9	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32548860	32548860	1463	2	T	A	A	49	49	BIRC6	A	4	4
TAF1B	9014	broad.mit.edu	36	2	9911908	9911908	+	Silent	SNP	C	T	T			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:9911908C>T	uc002qzz.1	+	c.306C>T	c.(304-306)AAC>AAT	p.N102N	TAF1B_uc010exc.1_Silent_p.N102N|TAF1B_uc002qzy.2_Silent_p.N102N|TAF1B_uc010exd.1_De_novo_Start_OutOfFrame	NM_005680	NP_005671	Q53T94	TAF1B_HUMAN	TBP-associated factor 1B	102					regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|breast(1)|pancreas(1)	3	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)													0.221053	49.029186	55.829778	21	74	CC		KEEP	---	---	---	---	capture			Silent	SNP	9911908	9911908	16041	2	C	T	T	19	19	TAF1B	T	1	1
CASR	846	broad.mit.edu	36	3	123463220	123463220	+	Silent	SNP	C	T	T			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:123463220C>T	uc003eew.2	+	c.648C>T	c.(646-648)GAC>GAT	p.D216D	CASR_uc003eev.2_Silent_p.D216D	NM_000388	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	216	Extracellular (Potential).				anatomical structure morphogenesis|calcium ion import|cellular calcium ion homeostasis|chemosensory behavior|detection of calcium ion|ossification	integral to plasma membrane	G-protein coupled receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)	4					Cinacalcet(DB01012)									0.247826	134.958926	148.273918	57	173	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(114;0.226)	Silent	SNP	123463220	123463220	2801	3	C	T	T	19	19	CASR	T	1	1
ADCY5	111	broad.mit.edu	36	3	124521254	124521254	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:124521254C>T	uc003egh.1	-	c.2213G>A	c.(2212-2214)CGC>CAC	p.R738H	ADCY5_uc003egg.1_Missense_Mutation_p.R371H|ADCY5_uc003egi.1_Missense_Mutation_p.R297H	NM_183357	NP_899200	O95622	ADCY5_HUMAN	adenylate cyclase 5	738	Cytoplasmic (Potential).				activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)	4														0.211111	40.792976	47.728068	19	71	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(114;0.0342)	Missense_Mutation	SNP	124521254	124521254	298	3	C	T	T	27	27	ADCY5	T	1	1
FGD5	152273	broad.mit.edu	36	3	14837755	14837755	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0749-01	TCGA-06-0749-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:14837755T>A	uc003bzc.1	+	c.1450T>A	c.(1450-1452)TAT>AAT	p.Y484N		NM_152536	NP_689749	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	725					actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(3)|kidney(1)|pancreas(1)	5														0.328671	119.881826	123.600631	47	96	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	14837755	14837755	6073	3	T	A	A	61	61	FGD5	A	4	4
NBEAL2	23218	broad.mit.edu	36	3	47018713	47018713	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:47018713C>G	uc003cqp.2	+	c.5082C>G	c.(5080-5082)AGC>AGG	p.S1694R	NBEAL2_uc010hjm.1_Missense_Mutation_p.S1071R|NBEAL2_uc010hjn.1_Missense_Mutation_p.S90R|NBEAL2_uc010hjo.1_5'Flank	NM_015175	NP_055990	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	1694							binding			ovary(1)	1		Acute lymphoblastic leukemia(5;0.0534)												0.285714	6.417763	6.983093	4	10	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)	Missense_Mutation	SNP	47018713	47018713	10585	3	C	G	G	26	26	NBEAL2	G	3	3
ZNF718	255403	broad.mit.edu	36	4	145414	145414	+	Silent	SNP	C	T	T			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:145414C>T	uc003fzt.2	+	c.939C>T	c.(937-939)TGC>TGT	p.C313C	ZNF595_uc003fzu.1_Intron|ZNF718_uc010iaz.1_Non-coding_Transcript|ZNF718_uc003fzw.2_Missense_Mutation_p.A93V	NM_001039127	NP_001034216	Q3SXZ3	ZN718_HUMAN	zinc finger protein 718	313	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)												0.212766	22.226438	25.808361	10	37	CC		KEEP	---	---	---	---	capture		Lung(54;0.0681)|Epithelial(2;0.0838)|all cancers(2;0.135)|LUSC - Lung squamous cell carcinoma(95;0.18)	Silent	SNP	145414	145414	18717	4	C	T	T	27	27	ZNF718	T	1	1
RBM47	54502	broad.mit.edu	36	4	40135116	40135116	+	Silent	SNP	G	A	A			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:40135116G>A	uc003gvc.2	-	c.552C>T	c.(550-552)TAC>TAT	p.Y184Y	RBM47_uc003gve.2_Non-coding_Transcript|RBM47_uc003gvd.2_Silent_p.Y184Y|RBM47_uc003gvg.1_Silent_p.Y184Y	NM_001098634	NP_001092104	A0AV96	RBM47_HUMAN	RNA binding motif protein 47 isoform a	184	RRM 2.					nucleus	nucleotide binding|RNA binding			breast(3)	3														0.277778	129.516686	138.273021	55	143	GG		KEEP	---	---	---	---	capture			Silent	SNP	40135116	40135116	13603	4	G	A	A	40	40	RBM47	A	1	1
PPEF2	5470	broad.mit.edu	36	4	77012251	77012251	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:77012251C>T	uc003hix.1	-	c.1600G>A	c.(1600-1602)GTG>ATG	p.V534M	PPEF2_uc003hiy.1_Non-coding_Transcript|PPEF2_uc003hiz.1_Missense_Mutation_p.V534M	NM_006239	NP_006230	O14830	PPE2_HUMAN	serine/threonine protein phosphatase with	534	Catalytic.				detection of stimulus involved in sensory perception|protein dephosphorylation|visual perception	cytoplasm|photoreceptor inner segment|photoreceptor outer segment	calcium ion binding|iron ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity			ovary(2)|lung(1)|central_nervous_system(1)	4						NSCLC(105;1359 1603 15961 44567 47947)								0.233577	76.835014	85.73208	32	105	CC		KEEP	---	---	---	---	capture	Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)		Missense_Mutation	SNP	77012251	77012251	12738	4	C	T	T	17	17	PPEF2	T	2	2
ADAMTS12	81792	broad.mit.edu	36	5	33631882	33631882	+	Silent	SNP	G	A	A			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:33631882G>A	uc003jia.1	-	c.2568C>T	c.(2566-2568)CGC>CGT	p.R856R	ADAMTS12_uc010iuq.1_Silent_p.R771R	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	856	TSP type-1 2.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|lung(1)|kidney(1)|skin(1)	7														0.300578	134.36122	140.491373	52	121	GG		KEEP	---	---	---	---	capture			Silent	SNP	33631882	33631882	258	5	G	A	A	38	38	ADAMTS12	A	1	1
OR2H1	26716	broad.mit.edu	36	6	29538384	29538384	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:29538384G>A	uc003nmi.1	+	c.859G>A	c.(859-861)GTA>ATA	p.V287I	OR2H1_uc003nmj.1_Missense_Mutation_p.V287I|OR2H1_uc010jri.1_Missense_Mutation_p.V209I|OR2H1_uc010jrj.1_Missense_Mutation_p.V209I|OR2H1_uc010jrk.1_Missense_Mutation_p.V287I	NM_030883	NP_112145	Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H,	287	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.376238	107.324951	108.682822	38	63	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29538384	29538384	11407	6	G	A	A	40	40	OR2H1	A	1	1
GABBR1	2550	broad.mit.edu	36	6	29707207	29707207	+	Silent	SNP	G	A	A			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:29707207G>A	uc003nmt.2	-	c.234C>T	c.(232-234)GTC>GTT	p.V78V	GABBR1_uc003nmu.2_Silent_p.V78V|GABBR1_uc003nmv.2_Silent_p.V78V|GABBR1_uc003nmw.2_5'UTR	NM_001470	NP_001461	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor 1	78	Sushi 1.|Extracellular (Potential).				gamma-aminobutyric acid signaling pathway|negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|extracellular region|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(5)|liver(1)	6					Baclofen(DB00181)|Progabide(DB00837)									0.206897	72.602273	86.466336	36	138	GG		KEEP	---	---	---	---	capture			Silent	SNP	29707207	29707207	6406	6	G	A	A	41	41	GABBR1	A	2	2
RIPK1	8737	broad.mit.edu	36	6	3049536	3049536	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:3049536C>T	uc010jni.1	+	c.994C>T	c.(994-996)CGG>TGG	p.R332W	RIPK1_uc003muv.2_Missense_Mutation_p.R169W|RIPK1_uc003muw.2_Missense_Mutation_p.R267W|RIPK1_uc003mux.1_Missense_Mutation_p.R332W	NM_003804	NP_003795	Q13546	RIPK1_HUMAN	receptor (TNFRSF)-interacting serine-threonine	332	Interaction with SQSTM1.				activation of caspase activity|activation of JUN kinase activity|activation of pro-apoptotic gene products|induction of apoptosis by extracellular signals|induction of necroptosis by extracellular signals|innate immune response|MyD88-independent toll-like receptor signaling pathway|positive regulation of anti-apoptosis|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of tumor necrosis factor production|protein autophosphorylation|regulation of ATP:ADP antiporter activity|regulation of oxygen and reactive oxygen species metabolic process|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|tumor necrosis factor-mediated signaling pathway	cytosol|death-inducing signaling complex|endosome membrane|mitochondrion|receptor complex	ATP binding|death domain binding|death receptor binding|protein serine/threonine kinase activity			large_intestine(3)|lung(1)|skin(1)	5	Ovarian(93;0.0386)	all_hematologic(90;0.0895)								138				0.23301	59.156	65.871395	24	79	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3049536	3049536	13857	6	C	T	T	23	23	RIPK1	T	1	1
ASZ1	136991	broad.mit.edu	36	7	116807278	116807278	+	Silent	SNP	T	C	C			TCGA-06-0749-01	TCGA-06-0749-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:116807278T>C	uc003vjb.2	-	c.1005A>G	c.(1003-1005)GTA>GTG	p.V335V		NM_130768	NP_570124	Q8WWH4	ASZ1_HUMAN	ankyrin repeat, SAM and basic leucine zipper	335					cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	pi-body	signal transducer activity			central_nervous_system(2)|ovary(1)	3	Lung NSC(10;0.00156)|all_lung(10;0.00175)													0.102273	9.608706	23.484029	9	79	TT		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(10;0.000512)		Silent	SNP	116807278	116807278	1088	7	T	C	C	53	53	ASZ1	C	4	4
CLCN1	1180	broad.mit.edu	36	7	142758855	142758855	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:142758855G>A	uc003wcr.1	+	c.2642G>A	c.(2641-2643)CGC>CAC	p.R881H		NM_000083	NP_000074	P35523	CLCN1_HUMAN	chloride channel 1, skeletal muscle	881	Cytoplasmic (By similarity).				muscle contraction	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			ovary(1)|breast(1)|central_nervous_system(1)	3	Melanoma(164;0.205)													0.25	67.954011	74.734844	30	90	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	142758855	142758855	3598	7	G	A	A	38	38	CLCN1	A	1	1
RAMP3	10268	broad.mit.edu	36	7	45183512	45183512	+	Silent	SNP	C	T	T			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:45183512C>T	uc003tnb.1	+	c.138C>T	c.(136-138)GAC>GAT	p.D46D	RAMP3_uc003tnc.1_Silent_p.D14D	NM_005856	NP_005847	O60896	RAMP3_HUMAN	receptor activity modifying protein 3 precursor	46	Extracellular (Potential).				intracellular protein transport|receptor-mediated endocytosis|regulation of G-protein coupled receptor protein signaling pathway	integral to plasma membrane|lysosome	protein transporter activity				0					Pramlintide(DB01278)									0.122302	14.968386	34.407131	17	122	CC		KEEP	---	---	---	---	capture			Silent	SNP	45183512	45183512	13483	7	C	T	T	17	17	RAMP3	T	2	2
TNRC18	84629	broad.mit.edu	36	7	5384134	5384134	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:5384134G>A	uc003soi.2	-	c.2200C>T	c.(2200-2202)CGG>TGG	p.R734W		NM_001080495	NP_001073964	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	734							DNA binding				0		Ovarian(82;0.142)												0.144144	24.470676	37.970296	16	95	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)	Missense_Mutation	SNP	5384134	5384134	16880	7	G	A	A	39	39	TNRC18	A	1	1
EGFR	1956	broad.mit.edu	36	7	55189315	55189315	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55189315G>A	uc003tqk.1	+	c.865G>A	c.(865-867)GCC>ACC	p.A289T	EGFR_uc003tqh.1_Missense_Mutation_p.A289T|EGFR_uc003tqi.1_Missense_Mutation_p.A289T|EGFR_uc003tqj.1_Missense_Mutation_p.A289T|EGFR_uc010kzg.1_Missense_Mutation_p.A244T	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	289	Approximate.|Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.V30_R297>G(10)|p.A289T(3)		lung(8200)|central_nervous_system(103)|upper_aerodigestive_tract(37)|prostate(32)|ovary(31)|thyroid(23)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|stomach(6)|urinary_tract(6)|skin(5)|adrenal_gland(5)|kidney(4)|soft_tissue(4)|bone(3)|NS(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)|pancreas(1)	8515	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)				Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8		608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.25	82.164679	91.024635	39	117	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Missense_Mutation	SNP	55189315	55189315	5156	7	G	A	A	46	46	EGFR	A	2	2
EGFR	1956	broad.mit.edu	36	7	55216516	55216516	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55216516G>A	uc003tqk.1	+	c.2320G>A	c.(2320-2322)GTG>ATG	p.V774M	EGFR_uc010kzg.1_Missense_Mutation_p.V729M	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	774	Cytoplasmic (Potential).|Protein kinase.				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.H773_V774insNPH(11)|p.H773_V774insH(3)|p.V774M(3)|p.H773_V774insPH(2)|p.H773_V774insGH(1)|p.H773_V774insG(1)|p.G729R(1)|p.H773_V774>LM(1)|p.V774L(1)|p.V774_C775insHV(1)|p.H773_V774insGNPH(1)|p.V774del(1)|p.G729E(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)			0.125475	38.777628	74.738036	33	230	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Missense_Mutation	SNP	55216516	55216516	5156	7	G	A	A	40	40	EGFR	A	1	1
MCM7	4176	broad.mit.edu	36	7	99532863	99532863	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:99532863G>A	uc003usw.1	-	c.1198C>T	c.(1198-1200)CGC>TGC	p.R400C	MCM7_uc003usv.1_Missense_Mutation_p.R224C|MCM7_uc003usx.1_Missense_Mutation_p.R224C	NM_005916	NP_005907	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	400	MCM.				cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|regulation of phosphorylation|response to DNA damage stimulus|S phase of mitotic cell cycle	chromatin|MCM complex	ATP binding|protein binding				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)				Atorvastatin(DB01076)									0.25	67.782354	73.911934	27	81	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99532863	99532863	9781	7	G	A	A	37	37	MCM7	A	1	1
KCNB2	9312	broad.mit.edu	36	8	74011468	74011468	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:74011468C>T	uc003xzb.1	+	c.1324C>T	c.(1324-1326)CGG>TGG	p.R442W		NM_004770	NP_004761	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related	442	Cytoplasmic (Potential).				regulation of smooth muscle contraction	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|protein binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|pancreas(1)	4	Breast(64;0.137)													0.294118	127.479912	133.931104	50	120	CC		KEEP	---	---	---	---	capture	Epithelial(68;0.105)		Missense_Mutation	SNP	74011468	74011468	8318	8	C	T	T	27	27	KCNB2	T	1	1
PRDM12	59335	broad.mit.edu	36	9	132546603	132546603	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0749-01	TCGA-06-0749-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:132546603A>C	uc004bzt.1	+	c.830A>C	c.(829-831)AAC>ACC	p.N277T		NM_021619	NP_067632	Q9H4Q4	PRD12_HUMAN	PR domain containing 12	277	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_hematologic(13;0.0433)|Acute lymphoblastic leukemia(5;0.0534)												0.2	6.316422	7.572152	3	12	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;0.000344)	Missense_Mutation	SNP	132546603	132546603	12895	9	A	C	C	2	2	PRDM12	C	4	4
BNC2	54796	broad.mit.edu	36	9	16409304	16409304	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0749-01	TCGA-06-0749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:16409304C>T	uc003zml.1	-	c.2983G>A	c.(2983-2985)GGG>AGG	p.G995R	BNC2_uc003zmm.2_3'UTR|BNC2_uc010mii.1_3'UTR|BNC2_uc003zmi.1_Missense_Mutation_p.G782R|BNC2_uc003zmj.1_3'UTR|BNC2_uc003zmk.1_Non-coding_Transcript	NM_017637	NP_060107	Q6ZN30	BNC2_HUMAN	basonuclin 2	995					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	zinc ion binding			ovary(2)|central_nervous_system(1)	3														0.220339	62.505152	70.989493	26	92	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(50;9.01e-08)	Missense_Mutation	SNP	16409304	16409304	1500	9	C	T	T	23	23	BNC2	T	1	1
TAF1L	138474	broad.mit.edu	36	9	32621824	32621824	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:32621824G>A	uc003zrg.1	-	c.3754C>T	c.(3754-3756)CGG>TGG	p.R1252W		NM_153809	NP_722516	Q8IZX4	TAF1L_HUMAN	TBP-associated factor RNA polymerase 1-like	1252					male meiosis|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	transcription factor TFIID complex	DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding|transcription activator activity			lung(8)|large_intestine(3)|central_nervous_system(3)|skin(2)|ovary(2)|breast(1)|pancreas(1)	20									p.R1252W(SNU407-Tumor)	234				0.574324	258.695975	259.412967	85	63	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)	Missense_Mutation	SNP	32621824	32621824	16044	9	G	A	A	38	38	TAF1L	A	1	1
PGM5	5239	broad.mit.edu	36	9	70304077	70304077	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0749-01	TCGA-06-0749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:70304077G>A	uc004agr.1	+	c.1594G>A	c.(1594-1596)GGC>AGC	p.G532S		NM_021965	NP_068800	Q15124	PGM5_HUMAN	phosphoglucomutase 5	532					cell adhesion|cellular calcium ion homeostasis|glucose metabolic process	costamere|dystrophin-associated glycoprotein complex|focal adhesion|intercalated disc|internal side of plasma membrane|sarcolemma|spot adherens junction|stress fiber|Z disc	intramolecular transferase activity, phosphotransferases|magnesium ion binding|structural molecule activity			ovary(1)|pancreas(1)	2														0.133333	10.95871	18.789719	8	52	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70304077	70304077	12224	9	G	A	A	39	39	PGM5	A	1	1
PTEN	5728	broad.mit.edu	36	10	89710718	89710718	+	Frame_Shift_Del	DEL	G	-	-			TCGA-06-0749-01	TCGA-06-0749-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:89710718_89710718delG	uc001kfb.1	+	c.889_889delG	c.(889-891)GATfs	p.D297fs		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	297	C2 tensin-type.				apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of focal adhesion assembly|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of cyclin-dependent protein kinase activity|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.G165_K342del(1)|p.G165_*404del(1)|p.W274_F341del(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)				31		264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.46			45	52				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	89710718	89710718	13192	10	G	-	-	45	45	PTEN	-	5	5
STAG2	10735	broad.mit.edu	36	X	123032727	123032728	+	Frame_Shift_Del	DEL	TA	-	-			TCGA-06-0749-01	TCGA-06-0749-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:123032727_123032728delTA	uc004eua.1	+	c.2406_2407delTA	c.(2404-2409)ATTATGfs	p.I802fs	STAG2_uc004etz.2_Frame_Shift_Del_p.I802fs|STAG2_uc004eub.1_Frame_Shift_Del_p.I802fs|STAG2_uc004euc.1_Frame_Shift_Del_p.I802fs|STAG2_uc004eud.1_Frame_Shift_Del_p.I802fs|STAG2_uc004eue.1_Frame_Shift_Del_p.I802fs	NM_001042749	NP_001036215	Q8N3U4	STAG2_HUMAN	stromal antigen 2 isoform a	802_803					cell division|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|negative regulation of DNA endoreduplication|sister chromatid cohesion	chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(4)|skin(1)	5														0.60			116	77				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	123032727	123032728	15761	23	TA	-	-	61	61	STAG2	-	5	5
