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
KCNJ5	3762	broad.mit.edu	36	11	128286793	128286793	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:128286793G>A	uc001qet.1	+	c.415G>A	c.(415-417)GCT>ACT	p.A139T	KCNJ5_uc009zck.1_Missense_Mutation_p.A139T|KCNJ5_uc001qew.1_Missense_Mutation_p.A139T	NM_000890	NP_000881	P48544	IRK5_HUMAN	potassium inwardly-rectifying channel J5	139					synaptic transmission	voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding				0	all_hematologic(175;0.0641)	Lung NSC(97;0.00038)|all_lung(97;0.000817)|Breast(109;0.00123)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)			Glibenclamide(DB01016)	Pancreas(108;2548 5082)|Esophageal Squamous(165;4544 6231)								0.512077	305.338484	305.365099	106	101	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(99;0.0059)|LUSC - Lung squamous cell carcinoma(976;0.021)|Lung(977;0.0215)	Missense_Mutation	SNP	128286793	128286793	8359	11	G	A	A	38	38	KCNJ5	A	1	1
RAG1	5896	broad.mit.edu	36	11	36552851	36552851	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:36552851G>A	uc001mwu.2	+	c.1421G>A	c.(1420-1422)CGT>CAT	p.R474H	RAG1_uc001mwt.2_Non-coding_Transcript|RAG1_uc009ykl.1_Missense_Mutation_p.R474H	NM_000448	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	474			R -> H (in OS/T(-)B(-)NK(+) SCID; atypical).		histone monoubiquitination|immune response|pre-B cell allelic exclusion|protein autoubiquitination|T cell differentiation in thymus|V(D)J recombination	nucleus	endonuclease activity|histone binding|protein homodimerization activity|sequence-specific DNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4	all_lung(20;0.226)	all_hematologic(20;0.107)				Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)				117				0.352941	151.911683	154.826048	54	99	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36552851	36552851	13463	11	G	A	A	40	40	RAG1	A	1	1
CACNA1C	775	broad.mit.edu	36	12	2545929	2545929	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0237-01	TCGA-06-0237-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:2545929T>G	uc009zdu.1	+	c.1589T>G	c.(1588-1590)GTG>GGG	p.V530G	CACNA1C_uc009zdv.1_Missense_Mutation_p.V527G|CACNA1C_uc001qkb.2_Missense_Mutation_p.V530G|CACNA1C_uc001qkc.2_Missense_Mutation_p.V530G|CACNA1C_uc001qke.2_Missense_Mutation_p.V530G|CACNA1C_uc001qkf.2_Missense_Mutation_p.V530G|CACNA1C_uc001qjz.2_Missense_Mutation_p.V530G|CACNA1C_uc001qkd.2_Missense_Mutation_p.V530G|CACNA1C_uc001qkg.2_Missense_Mutation_p.V530G|CACNA1C_uc009zdw.1_Missense_Mutation_p.V530G|CACNA1C_uc001qkh.2_Missense_Mutation_p.V530G|CACNA1C_uc001qkl.2_Missense_Mutation_p.V530G|CACNA1C_uc001qkn.2_Missense_Mutation_p.V530G|CACNA1C_uc001qko.2_Missense_Mutation_p.V530G|CACNA1C_uc001qkp.2_Missense_Mutation_p.V530G|CACNA1C_uc001qkr.2_Missense_Mutation_p.V530G|CACNA1C_uc001qku.2_Missense_Mutation_p.V530G|CACNA1C_uc001qkq.2_Missense_Mutation_p.V530G|CACNA1C_uc001qks.2_Missense_Mutation_p.V530G|CACNA1C_uc001qkt.2_Missense_Mutation_p.V530G|CACNA1C_uc001qka.1_Missense_Mutation_p.V65G|CACNA1C_uc001qki.1_Missense_Mutation_p.V266G|CACNA1C_uc001qkj.1_Missense_Mutation_p.V266G|CACNA1C_uc001qkk.1_Missense_Mutation_p.V266G|CACNA1C_uc001qkm.1_Missense_Mutation_p.V266G|CACNA1C_uc009zdy.1_Missense_Mutation_p.V195G|CACNA1C_uc001qkv.1_Missense_Mutation_p.V100G	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	530	II.|Helical; Name=S1 of repeat II; (Potential).				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11					Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)									0.428571	7.923076	7.954346	3	4	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Missense_Mutation	SNP	2545929	2545929	2656	12	T	G	G	59	59	CACNA1C	G	4	4
FAM113B	91523	broad.mit.edu	36	12	45916380	45916380	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:45916380G>C	uc001rpn.1	+	c.1267G>C	c.(1267-1269)GCC>CCC	p.A423P	FAM113B_uc001rpq.1_Missense_Mutation_p.A423P|FAM113B_uc009zko.1_Missense_Mutation_p.A423P	NM_138371	NP_612380	Q96HM7	F113B_HUMAN	hypothetical protein LOC91523	423	Pro-rich.						hydrolase activity			ovary(2)	2	Renal(347;0.138)|Lung SC(27;0.192)													0.291667	11.60455	12.490387	7	17	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45916380	45916380	5599	12	G	C	C	42	42	FAM113B	C	3	3
NBEA	26960	broad.mit.edu	36	13	35100290	35100290	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:35100290G>A	uc001uvb.1	+	c.7522G>A	c.(7522-7524)GGA>AGA	p.G2508R	NBEA_uc010abi.1_Missense_Mutation_p.G1164R|NBEA_uc001uvd.1_Missense_Mutation_p.G65R	NM_015678	NP_056493	Q8NFP9	NBEA_HUMAN	neurobeachin	2508	BEACH.					cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)												0.318182	42.733925	44.027053	14	30	GG		KEEP	---	---	---	---	capture		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)	Missense_Mutation	SNP	35100290	35100290	10583	13	G	A	A	35	35	NBEA	A	2	2
YPEL3	83719	broad.mit.edu	36	16	30013704	30013704	+	Silent	SNP	G	A	A			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:30013704G>A	uc002dwl.1	-	c.291C>T	c.(289-291)TGC>TGT	p.C97C	BOLA2_uc010bzb.1_Intron|BOLA2_uc010bzc.1_Intron|TBX6_uc002dwj.1_5'Flank|TBX6_uc002dwk.1_5'Flank|YPEL3_uc002dwm.1_Silent_p.C59C|YPEL3_uc002dwn.1_Silent_p.C97C	NM_031477	NP_113665	P61236	YPEL3_HUMAN	yippee-like 3	59						nucleolus					0														0.580952	182.028145	182.644876	61	44	GG		KEEP	---	---	---	---	capture			Silent	SNP	30013704	30013704	18074	16	G	A	A	38	38	YPEL3	A	1	1
RAB34	83871	broad.mit.edu	36	17	24066410	24066410	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:24066410G>C	uc002hcf.1	-	c.446C>G	c.(445-447)GCC>GGC	p.A149G	RAB34_uc002hcd.1_Missense_Mutation_p.A148G|RAB34_uc002hcc.2_Missense_Mutation_p.A149G|RAB34_uc002hce.1_Missense_Mutation_p.A148G|RAB34_uc002hcg.1_Missense_Mutation_p.A148G|RAB34_uc002hch.1_Missense_Mutation_p.A148G	NM_031934	NP_114140	Q9BZG1	RAB34_HUMAN	RAB39 isoform 1	148					protein transport|small GTPase mediated signal transduction	Golgi apparatus	GTP binding				0	Lung NSC(42;0.00431)					Pancreas(175;216 2049 29940 32498 41589)								0.225806	10.722023	12.866753	7	24	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	24066410	24066410	13383	17	G	C	C	42	42	RAB34	C	3	3
LIG3	3980	broad.mit.edu	36	17	30347717	30347717	+	Silent	SNP	C	T	T			TCGA-06-0237-01	TCGA-06-0237-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:30347717C>T	uc002hik.1	+	c.1755C>T	c.(1753-1755)TTC>TTT	p.F585F	LIG3_uc002hij.1_Silent_p.F585F	NM_013975	NP_039269	P49916	DNLI3_HUMAN	ligase III, DNA, ATP-dependent isoform alpha	585					base-excision repair|cell division|DNA ligation involved in DNA repair|DNA replication|reciprocal meiotic recombination|spermatogenesis	nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|protein binding|zinc ion binding			ovary(2)|large_intestine(1)|pancreas(1)	4		Ovarian(249;0.17)			Bleomycin(DB00290)									0.388186	281.237599	283.836766	92	145	CC		KEEP	---	---	---	---	capture			Silent	SNP	30347717	30347717	9108	17	C	T	T	30	30	LIG3	T	2	2
XYLT2	64132	broad.mit.edu	36	17	45792601	45792601	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:45792601G>A	uc002iqo.1	+	c.2548G>A	c.(2548-2550)GAC>AAC	p.D850N	XYLT2_uc010dbo.1_Non-coding_Transcript	NM_022167	NP_071450	Q9H1B5	XYLT2_HUMAN	xylosyltransferase II	850	Lumenal (Potential).				glycosaminoglycan biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	acetylglucosaminyltransferase activity|protein xylosyltransferase activity			pancreas(1)	1	Breast(11;7.18e-19)													0.435484	81.315816	81.540751	27	35	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45792601	45792601	18047	17	G	A	A	37	37	XYLT2	A	1	1
TP53	7157	broad.mit.edu	36	17	7518990	7518990	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0237-01	TCGA-06-0237-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7518990A>G	uc002gim.2	-	c.584T>C	c.(583-585)ATC>ACC	p.I195T	TP53_uc002gig.1_Missense_Mutation_p.I195T|TP53_uc002gih.1_Missense_Mutation_p.I195T|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.I63T|TP53_uc010cng.1_Missense_Mutation_p.I63T|TP53_uc002gii.1_Missense_Mutation_p.I63T|TP53_uc010cnh.1_Missense_Mutation_p.I195T|TP53_uc010cni.1_Missense_Mutation_p.I195T|TP53_uc002gij.2_Missense_Mutation_p.I195T|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_Missense_Mutation_p.I102T|TP53_uc002gio.2_Missense_Mutation_p.I63T	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	195	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		I -> F (in sporadic cancers; somatic mutation).|I -> L (in a sporadic cancer; somatic mutation).|I -> S (in sporadic cancers; somatic mutation).|I -> T (in sporadic cancers; somatic mutation).|I -> V (in a sporadic cancer; somatic mutation).|I -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|I -> N (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.I195T(58)|p.I195N(11)|p.0?(6)|p.I195S(4)|p.A189_V197delAPPQHLIRV(4)|p.I195fs*14(2)|p.I195fs*50(1)|p.P191fs*6(1)|p.I195_G199delIRVEG(1)|p.H193_I195delHLI(1)|p.H193_I195>AP(1)|p.I195fs*12(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)				Pancreas(47;798 1329 9957 10801)		111	p.I195S(SNU1077-Tumor)|p.I195T(KYSE180-Tumor)|p.H193fs(59M-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.457447	144.700737	144.849945	43	51	AA		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Missense_Mutation	SNP	7518990	7518990	16923	17	A	G	G	12	12	TP53	G	4	4
SALL3	27164	broad.mit.edu	36	18	74854963	74854963	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0237-01	TCGA-06-0237-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr18:74854963T>G	uc002lmt.1	+	c.1984T>G	c.(1984-1986)TCG>GCG	p.S662A	SALL3_uc010dra.1_Missense_Mutation_p.S269A	NM_171999	NP_741996	Q9BXA9	SALL3_HUMAN	sal-like 3	662					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)												0.73913	52.977298	54.164962	17	6	TT		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)	Missense_Mutation	SNP	74854963	74854963	14292	18	T	G	G	54	54	SALL3	G	4	4
CYP4F2	8529	broad.mit.edu	36	19	15850717	15850717	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:15850717G>A	uc002nbs.1	-	c.1427C>T	c.(1426-1428)GCG>GTG	p.A476V		NM_001082	NP_001073	P78329	CP4F2_HUMAN	cytochrome P450, family 4, subfamily F,	476					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														0.407767	118.527612	119.293652	42	61	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15850717	15850717	4353	19	G	A	A	38	38	CYP4F2	A	1	1
GIPC3	126326	broad.mit.edu	36	19	3537880	3537880	+	Silent	SNP	C	T	T			TCGA-06-0237-01	TCGA-06-0237-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:3537880C>T	uc002lyc.1	+	c.480C>T	c.(478-480)ATC>ATT	p.I160I		NM_133261	NP_573568	Q8TF64	GIPC3_HUMAN	GIPC PDZ domain containing family, member 3	160	PDZ.									breast(1)	1												OREG0025154	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.535714	91.847396	91.909027	30	26	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0025)|STAD - Stomach adenocarcinoma(1328;0.18)	Silent	SNP	3537880	3537880	6662	19	C	T	T	29	29	GIPC3	T	2	2
FFAR3	2865	broad.mit.edu	36	19	40542382	40542382	+	Silent	SNP	C	T	T			TCGA-06-0237-01	TCGA-06-0237-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:40542382C>T	uc002nzd.1	+	c.750C>T	c.(748-750)ATC>ATT	p.I250I	FFAR3_uc010edy.1_Silent_p.I250I	NM_005304	NP_005295	O14843	FFAR3_HUMAN	free fatty acid receptor 3	250	Extracellular (Potential).					integral to plasma membrane	G-protein coupled receptor activity|lipid binding				0	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)					Esophageal Squamous(185;1742 2042 21963 24215 27871)								0.200737	252.543476	297.771991	109	434	CC		KEEP	---	---	---	---	capture	Epithelial(14;1.29e-19)|OV - Ovarian serous cystadenocarcinoma(14;4.63e-18)|all cancers(14;5.19e-17)|LUSC - Lung squamous cell carcinoma(66;0.0221)		Silent	SNP	40542382	40542382	6066	19	C	T	T	32	32	FFAR3	T	2	2
CYP2B6	1555	broad.mit.edu	36	19	46207766	46207766	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0237-01	TCGA-06-0237-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:46207766A>T	uc002opr.1	+	c.850A>T	c.(850-852)AGC>TGC	p.S284C	CYP2A7_uc002opo.1_Intron	NM_000767	NP_000758	P20813	CP2B6_HUMAN	cytochrome P450, family 2, subfamily B,	284					cellular ketone metabolic process|exogenous drug catabolic process|oxidation-reduction process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)	1					Bupropion(DB01156)|Butalbital(DB00241)|Carbamazepine(DB00564)|Clopidogrel(DB00758)|Cyclophosphamide(DB00531)|Efavirenz(DB00625)|Ifosfamide(DB01181)|Memantine(DB01043)|Meperidine(DB00454)|Mephenytoin(DB00532)|Methadone(DB00333)|Methylphenobarbital(DB00849)|Midazolam(DB00683)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicotine(DB00184)|Orphenadrine(DB01173)|Phenytoin(DB00252)|Propofol(DB00818)|Ritonavir(DB00503)|Selegiline(DB01037)|Sertraline(DB01104)|Ticlopidine(DB00208)|Troleandomycin(DB01361)					56				0.280899	69.839779	73.678226	25	64	AA		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(20;0.00322)		Missense_Mutation	SNP	46207766	46207766	4329	19	A	T	T	7	7	CYP2B6	T	4	4
ARHGEF2	9181	broad.mit.edu	36	1	154194296	154194296	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0237-01	TCGA-06-0237-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:154194296T>C	uc001fmu.1	-	c.1679A>G	c.(1678-1680)GAC>GGC	p.D560G	ARHGEF2_uc001fmr.1_Missense_Mutation_p.D488G|ARHGEF2_uc001fms.1_Missense_Mutation_p.D515G|ARHGEF2_uc001fmt.1_Missense_Mutation_p.D516G	NM_004723	NP_004714	Q92974	ARHG2_HUMAN	rho/rac guanine nucleotide exchange factor 2	516	PH.				actin filament organization|apoptosis|cell division|cell morphogenesis|induction of apoptosis by extracellular signals|intracellular protein transport|mitosis|negative regulation of microtubule depolymerization|nerve growth factor receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|regulation of cell proliferation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|Golgi apparatus|microtubule|ruffle membrane|spindle|tight junction	microtubule binding|Rac GTPase binding|Rac guanyl-nucleotide exchange factor activity|zinc ion binding			ovary(1)	1	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					Melanoma(178;35 2768 6610 28839)								0.310345	10.858967	11.918024	9	20	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	154194296	154194296	917	1	T	C	C	58	58	ARHGEF2	C	4	4
USH2A	7399	broad.mit.edu	36	1	213999700	213999700	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0237-01	TCGA-06-0237-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:213999700C>T	uc001hku.1	-	c.11156G>A	c.(11155-11157)CGT>CAT	p.R3719H		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	3719	Fibronectin type-III 22.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|kidney(1)|central_nervous_system(1)	22														0.438202	235.826609	236.41858	78	100	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)	Missense_Mutation	SNP	213999700	213999700	17598	1	C	T	T	19	19	USH2A	T	1	1
OBSCN	84033	broad.mit.edu	36	1	226561312	226561312	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0237-01	TCGA-06-0237-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:226561312C>T	uc009xez.1	+	c.12014C>T	c.(12013-12015)GCG>GTG	p.A4005V	OBSCN_uc001hsn.1_Missense_Mutation_p.A4005V	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	4005	Ig-like 41.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			large_intestine(7)|breast(5)|ovary(4)|skin(2)|stomach(1)|central_nervous_system(1)|pancreas(1)	21		Prostate(94;0.0405)								4006				0.5	56.794878	56.794878	20	20	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	226561312	226561312	11217	1	C	T	T	27	27	OBSCN	T	1	1
RYR2	6262	broad.mit.edu	36	1	235879857	235879857	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:235879857G>A	uc001hyl.1	+	c.7570G>A	c.(7570-7572)GTC>ATC	p.V2524I		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	2524	Cytoplasmic (By similarity).|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)												0.328413	247.684622	254.757993	89	182	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.00606)		Missense_Mutation	SNP	235879857	235879857	14249	1	G	A	A	40	40	RYR2	A	1	1
AGRN	375790	broad.mit.edu	36	1	968815	968815	+	Silent	SNP	C	T	T			TCGA-06-0237-01	TCGA-06-0237-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:968815C>T	uc001ack.1	+	c.1638C>T	c.(1636-1638)TGC>TGT	p.C546C		NM_198576	NP_940978	O00468	AGRIN_HUMAN	agrin	546	Kazal-like 6.				axon guidance|clustering of voltage-gated sodium channels|muscarinic acetylcholine receptor signaling pathway|receptor clustering	basal lamina	laminin binding|structural constituent of cytoskeleton			central_nervous_system(2)|breast(1)	3	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)												0.431373	187.031257	187.65745	66	87	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)	Silent	SNP	968815	968815	400	1	C	T	T	27	27	AGRN	T	1	1
SLC17A9	63910	broad.mit.edu	36	20	61067431	61067431	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:61067431G>A	uc002yea.2	+	c.970G>A	c.(970-972)GTC>ATC	p.V324I	SLC17A9_uc002ydz.2_Missense_Mutation_p.V318I	NM_022082	NP_071365	Q9BYT1	S17A9_HUMAN	vesicular nucleotide transporter SLC17A9	324	Helical; (Potential).				exocytosis|transmembrane transport	integral to membrane	transporter activity	p.V324I(1)		ovary(1)	1														0.387858	660.170007	666.680514	230	363	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	61067431	61067431	14920	20	G	A	A	40	40	SLC17A9	A	1	1
EEF1A2	1917	broad.mit.edu	36	20	61592522	61592522	+	Silent	SNP	C	T	T			TCGA-06-0237-01	TCGA-06-0237-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:61592522C>T	uc002yfd.1	-	c.783G>A	c.(781-783)ACG>ACA	p.T261T	EEF1A2_uc002yfe.1_Silent_p.T261T|EEF1A2_uc010gkg.1_Silent_p.T261T	NM_001958	NP_001949	Q05639	EF1A2_HUMAN	eukaryotic translation elongation factor 1 alpha	261						nucleus	GTP binding|GTPase activity|protein binding|translation elongation factor activity				0	all_cancers(38;9.45e-12)													0.43956	119.895667	120.182523	40	51	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(10;1.22e-05)		Silent	SNP	61592522	61592522	5111	20	C	T	T	23	23	EEF1A2	T	1	1
DSCR6	53820	broad.mit.edu	36	21	37302336	37302336	+	Silent	SNP	G	A	A			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:37302336G>A	uc002yvv.1	+	c.114G>A	c.(112-114)CCG>CCA	p.P38P	DSCR6_uc002yvu.1_De_novo_Start_OutOfFrame|DSCR6_uc010gnd.1_De_novo_Start_InFrame	NM_018962	NP_061835	P57055	DSCR6_HUMAN	Down syndrome critical region protein 6	38						nucleus				breast(1)	1		Myeloproliferative disorder(46;0.0632)				Colon(134;194 1731 2725 51652 51982)								0.476636	156.319446	156.370131	51	56	GG		KEEP	---	---	---	---	capture			Silent	SNP	37302336	37302336	4957	21	G	A	A	40	40	DSCR6	A	1	1
SIK1	150094	broad.mit.edu	36	21	43665983	43665983	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:43665983G>T	uc002zdf.1	-	c.462C>A	c.(460-462)AAC>AAA	p.N154K		NM_173354	NP_775490	P57059	SIK1_HUMAN	SNF1-like kinase	154	Protein kinase.				anoikis|cell cycle|cell differentiation|intracellular protein kinase cascade|multicellular organismal development|protein phosphorylation|regulation of cell differentiation|regulation of mitotic cell cycle	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			lung(2)|testis(2)|ovary(1)|central_nervous_system(1)|skin(1)	7										671				0.492754	106.446698	106.44987	34	35	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43665983	43665983	14812	21	G	T	T	44	44	SIK1	T	3	3
FANCD2	2177	broad.mit.edu	36	3	10059272	10059272	+	Silent	SNP	G	A	A			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:10059272G>A	uc003buw.1	+	c.813G>A	c.(811-813)TCG>TCA	p.S271S	FANCD2_uc003bux.1_Silent_p.S271S|FANCD2_uc003buy.1_Silent_p.S271S	NM_033084	NP_149075	Q9BXW9	FACD2_HUMAN	Fanconi anemia complementation group D2 isoform	271	Interaction with FANCE.|Interaction with BRCA2.				DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4									p.S271S(639V-Tumor)	587				0.420495	361.381743	362.94152	119	164	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(96;0.148)	Silent	SNP	10059272	10059272	5901	3	G	A	A	40	40	FANCD2	A	1	1
PLS1	5357	broad.mit.edu	36	3	143887838	143887838	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0237-01	TCGA-06-0237-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:143887838T>G	uc010huv.1	+	c.911T>G	c.(910-912)CTG>CGG	p.L304R	PLS1_uc003euz.1_Missense_Mutation_p.L304R|PLS1_uc003eva.1_Missense_Mutation_p.L304R	NM_002670	NP_002661	Q14651	PLSI_HUMAN	plastin 1	304	Actin-binding 1.|CH 2.					cytoplasm	actin filament binding|calcium ion binding|structural constituent of cytoskeleton				0														0.411765	163.285607	164.206274	56	80	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	143887838	143887838	12533	3	T	G	G	55	55	PLS1	G	4	4
CRYGS	1427	broad.mit.edu	36	3	187739289	187739289	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:187739289G>T	uc003fqe.1	-	c.427C>A	c.(427-429)CCC>ACC	p.P143T	CRYGS_uc003fqf.1_Missense_Mutation_p.P143T	NM_017541	NP_060011	P22914	CRBS_HUMAN	crystallin, gamma S	143	Beta/gamma crystallin 'Greek key' 4.						structural constituent of eye lens				0	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)													0.408377	239.042087	240.433591	78	113	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(80;5.5e-22)	GBM - Glioblastoma multiforme(93;0.0906)	Missense_Mutation	SNP	187739289	187739289	4058	3	G	T	T	44	44	CRYGS	T	3	3
ASB5	140458	broad.mit.edu	36	4	177373835	177373835	+	Silent	SNP	A	G	G			TCGA-06-0237-01	TCGA-06-0237-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:177373835A>G	uc003iuq.1	-	c.900T>C	c.(898-900)TGT>TGC	p.C300C	ASB5_uc003iup.1_Silent_p.C247C	NM_080874	NP_543150	Q8WWX0	ASB5_HUMAN	ankyrin repeat and SOCS box-containing protein	300	SOCS box.				intracellular signal transduction						0		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)												0.395062	110.48713	111.266533	32	49	AA		KEEP	---	---	---	---	capture		all cancers(43;2.13e-20)|Epithelial(43;9.94e-18)|OV - Ovarian serous cystadenocarcinoma(60;2e-09)|GBM - Glioblastoma multiforme(59;0.000254)|STAD - Stomach adenocarcinoma(60;0.000653)|LUSC - Lung squamous cell carcinoma(193;0.0393)	Silent	SNP	177373835	177373835	1044	4	A	G	G	14	14	ASB5	G	4	4
CCDC158	339965	broad.mit.edu	36	4	77471568	77471568	+	Silent	SNP	C	T	T			TCGA-06-0237-01	TCGA-06-0237-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:77471568C>T	uc003hkb.2	-	c.2883G>A	c.(2881-2883)TCG>TCA	p.S961S	CCDC158_uc010ijg.1_Non-coding_Transcript	NM_001042784	NP_001036249	Q5M9N0	CD158_HUMAN	hypothetical protein LOC339965	961	Ser-rich.									ovary(2)|pancreas(1)	3														0.39834	292.259875	294.435679	96	145	CC		KEEP	---	---	---	---	capture			Silent	SNP	77471568	77471568	2912	4	C	T	T	19	19	CCDC158	T	1	1
HPSE	10855	broad.mit.edu	36	4	84442385	84442385	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0237-01	TCGA-06-0237-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:84442385C>T	uc003hoj.2	-	c.1267G>A	c.(1267-1269)GTG>ATG	p.V423M	HPSE_uc010ika.1_Missense_Mutation_p.V365M|HPSE_uc003hok.2_Missense_Mutation_p.V423M	NM_001098540	NP_006656	Q9Y251	HPSE_HUMAN	heparanase	423					carbohydrate metabolic process|proteoglycan metabolic process	extracellular region|lysosomal membrane	beta-glucuronidase activity|cation binding			ovary(1)	1		Hepatocellular(203;0.114)			Heparin(DB01109)									0.409722	176.69968	177.724452	59	85	CC		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(81;0.141)	Missense_Mutation	SNP	84442385	84442385	7636	4	C	T	T	19	19	HPSE	T	1	1
HSD17B4	3295	broad.mit.edu	36	5	118837994	118837994	+	Splice_Site_SNP	SNP	G	C	C			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:118837994G>C	uc003ksj.2	+	c.221_splice	c.e4-1	p.D74_splice	HSD17B4_uc003ksk.2_Splice_Site_SNP|HSD17B4_uc010jcn.1_5'Flank	NM_000414	NP_000405			hydroxysteroid (17-beta) dehydrogenase 4						bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	3-hydroxyacyl-CoA dehydrogenase activity|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity|estradiol 17-beta-dehydrogenase activity|isomerase activity|long-chain-enoyl-CoA hydratase activity|protein binding|sterol binding|sterol transporter activity			ovary(1)|pancreas(1)	2		all_cancers(142;0.0206)|Prostate(80;0.0322)			NADH(DB00157)	Colon(35;490 801 34689 41394 43344)								0.496183	226.672219	226.673908	65	66	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)	Splice_Site_SNP	SNP	118837994	118837994	7681	5	G	C	C	33	33	HSD17B4	C	5	3
PCDHAC1	56135	broad.mit.edu	36	5	140288016	140288016	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0237-01	TCGA-06-0237-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140288016T>C	uc003lih.1	+	c.1355T>C	c.(1354-1356)CTT>CCT	p.L452P	PCDHA1_uc003lha.1_Intron|PCDHA1_uc003lhb.1_Intron|PCDHA2_uc003lhd.1_Intron|PCDHA3_uc003lhf.1_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA4_uc003lhi.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.1_Intron|PCDHA6_uc003lho.1_Intron|PCDHA6_uc003lhn.1_Intron|PCDHA7_uc003lhq.1_Intron|PCDHA8_uc003lhs.1_Intron|PCDHA9_uc003lhu.1_Intron|PCDHA10_uc003lhx.1_Intron|PCDHA10_uc003lhw.1_Intron|PCDHA11_uc003lia.1_Intron|PCDHA12_uc003lic.1_Intron|PCDHA13_uc003lie.1_Intron|PCDHA13_uc003lif.1_Intron|PCDHAC1_uc003lig.1_Missense_Mutation_p.L452P	NM_018898	NP_061721	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1 isoform 1	452	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)	2														0.494792	343.935252	343.939553	95	97	TT		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140288016	140288016	11952	5	T	C	C	56	56	PCDHAC1	C	4	4
TCOF1	6949	broad.mit.edu	36	5	149749766	149749766	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:149749766G>C	uc003lry.1	+	c.3170G>C	c.(3169-3171)GGA>GCA	p.G1057A	TCOF1_uc003lrx.1_Missense_Mutation_p.G980A|TCOF1_uc003lrz.1_Missense_Mutation_p.G1057A|TCOF1_uc003lsa.1_Missense_Mutation_p.G980A	NM_001008657	NP_001008657	Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	1057					skeletal system development	nucleolus	protein binding|transporter activity			ovary(2)|large_intestine(1)	3		all_hematologic(541;0.224)												0.3	8.271871	8.978477	6	14	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Missense_Mutation	SNP	149749766	149749766	16234	5	G	C	C	41	41	TCOF1	C	3	3
KIF4B	285643	broad.mit.edu	36	5	154375567	154375567	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:154375567G>A	uc010jih.1	+	c.1955G>A	c.(1954-1956)CGT>CAT	p.R652H		NM_001099293	NP_001092763	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	652	Potential.				axon guidance|blood coagulation|microtubule-based movement	cytosol|microtubule|nuclear matrix	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1	Renal(175;0.00488)	Medulloblastoma(196;0.0523)												0.433735	213.480742	214.114734	72	94	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)		Missense_Mutation	SNP	154375567	154375567	8615	5	G	A	A	40	40	KIF4B	A	1	1
PLEKHG4B	153478	broad.mit.edu	36	5	235428	235428	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:235428G>A	uc003jak.2	+	c.3806G>A	c.(3805-3807)CGC>CAC	p.R1269H		NM_052909	NP_443141	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G	1269					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			skin(1)	1														0.28125	22.659743	24.037038	9	23	GG		KEEP	---	---	---	---	capture	all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)	Missense_Mutation	SNP	235428	235428	12498	5	G	A	A	38	38	PLEKHG4B	A	1	1
IL31RA	133396	broad.mit.edu	36	5	55239965	55239965	+	Silent	SNP	C	A	A			TCGA-06-0237-01	TCGA-06-0237-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:55239965C>A	uc003jql.1	+	c.1470C>A	c.(1468-1470)ATC>ATA	p.I490I	IL31RA_uc003jqk.2_Silent_p.I490I|IL31RA_uc003jqm.2_Silent_p.I458I|IL31RA_uc003jqn.2_Silent_p.I490I|IL31RA_uc010iwa.1_Silent_p.I458I|IL31RA_uc003jqo.1_Silent_p.I348I	NM_139017	NP_620586	Q8NI17	IL31R_HUMAN	gp130-like monocyte receptor	458	Extracellular (Potential).|Fibronectin type-III 5.				anti-apoptosis|defense response|homeostatic process|JAK-STAT cascade|macrophage differentiation|MAPKKK cascade|monocyte differentiation|negative regulation of macrophage activation|positive regulation of cell proliferation|positive regulation of transcription, DNA-dependent|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|transmembrane receptor protein tyrosine kinase signaling pathway	integral to membrane|plasma membrane	cytokine receptor activity|protein kinase binding|transcription coactivator activity			ovary(1)	1		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)												0.351852	106.314582	108.406603	38	70	CC		KEEP	---	---	---	---	capture			Silent	SNP	55239965	55239965	7992	5	C	A	A	32	32	IL31RA	A	3	3
DNAH8	1769	broad.mit.edu	36	6	38993699	38993699	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0237-01	TCGA-06-0237-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:38993699C>A	uc003ooe.1	+	c.9678C>A	c.(9676-9678)TTC>TTA	p.F3226L		NM_001371	NP_001362	Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy polypeptide 8	3226	Stalk (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(5)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	17										2979				0.516129	144.495352	144.516071	48	45	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38993699	38993699	4790	6	C	A	A	30	30	DNAH8	A	3	3
GTPBP2	54676	broad.mit.edu	36	6	43704770	43704770	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:43704770G>C	uc003ovt.1	-	c.108C>G	c.(106-108)TGC>TGG	p.C36W	GTPBP2_uc010jyv.1_5'Flank|GTPBP2_uc003ovs.1_Missense_Mutation_p.C36W|MAD2L1BP_uc003ovu.1_5'Flank	NM_019096	NP_061969	Q9BX10	GTPB2_HUMAN	GTP binding protein 2	36							GTP binding|GTPase activity			liver(1)	1	all_cancers(18;9.36e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004)					GBM(116;405 1620 28302 32150 44768)								0.529412	7.249899	7.238012	9	8	GG		KEEP	---	---	---	---	capture	all cancers(41;0.000501)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)		Missense_Mutation	SNP	43704770	43704770	7160	6	G	C	C	38	38	GTPBP2	C	3	3
JHDM1D	80853	broad.mit.edu	36	7	139437376	139437376	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0237-01	TCGA-06-0237-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:139437376C>T	uc003vvm.1	-	c.2813G>A	c.(2812-2814)CGT>CAT	p.R938H	JHDM1D_uc010lng.1_Non-coding_Transcript	NM_030647	NP_085150	Q6ZMT4	KDM7_HUMAN	jumonji C domain containing histone demethylase	938					midbrain development|oxidation-reduction process|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K27 specific)|histone demethylase activity (H3-K36 specific)|histone demethylase activity (H3-K9 specific)|histone demethylase activity (H4-K20 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1	Melanoma(164;0.0142)													0.218045	64.483605	74.176631	29	104	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	139437376	139437376	8252	7	C	T	T	19	19	JHDM1D	T	1	1
DNAH11	8701	broad.mit.edu	36	7	21605994	21605994	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0237-01	TCGA-06-0237-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:21605994T>C	uc003svc.1	+	c.2732T>C	c.(2731-2733)ATT>ACT	p.I911T		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	911	Stem (By similarity).				microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														0.307692	65.178879	67.319876	20	45	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21605994	21605994	4781	7	T	C	C	52	52	DNAH11	C	4	4
EGFR	1956	broad.mit.edu	36	7	55177569	55177569	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0237-01	TCGA-06-0237-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55177569T>G	uc003tqk.1	+	c.185T>G	c.(184-186)CTT>CGT	p.L62R	EGFR_uc003tqh.1_Missense_Mutation_p.L62R|EGFR_uc003tqi.1_Missense_Mutation_p.L62R|EGFR_uc003tqj.1_Missense_Mutation_p.L62R|EGFR_uc010kzg.1_Missense_Mutation_p.L62R	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	62	Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.V30_R297>G(5)|p.L62R(1)		lung(8200)|central_nervous_system(103)|upper_aerodigestive_tract(37)|prostate(32)|ovary(31)|thyroid(23)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|stomach(6)|urinary_tract(6)|skin(5)|adrenal_gland(5)|kidney(4)|soft_tissue(4)|bone(3)|NS(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)|pancreas(1)	8515	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)				Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8		608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.852476	2865.975785	2979.192605	809	140	TT		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Missense_Mutation	SNP	55177569	55177569	5156	7	T	G	G	56	56	EGFR	G	4	4
NPTX2	4885	broad.mit.edu	36	7	98094418	98094418	+	Silent	SNP	G	A	A			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:98094418G>A	uc003upl.1	+	c.894G>A	c.(892-894)GCG>GCA	p.A298A	NPTX2_uc010lfs.1_Non-coding_Transcript	NM_002523	NP_002514	P47972	NPTX2_HUMAN	neuronal pentraxin II	298	Pentaxin.				synaptic transmission	extracellular region	metal ion binding|sugar binding			central_nervous_system(2)	2	all_cancers(62;2.28e-09)|all_epithelial(64;4.86e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0128)|all_lung(186;0.0142)													0.27193	80.587047	85.925735	31	83	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.215)		Silent	SNP	98094418	98094418	11008	7	G	A	A	38	38	NPTX2	A	1	1
RP1L1	94137	broad.mit.edu	36	8	10506780	10506780	+	Silent	SNP	C	T	T			TCGA-06-0237-01	TCGA-06-0237-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:10506780C>T	uc003wtc.1	-	c.2238G>A	c.(2236-2238)TCG>TCA	p.S746S		NM_178857	NP_849188	A6NKC6	A6NKC6_HUMAN	retinitis pigmentosa 1-like 1	746					intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8														0.363636	130.977991	132.952954	44	77	CC		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(149;0.0811)	Silent	SNP	10506780	10506780	14012	8	C	T	T	23	23	RP1L1	T	1	1
SYTL5	94122	broad.mit.edu	36	X	37816333	37816333	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:37816333G>A	uc004ddx.1	+	c.419G>A	c.(418-420)CGA>CAA	p.R140Q	SYTL5_uc004ddu.1_Missense_Mutation_p.R140Q|SYTL5_uc004ddv.1_Missense_Mutation_p.R140Q|SYTL5_uc004ddw.1_Missense_Mutation_p.R140Q	NM_138780	NP_620135	Q8TDW5	SYTL5_HUMAN	synaptotagmin-like 5	140					intracellular protein transport	membrane	Rab GTPase binding|zinc ion binding				0														0.536232	235.15454	235.311559	74	64	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37816333	37816333	16007	23	G	A	A	37	37	SYTL5	A	1	1
SLC38A5	92745	broad.mit.edu	36	X	48202875	48202875	+	Silent	SNP	G	A	A			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:48202875G>A	uc010nid.1	-	c.1308C>T	c.(1306-1308)CCC>CCT	p.P436P	SLC38A5_uc004djk.2_Silent_p.P385P	NM_033518	NP_277053	Q8WUX1	S38A5_HUMAN	solute carrier family 38, member 5	436	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process|ion transport	integral to membrane|plasma membrane				ovary(3)	3														0.47619	30.24735	30.257796	10	11	GG		KEEP	---	---	---	---	capture			Silent	SNP	48202875	48202875	15104	23	G	A	A	47	47	SLC38A5	A	2	2
TGIF2LX	90316	broad.mit.edu	36	X	89063842	89063842	+	Silent	SNP	G	A	A			TCGA-06-0237-01	TCGA-06-0237-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:89063842G>A	uc004efe.1	+	c.102G>A	c.(100-102)TCG>TCA	p.S34S	TGIF2LX_uc010nmt.1_Silent_p.S34S	NM_138960	NP_620410	Q8IUE1	TF2LX_HUMAN	TGFB-induced factor homeobox 2-like, X-linked	34					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1														0.414634	155.538444	156.31111	51	72	GG		KEEP	---	---	---	---	capture			Silent	SNP	89063842	89063842	16355	23	G	A	A	37	37	TGIF2LX	A	1	1
NOL11	25926	broad.mit.edu	36	17	63164144	63164144	+	Frame_Shift_Del	DEL	C	-	-			TCGA-06-0237-01	TCGA-06-0237-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:63164144_63164144delC	uc002jgd.1	+	c.1277_1277delC	c.(1276-1278)ACAfs	p.T426fs	NOL11_uc010deu.1_Frame_Shift_Del_p.T21fs	NM_015462	NP_056277	Q9H8H0	NOL11_HUMAN	nucleolar protein 11	426						nucleolus					0	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)											0.44			113	146				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	63164144	63164144	10924	17	C	-	-	17	17	NOL11	-	5	5
SLC9A10	285335	broad.mit.edu	36	3	113488299	113488300	+	Frame_Shift_Ins	INS	-	A	A			TCGA-06-0237-01	TCGA-06-0237-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:113488299_113488300insA	uc003dyu.1	-	c.29_30insT	c.(28-30)TTCfs	p.F10fs	SLC9A10_uc010hqc.1_Frame_Shift_Ins_p.F10fs	NM_183061	NP_898884	Q4G0N8	S9A10_HUMAN	sperm-specific sodium proton exchanger	10	Helical; (Potential).				cell differentiation|multicellular organismal development|sodium ion transport|spermatogenesis	cilium|flagellar membrane|integral to membrane	solute:hydrogen antiporter activity			ovary(3)|breast(2)	5														0.38			32	52				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	113488299	113488300	15207	3	-	A	A	45	45	SLC9A10	A	5	5
QKI	9444	broad.mit.edu	36	6	163904742	163904745	+	Splice_Site_Del	DEL	GTAA	-	-			TCGA-06-0237-01	TCGA-06-0237-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:163904742_163904745delGTAA	uc003qui.1	+	c.e6_splice_site			QKI_uc003que.1_Frame_Shift_Del_p.G312fs|QKI_uc003quf.1_Splice_Site_Del|QKI_uc003qug.1_Splice_Site_Del|QKI_uc003quh.1_Splice_Site_Del|QKI_uc003quj.1_Splice_Site_Del	NM_006775	NP_006766			quaking homolog, KH domain RNA binding isoform						mRNA processing|mRNA transport|regulation of translation|RNA splicing	cytoplasm|nucleus|plasma membrane	RNA binding|SH3 domain binding			large_intestine(1)|ovary(1)	2		Breast(66;5e-05)|Prostate(117;0.0235)|all_neural(5;0.0416)|Ovarian(120;0.0448)|Glioma(2;0.203)		all cancers(1;4.4e-46)|OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|GBM - Glioblastoma multiforme(1;2.94e-19)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|Kidney(3;0.000199)|KIRC - Kidney renal clear cell carcinoma(3;0.000234)										0.40			79	121				---	---	---	---	capture_indel			Splice_Site_Del	DEL	163904742	163904745	13331	6	GTAA	-	-	44	44	QKI	-	5	5
HRCT1	646962	broad.mit.edu	36	9	35896584	35896586	+	In_Frame_Del	DEL	CCA	-	-			TCGA-06-0237-01	TCGA-06-0237-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:35896584_35896586delCCA	uc003zyr.1	+	c.300_302delCCA	c.(298-303)CTCCAC>CTC	p.H105del	LOC158376_uc003zys.1_5'Flank	NM_001039792	NP_001034881	Q6UXD1	HRCT1_HUMAN	histidine rich carboxyl terminus 1	105	His-rich.					integral to membrane					0														0.35			8	15				---	---	---	---	capture_indel			In_Frame_Del	DEL	35896584	35896586	7645	9	CCA	-	-	30	30	HRCT1	-	5	5
