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	TCGAscape_Amplification_Peaks	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_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	Oncotatorv0393GAF20hg19Feb2011dbSNPbuild132UniProtRelease2011_6	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	newbase	context_orig	context65	gene_name	categ	categ_ignoring_null_categ
CPN1	1369	broad.mit.edu	37	10	101814119	101814119	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:101814119G>C	uc001kql.2	-	c.1096C>G	c.(1096-1098)CAT>GAT	p.H366D		NM_001308	NP_001299	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1 precursor	366					proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			central_nervous_system(3)|pancreas(1)	4		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)										0.221239	70.911105	78.994045	25	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101814119	101814119	3947	10	G	C	C	C	611	47	CPN1	3	3
ERCC6	2074	broad.mit.edu	37	10	50667200	50667200	+	Silent	SNP	G	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:50667200G>A	uc001jhs.3	-	c.4143C>T	c.(4141-4143)TCC>TCT	p.S1381S	ERCC6_uc009xod.2_Silent_p.S541S|ERCC6_uc010qgr.1_Silent_p.S751S|ERCC6_uc001jhr.3_Silent_p.S749S	NM_000124	NP_000115	Q03468	ERCC6_HUMAN	excision repair cross-complementing rodent	1381					base-excision repair|positive regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair	nucleolus|soluble fraction|transcription elongation factor complex	ATP binding|chromatin binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein C-terminus binding|protein complex binding|protein N-terminus binding|transcription elongation regulator activity			breast(5)|ovary(2)|large_intestine(2)|lung(1)	10										738				0.259259	200.162167	215.737053	77	220	KEEP	---	---	---	---	capture		Silent	SNP	50667200	50667200	5410	10	G	A	A	A	496	39	ERCC6	1	1
DIP2C	22982	broad.mit.edu	37	10	532472	532472	+	Splice_Site_SNP	SNP	T	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:532472T>A	uc001ifp.2	-	c.86_splice	c.e2-1	p.G29_splice	DIP2C_uc009xhk.1_5'Flank	NM_014974	NP_055789			DIP2 disco-interacting protein 2 homolog C							nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)						1018				0.21875	89.34012	101.000012	35	125	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	532472	532472	4708	10	T	A	A	A	715	55	DIP2C	5	3
HECTD2	143279	broad.mit.edu	37	10	93220277	93220277	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:93220277C>A	uc010qnm.1	+	c.362C>A	c.(361-363)CCA>CAA	p.P121Q	LOC100188947_uc010qnl.1_Intron|HECTD2_uc001khk.2_Missense_Mutation_p.P121Q|HECTD2_uc001khl.2_Missense_Mutation_p.P121Q|HECTD2_uc001khm.2_Non-coding_Transcript|HECTD2_uc009xty.1_5'Flank	NM_182765	NP_877497	Q5U5R9	HECD2_HUMAN	HECT domain containing 2 isoform a	121					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	ubiquitin-protein ligase activity			skin(1)	1						NSCLC(12;376 469 1699 39910 41417)								0.27619	73.622501	78.363254	29	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	93220277	93220277	7323	10	C	A	A	A	273	21	HECTD2	2	2
TLL2	7093	broad.mit.edu	37	10	98188477	98188477	+	Silent	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:98188477G>T	uc001kml.1	-	c.549C>A	c.(547-549)GCC>GCA	p.A183A	TLL2_uc009xvf.1_Silent_p.A131A	NM_012465	NP_036597	Q9Y6L7	TLL2_HUMAN	tolloid-like 2 precursor	183	Metalloprotease (By similarity).				cell differentiation|multicellular organismal development|proteolysis	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)										0.319149	82.912324	85.646886	30	64	KEEP	---	---	---	---	capture		Silent	SNP	98188477	98188477	16476	10	G	T	T	T	600	47	TLL2	2	2
ATM	472	broad.mit.edu	37	11	108199895	108199895	+	Missense_Mutation	SNP	A	C	C			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:108199895A>C	uc001pkb.1	+	c.7237A>C	c.(7237-7239)AAG>CAG	p.K2413Q	ATM_uc009yxr.1_Missense_Mutation_p.K2413Q|C11orf65_uc010rvx.1_Intron|ATM_uc001pke.1_Missense_Mutation_p.K1065Q|ATM_uc001pkg.1_Missense_Mutation_p.K770Q	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	2413	FAT.				cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(24)|breast(14)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	238		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)						1073	TSP Lung(14;0.12)			0.125	14.786283	22.477649	7	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108199895	108199895	1128	11	A	C	C	C	65	5	ATM	4	4
OR4S2	219431	broad.mit.edu	37	11	55419045	55419046	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55419045_55419046CC>AA	uc001nhs.1	+	c.666_667CC>AA	c.(664-669)TCCCTG>TCAATG	p.L223M		NM_001004059	NP_001004059	Q8NH73	OR4S2_HUMAN	olfactory receptor, family 4, subfamily S,	223	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		all_epithelial(135;0.0748)												0.692308	320.270075	324.986722	99	44	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	55419045	55419046	11493	11	CC	AA	AA	AA	275	22	OR4S2	2	2
CDHR5	53841	broad.mit.edu	37	11	617417	617417	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:617417C>G	uc001lqj.2	-	c.2472G>C	c.(2470-2472)GAG>GAC	p.E824D	IRF7_uc009ycb.2_5'Flank|IRF7_uc010qwf.1_5'Flank|IRF7_uc001lqf.2_5'Flank|IRF7_uc010qwg.1_5'Flank|IRF7_uc001lqg.2_5'Flank|IRF7_uc001lqh.2_5'Flank|IRF7_uc001lqi.2_5'Flank|IRF7_uc010qwh.1_5'Flank|CDHR5_uc001lqk.2_Missense_Mutation_p.E630D|CDHR5_uc009ycc.2_Missense_Mutation_p.E658D|CDHR5_uc009ycd.2_Missense_Mutation_p.E818D|CDHR5_uc001lql.2_Missense_Mutation_p.E824D	NM_021924	NP_068743	Q9HBB8	CDHR5_HUMAN	mucin and cadherin-like isoform 1	824	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.4375	40.644205	40.753339	14	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	617417	617417	3251	11	C	G	G	G	311	24	CDHR5	3	3
DPF2	5977	broad.mit.edu	37	11	65107996	65107996	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:65107996A>T	uc001odn.2	+	c.173A>T	c.(172-174)GAA>GTA	p.E58V	DPF2_uc001odm.2_Missense_Mutation_p.E58V|DPF2_uc010roe.1_Missense_Mutation_p.E58V	NM_006268	NP_006259	Q92785	REQU_HUMAN	D4, zinc and double PHD fingers family 2	58					apoptosis|induction of apoptosis by extracellular signals|regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1														0.403941	225.30286	226.94131	82	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65107996	65107996	4901	11	A	T	T	T	117	9	DPF2	3	3
FAT3	120114	broad.mit.edu	37	11	92495049	92495049	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:92495049C>A	uc001pdj.3	+	c.3697C>A	c.(3697-3699)CCA>ACA	p.P1233T		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	1233	Cadherin 11.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)									TCGA Ovarian(4;0.039)			0.113846	29.856731	77.866895	37	288	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	92495049	92495049	5927	11	C	A	A	A	390	30	FAT3	2	2
ACACB	32	broad.mit.edu	37	12	109644622	109644622	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:109644622G>T	uc001tob.2	+	c.3021G>T	c.(3019-3021)ATG>ATT	p.M1007I	ACACB_uc001toc.2_Missense_Mutation_p.M1007I	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta	1007					acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|pancreas(1)	6					Biotin(DB00121)					1843				0.23913	124.301716	138.602061	55	175	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	109644622	109644622	108	12	G	T	T	T	585	45	ACACB	2	2
ANAPC7	51434	broad.mit.edu	37	12	110825555	110825555	+	Silent	SNP	G	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:110825555G>A	uc001tqo.2	-	c.765C>T	c.(763-765)ATC>ATT	p.I255I	ANAPC7_uc001tqp.3_Silent_p.I255I	NM_016238	NP_057322	Q9UJX3	APC7_HUMAN	anaphase-promoting complex subunit 7 isoform a	255					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm	binding				0														0.204301	41.670635	49.218891	19	74	KEEP	---	---	---	---	capture		Silent	SNP	110825555	110825555	609	12	G	A	A	A	577	45	ANAPC7	2	2
SDSL	113675	broad.mit.edu	37	12	113873352	113873352	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:113873352A>G	uc001tvi.2	+	c.662A>G	c.(661-663)GAC>GGC	p.D221G	SDSL_uc009zwh.2_Missense_Mutation_p.D221G	NM_138432	NP_612441	Q96GA7	SDSL_HUMAN	serine dehydratase-like	221					cellular amino acid metabolic process		L-serine ammonia-lyase activity|L-threonine ammonia-lyase activity|pyridoxal phosphate binding				0					Pyridoxal Phosphate(DB00114)									0.218935	95.011462	107.406488	37	132	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113873352	113873352	14462	12	A	G	G	G	130	10	SDSL	4	4
PEBP1	5037	broad.mit.edu	37	12	118577338	118577338	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:118577338G>T	uc001twu.1	+	c.328G>T	c.(328-330)GGG>TGG	p.G110W	PEBP1_uc010szc.1_Missense_Mutation_p.G110W	NM_002567	NP_002558	P30086	PEBP1_HUMAN	prostatic binding protein	110							ATP binding|phosphatidylethanolamine binding|serine-type endopeptidase inhibitor activity			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					NSCLC(44;94 1357 12187 49467)								0.272109	105.044047	111.921253	40	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118577338	118577338	12134	12	G	T	T	T	559	43	PEBP1	2	2
TMEM132B	114795	broad.mit.edu	37	12	126004076	126004076	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:126004076G>T	uc001uhe.1	+	c.1183G>T	c.(1183-1185)GTG>TTG	p.V395L		NM_052907	NP_443139	Q14DG7	T132B_HUMAN	transmembrane protein 132B	395	Extracellular (Potential).					integral to membrane				ovary(5)|large_intestine(1)|breast(1)|pancreas(1)	8	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)										0.302013	118.017152	123.23292	45	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	126004076	126004076	16577	12	G	T	T	T	572	44	TMEM132B	2	2
ZNF268	10795	broad.mit.edu	37	12	133727658	133727658	+	De_novo_Start_InFrame	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:133727658G>T	uc010tbv.1	+	c.-1006G>T	c.(-1008--1004)GAGGA>GATGA		ZNF10_uc009zzb.2_Missense_Mutation_p.E26D|ZNF10_uc001ulq.2_Missense_Mutation_p.E26D	ZNF268				RecName: Full=Zinc finger protein 268; AltName: Full=Zinc finger protein 3; AltName: Full=HZF3;						regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.000215)|all_epithelial(31;0.096)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)										0.301471	109.850292	114.621935	41	95	KEEP	---	---	---	---	capture		De_novo_Start_InFrame	SNP	133727658	133727658	18399	12	G	T	T	T	451	35	ZNF268	5	2
LRTM2	654429	broad.mit.edu	37	12	1943779	1943779	+	Silent	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:1943779C>T	uc001qjt.2	+	c.1005C>T	c.(1003-1005)TAC>TAT	p.Y335Y	CACNA2D4_uc001qjp.2_Intron|CACNA2D4_uc009zds.1_Intron|CACNA2D4_uc009zdt.1_Intron|CACNA2D4_uc009zdr.1_Intron|LRTM2_uc001qju.2_Silent_p.Y335Y|LRTM2_uc010sdx.1_Silent_p.Y335Y|LRTM2_uc001qjv.2_Silent_p.Y97Y	NM_001039029	NP_001034118	Q8N967	LRTM2_HUMAN	leucine-rich repeats and transmembrane domains 2	335	Cytoplasmic (Potential).					integral to membrane				large_intestine(1)	1	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000834)											0.447761	84.539861	84.698615	30	37	KEEP	---	---	---	---	capture		Silent	SNP	1943779	1943779	9421	12	C	T	T	T	246	19	LRTM2	1	1
SLCO1B1	10599	broad.mit.edu	37	12	21391919	21391919	+	Silent	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:21391919C>A	uc001req.3	+	c.1872C>A	c.(1870-1872)GTC>GTA	p.V624V		NM_006446	NP_006437	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family,	624	Extracellular (Potential).				bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|integral to plasma membrane|membrane fraction	bile acid transmembrane transporter activity|sodium-independent organic anion transmembrane transporter activity|thyroid hormone transmembrane transporter activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5					Digoxin(DB00390)|Gemfibrozil(DB01241)|Pravastatin(DB00175)									0.166667	13.096292	17.523013	7	35	KEEP	---	---	---	---	capture		Silent	SNP	21391919	21391919	15220	12	C	A	A	A	405	32	SLCO1B1	2	2
KRAS	3845	broad.mit.edu	37	12	25398285	25398285	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:25398285C>A	uc001rgp.1	-	c.34G>T	c.(34-36)GGT>TGT	p.G12C	KRAS_uc001rgq.1_Missense_Mutation_p.G12C|KRAS_uc001rgr.2_Non-coding_Transcript	NM_033360	NP_203524	P01116	RASK_HUMAN	c-K-ras2 protein isoform a precursor	12	GTP.		G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation).|G -> R (in lung cancer and bladder cancer; somatic mutation).|G -> S (in lung carcinoma and GASC; somatic mutation).|G -> A (in a colorectal cancer sample; somatic mutation).|G -> C (in lung carcinoma; somatic mutation).|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation).		activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding	p.G12C(2374)|p.G12S(1078)|p.G12R(674)|p.G12?(50)|p.G12F(33)|p.G12D(15)|p.G12N(6)|p.G12V(6)|p.G12L(5)|p.G12I(3)|p.G12W(3)|p.G12A(2)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12_G13insG(1)		large_intestine(11742)|pancreas(3256)|lung(2694)|biliary_tract(514)|ovary(437)|endometrium(339)|haematopoietic_and_lymphoid_tissue(303)|stomach(179)|thyroid(145)|prostate(85)|soft_tissue(75)|small_intestine(62)|upper_aerodigestive_tract(59)|cervix(49)|urinary_tract(48)|skin(38)|breast(27)|liver(21)|testis(17)|oesophagus(15)|central_nervous_system(8)|peritoneum(5)|kidney(5)|salivary_gland(5)|thymus(5)|eye(4)|gastrointestinal_tract_(site_indeterminate)(4)|autonomic_ganglia(2)|bone(2)|genital_tract(1)|penis(1)|adrenal_gland(1)	20148	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12C(CALU1_LUNG)|G12C(NCIH2030_LUNG)|G12C(LU99_LUNG)|G12C(NCIH1792_LUNG)|G12R(KP2_PANCREAS)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(NCIH2122_LUNG)|G12C(NCIH358_LUNG)|G12R(PSN1_PANCREAS)|G12C(KYSE410_OESOPHAGUS)|G12S(A549_LUNG)|G12R(HUPT3_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12C(HCC44_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(SW1463_LARGE_INTESTINE)|G12C(NCIH23_LUNG)|G12C(LU65_LUNG)|G12C(NCIH1373_LUNG)|G12C(MIAPACA2_PANCREAS)|G12R(HS274T_BREAST)|G12S(LS123_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(OV56_OVARY)|G12C(IALM_LUNG)	119	p.G12R(PSN1-Tumor)|p.G12C(NCIH1373-Tumor)|p.G12C(NCIH1792-Tumor)|p.G12S(KMS20-Tumor)|p.G12C(HCC44-Tumor)|p.G12C(HCC1171-Tumor)|p.G12C(SW837-Tumor)|p.G12C(LU65-Tumor)|p.G12R(HUPT3-Tumor)|p.G12S(A549-Tumor)|p.G12C(NCIH2122-Tumor)|p.G12R(KP2-Tumor)|p.G12C(OV56-Tumor)|p.G12C(IALM-Tumor)|p.G12C(SW1463-Tumor)|p.G12C(SW1573-Tumor)|p.G12R(NCIH1339-Tumor)|p.G12C(NCIH23-Tumor)|p.G12C(MIAPACA2-Tumor)|p.G12C(CALU1-Tumor)|p.G12C(NCIH2030-Tumor)|p.G12S(LS123-Tumor)|p.G12C(KYSE410-Tumor)|p.G12C(UMUC3-Tumor)|p.G12C(NCIH2291-Tumor)|p.G12R(TCCPAN2-Tumor)|p.G12C(KHM1B-Tumor)|p.G12C(LU99-Tumor)|p.G12C(NCIH358-Tumor)|p.G12C(NCIH1385-Tumor)|p.G12R(CAL62-Tumor)	262	TSP Lung(1;<1E-8)|Multiple Myeloma(2;<1E-6)			0.411765	20.821439	20.937168	7	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25398285	25398285	8753	12	C	A	A	A	273	21	KRAS	2	2
CACNA1C	775	broad.mit.edu	37	12	2800361	2800361	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:2800361T>C	uc009zdu.1	+	c.6662T>C	c.(6661-6663)CTG>CCG	p.L2221P	CACNA1C_uc009zdv.1_Missense_Mutation_p.L2135P|CACNA1C_uc001qkb.2_Missense_Mutation_p.L2138P|CACNA1C_uc001qkc.2_Missense_Mutation_p.L2157P|CACNA1C_uc001qke.2_Missense_Mutation_p.L2127P|CACNA1C_uc001qkf.2_Missense_Mutation_p.L2146P|CACNA1C_uc001qjz.2_Missense_Mutation_p.L2138P|CACNA1C_uc001qkd.2_Missense_Mutation_p.L2157P|CACNA1C_uc001qkg.2_Missense_Mutation_p.L2144P|CACNA1C_uc009zdw.1_Missense_Mutation_p.L2179P|CACNA1C_uc001qkh.2_Missense_Mutation_p.L2146P|CACNA1C_uc001qkl.2_Missense_Mutation_p.L2186P|CACNA1C_uc001qkn.2_Missense_Mutation_p.L2138P|CACNA1C_uc001qko.2_Missense_Mutation_p.L2158P|CACNA1C_uc001qkp.2_Missense_Mutation_p.L2138P|CACNA1C_uc001qkr.2_Missense_Mutation_p.L2155P|CACNA1C_uc001qku.2_Missense_Mutation_p.L2173P|CACNA1C_uc001qkq.2_Missense_Mutation_p.L2166P|CACNA1C_uc001qks.2_Missense_Mutation_p.L2138P|CACNA1C_uc001qkt.2_Missense_Mutation_p.L2157P|CACNA1C_uc001qki.1_Missense_Mutation_p.L1945P|CACNA1C_uc001qkj.1_Missense_Mutation_p.L1909P|CACNA1C_uc001qkk.1_Missense_Mutation_p.L1874P|CACNA1C_uc001qkm.1_Missense_Mutation_p.L1934P|CACNA1C_uc010sea.1_Missense_Mutation_p.L829P|CACNA1C_uc001qky.1_Missense_Mutation_p.L456P	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	2221	Cytoplasmic (Potential).				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)									0.2	10.761542	12.853985	5	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2800361	2800361	2656	12	T	C	C	C	715	55	CACNA1C	4	4
ADAMTS20	80070	broad.mit.edu	37	12	43860487	43860487	+	Silent	SNP	G	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:43860487G>A	uc010skx.1	-	c.1335C>T	c.(1333-1335)AAC>AAT	p.N445N		NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	445	Peptidase M12B.					proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)						2149				0.378378	41.639551	42.120353	14	23	KEEP	---	---	---	---	capture		Silent	SNP	43860487	43860487	267	12	G	A	A	A	464	36	ADAMTS20	2	2
TENC1	23371	broad.mit.edu	37	12	53452954	53452954	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:53452954G>T	uc001sbn.2	+	c.1559G>T	c.(1558-1560)AGC>ATC	p.S520I	TENC1_uc001sbl.2_Missense_Mutation_p.S386I|TENC1_uc001sbp.2_Missense_Mutation_p.S510I|TENC1_uc001sbq.2_Missense_Mutation_p.S5I|TENC1_uc001sbr.2_Non-coding_Transcript|TENC1_uc009zmr.2_Missense_Mutation_p.S5I|TENC1_uc001sbs.2_5'Flank	NM_015319	NP_056134	Q63HR2	TENC1_HUMAN	tensin like C1 domain containing phosphatase	510	Pro-rich.				intracellular signal transduction|negative regulation of cell proliferation	focal adhesion	metal ion binding|phosphoprotein phosphatase activity|protein binding			pancreas(1)	1														0.227273	33.400818	37.905037	15	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53452954	53452954	16285	12	G	T	T	T	442	34	TENC1	2	2
LACRT	90070	broad.mit.edu	37	12	55025579	55025579	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:55025579C>A	uc001sgi.1	-	c.298G>T	c.(298-300)GCA>TCA	p.A100S		NM_033277	NP_150593	Q9GZZ8	LACRT_HUMAN	lacritin precursor	100					calcineurin-NFAT signaling pathway|positive regulation of epithelial cell proliferation|positive regulation of NFAT protein import into nucleus|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of release of sequestered calcium ion into cytosol|positive regulation of secretion|protein localization in Golgi apparatus|tear secretion	extracellular region|stored secretory granule	collagen binding|fibronectin binding|glycoprotein binding|growth factor activity|laminin-1 binding|protein N-terminus binding			central_nervous_system(1)	1														0.272727	234.6712	250.060312	90	240	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55025579	55025579	8919	12	C	A	A	A	325	25	LACRT	2	2
GLIPR1	11010	broad.mit.edu	37	12	75884265	75884265	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:75884265A>G	uc001sxs.2	+	c.500A>G	c.(499-501)AAT>AGT	p.N167S	GLIPR1_uc009zsb.1_Missense_Mutation_p.M191V	NM_006851	NP_006842	P48060	GLIP1_HUMAN	GLI pathogenesis-related 1 precursor	167					cellular lipid metabolic process	extracellular region|integral to membrane				large_intestine(1)|ovary(1)	2														0.298507	60.172813	62.604913	20	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75884265	75884265	6709	12	A	G	G	G	52	4	GLIPR1	4	4
NALCN	259232	broad.mit.edu	37	13	101735223	101735224	+	Missense_Mutation	DNP	CT	AA	AA			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:101735223_101735224CT>AA	uc001vox.1	-	c.3701_3702AG>TT	c.(3700-3702)GAG>GTT	p.E1234V		NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	1234	Extracellular (Potential).					integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)													0.4375	103.609415	103.882544	35	45	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	101735223	101735224	10544	13	CT	AA	AA	AA	311	24	NALCN	2	2
PABPC3	5042	broad.mit.edu	37	13	25670895	25670895	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:25670895G>T	uc001upy.2	+	c.559G>T	c.(559-561)GCA>TCA	p.A187S		NM_030979	NP_112241	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	187					mRNA metabolic process	cytoplasm	nucleotide binding|poly(A) RNA binding			ovary(3)|skin(1)	4		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)										0.373832	113.06614	114.564439	40	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25670895	25670895	11780	13	G	T	T	T	546	42	PABPC3	2	2
MYH7	4625	broad.mit.edu	37	14	23885394	23885394	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:23885394A>T	uc001wjx.2	-	c.4772T>A	c.(4771-4773)CTG>CAG	p.L1591Q		NM_000257	NP_000248	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1591	Potential.				adult heart development|muscle filament sliding|regulation of heart rate|ventricular cardiac muscle tissue morphogenesis	focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(3)	3	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)										0.193676	106.449627	128.591737	49	204	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23885394	23885394	10434	14	A	T	T	T	91	7	MYH7	3	3
RPL10L	140801	broad.mit.edu	37	14	47120353	47120353	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:47120353C>G	uc001wwg.2	-	c.587G>C	c.(586-588)GGA>GCA	p.G196A		NM_080746	NP_542784	Q96L21	RL10L_HUMAN	ribosomal protein L10-like protein	196					spermatogenesis|translation	cytosolic large ribosomal subunit|nucleus	structural constituent of ribosome			ovary(1)	1														0.246032	93.753072	101.161379	31	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47120353	47120353	14035	14	C	G	G	G	390	30	RPL10L	3	3
TRIM9	114088	broad.mit.edu	37	14	51475811	51475811	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:51475811G>T	uc001wyy.2	-	c.1293C>A	c.(1291-1293)TTC>TTA	p.F431L	TRIM9_uc001wyx.3_Missense_Mutation_p.F431L|TRIM9_uc001wyz.3_Missense_Mutation_p.F431L	NM_052978	NP_443210	Q9C026	TRIM9_HUMAN	tripartite motif protein 9 isoform 2	431	COS.				proteasomal ubiquitin-dependent protein catabolic process	cell junction|cytoskeleton|dendrite|synaptic vesicle	protein homodimerization activity|ubiquitin-protein ligase activity|zinc ion binding			lung(1)|skin(1)	2	all_epithelial(31;0.00418)|Breast(41;0.148)													0.234375	71.663538	79.95004	30	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51475811	51475811	17099	14	G	T	T	T	477	37	TRIM9	1	1
C14orf149	112849	broad.mit.edu	37	14	59939767	59939767	+	Silent	SNP	T	C	C			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:59939767T>C	uc001xee.1	-	c.981A>G	c.(979-981)GTA>GTG	p.V327V		NM_144581	NP_653182	Q96EM0	PRCM_HUMAN	proline racemase-like	327							proline racemase activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.14)	L-Proline(DB00172)									0.303571	110.31706	114.16803	34	78	KEEP	---	---	---	---	capture		Silent	SNP	59939767	59939767	1800	14	T	C	C	C	626	49	C14orf149	4	4
RTN1	6252	broad.mit.edu	37	14	60074059	60074059	+	Silent	SNP	G	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:60074059G>A	uc001xen.1	-	c.1917C>T	c.(1915-1917)CGC>CGT	p.R639R	RTN1_uc001xem.1_Silent_p.R219R|RTN1_uc001xek.1_Silent_p.R71R|RTN1_uc001xel.1_Non-coding_Transcript|RTN1_uc010apl.1_Silent_p.R56R	NM_021136	NP_066959	Q16799	RTN1_HUMAN	reticulon 1 isoform A	639	Reticulon.				neuron differentiation	integral to endoplasmic reticulum membrane	signal transducer activity			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0968)										0.205882	14.604588	17.333266	7	27	KEEP	---	---	---	---	capture		Silent	SNP	60074059	60074059	14205	14	G	A	A	A	587	46	RTN1	2	2
KCNH5	27133	broad.mit.edu	37	14	63483638	63483638	+	Silent	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:63483638C>A	uc001xfx.2	-	c.108G>T	c.(106-108)GTG>GTT	p.V36V	KCNH5_uc001xfy.2_Silent_p.V36V|KCNH5_uc001xfz.1_5'UTR|KCNH5_uc001xga.2_5'UTR	NM_139318	NP_647479	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H,	36	Cytoplasmic (Potential).|PAS.				regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)										0.322034	53.201938	54.862616	19	40	KEEP	---	---	---	---	capture		Silent	SNP	63483638	63483638	8340	14	C	A	A	A	262	21	KCNH5	2	2
SERPINA3	12	broad.mit.edu	37	14	95090004	95090004	+	Silent	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:95090004C>T	uc001ydo.3	+	c.1200C>T	c.(1198-1200)GCC>GCT	p.A400A	SERPINA3_uc001ydr.2_Non-coding_Transcript|SERPINA3_uc001ydq.2_Silent_p.A375A|SERPINA3_uc001ydp.2_Silent_p.A375A|SERPINA3_uc001yds.2_Silent_p.A375A|SERPINA3_uc010avg.2_Silent_p.A375A	NM_001085	NP_001076	P01011	AACT_HUMAN	serpin peptidase inhibitor, clade A, member 3	375	RCL.				acute-phase response|maintenance of gastrointestinal epithelium|regulation of lipid metabolic process|regulation of proteolysis	extracellular region|nucleus	DNA binding|protein binding|serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)|large_intestine(1)	5		all_cancers(154;0.0525)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228)										0.264286	92.802095	99.841995	37	103	KEEP	---	---	---	---	capture		Silent	SNP	95090004	95090004	14578	14	C	T	T	T	262	21	SERPINA3	2	2
TRPM1	4308	broad.mit.edu	37	15	31329913	31329913	+	Splice_Site_SNP	SNP	C	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:31329913C>G	uc001zfm.2	-	c.2505_splice	c.e19+1	p.T835_splice	TRPM1_uc010azy.2_Splice_Site_SNP_p.T742_splice|TRPM1_uc001zfl.2_Splice_Site_SNP	NM_002420	NP_002411			transient receptor potential cation channel,						cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)										0.269565	99.137383	104.607713	31	84	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	31329913	31329913	17136	15	C	G	G	G	260	20	TRPM1	5	3
CASC5	57082	broad.mit.edu	37	15	40915482	40915482	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:40915482G>T	uc010bbs.1	+	c.3098G>T	c.(3097-3099)CGT>CTT	p.R1033L	CASC5_uc010ucq.1_Missense_Mutation_p.R857L|CASC5_uc001zme.2_Missense_Mutation_p.R1007L|CASC5_uc010bbt.1_Missense_Mutation_p.R1007L	NM_170589	NP_733468	Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5 isoform 1	1033	2 X 104 AA approximate repeats.				acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint	acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm	protein binding			breast(1)|central_nervous_system(1)	2		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)						629				0.337838	75.650872	77.372465	25	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40915482	40915482	2782	15	G	T	T	T	520	40	CASC5	1	1
SPPL2A	84888	broad.mit.edu	37	15	51017504	51017504	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:51017504C>A	uc001zyv.2	-	c.1163G>T	c.(1162-1164)AGA>ATA	p.R388I		NM_032802	NP_116191	Q8TCT8	PSL2_HUMAN	signal peptide peptidase-like 2A	388						integral to membrane	aspartic-type endopeptidase activity				0				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)		Melanoma(50;790 1209 4069 22965 33125)								0.333333	119.250164	122.500364	44	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51017504	51017504	15601	15	C	A	A	A	416	32	SPPL2A	2	2
WDR72	256764	broad.mit.edu	37	15	53992108	53992108	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:53992108C>A	uc002acj.2	-	c.1604G>T	c.(1603-1605)GGT>GTT	p.G535V	WDR72_uc010bfi.1_Missense_Mutation_p.G535V	NM_182758	NP_877435	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	535	WD 7.									lung(1)	1				all cancers(107;0.0511)										0.126761	21.441535	40.752464	18	124	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53992108	53992108	17895	15	C	A	A	A	234	18	WDR72	2	2
VPS13C	54832	broad.mit.edu	37	15	62239393	62239393	+	Silent	SNP	A	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:62239393A>G	uc002agz.2	-	c.4875T>C	c.(4873-4875)CAT>CAC	p.H1625H	VPS13C_uc002aha.2_Silent_p.H1582H|VPS13C_uc002ahb.1_Silent_p.H1625H|VPS13C_uc002ahc.1_Silent_p.H1582H	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A	1625					protein localization					ovary(2)	2														0.255319	34.6787	37.230333	12	35	KEEP	---	---	---	---	capture		Silent	SNP	62239393	62239393	17758	15	A	G	G	G	102	8	VPS13C	4	4
NEIL1	79661	broad.mit.edu	37	15	75641515	75641515	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:75641515G>T	uc002bae.2	+	c.527G>T	c.(526-528)CGC>CTC	p.R176L	NEIL1_uc002bad.2_Missense_Mutation_p.R90L	NM_024608	NP_078884	Q96FI4	NEIL1_HUMAN	nei endonuclease VIII-like 1	90					base-excision repair|negative regulation of nuclease activity|nucleotide-excision repair|response to oxidative stress	cytoplasm|nucleus	damaged DNA binding|DNA-(apurinic or apyrimidinic site) lyase activity|protein C-terminus binding|zinc ion binding				0														0.354167	45.559385	46.459861	17	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75641515	75641515	10717	15	G	T	T	T	494	38	NEIL1	1	1
CPEB1	64506	broad.mit.edu	37	15	83215263	83215263	+	Silent	SNP	A	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:83215263A>T	uc002bit.2	-	c.1698T>A	c.(1696-1698)ATT>ATA	p.I566I	CPEB1_uc002biq.2_Silent_p.I426I|CPEB1_uc002bir.2_Silent_p.I431I|CPEB1_uc002bis.2_Silent_p.I426I|CPEB1_uc010uod.1_Silent_p.I275I|CPEB1_uc010uoe.1_Silent_p.I504I|CPEB1_uc002biu.2_Silent_p.I528I|CPEB1_uc010uof.1_Silent_p.I426I|CPEB1_uc002biv.2_Silent_p.I501I|CPEB1_uc002bip.2_Silent_p.I275I	NM_001079533	NP_001073001	Q9BZB8	CPEB1_HUMAN	cytoplasmic polyadenylation element binding	506	RRM 2.|Necessary for stress granule assembly and correct localization in dcp1 bodies.				mRNA processing|regulation of translation	cell junction|cytoplasmic mRNA processing body|dendrite|postsynaptic density|postsynaptic membrane	nucleotide binding|RNA binding			ovary(1)|breast(1)	2			BRCA - Breast invasive adenocarcinoma(143;0.229)											0.430769	157.578629	158.121622	56	74	KEEP	---	---	---	---	capture		Silent	SNP	83215263	83215263	3938	15	A	T	T	T	60	5	CPEB1	3	3
ACAN	176	broad.mit.edu	37	15	89392926	89392926	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:89392926G>T	uc010upo.1	+	c.1990G>T	c.(1990-1992)GAC>TAC	p.D664Y	ACAN_uc002bmx.2_Missense_Mutation_p.D664Y|ACAN_uc010upp.1_Missense_Mutation_p.D664Y|ACAN_uc002bna.2_Non-coding_Transcript	NM_013227	NP_037359			aggrecan isoform 2 precursor											ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)											0.28	16.912389	18.001692	7	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	89392926	89392926	118	15	G	T	T	T	429	33	ACAN	2	2
SMG1	23049	broad.mit.edu	37	16	18882139	18882139	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:18882139C>T	uc002dfm.2	-	c.2374G>A	c.(2374-2376)GAT>AAT	p.D792N	SMG1_uc010bwb.2_Missense_Mutation_p.D652N	NM_015092	NP_055907	Q96Q15	SMG1_HUMAN	PI-3-kinase-related kinase SMG-1	792					DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|lung(4)|kidney(2)|stomach(1)|ovary(1)	13										1101				0.266667	11.192774	11.930692	4	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18882139	18882139	15293	16	C	T	T	T	416	32	SMG1	2	2
DCTN5	84516	broad.mit.edu	37	16	23669925	23669925	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:23669925C>T	uc002dly.1	+	c.215C>T	c.(214-216)CCA>CTA	p.P72L		NM_032486	NP_115875	Q9BTE1	DCTN5_HUMAN	dynactin 5	72						cytoplasm|cytoskeleton	transferase activity			upper_aerodigestive_tract(1)	1				GBM - Glioblastoma multiforme(48;0.0156)										0.204188	87.106804	102.627243	39	152	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23669925	23669925	4481	16	C	T	T	T	273	21	DCTN5	2	2
ERN2	10595	broad.mit.edu	37	16	23718140	23718140	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:23718140C>T	uc002dma.3	-	c.566G>A	c.(565-567)GGG>GAG	p.G189E	ERN2_uc010bxp.2_Missense_Mutation_p.G189E|ERN2_uc010bxq.1_5'UTR	NM_033266	NP_150296	Q76MJ5	ERN2_HUMAN	endoplasmic reticulum to nucleus signalling 2	141	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				GBM - Glioblastoma multiforme(48;0.0156)						225				0.196078	65.957682	79.133375	30	123	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23718140	23718140	5431	16	C	T	T	T	286	22	ERN2	2	2
ERN2	10595	broad.mit.edu	37	16	23718374	23718374	+	Silent	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:23718374C>T	uc002dma.3	-	c.477G>A	c.(475-477)CTG>CTA	p.L159L	ERN2_uc010bxp.2_Silent_p.L159L|ERN2_uc010bxq.1_5'UTR	NM_033266	NP_150296	Q76MJ5	ERN2_HUMAN	endoplasmic reticulum to nucleus signalling 2	111	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				GBM - Glioblastoma multiforme(48;0.0156)						225				0.127907	11.560609	23.176281	11	75	KEEP	---	---	---	---	capture		Silent	SNP	23718374	23718374	5431	16	C	T	T	T	262	21	ERN2	2	2
TNRC6A	27327	broad.mit.edu	37	16	24788604	24788604	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:24788604C>G	uc002dmm.2	+	c.514C>G	c.(514-516)CAG>GAG	p.Q172E	TNRC6A_uc010bxs.2_5'UTR	NM_014494	NP_055309	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	172					negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|micro-ribonucleoprotein complex	nucleotide binding|RNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0394)										0.188791	142.67698	173.427636	64	275	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24788604	24788604	16881	16	C	G	G	G	273	21	TNRC6A	3	3
ZNF423	23090	broad.mit.edu	37	16	49671383	49671383	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:49671383C>T	uc002efs.2	-	c.1680G>A	c.(1678-1680)ATG>ATA	p.M560I	ZNF423_uc010vgn.1_Missense_Mutation_p.M443I	NM_015069	NP_055884	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	560					cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	transcription activator activity|transcription repressor activity|zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4		all_cancers(37;0.0155)								386				0.208633	60.990777	71.925331	29	110	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49671383	49671383	18491	16	C	T	T	T	273	21	ZNF423	2	2
CES1	1066	broad.mit.edu	37	16	55853504	55853504	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:55853504C>A	uc002eil.2	-	c.849G>T	c.(847-849)ATG>ATT	p.M283I	CES1_uc010ccf.2_5'Flank|CES1_uc002eim.2_Missense_Mutation_p.M282I|CES1_uc002ein.2_Missense_Mutation_p.M282I	NM_001025195	NP_001020366	P23141	EST1_HUMAN	carboxylesterase 1 isoform a precursor	282					regulation of synaptic transmission|response to toxin	endoplasmic reticulum lumen	methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.13)|Epithelial(162;0.137)	Aminoglutethimide(DB00357)|Bezafibrate(DB01393)|Cholestyramine(DB01432)|Moexipril(DB00691)	NSCLC(162;1801 2756 42904 52896)								0.141538	70.90937	111.215889	46	279	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55853504	55853504	3402	16	C	A	A	A	273	21	CES1	2	2
ABAT	18	broad.mit.edu	37	16	8844285	8844285	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:8844285G>T	uc002czc.3	+	c.205G>T	c.(205-207)GAG>TAG	p.E69*	ABAT_uc002czd.3_Nonsense_Mutation_p.E69*|ABAT_uc010buh.2_Nonsense_Mutation_p.E11*|ABAT_uc010bui.2_Nonsense_Mutation_p.E69*	NM_020686	NP_065737	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase precursor	69					behavioral response to cocaine|gamma-aminobutyric acid catabolic process|neurotransmitter catabolic process|neurotransmitter secretion	4-aminobutyrate transaminase complex|mitochondrial matrix	(S)-3-amino-2-methylpropionate transaminase activity|4-aminobutyrate transaminase activity|protein homodimerization activity|pyridoxal phosphate binding|succinate-semialdehyde dehydrogenase binding				0					Divalproex sodium(DB00510)|Isoniazid(DB00951)|L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Pyruvic acid(DB00119)|Tiagabine(DB00906)|Valproic Acid(DB00313)|Vigabatrin(DB01080)									0.140244	33.02481	53.512032	23	141	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	8844285	8844285	28	16	G	T	T	T	429	33	ABAT	5	2
USP7	7874	broad.mit.edu	37	16	8988972	8988972	+	Silent	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:8988972C>T	uc002czl.2	-	c.2955G>A	c.(2953-2955)GAG>GAA	p.E985E	USP7_uc010uyk.1_Silent_p.E886E|USP7_uc002czj.2_Non-coding_Transcript|USP7_uc010uyj.1_Silent_p.E886E|USP7_uc002czk.2_Silent_p.E969E	NM_003470	NP_003461	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7	985					interspecies interaction between organisms|multicellular organismal development|protein deubiquitination|regulation of sequence-specific DNA binding transcription factor activity|ubiquitin-dependent protein catabolic process	cytoplasm|PML body	cysteine-type endopeptidase activity|p53 binding|protein C-terminus binding|transcription factor binding|ubiquitin protein ligase binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)	3														0.09589	41.282886	148.959039	63	594	KEEP	---	---	---	---	capture		Silent	SNP	8988972	8988972	17652	16	C	T	T	T	415	32	USP7	2	2
MYH2	4620	broad.mit.edu	37	17	10451096	10451096	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10451096C>A	uc010coi.2	-	c.142G>T	c.(142-144)GTC>TTC	p.V48F	MYH2_uc002gmp.3_Missense_Mutation_p.V48F|MYH2_uc010coj.2_Missense_Mutation_p.V48F	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	48	Myosin head-like.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|lung(1)|kidney(1)	11														0.434579	282.350737	283.147029	93	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10451096	10451096	10430	17	C	A	A	A	221	17	MYH2	2	2
PIRT	644139	broad.mit.edu	37	17	10728733	10728733	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10728733T>C	uc010col.2	-	c.230A>G	c.(229-231)TAC>TGC	p.Y77C		NM_001101387	NP_001094857	P0C851	PIRT_HUMAN	phosphoinositide-interacting regulator of	77						integral to membrane				ovary(1)	1														0.351351	90.343843	91.778932	26	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10728733	10728733	12369	17	T	C	C	C	741	57	PIRT	4	4
OR1A1	8383	broad.mit.edu	37	17	3119264	3119264	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:3119264C>T	uc010vrc.1	+	c.350C>T	c.(349-351)GCA>GTA	p.A117V		NM_014565	NP_055380	Q9P1Q5	OR1A1_HUMAN	olfactory receptor, family 1, subfamily A,	117	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.233645	53.123461	60.071292	25	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3119264	3119264	11355	17	C	T	T	T	325	25	OR1A1	2	2
C17orf98	388381	broad.mit.edu	37	17	36991511	36991511	+	Silent	SNP	G	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:36991511G>A	uc002hqv.2	-	c.396C>T	c.(394-396)CGC>CGT	p.R132R		NM_001080465	NP_001073934	A8MV24	CQ098_HUMAN	hypothetical protein LOC388381	132											0														0.190476	51.008067	64.183823	28	119	KEEP	---	---	---	---	capture		Silent	SNP	36991511	36991511	1953	17	G	A	A	A	587	46	C17orf98	2	2
TNS4	84951	broad.mit.edu	37	17	38644981	38644981	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:38644981T>A	uc010cxb.2	-	c.680A>T	c.(679-681)AAT>ATT	p.N227I		NM_032865	NP_116254	Q8IZW8	TENS4_HUMAN	tensin 4 precursor	227	Ser-rich.				apoptosis|protein localization	cytoplasm|cytoskeleton|focal adhesion	actin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)											0.422414	139.145939	139.756108	49	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38644981	38644981	16886	17	T	A	A	A	676	52	TNS4	3	3
HDAC5	10014	broad.mit.edu	37	17	42169750	42169750	+	Silent	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:42169750C>A	uc002iff.1	-	c.921G>T	c.(919-921)GGG>GGT	p.G307G	HDAC5_uc002ifd.1_Silent_p.G306G|HDAC5_uc002ife.1_Silent_p.G306G|HDAC5_uc010czp.1_Silent_p.G306G|HDAC5_uc002ifh.2_Silent_p.G306G	NM_001015053	NP_001015053	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5 isoform 3	306					B cell differentiation|cellular response to insulin stimulus|chromatin remodeling|chromatin silencing|inflammatory response|negative regulation of cell migration involved in sprouting angiogenesis|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of myotube differentiation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|regulation of protein binding|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein kinase C binding|repressing transcription factor binding|specific transcriptional repressor activity			ovary(1)	1		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)										0.205882	44.632098	52.805285	21	81	KEEP	---	---	---	---	capture		Silent	SNP	42169750	42169750	7293	17	C	A	A	A	275	22	HDAC5	2	2
LUC7L3	51747	broad.mit.edu	37	17	48823140	48823140	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:48823140G>T	uc002isq.2	+	c.753G>T	c.(751-753)AAG>AAT	p.K251N	LUC7L3_uc010wmw.1_Missense_Mutation_p.K175N|LUC7L3_uc002isr.2_Missense_Mutation_p.K251N|LUC7L3_uc002iss.2_Missense_Mutation_p.K251N	NM_016424	NP_057508	O95232	LC7L3_HUMAN	LUC7-like 3	251	Arg/Ser-rich.|Glu-rich.				apoptosis|mRNA processing|response to stress|RNA splicing	focal adhesion|nuclear speck	DNA binding|mRNA binding|protein binding				0														0.473684	54.545922	54.568928	18	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48823140	48823140	9460	17	G	T	T	T	438	34	LUC7L3	2	2
C17orf64	124773	broad.mit.edu	37	17	58506804	58506804	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:58506804T>C	uc002iyq.2	+	c.511T>C	c.(511-513)TGG>CGG	p.W171R		NM_181707	NP_859058	Q86WR6	CQ064_HUMAN	hypothetical protein LOC124773	171										breast(1)	1	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;5.81e-13)|all cancers(12;2.17e-11)|Colorectal(3;0.01)											0.412281	143.978395	144.749511	47	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58506804	58506804	1929	17	T	C	C	C	663	51	C17orf64	4	4
KCNH6	81033	broad.mit.edu	37	17	61619723	61619723	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:61619723G>T	uc002jay.2	+	c.2076G>T	c.(2074-2076)GAG>GAT	p.E692D	KCNH6_uc010wpl.1_Missense_Mutation_p.E569D|KCNH6_uc010wpm.1_Missense_Mutation_p.E692D|KCNH6_uc002jaz.1_Missense_Mutation_p.E639D	NM_030779	NP_110406	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H,	692	cNMP.|Cytoplasmic (Potential).				regulation of transcription, DNA-dependent|signal transduction						0					Ibutilide(DB00308)									0.344828	139.716248	142.794761	50	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61619723	61619723	8341	17	G	T	T	T	451	35	KCNH6	2	2
CHRNB1	1140	broad.mit.edu	37	17	7357633	7357633	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7357633T>C	uc002ghb.2	+	c.838T>C	c.(838-840)TCA>CCA	p.S280P	CHRNB1_uc010vty.1_Missense_Mutation_p.S208P|CHRNB1_uc010vtz.1_Missense_Mutation_p.S114P	NM_000747	NP_000738	P11230	ACHB_HUMAN	nicotinic acetylcholine receptor beta 1 subunit	280	Helical; (Potential).				behavioral response to nicotine|muscle contraction|muscle fiber development|neuromuscular synaptic transmission|postsynaptic membrane organization|regulation of membrane potential|synaptic transmission, cholinergic	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine binding|receptor activity			ovary(2)	2		Prostate(122;0.157)												0.473684	290.371742	290.474313	81	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7357633	7357633	3524	17	T	C	C	C	702	54	CHRNB1	4	4
GLP2R	9340	broad.mit.edu	37	17	9791285	9791285	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:9791285G>T	uc002gmd.1	+	c.1321G>T	c.(1321-1323)GGA>TGA	p.G441*		NM_004246	NP_004237	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor precursor	441	Helical; Name=7; (Potential).				G-protein signaling, coupled to cAMP nucleotide second messenger|positive regulation of cell proliferation	integral to membrane|plasma membrane				ovary(1)	1					Glucagon recombinant(DB00040)									0.421203	447.358711	449.251579	147	202	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	9791285	9791285	6721	17	G	T	T	T	611	47	GLP2R	5	2
TTC39C	125488	broad.mit.edu	37	18	21660779	21660779	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:21660779T>A	uc002kuw.2	+	c.691T>A	c.(691-693)TCC>ACC	p.S231T	TTC39C_uc002kuu.2_Missense_Mutation_p.S170T	NM_001135993	NP_001129465	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C isoform 1	231							binding			ovary(1)	1														0.238095	62.025329	68.602902	25	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21660779	21660779	17264	18	T	A	A	A	650	50	TTC39C	3	3
DCC	1630	broad.mit.edu	37	18	50592527	50592527	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:50592527C>A	uc002lfe.1	+	c.1252C>A	c.(1252-1254)CCT>ACT	p.P418T	DCC_uc010xdr.1_Missense_Mutation_p.P266T|DCC_uc010dpf.1_Missense_Mutation_p.P73T	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor	418	Extracellular (Potential).				apoptosis|induction of apoptosis	cytosol|integral to membrane				ovary(6)|large_intestine(1)|central_nervous_system(1)|skin(1)	9		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)										0.3	74.001239	77.581245	30	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50592527	50592527	4453	18	C	A	A	A	286	22	DCC	2	2
CCBE1	147372	broad.mit.edu	37	18	57363928	57363928	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:57363928C>T	uc002lib.2	-	c.145G>A	c.(145-147)GAG>AAG	p.E49K		NM_133459	NP_597716	Q6UXH8	CCBE1_HUMAN	collagen and calcium binding EGF domains 1	49					lymphangiogenesis|sprouting angiogenesis|venous blood vessel morphogenesis	collagen	calcium ion binding			ovary(1)	1		Colorectal(73;0.175)				NSCLC(137;1340 1860 15773 39604 51087)|Esophageal Squamous(139;339 1777 2926 19691 38524)						OREG0025022	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.288889	110.155873	115.559361	39	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57363928	57363928	2851	18	C	T	T	T	416	32	CCBE1	2	2
RTTN	25914	broad.mit.edu	37	18	67801779	67801779	+	Splice_Site_SNP	SNP	T	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:67801779T>A	uc002lkp.2	-	c.2886_splice	c.e23-1	p.W962_splice	RTTN_uc002lko.2_Splice_Site_SNP|RTTN_uc010xfb.1_Splice_Site_SNP_p.W50_splice	NM_173630	NP_775901			rotatin								binding			ovary(3)|pancreas(2)|breast(1)|central_nervous_system(1)	7		Esophageal squamous(42;0.129)												0.416667	14.97321	15.04587	5	7	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	67801779	67801779	14217	18	T	A	A	A	689	53	RTTN	5	3
TSHZ1	10194	broad.mit.edu	37	18	72999184	72999184	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:72999184G>T	uc002lly.2	+	c.1687G>T	c.(1687-1689)GGC>TGC	p.G563C		NM_005786	NP_005777	Q6ZSZ6	TSH1_HUMAN	teashirt family zinc finger 1	608					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)										0.253521	41.29493	45.231182	18	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72999184	72999184	17174	18	G	T	T	T	507	39	TSHZ1	1	1
SLC1A6	6511	broad.mit.edu	37	19	15061009	15061009	+	Nonstop_Mutation	SNP	A	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:15061009A>T	uc002naa.1	-	c.1693T>A	c.(1693-1695)TGA>AGA	p.*565R	SLC1A6_uc010dzu.1_Nonstop_Mutation_p.*487R|SLC1A6_uc010xod.1_Nonstop_Mutation_p.*501R	NM_005071	NP_005062	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity	565					synaptic transmission	integral to plasma membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|L-aspartate transmembrane transporter activity|sodium:dicarboxylate symporter activity			pancreas(3)|ovary(2)	5					L-Glutamic Acid(DB00142)									0.258065	20.985165	22.629888	8	23	KEEP	---	---	---	---	capture		Nonstop_Mutation	SNP	15061009	15061009	14932	19	A	T	T	T	78	6	SLC1A6	5	3
CYP4F2	8529	broad.mit.edu	37	19	15989716	15989716	+	Silent	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:15989716C>T	uc002nbs.1	-	c.1428G>A	c.(1426-1428)GCG>GCA	p.A476A	CYP4F2_uc010xot.1_Silent_p.A327A	NM_001082	NP_001073	P78329	CP4F2_HUMAN	cytochrome P450, family 4, subfamily F,	476					leukotriene metabolic process|long-chain fatty acid metabolic process|oxidation-reduction process|very long-chain fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	alkane 1-monooxygenase activity|electron carrier activity|heme binding|leukotriene-B4 20-monooxygenase activity|oxygen binding|protein binding			ovary(1)|skin(1)	2														0.284091	67.248857	70.925951	25	63	KEEP	---	---	---	---	capture		Silent	SNP	15989716	15989716	4353	19	C	T	T	T	288	23	CYP4F2	1	1
REXO1	57455	broad.mit.edu	37	19	1816518	1816518	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:1816518C>T	uc002lua.3	-	c.3368G>A	c.(3367-3369)CGT>CAT	p.R1123H	REXO1_uc010dsq.2_Missense_Mutation_p.R432H|REXO1_uc010xgs.1_Missense_Mutation_p.R109H|MIR1909_hsa-mir-1909|MI0008330_5'Flank	NM_020695	NP_065746	Q8N1G1	REXO1_HUMAN	transcription elongation factor B polypeptide 3	1123	Exonuclease.					nucleus	exonuclease activity|nucleic acid binding				0		Ovarian(11;1.78e-06)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)										0.166667	19.318288	25.634519	10	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1816518	1816518	13711	19	C	T	T	T	247	19	REXO1	1	1
GDF15	9518	broad.mit.edu	37	19	18499574	18499574	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:18499574C>A	uc002niv.2	+	c.756C>A	c.(754-756)AAC>AAA	p.N252K		NM_004864	NP_004855	Q99988	GDF15_HUMAN	growth differentiation factor 15	252					cell-cell signaling|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity			central_nervous_system(1)	1												OREG0025363	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.388889	20.919876	21.114896	7	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18499574	18499574	6581	19	C	A	A	A	220	17	GDF15	2	2
GMIP	51291	broad.mit.edu	37	19	19750925	19750925	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:19750925G>A	uc002nnd.2	-	c.506C>T	c.(505-507)ACA>ATA	p.T169I	GMIP_uc010xrb.1_Missense_Mutation_p.T169I|GMIP_uc010xrc.1_Missense_Mutation_p.T169I	NM_016573	NP_057657	Q9P107	GMIP_HUMAN	GEM interacting protein	169					negative regulation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	metal ion binding|protein binding|Rho GTPase activator activity			ovary(1)	1														0.3125	49.366271	51.375405	20	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19750925	19750925	6760	19	G	A	A	A	624	48	GMIP	2	2
ZNF430	80264	broad.mit.edu	37	19	21239980	21239980	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:21239980A>G	uc002npj.2	+	c.866A>G	c.(865-867)TAC>TGC	p.Y289C	ZNF430_uc002npk.2_Missense_Mutation_p.Y288C	NM_025189	NP_079465	Q9H8G1	ZN430_HUMAN	zinc finger protein 430	289	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.237705	88.321426	95.982941	29	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21239980	21239980	18497	19	A	G	G	G	182	14	ZNF430	4	4
ZNF676	163223	broad.mit.edu	37	19	22363671	22363671	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:22363671C>T	uc002nqs.1	-	c.848G>A	c.(847-849)TGT>TAT	p.C283Y		NM_001001411	NP_001001411	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	283	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)												0.305085	93.047664	97.051502	36	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22363671	22363671	18678	19	C	T	T	T	221	17	ZNF676	2	2
PSG8	440533	broad.mit.edu	37	19	43258471	43258471	+	Silent	SNP	T	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:43258471T>G	uc002ouo.2	-	c.1257A>C	c.(1255-1257)CCA>CCC	p.P419P	PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Intron|PSG8_uc010eim.2_Intron|PSG8_uc002oui.2_Intron|PSG8_uc002ouh.2_Intron|PSG8_uc010ein.2_Intron|PSG8_uc002ouj.3_Intron|PSG8_uc002ouk.3_Intron|PSG8_uc002oul.3_Intron|PSG8_uc002oum.3_Intron|PSG1_uc002oun.2_Intron|PSG8_uc002oup.3_Silent_p.P326P	NM_182707	NP_874366	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8 isoform	419						extracellular region					0		Prostate(69;0.00899)												0.261364	242.602422	260.778648	92	260	KEEP	---	---	---	---	capture		Silent	SNP	43258471	43258471	13114	19	T	G	G	G	704	55	PSG8	4	4
IRGC	56269	broad.mit.edu	37	19	44222905	44222905	+	Silent	SNP	G	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:44222905G>A	uc002oxh.2	+	c.195G>A	c.(193-195)GCG>GCA	p.A65A		NM_019612	NP_062558	Q6NXR0	IIGP5_HUMAN	immunity-related GTPase family, cinema	65	GTP.					membrane	GTP binding|hydrolase activity, acting on acid anhydrides			ovary(1)	1		Prostate(69;0.0435)				Colon(189;350 2037 11447 13433 38914)								0.491228	170.879396	170.88726	56	58	KEEP	---	---	---	---	capture		Silent	SNP	44222905	44222905	8141	19	G	A	A	A	496	39	IRGC	1	1
CRX	1406	broad.mit.edu	37	19	48342701	48342701	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:48342701G>T	uc002phq.3	+	c.377G>T	c.(376-378)AGA>ATA	p.R126I		NM_000554	NP_000545	O43186	CRX_HUMAN	cone-rod homeobox protein	126					organ morphogenesis|response to stimulus|visual perception		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|central_nervous_system(1)	2		all_cancers(25;2.76e-09)|all_epithelial(76;7.01e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000266)|all cancers(93;0.000788)|Epithelial(262;0.0226)|GBM - Glioblastoma multiforme(486;0.0521)		Pancreas(57;461 1196 22201 40716 47188)								0.443609	157.487901	157.858769	59	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48342701	48342701	4041	19	G	T	T	T	429	33	CRX	2	2
KLK7	5650	broad.mit.edu	37	19	51483127	51483127	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:51483127C>A	uc002puo.2	-	c.523G>T	c.(523-525)GAC>TAC	p.D175Y	KLK7_uc002pup.2_Missense_Mutation_p.D175Y|KLK7_uc010yco.1_Missense_Mutation_p.D49Y|KLK7_uc010eok.2_Missense_Mutation_p.D103Y	NM_139277	NP_644806	P49862	KLK7_HUMAN	stratum corneum chymotryptic enzyme	175	Peptidase S1.				epidermis development|proteolysis	extracellular region	serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00382)|GBM - Glioblastoma multiforme(134;0.00895)						155				0.458333	30.920118	30.956649	11	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51483127	51483127	8723	19	C	A	A	A	390	30	KLK7	2	2
ZNF83	55769	broad.mit.edu	37	19	53117543	53117543	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:53117543T>C	uc002pzu.3	-	c.275A>G	c.(274-276)CAC>CGC	p.H92R	ZNF83_uc002pzv.3_Missense_Mutation_p.H92R|ZNF83_uc010eps.2_Missense_Mutation_p.H92R|ZNF83_uc010ept.2_Missense_Mutation_p.H92R|ZNF83_uc010epu.2_Missense_Mutation_p.H92R|ZNF83_uc010epv.2_Missense_Mutation_p.H92R|ZNF83_uc010epw.2_Missense_Mutation_p.H92R|ZNF83_uc010epx.2_Missense_Mutation_p.H92R|ZNF83_uc010epy.2_Missense_Mutation_p.H92R|ZNF83_uc010epz.2_Missense_Mutation_p.H92R|ZNF83_uc010eqb.1_Missense_Mutation_p.H92R	NM_018300	NP_060770	P51522	ZNF83_HUMAN	zinc finger protein 83 isoform a	92					regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)										0.611111	189.944357	190.91799	55	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53117543	53117543	18782	19	T	C	C	C	767	59	ZNF83	4	4
MUC16	94025	broad.mit.edu	37	19	9068625	9068625	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9068625C>A	uc002mkp.2	-	c.18821G>T	c.(18820-18822)CGT>CTT	p.R6274L		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	6276	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.302158	121.714108	126.561968	42	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9068625	9068625	10367	19	C	A	A	A	247	19	MUC16	1	1
PHGDH	26227	broad.mit.edu	37	1	120263891	120263891	+	Silent	SNP	T	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:120263891T>A	uc001ehz.2	+	c.237T>A	c.(235-237)GGT>GGA	p.G79G	PHGDH_uc009whl.2_5'UTR|PHGDH_uc009whm.2_5'UTR|PHGDH_uc001eia.2_Silent_p.G79G|PHGDH_uc009whn.2_Silent_p.G79G|PHGDH_uc001eib.2_Silent_p.G45G	NM_006623	NP_006614	O43175	SERA_HUMAN	phosphoglycerate dehydrogenase	79					brain development|L-serine biosynthetic process|oxidation-reduction process		electron carrier activity|NAD binding|phosphoglycerate dehydrogenase activity			ovary(1)	1	all_cancers(5;1.18e-09)|all_epithelial(5;2.16e-10)|Melanoma(3;1.93e-05)|all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0347)		Lung(183;0.0111)|LUSC - Lung squamous cell carcinoma(189;0.0593)	NADH(DB00157)									0.113537	30.894	64.628446	26	203	KEEP	---	---	---	---	capture		Silent	SNP	120263891	120263891	12264	1	T	A	A	A	756	59	PHGDH	3	3
SPTA1	6708	broad.mit.edu	37	1	158624529	158624529	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158624529C>G	uc001fst.1	-	c.2908G>C	c.(2908-2910)GCT>CCT	p.A970P		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	970					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)													0.121495	20.297565	35.317731	13	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158624529	158624529	15630	1	C	G	G	G	338	26	SPTA1	3	3
RABGAP1L	9910	broad.mit.edu	37	1	174671252	174671252	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:174671252A>T	uc001gjx.2	+	c.2027A>T	c.(2026-2028)GAA>GTA	p.E676V	RABGAP1L_uc001gkb.3_5'UTR|RABGAP1L_uc001gkc.3_5'UTR|RABGAP1L_uc001gkd.3_Missense_Mutation_p.E2V	NM_014857	NP_055672	Q5R372	RBG1L_HUMAN	RAB GTPase activating protein 1-like isoform A	676	Rab-GAP TBC.				regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4														0.100629	7.684753	33.008729	16	143	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	174671252	174671252	13424	1	A	T	T	T	117	9	RABGAP1L	3	3
FAM5C	339479	broad.mit.edu	37	1	190203536	190203536	+	Silent	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:190203536C>A	uc001gse.1	-	c.690G>T	c.(688-690)CTG>CTT	p.L230L	FAM5C_uc010pot.1_Silent_p.L128L	NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C	230						extracellular region				lung(2)|ovary(1)|kidney(1)	4	Prostate(682;0.198)													0.432836	89.364623	89.628265	29	38	KEEP	---	---	---	---	capture		Silent	SNP	190203536	190203536	5817	1	C	A	A	A	262	21	FAM5C	2	2
HTR6	3362	broad.mit.edu	37	1	20005133	20005133	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:20005133C>G	uc001bcl.2	+	c.788C>G	c.(787-789)GCC>GGC	p.A263G		NM_000871	NP_000862	P50406	5HT6R_HUMAN	5-hydroxytryptamine (serotonin) receptor 6	263	Cytoplasmic (By similarity).				G-protein signaling, coupled to cyclic nucleotide second messenger|synaptic transmission	integral to plasma membrane	histamine receptor activity|protein binding			ovary(1)	1		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;5.81e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.00117)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)	Granisetron(DB00889)|Ondansetron(DB00904)|Sertindole(DB06144)	Esophageal Squamous(168;1879 2619 6848 21062)								0.188235	37.073436	44.790757	16	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20005133	20005133	7751	1	C	G	G	G	338	26	HTR6	3	3
CACNA1S	779	broad.mit.edu	37	1	201028377	201028377	+	Silent	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:201028377C>A	uc001gvv.2	-	c.3465G>T	c.(3463-3465)GTG>GTT	p.V1155V		NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,	1155	IV.|Helical; Name=S2 of repeat IV; (Potential).				axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)	4					Magnesium Sulfate(DB00653)|Verapamil(DB00661)									0.476923	187.33366	187.39442	62	68	KEEP	---	---	---	---	capture		Silent	SNP	201028377	201028377	2663	1	C	A	A	A	262	21	CACNA1S	2	2
PRSS38	339501	broad.mit.edu	37	1	228004983	228004983	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:228004983T>A	uc001hrh.2	+	c.385T>A	c.(385-387)TGG>AGG	p.W129R		NM_183062	NP_898885	A1L453	PRS38_HUMAN	marapsin 2 precursor	129	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)|pancreas(1)	2														0.633136	353.149382	355.781384	107	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	228004983	228004983	13077	1	T	A	A	A	767	59	PRSS38	3	3
OR2L2	26246	broad.mit.edu	37	1	248202145	248202145	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248202145G>T	uc001idw.2	+	c.576G>T	c.(574-576)TGG>TGT	p.W192C	OR2L13_uc001ids.2_Intron	NM_001004686	NP_001004686	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L,	192	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)	2	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)											0.186916	83.550978	103.143118	40	174	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248202145	248202145	11413	1	G	T	T	T	559	43	OR2L2	2	2
OR14C36	127066	broad.mit.edu	37	1	248512355	248512355	+	Silent	SNP	G	C	C			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248512355G>C	uc010pzl.1	+	c.279G>C	c.(277-279)GCG>GCC	p.A93A		NM_001001918	NP_001001918	Q8NHC7	O14CZ_HUMAN	olfactory receptor, family 14, subfamily C,	93	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)	2														0.271429	50.292321	53.591223	19	51	KEEP	---	---	---	---	capture		Silent	SNP	248512355	248512355	11352	1	G	C	C	C	496	39	OR14C36	3	3
NR0B2	8431	broad.mit.edu	37	1	27240194	27240194	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:27240194G>A	uc001bnf.2	-	c.238C>T	c.(238-240)CCT>TCT	p.P80S		NM_021969	NP_068804	Q15466	NR0B2_HUMAN	short heterodimer partner	80	Ligand-binding (By similarity).				cholesterol metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	DNA binding|protein domain specific binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription corepressor activity				0		all_cancers(24;1.23e-26)|all_epithelial(13;1.19e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;0.00017)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.01e-51)|OV - Ovarian serous cystadenocarcinoma(117;8.22e-30)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)										0.470588	21.168308	21.183058	8	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27240194	27240194	11019	1	G	A	A	A	546	42	NR0B2	2	2
AHDC1	27245	broad.mit.edu	37	1	27874554	27874554	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:27874554G>A	uc009vsy.2	-	c.4073C>T	c.(4072-4074)ACC>ATC	p.T1358I	AHDC1_uc009vsz.1_Missense_Mutation_p.T1358I	NM_001029882	NP_001025053	Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	1358							DNA binding			central_nervous_system(1)	1		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)										0.252525	58.925556	64.433693	25	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27874554	27874554	415	1	G	A	A	A	572	44	AHDC1	2	2
PRPF38A	84950	broad.mit.edu	37	1	52878240	52878240	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:52878240G>T	uc001ctv.3	+	c.553G>T	c.(553-555)GAA>TAA	p.E185*	PRPF38A_uc001ctw.3_5'UTR	NM_032864	NP_116253	Q8NAV1	PR38A_HUMAN	PRP38 pre-mRNA processing factor 38 (yeast)	185	Potential.				mRNA processing|RNA splicing	spliceosomal complex					0														0.117647	8.746739	18.523916	8	60	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	52878240	52878240	13010	1	G	T	T	T	533	41	PRPF38A	5	2
C1orf177	163747	broad.mit.edu	37	1	55279583	55279583	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:55279583C>G	uc001cyb.3	+	c.859C>G	c.(859-861)CGA>GGA	p.R287G	C1orf177_uc001cya.3_Missense_Mutation_p.R287G	NM_001110533	NP_001104003	Q3ZCV2	CA177_HUMAN	hypothetical protein LOC163747 isoform 2	287											0														0.21831	72.050684	82.435653	31	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55279583	55279583	2084	1	C	G	G	G	295	23	C1orf177	3	3
DOCK7	85440	broad.mit.edu	37	1	62941022	62941022	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:62941022T>A	uc001daq.2	-	c.5929A>T	c.(5929-5931)ATC>TTC	p.I1977F	DOCK7_uc001dan.2_Missense_Mutation_p.I1840F|DOCK7_uc001dao.2_Missense_Mutation_p.I1838F|DOCK7_uc001dap.2_Missense_Mutation_p.I1957F|DOCK7_uc001dam.2_Missense_Mutation_p.I1159F|DOCK7_uc010oov.1_Missense_Mutation_p.I718F|DOCK7_uc001dar.1_Missense_Mutation_p.I151F	NM_033407	NP_212132	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1988	DHR-2.				activation of Rac GTPase activity|axonogenesis|establishment of neuroblast polarity|microtubule cytoskeleton organization|positive regulation of peptidyl-serine phosphorylation	axon|basal part of cell|growth cone	GTP binding|guanyl-nucleotide exchange factor activity|Rac GTPase binding			ovary(2)	2														0.235294	39.07064	43.424767	16	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62941022	62941022	4876	1	T	A	A	A	650	50	DOCK7	3	3
ENTPD6	955	broad.mit.edu	37	20	25187965	25187965	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:25187965G>T	uc002wuj.2	+	c.308G>T	c.(307-309)GGG>GTG	p.G103V	ENTPD6_uc010zsy.1_Missense_Mutation_p.G103V|ENTPD6_uc010gdj.1_Missense_Mutation_p.G75V|ENTPD6_uc010zsz.1_Intron|ENTPD6_uc002wum.2_Missense_Mutation_p.G86V|ENTPD6_uc010zta.1_Missense_Mutation_p.G103V|ENTPD6_uc002wun.2_Missense_Mutation_p.G103V|ENTPD6_uc002wuk.2_Missense_Mutation_p.G102V|ENTPD6_uc002wul.2_Missense_Mutation_p.G102V|ENTPD6_uc010ztb.1_Missense_Mutation_p.G75V|ENTPD6_uc010ztc.1_Missense_Mutation_p.G75V|ENTPD6_uc002wuo.2_Intron|ENTPD6_uc010ztd.1_5'Flank	NM_001247	NP_001238	O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6	103	Lumenal (Potential).					Golgi membrane|integral to membrane	nucleoside-diphosphatase activity				0														0.1875	35.201163	43.975765	18	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25187965	25187965	5336	20	G	T	T	T	559	43	ENTPD6	2	2
CPXM1	56265	broad.mit.edu	37	20	2776024	2776024	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:2776024C>A	uc002wgu.2	-	c.1759G>T	c.(1759-1761)GAG>TAG	p.E587*	CPXM1_uc010gas.2_Nonsense_Mutation_p.E513*	NM_019609	NP_062555	Q96SM3	CPXM1_HUMAN	carboxypeptidase X, member 1 precursor	587					cell adhesion|proteolysis		metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2														0.215517	54.310625	62.980187	25	91	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	2776024	2776024	3976	20	C	A	A	A	377	29	CPXM1	5	2
FASTKD5	60493	broad.mit.edu	37	20	3127954	3127954	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:3127954G>A	uc002whz.2	-	c.1763C>T	c.(1762-1764)TCT>TTT	p.S588F	UBOX5_uc002whw.2_Intron|UBOX5_uc002whx.2_Intron|UBOX5_uc002why.1_Intron	NM_021826	NP_068598	Q7L8L6	FAKD5_HUMAN	FAST kinase domains 5	588					apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity				0														0.146597	47.087866	70.003813	28	163	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3127954	3127954	5924	20	G	A	A	A	429	33	FASTKD5	2	2
C20orf152	140894	broad.mit.edu	37	20	34572656	34572656	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:34572656C>A	uc002xer.1	+	c.672C>A	c.(670-672)GAC>GAA	p.D224E	C20orf152_uc002xes.1_Missense_Mutation_p.D224E|C20orf152_uc010gfp.1_Non-coding_Transcript	NM_080834	NP_543024	Q96M20	CT152_HUMAN	hypothetical protein LOC140894	224	cNMP.										0	Breast(12;0.00631)													0.448179	511.166837	512.00026	160	197	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34572656	34572656	2169	20	C	A	A	A	233	18	C20orf152	2	2
PTPRT	11122	broad.mit.edu	37	20	41101011	41101011	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:41101011G>T	uc010ggj.2	-	c.1345C>A	c.(1345-1347)CTG>ATG	p.L449M	PTPRT_uc002xkg.2_Missense_Mutation_p.L449M	NM_133170	NP_573400	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	449	Extracellular (Potential).|Fibronectin type-III 2.				homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			ovary(7)|lung(5)|skin(2)	14		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)								646				0.235294	47.552767	53.003151	20	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41101011	41101011	13270	20	G	T	T	T	451	35	PTPRT	2	2
PTPRT	11122	broad.mit.edu	37	20	41514452	41514452	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:41514452G>T	uc010ggj.2	-	c.209C>A	c.(208-210)CCC>CAC	p.P70H	PTPRT_uc002xkg.2_Missense_Mutation_p.P70H	NM_133170	NP_573400	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	70	Extracellular (Potential).|MAM.				homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			ovary(7)|lung(5)|skin(2)	14		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)								646				0.177083	33.959818	43.35752	17	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41514452	41514452	13270	20	G	T	T	T	559	43	PTPRT	2	2
KRTAP21-2	337978	broad.mit.edu	37	21	32119384	32119384	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:32119384C>A	uc011adh.1	-	c.137G>T	c.(136-138)GGC>GTC	p.G46V		NM_181617	NP_853648	Q3LI59	KR212_HUMAN	keratin associated protein 21-2	46						intermediate filament					0														0.283333	44.64915	47.179241	17	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32119384	32119384	8858	21	C	A	A	A	338	26	KRTAP21-2	2	2
TRPM2	7226	broad.mit.edu	37	21	45826567	45826567	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:45826567C>A	uc010gpt.1	+	c.2881C>A	c.(2881-2883)CGC>AGC	p.R961S	TRPM2_uc002zet.1_Missense_Mutation_p.R961S|TRPM2_uc002zeu.1_Missense_Mutation_p.R961S|TRPM2_uc002zew.1_Missense_Mutation_p.R961S|TRPM2_uc002zex.1_Missense_Mutation_p.R747S|TRPM2_uc002zey.1_Missense_Mutation_p.R474S	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,	961	Extracellular (Potential).					integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.333333	14.219748	14.674846	6	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45826567	45826567	17137	21	C	A	A	A	351	27	TRPM2	1	1
ZMAT5	55954	broad.mit.edu	37	22	30144421	30144421	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:30144421T>C	uc003agm.2	-	c.113A>G	c.(112-114)TAC>TGC	p.Y38C	ZMAT5_uc003agn.2_Missense_Mutation_p.Y38C|ZMAT5_uc003ago.1_Missense_Mutation_p.Y38C	NM_019103	NP_061976	Q9UDW3	ZMAT5_HUMAN	zinc finger, matrin type 5	38					mRNA processing|RNA splicing	cytoplasm|U12-type spliceosomal complex	nucleic acid binding|zinc ion binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(5;0.000597)|all cancers(5;0.0534)|Epithelial(10;0.0574)											0.352273	104.308821	105.997996	31	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30144421	30144421	18286	22	T	C	C	C	741	57	ZMAT5	4	4
APOL5	80831	broad.mit.edu	37	22	36123064	36123064	+	Silent	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:36123064C>T	uc003aof.2	+	c.949C>T	c.(949-951)CTG>TTG	p.L317L		NM_030642	NP_085145	Q9BWW9	APOL5_HUMAN	apolipoprotein L5	317					lipid metabolic process|lipid transport|lipoprotein metabolic process	cytoplasm|extracellular region	high-density lipoprotein particle binding|lipid binding|protein binding				0														0.288	103.13522	108.182379	36	89	KEEP	---	---	---	---	capture		Silent	SNP	36123064	36123064	820	22	C	T	T	T	311	24	APOL5	2	2
ZBED4	9889	broad.mit.edu	37	22	50280790	50280790	+	Silent	SNP	G	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:50280790G>A	uc003bix.2	+	c.3480G>A	c.(3478-3480)TTG>TTA	p.L1160L		NM_014838	NP_055653	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	1160						cytoplasm|nucleus	DNA binding|metal ion binding|protein dimerization activity			ovary(2)	2		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)										0.520833	73.572537	73.590458	25	23	KEEP	---	---	---	---	capture		Silent	SNP	50280790	50280790	18104	22	G	A	A	A	581	45	ZBED4	2	2
PCDP1	200373	broad.mit.edu	37	2	120383238	120383238	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:120383238G>A	uc002tmb.2	+	c.632G>A	c.(631-633)GGC>GAC	p.G211D	PCDP1_uc010yyq.1_Missense_Mutation_p.G341D	NM_001029996	NP_001025167	Q4G0U5	PCDP1_HUMAN	primary ciliary dyskinesia protein 1	497						cilium	calmodulin binding				0	Colorectal(110;0.196)													0.225225	57.511541	65.214685	25	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	120383238	120383238	11992	2	G	A	A	A	546	42	PCDP1	2	2
CNTNAP5	129684	broad.mit.edu	37	2	125530480	125530480	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:125530480G>C	uc010flu.2	+	c.2638G>C	c.(2638-2640)GCT>CCT	p.A880P	CNTNAP5_uc002tno.2_Missense_Mutation_p.A879P	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	879	Laminin G-like 3.|Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)										0.233831	140.225927	153.252768	47	154	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125530480	125530480	3788	2	G	C	C	C	546	42	CNTNAP5	3	3
FAM123C	205147	broad.mit.edu	37	2	131521154	131521154	+	Silent	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:131521154C>A	uc002trw.2	+	c.1509C>A	c.(1507-1509)GCC>GCA	p.A503A	FAM123C_uc010fmv.2_Silent_p.A503A|FAM123C_uc010fms.1_Silent_p.A503A|FAM123C_uc010fmt.1_Silent_p.A503A|FAM123C_uc010fmu.1_Silent_p.A503A	NM_152698	NP_689911	Q8N944	F123C_HUMAN	hypothetical protein LOC205147	503										pancreas(2)|ovary(1)	3	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.13)										0.205128	16.475041	19.624028	8	31	KEEP	---	---	---	---	capture		Silent	SNP	131521154	131521154	5621	2	C	A	A	A	262	21	FAM123C	2	2
KYNU	8942	broad.mit.edu	37	2	143676236	143676236	+	Silent	SNP	T	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:143676236T>G	uc002tvl.2	+	c.228T>G	c.(226-228)CTT>CTG	p.L76L	KYNU_uc002tvk.2_Silent_p.L76L|KYNU_uc010fnm.2_Silent_p.L76L	NM_003937	NP_003928	Q16719	KYNU_HUMAN	kynureninase (L-kynurenine hydrolase) isoform a	76					anthranilate metabolic process|NAD biosynthetic process|quinolinate biosynthetic process|response to interferon-gamma|response to vitamin B6	cytosol|mitochondrion|soluble fraction	kynureninase activity|protein homodimerization activity			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.072)	L-Alanine(DB00160)|Pyridoxal Phosphate(DB00114)									0.3	20.943904	21.657607	6	14	KEEP	---	---	---	---	capture		Silent	SNP	143676236	143676236	8910	2	T	G	G	G	808	63	KYNU	4	4
NEB	4703	broad.mit.edu	37	2	152426724	152426724	+	Silent	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:152426724G>T	uc010fnx.2	-	c.12198C>A	c.(12196-12198)ATC>ATA	p.I4066I	NEB_uc002txr.2_Silent_p.I489I	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	4066	Nebulin 111.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(1)|skin(1)|pancreas(1)	19				BRCA - Breast invasive adenocarcinoma(221;0.219)										0.195652	17.345442	21.322363	9	37	KEEP	---	---	---	---	capture		Silent	SNP	152426724	152426724	10701	2	G	T	T	T	525	41	NEB	2	2
PRPF40A	55660	broad.mit.edu	37	2	153519649	153519649	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:153519649T>A	uc002tyh.3	-	c.2126A>T	c.(2125-2127)GAA>GTA	p.E709V	PRPF40A_uc002tyg.3_Missense_Mutation_p.E165V|PRPF40A_uc010zcd.1_Missense_Mutation_p.E660V	NM_017892	NP_060362	O75400	PR40A_HUMAN	formin binding protein 3	736					mRNA processing|RNA splicing	nuclear matrix|nuclear speck	protein binding				0														0.238095	10.664198	11.980625	5	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	153519649	153519649	13014	2	T	A	A	A	806	62	PRPF40A	3	3
KCNH7	90134	broad.mit.edu	37	2	163241275	163241275	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:163241275G>T	uc002uch.1	-	c.2885C>A	c.(2884-2886)GCA>GAA	p.A962E		NM_033272	NP_150375	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H,	962	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	protein binding|signal transducer activity			ovary(3)	3					Ibutilide(DB00308)	GBM(196;1492 2208 17507 24132 45496)								0.235	113.511864	126.367589	47	153	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	163241275	163241275	8342	2	G	T	T	T	598	46	KCNH7	2	2
CSRNP3	80034	broad.mit.edu	37	2	166532856	166532856	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:166532856C>A	uc002udf.2	+	c.443C>A	c.(442-444)GCC>GAC	p.A148D	CSRNP3_uc002udg.2_Missense_Mutation_p.A148D	NM_024969	NP_079245	Q8WYN3	CSRN3_HUMAN	cysteine-serine-rich nuclear protein 3	148					apoptosis|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|large_intestine(1)	4														0.268559	316.903444	339.06363	123	335	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	166532856	166532856	4106	2	C	A	A	A	338	26	CSRNP3	2	2
SCN9A	6335	broad.mit.edu	37	2	167133845	167133845	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:167133845C>G	uc010fpl.2	-	c.2489G>C	c.(2488-2490)CGA>CCA	p.R830P		NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha	841	II.|Helical; Voltage-sensor; Name=S4 of repeat II; (Potential).					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)	11					Lamotrigine(DB00555)|Lidocaine(DB00281)									0.220779	48.637713	54.160222	17	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167133845	167133845	14407	2	C	G	G	G	403	31	SCN9A	3	3
COL3A1	1281	broad.mit.edu	37	2	189871100	189871100	+	Silent	SNP	T	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:189871100T>A	uc002uqj.1	+	c.3123T>A	c.(3121-3123)GGT>GGA	p.G1041G		NM_000090	NP_000081	P02461	CO3A1_HUMAN	collagen type III alpha 1 preproprotein	1041	Triple-helical region.				axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway	collagen type III|extracellular space	extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding			central_nervous_system(7)|ovary(4)|large_intestine(2)	13			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)|Palifermin(DB00039)					1079				0.282353	62.566512	66.182514	24	61	KEEP	---	---	---	---	capture		Silent	SNP	189871100	189871100	3826	2	T	A	A	A	756	59	COL3A1	3	3
DNAH7	56171	broad.mit.edu	37	2	196671525	196671525	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:196671525C>A	uc002utj.3	-	c.10115G>T	c.(10114-10116)TGG>TTG	p.W3372L		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3372					ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(2)	2														0.337838	71.848808	73.571421	25	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	196671525	196671525	4789	2	C	A	A	A	273	21	DNAH7	2	2
TTLL4	9654	broad.mit.edu	37	2	219603497	219603497	+	Silent	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:219603497C>T	uc002viy.2	+	c.1098C>T	c.(1096-1098)CCC>CCT	p.P366P	TTLL4_uc010zkl.1_Silent_p.P201P|TTLL4_uc010fvx.2_Silent_p.P366P	NM_014640	NP_055455	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	366					protein polyglutamylation	cilium|microtubule basal body	ATP binding|tubulin binding|tubulin-tyrosine ligase activity			ovary(2)	2		Renal(207;0.0915)		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)		GBM(172;1818 2053 15407 20943 49753)								0.230337	89.964368	101.850354	41	137	KEEP	---	---	---	---	capture		Silent	SNP	219603497	219603497	17284	2	C	T	T	T	262	21	TTLL4	2	2
TCF23	150921	broad.mit.edu	37	2	27375674	27375674	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:27375674C>A	uc010ylg.1	+	c.584C>A	c.(583-585)CCT>CAT	p.P195H		NM_175769	NP_786951	Q7RTU1	TCF23_HUMAN	transcription factor 23	195					cell differentiation|muscle organ development	nucleus	transcription regulator activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.383621	258.958045	261.698734	89	143	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27375674	27375674	16218	2	C	A	A	A	312	24	TCF23	2	2
LHCGR	3973	broad.mit.edu	37	2	48950635	48950635	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:48950635C>T	uc002rwu.3	-	c.496G>A	c.(496-498)GGA>AGA	p.G166R	GTF2A1L_uc002rwt.2_Intron|LHCGR_uc002rwv.2_Non-coding_Transcript	NM_000233	NP_000224	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	166	Extracellular (Potential).|LRR 3.				male genitalia development|male gonad development	endosome|integral to plasma membrane	luteinizing hormone receptor activity			ovary(3)|breast(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)									0.369048	98.902418	100.168885	31	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48950635	48950635	9088	2	C	T	T	T	312	24	LHCGR	2	2
C3orf30	152405	broad.mit.edu	37	3	118865094	118865094	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:118865094G>T	uc003ecb.1	+	c.58G>T	c.(58-60)GCT>TCT	p.A20S	IGSF11_uc003eby.2_5'Flank|IGSF11_uc003ebz.2_5'Flank|IGSF11_uc010hqs.2_5'Flank|C3orf30_uc011biw.1_Missense_Mutation_p.A20S	NM_152539	NP_689752	Q96M34	CC030_HUMAN	hypothetical protein LOC152405	20										ovary(2)	2				GBM - Glioblastoma multiforme(114;0.222)										0.272727	32.285373	34.330894	12	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118865094	118865094	2313	3	G	T	T	T	494	38	C3orf30	1	1
GPR156	165829	broad.mit.edu	37	3	119886829	119886829	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:119886829G>T	uc011bjf.1	-	c.1495C>A	c.(1495-1497)CCA>ACA	p.P499T	GPR156_uc011bjg.1_Missense_Mutation_p.P495T	NM_153002	NP_694547	Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156	499	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.19)										0.279778	248.92112	264.664971	101	260	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	119886829	119886829	6936	3	G	T	T	T	533	41	GPR156	2	2
PRR23B	389151	broad.mit.edu	37	3	138738935	138738935	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:138738935C>T	uc003esy.1	-	c.569G>A	c.(568-570)CGG>CAG	p.R190Q		NM_001013650	NP_001013672	Q6ZRT6	PR23B_HUMAN	proline rich 23B	190	Pro-rich.									breast(1)	1														0.232759	67.371781	74.952432	27	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	138738935	138738935	13043	3	C	T	T	T	299	23	PRR23B	1	1
ZIC4	84107	broad.mit.edu	37	3	147114235	147114235	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:147114235C>T	uc011bno.1	-	c.242G>A	c.(241-243)GGC>GAC	p.G81D	ZIC4_uc003ewc.1_5'UTR|ZIC4_uc003ewd.1_Missense_Mutation_p.G31D	NM_032153	NP_115529	Q8N9L1	ZIC4_HUMAN	zinc finger protein of the cerebellum 4	31						nucleus	DNA binding|zinc ion binding				0														0.166667	17.547865	23.231453	9	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	147114235	147114235	18272	3	C	T	T	T	338	26	ZIC4	2	2
BCHE	590	broad.mit.edu	37	3	165547581	165547581	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:165547581C>G	uc003fem.3	-	c.1241G>C	c.(1240-1242)CGT>CCT	p.R414P	BCHE_uc003fen.3_Intron	NM_000055	NP_000046	P06276	CHLE_HUMAN	butyrylcholinesterase precursor	414			R -> C (in BChE deficiency).		acetylcholine catabolic process|choline metabolic process|cocaine metabolic process|synaptic transmission, cholinergic	endoplasmic reticulum lumen|extracellular space|membrane	acetylcholinesterase activity|beta-amyloid binding|cholinesterase activity|enzyme binding			ovary(3)|pancreas(1)	4					Ambenonium(DB01122)|Atropine(DB00572)|Bambuterol(DB01408)|Chlorpromazine(DB00477)|Choline(DB00122)|Cinnarizine(DB00568)|Demecarium bromide(DB00944)|Dibucaine(DB00527)|Donepezil(DB00843)|Echothiophate Iodide(DB01057)|Edrophonium(DB01010)|Ethopropazine(DB00392)|Etomidate(DB00292)|Galantamine(DB00674)|Hexafluronium bromide(DB00941)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Mivacurium(DB01226)|Neostigmine(DB01400)|Pancuronium(DB01337)|Pralidoxime(DB00733)|Procainamide(DB01035)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Succinylcholine(DB00202)|Terbutaline(DB00871)|Trimethaphan(DB01116)									0.198113	56.717213	65.707431	21	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	165547581	165547581	1379	3	C	G	G	G	247	19	BCHE	3	3
TFRC	7037	broad.mit.edu	37	3	195798322	195798322	+	Missense_Mutation	SNP	T	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:195798322T>G	uc003fvz.3	-	c.632A>C	c.(631-633)TAC>TCC	p.Y211S	TFRC_uc003fwa.3_Missense_Mutation_p.Y211S|TFRC_uc010hzy.2_Missense_Mutation_p.Y130S|TFRC_uc011btr.1_5'UTR	NM_003234	NP_003225	P02786	TFR1_HUMAN	transferrin receptor	211	Extracellular (Potential).				cellular iron ion homeostasis|endocytosis|interspecies interaction between organisms|proteolysis|transferrin transport|transmembrane transport	coated pit|endosome|integral to plasma membrane|melanosome	peptidase activity|transferrin receptor activity			ovary(3)	3	all_cancers(143;1.94e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.36e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.17e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00233)						680				0.289855	184.734914	192.915916	60	147	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	195798322	195798322	16340	3	T	G	G	G	741	57	TFRC	4	4
KAT2B	8850	broad.mit.edu	37	3	20164279	20164279	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:20164279G>A	uc003cbq.2	+	c.1396G>A	c.(1396-1398)GCA>ACA	p.A466T		NM_003884	NP_003875	Q92831	KAT2B_HUMAN	K(lysine) acetyltransferase 2B	466					cell cycle arrest|cellular response to insulin stimulus|chromatin remodeling|histone H3 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|negative regulation of cell proliferation|transcription initiation from RNA polymerase I promoter	Ada2/Gcn5/Ada3 transcription activator complex|chromatin remodeling complex|PCAF complex	cyclin-dependent protein kinase inhibitor activity|histone acetyltransferase activity|histone deacetylase binding|protein kinase binding|transcription coactivator activity|transcription factor binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.232877	41.860972	46.613977	17	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20164279	20164279	8286	3	G	A	A	A	442	34	KAT2B	2	2
RPL15	6138	broad.mit.edu	37	3	23960893	23960893	+	Silent	SNP	T	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:23960893T>A	uc003ccn.2	+	c.516T>A	c.(514-516)CGT>CGA	p.R172R	NKIRAS1_uc003cck.2_Intron|NKIRAS1_uc003ccj.2_5'Flank|NKIRAS1_uc003ccl.2_5'Flank|NKIRAS1_uc003ccm.2_5'Flank|RPL15_uc011awi.1_3'UTR|RPL15_uc011awj.1_Missense_Mutation_p.W117R|RPL15_uc003cco.2_Intron|RPL15_uc003ccp.2_Silent_p.R172R|RPL15_uc003ccq.2_Silent_p.R172R|RPL15_uc003ccr.2_Silent_p.R172R	NM_002948	NP_002939	P61313	RL15_HUMAN	ribosomal protein L15	172					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|ribosome	RNA binding|structural constituent of ribosome			ovary(1)	1														0.155844	24.653237	33.358201	12	65	KEEP	---	---	---	---	capture		Silent	SNP	23960893	23960893	14041	3	T	A	A	A	756	59	RPL15	3	3
EOMES	8320	broad.mit.edu	37	3	27759217	27759217	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:27759217G>A	uc003cdy.3	-	c.1462C>T	c.(1462-1464)CGG>TGG	p.R488W	EOMES_uc003cdx.2_Missense_Mutation_p.R469W|EOMES_uc010hfn.2_3'UTR|EOMES_uc011axc.1_Missense_Mutation_p.R193W	NM_005442	NP_005433	O95936	EOMES_HUMAN	eomesodermin	469					CD8-positive, alpha-beta T cell differentiation involved in immune response|cell differentiation involved in embryonic placenta development|endoderm formation|mesoderm formation|mesodermal to mesenchymal transition involved in gastrulation|regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription activator activity			ovary(3)|breast(1)	4														0.145985	31.015402	47.520503	20	117	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27759217	27759217	5340	3	G	A	A	A	480	37	EOMES	1	1
TRIM71	131405	broad.mit.edu	37	3	32933097	32933097	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:32933097G>T	uc003cff.2	+	c.2401G>T	c.(2401-2403)GCT>TCT	p.A801S		NM_001039111	NP_001034200	Q2Q1W2	LIN41_HUMAN	tripartite motif-containing 71	801	NHL 5.				multicellular organismal development	cytoplasm	zinc ion binding			ovary(2)|large_intestine(1)	3														0.174242	41.922577	55.174737	23	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32933097	32933097	17093	3	G	T	T	T	442	34	TRIM71	2	2
ITIH4	3700	broad.mit.edu	37	3	52858333	52858333	+	Splice_Site_SNP	SNP	T	G	G	rs113532241		TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:52858333T>G	uc011bem.1	-	c.1046_splice	c.e9-1	p.G349_splice	ITIH4_uc011bel.1_Splice_Site_SNP_p.G79_splice|ITIH4_uc003dfy.2_Splice_Site_SNP_p.G213_splice|ITIH4_uc011ben.1_Splice_Site_SNP_p.G349_splice|ITIH4_uc003dfz.2_Splice_Site_SNP_p.G349_splice	NM_002218	NP_002209			inter-alpha (globulin) inhibitor H4						acute-phase response|hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)										0.167808	102.195772	132.723238	49	243	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	52858333	52858333	8210	3	T	G	G	G	715	55	ITIH4	5	4
ROBO2	6092	broad.mit.edu	37	3	77651390	77651390	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:77651390G>T	uc003dpz.2	+	c.2896G>T	c.(2896-2898)GAT>TAT	p.D966Y	ROBO2_uc003dpy.3_Missense_Mutation_p.D962Y|ROBO2_uc011bgj.1_Non-coding_Transcript|ROBO2_uc011bgk.1_Missense_Mutation_p.D966Y|ROBO2_uc003dqa.2_Missense_Mutation_p.D89Y	NM_002942	NP_002933	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2	962	Cytoplasmic (Potential).				apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development	axolemma|cell surface|integral to membrane	axon guidance receptor activity|identical protein binding			lung(5)|ovary(1)|large_intestine(1)|liver(1)	8				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)						1049				0.279661	77.52226	82.677332	33	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77651390	77651390	13993	3	G	T	T	T	533	41	ROBO2	2	2
ANK2	287	broad.mit.edu	37	4	114275531	114275531	+	Silent	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:114275531C>A	uc003ibe.3	+	c.5757C>A	c.(5755-5757)TCC>TCA	p.S1919S	ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc011cgc.1_Intron|ANK2_uc003ibg.3_Intron|ANK2_uc003ibh.3_Intron|ANK2_uc011cgd.1_5'Flank|ANK2_uc011cgb.1_Silent_p.S1934S	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	1886	Repeat-rich region.|Repeat A.				axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)	13		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)										0.352941	100.86997	102.814863	36	66	KEEP	---	---	---	---	capture		Silent	SNP	114275531	114275531	624	4	C	A	A	A	288	23	ANK2	1	1
BBS7	55212	broad.mit.edu	37	4	122789195	122789195	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:122789195C>A	uc003ied.2	-	c.43G>T	c.(43-45)GTA>TTA	p.V15L	BBS7_uc003iee.1_Missense_Mutation_p.V15L	NM_176824	NP_789794	Q8IWZ6	BBS7_HUMAN	Bardet-Biedl syndrome 7 protein isoform a	15					cilium morphogenesis|digestive tract morphogenesis|fat cell differentiation|heart looping|melanosome transport|pigment granule aggregation in cell center|response to stimulus|visual perception	BBSome|cilium membrane|cytoplasm	protein binding			ovary(1)	1														0.39	112.200246	113.260664	39	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122789195	122789195	1362	4	C	A	A	A	260	20	BBS7	2	2
TRPC3	7222	broad.mit.edu	37	4	122846200	122846200	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:122846200T>A	uc003ieg.2	-	c.1149A>T	c.(1147-1149)AAA>AAT	p.K383N	TRPC3_uc010inr.2_Missense_Mutation_p.K310N|TRPC3_uc003ief.2_Missense_Mutation_p.K310N|TRPC3_uc011cgl.1_Missense_Mutation_p.K47N	NM_001130698	NP_001124170	Q13507	TRPC3_HUMAN	transient receptor potential cation channel,	298	Cytoplasmic (Potential).				axon guidance|phototransduction|platelet activation	integral to plasma membrane	protein binding|store-operated calcium channel activity			ovary(2)	2														0.300578	140.138019	146.281102	52	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122846200	122846200	17130	4	T	A	A	A	777	60	TRPC3	3	3
NKX3-2	579	broad.mit.edu	37	4	13544075	13544075	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:13544075C>G	uc003gmx.2	-	c.544G>C	c.(544-546)GGC>CGC	p.G182R		NM_001189	NP_001180	P78367	NKX32_HUMAN	NK3 homeobox 2	182	Poly-Gly.				negative regulation of chondrocyte differentiation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	RNA polymerase II transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0														0.4	10.598693	10.68585	4	6	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13544075	13544075	10859	4	C	G	G	G	299	23	NKX3-2	3	3
KIAA1211	57482	broad.mit.edu	37	4	57181002	57181002	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:57181002C>G	uc003hbk.2	+	c.1334C>G	c.(1333-1335)TCC>TGC	p.S445C	KIAA1211_uc010iha.2_Missense_Mutation_p.S438C|KIAA1211_uc011bzz.1_Missense_Mutation_p.S355C|KIAA1211_uc003hbm.1_Missense_Mutation_p.S331C	NM_020722	NP_065773	Q6ZU35	K1211_HUMAN	hypothetical protein LOC57482	445	Glu-rich.									ovary(1)|skin(1)	2	Glioma(25;0.08)|all_neural(26;0.101)													0.361111	44.465935	45.076881	13	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57181002	57181002	8523	4	C	G	G	G	390	30	KIAA1211	3	3
LPHN3	23284	broad.mit.edu	37	4	62598758	62598758	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:62598758C>G	uc010ihh.2	+	c.681C>G	c.(679-681)AAC>AAG	p.N227K	LPHN3_uc003hcq.3_Missense_Mutation_p.N227K|LPHN3_uc010ihg.1_Missense_Mutation_p.N295K|LPHN3_uc003hcs.1_Missense_Mutation_p.N56K	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor	227	Extracellular (Potential).|Olfactomedin-like.				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.288889	41.956212	43.754158	13	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62598758	62598758	9290	4	C	G	G	G	220	17	LPHN3	3	3
UGT2B4	7363	broad.mit.edu	37	4	70361226	70361226	+	Silent	SNP	T	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:70361226T>A	uc003hek.3	-	c.354A>T	c.(352-354)ACA>ACT	p.T118T	UGT2B4_uc011cap.1_Intron|UGT2B4_uc003hel.3_Silent_p.T118T	NM_021139	NP_066962	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2B4 precursor	118					estrogen catabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity				0														0.25	8.619583	9.301005	3	9	KEEP	---	---	---	---	capture		Silent	SNP	70361226	70361226	17519	4	T	A	A	A	652	51	UGT2B4	3	3
ADAMTS3	9508	broad.mit.edu	37	4	73164047	73164047	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:73164047G>T	uc003hgk.1	-	c.2537C>A	c.(2536-2538)ACT>AAT	p.T846N	ADAMTS3_uc003hgl.2_Missense_Mutation_p.T187N	NM_014243	NP_055058	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1	846	TSP type-1 2.				collagen catabolic process|collagen fibril organization|proteolysis	proteinaceous extracellular matrix	heparin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			NSCLC(168;1941 2048 2918 13048 43078)								0.308824	61.248567	63.463905	21	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73164047	73164047	268	4	G	T	T	T	468	36	ADAMTS3	2	2
ACOX3	8310	broad.mit.edu	37	4	8407759	8407759	+	Silent	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:8407759C>A	uc010idk.2	-	c.699G>T	c.(697-699)CCG>CCT	p.P233P	ACOX3_uc003glc.3_Silent_p.P233P|ACOX3_uc003gld.3_Silent_p.P233P|ACOX3_uc003gle.1_Silent_p.P138P	NM_003501	NP_003492	O15254	ACOX3_HUMAN	acyl-Coenzyme A oxidase 3 isoform a	233					bile acid metabolic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|pristanoyl-CoA oxidase activity			central_nervous_system(1)	1														0.246696	149.650327	162.867796	56	171	KEEP	---	---	---	---	capture		Silent	SNP	8407759	8407759	161	4	C	A	A	A	392	31	ACOX3	1	1
PCDHB7	56129	broad.mit.edu	37	5	140554050	140554050	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140554050C>T	uc003lit.2	+	c.1634C>T	c.(1633-1635)GCG>GTG	p.A545V		NM_018940	NP_061763	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7 precursor	545	Extracellular (Potential).|Cadherin 5.				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|central_nervous_system(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.294118	71.145315	74.995274	30	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140554050	140554050	11967	5	C	T	T	T	351	27	PCDHB7	1	1
PCDHB9	56127	broad.mit.edu	37	5	140568110	140568110	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140568110G>T	uc003liw.1	+	c.1219G>T	c.(1219-1221)GGT>TGT	p.G407C		NM_019119	NP_061992	Q9Y5E1	PCDB9_HUMAN	protocadherin beta 9 precursor	407	Extracellular (Potential).|Cadherin 4.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.388535	172.142156	173.849798	61	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140568110	140568110	11969	5	G	T	T	T	451	35	PCDHB9	2	2
PCDHB11	56125	broad.mit.edu	37	5	140579492	140579492	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140579492G>T	uc003liy.2	+	c.145G>T	c.(145-147)GCA>TCA	p.A49S	PCDHB11_uc011daj.1_Intron	NM_018931	NP_061754	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11 precursor	49	Extracellular (Potential).|Cadherin 1.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.168605	50.703408	68.569271	29	143	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140579492	140579492	11956	5	G	T	T	T	546	42	PCDHB11	2	2
PCDHGA5	56110	broad.mit.edu	37	5	140744543	140744543	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140744543G>T	uc003lju.1	+	c.646G>T	c.(646-648)GAT>TAT	p.D216Y	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc011das.1_Missense_Mutation_p.D216Y	NM_018918	NP_061741	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5 isoform 1	216	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.225806	46.520085	52.947016	21	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140744543	140744543	11977	5	G	T	T	T	429	33	PCDHGA5	2	2
ARHGEF37	389337	broad.mit.edu	37	5	148989214	148989214	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:148989214G>T	uc003lra.1	+	c.414G>T	c.(412-414)GAG>GAT	p.E138D		NM_001001669	NP_001001669	A1IGU5	ARH37_HUMAN	hypothetical protein LOC389337	138	DH.				regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity				0														0.375839	156.957621	158.975875	56	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	148989214	148989214	921	5	G	T	T	T	438	34	ARHGEF37	2	2
ANXA6	309	broad.mit.edu	37	5	150483150	150483150	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:150483150G>A	uc003ltl.1	-	c.1943C>T	c.(1942-1944)TCT>TTT	p.S648F	ANXA6_uc011dcp.1_Missense_Mutation_p.S616F|ANXA6_uc003ltm.1_Missense_Mutation_p.S642F|ANXA6_uc003ltn.1_Missense_Mutation_p.S435F|ANXA6_uc003lto.1_Missense_Mutation_p.S235F	NM_001155	NP_001146	P08133	ANXA6_HUMAN	annexin VI isoform 1	648	Annexin 8.					melanosome	calcium ion binding|calcium-dependent phospholipid binding|protein binding				0		Medulloblastoma(196;0.0912)|all_hematologic(541;0.208)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)											0.189189	14.501699	17.847034	7	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150483150	150483150	730	5	G	A	A	A	429	33	ANXA6	2	2
NKX2-5	1482	broad.mit.edu	37	5	172659670	172659670	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:172659670C>T	uc003mcm.1	-	c.877G>A	c.(877-879)GTG>ATG	p.V293M		NM_004387	NP_004378	P52952	NKX25_HUMAN	NK2 transcription factor related, locus 5	293					adult heart development|atrial cardiac muscle cell development|atrial septum morphogenesis|heart looping|hemopoiesis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cardiac muscle cell apoptosis|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of myotube differentiation|pharyngeal system development|positive regulation of calcium ion transport via voltage-gated calcium channel activity|positive regulation of cardioblast differentiation|positive regulation of cell proliferation|positive regulation of heart contraction|positive regulation of neuron differentiation|positive regulation of sodium ion transport|positive regulation of survival gene product expression|positive regulation of transcription initiation from RNA polymerase II promoter|positive regulation of transcription via serum response element binding|regulation of cardiac muscle contraction|septum secundum development|spleen development|thyroid gland development|tongue development|vasculogenesis|ventricular septum morphogenesis	transcription factor complex	chromatin binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|serum response element binding|transcription activator activity|transcription factor binding|transcription repressor activity			central_nervous_system(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			Esophageal Squamous(72;810 1219 2387 13420 44943)								0.395349	49.663532	50.076238	17	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	172659670	172659670	10855	5	C	T	T	T	247	19	NKX2-5	1	1
DRD1	1812	broad.mit.edu	37	5	174870043	174870043	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:174870043G>T	uc003mcz.2	-	c.60C>A	c.(58-60)TTC>TTA	p.F20L		NM_000794	NP_000785	P21728	DRD1_HUMAN	dopamine receptor D1	20	Extracellular (Potential).				activation of adenylate cyclase activity by dopamine receptor signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|adult walking behavior|cerebral cortex GABAergic interneuron migration|dopamine metabolic process|elevation of cytosolic calcium ion concentration involved in G-protein signaling coupled to IP3 second messenger|mating behavior|positive regulation of cAMP biosynthetic process|positive regulation of cell migration|positive regulation of potassium ion transport|positive regulation of release of sequestered calcium ion into cytosol|positive regulation of synaptic transmission, glutamatergic|prepulse inhibition|regulation of dopamine uptake|response to drug|synapse assembly|visual learning	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction	protein binding			ovary(2)	2	all_cancers(89;0.00895)|Renal(175;0.000159)|Lung NSC(126;0.00625)|all_lung(126;0.0104)	Medulloblastoma(196;0.0208)|all_neural(177;0.0277)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)		Acetophenazine(DB01063)|Amantadine(DB00915)|Apomorphine(DB00714)|Carphenazine(DB01038)|Chlorprothixene(DB01239)|Clozapine(DB00363)|Cocaine(DB00907)|Dopamine(DB00988)|Fenoldopam(DB00800)|Flupenthixol(DB00875)|Fluphenazine(DB00623)|Haloperidol(DB00502)|Levodopa(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methylergonovine(DB00353)|Minaprine(DB00805)|Olanzapine(DB00334)|Pegademase bovine(DB00061)|Pergolide(DB01186)|Perphenazine(DB00850)|Prochlorperazine(DB00433)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Thiethylperazine(DB00372)|Thioridazine(DB00679)|Triflupromazine(DB00508)|Zuclopenthixol(DB01624)									0.342246	166.149286	170.258052	64	123	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	174870043	174870043	4940	5	G	T	T	T	425	33	DRD1	2	2
SFXN1	94081	broad.mit.edu	37	5	174936182	174936182	+	Silent	SNP	A	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:174936182A>T	uc003mda.2	+	c.312A>T	c.(310-312)ACA>ACT	p.T104T	SFXN1_uc003mdb.1_Silent_p.T43T	NM_022754	NP_073591	Q9H9B4	SFXN1_HUMAN	sideroflexin 1	104	Helical; (Potential).				iron ion homeostasis	integral to membrane	cation transmembrane transporter activity|protein binding			ovary(1)	1	all_cancers(89;0.00922)|Renal(175;0.000269)|Lung NSC(126;0.00515)|all_lung(126;0.00873)	Medulloblastoma(196;0.0399)|all_neural(177;0.0663)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)											0.218487	191.058317	217.129267	78	279	KEEP	---	---	---	---	capture		Silent	SNP	174936182	174936182	14685	5	A	T	T	T	80	7	SFXN1	3	3
FGFR4	2264	broad.mit.edu	37	5	176517431	176517431	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:176517431G>T	uc003mfl.2	+	c.132G>T	c.(130-132)GAG>GAT	p.E44D	FGFR4_uc003mfm.2_Missense_Mutation_p.E44D|FGFR4_uc011dfu.1_Missense_Mutation_p.E44D|FGFR4_uc011dfv.1_Non-coding_Transcript|FGFR4_uc003mfn.1_Missense_Mutation_p.E44D|FGFR4_uc011dfw.1_Missense_Mutation_p.E44D|FGFR4_uc003mfo.2_Missense_Mutation_p.E44D	NM_002011	NP_002002	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4 isoform 1	44	Ig-like C2-type 1.|Extracellular (Potential).				insulin receptor signaling pathway|positive regulation of cell proliferation|protein phosphorylation	integral to plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor receptor activity			lung(10)|breast(1)|central_nervous_system(1)|skin(1)	13	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)					219	TSP Lung(9;0.080)			0.445946	91.64968	91.839943	33	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	176517431	176517431	6105	5	G	T	T	T	438	34	FGFR4	2	2
GRM6	2916	broad.mit.edu	37	5	178410147	178410147	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:178410147C>G	uc003mjr.2	-	c.2200G>C	c.(2200-2202)GAC>CAC	p.D734H	GRM6_uc003mjq.2_Missense_Mutation_p.D137H	NM_000843	NP_000834	O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6 precursor	734	Extracellular (Potential).				detection of visible light|visual perception	integral to plasma membrane				ovary(2)|breast(1)|pancreas(1)	4	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)										0.183908	40.250082	48.40383	16	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	178410147	178410147	7080	5	C	G	G	G	390	30	GRM6	3	3
PRDM9	56979	broad.mit.edu	37	5	23527673	23527673	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:23527673C>A	uc003jgo.2	+	c.2476C>A	c.(2476-2478)CAC>AAC	p.H826N		NM_020227	NP_064612	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	826	C2H2-type 12.				meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleoplasm	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)|large_intestine(2)|pancreas(1)	6														0.295858	245.887934	258.684025	100	238	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23527673	23527673	12906	5	C	A	A	A	221	17	PRDM9	2	2
C6	729	broad.mit.edu	37	5	41160437	41160437	+	Silent	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:41160437G>T	uc003jmk.2	-	c.1491C>A	c.(1489-1491)ATC>ATA	p.I497I	C6_uc003jml.1_Silent_p.I497I	NM_000065	NP_000056	P13671	CO6_HUMAN	complement component 6 precursor	497	MACPF.				complement activation, classical pathway|cytolysis|innate immune response	membrane attack complex	protein binding			ovary(3)|central_nervous_system(2)	5		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)												0.300493	152.079157	159.307813	61	142	KEEP	---	---	---	---	capture		Silent	SNP	41160437	41160437	2416	5	G	T	T	T	525	41	C6	2	2
BHMT	635	broad.mit.edu	37	5	78426859	78426859	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:78426859G>T	uc003kfu.3	+	c.1141G>T	c.(1141-1143)GAG>TAG	p.E381*	BHMT_uc011cti.1_Nonsense_Mutation_p.E228*	NM_001713	NP_001704	Q93088	BHMT1_HUMAN	betaine-homocysteine methyltransferase	381					protein methylation|regulation of homocysteine metabolic process	cytoplasm	betaine-homocysteine S-methyltransferase activity|homocysteine S-methyltransferase activity|zinc ion binding			ovary(1)	1		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.88e-45)|Epithelial(54;8.07e-41)|all cancers(79;3.51e-36)	L-Methionine(DB00134)									0.349282	206.002498	210.195773	73	136	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	78426859	78426859	1450	5	G	T	T	T	481	37	BHMT	5	1
MSH3	4437	broad.mit.edu	37	5	80021292	80021292	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:80021292G>T	uc003kgz.2	+	c.1361G>T	c.(1360-1362)CGA>CTA	p.R454L		NM_002439	NP_002430	P20585	MSH3_HUMAN	mutS homolog 3	454					maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding			ovary(1)	1		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		Melanoma(88;1010 1399 13793 26548 36275)				1101				0.184524	73.235658	88.908713	31	137	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80021292	80021292	10264	5	G	T	T	T	481	37	MSH3	1	1
POLR3G	10622	broad.mit.edu	37	5	89802489	89802489	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:89802489G>C	uc003kjq.2	+	c.583G>C	c.(583-585)GAG>CAG	p.E195Q	POLR3G_uc011cuc.1_Missense_Mutation_p.E195Q	NM_006467	NP_006458	O15318	RPC7_HUMAN	polymerase (RNA) III (DNA directed) polypeptide	195	Glu-rich.				innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|regulation of transcription from RNA polymerase III promoter|response to virus	DNA-directed RNA polymerase III complex	DNA-directed RNA polymerase activity				0		all_cancers(142;5.03e-09)|all_epithelial(76;1.23e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(54;2.74e-31)|Epithelial(54;8.2e-26)|all cancers(79;3.86e-22)										0.128205	17.896628	28.400986	10	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	89802489	89802489	12662	5	G	C	C	C	429	33	POLR3G	3	3
GRIK2	2898	broad.mit.edu	37	6	102124642	102124642	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:102124642A>T	uc003pqp.3	+	c.686A>T	c.(685-687)GAT>GTT	p.D229V	GRIK2_uc003pqn.2_Missense_Mutation_p.D229V|GRIK2_uc003pqo.3_Missense_Mutation_p.D229V|GRIK2_uc010kcw.2_Missense_Mutation_p.D229V	NM_021956	NP_068775	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	229	Extracellular (Potential).				glutamate signaling pathway|induction of programmed cell death in response to chemical stimulus|neuron apoptosis|positive regulation of synaptic transmission|regulation of short-term neuronal synaptic plasticity	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|breast(1)|pancreas(1)	4		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	L-Glutamic Acid(DB00142)									0.176471	11.935193	15.284679	6	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102124642	102124642	7053	6	A	T	T	T	156	12	GRIK2	3	3
LAMA4	3910	broad.mit.edu	37	6	112452206	112452206	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:112452206A>T	uc003pvu.2	-	c.3932T>A	c.(3931-3933)CTG>CAG	p.L1311Q	LAMA4_uc003pvv.2_Missense_Mutation_p.L1304Q|LAMA4_uc003pvt.2_Missense_Mutation_p.L1304Q	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor	1311	Laminin G-like 3.				cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)										0.22	26.797396	30.407937	11	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112452206	112452206	8931	6	A	T	T	T	91	7	LAMA4	3	3
PLG	5340	broad.mit.edu	37	6	161152090	161152090	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:161152090A>T	uc003qtm.3	+	c.1264A>T	c.(1264-1266)ACA>TCA	p.T422S		NM_000301	NP_000292	P00747	PLMN_HUMAN	plasminogen	422	Kringle 4.				extracellular matrix disassembly|fibrinolysis|negative regulation of cell proliferation|negative regulation of cell-substrate adhesion|negative regulation of fibrinolysis|platelet activation|platelet degranulation|positive regulation of fibrinolysis|proteolysis|tissue remodeling	extracellular space|extrinsic to external side of plasma membrane|platelet alpha granule lumen	apolipoprotein binding|cell surface binding|serine-type endopeptidase activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Aminocaproic Acid(DB00513)|Streptokinase(DB00086)|Tranexamic Acid(DB00302)|Urokinase(DB00013)									0.301775	132.366429	138.293012	51	118	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	161152090	161152090	12512	6	A	T	T	T	130	10	PLG	3	3
BRP44L	51660	broad.mit.edu	37	6	166779514	166779514	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:166779514C>A	uc011egn.1	-	c.253G>T	c.(253-255)GCA>TCA	p.A85S	BRP44L_uc003qva.2_Non-coding_Transcript	NM_016098	NP_057182	Q9Y5U8	BR44L_HUMAN	brain protein 44-like	85						mitochondrion				central_nervous_system(1)	1		Breast(66;0.000148)|Prostate(117;0.109)|Ovarian(120;0.199)		OV - Ovarian serous cystadenocarcinoma(33;1.8e-19)|BRCA - Breast invasive adenocarcinoma(81;4.68e-06)|GBM - Glioblastoma multiforme(31;0.000122)										0.152778	20.700389	28.987773	11	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	166779514	166779514	1550	6	C	A	A	A	351	27	BRP44L	1	1
OR2B3	442184	broad.mit.edu	37	6	29054376	29054376	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:29054376G>T	uc003nlx.2	-	c.650C>A	c.(649-651)TCC>TAC	p.S217Y		NM_001005226	NP_001005226			olfactory receptor, family 2, subfamily B,												0														0.265823	101.969609	109.805093	42	116	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29054376	29054376	11396	6	G	T	T	T	533	41	OR2B3	2	2
CCHCR1	54535	broad.mit.edu	37	6	31112700	31112700	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:31112700C>A	uc003nsp.3	-	c.2027G>T	c.(2026-2028)CGG>CTG	p.R676L	CCHCR1_uc011dne.1_Missense_Mutation_p.R587L|CCHCR1_uc003nsq.3_Missense_Mutation_p.R640L|CCHCR1_uc003nsr.3_Missense_Mutation_p.R587L|CCHCR1_uc010jsk.1_Missense_Mutation_p.R587L	NM_001105564	NP_001099034	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1 isoform	587	Potential.				cell differentiation|multicellular organismal development	cytoplasm|nucleus	protein binding				0														0.385246	137.348908	138.737931	47	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31112700	31112700	3002	6	C	A	A	A	299	23	CCHCR1	1	1
TEAD3	7005	broad.mit.edu	37	6	35445092	35445092	+	Silent	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:35445092G>T	uc003oku.3	-	c.588C>A	c.(586-588)CTC>CTA	p.L196L	TEAD3_uc003okt.2_Silent_p.L85L|TEAD3_uc010jvx.2_Silent_p.L136L	NM_003214	NP_003205	Q99594	TEAD3_HUMAN	TEA domain family member 3	196	Pro-rich.|Transcriptional activation (Potential).				female pregnancy|hippo signaling cascade		DNA binding|protein binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding transcription factor activity			ovary(1)	1														0.163265	14.664918	19.948946	8	41	KEEP	---	---	---	---	capture		Silent	SNP	35445092	35445092	16267	6	G	T	T	T	574	45	TEAD3	2	2
DST	667	broad.mit.edu	37	6	56358869	56358869	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:56358869T>A	uc003pdf.2	-	c.13976A>T	c.(13975-13977)CAA>CTA	p.Q4659L	DST_uc003pcz.3_Missense_Mutation_p.Q4481L|DST_uc011dxj.1_Missense_Mutation_p.Q4510L|DST_uc011dxk.1_Missense_Mutation_p.Q4521L|DST_uc003pcy.3_Missense_Mutation_p.Q4155L|DST_uc003pda.3_5'Flank	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	6567	Spectrin 16.				cell adhesion|cell cycle arrest|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization	basement membrane|cytoplasmic membrane-bounded vesicle|hemidesmosome|microtubule plus end|nucleus	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein C-terminus binding			ovary(7)|central_nervous_system(6)	13	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)							2498				0.264706	45.618459	49.022128	18	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56358869	56358869	4967	6	T	A	A	A	819	63	DST	3	3
F13A1	2162	broad.mit.edu	37	6	6224937	6224937	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:6224937C>A	uc003mwv.2	-	c.955G>T	c.(955-957)GCT>TCT	p.A319S	F13A1_uc011dib.1_Missense_Mutation_p.A256S	NM_000129	NP_000120	P00488	F13A_HUMAN	coagulation factor XIII A1 subunit precursor	319					peptide cross-linking|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)									0.190244	80.083729	98.499796	39	166	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6224937	6224937	5534	6	C	A	A	A	325	25	F13A1	2	2
UBE2J1	51465	broad.mit.edu	37	6	90039406	90039406	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:90039406C>A	uc010kcb.2	-	c.949G>T	c.(949-951)GAG>TAG	p.E317*	UBE2J1_uc003pnc.2_Nonsense_Mutation_p.E317*	NM_016021	NP_057105	Q9Y385	UB2J1_HUMAN	ubiquitin-conjugating enzyme E2, J1	317	Lumenal (Potential).				post-translational protein modification	endoplasmic reticulum membrane|integral to membrane	ATP binding|ubiquitin-protein ligase activity				0		all_cancers(76;1.65e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;2.5e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0139)										0.327273	45.824826	47.283451	18	37	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	90039406	90039406	17417	6	C	A	A	A	377	29	UBE2J1	5	2
CTTNBP2	83992	broad.mit.edu	37	7	117359591	117359591	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:117359591C>A	uc003vjf.2	-	c.4611G>T	c.(4609-4611)ATG>ATT	p.M1537I		NM_033427	NP_219499	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1537										ovary(4)	4	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)										0.264516	109.597294	117.372221	41	114	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117359591	117359591	4204	7	C	A	A	A	221	17	CTTNBP2	2	2
SPAM1	6677	broad.mit.edu	37	7	123599549	123599549	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:123599549G>T	uc003vle.2	+	c.1056G>T	c.(1054-1056)TTG>TTT	p.L352F	SPAM1_uc011koa.1_Missense_Mutation_p.L8F|SPAM1_uc003vld.2_Missense_Mutation_p.L352F|SPAM1_uc003vlf.3_Missense_Mutation_p.L352F|SPAM1_uc010lku.2_Missense_Mutation_p.L352F	NM_003117	NP_003108	P38567	HYALP_HUMAN	sperm adhesion molecule 1 isoform 1	352					binding of sperm to zona pellucida|carbohydrate metabolic process|cell adhesion|fusion of sperm to egg plasma membrane	anchored to membrane|plasma membrane	hyalurononglucosaminidase activity			ovary(3)|kidney(1)	4					Hyaluronidase(DB00070)									0.255814	27.807607	30.131141	11	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123599549	123599549	15489	7	G	T	T	T	594	46	SPAM1	2	2
OR2A5	393046	broad.mit.edu	37	7	143748183	143748183	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:143748183C>A	uc011ktw.1	+	c.689C>A	c.(688-690)TCT>TAT	p.S230Y		NM_012365	NP_036497	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A,	230	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3	Melanoma(164;0.0783)													0.290323	153.406924	161.976524	63	154	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	143748183	143748183	11387	7	C	A	A	A	416	32	OR2A5	2	2
OR2A14	135941	broad.mit.edu	37	7	143826247	143826247	+	Silent	SNP	G	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:143826247G>A	uc011kua.1	+	c.42G>A	c.(40-42)CCG>CCA	p.P14P		NM_001001659	NP_001001659	Q96R47	O2A14_HUMAN	olfactory receptor, family 2, subfamily A,	14	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Melanoma(164;0.0783)													0.278261	84.367667	89.444083	32	83	KEEP	---	---	---	---	capture		Silent	SNP	143826247	143826247	11382	7	G	A	A	A	483	38	OR2A14	1	1
SSPO	23145	broad.mit.edu	37	7	149519646	149519646	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:149519646G>C	uc010lpk.2	+	c.13136G>C	c.(13135-13137)TGC>TCC	p.C4379S	SSPO_uc010lpm.1_Intron|SSPO_uc003wgg.2_Intron|SSPO_uc003wgh.2_Non-coding_Transcript|SSPO_uc003wgi.1_Intron	NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	4379	TSP type-1 22.				cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)											0.238095	15.766204	17.080539	5	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	149519646	149519646	15705	7	G	C	C	C	598	46	SSPO	3	3
GIMAP8	155038	broad.mit.edu	37	7	150171185	150171185	+	Silent	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:150171185C>T	uc003whj.2	+	c.768C>T	c.(766-768)CGC>CGT	p.R256R		NM_175571	NP_783161	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	256						endoplasmic reticulum|Golgi apparatus|mitochondrion	GTP binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)										0.234637	95.251595	106.790456	42	137	KEEP	---	---	---	---	capture		Silent	SNP	150171185	150171185	6653	7	C	T	T	T	340	27	GIMAP8	1	1
AMZ1	155185	broad.mit.edu	37	7	2748319	2748319	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:2748319C>A	uc003smr.1	+	c.570C>A	c.(568-570)AGC>AGA	p.S190R	AMZ1_uc003sms.1_Missense_Mutation_p.S190R|AMZ1_uc011jwa.1_5'UTR	NM_133463	NP_597720	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	190							metallopeptidase activity|zinc ion binding				0		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)										0.5	294.336972	294.336972	101	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2748319	2748319	599	7	C	A	A	A	363	28	AMZ1	2	2
ABCA13	154664	broad.mit.edu	37	7	48443360	48443360	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:48443360C>T	uc003toq.2	+	c.11954C>T	c.(11953-11955)TCC>TTC	p.S3985F	ABCA13_uc010kys.1_Missense_Mutation_p.S1059F|ABCA13_uc003tos.1_Missense_Mutation_p.S811F|ABCA13_uc010kyt.1_Non-coding_Transcript	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	3985	ABC transporter 1.				transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10														0.421687	100.894245	101.341645	35	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48443360	48443360	32	7	C	T	T	T	390	30	ABCA13	2	2
KLHL38	340359	broad.mit.edu	37	8	124664403	124664403	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:124664403G>A	uc003yqs.1	-	c.764C>T	c.(763-765)GCC>GTC	p.A255V		NM_001081675	NP_001075144	Q2WGJ6	KLH38_HUMAN	kelch-like 38	255											0														0.165468	40.641321	55.400345	23	116	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124664403	124664403	8704	8	G	A	A	A	546	42	KLHL38	2	2
WRN	7486	broad.mit.edu	37	8	30999265	30999265	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:30999265G>T	uc003xio.3	+	c.3207G>T	c.(3205-3207)TTG>TTT	p.L1069F	WRN_uc010lvk.2_Missense_Mutation_p.L536F	NM_000553	NP_000544	Q14191	WRN_HUMAN	Werner syndrome protein	1069					base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance	centrosome|nucleolus|nucleoplasm	3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding			ovary(2)|kidney(2)|large_intestine(1)	5		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		Ovarian(18;161 598 2706 14834 27543)				832				0.210526	21.804821	26.308932	12	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30999265	30999265	17976	8	G	T	T	T	620	48	WRN	2	2
ANK1	286	broad.mit.edu	37	8	41563717	41563717	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:41563717C>T	uc003xom.2	-	c.2140G>A	c.(2140-2142)GTT>ATT	p.V714I	NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoh.2_5'UTR|ANK1_uc003xoi.2_Missense_Mutation_p.V681I|ANK1_uc003xoj.2_Missense_Mutation_p.V681I|ANK1_uc003xok.2_Missense_Mutation_p.V681I|ANK1_uc003xol.2_Missense_Mutation_p.V681I	NM_001142446	NP_001135918	P16157	ANK1_HUMAN	ankyrin 1 isoform 9	681	ANK 20.|89 kDa domain.				axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|lung(2)|central_nervous_system(2)|breast(1)	8	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)											0.207547	24.895416	29.095921	11	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41563717	41563717	623	8	C	T	T	T	247	19	ANK1	1	1
RP1	6101	broad.mit.edu	37	8	55541741	55541741	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:55541741G>T	uc003xsd.1	+	c.5299G>T	c.(5299-5301)GCA>TCA	p.A1767S	RP1_uc011ldy.1_Intron	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	1767					cell projection organization|intracellular signal transduction|phototransduction, visible light|visual perception	cilium axoneme|cytoplasm|microtubule|photoreceptor connecting cilium|photoreceptor outer segment				ovary(4)|pancreas(1)	5		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			Colon(91;1014 1389 7634 14542 40420)								0.261364	57.872793	62.418	23	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55541741	55541741	14011	8	G	T	T	T	598	46	RP1	2	2
RP1	6101	broad.mit.edu	37	8	55542007	55542007	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:55542007G>T	uc003xsd.1	+	c.5565G>T	c.(5563-5565)AAG>AAT	p.K1855N	RP1_uc011ldy.1_Intron	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	1855					cell projection organization|intracellular signal transduction|phototransduction, visible light|visual perception	cilium axoneme|cytoplasm|microtubule|photoreceptor connecting cilium|photoreceptor outer segment				ovary(4)|pancreas(1)	5		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			Colon(91;1014 1389 7634 14542 40420)								0.123077	8.648988	17.692939	8	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55542007	55542007	14011	8	G	T	T	T	451	35	RP1	2	2
PREX2	80243	broad.mit.edu	37	8	68956798	68956798	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:68956798G>A	uc003xxv.1	+	c.916G>A	c.(916-918)GAA>AAA	p.E306K	PREX2_uc003xxu.1_Missense_Mutation_p.E306K|PREX2_uc011lez.1_Missense_Mutation_p.E241K	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a	306	PH.				G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			large_intestine(4)|pancreas(3)|lung(2)|skin(2)|ovary(1)|kidney(1)	13										1011				0.195652	37.392219	45.34088	18	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	68956798	68956798	12920	8	G	A	A	A	533	41	PREX2	2	2
ZFHX4	79776	broad.mit.edu	37	8	77763196	77763196	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:77763196G>T	uc003yav.2	+	c.3904G>T	c.(3904-3906)GAG>TAG	p.E1302*	ZFHX4_uc003yau.1_Nonsense_Mutation_p.E1347*|ZFHX4_uc003yaw.1_Nonsense_Mutation_p.E1302*	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1302					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)											0.272727	28.377172	30.428225	12	32	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	77763196	77763196	18223	8	G	T	T	T	533	41	ZFHX4	5	2
TMEM55A	55529	broad.mit.edu	37	8	92033633	92033633	+	Splice_Site_SNP	SNP	C	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:92033633C>G	uc003yes.2	-	c.107_splice	c.e2-1	p.A36_splice		NM_018710	NP_061180			transmembrane protein 55A							integral to membrane|late endosome membrane|lysosomal membrane	hydrolase activity				0			BRCA - Breast invasive adenocarcinoma(11;0.033)											0.217391	67.911958	76.380004	25	90	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	92033633	92033633	16720	8	C	G	G	G	364	28	TMEM55A	5	3
KCNS2	3788	broad.mit.edu	37	8	99440446	99440446	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:99440446A>G	uc003yin.2	+	c.239A>G	c.(238-240)TAC>TGC	p.Y80C		NM_020697	NP_065748	Q9ULS6	KCNS2_HUMAN	potassium voltage-gated channel,	80	Cytoplasmic (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)	1	Breast(36;2.4e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.0448)			Pancreas(138;844 2489 9202 24627)								0.465863	416.801339	417.05143	116	133	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99440446	99440446	8394	8	A	G	G	G	182	14	KCNS2	4	4
OR13D1	286365	broad.mit.edu	37	9	107457252	107457252	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:107457252G>A	uc011lvs.1	+	c.550G>A	c.(550-552)GGC>AGC	p.G184S		NM_001004484	NP_001004484	Q8NGV5	O13D1_HUMAN	olfactory receptor, family 13, subfamily D,	184	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.161677	55.922041	74.099515	27	140	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107457252	107457252	11346	9	G	A	A	A	455	35	OR13D1	2	2
PTPN3	5774	broad.mit.edu	37	9	112141905	112141905	+	Nonsense_Mutation	SNP	G	C	C			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:112141905G>C	uc004bed.2	-	c.2673C>G	c.(2671-2673)TAC>TAG	p.Y891*	PTPN3_uc004beb.2_Nonsense_Mutation_p.Y760*|PTPN3_uc004bec.2_Nonsense_Mutation_p.Y715*|PTPN3_uc010mtu.2_Non-coding_Transcript|PTPN3_uc011lwg.1_Nonsense_Mutation_p.Y846*|PTPN3_uc011lwh.1_Nonsense_Mutation_p.Y737*|PTPN3_uc011lwd.1_Nonsense_Mutation_p.Y359*|PTPN3_uc011lwe.1_Nonsense_Mutation_p.Y604*|PTPN3_uc011lwf.1_Nonsense_Mutation_p.Y559*	NM_002829	NP_002820	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type	891	Tyrosine-protein phosphatase.				negative regulation of membrane protein ectodomain proteolysis|negative regulation of mitotic cell cycle	cytoplasm|cytoskeleton|internal side of plasma membrane	ATPase binding|cytoskeletal protein binding|phosphotyrosine binding|protein tyrosine phosphatase activity			ovary(3)	3														0.313253	84.50649	87.090737	26	57	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	112141905	112141905	13246	9	G	C	C	C	620	48	PTPN3	5	3
KIAA0368	23392	broad.mit.edu	37	9	114176921	114176921	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:114176921T>A	uc004bfe.1	-	c.2309A>T	c.(2308-2310)TAC>TTC	p.Y770F	KIAA0368_uc010muc.1_Missense_Mutation_p.Y592F	NM_001080398	NP_001073867			KIAA0368 protein												0														0.166667	49.033343	66.098163	27	135	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	114176921	114176921	8478	9	T	A	A	A	741	57	KIAA0368	3	3
OR1K1	392392	broad.mit.edu	37	9	125563312	125563312	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:125563312C>T	uc011lze.1	+	c.911C>T	c.(910-912)GCC>GTC	p.A304V		NM_080859	NP_543135	Q8NGR3	OR1K1_HUMAN	olfactory receptor, family 1, subfamily K,	304	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.170732	28.797114	37.205908	14	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125563312	125563312	11368	9	C	T	T	T	338	26	OR1K1	2	2
RC3H2	54542	broad.mit.edu	37	9	125613500	125613500	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:125613500C>A	uc010mwc.1	-	c.3240G>T	c.(3238-3240)TTG>TTT	p.L1080F	RC3H2_uc004bnc.2_Non-coding_Transcript	NM_001100588	NP_001094058	Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type zinc finger domains 2	1080						cell surface|endomembrane system|membrane|membrane fraction|perinuclear region of cytoplasm	DNA binding|zinc ion binding			ovary(1)	1														0.217391	80.532311	92.39325	35	126	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125613500	125613500	13636	9	C	A	A	A	272	21	RC3H2	2	2
FRMPD1	22844	broad.mit.edu	37	9	37692711	37692711	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:37692711C>G	uc004aag.1	+	c.73C>G	c.(73-75)CTT>GTT	p.L25V	FRMPD1_uc004aah.1_Missense_Mutation_p.L25V	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	25						cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|breast(1)	7				GBM - Glioblastoma multiforme(29;0.00655)										0.270115	139.244608	147.541513	47	127	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37692711	37692711	6307	9	C	G	G	G	364	28	FRMPD1	3	3
VPS13A	23230	broad.mit.edu	37	9	79910762	79910762	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:79910762G>T	uc004akr.2	+	c.3812G>T	c.(3811-3813)AGA>ATA	p.R1271I	VPS13A_uc004akp.3_Missense_Mutation_p.R1271I|VPS13A_uc004akq.3_Missense_Mutation_p.R1271I|VPS13A_uc004aks.2_Missense_Mutation_p.R1232I|VPS13A_uc010mpo.1_5'UTR	NM_033305	NP_150648	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13A isoform A	1271	TPR 4.				Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	7														0.216667	29.438679	33.884583	13	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79910762	79910762	17756	9	G	T	T	T	455	35	VPS13A	2	2
BCORL1	63035	broad.mit.edu	37	X	129148736	129148736	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:129148736C>G	uc004evb.1	+	c.1988C>G	c.(1987-1989)TCT>TGT	p.S663C	BCORL1_uc010nrd.1_Missense_Mutation_p.S565C	NM_021946	NP_068765	Q5H9F3	BCORL_HUMAN	BCL6 co-repressor-like 1	663					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(4)|breast(2)|lung(1)	7														0.295652	103.702213	107.999329	34	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	129148736	129148736	1408	23	C	G	G	G	416	32	BCORL1	3	3
GPR112	139378	broad.mit.edu	37	X	135432428	135432428	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:135432428T>C	uc004ezu.1	+	c.6563T>C	c.(6562-6564)GTT>GCT	p.V2188A	GPR112_uc010nsb.1_Missense_Mutation_p.V1983A|GPR112_uc010nsc.1_Missense_Mutation_p.V1955A	NM_153834	NP_722576	Q8IZF6	GP112_HUMAN	G-protein coupled receptor 112	2188	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(5)|large_intestine(2)|lung(1)|breast(1)|skin(1)|pancreas(1)	11	Acute lymphoblastic leukemia(192;0.000127)									487				0.387255	267.394432	269.661356	79	125	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135432428	135432428	6903	23	T	C	C	C	780	60	GPR112	4	4
POLA1	5422	broad.mit.edu	37	X	24844572	24844572	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:24844572G>A	uc004dbl.2	+	c.3572G>A	c.(3571-3573)AGG>AAG	p.R1191K		NM_016937	NP_058633	P09884	DPOLA_HUMAN	DNA-directed DNA polymerase alpha 1	1191					cell proliferation|DNA replication checkpoint|DNA replication, synthesis of RNA primer|DNA-dependent DNA replication initiation|double-strand break repair via nonhomologous end joining|interspecies interaction between organisms|lagging strand elongation|leading strand elongation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|cytoplasm|nuclear envelope|nuclear matrix|nucleolus|nucleoplasm	chromatin binding|DNA-directed DNA polymerase activity|metal ion binding|nucleoside binding			ovary(2)|skin(1)	3					Clofarabine(DB00631)|Fludarabine(DB01073)									0.545455	40.601483	40.64093	12	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24844572	24844572	12615	23	G	A	A	A	455	35	POLA1	2	2
KDM5C	8242	broad.mit.edu	37	X	53230770	53230770	+	Nonsense_Mutation	SNP	G	A	A			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:53230770G>A	uc004drz.2	-	c.2023C>T	c.(2023-2025)CAA>TAA	p.Q675*	KDM5C_uc011moc.1_Non-coding_Transcript|KDM5C_uc011mod.1_Nonsense_Mutation_p.Q608*|KDM5C_uc004dsa.2_Nonsense_Mutation_p.Q674*	NM_004187	NP_004178	P41229	KDM5C_HUMAN	jumonji, AT rich interactive domain 1C isoform	675					chromatin modification|oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			kidney(9)|ovary(5)|salivary_gland(1)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|oesophagus(1)	18														0.483871	131.162345	131.183743	45	48	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	53230770	53230770	8441	23	G	A	A	A	598	46	KDM5C	5	2
ZNF711	7552	broad.mit.edu	37	X	84510681	84510681	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:84510681A>T	uc004eeq.2	+	c.496A>T	c.(496-498)AAT>TAT	p.N166Y	ZNF711_uc004eeo.2_Missense_Mutation_p.N166Y|ZNF711_uc004eep.2_Missense_Mutation_p.N166Y	NM_021998	NP_068838	Q9Y462	ZN711_HUMAN	zinc finger protein 711	166					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|transcription regulator activity|zinc ion binding			ovary(3)	3														0.716216	169.201567	172.308086	53	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	84510681	84510681	18712	23	A	T	T	T	169	13	ZNF711	3	3
CHM	1121	broad.mit.edu	37	X	85233802	85233802	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:85233802T>C	uc004eet.2	-	c.283A>G	c.(283-285)ATT>GTT	p.I95V	CHM_uc011mqz.1_Intron|CHM_uc004eeu.3_Non-coding_Transcript|CHM_uc004eev.3_Missense_Mutation_p.I95V	NM_000390	NP_000381	P24386	RAE1_HUMAN	choroideremia isoform a	95					intracellular protein transport|protein geranylgeranylation|response to stimulus|visual perception	Rab-protein geranylgeranyltransferase complex	GTPase activator activity|Rab geranylgeranyltransferase activity			ovary(1)	1		all_lung(315;5.41e-06)												0.322581	66.582668	68.313195	20	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85233802	85233802	3484	23	T	C	C	C	637	49	CHM	4	4
PCDH11X	27328	broad.mit.edu	37	X	91134263	91134263	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:91134263C>G	uc004efk.1	+	c.3024C>G	c.(3022-3024)CAC>CAG	p.H1008Q	PCDH11X_uc004efl.1_Missense_Mutation_p.H1008Q|PCDH11X_uc004efo.1_Missense_Mutation_p.H1008Q|PCDH11X_uc010nmv.1_Missense_Mutation_p.H1008Q|PCDH11X_uc004efm.1_Missense_Mutation_p.H1008Q|PCDH11X_uc004efn.1_Missense_Mutation_p.H1008Q|PCDH11X_uc004efh.1_Missense_Mutation_p.H1008Q|PCDH11X_uc004efj.1_Missense_Mutation_p.H1008Q	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	1008	Cytoplasmic (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						NSCLC(38;925 1092 2571 38200 45895)								0.288043	170.607837	178.014576	53	131	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	91134263	91134263	11928	23	C	G	G	G	220	17	PCDH11X	3	3
PYROXD1	79912	broad.mit.edu	37	12	21621675	21621677	+	In_Frame_Del	DEL	ATT	-	-			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:21621675_21621677delATT	uc001rew.2	+	c.1490_1492delATT	c.(1489-1494)GATTAT>GAT	p.Y498del	PYROXD1_uc009ziq.2_In_Frame_Del_p.Y239del|PYROXD1_uc009zir.2_In_Frame_Del_p.Y204del	NM_024854	NP_079130	Q8WU10	PYRD1_HUMAN	pyridine nucleotide-disulphide oxidoreductase	498					oxidation-reduction process		oxidoreductase activity			ovary(1)	1														0.44			4	5		---	---	---	---	capture_indel		In_Frame_Del	DEL	21621675	21621677	13324	12	ATT	-	-	-	156	12	PYROXD1	5	5
IARS2	55699	broad.mit.edu	37	1	220267786	220267786	+	Frame_Shift_Del	DEL	G	-	-			TCGA-05-4244-01	TCGA-05-4244-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:220267786_220267786delG	uc001hmc.2	+	c.228_228delG	c.(226-228)CTGfs	p.L76fs		NM_018060	NP_060530	Q9NSE4	SYIM_HUMAN	mitochondrial isoleucine tRNA synthetase	76					isoleucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|isoleucine-tRNA ligase activity			ovary(2)	2				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)									0.31			15	33		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	220267786	220267786	7774	1	G	-	-	-	600	47	IARS2	5	5
