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
PITX3	5309	broad.mit.edu	36	10	103980686	103980686	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:103980686C>G	uc001kuu.1	-	c.484G>C	c.(484-486)GCC>CCC	p.A162P		NM_005029	NP_005020	O75364	PITX3_HUMAN	paired-like homeodomain 3	162					dopaminergic neuron differentiation|lens morphogenesis in camera-type eye|midbrain development|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription activator activity				0		Colorectal(252;0.00957)												0.333333	6.41912	6.641967	3	6	CC		KEEP	---	---	---	---	capture		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)	Missense_Mutation	SNP	103980686	103980686	12380	10	C	G	G	25	25	PITX3	G	3	3
GALNTL4	374378	broad.mit.edu	36	11	11355358	11355358	+	Silent	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:11355358G>A	uc001mjo.1	-	c.924C>T	c.(922-924)TAC>TAT	p.Y308Y		NM_198516	NP_940918	Q6P9A2	GLTL4_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	308	Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0														0.376147	114.26262	115.724155	41	68	GG		KEEP	---	---	---	---	capture		all cancers(16;3.67e-05)|Epithelial(150;0.000184)	Silent	SNP	11355358	11355358	6487	11	G	A	A	44	44	GALNTL4	A	2	2
C2CD2L	9854	broad.mit.edu	36	11	118489850	118489850	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:118489850G>A	uc001pvn.1	+	c.1568G>A	c.(1567-1569)CGG>CAG	p.R523Q	C2CD2L_uc001pvo.1_Missense_Mutation_p.R522Q	NM_014807	NP_055622	O14523	C2C2L_HUMAN	transmembrane protein 24	522						integral to membrane					0														0.504854	165.114719	165.117143	52	51	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	118489850	118489850	2236	11	G	A	A	39	39	C2CD2L	A	1	1
OR6M1	390261	broad.mit.edu	36	11	123181617	123181617	+	Silent	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:123181617G>A	uc001pzh.1	-	c.651C>T	c.(649-651)TAC>TAT	p.Y217Y		NM_001005325	NP_001005325	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M,	217	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)												0.380952	67.09433	67.87377	24	39	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)	Silent	SNP	123181617	123181617	11615	11	G	A	A	48	48	OR6M1	A	2	2
OR10G9	219870	broad.mit.edu	36	11	123399724	123399724	+	Silent	SNP	C	T	T			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:123399724C>T	uc001pzo.1	+	c.795C>T	c.(793-795)GAC>GAT	p.D265D		NM_001001953	NP_001001953	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G,	265	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)												0.410569	296.603123	298.326889	101	145	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)	Silent	SNP	123399724	123399724	11310	11	C	T	T	19	19	OR10G9	T	1	1
RIC8A	60626	broad.mit.edu	36	11	199578	199578	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:199578G>A	uc001lof.1	+	c.304G>A	c.(304-306)GAG>AAG	p.E102K	BET1L_uc001loe.2_5'Flank|BET1L_uc001lod.2_5'Flank|RIC8A_uc001log.1_Missense_Mutation_p.E102K|RIC8A_uc001loh.1_Missense_Mutation_p.E95K	NM_021932	NP_068751	Q9NPQ8	RIC8A_HUMAN	resistance to inhibitors of cholinesterase 8	102						cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity				0		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)												0.456522	125.737134	125.888843	42	50	GG		KEEP	---	---	---	---	capture		all cancers(45;4.45e-27)|Epithelial(43;2.94e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.86e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)	Missense_Mutation	SNP	199578	199578	13830	11	G	A	A	45	45	RIC8A	A	2	2
OR4A47	403253	broad.mit.edu	36	11	48467102	48467102	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0744-01	TCGA-06-0744-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:48467102T>C	uc001ngw.1	+	c.182T>C	c.(181-183)CTT>CCT	p.L61P		NM_001005512	NP_001005512	Q6IF82	O4A47_HUMAN	olfactory receptor, family 4, subfamily A,	61	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.432432	165.203852	165.641222	48	63	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48467102	48467102	11448	11	T	C	C	56	56	OR4A47	C	4	4
OR5I1	10798	broad.mit.edu	36	11	55460432	55460432	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55460432G>C	uc001nic.1	-	c.21C>G	c.(19-21)AAC>AAG	p.N7K		NM_006637	NP_006628	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I,	7	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.633333	71.233842	71.702878	19	11	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55460432	55460432	11574	11	G	C	C	36	36	OR5I1	C	3	3
SLC22A8	9376	broad.mit.edu	36	11	62523882	62523882	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:62523882C>T	uc001nwo.1	-	c.446G>A	c.(445-447)CGC>CAC	p.R149H	SLC22A8_uc001nwn.1_5'Flank|SLC22A8_uc009yom.1_Missense_Mutation_p.R26H|SLC22A8_uc009yon.1_Missense_Mutation_p.R149H|SLC22A8_uc001nwp.2_Missense_Mutation_p.R149H	NM_004254	NP_004245	Q8TCC7	S22A8_HUMAN	solute carrier family 22 member 8	149	Cytoplasmic (Potential).				response to toxin	basolateral plasma membrane|integral to plasma membrane|membrane fraction	inorganic anion exchanger activity|organic anion transmembrane transporter activity			ovary(1)	1														0.385965	64.151214	64.795505	22	35	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	62523882	62523882	14957	11	C	T	T	27	27	SLC22A8	T	1	1
TSPAN9	10867	broad.mit.edu	36	12	3258425	3258425	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0744-01	TCGA-06-0744-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:3258425A>G	uc001qlp.1	+	c.262A>G	c.(262-264)ATC>GTC	p.I88V		NM_006675	NP_006666	O75954	TSN9_HUMAN	tetraspanin 9	88	Helical; (Potential).					integral to plasma membrane|membrane fraction				ovary(1)	1														0.426966	109.687032	110.109591	38	51	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(31;0.00153)|COAD - Colon adenocarcinoma(12;0.0831)		Missense_Mutation	SNP	3258425	3258425	17205	12	A	G	G	8	8	TSPAN9	G	4	4
KERA	11081	broad.mit.edu	36	12	89974181	89974181	+	Silent	SNP	G	C	C			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:89974181G>C	uc001tbl.1	-	c.9C>G	c.(7-9)GGC>GGG	p.G3G		NM_007035	NP_008966	O60938	KERA_HUMAN	keratocan	3					response to stimulus|visual perception	proteinaceous extracellular matrix					0														0.222222	7.007275	8.274593	4	14	GG		KEEP	---	---	---	---	capture			Silent	SNP	89974181	89974181	8449	12	G	C	C	46	46	KERA	C	3	3
CDC42BPB	9578	broad.mit.edu	36	14	102510200	102510200	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:102510200G>A	uc001ymi.1	-	c.1547C>T	c.(1546-1548)GCG>GTG	p.A516V		NM_006035	NP_006026	Q9Y5S2	MRCKB_HUMAN	CDC42-binding protein kinase beta	516	Potential.				actin cytoskeleton reorganization|establishment or maintenance of cell polarity|intracellular signal transduction|protein phosphorylation	cell leading edge|cell-cell junction|cytoplasm|cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(3)|lung(2)|ovary(1)|breast(1)|skin(1)	8		Melanoma(154;0.155)								1085				0.486486	51.94464	51.950603	18	19	GG		KEEP	---	---	---	---	capture		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)	Missense_Mutation	SNP	102510200	102510200	3201	14	G	A	A	38	38	CDC42BPB	A	1	1
AHNAK2	113146	broad.mit.edu	36	14	104480091	104480091	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:104480091G>A	uc010axc.1	-	c.12742C>T	c.(12742-12744)CCC>TCC	p.P4248S	AHNAK2_uc001ypx.2_Missense_Mutation_p.P4148S	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4248						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)												0.426829	427.767516	429.268951	140	188	GG		KEEP	---	---	---	---	capture	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)		Missense_Mutation	SNP	104480091	104480091	418	14	G	A	A	43	43	AHNAK2	A	2	2
PSMB11	122706	broad.mit.edu	36	14	22581656	22581656	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:22581656G>A	uc010ake.1	+	c.382G>A	c.(382-384)GCT>ACT	p.A128T		NM_001099780	NP_001093250	A5LHX3	PSB11_HUMAN	proteasome subunit beta5t	128					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex	threonine-type endopeptidase activity				0	all_cancers(95;3.3e-05)													0.5	142.8148	142.8148	51	51	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(265;0.00643)	Missense_Mutation	SNP	22581656	22581656	13129	14	G	A	A	46	46	PSMB11	A	2	2
ARHGAP5	394	broad.mit.edu	36	14	31631243	31631243	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0744-01	TCGA-06-0744-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr14:31631243A>C	uc001wrl.1	+	c.1617A>C	c.(1615-1617)GAA>GAC	p.E539D	ARHGAP5_uc001wrm.1_Missense_Mutation_p.E539D|ARHGAP5_uc001wrn.1_Missense_Mutation_p.E539D|ARHGAP5_uc001wro.1_Intron|ARHGAP5_uc001wrp.1_Intron	NM_001173	NP_001025226	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5 isoform b	539					cell adhesion|Rho protein signal transduction	cytosol|membrane	GTP binding|GTPase activity|Rho GTPase activator activity|SH2 domain binding			ovary(3)|central_nervous_system(1)	4	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)					NSCLC(9;77 350 3443 29227 41353)								0.106667	8.543194	20.065137	8	67	AA		KEEP	---	---	---	---	capture	LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)	Missense_Mutation	SNP	31631243	31631243	900	14	A	C	C	4	4	ARHGAP5	C	4	4
LRFN5	145581	broad.mit.edu	36	14	41430582	41430582	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:41430582G>A	uc001wvm.1	+	c.1765G>A	c.(1765-1767)GTG>ATG	p.V589M	LRFN5_uc010ana.1_Intron	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III	589	Cytoplasmic (Potential).					integral to membrane				ovary(5)|pancreas(2)|central_nervous_system(1)	8														0.397959	113.603491	114.496394	39	59	GG		KEEP	---	---	---	---	capture	LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)	Missense_Mutation	SNP	41430582	41430582	9314	14	G	A	A	40	40	LRFN5	A	1	1
OR4N4	283694	broad.mit.edu	36	15	19884434	19884434	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:19884434G>A	uc001yuc.1	+	c.598G>A	c.(598-600)GTC>ATC	p.V200I	LOC727924_uc001yub.1_Intron|OR4N4_uc001yue.2_Missense_Mutation_p.V200I	NM_001005241	NP_001005241	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N,	200	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(4)	4		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)												0.317647	145.914879	150.92705	54	116	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)	Missense_Mutation	SNP	19884434	19884434	11488	15	G	A	A	44	44	OR4N4	A	2	2
SYNM	23336	broad.mit.edu	36	15	97489566	97489566	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:97489566C>A	uc002bup.1	+	c.3478C>A	c.(3478-3480)CAG>AAG	p.Q1160K	SYNM_uc002buo.1_Intron|SYNM_uc002buq.1_Intron	NM_145728	NP_663780	O15061	SYNEM_HUMAN	desmuslin isoform A	1160	Tail.|Interaction with TLN1 and VCL.				intermediate filament cytoskeleton organization	adherens junction|costamere|intermediate filament|neurofilament cytoskeleton	intermediate filament binding|structural constituent of cytoskeleton|structural constituent of muscle|vinculin binding			ovary(3)|central_nervous_system(1)	4						Pancreas(125;1071 1762 21750 40003 40381)								0.37931	61.53295	62.275202	22	36	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	97489566	97489566	15976	15	C	A	A	29	29	SYNM	A	3	3
ERN2	10595	broad.mit.edu	36	16	23625681	23625681	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:23625681G>A	uc002dma.2	-	c.526C>T	c.(526-528)CGG>TGG	p.R176W	ERN2_uc010bxp.1_Missense_Mutation_p.R176W|ERN2_uc010bxq.1_5'UTR	NM_033266	NP_150296	Q76MJ5	ERN2_HUMAN	endoplasmic reticulum to nucleus signalling 2	128	Lumenal (Potential).				apoptosis|induction of apoptosis|mRNA processing|negative regulation of transcription, DNA-dependent|protein phosphorylation|rRNA catabolic process|transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein serine/threonine kinase activity			large_intestine(2)|lung(2)|ovary(2)	6									p.R176W(RCHACV-Tumor)	225				0.472222	112.353651	112.401158	34	38	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(48;0.0156)	Missense_Mutation	SNP	23625681	23625681	5431	16	G	A	A	39	39	ERN2	A	1	1
TNFRSF12A	51330	broad.mit.edu	36	16	3010407	3010407	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:3010407G>C	uc002csv.2	+	c.8G>C	c.(7-9)CGG>CCG	p.R3P	CLDN6_uc002csu.2_5'Flank|TNFRSF12A_uc002csw.2_Missense_Mutation_p.R3P	NM_016639	NP_057723	Q9NP84	TNR12_HUMAN	tumor necrosis factor receptor superfamily,	3					angiogenesis|apoptosis	integral to membrane	receptor activity				0										264				0.454545	6.758205	6.801867	5	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3010407	3010407	16827	16	G	C	C	39	39	TNFRSF12A	C	3	3
TP53	7157	broad.mit.edu	36	17	7519119	7519119	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0744-01	TCGA-06-0744-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7519119T>C	uc002gim.2	-	c.536A>G	c.(535-537)CAT>CGT	p.H179R	TP53_uc002gig.1_Missense_Mutation_p.H179R|TP53_uc002gih.1_Missense_Mutation_p.H179R|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.H47R|TP53_uc010cng.1_Missense_Mutation_p.H47R|TP53_uc002gii.1_Missense_Mutation_p.H47R|TP53_uc010cnh.1_Missense_Mutation_p.H179R|TP53_uc010cni.1_Missense_Mutation_p.H179R|TP53_uc002gij.2_Missense_Mutation_p.H179R|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.H86R|TP53_uc002gio.2_Missense_Mutation_p.H47R	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	179	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).	Zinc.	H -> Q (in sporadic cancers; somatic mutation).|H -> N (in sporadic cancers; somatic mutation).|H -> R (in sporadic cancers; somatic mutation).|HH -> QS (in a sporadic cancer; somatic mutation).|H -> L (in sporadic cancers; somatic mutation).|H -> D (in sporadic cancers; somatic mutation).|H -> P (in sporadic cancers; somatic mutation).|H -> Y (in LFS; germline mutation and in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.H179R(98)|p.H179L(31)|p.P177_C182delPHHERC(7)|p.0?(6)|p.C176_R181delCPHHER(3)|p.H179P(3)|p.R175_E180delRCPHHE(3)|p.P177fs*3(2)|p.V173fs*59(2)|p.R174fs*1(2)|p.H179fs*68(1)|p.C176fs*65(1)|p.P177_H179delPHH(1)|p.V173fs*23(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171_H179delEVVRRCPHH(1)|p.R174_E180>K(1)|p.P177_E180delPHHE(1)|p.E171fs*1(1)|p.R174fs*3(1)|p.E171fs*61(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)				Pancreas(47;798 1329 9957 10801)		111	p.H179R(HS729-Tumor)|p.H179R(NCIH1568-Tumor)|p.H179R(YAPC-Tumor)|p.R174fs(THP1-Tumor)|p.H179R(KM12-Tumor)|p.H179R(KYSE450-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.48913	140.667491	140.676998	45	47	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Missense_Mutation	SNP	7519119	7519119	16923	17	T	C	C	51	51	TP53	C	4	4
SIGLEC15	284266	broad.mit.edu	36	18	41672922	41672922	+	Silent	SNP	C	T	T			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:41672922C>T	uc002lbl.1	+	c.738C>T	c.(736-738)TCC>TCT	p.S246S		NM_213602	NP_998767	Q6ZMC9	SIG15_HUMAN	sialic acid binding Ig-like lectin 15	246	Extracellular (Potential).|Ig-like C2-type.					integral to membrane					0														0.357143	14.088825	14.332655	5	9	CC		KEEP	---	---	---	---	capture			Silent	SNP	41672922	41672922	14805	18	C	T	T	23	23	SIGLEC15	T	1	1
SERPINB4	6318	broad.mit.edu	36	18	59457991	59457991	+	Splice_Site_SNP	SNP	C	T	T			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:59457991C>T	uc002ljf.1	-	c.470_splice	c.e6-1	p.E157_splice	SERPINB4_uc002lje.1_Splice_Site_SNP_p.E157_splice|SERPINB4_uc002ljg.1_Intron|SERPINB4_uc002ljh.1_Splice_Site_SNP_p.E157_splice	NM_002974	NP_002965			serine (or cysteine) proteinase inhibitor, clade						immune response|regulation of proteolysis	cytoplasm|extracellular region	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)|lung(1)	2										163				0.408163	122.777399	123.500604	40	58	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	59457991	59457991	14591	18	C	T	T	32	32	SERPINB4	T	5	2
LAMA1	284217	broad.mit.edu	36	18	7027694	7027694	+	Silent	SNP	C	T	T			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:7027694C>T	uc002knm.1	-	c.1620G>A	c.(1618-1620)CCG>CCA	p.P540P		NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	540	Laminin IV type A 1.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|breast(2)|pancreas(2)|central_nervous_system(1)	17		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)					1597				0.494253	132.525314	132.527733	43	44	CC		KEEP	---	---	---	---	capture			Silent	SNP	7027694	7027694	8928	18	C	T	T	19	19	LAMA1	T	1	1
ZNF493	284443	broad.mit.edu	36	19	21398782	21398782	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:21398782G>A	uc002npw.1	+	c.1481G>A	c.(1480-1482)TGT>TAT	p.C494Y	ZNF493_uc002npx.1_Missense_Mutation_p.C366Y|ZNF493_uc002npy.1_Missense_Mutation_p.C366Y|ZNF493_uc010ect.1_Missense_Mutation_p.C366Y	NM_001076678	NP_787106	Q6ZR52	ZN493_HUMAN	zinc finger protein 493 isoform 3	366	C2H2-type 13.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1														0.307692	64.168862	66.741448	24	54	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21398782	21398782	18538	19	G	A	A	48	48	ZNF493	A	2	2
PNKP	11284	broad.mit.edu	36	19	55062236	55062236	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0744-01	TCGA-06-0744-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:55062236T>G	uc002pqh.1	-	c.38A>C	c.(37-39)GAG>GCG	p.E13A	PNKP_uc002pqg.1_5'Flank|PNKP_uc002pqi.1_5'UTR|PNKP_uc002pqj.1_Missense_Mutation_p.E13A|PNKP_uc010enm.1_Missense_Mutation_p.E13A|PNKP_uc002pqk.1_Missense_Mutation_p.E13A	NM_007254	NP_009185	Q96T60	PNKP_HUMAN	polynucleotide kinase 3'-phosphatase	13					DNA damage response, detection of DNA damage|DNA-dependent DNA replication|nucleotide-excision repair, DNA damage removal|response to oxidative stress|response to radiation	nucleolus	ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|damaged DNA binding|double-stranded DNA binding|endonuclease activity|nucleotide kinase activity|polynucleotide 3'-phosphatase activity|protein binding			ovary(1)|kidney(1)	2		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)												0.181818	12.341365	15.471439	6	27	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.0118)|OV - Ovarian serous cystadenocarcinoma(262;0.0134)	Missense_Mutation	SNP	55062236	55062236	12573	19	T	G	G	54	54	PNKP	G	4	4
PRR22	163154	broad.mit.edu	36	19	5734047	5734047	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:5734047C>G	uc002mdb.1	-	c.1205G>C	c.(1204-1206)GGC>GCC	p.G402A		NM_153359	NP_699190	Q8IZ63	PRR22_HUMAN	hypothetical protein LOC163154 isoform 2	402											0														0.428571	14.341651	14.404945	6	8	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5734047	5734047	13041	19	C	G	G	26	26	PRR22	G	3	3
A1BG	1	broad.mit.edu	36	19	63555504	63555504	+	Silent	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:63555504G>A	uc002qsd.2	-	c.570C>T	c.(568-570)GGC>GGT	p.G190G	A1BG-AS_uc002qse.2_Intron|A1BG_uc002qsf.1_Non-coding_Transcript|A1BG-AS_uc002qsg.1_Non-coding_Transcript	NM_130786	NP_570602	P04217	A1BG_HUMAN	alpha 1B-glycoprotein precursor	190	Ig-like V-type 2.					extracellular region					0		all_cancers(17;3.04e-16)|all_epithelial(17;7.77e-12)|Lung NSC(17;3.25e-05)|Colorectal(82;5.46e-05)|all_lung(17;0.000129)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(17;0.157)												0.324786	205.639739	211.953784	76	158	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0269)	Silent	SNP	63555504	63555504	1	19	G	A	A	38	38	A1BG	A	1	1
NOTCH2	4853	broad.mit.edu	36	1	120413536	120413537	+	Missense_Mutation	DNP	GC	AA	AA			TCGA-06-0744-01	TCGA-06-0744-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:120413536_120413537GC>AA	uc001eik.1	-	c.7_8GC>TT	c.(7-9)GCC>TTC	p.A3F	NOTCH2_uc001eil.2_Missense_Mutation_p.A3F|NOTCH2_uc001eim.2_5'UTR	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein	3					anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			haematopoietic_and_lymphoid_tissue(7)|ovary(4)|lung(3)|central_nervous_system(2)|kidney(2)|breast(1)	19	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)								581				0.190476	7.285719	9.169586	4	17	GG		KEEP	---	---	---	---	capture		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)	Missense_Mutation	DNP	120413536	120413537	10951	1	GC	AA	AA	42	42	NOTCH2	AA	2	2
ARHGEF2	9181	broad.mit.edu	36	1	154194296	154194296	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0744-01	TCGA-06-0744-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:154194296T>C	uc001fmu.1	-	c.1679A>G	c.(1678-1680)GAC>GGC	p.D560G	ARHGEF2_uc001fmr.1_Missense_Mutation_p.D488G|ARHGEF2_uc001fms.1_Missense_Mutation_p.D515G|ARHGEF2_uc001fmt.1_Missense_Mutation_p.D516G	NM_004723	NP_004714	Q92974	ARHG2_HUMAN	rho/rac guanine nucleotide exchange factor 2	516	PH.				actin filament organization|apoptosis|cell division|cell morphogenesis|induction of apoptosis by extracellular signals|intracellular protein transport|mitosis|negative regulation of microtubule depolymerization|nerve growth factor receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|regulation of cell proliferation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|Golgi apparatus|microtubule|ruffle membrane|spindle|tight junction	microtubule binding|Rac GTPase binding|Rac guanyl-nucleotide exchange factor activity|zinc ion binding			ovary(1)	1	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					Melanoma(178;35 2768 6610 28839)								0.307692	7.709944	8.1307	4	9	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	154194296	154194296	917	1	T	C	C	58	58	ARHGEF2	C	4	4
ARID4B	51742	broad.mit.edu	36	1	233412118	233412118	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0744-01	TCGA-06-0744-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:233412118A>T	uc001hwq.1	-	c.2739T>A	c.(2737-2739)GAT>GAA	p.D913E	ARID4B_uc001hwr.1_Missense_Mutation_p.D827E|ARID4B_uc001hws.2_Missense_Mutation_p.D827E|ARID4B_uc001hwt.2_Missense_Mutation_p.D594E|ARID4B_uc001hwp.1_5'UTR	NM_016374	NP_057458	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B isoform 1	913					chromatin assembly or disassembly|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|cytoplasm|nucleus	chromatin binding|DNA binding|protein binding			ovary(2)|lung(1)	3	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)												0.486486	301.248118	301.277324	90	95	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)		Missense_Mutation	SNP	233412118	233412118	935	1	A	T	T	8	8	ARID4B	T	4	4
CSMD2	114784	broad.mit.edu	36	1	33840719	33840719	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0744-01	TCGA-06-0744-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:33840719T>C	uc001bxm.1	-	c.6547A>G	c.(6547-6549)AAC>GAC	p.N2183D	CSMD2_uc001bxn.1_Missense_Mutation_p.N2185D|CSMD2_uc001bxo.1_Missense_Mutation_p.N1056D	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2185	Extracellular (Potential).|CUB 13.					integral to membrane|plasma membrane	protein binding			ovary(5)|pancreas(1)	6		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)												0.333333	6.42006	6.642436	3	6	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33840719	33840719	4086	1	T	C	C	62	62	CSMD2	C	4	4
TGM3	7053	broad.mit.edu	36	20	2260895	2260895	+	Silent	SNP	C	T	T	rs34234428	by-frequency	TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:2260895C>T	uc002wfx.2	+	c.1581C>T	c.(1579-1581)AAC>AAT	p.N527N		NM_003245	NP_003236	Q08188	TGM3_HUMAN	transglutaminase 3 precursor	527					cell envelope organization|hair follicle morphogenesis|keratinization|peptide cross-linking|protein tetramerization	cytoplasm|extrinsic to internal side of plasma membrane	acyltransferase activity|calcium ion binding|GDP binding|GTP binding|GTPase activity|magnesium ion binding|protein-glutamine gamma-glutamyltransferase activity			large_intestine(4)|ovary(3)|breast(1)	8					L-Glutamine(DB00130)									0.382979	51.139984	51.703866	18	29	CC		KEEP	---	---	---	---	capture			Silent	SNP	2260895	2260895	16359	20	C	T	T	19	19	TGM3	T	1	1
CHRNA4	1137	broad.mit.edu	36	20	61448544	61448544	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:61448544C>T	uc002yes.2	-	c.1874G>A	c.(1873-1875)GGC>GAC	p.G625D	CHRNA4_uc002yet.1_Missense_Mutation_p.G449D|CHRNA4_uc010gke.1_Missense_Mutation_p.G554D|CHRNA4_uc002yev.1_Missense_Mutation_p.G449D|CHRNA4_uc010gkf.1_Missense_Mutation_p.G449D	NM_000744	NP_000735	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 subunit	625					B cell activation|behavioral response to nicotine|calcium ion transport|cognition|DNA repair|membrane depolarization|regulation of action potential|regulation of dopamine secretion|regulation of inhibitory postsynaptic membrane potential|response to hypoxia|response to oxidative stress|sensory perception of pain|synaptic transmission, cholinergic	cell junction|dendrite|external side of plasma membrane|membrane fraction|neuronal cell body|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			central_nervous_system(1)	1	all_cancers(38;1.71e-10)				Nicotine(DB00184)|Varenicline(DB01273)									0.444444	34.396355	34.468875	12	15	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	61448544	61448544	3519	20	C	T	T	26	26	CHRNA4	T	2	2
IL17RA	23765	broad.mit.edu	36	22	15969929	15969929	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0744-01	TCGA-06-0744-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr22:15969929A>G	uc002zly.1	+	c.1820A>G	c.(1819-1821)GAG>GGG	p.E607G	IL17RA_uc010gqt.1_Missense_Mutation_p.E555G	NM_014339	NP_055154	Q96F46	I17RA_HUMAN	interleukin 17A receptor precursor	607	Cytoplasmic (Potential).				fibroblast activation|positive regulation of interleukin-23 production	integral to plasma membrane	interleukin-17 receptor activity				0		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)												0.266667	8.694962	9.431804	4	11	AA		KEEP	---	---	---	---	capture		Colorectal(9;0.241)	Missense_Mutation	SNP	15969929	15969929	7940	22	A	G	G	11	11	IL17RA	G	4	4
ACVR2A	92	broad.mit.edu	36	2	148392613	148392613	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0744-01	TCGA-06-0744-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:148392613A>C	uc002twg.1	+	c.944A>C	c.(943-945)AAA>ACA	p.K315T	ACVR2A_uc002twh.1_Missense_Mutation_p.K315T	NM_001616	NP_001607	P27037	AVR2A_HUMAN	activin A receptor, type IIA precursor	315	Cytoplasmic (Potential).|Protein kinase.				activin receptor signaling pathway|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of erythrocyte differentiation|positive regulation of osteoblast differentiation|positive regulation of protein phosphorylation|protein phosphorylation	cytoplasm|inhibin-betaglycan-ActRII complex|integral to plasma membrane	ATP binding|coreceptor activity|inhibin beta-A binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity			stomach(8)|large_intestine(2)|kidney(1)	11										196				0.222222	11.105577	13.059646	6	21	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.0969)	Missense_Mutation	SNP	148392613	148392613	224	2	A	C	C	1	1	ACVR2A	C	4	4
TTN	7273	broad.mit.edu	36	2	179121169	179121169	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179121169G>A	uc002umr.1	-	c.85726C>T	c.(85726-85728)CGG>TGG	p.R28576W	TTN_uc002ums.1_Missense_Mutation_p.R22271W|TTN_uc010frc.1_Missense_Mutation_p.R22204W|TTN_uc010frd.1_Missense_Mutation_p.R22079W	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	29503										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				0.450593	338.125184	338.660218	114	139	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179121169	179121169	17290	2	G	A	A	39	39	TTN	A	1	1
SPEG	10290	broad.mit.edu	36	2	220017651	220017651	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:220017651G>A	uc010fwg.1	+	c.421G>A	c.(421-423)GTG>ATG	p.V141M	SPEG_uc002vlm.2_Non-coding_Transcript|SPEG_uc010fwh.1_De_novo_Start_InFrame|SPEG_uc002vln.1_De_novo_Start_InFrame	NM_005876	NP_005867	Q15772	SPEG_HUMAN	SPEG complex locus	141					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				0.444444	88.174057	88.369516	32	40	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	220017651	220017651	15548	2	G	A	A	48	48	SPEG	A	2	2
DOCK10	55619	broad.mit.edu	36	2	225414823	225414823	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0744-01	TCGA-06-0744-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:225414823T>C	uc010fwz.1	-	c.2603A>G	c.(2602-2604)CAA>CGA	p.Q868R	DOCK10_uc002vob.2_Missense_Mutation_p.Q862R	NM_014689	NP_055504	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	868	DHR-1.						GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)												0.423729	227.983301	228.883417	75	102	TT		KEEP	---	---	---	---	capture		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)	Missense_Mutation	SNP	225414823	225414823	4869	2	T	C	C	63	63	DOCK10	C	4	4
DGKD	8527	broad.mit.edu	36	2	234033665	234033665	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:234033665G>A	uc002vui.1	+	c.2916G>A	c.(2914-2916)ATG>ATA	p.M972I	DGKD_uc002vuj.1_Missense_Mutation_p.M928I|DGKD_uc010fyi.1_Non-coding_Transcript	NM_152879	NP_690618	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa isoform 2	972					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)									0.435185	130.90618	131.301594	47	61	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	234033665	234033665	4646	2	G	A	A	46	46	DGKD	A	2	2
C2orf78	388960	broad.mit.edu	36	2	73896481	73896481	+	Silent	SNP	C	T	T			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:73896481C>T	uc002sjr.1	+	c.1623C>T	c.(1621-1623)AGC>AGT	p.S541S		NM_001080474	NP_001073943	A6NCI8	CB078_HUMAN	hypothetical protein LOC388960	541										ovary(2)	2														0.511111	67.621446	67.626234	23	22	CC		KEEP	---	---	---	---	capture			Silent	SNP	73896481	73896481	2285	2	C	T	T	27	27	C2orf78	T	1	1
C2orf89	129293	broad.mit.edu	36	2	84904664	84904664	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:84904664G>A	uc002sou.2	-	c.1111C>T	c.(1111-1113)CGG>TGG	p.R371W		NM_001080824	NP_001074293	Q86V40	CB089_HUMAN	hypothetical protein LOC129293	420	Extracellular (Potential).					integral to membrane				ovary(1)	1														0.409091	25.667079	25.826718	9	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	84904664	84904664	2295	2	G	A	A	39	39	C2orf89	A	1	1
TMEM45A	55076	broad.mit.edu	36	3	101758306	101758306	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0744-01	TCGA-06-0744-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:101758306A>G	uc003dua.1	+	c.251A>G	c.(250-252)GAG>GGG	p.E84G	TMEM45A_uc003dtz.1_Missense_Mutation_p.E68G	NM_018004	NP_060474	Q9NWC5	TM45A_HUMAN	transmembrane protein 45A	68	Helical; (Potential).					integral to membrane				ovary(1)	1														0.304348	13.697676	14.49674	7	16	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	101758306	101758306	16708	3	A	G	G	11	11	TMEM45A	G	4	4
UROC1	131669	broad.mit.edu	36	3	127702359	127702359	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:127702359G>C	uc010hsi.1	-	c.1194C>G	c.(1192-1194)GAC>GAG	p.D398E	UROC1_uc003eiz.1_Missense_Mutation_p.D338E	NM_144639	NP_653240	Q96N76	HUTU_HUMAN	urocanase domain containing 1	338					histidine catabolic process	cytosol	urocanate hydratase activity			ovary(1)	1														0.401961	133.659887	134.515467	41	61	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(114;0.17)	Missense_Mutation	SNP	127702359	127702359	17590	3	G	C	C	44	44	UROC1	C	3	3
ATR	545	broad.mit.edu	36	3	143762848	143762848	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:143762848C>T	uc003eux.2	-	c.1276G>A	c.(1276-1278)GGA>AGA	p.G426R		NM_001184	NP_001175	Q13535	ATR_HUMAN	ataxia telangiectasia and Rad3 related protein	426					cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity			lung(5)|breast(4)|ovary(3)|skin(2)|stomach(1)|central_nervous_system(1)|liver(1)	17										936				0.364407	122.885132	124.796738	43	75	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	143762848	143762848	1223	3	C	T	T	21	21	ATR	T	2	2
KNG1	3827	broad.mit.edu	36	3	187939810	187939810	+	Splice_Site_SNP	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:187939810G>A	uc010hyt.1	+	c.1039_splice	c.e9-1	p.Q347_splice	KNG1_uc003fqr.1_Splice_Site_SNP_p.Q347_splice	NM_001102416	NP_001095886			kininogen 1 isoform 1						blood coagulation, intrinsic pathway|diuresis|elevation of cytosolic calcium ion concentration|inflammatory response|natriuresis|negative regulation of blood coagulation|negative regulation of cell adhesion|platelet activation|platelet degranulation|positive regulation of apoptosis|smooth muscle contraction|vasodilation	extracellular space|plasma membrane|platelet alpha granule lumen	cysteine-type endopeptidase inhibitor activity|heparin binding|receptor binding|zinc ion binding				0	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)				Ouabain(DB01092)									0.428571	76.022772	76.264287	24	32	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)	Splice_Site_SNP	SNP	187939810	187939810	8741	3	G	A	A	34	34	KNG1	A	5	2
IQCF3	401067	broad.mit.edu	36	3	51838761	51838761	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:51838761G>A	uc010hlx.1	+	c.59G>A	c.(58-60)CGG>CAG	p.R20Q	IQCF1_uc003dbq.2_Intron|IQCF3_uc010hlw.1_Non-coding_Transcript|IQCF3_uc003dbs.2_Missense_Mutation_p.R20Q	NM_001085479	NP_001078948	P0C7M6	IQCF3_HUMAN	IQ motif containing F3	20										ovary(1)	1														0.466667	46.052896	46.081224	14	16	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Missense_Mutation	SNP	51838761	51838761	8110	3	G	A	A	39	39	IQCF3	A	1	1
POU1F1	5449	broad.mit.edu	36	3	87408249	87408249	+	Silent	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:87408249G>A	uc010hoj.1	-	c.54C>T	c.(52-54)GAC>GAT	p.D18D	POU1F1_uc003dqq.1_Silent_p.D18D	NM_001122757	NP_001116229	P28069	PIT1_HUMAN	pituitary specific transcription factor 1	18					negative regulation of cell proliferation|positive regulation of gene-specific transcription|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			central_nervous_system(1)|skin(1)	2	all_cancers(8;0.104)|Lung SC(3;0.184)	Lung NSC(201;0.0777)												0.552632	129.553762	129.736606	42	34	GG		KEEP	---	---	---	---	capture		LUSC - Lung squamous cell carcinoma(29;0.00229)|Lung(72;0.00677)	Silent	SNP	87408249	87408249	12699	3	G	A	A	40	40	POU1F1	A	1	1
CENPE	1062	broad.mit.edu	36	4	104299258	104299258	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:104299258C>T	uc003hxb.1	-	c.2836G>A	c.(2836-2838)GAC>AAC	p.D946N	CENPE_uc003hxc.1_Missense_Mutation_p.D921N	NM_001813	NP_001804	Q02224	CENPE_HUMAN	centromere protein E	946	Potential.				blood coagulation|cell division|kinetochore assembly|microtubule-based movement|mitotic chromosome movement towards spindle pole|mitotic metaphase|mitotic metaphase plate congression|mitotic prometaphase|multicellular organismal development|positive regulation of protein kinase activity	condensed chromosome kinetochore|cytosol|microtubule|nucleus|spindle	ATP binding|kinetochore binding|microtubule motor activity			ovary(5)|breast(4)	9														0.413793	71.584766	71.962209	24	34	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)	Missense_Mutation	SNP	104299258	104299258	3363	4	C	T	T	30	30	CENPE	T	2	2
EXOSC9	5393	broad.mit.edu	36	4	122954536	122954536	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:122954536G>C	uc003idz.1	+	c.1040G>C	c.(1039-1041)TGG>TCG	p.W347S	EXOSC9_uc003iea.1_Missense_Mutation_p.W347S|EXOSC9_uc003ieb.1_Missense_Mutation_p.W331S|EXOSC9_uc010inp.1_Non-coding_Transcript	NM_001034194	NP_001029366	Q06265	EXOS9_HUMAN	exosome component 9 isoform 1	347					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|immune response|nuclear mRNA surveillance|nuclear polyadenylation-dependent rRNA catabolic process|positive regulation of cell growth|rRNA processing	cytosol|nuclear exosome (RNase complex)|nucleolus|nucleolus|nucleus	3'-5'-exoribonuclease activity|AU-rich element binding|protein binding				0														0.450549	132.063624	132.257599	41	50	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	122954536	122954536	5515	4	G	C	C	47	47	EXOSC9	C	3	3
GYPA	2993	broad.mit.edu	36	4	145257471	145257471	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:145257471G>A	uc003ijo.2	-	c.343C>T	c.(343-345)CGC>TGC	p.R115C	GYPA_uc003ijn.2_Intron|GYPA_uc010ioq.1_Missense_Mutation_p.R102C|GYPA_uc003ijp.2_Missense_Mutation_p.R83C|GYPA_uc010ior.1_Missense_Mutation_p.R50C|GYPA_uc010ios.1_Missense_Mutation_p.R70C	NM_002099	NP_002090	P02724	GLPA_HUMAN	glycophorin A precursor	115	Cytoplasmic.				interspecies interaction between organisms	membrane fraction				central_nervous_system(2)	2	all_hematologic(180;0.15)													0.357143	114.26197	116.2779	40	72	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	145257471	145257471	7188	4	G	A	A	37	37	GYPA	A	1	1
ADAM29	11086	broad.mit.edu	36	4	176133770	176133770	+	Nonsense_Mutation	SNP	C	A	A			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:176133770C>A	uc003iuc.1	+	c.519C>A	c.(517-519)TGC>TGA	p.C173*	ADAM29_uc003iud.1_Nonsense_Mutation_p.C173*|ADAM29_uc003iue.1_Nonsense_Mutation_p.C173*|ADAM29_uc010irr.1_Nonsense_Mutation_p.C173*	NM_014269	NP_055084	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29 preproprotein	173					proteolysis|spermatogenesis	integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			ovary(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(1)	10		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)				Ovarian(140;1727 1835 21805 25838 41440)				106				0.424528	133.055999	133.583047	45	61	CC		KEEP	---	---	---	---	capture		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)	Nonsense_Mutation	SNP	176133770	176133770	248	4	C	A	A	26	26	ADAM29	A	5	3
CCDC110	256309	broad.mit.edu	36	4	186618237	186618237	+	Silent	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:186618237G>A	uc003ixu.2	-	c.498C>T	c.(496-498)TCC>TCT	p.S166S	CCDC110_uc003ixv.2_Silent_p.S129S	NM_152775	NP_689988	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	166						nucleus					0		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)												0.340426	96.473074	98.587927	32	62	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)	Silent	SNP	186618237	186618237	2867	4	G	A	A	39	39	CCDC110	A	1	1
JAKMIP1	152789	broad.mit.edu	36	4	6158175	6158175	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:6158175G>A	uc010idb.1	-	c.550C>T	c.(550-552)CGT>TGT	p.R184C	JAKMIP1_uc010idc.1_Intron|JAKMIP1_uc010idd.1_Missense_Mutation_p.R184C|JAKMIP1_uc003giu.2_Missense_Mutation_p.R184C|JAKMIP1_uc003giv.2_Missense_Mutation_p.R184C|JAKMIP1_uc010ide.1_Missense_Mutation_p.R184C	NM_001099433	NP_001092903	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein	184	Potential.|Mediates association with microtubules.				protein transport	cytoplasm|membrane|microtubule|peripheral to membrane of membrane fraction|ribonucleoprotein complex	GABA receptor binding|RNA binding			large_intestine(1)|ovary(1)|pancreas(1)	3														0.173913	6.886215	9.195177	4	19	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6158175	6158175	8244	4	G	A	A	38	38	JAKMIP1	A	1	1
PCDHA8	56140	broad.mit.edu	36	5	140202964	140202964	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140202964G>T	uc003lhs.1	+	c.1874G>T	c.(1873-1875)GGG>GTG	p.G625V	PCDHA1_uc003lha.1_Intron|PCDHA1_uc003lhb.1_Intron|PCDHA2_uc003lhd.1_Intron|PCDHA3_uc003lhf.1_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA4_uc003lhi.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.1_Intron|PCDHA6_uc003lho.1_Intron|PCDHA6_uc003lhn.1_Intron|PCDHA7_uc003lhq.1_Intron|PCDHA8_uc003lhr.1_Missense_Mutation_p.G625V	NM_018911	NP_061734	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8 isoform 1 precursor	625	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding				0														0.54955	177.55134	177.804566	61	50	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140202964	140202964	11950	5	G	T	T	43	43	PCDHA8	T	3	3
NMUR2	56923	broad.mit.edu	36	5	151752108	151752108	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:151752108C>T	uc003luv.2	-	c.1085G>A	c.(1084-1086)CGG>CAG	p.R362Q		NM_020167	NP_064552	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	362	Cytoplasmic (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|arachidonic acid secretion|calcium ion transport|central nervous system development|elevation of cytosolic calcium ion concentration|regulation of smooth muscle contraction	integral to membrane|plasma membrane	GTP binding|intracellular calcium activated chloride channel activity|neuromedin U receptor activity			ovary(2)	2		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)												0.736842	240.88831	245.707783	70	25	CC		KEEP	---	---	---	---	capture	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)		Missense_Mutation	SNP	151752108	151752108	10910	5	C	T	T	23	23	NMUR2	T	1	1
ERGIC1	57222	broad.mit.edu	36	5	172283653	172283653	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:172283653G>C	uc003mbw.2	+	c.415G>C	c.(415-417)GCC>CCC	p.A139P	ERGIC1_uc003mby.2_Missense_Mutation_p.A47P	NM_001031711	NP_001026881	Q969X5	ERGI1_HUMAN	endoplasmic reticulum-golgi intermediate	139	Lumenal (Potential).				ER to Golgi vesicle-mediated transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	protein binding			ovary(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)												0.210526	7.386988	8.862707	4	15	GG		KEEP	---	---	---	---	capture	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)		Missense_Mutation	SNP	172283653	172283653	5416	5	G	C	C	34	34	ERGIC1	C	3	3
ADAMTS12	81792	broad.mit.edu	36	5	33612749	33612749	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:33612749C>T	uc003jia.1	-	c.3139G>A	c.(3139-3141)GCA>ACA	p.A1047T	ADAMTS12_uc010iuq.1_Missense_Mutation_p.A962T	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1047	Spacer 2.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|lung(1)|kidney(1)|skin(1)	7														0.448	160.27486	160.570292	56	69	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33612749	33612749	258	5	C	T	T	28	28	ADAMTS12	T	2	2
ADAMTS12	81792	broad.mit.edu	36	5	33719790	33719790	+	Silent	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:33719790G>A	uc003jia.1	-	c.762C>T	c.(760-762)GCC>GCT	p.A254A	ADAMTS12_uc010iuq.1_Silent_p.A254A	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	254	Peptidase M12B.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|lung(1)|kidney(1)|skin(1)	7														0.420635	161.761915	162.4521	53	73	GG		KEEP	---	---	---	---	capture			Silent	SNP	33719790	33719790	258	5	G	A	A	39	39	ADAMTS12	A	1	1
OSMR	9180	broad.mit.edu	36	5	38960427	38960427	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:38960427C>T	uc003jln.1	+	c.2017C>T	c.(2017-2019)CCA>TCA	p.P673S		NM_003999	NP_003990	Q99650	OSMR_HUMAN	oncostatin M receptor	673	Fibronectin type-III 4.|Extracellular (Potential).				cell proliferation|positive regulation of acute inflammatory response|positive regulation of cell proliferation	oncostatin-M receptor complex	growth factor binding|oncostatin-M receptor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4	all_lung(31;0.000365)													0.304636	128.790285	133.933822	46	105	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38960427	38960427	11703	5	C	T	T	22	22	OSMR	T	2	2
CMYA5	202333	broad.mit.edu	36	5	79070787	79070787	+	Silent	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:79070787G>A	uc003kgc.1	+	c.10443G>A	c.(10441-10443)TTG>TTA	p.L3481L		NM_153610	NP_705838	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3481						perinuclear region of cytoplasm				ovary(6)|pancreas(2)|lung(1)	9		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)												0.571429	53.403229	53.527604	16	12	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)	Silent	SNP	79070787	79070787	3728	5	G	A	A	47	47	CMYA5	A	2	2
TRIM40	135644	broad.mit.edu	36	6	30222866	30222866	+	Silent	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:30222866G>A	uc003npk.2	+	c.567G>A	c.(565-567)GCG>GCA	p.A189A	TRIM40_uc003npm.2_Silent_p.A160A	NM_138700	NP_619645	Q6P9F5	TRI40_HUMAN	tripartite motif-containing 40	189						intracellular	zinc ion binding			ovary(1)	1														0.45614	80.745	80.840268	26	31	GG		KEEP	---	---	---	---	capture			Silent	SNP	30222866	30222866	17059	6	G	A	A	39	39	TRIM40	A	1	1
TRIM10	10107	broad.mit.edu	36	6	30234991	30234991	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0744-01	TCGA-06-0744-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:30234991T>C	uc003npo.2	-	c.440A>G	c.(439-441)CAT>CGT	p.H147R	TRIM10_uc003npn.1_Missense_Mutation_p.H147R	NM_006778	NP_006769	Q9UDY6	TRI10_HUMAN	tripartite motif-containing 10 isoform 1	147						cytoplasm	zinc ion binding				0														0.457627	77.794345	77.888888	27	32	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30234991	30234991	17030	6	T	C	C	51	51	TRIM10	C	4	4
PGC	5225	broad.mit.edu	36	6	41812709	41812709	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:41812709G>T	uc003ora.1	-	c.1026C>A	c.(1024-1026)TAC>TAA	p.Y342*	TFEB_uc003oqu.1_5'Flank	NM_002630	NP_002621	P20142	PEPC_HUMAN	progastricsin (pepsinogen C)	342					digestion|proteolysis	extracellular space	aspartic-type endopeptidase activity				0	Ovarian(28;0.0355)|Colorectal(47;0.121)													0.25	7.393186	8.303555	4	12	GG		KEEP	---	---	---	---	capture	Epithelial(12;0.000132)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)		Nonsense_Mutation	SNP	41812709	41812709	12208	6	G	T	T	36	36	PGC	T	5	3
GPR115	221393	broad.mit.edu	36	6	47789678	47789678	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:47789678C>A	uc003oyz.1	+	c.909C>A	c.(907-909)CAC>CAA	p.H303Q	GPR115_uc003oza.1_Missense_Mutation_p.H246Q|GPR115_uc003ozb.1_Missense_Mutation_p.H246Q	NM_153838	NP_722580	Q8IZF3	GP115_HUMAN	G-protein coupled receptor 115	246	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)|breast(1)	4						GBM(22;431 510 9010 26644 32828)								0.490741	166.16944	166.177555	53	55	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47789678	47789678	6906	6	C	A	A	17	17	GPR115	A	3	3
DOPEY1	23033	broad.mit.edu	36	6	83887193	83887193	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:83887193C>T	uc003pjs.1	+	c.1063C>T	c.(1063-1065)CGC>TGC	p.R355C	DOPEY1_uc010kbl.1_Missense_Mutation_p.R346C	NM_015018	NP_055833	Q5JWR5	DOP1_HUMAN	dopey family member 1	355					protein transport					ovary(2)|breast(1)	3		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)												0.351351	38.365945	39.086183	13	24	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(397;0.053)	Missense_Mutation	SNP	83887193	83887193	4891	6	C	T	T	31	31	DOPEY1	T	1	1
MUC17	140453	broad.mit.edu	36	7	100462668	100462668	+	Silent	SNP	T	C	C			TCGA-06-0744-01	TCGA-06-0744-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:100462668T>C	uc003uxp.1	+	c.1251T>C	c.(1249-1251)CCT>CCC	p.P417P	MUC17_uc010lho.1_Non-coding_Transcript	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17	417	Extracellular (Potential).|59 X approximate tandem repeats.|4.|Ser-rich.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|breast(3)|lung(2)	19	Lung NSC(181;0.136)|all_lung(186;0.182)													0.277899	336.438773	356.717344	127	330	TT		KEEP	---	---	---	---	capture			Silent	SNP	100462668	100462668	10368	7	T	C	C	55	55	MUC17	C	4	4
ARHGEF35	445328	broad.mit.edu	36	7	143515127	143515127	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0744-01	TCGA-06-0744-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:143515127A>T	uc003wdz.1	-	c.1283T>A	c.(1282-1284)CTC>CAC	p.L428H	ARHGEF35_uc010lpd.1_Missense_Mutation_p.L428H	NM_001003702	NP_001003702	A5YM69	ARG35_HUMAN	hypothetical protein LOC445328	428											0														0.2625	53.135613	57.220017	21	59	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	143515127	143515127	920	7	A	T	T	11	11	ARHGEF35	T	4	4
ELMO1	9844	broad.mit.edu	36	7	37219577	37219577	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:37219577C>T	uc003tfk.1	-	c.842G>A	c.(841-843)CGA>CAA	p.R281Q	ELMO1_uc010kxg.1_Missense_Mutation_p.R281Q	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1	281					actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)	3														0.673913	207.383994	209.858015	62	30	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37219577	37219577	5257	7	C	T	T	31	31	ELMO1	T	1	1
ELMO1	9844	broad.mit.edu	36	7	37265440	37265440	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:37265440G>A	uc003tfk.1	-	c.284C>T	c.(283-285)TCG>TTG	p.S95L	ELMO1_uc010kxg.1_Missense_Mutation_p.S95L	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1	95					actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)	3														0.292135	68.625165	72.062741	26	63	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37265440	37265440	5257	7	G	A	A	37	37	ELMO1	A	1	1
WBSCR17	64409	broad.mit.edu	36	7	70518965	70518965	+	Silent	SNP	C	T	T			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:70518965C>T	uc003tvy.1	+	c.744C>T	c.(742-744)CAC>CAT	p.H248H	WBSCR17_uc003tvz.1_De_novo_Start_OutOfFrame	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide	248	Catalytic subdomain A.|Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)												0.237113	55.516135	61.615797	23	74	CC		KEEP	---	---	---	---	capture			Silent	SNP	70518965	70518965	17836	7	C	T	T	19	19	WBSCR17	T	1	1
NSUN5	55695	broad.mit.edu	36	7	72359570	72359570	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:72359570G>A	uc003txv.1	-	c.337C>T	c.(337-339)CGG>TGG	p.R113W	FKBP6_uc003twz.2_Intron|NSUN5_uc003txw.1_Missense_Mutation_p.R113W|NSUN5_uc003txx.1_Missense_Mutation_p.R75W	NM_148956	NP_683759	Q96P11	NSUN5_HUMAN	NOL1/NOP2/Sun domain family, member 5 isoform 1	113							methyltransferase activity				0		Lung NSC(55;0.163)												0.24	44.216141	48.841359	18	57	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	72359570	72359570	11086	7	G	A	A	37	37	NSUN5	A	1	1
SAMD9	54809	broad.mit.edu	36	7	92572140	92572140	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:92572140C>A	uc003umf.1	-	c.1207G>T	c.(1207-1209)GAT>TAT	p.D403Y	SAMD9_uc003umg.1_Missense_Mutation_p.D403Y|SAMD9_uc010lfa.1_Missense_Mutation_p.D403Y	NM_017654	NP_060124	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	403						cytoplasm				ovary(3)|breast(1)|central_nervous_system(1)	5	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)													0.219512	40.603168	46.547901	18	64	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.000302)		Missense_Mutation	SNP	92572140	92572140	14306	7	C	A	A	32	32	SAMD9	A	3	3
PON1	5444	broad.mit.edu	36	7	94769470	94769470	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0744-01	TCGA-06-0744-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:94769470T>A	uc003uns.1	-	c.892A>T	c.(892-894)AAT>TAT	p.N298Y		NM_000446	NP_000437	P27169	PON1_HUMAN	paraoxonase 1 precursor	298					aromatic compound catabolic process|carboxylic acid catabolic process|organophosphate catabolic process|phosphatidylcholine metabolic process|positive regulation of binding|positive regulation of cholesterol efflux|positive regulation of transporter activity|response to external stimulus	spherical high-density lipoprotein particle	aryldialkylphosphatase activity|arylesterase activity|calcium ion binding|phospholipid binding|protein homodimerization activity			pancreas(1)	1	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)				Atorvastatin(DB01076)|Cefazolin(DB01327)	GBM(119;715 1622 17358 22490 33240)								0.29703	75.105503	78.829454	30	71	TT		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.0031)		Missense_Mutation	SNP	94769470	94769470	12677	7	T	A	A	62	62	PON1	A	4	4
RIMS2	9699	broad.mit.edu	36	8	105070773	105070773	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:105070773C>T	uc003yls.2	+	c.2326C>T	c.(2326-2328)CGA>TGA	p.R776*	RIMS2_uc003ylp.2_Nonsense_Mutation_p.R998*|RIMS2_uc003ylw.2_Nonsense_Mutation_p.R790*|RIMS2_uc003ylq.2_Nonsense_Mutation_p.R790*|RIMS2_uc003ylr.2_Nonsense_Mutation_p.R837*	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	1060					intracellular protein transport	cell junction|presynaptic membrane	Rab GTPase binding|zinc ion binding			ovary(6)|lung(2)|breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)|pancreas(1)	14										728				0.433824	184.912705	185.430213	59	77	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)		Nonsense_Mutation	SNP	105070773	105070773	13845	8	C	T	T	23	23	RIMS2	T	5	1
OC90	729330	broad.mit.edu	36	8	133106077	133106077	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:133106077C>G	uc003ytg.1	-	c.1267G>C	c.(1267-1269)GCA>CCA	p.A423P		NM_001080399	NP_001073868	Q02509	OC90_HUMAN	otoconin 90	439	Phospholipase A2-like 3.				lipid catabolic process|phospholipid metabolic process		calcium ion binding|phospholipase A2 activity			ovary(2)|skin(1)	3	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)													0.25	7.291174	8.2023	4	12	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(115;0.000805)		Missense_Mutation	SNP	133106077	133106077	11219	8	C	G	G	28	28	OC90	G	3	3
DLGAP2	9228	broad.mit.edu	36	8	1604145	1604145	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0744-01	TCGA-06-0744-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:1604145A>C	uc003wpl.1	+	c.1814A>C	c.(1813-1815)CAC>CCC	p.H605P	DLGAP2_uc003wpm.1_Missense_Mutation_p.H605P	NM_004745	NP_004736	Q9P1A6	DLGP2_HUMAN	discs large-associated protein 2	684					nerve-nerve synaptic transmission	cell junction|neurofilament|postsynaptic density|postsynaptic membrane	protein binding				0		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)												0.5	8.021517	8.021517	3	3	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)	Missense_Mutation	SNP	1604145	1604145	4740	8	A	C	C	6	6	DLGAP2	C	4	4
DOCK5	80005	broad.mit.edu	36	8	25223869	25223869	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:25223869G>A	uc003xeg.1	+	c.1222G>A	c.(1222-1224)GGT>AGT	p.G408S	DOCK5_uc010luf.1_Non-coding_Transcript|DOCK5_uc003xei.1_5'UTR|DOCK5_uc003xeh.1_Missense_Mutation_p.G122S	NM_024940	NP_079216	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	408						cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)				Pancreas(145;34 1887 3271 10937 30165)								0.356164	81.931051	83.260991	26	47	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)	Missense_Mutation	SNP	25223869	25223869	4874	8	G	A	A	39	39	DOCK5	A	1	1
RAB11FIP1	80223	broad.mit.edu	36	8	37849163	37849163	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:37849163G>A	uc003xkm.1	-	c.2315C>T	c.(2314-2316)GCG>GTG	p.A772V	RAB11FIP1_uc010lvz.1_Intron|RAB11FIP1_uc003xkl.1_Missense_Mutation_p.A101V|RAB11FIP1_uc003xkn.1_Intron|RAB11FIP1_uc003xko.1_Missense_Mutation_p.A101V|RAB11FIP1_uc003xkp.1_Intron	NM_001002814	NP_001002814	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 isoform 3	772					protein transport	centrosome|phagocytic vesicle membrane|recycling endosome	protein binding			ovary(1)	1		Lung NSC(58;0.118)|all_lung(54;0.195)												0.476821	213.126517	213.193559	72	79	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(8;3.62e-11)		Missense_Mutation	SNP	37849163	37849163	13352	8	G	A	A	38	38	RAB11FIP1	A	1	1
PGCP	10404	broad.mit.edu	36	8	97866727	97866727	+	Silent	SNP	T	A	A			TCGA-06-0744-01	TCGA-06-0744-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:97866727T>A	uc003yhw.1	+	c.426T>A	c.(424-426)CCT>CCA	p.P142P	PGCP_uc010mbe.1_Silent_p.P142P	NM_016134	NP_057218	Q9Y646	PGCP_HUMAN	plasma glutamate carboxypeptidase	142					peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity				0	Breast(36;1.86e-05)													0.447368	49.069447	49.161188	17	21	TT		KEEP	---	---	---	---	capture			Silent	SNP	97866727	97866727	12209	8	T	A	A	54	54	PGCP	A	4	4
ANKS6	203286	broad.mit.edu	36	9	100570268	100570268	+	Silent	SNP	C	T	T			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:100570268C>T	uc004ayu.1	-	c.2058G>A	c.(2056-2058)CGG>CGA	p.R686R	ANKS6_uc004ayt.1_Silent_p.R385R|ANKS6_uc004ayv.1_Silent_p.R148R|ANKS6_uc004ayw.1_Silent_p.R268R|ANKS6_uc004ayx.1_Non-coding_Transcript|ANKS6_uc004ayy.1_Non-coding_Transcript	NM_173551	NP_775822	Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain	686	Ser-rich.									ovary(2)	2		Acute lymphoblastic leukemia(62;0.0527)												0.38	50.710297	51.34241	19	31	CC		KEEP	---	---	---	---	capture			Silent	SNP	100570268	100570268	700	9	C	T	T	18	18	ANKS6	T	2	2
GRIN3A	116443	broad.mit.edu	36	9	103539456	103539456	+	Silent	SNP	G	A	A			TCGA-06-0744-01	TCGA-06-0744-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:103539456G>A	uc004bbp.1	-	c.627C>T	c.(625-627)CTC>CTT	p.L209L	GRIN3A_uc004bbq.1_Silent_p.L209L	NM_133445	NP_597702	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic,	209	Extracellular (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|neuron projection|neuronal cell body|outer membrane-bounded periplasmic space|postsynaptic density|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|glycine binding|identical protein binding|N-methyl-D-aspartate selective glutamate receptor activity|protein phosphatase 2A binding			ovary(4)|central_nervous_system(1)|pancreas(1)	6		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Ketamine(DB01221)|L-Glutamic Acid(DB00142)|Memantine(DB01043)|Meperidine(DB00454)|Methadone(DB00333)|Orphenadrine(DB01173)|Procaine(DB00721)|Riluzole(DB00740)					27				0.761905	104.500074	107.12469	32	10	GG		KEEP	---	---	---	---	capture			Silent	SNP	103539456	103539456	7062	9	G	A	A	37	37	GRIN3A	A	1	1
C9orf156	51531	broad.mit.edu	36	9	99712240	99712240	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:99712240C>A	uc004axv.1	-	c.889G>T	c.(889-891)GTC>TTC	p.V297F	C9orf156_uc004axw.1_Missense_Mutation_p.V194F|C9orf156_uc004axx.1_Missense_Mutation_p.V151F|C9orf156_uc010msq.1_Missense_Mutation_p.V194F	NM_016481	NP_057565	Q9BU70	NAP1_HUMAN	Nef associated protein 1	297					interspecies interaction between organisms		hydrolase activity				0		Acute lymphoblastic leukemia(62;0.158)												0.435294	118.966967	119.276244	37	48	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99712240	99712240	2579	9	C	A	A	20	20	C9orf156	A	3	3
CXorf57	55086	broad.mit.edu	36	X	105767661	105767661	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:105767661C>T	uc004emi.2	+	c.1424C>T	c.(1423-1425)CCG>CTG	p.P475L	CXorf57_uc004emj.2_Missense_Mutation_p.P475L|CXorf57_uc004emh.2_Missense_Mutation_p.P475L	NM_018015	NP_060485	Q6NSI4	CX057_HUMAN	hypothetical protein LOC55086	475										ovary(1)|lung(1)|breast(1)	3														0.823529	100.022261	103.380174	28	6	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	105767661	105767661	4277	23	C	T	T	23	23	CXorf57	T	1	1
ZC3H12B	340554	broad.mit.edu	36	X	64639529	64639529	+	Nonsense_Mutation	SNP	C	A	A			TCGA-06-0744-01	TCGA-06-0744-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:64639529C>A	uc010nko.1	+	c.2193C>A	c.(2191-2193)TAC>TAA	p.Y731*		NM_001010888	NP_001010888	Q5HYM0	ZC12B_HUMAN	zinc finger CCCH-type containing 12B	731							endonuclease activity|nucleic acid binding|zinc ion binding			lung(1)|kidney(1)|pancreas(1)	3														0.272727	11.210287	12.26651	6	16	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	64639529	64639529	18150	23	C	A	A	18	18	ZC3H12B	A	5	3
HDHD2	84064	broad.mit.edu	36	18	42889105	42889108	+	Frame_Shift_Del	DEL	TAAG	-	-			TCGA-06-0744-01	TCGA-06-0744-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:42889105_42889108delTAAG	uc002lcs.1	-	c.723_726delCTTA	c.(721-726)TACTTAfs	p.Y241fs	HDHD2_uc002lct.1_Frame_Shift_Del_p.Y151fs	NM_032124	NP_115500	Q9H0R4	HDHD2_HUMAN	haloacid dehalogenase-like hydrolase domain	241_242							hydrolase activity				0														0.42			33	45				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	42889105	42889108	7306	18	TAAG	-	-	61	61	HDHD2	-	5	5
NIT2	56954	broad.mit.edu	36	3	101536275	101536285	+	Splice_Site_Del	DEL	CGGATCTCCAG	-	-			TCGA-06-0744-01	TCGA-06-0744-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:101536275_101536285delCGGATCTCCAG	uc003dtv.1	+	c.e2_splice_site				NM_020202	NP_064587			nitrilase family, member 2						nitrogen compound metabolic process		omega-amidase activity			ovary(1)	1														0.39			13	20				---	---	---	---	capture_indel			Splice_Site_Del	DEL	101536275	101536285	10835	3	CGGATCTCCAG	-	-	23	23	NIT2	-	5	5
ADCK5	203054	broad.mit.edu	36	8	145588343	145588357	+	Splice_Site_Del	DEL	GGGGGTGCAAGGTGA	-	-			TCGA-06-0744-01	TCGA-06-0744-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:145588343_145588357delGGGGGTGCAAGGTGA	uc003zch.1	+	c.e12_splice_site			ADCK5_uc003zcg.1_Intron|ADCK5_uc003zci.1_Splice_Site_Del	NM_174922	NP_777582			aarF domain containing kinase 5							integral to membrane	protein serine/threonine kinase activity				0	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;8.96e-41)|Epithelial(56;4.08e-40)|all cancers(56;4.51e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)							90				0.43			3	4				---	---	---	---	capture_indel			Splice_Site_Del	DEL	145588343	145588357	292	8	GGGGGTGCAAGGTGA	-	-	47	47	ADCK5	-	5	5
PHF2	5253	broad.mit.edu	36	9	95478825	95478826	+	In_Frame_Ins	INS	-	CCTGCCTCCACCACA	CCTGCCTCCACCACA			TCGA-06-0744-01	TCGA-06-0744-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:95478825_95478826insCCTGCCTCCACCACA	uc004aub.1	+	c.2961_2962insCCTGCCTCCACCACA	c.(2959-2964)insCCTGCCTCCACCACA	p.992_993insPASTT	PHF2_uc004auc.2_In_Frame_Ins_p.412_413insPASTT	NM_005392	NP_005383	O75151	PHF2_HUMAN	PHD finger protein 2	992_993	Ser/Thr-rich.				negative regulation of chromatin silencing at rDNA|transcription, DNA-dependent	nucleolus	methylated histone residue binding|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)										0.36			4	7				---	---	---	---	capture_indel			In_Frame_Ins	INS	95478825	95478826	12253	9	-	CCTGCCTCCACCACA	CCTGCCTCCACCACA	22	22	PHF2	CCTGCCTCCACCACA	5	5
