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
NFRKB	4798	broad.mit.edu	36	11	129250550	129250550	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1456-01	TCGA-14-1456-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:129250550C>G	uc001qfg.1	-	c.1841G>C	c.(1840-1842)CGA>CCA	p.R614P	NFRKB_uc009zcr.1_5'Flank|NFRKB_uc001qfh.1_Missense_Mutation_p.R612P|NFRKB_uc001qfi.1_Missense_Mutation_p.R589P	NM_006165	NP_006156	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	589					inflammatory response|transcription from RNA polymerase II promoter	nucleus	DNA binding|protease binding|specific RNA polymerase II transcription factor activity			ovary(3)	3	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)												0.25	7.140924	7.808395	3	9	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)	Missense_Mutation	SNP	129250550	129250550	10784	11	C	G	G	31	31	NFRKB	G	3	3
DCHS1	8642	broad.mit.edu	36	11	6607847	6607847	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1456-01	TCGA-14-1456-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:6607847G>C	uc001mem.1	-	c.4754C>G	c.(4753-4755)GCA>GGA	p.A1585G		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	1585	Cadherin 15.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)												0.3125	11.967178	12.469148	5	11	GG		KEEP	---	---	---	---	capture		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	Missense_Mutation	SNP	6607847	6607847	4458	11	G	C	C	46	46	DCHS1	C	3	3
GDPD5	81544	broad.mit.edu	36	11	74831892	74831892	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1456-01	TCGA-14-1456-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:74831892C>G	uc001owo.2	-	c.885G>C	c.(883-885)AGG>AGC	p.R295S	GDPD5_uc009yuc.1_Missense_Mutation_p.R157S|GDPD5_uc009yud.1_Missense_Mutation_p.R176S|GDPD5_uc001owp.2_Missense_Mutation_p.R295S|GDPD5_uc009yue.1_Missense_Mutation_p.R183S|GDPD5_uc001own.2_Missense_Mutation_p.R50S	NM_030792	NP_110419	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain	295	Extracellular (Potential).|GDPD.				glycerol metabolic process|lipid metabolic process|nervous system development	endomembrane system|growth cone|integral to membrane|perinuclear region of cytoplasm	glycerophosphodiester phosphodiesterase activity			ovary(1)	1														0.210526	7.488142	8.962687	4	15	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74831892	74831892	6595	11	C	G	G	26	26	GDPD5	G	3	3
TDRD9	122402	broad.mit.edu	36	14	103542742	103542742	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1456-01	TCGA-14-1456-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:103542742C>G	uc001yom.2	+	c.1886C>G	c.(1885-1887)GCT>GGT	p.A629G	TDRD9_uc001yon.2_Missense_Mutation_p.A367G|TDRD9_uc010awx.1_Missense_Mutation_p.A344G	NM_153046	NP_694591	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	629					cell differentiation|DNA methylation involved in gamete generation|fertilization|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	nucleus|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(2)|central_nervous_system(1)	3		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)												0.181818	7.953478	11.080059	6	27	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	103542742	103542742	16263	14	C	G	G	28	28	TDRD9	G	3	3
SLC27A2	11001	broad.mit.edu	36	15	48302545	48302545	+	Missense_Mutation	SNP	A	G	G			TCGA-14-1456-01	TCGA-14-1456-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:48302545A>G	uc001zxw.1	+	c.1064A>G	c.(1063-1065)GAC>GGC	p.D355G	SLC27A2_uc010bes.1_Missense_Mutation_p.D302G|SLC27A2_uc001zxx.1_Missense_Mutation_p.D120G	NM_003645	NP_003636	O14975	S27A2_HUMAN	solute carrier family 27 (fatty acid	355	Cytoplasmic (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)												0.379518	201.030602	203.16213	63	103	AA		KEEP	---	---	---	---	capture		all cancers(107;1.16e-06)|GBM - Glioblastoma multiforme(94;0.000113)	Missense_Mutation	SNP	48302545	48302545	15023	15	A	G	G	10	10	SLC27A2	G	4	4
SEC11A	23478	broad.mit.edu	36	15	83035820	83035820	+	Silent	SNP	C	T	T			TCGA-14-1456-01	TCGA-14-1456-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:83035820C>T	uc002blb.1	-	c.111G>A	c.(109-111)AAG>AAA	p.K37K	SEC11A_uc002blc.1_Silent_p.K11K	NM_014300	NP_055115	P67812	SC11A_HUMAN	SEC11-like 1	37	Lumenal (Potential).				energy reserve metabolic process|regulation of insulin secretion|signal peptide processing	endoplasmic reticulum membrane|integral to membrane|microsome	protein binding|serine-type peptidase activity			ovary(1)	1														0.21978	51.04908	57.631794	20	71	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(143;0.199)		Silent	SNP	83035820	83035820	14464	15	C	T	T	24	24	SEC11A	T	2	2
KCTD2	23510	broad.mit.edu	36	17	70555185	70555185	+	Missense_Mutation	SNP	A	G	G			TCGA-14-1456-01	TCGA-14-1456-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:70555185A>G	uc002jmp.1	+	c.245A>G	c.(244-246)TAC>TGC	p.Y82C	KCTD2_uc010dfy.1_Intron|KCTD2_uc010dfz.1_Intron|ATP5H_uc002jmn.1_5'Flank|ATP5H_uc002jmo.1_5'Flank|KCTD2_uc002jmq.1_Non-coding_Transcript	NM_015353	NP_056168	Q14681	KCTD2_HUMAN	potassium channel tetramerisation domain	82	BTB.					voltage-gated potassium channel complex	voltage-gated potassium channel activity				0	all_lung(278;0.226)													0.390244	52.293993	52.725477	16	25	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70555185	70555185	8413	17	A	G	G	14	14	KCTD2	G	4	4
ASNA1	439	broad.mit.edu	36	19	12709333	12709333	+	Missense_Mutation	SNP	T	G	G			TCGA-14-1456-01	TCGA-14-1456-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:12709333T>G	uc002muv.1	+	c.14T>G	c.(13-15)GTG>GGG	p.V5G	ASNA1_uc002muw.1_Missense_Mutation_p.V5G|C19orf43_uc002muu.1_5'Flank	NM_004317	NP_004308	O43681	ASNA_HUMAN	arsA arsenite transporter, ATP-binding, homolog	5					cellular metal ion homeostasis	endoplasmic reticulum|nucleolus|soluble fraction	arsenite transmembrane transporter activity|ATP binding|hydrolase activity|metal ion binding			ovary(2)	2					Adenosine triphosphate(DB00171)									0.416667	7.17651	7.269212	5	7	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12709333	12709333	1066	19	T	G	G	59	59	ASNA1	G	4	4
LRFN3	79414	broad.mit.edu	36	19	41122878	41122878	+	Silent	SNP	G	C	C			TCGA-14-1456-01	TCGA-14-1456-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:41122878G>C	uc002oco.1	+	c.711G>C	c.(709-711)TCG>TCC	p.S237S		NM_024509	NP_078785	Q9BTN0	LRFN3_HUMAN	leucine rich repeat and fibronectin type III	237	Extracellular (Potential).				cell adhesion	axon|cell junction|dendrite|integral to membrane|postsynaptic membrane|presynaptic membrane					0	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)													0.195122	7.110847	10.611193	8	33	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(66;0.06)		Silent	SNP	41122878	41122878	9312	19	G	C	C	38	38	LRFN3	C	3	3
CCDC27	148870	broad.mit.edu	36	1	3670243	3670243	+	Missense_Mutation	SNP	C	A	A			TCGA-14-1456-01	TCGA-14-1456-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:3670243C>A	uc001akv.1	+	c.1435C>A	c.(1435-1437)CAA>AAA	p.Q479K		NM_152492	NP_689705	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	479											0	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)												0.363636	14.539063	14.919751	8	14	CC		KEEP	---	---	---	---	capture		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)	Missense_Mutation	SNP	3670243	3670243	2923	1	C	A	A	17	17	CCDC27	A	3	3
CHD6	84181	broad.mit.edu	36	20	39483194	39483194	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1456-01	TCGA-14-1456-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:39483194C>T	uc002xka.1	-	c.5495G>A	c.(5494-5496)TGT>TAT	p.C1832Y		NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1832					chromatin assembly or disassembly|chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|lung(2)|central_nervous_system(1)|skin(1)	10		Myeloproliferative disorder(115;0.00425)												0.344059	379.611946	388.284775	139	265	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	39483194	39483194	3463	20	C	T	T	17	17	CHD6	T	2	2
PREX1	57580	broad.mit.edu	36	20	46701364	46701364	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1456-01	TCGA-14-1456-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:46701364C>T	uc002xtw.1	-	c.2632G>A	c.(2632-2634)GGC>AGC	p.G878S	PREX1_uc002xtv.1_Missense_Mutation_p.G175S	NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,	878					actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6														0.344828	55.376128	56.612286	20	38	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)		Missense_Mutation	SNP	46701364	46701364	12919	20	C	T	T	23	23	PREX1	T	1	1
IDH1	3417	broad.mit.edu	36	2	208821357	208821357	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1456-01	TCGA-14-1456-01	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						Pancreas(158;264 1958 3300 35450 36047)				134				0.282443	94.62477	100.19222	37	94	CC		KEEP	---	---	---	---	capture		Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)	Missense_Mutation	SNP	208821357	208821357	7794	2	C	T	T	19	19	IDH1	T	1	1
CRYBA2	1412	broad.mit.edu	36	2	219565117	219565117	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1456-01	TCGA-14-1456-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:219565117C>G	uc002vjj.1	-	c.254G>C	c.(253-255)AGC>ACC	p.S85T	CRYBA2_uc002vjk.1_Missense_Mutation_p.S85T	NM_057094	NP_476435	P53672	CRBA2_HUMAN	crystallin, beta A2	85	Beta/gamma crystallin 'Greek key' 2.						structural constituent of eye lens				0		Renal(207;0.0474)												0.454545	12.767649	12.788045	5	6	CC		KEEP	---	---	---	---	capture		Epithelial(149;9.77e-07)|all cancers(144;0.000167)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Missense_Mutation	SNP	219565117	219565117	4047	2	C	G	G	28	28	CRYBA2	G	3	3
SPP2	6694	broad.mit.edu	36	2	234632242	234632242	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1456-01	TCGA-14-1456-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:234632242C>G	uc002vvk.1	+	c.234C>G	c.(232-234)AAC>AAG	p.N78K	SPP2_uc010fyl.1_5'UTR	NM_006944	NP_008875	Q13103	SPP24_HUMAN	secreted phosphoprotein 2, 24kDa precursor	78					bone remodeling|skeletal system development	extracellular region	endopeptidase inhibitor activity				0		Breast(86;0.0109)|Renal(207;0.019)|all_lung(227;0.13)|all_hematologic(139;0.182)												0.354839	220.397797	223.851703	66	120	CC		KEEP	---	---	---	---	capture		Epithelial(121;5.73e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000166)|Lung(119;0.00539)|LUSC - Lung squamous cell carcinoma(224;0.00846)	Missense_Mutation	SNP	234632242	234632242	15600	2	C	G	G	20	20	SPP2	G	3	3
PER2	8864	broad.mit.edu	36	2	238822498	238822498	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1456-01	TCGA-14-1456-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:238822498G>A	uc002vyc.1	-	c.3562C>T	c.(3562-3564)CGC>TGC	p.R1188C		NM_022817	NP_073728	O15055	PER2_HUMAN	period 2	1188	CRY binding domain (By similarity).				circadian rhythm|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|signal transducer activity			breast(1)	1		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)												0.413534	463.260362	465.846295	165	234	GG		KEEP	---	---	---	---	capture		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)	Missense_Mutation	SNP	238822498	238822498	12151	2	G	A	A	38	38	PER2	A	1	1
PIK3R1	5295	broad.mit.edu	36	5	67624903	67624903	+	Missense_Mutation	SNP	A	G	G			TCGA-14-1456-01	TCGA-14-1456-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:67624903A>G	uc003jva.1	+	c.1135A>G	c.(1135-1137)AAA>GAA	p.K379E	PIK3R1_uc003jvb.1_Missense_Mutation_p.K379E|PIK3R1_uc003jvc.1_Missense_Mutation_p.K79E|PIK3R1_uc003jvd.1_Missense_Mutation_p.K109E|PIK3R1_uc003jve.1_Missense_Mutation_p.K58E	NM_181523	NP_852664	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1	379	SH2 1.				epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex	1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding	p.?(1)		endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(5)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1)	99		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)			Isoproterenol(DB01064)					370	TCGA GBM(4;<1E-8)			0.222222	45.407062	51.156494	18	63	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Missense_Mutation	SNP	67624903	67624903	12342	5	A	G	G	5	5	PIK3R1	G	4	4
ARSK	153642	broad.mit.edu	36	5	94962486	94962486	+	Missense_Mutation	SNP	T	C	C			TCGA-14-1456-01	TCGA-14-1456-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:94962486T>C	uc003kld.1	+	c.1276T>C	c.(1276-1278)TAT>CAT	p.Y426H	ARSK_uc010jbg.1_Missense_Mutation_p.Y267H	NM_198150	NP_937793	Q6UWY0	ARSK_HUMAN	arylsulfatase K	426						extracellular region	arylsulfatase activity|metal ion binding			pancreas(1)	1		all_cancers(142;3.38e-06)|all_epithelial(76;6.57e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)												0.420408	357.492885	358.844335	103	142	TT		KEEP	---	---	---	---	capture		all cancers(79;6.5e-16)	Missense_Mutation	SNP	94962486	94962486	1014	5	T	C	C	49	49	ARSK	C	4	4
CD2AP	23607	broad.mit.edu	36	6	47655137	47655137	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1456-01	TCGA-14-1456-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:47655137C>T	uc003oyw.1	+	c.961C>T	c.(961-963)CCA>TCA	p.P321S		NM_012120	NP_036252	Q9Y5K6	CD2AP_HUMAN	CD2-associated protein	321	SH3 3.				cell division|mitosis|protein complex assembly|signal transduction|substrate-dependent cell migration, cell extension	cytoplasm|filamentous actin|nucleolus|plasma membrane|ruffle	SH3 domain binding|structural constituent of cytoskeleton			ovary(1)	1														0.364486	107.473211	109.209897	39	68	CC		KEEP	---	---	---	---	capture	Lung(136;0.105)|LUSC - Lung squamous cell carcinoma(51;0.138)		Missense_Mutation	SNP	47655137	47655137	3122	6	C	T	T	30	30	CD2AP	T	2	2
EGFR	1956	broad.mit.edu	36	7	55186515	55186515	+	Silent	SNP	C	T	T			TCGA-14-1456-01	TCGA-14-1456-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55186515C>T	uc003tqk.1	+	c.594C>T	c.(592-594)AGC>AGT	p.S198S	EGFR_uc003tqh.1_Silent_p.S198S|EGFR_uc003tqi.1_Silent_p.S198S|EGFR_uc003tqj.1_Silent_p.S198S|EGFR_uc010kzg.1_Silent_p.S153S|EGFR_uc003tql.1_5'Flank	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	198	Approximate.|Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.V30_R297>G(10)		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)			0.227273	135.225524	151.728009	55	187	CC		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)		Silent	SNP	55186515	55186515	5156	7	C	T	T	28	28	EGFR	T	2	2
EGFR	1956	broad.mit.edu	36	7	55189316	55189316	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1456-01	TCGA-14-1456-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55189316C>T	uc003tqk.1	+	c.866C>T	c.(865-867)GCC>GTC	p.A289V	EGFR_uc003tqh.1_Missense_Mutation_p.A289V|EGFR_uc003tqi.1_Missense_Mutation_p.A289V|EGFR_uc003tqj.1_Missense_Mutation_p.A289V|EGFR_uc010kzg.1_Missense_Mutation_p.A244V	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	289	Approximate.|Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.A289V(20)|p.V30_R297>G(10)|p.A289D(3)		lung(8200)|central_nervous_system(103)|upper_aerodigestive_tract(37)|prostate(32)|ovary(31)|thyroid(23)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|stomach(6)|urinary_tract(6)|skin(5)|adrenal_gland(5)|kidney(4)|soft_tissue(4)|bone(3)|NS(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)|pancreas(1)	8515	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)				Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8	p.A289V(HEC6-Tumor)|p.A289D(HS683-Tumor)|p.A289V(RL952-Tumor)	608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.234375	72.483419	80.747714	30	98	CC		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	55189316	55189316	5156	7	C	T	T	26	26	EGFR	T	2	2
SULF1	23213	broad.mit.edu	36	8	70650789	70650789	+	Missense_Mutation	SNP	A	C	C			TCGA-14-1456-01	TCGA-14-1456-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:70650789A>C	uc010lza.1	+	c.203A>C	c.(202-204)AAG>ACG	p.K68T	SULF1_uc003xyd.2_Missense_Mutation_p.K68T|SULF1_uc003xye.2_Missense_Mutation_p.K68T|SULF1_uc003xyf.2_Missense_Mutation_p.K68T|SULF1_uc003xyg.2_Missense_Mutation_p.K68T	NM_015170	NP_055985	Q8IWU6	SULF1_HUMAN	sulfatase 1	68					apoptosis|bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			ovary(2)|central_nervous_system(2)|pancreas(1)	5	Breast(64;0.0654)									473				0.19403	29.13239	34.989183	13	54	AA		KEEP	---	---	---	---	capture	Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)		Missense_Mutation	SNP	70650789	70650789	15890	8	A	C	C	3	3	SULF1	C	4	4
GABBR2	9568	broad.mit.edu	36	9	100092701	100092701	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1456-01	TCGA-14-1456-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:100092701C>G	uc004ays.1	-	c.2812G>C	c.(2812-2814)GTC>CTC	p.V938L		NM_005458	NP_005449	O75899	GABR2_HUMAN	G protein-coupled receptor 51	938	Cytoplasmic (Potential).				negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)	2		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)									0.333333	21.919178	22.435202	7	14	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100092701	100092701	6407	9	C	G	G	18	18	GABBR2	G	3	3
PLXNB3	5365	broad.mit.edu	36	X	152689227	152689227	+	Missense_Mutation	SNP	G	T	T			TCGA-14-1456-01	TCGA-14-1456-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:152689227G>T	uc004fii.1	+	c.1946G>T	c.(1945-1947)AGT>ATT	p.S649I	PLXNB3_uc010nuk.1_Missense_Mutation_p.S672I	NM_005393	NP_005384	Q9ULL4	PLXB3_HUMAN	plexin B3	649	Extracellular (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	protein binding|receptor activity			lung(1)	1	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)													0.222222	6.871584	8.172684	4	14	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152689227	152689227	12551	23	G	T	T	36	36	PLXNB3	T	3	3
DNASE1L1	1774	broad.mit.edu	36	X	153286608	153286608	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1456-01	TCGA-14-1456-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:153286608C>G	uc004fks.1	-	c.146G>C	c.(145-147)CGC>CCC	p.R49P	DNASE1L1_uc004fkt.1_Missense_Mutation_p.R49P|DNASE1L1_uc004fku.1_Missense_Mutation_p.R49P|DNASE1L1_uc004fkv.1_Missense_Mutation_p.R49P|DNASE1L1_uc004fkw.1_Missense_Mutation_p.R49P	NM_006730	NP_006721	P49184	DNSL1_HUMAN	deoxyribonuclease I-like 1 precursor	49					DNA catabolic process	endoplasmic reticulum	DNA binding|endodeoxyribonuclease activity, producing 5'-phosphomonoesters				0	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)													0.227273	6.618079	8.092967	5	17	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153286608	153286608	4844	23	C	G	G	27	27	DNASE1L1	G	3	3
NLGN4X	57502	broad.mit.edu	36	X	5831320	5831320	+	Missense_Mutation	SNP	T	G	G			TCGA-14-1456-01	TCGA-14-1456-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:5831320T>G	uc010ndi.1	-	c.1510A>C	c.(1510-1512)ACC>CCC	p.T504P	NLGN4X_uc004crp.1_Missense_Mutation_p.T487P|NLGN4X_uc010ndh.1_Missense_Mutation_p.T467P|NLGN4X_uc004crq.1_Missense_Mutation_p.T467P|NLGN4X_uc004crr.1_Missense_Mutation_p.T467P|NLGN4X_uc010ndj.1_Missense_Mutation_p.T467P	NM_181332	NP_851849	Q8N0W4	NLGNX_HUMAN	X-linked neuroligin 4	467	Extracellular (Potential).				brainstem development|cell adhesion|cell-cell junction organization|cerebellum development|male courtship behavior|positive regulation of organ growth|regulation of excitatory postsynaptic membrane potential|regulation of synaptic transmission|social behavior|synapse assembly|territorial aggressive behavior|vocalization behavior	cell surface|dendrite|integral to plasma membrane|synapse	carboxylesterase activity|chloride ion binding|neurexin binding|protein homodimerization activity			large_intestine(1)|skin(1)	2														0.25641	10.370555	12.632382	10	29	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5831320	5831320	10867	23	T	G	G	59	59	NLGN4X	G	4	4
TBX22	50945	broad.mit.edu	36	X	79168951	79168951	+	Silent	SNP	C	A	A			TCGA-14-1456-01	TCGA-14-1456-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:79168951C>A	uc010nmg.1	+	c.726C>A	c.(724-726)CCC>CCA	p.P242P	TBX22_uc004edi.1_Silent_p.P122P|TBX22_uc004edj.1_Silent_p.P242P	NM_001109878	NP_001103349	Q9Y458	TBX22_HUMAN	T-box 22 isoform 1	242	T-box.				multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity			large_intestine(3)|central_nervous_system(2)|lung(1)|ovary(1)	7										298				0.123288	10.920749	21.059658	9	64	CC		KEEP	---	---	---	---	capture			Silent	SNP	79168951	79168951	16184	23	C	A	A	21	21	TBX22	A	3	3
ZNF784	147808	broad.mit.edu	36	19	60825600	60825601	+	Frame_Shift_Ins	INS	-	C	C			TCGA-14-1456-01	TCGA-14-1456-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:60825600_60825601insC	uc002qll.1	-	c.300_301insG	c.(298-303)CCGAGCfs	p.P100fs	ZNF784_uc010etb.1_Frame_Shift_Ins_p.R16fs	NM_203374	NP_976308	Q8NCA9	ZN784_HUMAN	zinc finger protein 784	100_101	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.105)										0.33			7	14				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	60825600	60825601	18754	19	-	C	C	54	54	ZNF784	C	5	5
IRF5	3663	broad.mit.edu	36	7	128374603	128374617	+	Splice_Site_Del	DEL	ACTCTGCGGCCGCCT	-	-			TCGA-14-1456-01	TCGA-14-1456-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:128374603_128374617delACTCTGCGGCCGCCT	uc003vog.1	+	c.e7_splice_site			IRF5_uc010llr.1_In_Frame_Del_p.LCGRL162del|IRF5_uc010lls.1_In_Frame_Del_p.LCGRL162del|IRF5_uc003voh.1_Splice_Site_Del|IRF5_uc010llt.1_Intron|IRF5_uc003voi.1_Splice_Site_Del|IRF5_uc003vok.2_3'UTR|IRF5_uc010llu.1_In_Frame_Del_p.LCGRL162del|IRF5_uc003voj.2_Splice_Site_Del|IRF5_uc010llv.1_3'UTR|IRF5_uc010llw.1_In_Frame_Del_p.LCGRL162del	NM_002200	NP_002191			interferon regulatory factor 5 isoform a						interferon-gamma-mediated signaling pathway|regulation of transcription, DNA-dependent|type I interferon-mediated signaling pathway	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0														0.52			15	14				---	---	---	---	capture_indel			Splice_Site_Del	DEL	128374603	128374617	8136	7	ACTCTGCGGCCGCCT	-	-	6	6	IRF5	-	5	5
