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
OR52E8	390079	broad.mit.edu	36	11	5834707	5834707	+	Missense_Mutation	SNP	G	C	C			TCGA-12-1093-01	TCGA-12-1093-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:5834707G>C	uc001mbz.1	-	c.802C>G	c.(802-804)CGT>GGT	p.R268G	TRIM5_uc001mbq.1_Intron	NM_001005168	NP_001005168	Q6IFG1	O52E8_HUMAN	olfactory receptor, family 52, subfamily E,	268	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.114)		Epithelial(150;2.37e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)										0.175439	42.010194	53.373989	20	94	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5834707	5834707	11528	11	G	C	C	37	37	OR52E8	C	3	3
MS4A5	64232	broad.mit.edu	36	11	59954929	59954929	+	Missense_Mutation	SNP	C	G	G			TCGA-12-1093-01	TCGA-12-1093-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:59954929C>G	uc001npo.1	+	c.238C>G	c.(238-240)CCC>GCC	p.P80A		NM_023945	NP_076434	Q9H3V2	MS4A5_HUMAN	membrane-spanning 4-domains, subfamily A, member	80	Extracellular (Potential).					integral to membrane	receptor activity			large_intestine(1)|ovary(1)	2														0.162393	38.349477	51.029951	19	98	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59954929	59954929	10256	11	C	G	G	30	30	MS4A5	G	3	3
NOS1	4842	broad.mit.edu	36	12	116208411	116208411	+	Missense_Mutation	SNP	T	G	G			TCGA-12-1093-01	TCGA-12-1093-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:116208411T>G	uc001twm.1	-	c.1171A>C	c.(1171-1173)AAA>CAA	p.K391Q		NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1 (neuronal)	391					arginine catabolic process|multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|oxidation-reduction process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(2)|pancreas(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)	Esophageal Squamous(162;1748 2599 51982 52956)								0.146245	75.419848	105.839775	37	216	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	116208411	116208411	10944	12	T	G	G	63	63	NOS1	G	4	4
KCNA5	3741	broad.mit.edu	36	12	5025364	5025364	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1093-01	TCGA-12-1093-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:5025364G>A	uc001qni.1	+	c.1790G>A	c.(1789-1791)CGG>CAG	p.R597Q		NM_002234	NP_002225	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related	597						Golgi apparatus|voltage-gated potassium channel complex	delayed rectifier potassium channel activity			ovary(2)|breast(2)	4														0.680556	172.400376	174.487126	49	23	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5025364	5025364	8311	12	G	A	A	39	39	KCNA5	A	1	1
FLT3	2322	broad.mit.edu	36	13	27534162	27534162	+	Missense_Mutation	SNP	C	G	G			TCGA-12-1093-01	TCGA-12-1093-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:27534162C>G	uc001urw.1	-	c.210G>C	c.(208-210)CAG>CAC	p.Q70H	FLT3_uc010aao.1_Non-coding_Transcript	NM_004119	NP_004110	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	70	Extracellular (Potential).				positive regulation of cell proliferation	integral to plasma membrane	ATP binding|vascular endothelial growth factor receptor activity	p.599_560>LTGSSDNEYFYVDFREYEY(1)		haematopoietic_and_lymphoid_tissue(8072)|ovary(2)|lung(1)|central_nervous_system(1)	8076	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Sorafenib(DB00398)|Sunitinib(DB01268)					630				0.190476	141.21537	169.432908	60	255	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27534162	27534162	6184	13	C	G	G	32	32	FLT3	G	3	3
OR4K5	79317	broad.mit.edu	36	14	19459253	19459253	+	Silent	SNP	C	T	T			TCGA-12-1093-01	TCGA-12-1093-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:19459253C>T	uc001vwi.1	+	c.648C>T	c.(646-648)AGC>AGT	p.S216S		NM_001005483	NP_001005483	Q8NGD3	OR4K5_HUMAN	olfactory receptor, family 4, subfamily K,	216	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)										0.092971	17.547119	91.068974	41	400	CC		KEEP	---	---	---	---	capture			Silent	SNP	19459253	19459253	11483	14	C	T	T	28	28	OR4K5	T	2	2
SALL2	6297	broad.mit.edu	36	14	21062967	21062967	+	Silent	SNP	G	T	T			TCGA-12-1093-01	TCGA-12-1093-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:21062967G>T	uc001wbe.1	-	c.735C>A	c.(733-735)ATC>ATA	p.I245I	SALL2_uc001wbf.2_Intron|SALL2_uc001wbg.1_Intron	NM_005407	NP_005398	Q9Y467	SALL2_HUMAN	sal-like 2	245							DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|large_intestine(1)	3	all_cancers(95;0.000662)			GBM - Glioblastoma multiforme(265;0.0151)										0.159292	31.576065	44.077615	18	95	GG		KEEP	---	---	---	---	capture			Silent	SNP	21062967	21062967	14291	14	G	T	T	45	45	SALL2	T	3	3
DUOX2	50506	broad.mit.edu	36	15	43187577	43187577	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1093-01	TCGA-12-1093-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:43187577G>A	uc010bea.1	-	c.1534C>T	c.(1534-1536)CGG>TGG	p.R512W	DUOX2_uc001zun.1_Missense_Mutation_p.R512W	NM_014080	NP_054799	Q9NRD8	DUOX2_HUMAN	dual oxidase 2 precursor	512	Extracellular (Potential).|Peroxidase-like; mediates peroxidase activity (By similarity).				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide catabolic process|oxidation-reduction process|response to cAMP|response to virus	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|peroxidase activity			ovary(2)|pancreas(1)	3		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)										0.384615	45.416206	45.87128	15	24	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43187577	43187577	4986	15	G	A	A	38	38	DUOX2	A	1	1
SLC27A2	11001	broad.mit.edu	36	15	48282043	48282043	+	Silent	SNP	C	T	T			TCGA-12-1093-01	TCGA-12-1093-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:48282043C>T	uc001zxw.1	+	c.756C>T	c.(754-756)AGC>AGT	p.S252S	SLC27A2_uc010bes.1_Intron|SLC27A2_uc001zxx.1_Silent_p.S17S	NM_003645	NP_003636	O14975	S27A2_HUMAN	solute carrier family 27 (fatty acid	252	Lumenal (Potential).				bile acid biosynthetic process|fatty acid alpha-oxidation	endoplasmic reticulum membrane|integral to membrane|peroxisomal matrix|peroxisomal membrane	ATP binding|long-chain fatty acid-CoA ligase activity|phytanate-CoA ligase activity|pristanate-CoA ligase activity			ovary(1)	1		all_lung(180;0.00177)		all cancers(107;1.16e-06)|GBM - Glioblastoma multiforme(94;0.000113)										0.220779	112.698148	129.286184	51	180	CC		KEEP	---	---	---	---	capture			Silent	SNP	48282043	48282043	15023	15	C	T	T	27	27	SLC27A2	T	1	1
DIS3L	115752	broad.mit.edu	36	15	64386307	64386307	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1093-01	TCGA-12-1093-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:64386307C>T	uc002app.1	+	c.136C>T	c.(136-138)CGG>TGG	p.R46W	DIS3L_uc002apq.1_Missense_Mutation_p.R129W|DIS3L_uc010bho.1_De_novo_Start_OutOfFrame	NM_133375	NP_588616	Q8TF46	DI3L1_HUMAN	DIS3 mitotic control homolog (S.	129					rRNA catabolic process	cytoplasm|exosome (RNase complex)	exonuclease activity|ribonuclease activity|RNA binding			ovary(2)	2														0.209091	51.168903	59.786297	23	87	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	64386307	64386307	4715	15	C	T	T	19	19	DIS3L	T	1	1
CIITA	4261	broad.mit.edu	36	16	10908282	10908282	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1093-01	TCGA-12-1093-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:10908282G>A	uc002daj.2	+	c.1435G>A	c.(1435-1437)GTG>ATG	p.V479M	CIITA_uc002dag.2_Missense_Mutation_p.V478M|CIITA_uc002dah.2_Missense_Mutation_p.V430M|CIITA_uc010bup.1_Intron|CIITA_uc002dai.2_Missense_Mutation_p.V478M|CIITA_uc002dak.2_Intron	NM_000246	NP_000237	P33076	C2TA_HUMAN	class II transactivator	478	NACHT.				interferon-gamma-mediated signaling pathway|negative regulation of collagen biosynthetic process|negative regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of MHC class I biosynthetic process|positive regulation of MHC class II biosynthetic process|response to antibiotic|transcription, DNA-dependent	nucleus	activating transcription factor binding|ATP binding|promoter binding|protein C-terminus binding|protein complex binding|RNA polymerase II transcription factor activity|transcription activator activity|transcription coactivator activity|transcription repressor activity			central_nervous_system(1)	1										532				0.240964	100.821201	110.982307	40	126	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10908282	10908282	3562	16	G	A	A	40	40	CIITA	A	1	1
PKD1L2	114780	broad.mit.edu	36	16	79798676	79798676	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1093-01	TCGA-12-1093-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:79798676G>A	uc002fgh.1	-	c.826C>T	c.(826-828)CTC>TTC	p.L276F	PKD1L2_uc002fgj.1_Missense_Mutation_p.L276F	NM_052892	NP_443124	Q7Z442	PK1L2_HUMAN	polycystin 1-like 2 isoform a	276	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.518519	41.146481	41.154389	14	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	79798676	79798676	12389	16	G	A	A	34	34	PKD1L2	A	2	2
TUSC5	286753	broad.mit.edu	36	17	1148299	1148299	+	Missense_Mutation	SNP	G	T	T			TCGA-12-1093-01	TCGA-12-1093-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:1148299G>T	uc002fsi.1	+	c.525G>T	c.(523-525)CAG>CAT	p.Q175H		NM_172367	NP_758955	Q8IXB3	TUSC5_HUMAN	LOST1	175					response to biotic stimulus	integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)										0.363636	7.691258	7.873389	4	7	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1148299	1148299	17335	17	G	T	T	33	33	TUSC5	T	3	3
KRT31	3881	broad.mit.edu	36	17	36807046	36807046	+	Missense_Mutation	SNP	C	G	G			TCGA-12-1093-01	TCGA-12-1093-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36807046C>G	uc002hwn.1	-	c.272G>C	c.(271-273)CGG>CCG	p.R91P	KRT31_uc010cxn.1_Missense_Mutation_p.R91P	NM_002277	NP_002268	Q15323	K1H1_HUMAN	keratin 31	91	Coil 1A.|Rod.				epidermis development	intermediate filament	protein binding|structural constituent of cytoskeleton				0		Breast(137;0.000496)												0.24	9.932422	11.480962	6	19	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36807046	36807046	8782	17	C	G	G	23	23	KRT31	G	3	3
MAP3K14	9020	broad.mit.edu	36	17	40707384	40707384	+	Missense_Mutation	SNP	C	A	A			TCGA-12-1093-01	TCGA-12-1093-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:40707384C>A	uc002iiw.1	-	c.1441G>T	c.(1441-1443)GTC>TTC	p.V481F	MAP3K14_uc002iiu.1_5'Flank|MAP3K14_uc010daj.1_Non-coding_Transcript|MAP3K14_uc002iiv.1_Missense_Mutation_p.V65F	NM_003954	NP_003945	Q99558	M3K14_HUMAN	mitogen-activated protein kinase kinase kinase	481	Interaction with ZFP91.|Protein kinase.				cellular response to mechanical stimulus|I-kappaB kinase/NF-kappaB cascade|immune response|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein phosphorylation|T cell costimulation	cytosol	ATP binding|MAP kinase kinase kinase activity|NF-kappaB-inducing kinase activity|protein binding			central_nervous_system(3)|ovary(1)|lung(1)	5										697				0.357143	18.226876	18.736244	10	18	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40707384	40707384	9631	17	C	A	A	18	18	MAP3K14	A	3	3
SUPT4H1	6827	broad.mit.edu	36	17	53779917	53779917	+	Silent	SNP	G	A	A			TCGA-12-1093-01	TCGA-12-1093-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:53779917G>A	uc002iwe.1	-	c.204C>T	c.(202-204)GAC>GAT	p.D68D	SUPT4H1_uc002iwd.1_Non-coding_Transcript	NM_003168	NP_003159	P63272	SPT4H_HUMAN	suppressor of Ty 4 homolog 1	68					chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	negative transcription elongation factor activity|positive transcription elongation factor activity|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	Medulloblastoma(34;0.127)|all_neural(34;0.237)					NSCLC(25;723 896 19867 29219 40028)								0.180851	71.830579	89.837114	34	154	GG		KEEP	---	---	---	---	capture			Silent	SNP	53779917	53779917	15918	17	G	A	A	48	48	SUPT4H1	A	2	2
CALR3	125972	broad.mit.edu	36	19	16462301	16462301	+	Missense_Mutation	SNP	C	A	A			TCGA-12-1093-01	TCGA-12-1093-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:16462301C>A	uc002ned.2	-	c.274G>T	c.(274-276)GTT>TTT	p.V92F	MED26_uc002nee.2_Intron	NM_145046	NP_659483	Q96L12	CALR3_HUMAN	calreticulin 3	92	N-domain.				protein folding	endoplasmic reticulum lumen	calcium ion binding|sugar binding|unfolded protein binding				0														0.465909	371.69415	371.961199	123	141	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16462301	16462301	2710	19	C	A	A	18	18	CALR3	A	3	3
HRC	3270	broad.mit.edu	36	19	54349908	54349908	+	Silent	SNP	C	T	T			TCGA-12-1093-01	TCGA-12-1093-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:54349908C>T	uc002pmv.1	-	c.399G>A	c.(397-399)GGG>GGA	p.G133G	TRPM4_uc002pmw.1_5'Flank|TRPM4_uc010emu.1_5'Flank|TRPM4_uc002pmx.1_5'Flank|TRPM4_uc010emv.1_5'Flank	NM_002152	NP_002143	P23327	SRCH_HUMAN	histidine rich calcium binding protein	133	4 X tandem repeats, acidic.|6 X approximate tandem repeats.				muscle contraction	sarcoplasmic reticulum lumen	calcium ion binding			ovary(1)	1		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		Melanoma(37;75 1097 24567 25669 30645)								0.245283	29.647649	32.78149	13	40	CC		KEEP	---	---	---	---	capture			Silent	SNP	54349908	54349908	7644	19	C	T	T	26	26	HRC	T	2	2
ZNF836	162962	broad.mit.edu	36	19	57350535	57350535	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1093-01	TCGA-12-1093-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:57350535G>A	uc002pyo.2	-	c.2213C>T	c.(2212-2214)ACG>ATG	p.T738M	ZNF836_uc010epl.1_Missense_Mutation_p.T738M	NM_001102657	NP_001096127	Q6ZNA1	ZN836_HUMAN	zinc finger protein 836	738	C2H2-type 19.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.136364	82.28273	127.331287	48	304	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	57350535	57350535	18786	19	G	A	A	40	40	ZNF836	A	1	1
NLRP8	126205	broad.mit.edu	36	19	61165247	61165247	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1093-01	TCGA-12-1093-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:61165247C>T	uc002qmh.1	+	c.2045C>T	c.(2044-2046)GCG>GTG	p.A682V	NLRP8_uc010etg.1_Missense_Mutation_p.A682V	NM_176811	NP_789781	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	682						cytoplasm	ATP binding			ovary(4)|breast(3)|large_intestine(1)|kidney(1)|skin(1)	10		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)										0.129032	54.099464	91.495624	36	243	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	61165247	61165247	10886	19	C	T	T	27	27	NLRP8	T	1	1
CD209	30835	broad.mit.edu	36	19	7714042	7714042	+	Silent	SNP	G	A	A			TCGA-12-1093-01	TCGA-12-1093-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:7714042G>A	uc002mht.1	-	c.1098C>T	c.(1096-1098)GAC>GAT	p.D366D	CD209_uc010dvp.1_3'UTR|CD209_uc002mhs.1_Silent_p.D296D|CD209_uc002mhq.1_Silent_p.D366D|CD209_uc002mhr.1_Silent_p.D342D|CD209_uc002mhu.1_Silent_p.D274D|CD209_uc010dvq.1_Silent_p.D360D|CD209_uc002mhv.1_Silent_p.D342D|CD209_uc002mhw.1_Silent_p.D230D|CD209_uc002mhx.1_Silent_p.D322D|CD209_uc010dvr.1_Silent_p.D130D	NM_021155	NP_066978	Q9NNX6	CD209_HUMAN	CD209 molecule isoform 1	366	Extracellular (Probable).|C-type lectin.	Calcium.		D->A: Loss of binding to ICAM3 and HIV-1 gp120.	cell-cell recognition|endocytosis|heterophilic cell-cell adhesion|innate immune response|intracellular signal transduction|intracellular virion transport|leukocyte cell-cell adhesion|peptide antigen transport|viral genome replication|virion attachment to host cell surface receptor	cytoplasm|extracellular region|integral to membrane|plasma membrane	mannose binding|metal ion binding|peptide antigen binding|receptor activity|virion binding				0														0.196078	178.379799	213.500794	80	328	GG		KEEP	---	---	---	---	capture			Silent	SNP	7714042	7714042	3111	19	G	A	A	40	40	CD209	A	1	1
TCHH	7062	broad.mit.edu	36	1	150347187	150347187	+	Silent	SNP	G	C	C			TCGA-12-1093-01	TCGA-12-1093-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150347187G>C	uc001ezp.2	-	c.5130C>G	c.(5128-5130)CTC>CTG	p.L1710L	TCHH_uc009wne.1_Silent_p.L1710L	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	1710	23 X 26 AA approximate tandem repeats.				keratinization	cytoskeleton	calcium ion binding			ovary(3)|kidney(1)|central_nervous_system(1)	5	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.113095	20.493201	45.371767	19	149	GG		KEEP	---	---	---	---	capture			Silent	SNP	150347187	150347187	16226	1	G	C	C	41	41	TCHH	C	3	3
IL6R	3570	broad.mit.edu	36	1	152687242	152687242	+	Missense_Mutation	SNP	G	T	T			TCGA-12-1093-01	TCGA-12-1093-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:152687242G>T	uc001fez.1	+	c.967G>T	c.(967-969)GCT>TCT	p.A323S	IL6R_uc001ffa.1_Missense_Mutation_p.A323S	NM_000565	NP_000556	P08887	IL6RA_HUMAN	interleukin 6 receptor isoform 1 precursor	323	Extracellular (Potential).				acute-phase response|ciliary neurotrophic factor-mediated signaling pathway|defense response to Gram-negative bacterium|defense response to Gram-positive bacterium|endocrine pancreas development|hepatic immune response|monocyte chemotaxis|negative regulation of collagen biosynthetic process|negative regulation of interleukin-8 production|neutrophil mediated immunity|positive regulation of activation of Janus kinase activity|positive regulation of anti-apoptosis|positive regulation of chemokine production|positive regulation of chemokine production|positive regulation of interleukin-6 production|positive regulation of leukocyte chemotaxis|positive regulation of leukocyte chemotaxis|positive regulation of MAPKKK cascade|positive regulation of osteoblast differentiation|positive regulation of smooth muscle cell proliferation|positive regulation of tyrosine phosphorylation of Stat3 protein|regulation of apoptosis	apical plasma membrane|basolateral plasma membrane|extracellular space|interleukin-6 receptor complex	ciliary neurotrophic factor binding|enzyme binding|protein homodimerization activity			ovary(3)|breast(1)	4	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)											0.220339	93.929484	106.677029	39	138	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152687242	152687242	8003	1	G	T	T	34	34	IL6R	T	3	3
ASPM	259266	broad.mit.edu	36	1	195360086	195360086	+	Splice_Site_SNP	SNP	T	A	A			TCGA-12-1093-01	TCGA-12-1093-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:195360086T>A	uc001gtu.1	-	c.e13_splice_site			ASPM_uc001gtv.1_Splice_Site_SNP|ASPM_uc001gtw.2_Intron	NM_018136	NP_060606			asp (abnormal spindle)-like, microcephaly						mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6														0.285714	6.793081	7.371504	4	10	TT		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	195360086	195360086	1075	1	T	A	A	53	53	ASPM	A	5	4
CNTN2	6900	broad.mit.edu	36	1	203300958	203300958	+	Missense_Mutation	SNP	A	C	C			TCGA-12-1093-01	TCGA-12-1093-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:203300958A>C	uc001hbr.1	+	c.1640A>C	c.(1639-1641)GAC>GCC	p.D547A	CNTN2_uc001hbq.1_Missense_Mutation_p.D438A|CNTN2_uc001hbs.1_Missense_Mutation_p.D335A	NM_005076	NP_005067	Q02246	CNTN2_HUMAN	contactin 2 precursor	547	Ig-like C2-type 6.				axon guidance|clustering of voltage-gated potassium channels	anchored to membrane|juxtaparanode region of axon|myelin sheath|node of Ranvier|synapse part	identical protein binding			ovary(1)	1	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			Melanoma(183;2548 2817 37099 41192)								0.116438	7.062836	28.240262	17	129	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	203300958	203300958	3779	1	A	C	C	10	10	CNTN2	C	4	4
ALPL	249	broad.mit.edu	36	1	21762191	21762191	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1093-01	TCGA-12-1093-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:21762191C>T	uc001bet.1	+	c.299C>T	c.(298-300)ACG>ATG	p.T100M	ALPL_uc001beu.2_Missense_Mutation_p.T100M	NM_000478	NP_001120973	P05186	PPBT_HUMAN	tissue-nonspecific alkaline phosphatase	100					response to vitamin D|skeletal system development	anchored to membrane|cytoplasm|integral to membrane|plasma membrane	alkaline phosphatase activity|metal ion binding			ovary(2)|central_nervous_system(2)	4		all_lung(284;2.19e-05)|Lung NSC(340;2.22e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;8.7e-28)|COAD - Colon adenocarcinoma(152;1.57e-05)|GBM - Glioblastoma multiforme(114;2.66e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000177)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00856)|READ - Rectum adenocarcinoma(331;0.0623)|Lung(427;0.146)	Amifostine(DB01143)									0.414634	47.771164	48.030545	17	24	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21762191	21762191	550	1	C	T	T	19	19	ALPL	T	1	1
PTPRT	11122	broad.mit.edu	36	20	40739983	40739983	+	Nonsense_Mutation	SNP	G	A	A			TCGA-12-1093-01	TCGA-12-1093-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:40739983G>A	uc010ggj.1	-	c.1090C>T	c.(1090-1092)CGA>TGA	p.R364*	PTPRT_uc002xkg.1_Nonsense_Mutation_p.R364*	NM_133170	NP_573400	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	364	Extracellular (Potential).|Fibronectin type-III 1.				homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			ovary(7)|lung(5)|skin(2)	14		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)								646				0.132743	23.3554	38.149733	15	98	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	40739983	40739983	13270	20	G	A	A	40	40	PTPRT	A	5	1
C2orf48	348738	broad.mit.edu	36	2	10268032	10268032	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1093-01	TCGA-12-1093-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:10268032G>A	uc002rai.1	+	c.338G>A	c.(337-339)AGA>AAA	p.R113K		NM_182626	NP_872432	Q96LS8	CB048_HUMAN	hypothetical protein LOC348738	113											0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.188)										0.16	6.682079	9.437307	4	21	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10268032	10268032	2258	2	G	A	A	33	33	C2orf48	A	2	2
SPHKAP	80309	broad.mit.edu	36	2	228591698	228591698	+	Missense_Mutation	SNP	T	G	G			TCGA-12-1093-01	TCGA-12-1093-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:228591698T>G	uc002vpq.1	-	c.2116A>C	c.(2116-2118)ATG>CTG	p.M706L	SPHKAP_uc002vpp.1_Missense_Mutation_p.M706L	NM_030623	NP_085126	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	706						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)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)										0.131222	18.899945	48.192316	29	192	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	228591698	228591698	15560	2	T	G	G	52	52	SPHKAP	G	4	4
BIRC6	57448	broad.mit.edu	36	2	32479803	32479803	+	Missense_Mutation	SNP	T	G	G			TCGA-12-1093-01	TCGA-12-1093-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:32479803T>G	uc010ezu.1	+	c.1103T>G	c.(1102-1104)TTG>TGG	p.L368W		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	368					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				0.112013	91.553322	183.133835	69	547	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32479803	32479803	1463	2	T	G	G	63	63	BIRC6	G	4	4
BIRC6	57448	broad.mit.edu	36	2	32653879	32653879	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1093-01	TCGA-12-1093-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:32653879G>A	uc010ezu.1	+	c.13297G>A	c.(13297-13299)GTT>ATT	p.V4433I		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	4433					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				0.224	65.934965	74.688238	28	97	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32653879	32653879	1463	2	G	A	A	48	48	BIRC6	A	2	2
MOGS	7841	broad.mit.edu	36	2	74542883	74542883	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1093-01	TCGA-12-1093-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:74542883G>A	uc010ffj.1	-	c.1541C>T	c.(1540-1542)ACC>ATC	p.T514I	MOGS_uc010ffh.1_Missense_Mutation_p.T239I|MOGS_uc010ffi.1_Missense_Mutation_p.T408I	NM_006302	NP_006293	Q13724	MOGS_HUMAN	mannosyl-oligosaccharide glucosidase	514	Lumenal (Potential).				oligosaccharide metabolic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane|membrane fraction	mannosyl-oligosaccharide glucosidase activity				0														0.260504	79.36693	85.549024	31	88	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74542883	74542883	10088	2	G	A	A	44	44	MOGS	A	2	2
SH3BP5	9467	broad.mit.edu	36	3	15347050	15347050	+	Missense_Mutation	SNP	T	C	C			TCGA-12-1093-01	TCGA-12-1093-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:15347050T>C	uc003bzp.1	-	c.166A>G	c.(166-168)ACG>GCG	p.T56A	SH3BP5_uc010hem.1_Intron|SH3BP5_uc003bzq.1_5'UTR|SH3BP5_uc003bzr.1_5'UTR	NM_004844	NP_001018009	O60239	3BP5_HUMAN	SH3-domain binding protein 5 (BTK-associated)	56	Glu-rich.				intracellular signal transduction	mitochondrion	protein kinase inhibitor activity|SH3 domain binding				0														0.3	22.160098	23.23452	9	21	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15347050	15347050	14738	3	T	C	C	59	59	SH3BP5	C	4	4
TIPARP	25976	broad.mit.edu	36	3	157894598	157894598	+	Missense_Mutation	SNP	A	G	G			TCGA-12-1093-01	TCGA-12-1093-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:157894598A>G	uc003fav.1	+	c.1013A>G	c.(1012-1014)AAT>AGT	p.N338S	TIPARP_uc003faw.1_Missense_Mutation_p.N338S	NM_015508	NP_056323	Q7Z3E1	PARPT_HUMAN	TCDD-inducible poly(ADP-ribose) polymerase	338	WWE.						NAD+ ADP-ribosyltransferase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			Ovarian(171;276 1987 3319 6837 11197)								0.112	15.463104	34.051745	14	111	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	157894598	157894598	16453	3	A	G	G	4	4	TIPARP	G	4	4
SCN11A	11280	broad.mit.edu	36	3	38926643	38926643	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1093-01	TCGA-12-1093-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:38926643G>A	uc010hhm.1	-	c.1019C>T	c.(1018-1020)ACG>ATG	p.T340M		NM_014139	NP_054858	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha	340	I.				response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(1)|pancreas(1)|skin(1)	3				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)									0.192661	43.907404	53.527975	21	88	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38926643	38926643	14395	3	G	A	A	40	40	SCN11A	A	1	1
CACNA1D	776	broad.mit.edu	36	3	53756424	53756424	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1093-01	TCGA-12-1093-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:53756424C>T	uc003dgu.2	+	c.3283C>T	c.(3283-3285)CGG>TGG	p.R1095W	CACNA1D_uc003dgv.2_Missense_Mutation_p.R1075W|CACNA1D_uc003dgy.2_Missense_Mutation_p.R1075W|CACNA1D_uc003dgw.2_Missense_Mutation_p.R742W|CACNA1D_uc003dgx.1_Missense_Mutation_p.R223W	NM_000720	NP_000711	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type,	1075	Extracellular (Potential).|Dihydropyridine binding (By similarity).|III.				axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|liver(1)	7				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)									0.151515	16.511545	24.186194	10	56	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53756424	53756424	2657	3	C	T	T	19	19	CACNA1D	T	1	1
RPP14	11102	broad.mit.edu	36	3	58271333	58271333	+	Nonsense_Mutation	SNP	C	A	A			TCGA-12-1093-01	TCGA-12-1093-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:58271333C>A	uc010hnh.1	+	c.137C>A	c.(136-138)TCG>TAG	p.S46*	RPP14_uc010hni.1_5'UTR|RPP14_uc003dju.2_Nonsense_Mutation_p.S46*|RPP14_uc003djv.2_5'UTR|RPP14_uc003djw.2_5'UTR	NM_001098783	NP_008973	O95059	RPP14_HUMAN	ribonuclease P 14kDa subunit	46					tRNA processing	nucleus	identical protein binding|ribonuclease P activity|RNA binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000187)|KIRC - Kidney renal clear cell carcinoma(10;0.0102)|Kidney(10;0.0118)|OV - Ovarian serous cystadenocarcinoma(275;0.191)										0.132743	52.089347	81.690424	30	196	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	58271333	58271333	14088	3	C	A	A	31	31	RPP14	A	5	3
CRYBG3	131544	broad.mit.edu	36	3	99078751	99078751	+	Missense_Mutation	SNP	A	G	G			TCGA-12-1093-01	TCGA-12-1093-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:99078751A>G	uc003drx.1	+	c.179A>G	c.(178-180)CAA>CGA	p.Q60R		NM_153605	NP_705833			beta-gamma crystallin domain containing 3												0														0.197368	24.275231	30.769493	15	61	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99078751	99078751	4052	3	A	G	G	5	5	CRYBG3	G	4	4
ZNF518B	85460	broad.mit.edu	36	4	10054420	10054420	+	Silent	SNP	C	T	T			TCGA-12-1093-01	TCGA-12-1093-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:10054420C>T	uc003gmn.1	-	c.2631G>A	c.(2629-2631)GGG>GGA	p.G877G	ZNF518B_uc010idn.1_Silent_p.G877G	NM_053042	NP_444270	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	877					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3														0.233333	32.418606	36.325494	14	46	CC		KEEP	---	---	---	---	capture			Silent	SNP	10054420	10054420	18557	4	C	T	T	30	30	ZNF518B	T	2	2
ZCCHC4	29063	broad.mit.edu	36	4	24972699	24972699	+	Missense_Mutation	SNP	A	G	G			TCGA-12-1093-01	TCGA-12-1093-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:24972699A>G	uc003grl.2	+	c.1132A>G	c.(1132-1134)AGA>GGA	p.R378G	ZCCHC4_uc003grn.2_Missense_Mutation_p.R144G	NM_024936	NP_079212	Q9H5U6	ZCHC4_HUMAN	zinc finger, CCHC domain containing 4	378							methyltransferase activity|nucleic acid binding|zinc ion binding			ovary(2)	2		Breast(46;0.0503)												0.294118	14.067485	14.712948	5	12	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	24972699	24972699	18178	4	A	G	G	7	7	ZCCHC4	G	4	4
ADAMTS16	170690	broad.mit.edu	36	5	5235239	5235239	+	Missense_Mutation	SNP	C	A	A			TCGA-12-1093-01	TCGA-12-1093-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:5235239C>A	uc003jdl.1	+	c.584C>A	c.(583-585)GCC>GAC	p.A195D	ADAMTS16_uc003jdj.1_Missense_Mutation_p.A195D|ADAMTS16_uc003jdk.1_Missense_Mutation_p.A195D	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1	195					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8														0.23	54.17401	60.857479	23	77	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5235239	5235239	262	5	C	A	A	26	26	ADAMTS16	A	3	3
MCHR2	84539	broad.mit.edu	36	6	100475830	100475830	+	Missense_Mutation	SNP	G	C	C			TCGA-12-1093-01	TCGA-12-1093-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:100475830G>C	uc003pqh.1	-	c.730C>G	c.(730-732)CAG>GAG	p.Q244E	MCHR2_uc003pqi.1_Missense_Mutation_p.Q244E	NM_001040179	NP_115892	Q969V1	MCHR2_HUMAN	melanin-concentrating hormone receptor 2	244	Cytoplasmic (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)		BRCA - Breast invasive adenocarcinoma(108;0.0429)										0.103627	23.758406	53.940245	20	173	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100475830	100475830	9772	6	G	C	C	48	48	MCHR2	C	3	3
IMPG1	3617	broad.mit.edu	36	6	76717443	76717443	+	Silent	SNP	A	T	T			TCGA-12-1093-01	TCGA-12-1093-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:76717443A>T	uc003pik.1	-	c.1380T>A	c.(1378-1380)ACT>ACA	p.T460T		NM_001563	NP_001554	Q17R60	IMPG1_HUMAN	interphotoreceptor matrix proteoglycan 1	460					visual perception	proteinaceous extracellular matrix	extracellular matrix structural constituent|receptor activity			ovary(2)	2		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				Pancreas(37;839 1141 2599 26037)								0.10274	11.919476	34.884349	15	131	AA		KEEP	---	---	---	---	capture			Silent	SNP	76717443	76717443	8029	6	A	T	T	7	7	IMPG1	T	4	4
TRAPPC9	83696	broad.mit.edu	36	8	141530611	141530611	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1093-01	TCGA-12-1093-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:141530611G>A	uc003yvh.1	-	c.338C>T	c.(337-339)ACG>ATG	p.T113M	TRAPPC9_uc003yvi.1_Missense_Mutation_p.T15M|TRAPPC9_uc003yvj.1_Missense_Mutation_p.T15M	NM_031466	NP_113654	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	15					cell differentiation	endoplasmic reticulum|Golgi apparatus					0														0.225806	49.424859	55.849456	21	72	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	141530611	141530611	17009	8	G	A	A	40	40	TRAPPC9	A	1	1
TNFRSF10B	8795	broad.mit.edu	36	8	22936363	22936363	+	Silent	SNP	G	A	A			TCGA-12-1093-01	TCGA-12-1093-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:22936363G>A	uc003xcu.1	-	c.1089C>T	c.(1087-1089)CTC>CTT	p.L363L	TNFRSF10B_uc003xcs.1_Silent_p.L128L|TNFRSF10B_uc003xct.1_Silent_p.L334L|TNFRSF10B_uc003xcv.1_Silent_p.L261L	NM_003842	NP_003833	O14763	TR10B_HUMAN	tumor necrosis factor receptor superfamily,	363	Death.|Cytoplasmic (Potential).				activation of caspase activity|activation of NF-kappaB-inducing kinase activity|activation of pro-apoptotic gene products|cell surface receptor linked signaling pathway|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane|plasma membrane	caspase activator activity|receptor activity|TRAIL binding				0		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0179)|COAD - Colon adenocarcinoma(73;0.0703)		GBM(94;1064 1342 1839 21060 42553)				305				0.350254	379.121182	386.919821	138	256	GG		KEEP	---	---	---	---	capture			Silent	SNP	22936363	22936363	16822	8	G	A	A	45	45	TNFRSF10B	A	2	2
TSC1	7248	broad.mit.edu	36	9	134786569	134786569	+	Splice_Site_SNP	SNP	A	G	G			TCGA-12-1093-01	TCGA-12-1093-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:134786569A>G	uc004cca.1	-	c.e8_splice_site			TSC1_uc004ccb.2_Splice_Site_SNP|TSC1_uc004ccc.1_Splice_Site_SNP|TSC1_uc004ccd.1_Splice_Site_SNP|TSC1_uc004cce.1_Splice_Site_SNP	NM_000368	NP_000359			tuberous sclerosis 1 protein isoform 1						activation of Rho GTPase activity|cell cycle arrest|cell-matrix adhesion|insulin receptor signaling pathway|negative regulation of cell proliferation|negative regulation of protein ubiquitination|negative regulation of TOR signaling cascade|negative regulation of translation|positive regulation of focal adhesion assembly|regulation of phosphoprotein phosphatase activity|regulation of stress fiber assembly|rRNA export from nucleus	cell cortex|lamellipodium|membrane|TSC1-TSC2 complex	chaperone binding|protein N-terminus binding	p.?(1)		lung(3)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)|ovary(1)|bone(1)	9				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)						536				0.13	22.915252	36.227667	13	87	AA		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	134786569	134786569	17156	9	A	G	G	14	14	TSC1	G	5	4
CDKN2A	1029	broad.mit.edu	36	9	21961028	21961028	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1093-01	TCGA-12-1093-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:21961028C>T	uc003zpl.1	-	c.496G>A	c.(496-498)GGG>AGG	p.G166R	MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpk.1_Nonsense_Mutation_p.W110*|CDKN2A_uc003zpj.1_3'UTR|CDKN2A_uc010miu.1_Non-coding_Transcript	NM_058195	NP_478102	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A isoform 4	Error:Variant_position_missing_in_P42771_after_alignment					cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding	p.0?(425)|p.W110*(30)|p.H83fs*2(2)|p.D105fs*8(1)|p.A68fs*3(1)|p.W110C(1)		haematopoietic_and_lymphoid_tissue(647)|skin(417)|upper_aerodigestive_tract(405)|central_nervous_system(380)|lung(319)|pancreas(237)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|ovary(76)|soft_tissue(73)|biliary_tract(71)|bone(70)|breast(46)|stomach(44)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|large_intestine(9)|salivary_gland(8)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1)	3636		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)				17	p.W110*(CHL1-Tumor)|p.W110*(YD10B-Tumor)	76	TSP Lung(5;3.83e-07)			0.230769	10.638116	12.36638	6	20	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21961028	21961028	3290	9	C	T	T	22	22	CDKN2A	T	2	2
P2RY10	27334	broad.mit.edu	36	X	78103574	78103574	+	Missense_Mutation	SNP	G	T	T			TCGA-12-1093-01	TCGA-12-1093-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:78103574G>T	uc004ede.1	+	c.901G>T	c.(901-903)GAT>TAT	p.D301Y	P2RY10_uc004edf.1_Missense_Mutation_p.D301Y|P2RY10_uc010nmf.1_Missense_Mutation_p.D301Y	NM_014499	NP_938147	O00398	P2Y10_HUMAN	G-protein coupled purinergic receptor P2Y10	301	Helical; Name=7; (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled	p.D301N(1)		ovary(2)|lung(1)	3														0.134872	138.363654	244.792952	111	712	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	78103574	78103574	11760	23	G	T	T	41	41	P2RY10	T	3	3
DOCK1	1793	broad.mit.edu	36	10	129135669	129135679	+	Frame_Shift_Del	DEL	CGGGGGCGGAC	-	-			TCGA-12-1093-01	TCGA-12-1093-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:129135669_129135679delCGGGGGCGGAC	uc001ljt.1	+	c.5372_5382delCGGGGGCGGAC	c.(5371-5382)ACGGGGGCGGACfs	p.T1791fs	DOCK1_uc009yaq.1_Frame_Shift_Del_p.D790fs|DOCK1_uc001ljw.1_5'Flank	NM_001380	NP_001371	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1791_1794	Interaction with NCK2 second and third SH3 domain (minor).				apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)										0.39			187	294				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	129135669	129135679	4868	10	CGGGGGCGGAC	-	-	19	19	DOCK1	-	5	5
C10orf93	255352	broad.mit.edu	36	10	134605120	134605141	+	Frame_Shift_Del	DEL	CCCTGCACAGGTGCGCTCGGCC	-	-			TCGA-12-1093-01	TCGA-12-1093-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:134605120_134605141delCCCTGCACAGGTGCGCTCGGCC	uc001llt.1	-	c.76_97delGGCCGAGCGCACCTGTGCAGGG	c.(76-99)GGCCGAGCGCACCTGTGCAGGGCCfs	p.G26fs	C10orf93_uc001llu.2_Frame_Shift_Del_p.G84fs	NM_173572	NP_775843	Q5SR76	CJ093_HUMAN	hypothetical protein LOC255352	84_91	TPR 1.						binding			pancreas(1)	1		all_cancers(35;1.8e-07)|all_epithelial(44;6.22e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Colorectal(31;0.119)|Glioma(114;0.172)|Melanoma(40;0.175)		Epithelial(32;4.28e-05)|OV - Ovarian serous cystadenocarcinoma(35;4.31e-05)|all cancers(32;5.02e-05)										0.37			23	40				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	134605120	134605141	1662	10	CCCTGCACAGGTGCGCTCGGCC	-	-	26	26	C10orf93	-	5	5
MRC2	9902	broad.mit.edu	36	17	58095949	58095951	+	In_Frame_Del	DEL	AAG	-	-			TCGA-12-1093-01	TCGA-12-1093-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:58095949_58095951delAAG	uc002jad.1	+	c.427_429delAAG	c.(427-429)AAGdel	p.K143del	MRC2_uc002jac.1_In_Frame_Del_p.K143del	NM_006039	NP_006030	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	143	Extracellular (Potential).|Ricin B-type lectin.				endocytosis	integral to membrane	receptor activity|sugar binding			ovary(1)|central_nervous_system(1)	2														0.45			9	11				---	---	---	---	capture_indel			In_Frame_Del	DEL	58095949	58095951	10150	17	AAG	-	-	5	5	MRC2	-	5	5
ZNF556	80032	broad.mit.edu	36	19	2829099	2829117	+	Frame_Shift_Del	DEL	GTCCTCATCTTTACACAAA	-	-			TCGA-12-1093-01	TCGA-12-1093-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:2829099_2829117delGTCCTCATCTTTACACAAA	uc002lwp.1	+	c.1143_1161delGTCCTCATCTTTACACAAA	c.(1141-1161)TGGTCCTCATCTTTACACAAAfs	p.W381fs	ZNF556_uc002lwq.2_Frame_Shift_Del_p.W380fs	NM_024967	NP_079243	Q9HAH1	ZN556_HUMAN	zinc finger protein 556	381_387	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				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)										0.39			36	57				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	2829099	2829117	18582	19	GTCCTCATCTTTACACAAA	-	-	44	44	ZNF556	-	5	5
HNF4A	3172	broad.mit.edu	36	20	42486233	42486245	+	Frame_Shift_Del	DEL	ATCGAGCAGATCC	-	-			TCGA-12-1093-01	TCGA-12-1093-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:42486233_42486245delATCGAGCAGATCC	uc002xma.1	+	c.1054_1066delATCGAGCAGATCC	c.(1054-1068)ATCGAGCAGATCCAGfs	p.I352fs	HNF4A_uc002xlt.1_Frame_Shift_Del_p.I330fs|HNF4A_uc002xlu.1_Frame_Shift_Del_p.I330fs|HNF4A_uc002xlv.1_Frame_Shift_Del_p.I330fs|HNF4A_uc002xly.1_Frame_Shift_Del_p.I352fs|HNF4A_uc002xlz.1_Frame_Shift_Del_p.I352fs|HNF4A_uc010ggq.1_Frame_Shift_Del_p.I345fs	NM_000457	NP_000448	P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4 alpha isoform b	352_356					blood coagulation|endocrine pancreas development|glucose homeostasis|negative regulation of cell growth|negative regulation of cell proliferation|ornithine metabolic process|phospholipid homeostasis|positive regulation of cholesterol homeostasis|positive regulation of gene-specific transcription from RNA polymerase II promoter|regulation of growth hormone receptor signaling pathway|regulation of insulin secretion|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to glucose stimulus|triglyceride homeostasis|xenobiotic metabolic process	cytoplasm	activating transcription factor binding|promoter binding|protein homodimerization activity|receptor binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|steroid hormone receptor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			Colon(79;2 1269 8820 14841 52347)								0.53			155	137				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	42486233	42486245	7545	20	ATCGAGCAGATCC	-	-	12	12	HNF4A	-	5	5
UNC5A	90249	broad.mit.edu	36	5	176238964	176238970	+	Frame_Shift_Del	DEL	CCCAGCC	-	-			TCGA-12-1093-01	TCGA-12-1093-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:176238964_176238970delCCCAGCC	uc003mey.1	+	c.2232_2238delCCCAGCC	c.(2230-2238)GTCCCAGCCfs	p.V744fs		NM_133369	NP_588610	Q6ZN44	UNC5A_HUMAN	netrin receptor Unc5h1	744_746	Cytoplasmic (Potential).				apoptosis|axon guidance|regulation of apoptosis	integral to membrane|plasma membrane					0	all_cancers(89;0.000119)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)											0.90			235	27				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	176238964	176238970	17549	5	CCCAGCC	-	-	30	30	UNC5A	-	5	5
HIP1	3092	broad.mit.edu	36	7	75026979	75026989	+	Frame_Shift_Del	DEL	CTCAGACAGGC	-	-			TCGA-12-1093-01	TCGA-12-1093-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:75026979_75026989delCTCAGACAGGC	uc003uds.1	-	c.1358_1368delGCCTGTCTGAG	c.(1357-1368)AGCCTGTCTGAGfs	p.S453fs		NM_005338	NP_005329	O00291	HIP1_HUMAN	huntingtin interacting protein 1	453_456	Potential.|pDED.				activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			pancreas(2)|ovary(1)|central_nervous_system(1)	4										1179				0.39			18	28				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	75026979	75026989	7399	7	CTCAGACAGGC	-	-	32	32	HIP1	-	5	5
