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
C10orf72	196740	broad.mit.edu	36	10	49955324	49955324	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:49955324G>A	uc001jhf.2	-	c.580C>T	c.(580-582)CTC>TTC	p.L194F		NM_001031746	NP_001026916	Q8IW00	CJ072_HUMAN	hypothetical protein LOC196740 isoform 1	194	Helical; (Potential).					integral to membrane|plasma membrane				large_intestine(1)|liver(1)	2														0.734694	127.62198	130.060328	36	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49955324	49955324	1652	10	G	A	A	34	34	C10orf72	A	2	2
FAM55D	54827	broad.mit.edu	36	11	113958316	113958316	+	Missense_Mutation	SNP	C	A	A			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:113958316C>A	uc001ppc.1	-	c.734G>T	c.(733-735)AGG>ATG	p.R245M	FAM55D_uc001ppd.1_Intron	NM_001077639	NP_001071107	Q6UWF7	FA55D_HUMAN	hypothetical protein LOC54827 isoform 1	245						extracellular region				ovary(2)	2		all_cancers(61;8.53e-16)|all_epithelial(67;1.71e-08)|all_hematologic(158;3.05e-05)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0194)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)												0.489209	212.389407	212.403641	68	71	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;2.82e-06)|Epithelial(105;0.000129)|all cancers(92;0.000938)	Missense_Mutation	SNP	113958316	113958316	5809	11	C	A	A	24	24	FAM55D	A	3	3
MRGPRE	116534	broad.mit.edu	36	11	3206173	3206173	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:3206173C>T	uc001lxq.2	-	c.430G>A	c.(430-432)GCC>ACC	p.A144T	MRGPRE_uc009ydy.1_Missense_Mutation_p.A144T	NM_001039165	NP_001034254	Q86SM8	MRGRE_HUMAN	MAS-related GPR, member E	144	Helical; Name=4; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			large_intestine(1)|ovary(1)	2		Medulloblastoma(188;0.00106)|all_epithelial(84;0.00111)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)												0.75	18.652835	19.106868	6	2	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.00529)|LUSC - Lung squamous cell carcinoma(625;0.19)	Missense_Mutation	SNP	3206173	3206173	10156	11	C	T	T	27	27	MRGPRE	T	1	1
OR8K3	219473	broad.mit.edu	36	11	55842601	55842601	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55842601G>A	uc001niq.1	+	c.243G>A	c.(241-243)ATG>ATA	p.M81I		NM_001005202	NP_001005202	Q8NH51	OR8K3_HUMAN	olfactory receptor, family 8, subfamily K,	81	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|large_intestine(1)|central_nervous_system(1)	4	Esophageal squamous(21;0.00448)													0.214286	101.665419	118.565608	48	176	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55842601	55842601	11655	11	G	A	A	48	48	OR8K3	A	2	2
MAP4K2	5871	broad.mit.edu	36	11	64314246	64314246	+	Silent	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:64314246G>A	uc001obh.1	-	c.2238C>T	c.(2236-2238)ATC>ATT	p.I746I	MAP4K2_uc001obg.1_Non-coding_Transcript|MAP4K2_uc001obi.1_Silent_p.I738I	NM_004579	NP_004570	Q12851	M4K2_HUMAN	mitogen-activated protein kinase kinase kinase	746	CNH.				immune response|JNK cascade|protein phosphorylation|vesicle targeting	basolateral plasma membrane|Golgi membrane|soluble fraction	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(1)|pancreas(1)	2										392				0.364706	91.604033	92.97175	31	54	GG		KEEP	---	---	---	---	capture			Silent	SNP	64314246	64314246	9643	11	G	A	A	37	37	MAP4K2	A	1	1
PAH	5053	broad.mit.edu	36	12	101770744	101770744	+	Missense_Mutation	SNP	T	A	A			TCGA-12-1597-01	TCGA-12-1597-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:101770744T>A	uc001tjq.1	-	c.821A>T	c.(820-822)AAG>ATG	p.K274M		NM_000277	NP_000268	P00439	PH4H_HUMAN	phenylalanine hydroxylase	274			K -> E.		catecholamine biosynthetic process|L-phenylalanine catabolic process|neurotransmitter biosynthetic process|oxidation-reduction process	cytosol	phenylalanine 4-monooxygenase activity			ovary(4)	4					Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Levodopa(DB01235)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)									0.34188	110.659835	113.246761	40	77	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	101770744	101770744	11810	12	T	A	A	56	56	PAH	A	4	4
KRT4	3851	broad.mit.edu	36	12	51493751	51493751	+	Missense_Mutation	SNP	G	T	T			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:51493751G>T	uc001saz.1	-	c.581C>A	c.(580-582)ACC>AAC	p.T194N		NM_002272	NP_002263	P19013	K2C4_HUMAN	keratin 4	134	Head.				cytoskeleton organization|epithelial cell differentiation|negative regulation of epithelial cell proliferation	keratin filament	structural molecule activity			ovary(4)	4						Pancreas(190;284 2995 41444 45903)								0.112583	21.064123	43.441996	17	134	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51493751	51493751	8792	12	G	T	T	44	44	KRT4	T	3	3
OR6C1	390321	broad.mit.edu	36	12	54000860	54000860	+	Silent	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:54000860G>A	uc001sgu.1	+	c.210G>A	c.(208-210)TCG>TCA	p.S70S		NM_001005182	NP_001005182	Q96RD1	OR6C1_HUMAN	olfactory receptor, family 6, subfamily C,	70	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|ovary(1)	2														0.396825	146.522345	147.696171	50	76	GG		KEEP	---	---	---	---	capture			Silent	SNP	54000860	54000860	11600	12	G	A	A	40	40	OR6C1	A	1	1
EXOSC8	11340	broad.mit.edu	36	13	36478266	36478266	+	Missense_Mutation	SNP	A	C	C			TCGA-12-1597-01	TCGA-12-1597-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr13:36478266A>C	uc001uwa.1	+	c.359A>C	c.(358-360)CAG>CCG	p.Q120P	EXOSC8_uc001uvz.1_Non-coding_Transcript|EXOSC8_uc001uwb.1_Missense_Mutation_p.Q120P|EXOSC8_uc001uwc.1_Non-coding_Transcript	NM_181503	NP_852480	Q96B26	EXOS8_HUMAN	exosome component 8	120					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA processing	cytosol|exosome (RNase complex)|nucleolus	3'-5'-exoribonuclease activity|AU-rich element binding|identical protein binding			pancreas(1)	1		Lung NSC(96;6.57e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)												0.105882	10.509673	23.626645	9	76	AA		KEEP	---	---	---	---	capture		all cancers(112;3.67e-07)|Epithelial(112;1.31e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00699)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0411)	Missense_Mutation	SNP	36478266	36478266	5514	13	A	C	C	7	7	EXOSC8	C	4	4
FANCM	57697	broad.mit.edu	36	14	44675001	44675001	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:44675001G>A	uc001wwd.2	+	c.17G>A	c.(16-18)AGA>AAA	p.R6K	FANCM_uc001wwc.2_Missense_Mutation_p.R6K|FANCM_uc010anf.1_Missense_Mutation_p.R6K|FKBP3_uc001wwb.1_5'Flank	NM_020937	NP_065988	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	6					DNA repair	Fanconi anaemia nuclear complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding			ovary(2)|breast(1)	3										793				0.38	112.869783	114.15147	38	62	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44675001	44675001	5907	14	G	A	A	33	33	FANCM	A	2	2
NAA30	122830	broad.mit.edu	36	14	56927987	56927987	+	Missense_Mutation	SNP	C	G	G			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:56927987C>G	uc001xcx.2	+	c.559C>G	c.(559-561)CTG>GTG	p.L187V	NAA30_uc010aow.1_Intron	NM_001011713	NP_001011713	Q147X3	NAA30_HUMAN	N-acetyltransferase 12	187						cytoplasm	peptide alpha-N-acetyltransferase activity				0														0.25	11.542566	13.41317	8	24	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56927987	56927987	10517	14	C	G	G	28	28	NAA30	G	3	3
PAPLN	89932	broad.mit.edu	36	14	72803009	72803009	+	Missense_Mutation	SNP	T	G	G			TCGA-12-1597-01	TCGA-12-1597-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:72803009T>G	uc001xnw.2	+	c.3230T>G	c.(3229-3231)GTA>GGA	p.V1077G	PAPLN_uc010arm.1_Missense_Mutation_p.V303G|PAPLN_uc010arn.1_Intron	NM_173462	NP_775733	O95428	PPN_HUMAN	papilin	1104	Ig-like C2-type 2.					proteinaceous extracellular matrix	metalloendopeptidase activity|serine-type endopeptidase inhibitor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2														0.189189	7.418814	10.898437	7	30	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)	Missense_Mutation	SNP	72803009	72803009	11845	14	T	G	G	57	57	PAPLN	G	4	4
MGA	23269	broad.mit.edu	36	15	39819582	39819582	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:39819582C>T	uc001zoh.1	+	c.4621C>T	c.(4621-4623)CGT>TGT	p.R1541C		NM_001080541	NP_001074010	Q8IWI9	MGAP_HUMAN	MAX gene associated	1492					regulation of transcription, DNA-dependent	MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|skin(1)	11		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)								606				0.168317	33.416851	43.93731	17	84	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Missense_Mutation	SNP	39819582	39819582	9930	15	C	T	T	19	19	MGA	T	1	1
SALL1	6299	broad.mit.edu	36	16	49728535	49728535	+	Missense_Mutation	SNP	C	G	G			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:49728535C>G	uc002egt.2	-	c.3964G>C	c.(3964-3966)GTC>CTC	p.V1322L	SALL1_uc010cbt.1_Missense_Mutation_p.V1225L|SALL1_uc010cbu.1_3'UTR|SALL1_uc010cbv.1_Missense_Mutation_p.V174L	NM_001127892	NP_001121364	Q9NSC2	SALL1_HUMAN	sal-like 1 isoform b	1322					adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development	chromocenter|cytoplasm|heterochromatin|nucleus	beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription repressor activity|zinc ion binding			ovary(3)	3		all_cancers(37;0.0322)				GBM(103;1352 1446 1855 4775 8890)								0.321429	60.034699	61.618357	18	38	CC		KEEP	---	---	---	---	capture	COAD - Colon adenocarcinoma(2;0.24)		Missense_Mutation	SNP	49728535	49728535	14290	16	C	G	G	19	19	SALL1	G	3	3
GNAO1	2775	broad.mit.edu	36	16	54932285	54932285	+	Missense_Mutation	SNP	C	G	G			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:54932285C>G	uc002eit.2	+	c.762C>G	c.(760-762)ATC>ATG	p.I254M	GNAO1_uc002eiu.2_Intron	NM_138736	NP_620073	P09471	GNAO_HUMAN	guanine nucleotide binding protein, alpha	254					dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|muscle contraction	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|metabotropic serotonin receptor binding|signal transducer activity				0		all_neural(199;0.159)												0.437778	696.629401	698.145484	197	253	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54932285	54932285	6777	16	C	G	G	32	32	GNAO1	G	3	3
FBXO31	79791	broad.mit.edu	36	16	85925339	85925339	+	Missense_Mutation	SNP	G	C	C			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:85925339G>C	uc002fjw.1	-	c.1051C>G	c.(1051-1053)CGG>GGG	p.R351G	FBXO31_uc002fjv.1_Missense_Mutation_p.R243G	NM_024735	NP_079011	Q5XUX0	FBX31_HUMAN	F-box protein 31	351					cell cycle|cyclin catabolic process|mitotic cell cycle G1/S transition DNA damage checkpoint|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	SCF ubiquitin ligase complex	cyclin binding			lung(1)	1														0.165138	44.483638	56.079437	18	91	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(80;0.0272)	Missense_Mutation	SNP	85925339	85925339	5978	16	G	C	C	37	37	FBXO31	C	3	3
SSH2	85464	broad.mit.edu	36	17	25001838	25001838	+	Missense_Mutation	SNP	C	A	A			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:25001838C>A	uc002heo.1	-	c.1105G>T	c.(1105-1107)GCG>TCG	p.A369S	SSH2_uc002hep.1_Missense_Mutation_p.A369S	NM_033389	NP_203747	Q76I76	SSH2_HUMAN	slingshot 2	369	Tyrosine-protein phosphatase.				actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0														0.1125	19.827086	43.556213	18	142	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	25001838	25001838	15701	17	C	A	A	26	26	SSH2	A	3	3
ACACA	31	broad.mit.edu	36	17	32714344	32714344	+	Nonsense_Mutation	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:32714344G>A	uc002hno.1	-	c.547C>T	c.(547-549)CGA>TGA	p.R183*	ACACA_uc002hnk.1_Nonsense_Mutation_p.R68*|ACACA_uc002hnl.1_Nonsense_Mutation_p.R88*|ACACA_uc002hnm.1_Nonsense_Mutation_p.R146*|ACACA_uc002hnn.1_Nonsense_Mutation_p.R146*|ACACA_uc010cuz.1_Nonsense_Mutation_p.R146*|ACACA_uc002hnq.2_Nonsense_Mutation_p.R68*	NM_198834	NP_942135	Q13085	ACACA_HUMAN	acetyl-Coenzyme A carboxylase alpha isoform 1	146	Biotin carboxylation.				acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)			p.R183*(NCIH2122-Tumor)	742				0.301887	91.259649	94.974191	32	74	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	32714344	32714344	107	17	G	A	A	37	37	ACACA	A	5	1
BCL6B	255877	broad.mit.edu	36	17	6870649	6870649	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:6870649C>T	uc010clt.1	+	c.1042C>T	c.(1042-1044)CGT>TGT	p.R348C	BCL6B_uc002geg.2_Missense_Mutation_p.R347C	NM_181844	NP_862827	Q8N143	BCL6B_HUMAN	B-cell CLL/lymphoma 6, member B (zinc finger	347	C2H2-type 1.					nucleus	zinc ion binding			skin(1)	1														0.386076	186.938755	188.735293	61	97	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6870649	6870649	1398	17	C	T	T	31	31	BCL6B	T	1	1
RNF157	114804	broad.mit.edu	36	17	71669318	71669318	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:71669318G>A	uc002jqz.1	-	c.958C>T	c.(958-960)CGG>TGG	p.R320W	RNF157_uc002jra.1_Missense_Mutation_p.R320W	NM_052916	NP_443148	Q96PX1	RN157_HUMAN	ring finger protein 157	320							zinc ion binding			ovary(1)	1						GBM(186;507 2120 27388 27773 52994)								0.294872	66.194506	69.131139	23	55	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(166;0.187)		Missense_Mutation	SNP	71669318	71669318	13931	17	G	A	A	39	39	RNF157	A	1	1
ATP4A	495	broad.mit.edu	36	19	40738476	40738476	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:40738476C>T	uc002oal.1	-	c.1948G>A	c.(1948-1950)GAG>AAG	p.E650K	ATP4A_uc010eee.1_5'UTR	NM_000704	NP_000695	P20648	ATP4A_HUMAN	hydrogen/potassium-exchanging ATPase 4A	650	Cytoplasmic (Potential).				ATP biosynthetic process|ATP hydrolysis coupled proton transport	integral to plasma membrane	ATP binding|hydrogen:potassium-exchanging ATPase activity|magnesium ion binding				0	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)				Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)|Trifluoperazine(DB00831)									0.354305	305.451739	311.095636	107	195	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(66;0.0724)		Missense_Mutation	SNP	40738476	40738476	1164	19	C	T	T	31	31	ATP4A	T	1	1
NGF	4803	broad.mit.edu	36	1	115630354	115630354	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:115630354G>A	uc001efu.1	-	c.586C>T	c.(586-588)CAC>TAC	p.H196Y	NGF_uc009wgx.1_Missense_Mutation_p.H196Y	NM_002506	NP_002497	P01138	NGF_HUMAN	nerve growth factor, beta polypeptide precursor	196					activation of MAPKK activity|activation of phospholipase C activity|anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|negative regulation of cell cycle|nerve growth factor processing|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|Ras protein signal transduction	endosome|Golgi lumen	growth factor activity|nerve growth factor receptor binding			upper_aerodigestive_tract(1)	1	Lung SC(450;0.211)	all_cancers(81;1.07e-06)|all_epithelial(167;4.43e-06)|all_lung(203;2.86e-05)|Lung NSC(69;4.99e-05)			Clenbuterol(DB01407)					36				0.493333	108.468419	108.471393	37	38	GG		KEEP	---	---	---	---	capture		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)	Missense_Mutation	SNP	115630354	115630354	10795	1	G	A	A	46	46	NGF	A	2	2
SPTA1	6708	broad.mit.edu	36	1	156908558	156908558	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:156908558C>T	uc001fst.1	-	c.1403G>A	c.(1402-1404)CGT>CAT	p.R468H		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	468	Spectrin 5.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.179775	33.94742	42.53093	16	73	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	156908558	156908558	15630	1	C	T	T	19	19	SPTA1	T	1	1
NPL	80896	broad.mit.edu	36	1	181052516	181052516	+	Missense_Mutation	SNP	G	C	C			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:181052516G>C	uc009wyb.1	+	c.409G>C	c.(409-411)GCC>CCC	p.A137P	NPL_uc001gpo.1_Missense_Mutation_p.A118P|NPL_uc009wyc.1_Missense_Mutation_p.A137P|NPL_uc001gpp.2_Missense_Mutation_p.A137P|NPL_uc001gpq.1_Missense_Mutation_p.A137P	NM_030769	NP_110396	Q9BXD5	NPL_HUMAN	N-acetylneuraminate pyruvate lyase	137					carbohydrate metabolic process	cytoplasm	N-acetylneuraminate lyase activity			ovary(1)|central_nervous_system(1)	2														0.217391	7.43211	9.080849	5	18	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	181052516	181052516	10990	1	G	C	C	46	46	NPL	C	3	3
FAM5C	339479	broad.mit.edu	36	1	188333828	188333828	+	Silent	SNP	C	T	T			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:188333828C>T	uc001gse.1	-	c.2244G>A	c.(2242-2244)GCG>GCA	p.A748A		NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C	748						extracellular region				lung(2)|ovary(1)|kidney(1)	4	Prostate(682;0.198)													0.380488	230.711786	233.27585	78	127	CC		KEEP	---	---	---	---	capture			Silent	SNP	188333828	188333828	5817	1	C	T	T	19	19	FAM5C	T	1	1
OBSCN	84033	broad.mit.edu	36	1	226533105	226533105	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:226533105G>A	uc009xez.1	+	c.6952G>A	c.(6952-6954)GCC>ACC	p.A2318T	OBSCN_uc001hsn.1_Missense_Mutation_p.A2318T|OBSCN_uc001hsp.1_Missense_Mutation_p.A17T|OBSCN_uc001hsq.1_5'Flank	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	2318	Ig-like 23.				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				0.555556	74.483081	74.605737	25	20	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	226533105	226533105	11217	1	G	A	A	38	38	OBSCN	A	1	1
KIAA0754	643314	broad.mit.edu	36	1	39651876	39651876	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:39651876G>A	uc009vvt.1	+	c.3352G>A	c.(3352-3354)GCC>ACC	p.A1118T	MACF1_uc009vvo.1_Intron|MACF1_uc009vvp.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc009vvr.1_Intron|MACF1_uc009vvs.1_Intron	NM_015038	NP_055853	O94854	K0754_HUMAN	hypothetical protein LOC643314	982	9.|Ala-rich.										0	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)												0.266667	8.200468	8.934384	4	11	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)		Missense_Mutation	SNP	39651876	39651876	8499	1	G	A	A	38	38	KIAA0754	A	1	1
DMRTB1	63948	broad.mit.edu	36	1	53698227	53698227	+	Nonsense_Mutation	SNP	C	A	A			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:53698227C>A	uc001cvq.1	+	c.513C>A	c.(511-513)TAC>TAA	p.Y171*		NM_033067	NP_149056	Q96MA1	DMRTB_HUMAN	DMRT-like family B with proline-rich C-terminal,	171	Pro-rich.				regulation of transcription, DNA-dependent|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity				0														0.307692	7.590877	8.022184	4	9	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	53698227	53698227	4770	1	C	A	A	18	18	DMRTB1	A	5	3
C1orf173	127254	broad.mit.edu	36	1	74811101	74811101	+	Missense_Mutation	SNP	C	G	G			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:74811101C>G	uc001dgg.1	-	c.2881G>C	c.(2881-2883)GAC>CAC	p.D961H		NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	961	Glu-rich.									ovary(3)|central_nervous_system(1)	4														0.092715	14.432788	39.634735	14	137	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74811101	74811101	2081	1	C	G	G	30	30	C1orf173	G	3	3
C1orf173	127254	broad.mit.edu	36	1	74828238	74828238	+	Missense_Mutation	SNP	C	A	A			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:74828238C>A	uc001dgg.1	-	c.1841G>T	c.(1840-1842)AGT>ATT	p.S614I	C1orf173_uc001dgi.2_Missense_Mutation_p.S408I	NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	614	Glu-rich.									ovary(3)|central_nervous_system(1)	4														0.348993	144.141821	147.145992	52	97	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74828238	74828238	2081	1	C	A	A	20	20	C1orf173	A	3	3
C20orf20	55257	broad.mit.edu	36	20	60901367	60901367	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:60901367G>A	uc002ydi.1	+	c.542G>A	c.(541-543)CGG>CAG	p.R181Q		NM_018270	NP_060740	Q9NV56	MRGBP_HUMAN	MRG-binding protein	181					chromatin modification|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	H4/H2A histone acetyltransferase complex					0	Breast(26;3.65e-08)													0.192913	113.279443	135.600751	49	205	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	60901367	60901367	2181	20	G	A	A	39	39	C20orf20	A	1	1
EEF1A2	1917	broad.mit.edu	36	20	61590726	61590726	+	Missense_Mutation	SNP	T	G	G			TCGA-12-1597-01	TCGA-12-1597-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr20:61590726T>G	uc002yfd.1	-	c.1253A>C	c.(1252-1254)TAC>TCC	p.Y418S	EEF1A2_uc002yfe.1_Missense_Mutation_p.Y418S|EEF1A2_uc010gkg.1_Intron	NM_001958	NP_001949	Q05639	EF1A2_HUMAN	eukaryotic translation elongation factor 1 alpha	418						nucleus	GTP binding|GTPase activity|protein binding|translation elongation factor activity				0	all_cancers(38;9.45e-12)													0.25	8.216562	10.408639	9	27	TT		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(10;1.22e-05)		Missense_Mutation	SNP	61590726	61590726	5111	20	T	G	G	57	57	EEF1A2	G	4	4
KRTAP10-8	386681	broad.mit.edu	36	21	44856721	44856721	+	Silent	SNP	C	T	T			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:44856721C>T	uc002zfo.1	+	c.276C>T	c.(274-276)GAC>GAT	p.D92D	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198695	NP_941968	P60410	KR108_HUMAN	keratin associated protein 10-8	92	19 X 5 AA repeats of C-C-X(3).					keratin filament				large_intestine(1)|breast(1)	2														0.468254	178.329207	178.437814	59	67	CC		KEEP	---	---	---	---	capture			Silent	SNP	44856721	44856721	8830	21	C	T	T	20	20	KRTAP10-8	T	2	2
APOBEC3A	200315	broad.mit.edu	36	22	37685598	37685598	+	Silent	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:37685598G>A	uc003awn.1	+	c.135G>A	c.(133-135)TCG>TCA	p.S45S		NM_145699	NP_663745	P31941	ABC3A_HUMAN	phorbolin 1	45							hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines|zinc ion binding			ovary(1)	1	Melanoma(58;0.04)													0.345238	88.350748	90.126863	29	55	GG		KEEP	---	---	---	---	capture			Silent	SNP	37685598	37685598	800	22	G	A	A	39	39	APOBEC3A	A	1	1
MCAT	27349	broad.mit.edu	36	22	41868919	41868919	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:41868919G>A	uc003bdl.1	-	c.380C>T	c.(379-381)GCA>GTA	p.A127V	MCAT_uc003bdm.1_Missense_Mutation_p.A127V	NM_173467	NP_775738	Q8IVS2	FABD_HUMAN	mitochondrial malonyltransferase isoform a	127					fatty acid biosynthetic process	mitochondrion	[acyl-carrier-protein] S-malonyltransferase activity|binding			ovary(1)	1		Ovarian(80;0.0694)												0.277778	11.065209	11.866562	5	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41868919	41868919	9761	22	G	A	A	46	46	MCAT	A	2	2
ST6GAL2	84620	broad.mit.edu	36	2	106826680	106826680	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:106826680C>T	uc002tdr.1	-	c.186G>A	c.(184-186)ATG>ATA	p.M62I	ST6GAL2_uc002tds.2_Missense_Mutation_p.M62I	NM_032528	NP_115917	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide	62	Lumenal (Potential).				growth|multicellular organismal development|oligosaccharide metabolic process|protein glycosylation	Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			pancreas(6)|ovary(3)	9														0.488889	67.346528	67.351414	22	23	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	106826680	106826680	15740	2	C	T	T	21	21	ST6GAL2	T	2	2
TTN	7273	broad.mit.edu	36	2	179163008	179163008	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179163008C>T	uc002umr.1	-	c.53986G>A	c.(53986-53988)GTT>ATT	p.V17996I	TTN_uc002ums.1_Missense_Mutation_p.V11691I|TTN_uc010frc.1_Missense_Mutation_p.V11624I|TTN_uc010frd.1_Missense_Mutation_p.V11499I	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	18923										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153										8722				0.373239	151.546896	153.547436	53	89	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179163008	179163008	17290	2	C	T	T	19	19	TTN	T	1	1
TTN	7273	broad.mit.edu	36	2	179293107	179293107	+	Missense_Mutation	SNP	A	G	G			TCGA-12-1597-01	TCGA-12-1597-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179293107A>G	uc002umr.1	-	c.19775T>C	c.(19774-19776)ATC>ACC	p.I6592T	TTN_uc002ums.1_Intron|TTN_uc010frc.1_Intron|TTN_uc010frd.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.I3253T	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	7519										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153										8722				0.455285	194.991375	195.204974	56	67	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179293107	179293107	17290	2	A	G	G	12	12	TTN	G	4	4
MYT1L	23040	broad.mit.edu	36	2	1905191	1905191	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:1905191C>T	uc002qxe.1	-	c.1357G>A	c.(1357-1359)GCC>ACC	p.A453T	MYT1L_uc002qxd.1_Missense_Mutation_p.A453T|MYT1L_uc010ewl.1_Non-coding_Transcript	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	453					cell differentiation|nervous system development|regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)												0.48	296.488841	296.558353	96	104	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)	Missense_Mutation	SNP	1905191	1905191	10502	2	C	T	T	26	26	MYT1L	T	2	2
SPEG	10290	broad.mit.edu	36	2	220054614	220054614	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:220054614G>A	uc010fwg.1	+	c.5533G>A	c.(5533-5535)GCA>ACA	p.A1845T		NM_005876	NP_005867	Q15772	SPEG_HUMAN	SPEG complex locus	1845	Protein kinase 1.				muscle organ development|negative regulation of cell proliferation|protein phosphorylation	nucleus	ATP binding|protein serine/threonine kinase activity			ovary(4)|stomach(2)|central_nervous_system(1)	7		Renal(207;0.0183)								482				0.183333	23.688213	29.336117	11	49	GG		KEEP	---	---	---	---	capture		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)	Missense_Mutation	SNP	220054614	220054614	15548	2	G	A	A	38	38	SPEG	A	1	1
DGKD	8527	broad.mit.edu	36	2	234025381	234025381	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:234025381G>A	uc002vui.1	+	c.2200G>A	c.(2200-2202)GGT>AGT	p.G734S	DGKD_uc002vuj.1_Missense_Mutation_p.G690S|DGKD_uc010fyh.1_Missense_Mutation_p.G601S|DGKD_uc010fyi.1_Non-coding_Transcript	NM_152879	NP_690618	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa isoform 2	734					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell growth|diacylglycerol metabolic process|endocytosis|epidermal growth factor receptor signaling pathway|multicellular organismal development|platelet activation|protein homooligomerization|protein transport|response to organic substance|second-messenger-mediated signaling	cytoplasm|cytoplasmic membrane-bounded vesicle|plasma membrane|plasma membrane	ATP binding|diacylglycerol binding|diacylglycerol kinase activity|metal ion binding|protein heterodimerization activity|protein homodimerization activity			central_nervous_system(2)|pancreas(1)|lung(1)|skin(1)	5		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)			Phosphatidylserine(DB00144)									0.419355	122.024048	122.547835	39	54	GG		KEEP	---	---	---	---	capture		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Missense_Mutation	SNP	234025381	234025381	4646	2	G	A	A	39	39	DGKD	A	1	1
KIF1A	547	broad.mit.edu	36	2	241329424	241329424	+	Silent	SNP	T	G	G			TCGA-12-1597-01	TCGA-12-1597-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:241329424T>G	uc010fzk.1	-	c.3684A>C	c.(3682-3684)GGA>GGC	p.G1228G	KIF1A_uc002vzy.1_Silent_p.G1127G|KIF1A_uc002vzz.1_Silent_p.G1228G	NM_004321	NP_004312	Q12756	KIF1A_HUMAN	axonal transport of synaptic vesicles	1127					anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)												0.625	7.032014	7.110249	5	3	TT		KEEP	---	---	---	---	capture		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)	Silent	SNP	241329424	241329424	8594	2	T	G	G	58	58	KIF1A	G	4	4
FAM98A	25940	broad.mit.edu	36	2	33663860	33663860	+	Silent	SNP	G	A	A	rs34080556	unknown	TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:33663860G>A	uc002rpa.1	-	c.1044C>T	c.(1042-1044)TAC>TAT	p.Y348Y	FAM98A_uc002roz.1_Silent_p.Y186Y	NM_015475	NP_056290	Q8NCA5	FA98A_HUMAN	hypothetical protein LOC25940	349	Gly-rich.									ovary(1)	1	all_hematologic(175;0.115)													0.26087	61.794488	66.533559	24	68	GG		KEEP	---	---	---	---	capture			Silent	SNP	33663860	33663860	5892	2	G	A	A	40	40	FAM98A	A	1	1
SNRNP200	23020	broad.mit.edu	36	2	96321311	96321311	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:96321311G>A	uc002svu.1	-	c.2215C>T	c.(2215-2217)CGG>TGG	p.R739W	SNRNP200_uc002svw.1_5'Flank	NM_014014	NP_054733	O75643	U520_HUMAN	activating signal cointegrator 1 complex subunit	739	Helicase C-terminal 1.				cis assembly of pre-catalytic spliceosome|response to stimulus|visual perception	catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding	p.R739W(1)		ovary(5)|large_intestine(1)|skin(1)	7														0.235294	42.968496	47.323525	16	52	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	96321311	96321311	15352	2	G	A	A	39	39	SNRNP200	A	1	1
MST1R	4486	broad.mit.edu	36	3	49915453	49915453	+	Silent	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:49915453G>A	uc003cxy.2	-	c.594C>T	c.(592-594)TAC>TAT	p.Y198Y		NM_002447	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor precursor	198	Extracellular (Potential).|Sema.				cellular component movement|defense response|multicellular organismal development|positive regulation of cell proliferation|protein phosphorylation|single fertilization|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|macrophage colony-stimulating factor receptor activity|protein binding			ovary(5)|lung(1)	6										205				0.434783	59.494614	59.664808	20	26	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)	Silent	SNP	49915453	49915453	10284	3	G	A	A	40	40	MST1R	A	1	1
CPZ	8532	broad.mit.edu	36	4	8656676	8656676	+	Silent	SNP	C	T	T			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:8656676C>T	uc003glm.1	+	c.570C>T	c.(568-570)TAC>TAT	p.Y190Y	CPZ_uc003gll.1_Non-coding_Transcript|CPZ_uc003glo.1_Silent_p.Y179Y|CPZ_uc003gln.1_Silent_p.Y53Y|CPZ_uc003glp.1_Non-coding_Transcript	NM_001014447	NP_001014448	Q66K79	CBPZ_HUMAN	carboxypeptidase Z isoform 1	190					proteolysis|Wnt receptor signaling pathway	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)|pancreas(1)	3														0.444444	49.097483	49.193858	16	20	CC		KEEP	---	---	---	---	capture			Silent	SNP	8656676	8656676	3978	4	C	T	T	19	19	CPZ	T	1	1
KCNN2	3781	broad.mit.edu	36	5	113768267	113768267	+	Silent	SNP	C	T	T			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:113768267C>T	uc003kqo.1	+	c.816C>T	c.(814-816)GTC>GTT	p.V272V		NM_021614	NP_067627	Q9H2S1	KCNN2_HUMAN	small conductance calcium-activated potassium	272	Helical; Name=Segment S4; (Potential).					integral to membrane	calmodulin binding|small conductance calcium-activated potassium channel activity			ovary(2)	2		all_cancers(142;2.86e-05)|all_epithelial(76;9.33e-06)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Breast(839;0.159)|Lung NSC(810;0.174)|all_lung(232;0.206)												0.180412	69.697459	88.337277	35	159	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(64;1.89e-08)|Epithelial(69;2.04e-08)|all cancers(49;3.74e-06)|COAD - Colon adenocarcinoma(37;0.142)|Colorectal(14;0.195)	Silent	SNP	113768267	113768267	8384	5	C	T	T	29	29	KCNN2	T	2	2
MAT2B	27430	broad.mit.edu	36	5	162865285	162865285	+	Silent	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:162865285G>A	uc003lzk.1	+	c.15G>A	c.(13-15)GAG>GAA	p.E5E	MAT2B_uc003lzj.1_Intron|MAT2B_uc003lzl.1_Silent_p.E5E	NM_013283	NP_037415	Q9NZL9	MAT2B_HUMAN	methionine adenosyltransferase II, beta isoform	5					extracellular polysaccharide biosynthetic process|methylation|S-adenosylmethionine biosynthetic process|xenobiotic metabolic process	cytosol|methionine adenosyltransferase complex|nucleus	dTDP-4-dehydrorhamnose reductase activity|methionine adenosyltransferase regulator activity|protein binding				0	Renal(175;0.000281)	Medulloblastoma(196;0.0208)|all_neural(177;0.0765)			L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)							OREG0017003	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.416667	13.969226	14.042732	5	7	GG		KEEP	---	---	---	---	capture	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.027)|OV - Ovarian serous cystadenocarcinoma(192;0.0406)|Epithelial(171;0.0797)	Silent	SNP	162865285	162865285	9715	5	G	A	A	33	33	MAT2B	A	2	2
HCN1	348980	broad.mit.edu	36	5	45298200	45298200	+	Silent	SNP	C	T	T			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:45298200C>T	uc003jok.1	-	c.2253G>A	c.(2251-2253)CCG>CCA	p.P751P		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	751	Gln-rich.|Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1														0.462963	74.37401	74.437843	25	29	CC		KEEP	---	---	---	---	capture			Silent	SNP	45298200	45298200	7278	5	C	T	T	19	19	HCN1	T	1	1
SLC17A1	6568	broad.mit.edu	36	6	25927748	25927748	+	Nonsense_Mutation	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:25927748G>A	uc003nfh.2	-	c.499C>T	c.(499-501)CGA>TGA	p.R167*	SLC17A1_uc010jqb.1_Nonsense_Mutation_p.R167*|SLC17A1_uc010jqc.1_Nonsense_Mutation_p.R165*	NM_005074	NP_005065	Q14916	NPT1_HUMAN	solute carrier family 17 (sodium phosphate),	167					sodium ion transport|urate metabolic process	integral to plasma membrane|membrane fraction	sodium-dependent phosphate transmembrane transporter activity|symporter activity			ovary(3)|pancreas(1)	4														0.300813	101.513014	105.881501	37	86	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	25927748	25927748	14912	6	G	A	A	40	40	SLC17A1	A	5	1
PGBD1	84547	broad.mit.edu	36	6	28377703	28377703	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:28377703G>A	uc003nky.1	+	c.2093G>A	c.(2092-2094)TGC>TAC	p.C698Y	PGBD1_uc003nkz.1_Missense_Mutation_p.C698Y	NM_032507	NP_115896	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	698					regulation of transcription, DNA-dependent|viral reproduction	membrane|nucleus	scavenger receptor activity|sequence-specific DNA binding transcription factor activity			ovary(4)	4														0.411458	226.078235	227.395868	79	113	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	28377703	28377703	12203	6	G	A	A	46	46	PGBD1	A	2	2
C7orf52	375607	broad.mit.edu	36	7	100604567	100604567	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:100604567G>A	uc003uxy.1	-	c.242C>T	c.(241-243)CCT>CTT	p.P81L	C7orf52_uc003uxz.1_Missense_Mutation_p.P81L|C7orf52_uc003uya.1_Missense_Mutation_p.P81L|C7orf52_uc003uyb.1_Missense_Mutation_p.P81L	NM_198571	NP_940973	Q8N8M0	CG052_HUMAN	hypothetical protein LOC375607	81	N-acetyltransferase.						N-acetyltransferase activity			ovary(1)	1	Lung NSC(181;0.168)|all_lung(186;0.215)													0.277778	13.160266	14.826672	10	26	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100604567	100604567	2508	7	G	A	A	35	35	C7orf52	A	2	2
PPP1R3A	5506	broad.mit.edu	36	7	113306499	113306499	+	Silent	SNP	A	G	G			TCGA-12-1597-01	TCGA-12-1597-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:113306499A>G	uc010ljy.1	-	c.1884T>C	c.(1882-1884)AAT>AAC	p.N628N		NM_002711	NP_002702	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory (inhibitor)	628					glycogen metabolic process	integral to membrane				ovary(9)|pancreas(7)|skin(2)|breast(2)|lung(1)	21										235				0.28692	186.402762	196.05519	68	169	AA		KEEP	---	---	---	---	capture			Silent	SNP	113306499	113306499	12806	7	A	G	G	8	8	PPP1R3A	G	4	4
KLF14	136259	broad.mit.edu	36	7	130068674	130068674	+	Missense_Mutation	SNP	C	G	G			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:130068674C>G	uc003vqk.1	-	c.727G>C	c.(727-729)GCC>CCC	p.A243P		NM_138693	NP_619638	Q8TD94	KLF14_HUMAN	Kruppel-like factor 14	243	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Melanoma(18;0.0435)													0.230769	7.618868	8.482017	3	10	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	130068674	130068674	8654	7	C	G	G	26	26	KLF14	G	3	3
TRPV6	55503	broad.mit.edu	36	7	142283533	142283533	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:142283533G>A	uc003wbx.1	-	c.932C>T	c.(931-933)ACG>ATG	p.T311M	TRPV6_uc003wbw.1_Missense_Mutation_p.T97M|TRPV6_uc010lou.1_Missense_Mutation_p.T182M	NM_018646	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel,	311	Cytoplasmic (Potential).				regulation of calcium ion-dependent exocytosis	integral to plasma membrane	calcium channel activity|calmodulin binding			ovary(1)	1	Melanoma(164;0.059)													0.283951	107.679658	114.474579	46	116	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	142283533	142283533	17151	7	G	A	A	40	40	TRPV6	A	1	1
CNTNAP2	26047	broad.mit.edu	36	7	146371987	146371987	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:146371987C>T	uc003weu.1	+	c.458C>T	c.(457-459)CCG>CTG	p.P153L		NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor	153	F5/8 type C.|Extracellular (Potential).				behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)												0.302419	219.832237	228.474012	75	173	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.0319)		Missense_Mutation	SNP	146371987	146371987	3785	7	C	T	T	23	23	CNTNAP2	T	1	1
TRIL	9865	broad.mit.edu	36	7	28963436	28963436	+	Missense_Mutation	SNP	T	G	G			TCGA-12-1597-01	TCGA-12-1597-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:28963436T>G	uc003szt.1	-	c.752A>C	c.(751-753)CAC>CCC	p.H251P		NM_014817	NP_055632	Q7L0X0	TRIL_HUMAN	hypothetical protein LOC9865	251	Extracellular (Potential).|LRR 8.				inflammatory response|innate immune response|regulation of cytokine production involved in immune response|toll-like receptor 4 signaling pathway	lipopolysaccharide receptor complex	lipopolysaccharide binding				0														0.333333	11.399112	12.036854	8	16	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	28963436	28963436	17029	7	T	G	G	59	59	TRIL	G	4	4
DLC1	10395	broad.mit.edu	36	8	12990421	12990421	+	Missense_Mutation	SNP	T	C	C			TCGA-12-1597-01	TCGA-12-1597-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:12990421T>C	uc003wwm.1	-	c.4238A>G	c.(4237-4239)CAG>CGG	p.Q1413R	DLC1_uc003wwl.1_Missense_Mutation_p.Q1010R|DLC1_uc003wwk.1_Missense_Mutation_p.Q976R	NM_182643	NP_872584	Q96QB1	RHG07_HUMAN	deleted in liver cancer 1 isoform 1	1413	START.				actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding			ovary(3)|pancreas(2)|lung(1)|kidney(1)	7										739				0.37156	262.315427	265.476327	81	137	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12990421	12990421	4730	8	T	C	C	55	55	DLC1	C	4	4
ADAM2	2515	broad.mit.edu	36	8	39726349	39726349	+	Silent	SNP	A	G	G			TCGA-12-1597-01	TCGA-12-1597-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:39726349A>G	uc003xnj.1	-	c.1869T>C	c.(1867-1869)GAT>GAC	p.D623D	ADAM2_uc003xnk.1_Silent_p.D604D|ADAM2_uc003xnl.1_Silent_p.D467D	NM_001464	NP_001455	Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2 proprotein	623	Extracellular (Potential).|EGF-like.				cell adhesion|fusion of sperm to egg plasma membrane|proteolysis	integral to plasma membrane	integrin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)												0.260274	119.493087	127.081859	38	108	AA		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)	Silent	SNP	39726349	39726349	242	8	A	G	G	16	16	ADAM2	G	4	4
FAM75A5	727905	broad.mit.edu	36	9	65247351	65247351	+	Missense_Mutation	SNP	G	A	A	rs3897277	unknown	TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:65247351G>A	uc004adx.2	-	c.284C>T	c.(283-285)TCG>TTG	p.S95L		NM_015667	NP_056482	Q5VU36	F75A5_HUMAN	hypothetical protein LOC26165	95						integral to membrane					0														0.725	98.793461	100.619338	29	11	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65247351	65247351	5846	9	G	A	A	37	37	FAM75A5	A	1	1
PGM5	5239	broad.mit.edu	36	9	70189272	70189272	+	Missense_Mutation	SNP	C	A	A			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:70189272C>A	uc004agr.1	+	c.563C>A	c.(562-564)CCA>CAA	p.P188Q		NM_021965	NP_068800	Q15124	PGM5_HUMAN	phosphoglucomutase 5	188					cell adhesion|cellular calcium ion homeostasis|glucose metabolic process	costamere|dystrophin-associated glycoprotein complex|focal adhesion|intercalated disc|internal side of plasma membrane|sarcolemma|spot adherens junction|stress fiber|Z disc	intramolecular transferase activity, phosphotransferases|magnesium ion binding|structural molecule activity			ovary(1)|pancreas(1)	2														0.423913	121.61259	122.076476	39	53	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70189272	70189272	12224	9	C	A	A	21	21	PGM5	A	3	3
WNK2	65268	broad.mit.edu	36	9	95119670	95119670	+	Silent	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:95119670G>A	uc004ati.1	+	c.6675G>A	c.(6673-6675)GCG>GCA	p.A2225A	WNK2_uc004atj.1_Silent_p.A2188A|WNK2_uc004atk.2_Silent_p.A1713A	NM_006648	NP_006639	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	2225					intracellular protein kinase cascade|protein phosphorylation		ATP binding|protein binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|stomach(1)|large_intestine(1)|central_nervous_system(1)	7										1420				0.283019	38.944001	41.160688	15	38	GG		KEEP	---	---	---	---	capture			Silent	SNP	95119670	95119670	17952	9	G	A	A	38	38	WNK2	A	1	1
TAF7L	54457	broad.mit.edu	36	X	100417679	100417679	+	Missense_Mutation	SNP	C	A	A			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:100417679C>A	uc004ehb.1	-	c.1249G>T	c.(1249-1251)GAT>TAT	p.D417Y	TAF7L_uc004eha.1_Missense_Mutation_p.D257Y	NM_024885	NP_079161	Q5H9L4	TAF7L_HUMAN	TATA box binding protein-associated factor, RNA	417	Potential.				cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|spermatogenesis|transcription initiation from RNA polymerase II promoter	cytoplasm|transcription factor TFIID complex	binding|general RNA polymerase II transcription factor activity			breast(1)	1						Ovarian(104;431 1530 3210 15406 18594)								0.105634	9.514769	31.47077	15	127	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100417679	100417679	16054	23	C	A	A	30	30	TAF7L	A	3	3
SRPK3	26576	broad.mit.edu	36	X	152703467	152703467	+	Silent	SNP	A	G	G			TCGA-12-1597-01	TCGA-12-1597-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:152703467A>G	uc004fik.1	+	c.1515A>G	c.(1513-1515)GAA>GAG	p.E505E	SRPK3_uc004fil.1_Silent_p.E439E|SRPK3_uc004fim.1_Silent_p.E405E|SRPK3_uc010nul.1_Silent_p.E363E|SRPK3_uc004fin.1_Silent_p.E438E	NM_014370	NP_055185	Q9UPE1	SRPK3_HUMAN	SFRS protein kinase 3	439	Protein kinase.				cell differentiation|muscle organ development|muscle tissue development|protein phosphorylation		ATP binding|protein serine/threonine kinase activity			pancreas(2)|lung(1)	3	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)					Esophageal Squamous(167;766 3400 32156)				307				0.371901	133.219572	134.971963	45	76	AA		KEEP	---	---	---	---	capture			Silent	SNP	152703467	152703467	15675	23	A	G	G	4	4	SRPK3	G	4	4
MTCP1	4515	broad.mit.edu	36	X	153947237	153947237	+	Nonsense_Mutation	SNP	G	A	A			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:153947237G>A	uc004fmx.1	-	c.127C>T	c.(127-129)CGA>TGA	p.R43*	MTCP1_uc004fmy.1_Intron|MTCP1_uc004fmz.1_Nonsense_Mutation_p.R43*	NM_001018025	NP_001018025	P56278	MTCP1_HUMAN	mature T-cell proliferation 1 isoform p13	43					cell proliferation						0	all_cancers(53;3.51e-17)|all_epithelial(53;5.13e-11)|all_lung(58;3.84e-07)|Lung NSC(58;1.2e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)									36				0.427536	177.20693	177.837871	59	79	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	153947237	153947237	10308	23	G	A	A	40	40	MTCP1	A	5	1
CXorf59	286464	broad.mit.edu	36	X	36013387	36013387	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:36013387C>T	uc004ddk.1	+	c.452C>T	c.(451-453)TCG>TTG	p.S151L		NM_173695	NP_775966	Q8N9S7	CX059_HUMAN	hypothetical protein LOC286464	151						integral to membrane				central_nervous_system(1)	1														0.413223	155.427426	156.223415	50	71	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36013387	36013387	4279	23	C	T	T	31	31	CXorf59	T	1	1
FAM47C	442444	broad.mit.edu	36	X	36938542	36938542	+	Missense_Mutation	SNP	G	T	T			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:36938542G>T	uc004ddl.1	+	c.2138G>T	c.(2137-2139)AGT>ATT	p.S713I		NM_001013736	NP_001013758	Q5HY64	FA47C_HUMAN	hypothetical protein LOC442444	713										ovary(3)	3														0.397849	108.147734	108.998895	37	56	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36938542	36938542	5792	23	G	T	T	36	36	FAM47C	T	3	3
MAGIX	79917	broad.mit.edu	36	X	48909503	48909503	+	Missense_Mutation	SNP	G	C	C			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:48909503G>C	uc010nin.1	+	c.826G>C	c.(826-828)GCC>CCC	p.A276P	MAGIX_uc010nio.1_Missense_Mutation_p.A200P|MAGIX_uc004dmt.2_Missense_Mutation_p.A195P|MAGIX_uc004dmu.2_Missense_Mutation_p.A217P|MAGIX_uc004dmw.2_Missense_Mutation_p.A204P	NM_024859	NP_079135	Q9H6Y5	MAGIX_HUMAN	MAGI family member, X-linked isoform a	276											0														0.3	6.337794	6.686104	3	7	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48909503	48909503	9576	23	G	C	C	42	42	MAGIX	C	3	3
MED12	9968	broad.mit.edu	36	X	70259137	70259137	+	Missense_Mutation	SNP	G	C	C			TCGA-12-1597-01	TCGA-12-1597-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:70259137G>C	uc004dyy.1	+	c.1303G>C	c.(1303-1305)GTT>CTT	p.V435L	MED12_uc004dyz.1_Missense_Mutation_p.V435L|MED12_uc004dza.1_Missense_Mutation_p.V282L	NM_005120	NP_005111	Q93074	MED12_HUMAN	mediator complex subunit 12	435					androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription mediator activity|thyroid hormone receptor binding|transcription activator activity|vitamin D receptor binding			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4	Renal(35;0.156)													0.534091	169.92997	170.018789	47	41	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70259137	70259137	9817	23	G	C	C	36	36	MED12	C	3	3
FGF16	8823	broad.mit.edu	36	X	76598531	76598531	+	Silent	SNP	C	T	T			TCGA-12-1597-01	TCGA-12-1597-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:76598531C>T	uc004ecn.1	+	c.213C>T	c.(211-213)TAC>TAT	p.Y71Y		NM_003868	NP_003859	O43320	FGF16_HUMAN	fibroblast growth factor 16	162					cell-cell signaling|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|metabolic process|organ morphogenesis|response to temperature stimulus	extracellular space	growth factor activity				0														0.20979	68.689079	79.821817	30	113	CC		KEEP	---	---	---	---	capture			Silent	SNP	76598531	76598531	6081	23	C	T	T	19	19	FGF16	T	1	1
PTEN	5728	broad.mit.edu	36	10	89707684	89707684	+	Frame_Shift_Del	DEL	C	-	-			TCGA-12-1597-01	TCGA-12-1597-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:89707684_89707684delC	uc001kfb.1	+	c.729_729delC	c.(727-729)TTCfs	p.F243fs		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	243	C2 tensin-type.				apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of focal adhesion assembly|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of cyclin-dependent protein kinase activity|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.F243fs*9(1)|p.G165_*404del(1)|p.R234fs*9(1)|p.G165_K342del(1)|p.F243S(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)				31		264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.70			63	27				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	89707684	89707684	13192	10	C	-	-	30	30	PTEN	-	5	5
BPTF	2186	broad.mit.edu	36	17	63320234	63320237	+	Frame_Shift_Del	DEL	GACT	-	-			TCGA-12-1597-01	TCGA-12-1597-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:63320234_63320237delGACT	uc002jgf.1	+	c.2342_2345delGACT	c.(2341-2346)AGACTGfs	p.R781fs	BPTF_uc002jge.1_Frame_Shift_Del_p.R907fs	NM_182641	NP_872579	Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	907_908	Interaction with MAZ.				brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene-specific transcription|transcription, DNA-dependent	cytoplasm|NURF complex	sequence-specific DNA binding|transcription factor binding|transcription regulator activity|zinc ion binding			ovary(2)	2	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)											0.47			69	79				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	63320234	63320237	1523	17	GACT	-	-	33	33	BPTF	-	5	5
SMAD7	4092	broad.mit.edu	36	18	44701855	44701855	+	Frame_Shift_Del	DEL	G	-	-			TCGA-12-1597-01	TCGA-12-1597-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:44701855_44701855delG	uc002ldg.1	-	c.1166_1166delC	c.(1165-1167)CCGfs	p.P389fs	SMAD7_uc002ldf.1_Frame_Shift_Del_p.P201fs	NM_005904	NP_005895	O15105	SMAD7_HUMAN	SMAD family member 7	389	MH2.				adherens junction assembly|artery morphogenesis|BMP signaling pathway|cellular protein complex localization|negative regulation of BMP signaling pathway|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of pathway-restricted SMAD protein phosphorylation|negative regulation of peptidyl-serine phosphorylation|negative regulation of peptidyl-threonine phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by competitive promoter binding|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of ubiquitin-protein ligase activity|pathway-restricted SMAD protein phosphorylation|positive regulation of anti-apoptosis|positive regulation of cell-cell adhesion|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein stabilization|regulation of activin receptor signaling pathway|regulation of ventricular cardiomyocyte membrane depolarization|response to laminar fluid shear stress|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	centrosome|cytosol|nucleolus|plasma membrane|transcription factor complex	activin binding|beta-catenin binding|I-SMAD binding|promoter binding|sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding				0	Colorectal(1;0.0518)									78				0.37			20	34				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	44701855	44701855	15261	18	G	-	-	39	39	SMAD7	-	5	5
