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
RSU1	6251	broad.mit.edu	36	10	16777096	16777096	+	Silent	SNP	G	T	T			TCGA-14-1821-01	TCGA-14-1821-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:16777096G>T	uc001iok.1	-	c.663C>A	c.(661-663)CCC>CCA	p.P221P	RSU1_uc001iol.1_Silent_p.P221P|RSU1_uc001iom.1_Silent_p.P168P	NM_152724	NP_689937	Q15404	RSU1_HUMAN	ras suppressor protein 1 isoform 2	221					cell junction assembly|signal transduction	cytosol	protein binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(1;7.54e-08)										0.419048	131.071314	131.67391	44	61	GG		KEEP	---	---	---	---	capture			Silent	SNP	16777096	16777096	14196	10	G	T	T	47	47	RSU1	T	3	3
ARMC4	55130	broad.mit.edu	36	10	28264183	28264183	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1821-01	TCGA-14-1821-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:28264183G>A	uc009xky.1	-	c.2257C>T	c.(2257-2259)CGG>TGG	p.R753W	ARMC4_uc001itz.1_Missense_Mutation_p.R753W	NM_018076	NP_060546	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	753	ARM 5.						binding			ovary(4)	4														0.508197	205.451789	205.459003	62	60	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	28264183	28264183	971	10	G	A	A	37	37	ARMC4	A	1	1
OR4C11	219429	broad.mit.edu	36	11	55127709	55127709	+	Silent	SNP	C	T	T			TCGA-14-1821-01	TCGA-14-1821-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55127709C>T	uc001nhq.1	-	c.717G>A	c.(715-717)ACG>ACA	p.T239T		NM_001004700	NP_001004700	Q6IEV9	OR4CB_HUMAN	olfactory receptor, family 4, subfamily C,	239	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.513661	294.143175	294.172761	94	89	CC		KEEP	---	---	---	---	capture			Silent	SNP	55127709	55127709	11451	11	C	T	T	19	19	OR4C11	T	1	1
BBS1	582	broad.mit.edu	36	11	66045424	66045424	+	Splice_Site_SNP	SNP	G	T	T			TCGA-14-1821-01	TCGA-14-1821-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:66045424G>T	uc001oii.1	+	c.e9_splice_site			ZDHHC24_uc001oim.1_Non-coding_Transcript|ZDHHC24_uc009yrg.1_3'UTR|BBS1_uc001oij.1_Splice_Site_SNP|BBS1_uc001oik.1_Splice_Site_SNP|BBS1_uc001oil.1_Intron	NM_024649	NP_078925			Bardet-Biedl syndrome 1						photoreceptor cell maintenance|response to stimulus|retina homeostasis|sensory cilium assembly	BBSome|cilium membrane|cytoplasm	protein binding			ovary(1)	1						GBM(152;173 2612 9770 10137)								0.21875	6.482507	8.869565	7	25	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	66045424	66045424	1356	11	G	T	T	44	44	BBS1	T	5	3
DNAJC14	85406	broad.mit.edu	36	12	54508572	54508572	+	Silent	SNP	A	C	C			TCGA-14-1821-01	TCGA-14-1821-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:54508572A>C	uc001shu.1	-	c.138T>G	c.(136-138)GCT>GCG	p.A46A	DNAJC14_uc001shx.1_Silent_p.A46A|DNAJC14_uc009zob.1_Silent_p.A46A|DNAJC14_uc001shy.1_Silent_p.A46A	NM_032364	NP_115740	Q6Y2X3	DJC14_HUMAN	dopamine receptor interacting protein	46					protein folding|protein transport	endoplasmic reticulum membrane|integral to membrane	heat shock protein binding|unfolded protein binding			ovary(2)|large_intestine(1)	3														0.323529	30.512658	31.452855	11	23	AA		KEEP	---	---	---	---	capture			Silent	SNP	54508572	54508572	4816	12	A	C	C	11	11	DNAJC14	C	4	4
SYNE2	23224	broad.mit.edu	36	14	63752832	63752832	+	Missense_Mutation	SNP	T	G	G			TCGA-14-1821-01	TCGA-14-1821-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:63752832T>G	uc001xgl.1	+	c.19516T>G	c.(19516-19518)TCC>GCC	p.S6506A	SYNE2_uc001xgm.1_Missense_Mutation_p.S6483A|SYNE2_uc010apy.1_Missense_Mutation_p.S2868A|SYNE2_uc001xgn.1_Missense_Mutation_p.S1445A|SYNE2_uc001xgo.1_Non-coding_Transcript|SYNE2_uc010aqa.1_Missense_Mutation_p.S453A|SYNE2_uc001xgq.1_Missense_Mutation_p.S848A|SYNE2_uc001xgr.1_Missense_Mutation_p.S266A|SYNE2_uc001xgs.1_Missense_Mutation_p.S140A|SYNE2_uc001xgt.1_Missense_Mutation_p.S14A	NM_182914	NP_878918	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	6483	Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)										0.492063	193.611965	193.619365	62	64	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63752832	63752832	15967	14	T	G	G	58	58	SYNE2	G	4	4
EIF4A1	1973	broad.mit.edu	36	17	7416905	7416905	+	Nonsense_Mutation	SNP	C	T	T			TCGA-14-1821-01	TCGA-14-1821-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7416905C>T	uc002gho.1	+	c.22C>T	c.(22-24)CGA>TGA	p.R8*	EIF4A1_uc002ghr.1_Nonsense_Mutation_p.R8*|EIF4A1_uc002ghq.1_Nonsense_Mutation_p.R8*|EIF4A1_uc002ghp.1_Nonsense_Mutation_p.R8*|SNORA48_uc002ghs.1_5'Flank	NM_001416	NP_001407	P60842	IF4A1_HUMAN	eukaryotic translation initiation factor 4A	8					nuclear-transcribed mRNA poly(A) tail shortening	cytosol|eukaryotic translation initiation factor 4F complex	ATP binding|ATP-dependent helicase activity|mRNA binding|protein binding|RNA cap binding|translation initiation factor activity			ovary(1)	1						Melanoma(120;278 1668 15796 27423 46368)				115				0.416667	255.1702	256.332465	80	112	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	7416905	7416905	5215	17	C	T	T	23	23	EIF4A1	T	5	1
TP53	7157	broad.mit.edu	36	17	7518933	7518933	+	Missense_Mutation	SNP	T	C	C			TCGA-14-1821-01	TCGA-14-1821-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7518933T>C	uc002gim.2	-	c.641A>G	c.(640-642)CAT>CGT	p.H214R	TP53_uc002gig.1_Missense_Mutation_p.H214R|TP53_uc002gih.1_Missense_Mutation_p.H214R|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.H82R|TP53_uc010cng.1_Missense_Mutation_p.H82R|TP53_uc002gii.1_Missense_Mutation_p.H82R|TP53_uc010cnh.1_Missense_Mutation_p.H214R|TP53_uc010cni.1_Missense_Mutation_p.H214R|TP53_uc002gij.2_Missense_Mutation_p.H214R|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_Missense_Mutation_p.H121R|TP53_uc002gio.2_Missense_Mutation_p.H82R	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	214	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		H -> Y (in sporadic cancers; somatic mutation).|H -> D (in sporadic cancers; somatic mutation).|H -> R (in sporadic cancers; somatic mutation).|H -> Q (in sporadic cancers; somatic mutation).|H -> P (in a sporadic cancer; 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.H214R(44)|p.0?(6)|p.H214fs*5(2)|p.D208fs*1(1)|p.T211fs*28(1)|p.R213_S215>X(1)|p.D207_V216del10(1)|p.R213fs*32(1)|p.T211_S215delTFRHS(1)|p.R209fs*6(1)|p.D208_V216delDRNTFRHSV(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)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		Pancreas(47;798 1329 9957 10801)		111	p.H214R(T.T-Tumor)|p.H214R(NCIH1963-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.906977	524.910162	553.579425	156	16	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7518933	7518933	16923	17	T	C	C	51	51	TP53	C	4	4
MYT1	4661	broad.mit.edu	36	20	62307559	62307559	+	Nonsense_Mutation	SNP	C	G	G			TCGA-14-1821-01	TCGA-14-1821-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:62307559C>G	uc002yii.1	+	c.359C>G	c.(358-360)TCA>TGA	p.S120*	MYT1_uc002yih.2_Nonsense_Mutation_p.S120*|MYT1_uc002yij.1_5'Flank	NM_004535	NP_004526	Q01538	MYT1_HUMAN	myelin transcription factor 1	120					cell differentiation|nervous system development|regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					GBM(59;481 1041 20555 21139 33705)				1819				0.432432	52.596619	52.743354	16	21	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	62307559	62307559	10501	20	C	G	G	29	29	MYT1	G	5	3
SF3B1	23451	broad.mit.edu	36	2	197973254	197973254	+	Silent	SNP	A	T	T			TCGA-14-1821-01	TCGA-14-1821-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:197973254A>T	uc002uue.1	-	c.2868T>A	c.(2866-2868)TCT>TCA	p.S956S		NM_012433	NP_036565	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1 isoform 1	956					nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nuclear speck|U12-type spliceosomal complex	protein binding			pancreas(3)|ovary(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.246)											0.439153	249.792804	250.402974	83	106	AA		KEEP	---	---	---	---	capture			Silent	SNP	197973254	197973254	14638	2	A	T	T	11	11	SF3B1	T	4	4
IDH1	3417	broad.mit.edu	36	2	208821357	208821357	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1821-01	TCGA-14-1821-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:208821357C>T	uc002vcs.1	-	c.395G>A	c.(394-396)CGT>CAT	p.R132H	IDH1_uc002vct.1_Missense_Mutation_p.R132H|IDH1_uc002vcu.1_Missense_Mutation_p.R132H	NM_005896	NP_005887	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132		Substrate.	R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).		2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity	p.R132H(1725)|p.R132?(210)|p.R132C(92)|p.R132L(48)|p.R132G(26)|p.R132S(11)|p.R132V(1)|p.G131_R132>VL(1)		central_nervous_system(1848)|haematopoietic_and_lymphoid_tissue(593)|large_intestine(4)|skin(2)|prostate(2)|autonomic_ganglia(1)|soft_tissue(1)	2451				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		Pancreas(158;264 1958 3300 35450 36047)				134				0.456	180.235366	180.448486	57	68	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	208821357	208821357	7794	2	C	T	T	19	19	IDH1	T	1	1
AGBL5	60509	broad.mit.edu	36	2	27133706	27133706	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1821-01	TCGA-14-1821-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:27133706C>T	uc002rie.1	+	c.1567C>T	c.(1567-1569)CGC>TGC	p.R523C	AGBL5_uc002rid.1_Missense_Mutation_p.R523C|AGBL5_uc002rif.1_Non-coding_Transcript	NM_021831	NP_068603	Q8NDL9	CBPC5_HUMAN	ATP/GTP binding protein-like 5 isoform 1	523					protein branching point deglutamylation|proteolysis	cytosol|nucleus	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.527778	58.212458	58.235919	19	17	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27133706	27133706	381	2	C	T	T	19	19	AGBL5	T	1	1
SENP7	57337	broad.mit.edu	36	3	102619220	102619220	+	Missense_Mutation	SNP	A	C	C			TCGA-14-1821-01	TCGA-14-1821-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:102619220A>C	uc003dut.1	-	c.389T>G	c.(388-390)GTG>GGG	p.V130G	SENP7_uc003duu.1_Missense_Mutation_p.V130G|SENP7_uc003duv.1_Missense_Mutation_p.V97G|SENP7_uc003duw.1_Intron|SENP7_uc003dux.1_Intron	NM_020654	NP_065705	Q9BQF6	SENP7_HUMAN	sentrin/SUMO-specific protease 7 isoform 1	130					proteolysis	nucleus	cysteine-type peptidase activity			ovary(2)|lung(1)	3														0.458791	522.617372	523.160108	167	197	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102619220	102619220	14537	3	A	C	C	6	6	SENP7	C	4	4
GFM1	85476	broad.mit.edu	36	3	159865856	159865856	+	Missense_Mutation	SNP	T	G	G			TCGA-14-1821-01	TCGA-14-1821-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:159865856T>G	uc003fce.1	+	c.1417T>G	c.(1417-1419)TTT>GTT	p.F473V	GFM1_uc003fcd.2_Missense_Mutation_p.F473V|GFM1_uc003fcf.1_Non-coding_Transcript|GFM1_uc003fcg.1_Missense_Mutation_p.F404V	NM_024996	NP_079272	Q96RP9	EFGM_HUMAN	G elongation factor, mitochondrial 1	473					mitochondrial translational elongation	mitochondrion	GTP binding|GTPase activity|translation elongation factor activity			ovary(3)|central_nervous_system(1)	4			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)											0.257143	6.943368	9.040171	9	26	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	159865856	159865856	6609	3	T	G	G	60	60	GFM1	G	4	4
PDGFRA	5156	broad.mit.edu	36	4	54838905	54838905	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1821-01	TCGA-14-1821-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:54838905C>G	uc003han.2	+	c.1977C>G	c.(1975-1977)AAC>AAG	p.N659K	PDGFRA_uc003haa.1_Missense_Mutation_p.N419K|PDGFRA_uc010igq.1_Missense_Mutation_p.N553K|PDGFRA_uc003ham.2_Non-coding_Transcript|PDGFRA_uc003hao.1_Missense_Mutation_p.N38K	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	659	Protein kinase.|Cytoplasmic (Potential).				cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity	p.N659K(12)|p.N659Y(2)		soft_tissue(532)|small_intestine(40)|stomach(16)|central_nervous_system(13)|lung(9)|haematopoietic_and_lymphoid_tissue(7)|ovary(3)|skin(2)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|bone(1)	625	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	Pancreas(151;208 1913 7310 23853 37092)				1045	TSP Lung(21;0.16)			0.692308	385.507246	391.074512	117	52	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54838905	54838905	12082	4	C	G	G	20	20	PDGFRA	G	3	3
C5orf42	65250	broad.mit.edu	36	5	37234609	37234609	+	Silent	SNP	T	C	C			TCGA-14-1821-01	TCGA-14-1821-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:37234609T>C	uc003jkq.1	-	c.267A>G	c.(265-267)GCA>GCG	p.A89A		NM_023073	NP_075561	B7ZLV7	B7ZLV7_HUMAN	hypothetical protein LOC65250	121										ovary(4)|breast(2)	6	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)											0.549296	363.88772	364.338819	117	96	TT		KEEP	---	---	---	---	capture			Silent	SNP	37234609	37234609	2399	5	T	C	C	59	59	C5orf42	C	4	4
CPNE5	57699	broad.mit.edu	36	6	36874214	36874214	+	Missense_Mutation	SNP	T	C	C			TCGA-14-1821-01	TCGA-14-1821-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:36874214T>C	uc003omr.1	-	c.323A>G	c.(322-324)AAA>AGA	p.K108R	CPNE5_uc003oms.1_Missense_Mutation_p.K70R	NM_020939	NP_065990	Q9HCH3	CPNE5_HUMAN	copine V	108	C2 1.									skin(1)	1										537				0.508772	188.26633	188.272342	58	56	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36874214	36874214	3953	6	T	C	C	64	64	CPNE5	C	4	4
GRHL2	79977	broad.mit.edu	36	8	102713757	102713757	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1821-01	TCGA-14-1821-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:102713757G>C	uc010mbu.1	+	c.1473G>C	c.(1471-1473)CAG>CAC	p.Q491H		NM_024915	NP_079191	Q6ISB3	GRHL2_HUMAN	transcription factor CP2-like 3	491					regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(2)|skin(1)	3	all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05)		Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213)									OREG0018909	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.47619	99.948195	99.97907	30	33	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102713757	102713757	7042	8	G	C	C	33	33	GRHL2	C	3	3
ABCA1	19	broad.mit.edu	36	9	106623562	106623562	+	Missense_Mutation	SNP	T	C	C			TCGA-14-1821-01	TCGA-14-1821-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:106623562T>C	uc004bcl.1	-	c.2875A>G	c.(2875-2877)ATC>GTC	p.I959V		NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1	959	ABC transporter 1.				Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol binding|cholesterol transporter activity|phospholipid binding|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|ovary(4)|central_nervous_system(1)|pancreas(1)	10				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)									0.260274	42.886383	46.68987	19	54	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	106623562	106623562	29	9	T	C	C	51	51	ABCA1	C	4	4
AGTPBP1	23287	broad.mit.edu	36	9	87437583	87437583	+	Nonsense_Mutation	SNP	G	T	T			TCGA-14-1821-01	TCGA-14-1821-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:87437583G>T	uc010mqc.1	-	c.1709C>A	c.(1708-1710)TCG>TAG	p.S570*	AGTPBP1_uc004aod.2_Nonsense_Mutation_p.S236*|AGTPBP1_uc004aoe.2_Nonsense_Mutation_p.S552*	NM_015239	NP_056054	Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	610					C-terminal protein deglutamylation|cerebellar Purkinje cell differentiation|eye photoreceptor cell differentiation|mitochondrion organization|neuromuscular process|olfactory bulb development|protein side chain deglutamylation|proteolysis	cytosol|mitochondrion|nucleus	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(4)|large_intestine(2)	6														0.30625	282.234992	292.944978	98	222	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	87437583	87437583	403	9	G	T	T	37	37	AGTPBP1	T	5	3
GPC4	2239	broad.mit.edu	36	X	132264726	132264726	+	Missense_Mutation	SNP	A	C	C			TCGA-14-1821-01	TCGA-14-1821-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:132264726A>C	uc004exc.1	-	c.1506T>G	c.(1504-1506)TGT>TGG	p.C502W		NM_001448	NP_001439	O75487	GPC4_HUMAN	glypican 4	502					anatomical structure morphogenesis|cell proliferation	anchored to membrane|external side of plasma membrane|extracellular space|insoluble fraction|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	Acute lymphoblastic leukemia(192;0.000127)													0.3	7.921823	8.278809	3	7	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	132264726	132264726	6874	23	A	C	C	6	6	GPC4	C	4	4
F8	2157	broad.mit.edu	36	X	153811414	153811414	+	Missense_Mutation	SNP	T	A	A			TCGA-14-1821-01	TCGA-14-1821-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:153811414T>A	uc004fmt.1	-	c.3845A>T	c.(3844-3846)AAA>ATA	p.K1282I		NM_000132	NP_000123	P00451	FA8_HUMAN	coagulation factor VIII isoform a precursor	1282	B.				acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|oxidation-reduction process|platelet activation|platelet degranulation	extracellular space|plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity|protein binding			ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	11	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)					359				0.980892	572.389958	577.395091	154	3	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153811414	153811414	5544	23	T	A	A	64	64	F8	A	4	4
ARAF	369	broad.mit.edu	36	X	47311076	47311076	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1821-01	TCGA-14-1821-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:47311076G>A	uc010nhs.1	+	c.652G>A	c.(652-654)GTC>ATC	p.V218I	ARAF_uc004dic.1_5'UTR	NM_001654	NP_001645	P10398	ARAF_HUMAN	v-raf murine sarcoma 3611 viral oncogene	218					intracellular signal transduction|negative regulation of apoptosis|positive regulation of peptidyl-serine phosphorylation|protein phosphorylation		ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity			large_intestine(3)|lung(1)|ovary(1)	5					Adenosine triphosphate(DB00171)				p.V218I(HEC251-Tumor)	119				1	76.03529	76.035289	20	0	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47311076	47311076	848	23	G	A	A	40	40	ARAF	A	1	1
NEIL1	79661	broad.mit.edu	36	15	73428634	73428635	+	Frame_Shift_Del	DEL	TA	-	-			TCGA-14-1821-01	TCGA-14-1821-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:73428634_73428635delTA	uc002bae.1	+	c.593_594delTA	c.(592-594)CTAfs	p.L198fs	NEIL1_uc002bad.1_Frame_Shift_Del_p.L112fs	NM_024608	NP_078884	Q96FI4	NEIL1_HUMAN	nei endonuclease VIII-like 1	112					base-excision repair|negative regulation of nuclease activity|nucleotide-excision repair|response to oxidative stress	cytoplasm|nucleus	damaged DNA binding|DNA-(apurinic or apyrimidinic site) lyase activity|protein C-terminus binding|zinc ion binding				0														0.38			8	13				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	73428634	73428635	10717	15	TA	-	-	53	53	NEIL1	-	5	5
