Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
GPR123	84435	broad.mit.edu	36	10	134736504	134736504	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:134736504C>T	uc001llw.1	+	c.548C>T	c.(547-549)TCC>TTC	p.S183F				Q86SQ6	GP123_HUMAN	Probable G-protein coupled receptor 123.	Error:Variant_position_missing_in_Q86SQ6_after_alignment						integral to membrane|plasma membrane	G-protein coupled receptor activity				0		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)												0.571429	12.900833	12.931942	4	3	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)	Missense_Mutation	SNP	134736504	134736504	6911	10	C	T	T	30	30	GPR123	T	2	2
DUSP13	51207	broad.mit.edu	36	10	76525452	76525452	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:76525452C>T	uc001jwu.1	-	c.560G>A	c.(559-561)GGA>GAA	p.G187E	DUSP13_uc001jwr.1_Missense_Mutation_p.G94E|DUSP13_uc001jws.1_3'UTR|DUSP13_uc001jww.1_Missense_Mutation_p.G144E|DUSP13_uc009xrs.1_Missense_Mutation_p.G187E|DUSP13_uc001jwt.1_Missense_Mutation_p.G187E|DUSP13_uc001jwv.1_Missense_Mutation_p.G94E	NM_001007273	NP_057448	Q6B8I1	MDSP_HUMAN	testis and skeletal muscle-specific dual	85	Tyrosine-protein phosphatase.					cytoplasm	protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					NSCLC(174;1655 2059 12324 40663 42963)								0.586538	192.081619	192.76001	61	43	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	76525452	76525452	4998	10	C	T	T	30	30	DUSP13	T	2	2
MUC5B	727897	broad.mit.edu	36	11	1221375	1221375	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:1221375C>A	uc001ltb.2	+	c.6698C>A	c.(6697-6699)CCT>CAT	p.P2233H		NM_002458	NP_002449	Q9HC84	MUC5B_HUMAN	mucin 5, subtype B, tracheobronchial	2230	7 X Cys-rich subdomain repeats.|Thr-rich.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)												0.220779	37.930738	43.460115	17	60	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)	Missense_Mutation	SNP	1221375	1221375	10373	11	C	A	A	24	24	MUC5B	A	3	3
NFRKB	4798	broad.mit.edu	36	11	129256930	129256930	+	Nonsense_Mutation	SNP	G	C	C			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:129256930G>C	uc001qfg.1	-	c.1295C>G	c.(1294-1296)TCA>TGA	p.S432*	NFRKB_uc001qfh.1_Nonsense_Mutation_p.S430*|NFRKB_uc001qfi.1_Nonsense_Mutation_p.S407*	NM_006165	NP_006156	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	407					inflammatory response|transcription from RNA polymerase II promoter	nucleus	DNA binding|protease binding|specific RNA polymerase II transcription factor activity			ovary(3)	3	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)										OREG0021512	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.191489	21.249528	25.427196	9	38	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)	Nonsense_Mutation	SNP	129256930	129256930	10784	11	G	C	C	45	45	NFRKB	C	5	3
ANO5	203859	broad.mit.edu	36	11	22248493	22248493	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:22248493G>T	uc001mqi.1	+	c.1958G>T	c.(1957-1959)AGT>ATT	p.S653I	ANO5_uc001mqj.1_Missense_Mutation_p.S652I	NM_213599	NP_998764	Q75V66	ANO5_HUMAN	anoctamin 5 isoform a	653	Extracellular (Potential).					chloride channel complex|endoplasmic reticulum membrane	chloride channel activity			central_nervous_system(3)|ovary(1)	4														0.396694	137.771264	138.902171	48	73	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22248493	22248493	708	11	G	T	T	36	36	ANO5	T	3	3
GAS2	2620	broad.mit.edu	36	11	22704422	22704422	+	Silent	SNP	G	A	A			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:22704422G>A	uc009yie.1	+	c.276G>A	c.(274-276)CCG>CCA	p.P92P	GAS2_uc001mqm.1_Silent_p.P92P|GAS2_uc001mqn.1_Non-coding_Transcript|GAS2_uc001mqo.1_Silent_p.P92P	NM_177553	NP_808221	O43903	GAS2_HUMAN	growth arrest-specific 2	92	CH.				cell cycle arrest|cellular component disassembly involved in apoptosis|regulation of cell shape	actin filament|cytosol|membrane				ovary(1)	1														0.475524	203.590972	203.665273	68	75	GG		KEEP	---	---	---	---	capture			Silent	SNP	22704422	22704422	6509	11	G	A	A	40	40	GAS2	A	1	1
RAG1	5896	broad.mit.edu	36	11	36553028	36553028	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:36553028C>T	uc001mwu.2	+	c.1598C>T	c.(1597-1599)ACT>ATT	p.T533I	RAG1_uc001mwt.2_Non-coding_Transcript|RAG1_uc009ykl.1_Missense_Mutation_p.T533I	NM_000448	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	533					histone monoubiquitination|immune response|pre-B cell allelic exclusion|protein autoubiquitination|T cell differentiation in thymus|V(D)J recombination	nucleus	endonuclease activity|histone binding|protein homodimerization activity|sequence-specific DNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4	all_lung(20;0.226)	all_hematologic(20;0.107)				Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)				117				0.361111	114.793434	116.628023	39	69	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36553028	36553028	13463	11	C	T	T	20	20	RAG1	T	2	2
OR4X1	390113	broad.mit.edu	36	11	48242591	48242591	+	Silent	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:48242591C>T	uc001ngt.1	+	c.603C>T	c.(601-603)GGC>GGT	p.G201G		NM_001004726	NP_001004726	Q8NH49	OR4X1_HUMAN	olfactory receptor, family 4, subfamily X,	201	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2														0.405797	78.581483	79.117808	28	41	CC		KEEP	---	---	---	---	capture			Silent	SNP	48242591	48242591	11494	11	C	T	T	27	27	OR4X1	T	1	1
OR56A4	120793	broad.mit.edu	36	11	5980496	5980496	+	Silent	SNP	G	A	A			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:5980496G>A	uc001mce.1	-	c.459C>T	c.(457-459)TTC>TTT	p.F153F		NM_001005179	NP_001005179	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, subfamily A,	101	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)												0.297619	64.642116	67.718274	25	59	GG		KEEP	---	---	---	---	capture		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	Silent	SNP	5980496	5980496	11545	11	G	A	A	41	41	OR56A4	A	2	2
TRIM3	10612	broad.mit.edu	36	11	6426862	6426862	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:6426862C>T	uc001mdh.1	-	c.2207G>A	c.(2206-2208)TGC>TAC	p.C736Y	TRIM3_uc001mdi.1_Missense_Mutation_p.C736Y|TRIM3_uc009yfd.1_Missense_Mutation_p.C736Y	NM_006458	NP_150594	O75382	TRIM3_HUMAN	tripartite motif-containing 3	736	NHL 6.				nervous system development|protein transport	early endosome	protein C-terminus binding|zinc ion binding	p.C736Y(1)		central_nervous_system(2)|large_intestine(1)|ovary(1)|skin(1)	5		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)				Melanoma(6;5 510 1540 25169 29084)								0.32	37.584953	39.02311	16	34	CC		KEEP	---	---	---	---	capture		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)	Missense_Mutation	SNP	6426862	6426862	17048	11	C	T	T	25	25	TRIM3	T	2	2
THRSP	7069	broad.mit.edu	36	11	77452786	77452786	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:77452786G>C	uc001oyx.1	+	c.211G>C	c.(211-213)GAC>CAC	p.D71H	THRSP_uc009yuv.1_Missense_Mutation_p.D71H	NM_003251	NP_003242	Q92748	THRSP_HUMAN	thyroid hormone-responsive protein	71					lipid biosynthetic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus				breast(1)	1	all_cancers(14;2.23e-19)|all_epithelial(13;7.49e-22)|Breast(9;6.38e-17)|Ovarian(111;0.152)									11				0.361538	141.603393	143.790741	47	83	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(8;2.15e-25)		Missense_Mutation	SNP	77452786	77452786	16404	11	G	C	C	41	41	THRSP	C	3	3
LRDD	55367	broad.mit.edu	36	11	790589	790589	+	Silent	SNP	G	A	A			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:790589G>A	uc001lro.1	-	c.1995C>T	c.(1993-1995)GGC>GGT	p.G665G	SLC25A22_uc009yci.1_5'Flank|SLC25A22_uc001lrj.1_5'Flank|LRDD_uc009yck.1_Non-coding_Transcript|LRDD_uc001lrk.1_Silent_p.G665G|LRDD_uc001lrl.1_Silent_p.G508G|LRDD_uc001lrm.1_Silent_p.G352G|LRDD_uc001lrn.1_Silent_p.G508G|LRDD_uc001lrp.1_Silent_p.G327G	NM_145886	NP_665893	Q9HB75	PIDD_HUMAN	leucine rich repeat and death domain containing	665					apoptosis|signal transduction	cytoplasm|nucleus	death receptor binding				0		all_cancers(49;1.13e-08)|all_epithelial(84;2.95e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.159)|all_lung(207;0.198)												0.4375	34.836031	34.946326	14	18	GG		KEEP	---	---	---	---	capture		all cancers(45;1.45e-25)|Epithelial(43;1.17e-24)|OV - Ovarian serous cystadenocarcinoma(40;6.76e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Silent	SNP	790589	790589	9309	11	G	A	A	38	38	LRDD	A	1	1
PRCP	5547	broad.mit.edu	36	11	82248667	82248667	+	Silent	SNP	C	T	T	rs71788174	unknown	TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:82248667C>T	uc001ozr.1	-	c.372G>A	c.(370-372)ACG>ACA	p.T124T	PRCP_uc001ozs.1_Silent_p.T103T	NM_199418	NP_955450	P42785	PCP_HUMAN	prolylcarboxypeptidase isoform 2 preproprotein	103					blood coagulation, intrinsic pathway|proteolysis	lysosome|plasma membrane	protein binding|serine-type carboxypeptidase activity				0														0.291667	39.037884	40.899586	14	34	CC		KEEP	---	---	---	---	capture			Silent	SNP	82248667	82248667	12891	11	C	T	T	23	23	PRCP	T	1	1
TBX3	6926	broad.mit.edu	36	12	113605272	113605272	+	Silent	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:113605272C>T	uc001tvt.1	-	c.117G>A	c.(115-117)CCG>CCA	p.P39P	TBX3_uc001tvu.1_Silent_p.P39P	NM_016569	NP_057653	O15119	TBX3_HUMAN	T-box 3 protein isoform 2	39					anterior/posterior axis specification, embryo|anti-apoptosis|cell aging|embryonic arm morphogenesis|embryonic digit morphogenesis|female genitalia development|follicle-stimulating hormone secretion|luteinizing hormone secretion|male genitalia development|mesoderm morphogenesis|negative regulation of myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle|positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter|skeletal system development	nucleus	general transcriptional repressor activity|RNA polymerase II transcription factor activity|sequence-specific DNA binding			ovary(2)	2	Medulloblastoma(191;0.163)|all_neural(191;0.178)													0.413793	66.988556	67.364989	24	34	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(302;0.0574)	Silent	SNP	113605272	113605272	16185	12	C	T	T	19	19	TBX3	T	1	1
GCN1L1	10985	broad.mit.edu	36	12	119084204	119084204	+	Silent	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:119084204C>T	uc001txo.1	-	c.2205G>A	c.(2203-2205)CCG>CCA	p.P735P		NM_006836	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis	735					regulation of translation	ribosome	protein binding|translation factor activity, nucleic acid binding			ovary(3)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)													0.303571	45.053887	46.982309	17	39	CC		KEEP	---	---	---	---	capture			Silent	SNP	119084204	119084204	6565	12	C	T	T	23	23	GCN1L1	T	1	1
ESPL1	9700	broad.mit.edu	36	12	51970443	51970443	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:51970443G>A	uc001sck.2	+	c.5287G>A	c.(5287-5289)GCA>ACA	p.A1763T	ESPL1_uc001scj.2_Missense_Mutation_p.A1438T	NM_012291	NP_036423	Q14674	ESPL1_HUMAN	extra spindle poles like 1	1763					apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)	2						Colon(53;1069 1201 2587 5382)								0.35443	75.523666	76.978635	28	51	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51970443	51970443	5446	12	G	A	A	42	42	ESPL1	A	2	2
LRP1	4035	broad.mit.edu	36	12	55884462	55884462	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:55884462C>T	uc001snd.1	+	c.10954C>T	c.(10954-10956)CGG>TGG	p.R3652W		NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	3652	Extracellular (Potential).|LDL-receptor class A 29.				apoptotic cell clearance|multicellular organismal development|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein particle receptor binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(7)|large_intestine(2)|pancreas(2)|skin(1)|central_nervous_system(1)	13					Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)					1456				0.295082	42.64956	44.928403	18	43	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(357;0.0103)	Missense_Mutation	SNP	55884462	55884462	9324	12	C	T	T	27	27	LRP1	T	1	1
SLC26A10	65012	broad.mit.edu	36	12	56301863	56301863	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:56301863C>A	uc001spe.1	+	c.679C>A	c.(679-681)CCC>ACC	p.P227T	SLC26A10_uc001spf.2_Non-coding_Transcript|SLC26A10_uc009zpz.1_5'Flank	NM_133489	NP_597996	Q8NG04	S2610_HUMAN	solute carrier family 26, member 10	227						integral to membrane	antiporter activity			large_intestine(1)|central_nervous_system(1)	2	Melanoma(17;0.122)											OREG0021948	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.24	7.409348	8.989254	6	19	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56301863	56301863	15012	12	C	A	A	18	18	SLC26A10	A	3	3
ANO4	121601	broad.mit.edu	36	12	99860325	99860325	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:99860325C>T	uc001thx.1	+	c.337C>T	c.(337-339)CGA>TGA	p.R113*	ANO4_uc001thw.1_Nonsense_Mutation_p.R78*	NM_178826	NP_849148	Q32M45	ANO4_HUMAN	anoctamin 4	113	Extracellular (Potential).					chloride channel complex	chloride channel activity			ovary(4)	4														0.306569	112.498938	117.069608	42	95	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	99860325	99860325	707	12	C	T	T	31	31	ANO4	T	5	1
MDGA2	161357	broad.mit.edu	36	14	46496459	46496459	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:46496459G>A	uc001wwj.2	-	c.1750C>T	c.(1750-1752)CGG>TGG	p.R584W	MDGA2_uc001wwi.2_Missense_Mutation_p.R355W|MDGA2_uc010ani.1_Missense_Mutation_p.R144W	NM_001113498	NP_001106970	Q7Z553	MDGA2_HUMAN	MAM domain containing 1 isoform 1	584	Ig-like 6.				spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(3)|large_intestine(1)|pancreas(1)	5														0.32967	80.327724	82.663552	30	61	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46496459	46496459	9796	14	G	A	A	40	40	MDGA2	A	1	1
BAHD1	22893	broad.mit.edu	36	15	38538908	38538908	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0122-01	TCGA-06-0122-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:38538908T>C	uc001zlu.2	+	c.953T>C	c.(952-954)ATG>ACG	p.M318T	BAHD1_uc001zlt.2_Missense_Mutation_p.M318T|BAHD1_uc010bbp.1_Missense_Mutation_p.M318T|BAHD1_uc001zlv.2_Missense_Mutation_p.M318T	NM_014952	NP_055767	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	318	Pro-rich.				heterochromatin formation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin silencing complex|chromosome	chromatin binding|DNA binding|protein binding				0		all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)												0.336735	91.858141	94.162312	33	65	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(113;3.46e-06)|BRCA - Breast invasive adenocarcinoma(123;0.08)	Missense_Mutation	SNP	38538908	38538908	1318	15	T	C	C	51	51	BAHD1	C	4	4
CYP19A1	1588	broad.mit.edu	36	15	49294718	49294718	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:49294718G>A	uc001zyz.2	-	c.862C>T	c.(862-864)CGT>TGT	p.R288C	CYP19A1_uc001zza.2_Missense_Mutation_p.R288C|CYP19A1_uc001zzb.2_Missense_Mutation_p.R288C	NM_031226	NP_112503	P11511	CP19A_HUMAN	cytochrome P450, family 19	288					estrogen biosynthetic process|oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|membrane fraction	aromatase activity|electron carrier activity|heme binding|oxygen binding|steroid hydroxylase activity				0					Aminoglutethimide(DB00357)|Anastrozole(DB01217)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Diethylstilbestrol(DB00255)|Exemestane(DB00990)|Letrozole(DB01006)|Testolactone(DB00894)|Testosterone(DB00624)	Melanoma(142;1016 1807 39614 48966 51721)				147				0.315789	61.96529	64.263522	24	52	GG		KEEP	---	---	---	---	capture		all cancers(107;0.000372)|GBM - Glioblastoma multiforme(94;0.0128)	Missense_Mutation	SNP	49294718	49294718	4313	15	G	A	A	40	40	CYP19A1	A	1	1
CILP	8483	broad.mit.edu	36	15	63277398	63277398	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:63277398C>T	uc002aon.2	-	c.2279G>A	c.(2278-2280)CGG>CAG	p.R760Q		NM_003613	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein	760					negative regulation of insulin-like growth factor receptor signaling pathway	extracellular matrix part|extracellular space|proteinaceous extracellular matrix				ovary(4)|pancreas(2)	6														0.382514	205.924503	208.132463	70	113	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63277398	63277398	3563	15	C	T	T	23	23	CILP	T	1	1
ABCC6	368	broad.mit.edu	36	16	16167015	16167015	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0122-01	TCGA-06-0122-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:16167015A>G	uc002den.2	-	c.3272T>C	c.(3271-3273)ATC>ACC	p.I1091T	ABCC6_uc010bvo.1_Non-coding_Transcript	NM_001171	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C, member 6	1091	Helical; Name=15; (By similarity).|ABC transmembrane type-1 2.				response to drug|visual perception	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(1)	1														0.333333	9.307304	9.768669	6	12	AA		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Missense_Mutation	SNP	16167015	16167015	58	16	A	G	G	12	12	ABCC6	G	4	4
OGFOD1	55239	broad.mit.edu	36	16	55062094	55062094	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:55062094C>T	uc002ejb.1	+	c.1175C>T	c.(1174-1176)ACT>ATT	p.T392I	OGFOD1_uc002ejc.1_Missense_Mutation_p.T252I	NM_018233	NP_060703	Q8N543	OGFD1_HUMAN	2-oxoglutarate and iron-dependent oxygenase	392					oxidation-reduction process		iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0					Vitamin C(DB00126)									0.285714	9.192968	9.770749	4	10	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55062094	55062094	11246	16	C	T	T	20	20	OGFOD1	T	2	2
COX10	1352	broad.mit.edu	36	17	14050998	14050998	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:14050998C>T	uc002gof.2	+	c.1075C>T	c.(1075-1077)CGC>TGC	p.R359C		NM_001303	NP_001294	Q12887	COX10_HUMAN	heme A:farnesyltransferase	359					heme a biosynthetic process|heme O biosynthetic process|mitochondrial electron transport, cytochrome c to oxygen|respiratory chain complex IV assembly	integral to membrane|mitochondrial membrane	protoheme IX farnesyltransferase activity				0		all_lung(20;0.06)|Lung SC(565;0.168)												0.290909	78.279665	82.576295	32	78	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)	Missense_Mutation	SNP	14050998	14050998	3900	17	C	T	T	27	27	COX10	T	1	1
SYNRG	11276	broad.mit.edu	36	17	33003017	33003017	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:33003017C>G	uc002hoa.1	-	c.1470G>C	c.(1468-1470)CAG>CAC	p.Q490H	SYNRG_uc002hob.1_Missense_Mutation_p.Q490H|SYNRG_uc002hoc.1_Missense_Mutation_p.Q411H|SYNRG_uc002hod.1_Missense_Mutation_p.Q412H|SYNRG_uc002hoe.1_Missense_Mutation_p.Q412H|SYNRG_uc002hog.1_Missense_Mutation_p.Q624H|SYNRG_uc002hof.1_Missense_Mutation_p.Q202H|SYNRG_uc010cvd.1_Missense_Mutation_p.Q290H	NM_007247	NP_009178	Q9UMZ2	SYNRG_HUMAN	AP1 gamma subunit binding protein 1 isoform 1	490					endocytosis|intracellular protein transport	AP-1 adaptor complex	calcium ion binding			ovary(2)	2														0.302752	101.432424	105.218434	33	76	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33003017	33003017	15981	17	C	G	G	28	28	SYNRG	G	3	3
KRT34	3885	broad.mit.edu	36	17	36788871	36788871	+	Silent	SNP	G	A	A			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36788871G>A	uc002hwm.1	-	c.1086C>T	c.(1084-1086)AAC>AAT	p.N362N		NM_021013	NP_066293	O76011	KRT34_HUMAN	keratin 34	362	Rod.|Coil 2.				epidermis development	intermediate filament	protein binding|structural molecule activity			central_nervous_system(1)	1		Breast(137;0.000496)												0.348148	129.483038	132.231001	47	88	GG		KEEP	---	---	---	---	capture			Silent	SNP	36788871	36788871	8786	17	G	A	A	40	40	KRT34	A	1	1
ARMC7	79637	broad.mit.edu	36	17	70636612	70636612	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:70636612C>T	uc002jmw.1	+	c.481C>T	c.(481-483)CAG>TAG	p.Q161*	ARMC7_uc010dga.1_Non-coding_Transcript	NM_024585	NP_078861	Q9H6L4	ARMC7_HUMAN	armadillo repeat containing 7	161							binding			pancreas(1)	1	all_lung(278;0.14)|Lung NSC(278;0.168)													0.361111	31.162237	31.774444	13	23	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)		Nonsense_Mutation	SNP	70636612	70636612	974	17	C	T	T	17	17	ARMC7	T	5	2
GALR1	2587	broad.mit.edu	36	18	73091634	73091634	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:73091634G>A	uc002lms.2	+	c.142G>A	c.(142-144)GTG>ATG	p.V48M		NM_001480	NP_001471	P47211	GALR1_HUMAN	galanin receptor 1	48	Helical; Name=1; (Potential).				digestion|negative regulation of adenylate cyclase activity	integral to membrane|plasma membrane	galanin receptor activity				0		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)												0.230769	20.757724	23.346479	9	30	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(15;1.03e-06)|BRCA - Breast invasive adenocarcinoma(31;0.104)	Missense_Mutation	SNP	73091634	73091634	6491	18	G	A	A	48	48	GALR1	A	2	2
ANKRD12	23253	broad.mit.edu	36	18	9270962	9270962	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0122-01	TCGA-06-0122-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr18:9270962A>C	uc002knv.2	+	c.6027A>C	c.(6025-6027)CAA>CAC	p.Q2009H	ANKRD12_uc002knw.2_Missense_Mutation_p.Q1986H|ANKRD12_uc002knx.2_Missense_Mutation_p.Q1986H	NM_015208	NP_056023	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12 isoform 1	2009						nucleus				ovary(2)|central_nervous_system(1)	3														0.343137	106.298871	108.513777	35	67	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	9270962	9270962	643	18	A	C	C	2	2	ANKRD12	C	4	4
C19orf44	84167	broad.mit.edu	36	19	16473069	16473069	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:16473069C>T	uc002neh.1	+	c.466C>T	c.(466-468)CGT>TGT	p.R156C	MED26_uc002nee.2_Intron|C19orf44_uc002nef.1_Missense_Mutation_p.R156C|C19orf44_uc002neg.2_Missense_Mutation_p.R156C|C19orf44_uc010eai.1_Non-coding_Transcript	NM_032207	NP_115583	Q9H6X5	CS044_HUMAN	hypothetical protein LOC84167	156											0														0.208696	56.239005	65.272751	24	91	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16473069	16473069	1991	19	C	T	T	23	23	C19orf44	T	1	1
KLHL26	55295	broad.mit.edu	36	19	18640533	18640533	+	Silent	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:18640533C>T	uc002njz.1	+	c.1326C>T	c.(1324-1326)TAC>TAT	p.Y442Y		NM_018316	NP_060786	Q53HC5	KLH26_HUMAN	kelch-like 26	442	Kelch 3.									ovary(1)	1														0.212121	14.305811	16.835501	7	26	CC		KEEP	---	---	---	---	capture			Silent	SNP	18640533	18640533	8693	19	C	T	T	19	19	KLHL26	T	1	1
APLP1	333	broad.mit.edu	36	19	41055341	41055341	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:41055341C>T	uc002ocf.1	+	c.967C>T	c.(967-969)CGC>TGC	p.R323C	APLP1_uc002oce.1_Missense_Mutation_p.R323C|APLP1_uc002ocg.1_Missense_Mutation_p.R226C	NM_001024807	NP_001019978	P51693	APLP1_HUMAN	amyloid precursor-like protein 1 isoform 1	323	Heparin-binding (By similarity).|Extracellular (Potential).				apoptosis|cell adhesion|cellular response to norepinephrine stimulus|endocytosis|inhibition of adenylate cyclase activity by G-protein signaling pathway|negative regulation of cAMP biosynthetic process|nervous system development|organ morphogenesis	basement membrane|integral to membrane|perinuclear region of cytoplasm|plasma membrane	alpha-2A adrenergic receptor binding|alpha-2B adrenergic receptor binding|alpha-2C adrenergic receptor binding|heparin binding|identical protein binding|metal ion binding			ovary(2)	2	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)													0.218045	63.610668	73.353675	29	104	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(66;0.0515)		Missense_Mutation	SNP	41055341	41055341	789	19	C	T	T	27	27	APLP1	T	1	1
ZNF229	7772	broad.mit.edu	36	19	49624996	49624996	+	Silent	SNP	G	A	A			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:49624996G>A	uc002oze.1	-	c.1800C>T	c.(1798-1800)TAC>TAT	p.Y600Y	ZNF229_uc010ejk.1_Silent_p.Y254Y|ZNF229_uc010ejl.1_Silent_p.Y594Y	NM_014518	NP_055333	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	600	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2		Prostate(69;0.0352)												0.241379	65.143109	72.22162	28	88	GG		KEEP	---	---	---	---	capture			Silent	SNP	49624996	49624996	18373	19	G	A	A	40	40	ZNF229	A	1	1
POLD1	5424	broad.mit.edu	36	19	55608575	55608575	+	Nonsense_Mutation	SNP	C	A	A			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:55608575C>A	uc010eny.1	+	c.2313C>A	c.(2311-2313)TAC>TAA	p.Y771*	POLD1_uc002psb.2_Nonsense_Mutation_p.Y745*|POLD1_uc002psc.2_Nonsense_Mutation_p.Y745*|POLD1_uc010enx.1_Non-coding_Transcript	NM_002691	NP_002682	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic	745					base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|DNA synthesis involved in DNA repair|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|response to UV|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	delta DNA polymerase complex|nucleoplasm|nucleotide-excision repair complex	3'-5'-exodeoxyribonuclease activity|chromatin binding|DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding|protein binding			central_nervous_system(1)	1		all_neural(266;0.0571)												0.222222	6.593375	7.874264	4	14	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)	Nonsense_Mutation	SNP	55608575	55608575	12618	19	C	A	A	17	17	POLD1	A	5	3
SPIB	6689	broad.mit.edu	36	19	55617956	55617956	+	Silent	SNP	G	A	A			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:55617956G>A	uc002psd.1	+	c.189G>A	c.(187-189)CCG>CCA	p.P63P	SPIB_uc002pse.1_Silent_p.P63P	NM_003121	NP_003112	Q01892	SPIB_HUMAN	Spi-B transcription factor (Spi-1/PU.1 related)	63					regulation of transcription from RNA polymerase II promoter	cytoplasm|microtubule cytoskeleton|nucleus	RNA polymerase II transcription factor activity|sequence-specific DNA binding			kidney(1)	1		all_neural(266;0.131)												0.261261	71.459263	77.162976	29	82	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)	Silent	SNP	55617956	55617956	15562	19	G	A	A	39	39	SPIB	A	1	1
SIGLEC9	27180	broad.mit.edu	36	19	56322309	56322309	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:56322309G>A	uc002pvu.1	+	c.959G>A	c.(958-960)TGC>TAC	p.C320Y		NM_014441	NP_055256	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	320	Extracellular (Potential).|Ig-like C2-type 2.				cell adhesion|cell surface receptor linked signaling pathway	integral to plasma membrane	sugar binding				0		all_neural(266;0.0529)												0.315789	61.2681	63.564529	24	52	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)	Missense_Mutation	SNP	56322309	56322309	14810	19	G	A	A	46	46	SIGLEC9	A	2	2
ZNF417	147687	broad.mit.edu	36	19	63115244	63115244	+	Silent	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:63115244C>T	uc002qqq.1	-	c.159G>A	c.(157-159)TCG>TCA	p.S53S	ZNF417_uc002qqr.1_Silent_p.S52S	NM_152475	NP_689688	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	53	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)												0.164384	20.151864	27.962765	12	61	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0151)	Silent	SNP	63115244	63115244	18487	19	C	T	T	27	27	ZNF417	T	1	1
OR7G2	390882	broad.mit.edu	36	19	9074120	9074120	+	Nonsense_Mutation	SNP	G	C	C			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:9074120G>C	uc002mkr.1	-	c.863C>G	c.(862-864)TCA>TGA	p.S288*		NM_001005193	NP_001005193	Q8NG99	OR7G2_HUMAN	olfactory receptor, family 7, subfamily G,	267	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						Esophageal Squamous(67;143 1448 28637 40648)								0.233645	66.720135	73.667482	25	82	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	9074120	9074120	11634	19	G	C	C	45	45	OR7G2	C	5	3
MTOR	2475	broad.mit.edu	36	1	11096982	11096982	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0122-01	TCGA-06-0122-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:11096982A>T	uc001asd.1	-	c.7280T>A	c.(7279-7281)CTG>CAG	p.L2427Q	MTOR_uc001asc.1_Missense_Mutation_p.L632Q	NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	2427	PI3K/PI4K.				cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|ovary(4)|kidney(3)|large_intestine(2)|skin(2)|lung(1)	19									p.L632R(ST486-Tumor)	1389				0.294737	75.762555	79.344083	28	67	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11096982	11096982	10347	1	A	T	T	7	7	MTOR	T	4	4
SPAG17	200162	broad.mit.edu	36	1	118349561	118349561	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0122-01	TCGA-06-0122-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:118349561T>G	uc001ehk.1	-	c.4775A>C	c.(4774-4776)CAG>CCG	p.Q1592P	SPAG17_uc009whi.1_Missense_Mutation_p.Q102P	NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1592						cilium|flagellar axoneme|microtubule				ovary(2)|large_intestine(1)	3	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)												0.273684	61.89349	66.289954	26	69	TT		KEEP	---	---	---	---	capture		Lung(183;0.0858)	Missense_Mutation	SNP	118349561	118349561	15482	1	T	G	G	55	55	SPAG17	G	4	4
APH1A	51107	broad.mit.edu	36	1	148506106	148506106	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:148506106G>A	uc001eua.1	-	c.602C>T	c.(601-603)TCG>TTG	p.S201L	APH1A_uc001ety.1_Missense_Mutation_p.S201L|APH1A_uc001etz.1_Missense_Mutation_p.S201L|APH1A_uc001eub.1_Missense_Mutation_p.S85L	NM_016022	NP_057106	Q96BI3	APH1A_HUMAN	anterior pharynx defective 1 homolog A isoform	201	Helical; Name=6; (Potential).				amyloid precursor protein catabolic process|apoptosis|induction of apoptosis by extracellular signals|membrane protein ectodomain proteolysis|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|positive regulation of catalytic activity|protein processing	endoplasmic reticulum membrane|Golgi cisterna membrane|integral to plasma membrane	protein binding			ovary(1)	1	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)													0.324324	100.064583	103.103358	36	75	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.171)		Missense_Mutation	SNP	148506106	148506106	781	1	G	A	A	37	37	APH1A	A	1	1
FLG2	388698	broad.mit.edu	36	1	150592337	150592337	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150592337G>A	uc001ezw.2	-	c.4549C>T	c.(4549-4551)CAT>TAT	p.H1517Y		NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	1517							calcium ion binding|structural molecule activity			ovary(9)|breast(1)	10	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.358757	330.990647	337.223794	127	227	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150592337	150592337	6161	1	G	A	A	48	48	FLG2	A	2	2
PPOX	5498	broad.mit.edu	36	1	159404845	159404845	+	Splice_Site_SNP	SNP	G	T	T			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:159404845G>T	uc001fyj.2	+	c.472_splice	c.e6-1	p.V158_splice	PPOX_uc001fyn.2_Intron|PPOX_uc001fyg.2_Splice_Site_SNP_p.V158_splice|PPOX_uc001fyk.2_Splice_Site_SNP|PPOX_uc001fyl.2_Splice_Site_SNP_p.V124_splice|PPOX_uc001fyh.2_Splice_Site_SNP|PPOX_uc009wuc.1_Splice_Site_SNP|PPOX_uc001fym.2_Intron|PPOX_uc001fyi.2_De_novo_Start_OutOfFrame	NM_001122764	NP_001116236			protoporphyrinogen oxidase						heme biosynthetic process|oxidation-reduction process	intrinsic to mitochondrial inner membrane|mitochondrial intermembrane space	flavin adenine dinucleotide binding|oxygen-dependent protoporphyrinogen oxidase activity			ovary(1)	1	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)													0.335329	148.846527	152.854341	56	111	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(70;0.00275)		Splice_Site_SNP	SNP	159404845	159404845	12783	1	G	T	T	35	35	PPOX	T	5	3
HMCN1	83872	broad.mit.edu	36	1	184358766	184358766	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:184358766C>T	uc001grq.1	+	c.12290C>T	c.(12289-12291)ACG>ATG	p.T4097M		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1	4097	Ig-like C2-type 40.				bioluminescence|protein-chromophore linkage|response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)	22														0.323529	87.542971	90.360988	33	69	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	184358766	184358766	7511	1	C	T	T	19	19	HMCN1	T	1	1
UBR4	23352	broad.mit.edu	36	1	19364767	19364767	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:19364767C>T	uc001bbi.1	-	c.4181G>A	c.(4180-4182)CGT>CAT	p.R1394H	UBR4_uc001bbm.1_Missense_Mutation_p.R605H	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	1394			R -> H (in a breast cancer sample; somatic mutation).		interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding	p.R1394H(2)		kidney(10)|ovary(7)|breast(4)|pancreas(2)	23		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)												0.385965	61.52483	62.177853	22	35	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)	Missense_Mutation	SNP	19364767	19364767	17462	1	C	T	T	19	19	UBR4	T	1	1
RYR2	6262	broad.mit.edu	36	1	235878397	235878397	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:235878397C>T	uc001hyl.1	+	c.7373C>T	c.(7372-7374)GCG>GTG	p.A2458V		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	2458	Cytoplasmic (By similarity).|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)												0.526316	30.150161	30.161578	10	9	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.00606)		Missense_Mutation	SNP	235878397	235878397	14249	1	C	T	T	27	27	RYR2	T	1	1
EYA3	2140	broad.mit.edu	36	1	28234661	28234661	+	Silent	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:28234661C>T	uc001bpi.1	-	c.342G>A	c.(340-342)ACG>ACA	p.T114T	EYA3_uc001bpj.2_Silent_p.T114T|EYA3_uc001bpk.1_Non-coding_Transcript	NM_001990	NP_001981	Q99504	EYA3_HUMAN	eyes absent 3	114					anatomical structure morphogenesis|double-strand break repair|histone dephosphorylation|multicellular organismal development|positive regulation of DNA repair|regulation of transcription, DNA-dependent|response to ionizing radiation|transcription, DNA-dependent|visual perception	cytoplasm	metal ion binding|protein binding|protein tyrosine phosphatase activity			ovary(2)	2		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000432)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)												0.335025	179.187614	183.932804	66	131	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0484)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;2.8e-06)|STAD - Stomach adenocarcinoma(196;0.00364)|KIRC - Kidney renal clear cell carcinoma(1967;0.00378)|BRCA - Breast invasive adenocarcinoma(304;0.00718)|READ - Rectum adenocarcinoma(331;0.0642)	Silent	SNP	28234661	28234661	5524	1	C	T	T	19	19	EYA3	T	1	1
ZSCAN20	7579	broad.mit.edu	36	1	33732897	33732897	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:33732897C>T	uc001bxj.2	+	c.2366C>T	c.(2365-2367)ACG>ATG	p.T789M	ZSCAN20_uc009vui.1_Missense_Mutation_p.T788M	NM_145238	NP_660281	P17040	ZSC20_HUMAN	zinc finger protein 31	789					regulation of transcription, DNA-dependent|viral reproduction	mitochondrion|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)												0.391892	164.002022	165.520807	58	90	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33732897	33732897	18836	1	C	T	T	19	19	ZSCAN20	T	1	1
EPHA10	284656	broad.mit.edu	36	1	38000078	38000078	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:38000078C>T	uc009vvi.1	-	c.436G>A	c.(436-438)GGC>AGC	p.G146S	EPHA10_uc001cbw.2_Missense_Mutation_p.G146S	NM_001099439	NP_001092909	Q5JZY3	EPHAA_HUMAN	EPH receptor A10 isofom 3	146	Extracellular (Potential).				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular region|integral to membrane|integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding|transmembrane-ephrin receptor activity			breast(3)|stomach(1)	4	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)								328				0.333333	82.212541	84.662791	33	66	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38000078	38000078	5359	1	C	T	T	23	23	EPHA10	T	1	1
SGIP1	84251	broad.mit.edu	36	1	66967554	66967554	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:66967554G>A	uc001dcr.1	+	c.1762G>A	c.(1762-1764)GGA>AGA	p.G588R	SGIP1_uc001dcs.1_Missense_Mutation_p.G188R|SGIP1_uc001dct.1_Missense_Mutation_p.G190R|SGIP1_uc009wat.1_Missense_Mutation_p.G382R|SGIP1_uc001dcu.1_Missense_Mutation_p.G93R	NM_032291	NP_115667	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting	588					intracellular protein transport|positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess|vesicle-mediated transport	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3														0.40404	117.781024	118.577596	40	59	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	66967554	66967554	14697	1	G	A	A	39	39	SGIP1	A	1	1
XKR7	343702	broad.mit.edu	36	20	30048114	30048114	+	Silent	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:30048114C>T	uc002wxe.1	+	c.933C>T	c.(931-933)GCC>GCT	p.A311A		NM_001011718	NP_001011718	Q5GH72	XKR7_HUMAN	XK, Kell blood group complex subunit-related	311						integral to membrane				ovary(1)|breast(1)	2														0.238938	66.166223	73.201615	27	86	CC		KEEP	---	---	---	---	capture	Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)		Silent	SNP	30048114	30048114	18017	20	C	T	T	23	23	XKR7	T	1	1
KIAA1755	85449	broad.mit.edu	36	20	36303233	36303233	+	Silent	SNP	G	C	C			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:36303233G>C	uc002xhy.1	-	c.714C>G	c.(712-714)GGC>GGG	p.G238G	KIAA1755_uc002xhz.1_Silent_p.G238G	NM_001029864	NP_001025035	Q5JYT7	K1755_HUMAN	hypothetical protein LOC85449	238										ovary(4)|pancreas(1)	5		Myeloproliferative disorder(115;0.00874)												0.315068	138.493978	142.937814	46	100	GG		KEEP	---	---	---	---	capture			Silent	SNP	36303233	36303233	8568	20	G	C	C	46	46	KIAA1755	C	3	3
ZSWIM3	140831	broad.mit.edu	36	20	43940188	43940188	+	Silent	SNP	C	G	G			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:43940188C>G	uc002xqd.1	+	c.1584C>G	c.(1582-1584)GGC>GGG	p.G528G		NM_080752	NP_542790	Q96MP5	ZSWM3_HUMAN	zinc finger, SWIM domain containing 3	528							zinc ion binding			ovary(2)	2		Myeloproliferative disorder(115;0.0122)												0.322581	58.405825	60.124342	20	42	CC		KEEP	---	---	---	---	capture			Silent	SNP	43940188	43940188	18846	20	C	G	G	28	28	ZSWIM3	G	3	3
TSHZ2	128553	broad.mit.edu	36	20	51305264	51305264	+	Silent	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:51305264C>T	uc002xwo.2	+	c.1860C>T	c.(1858-1860)CAC>CAT	p.H620H		NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	620					multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4														0.193548	47.631777	58.499908	24	100	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(23;0.1)		Silent	SNP	51305264	51305264	17175	20	C	T	T	19	19	TSHZ2	T	1	1
CHGB	1114	broad.mit.edu	36	20	5852743	5852743	+	Silent	SNP	C	T	T	rs56291961	unknown	TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:5852743C>T	uc002wmg.1	+	c.1953C>T	c.(1951-1953)GAC>GAT	p.D651D		NM_001819	NP_001810	P05060	SCG1_HUMAN	chromogranin B precursor	651						extracellular space	hormone activity			breast(3)|ovary(1)	4														0.257143	22.065721	23.932606	9	26	CC		KEEP	---	---	---	---	capture			Silent	SNP	5852743	5852743	3473	20	C	T	T	19	19	CHGB	T	1	1
TIMP3	7078	broad.mit.edu	36	22	31585261	31585261	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0122-01	TCGA-06-0122-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr22:31585261A>C	uc003anb.1	+	c.533A>C	c.(532-534)CAG>CCG	p.Q178P	SYN3_uc003amx.1_Intron|SYN3_uc003amy.1_Intron|SYN3_uc003amz.1_Intron	NM_000362	NP_000353	P35625	TIMP3_HUMAN	tissue inhibitor of metalloproteinase 3	178	Mediates interaction with EFEMP1.				negative regulation of membrane protein ectodomain proteolysis|visual perception		metal ion binding|metalloendopeptidase inhibitor activity|protein binding			lung(1)	1										10				0.418605	48.636865	48.886491	18	25	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31585261	31585261	16448	22	A	C	C	7	7	TIMP3	C	4	4
PCDP1	200373	broad.mit.edu	36	2	120085765	120085765	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:120085765C>T	uc002tmb.1	+	c.430C>T	c.(430-432)CGG>TGG	p.R144W		NM_001029996	NP_001025167	Q4G0U5	PCDP1_HUMAN	primary ciliary dyskinesia protein 1	430						cilium	calmodulin binding				0	Colorectal(110;0.196)													0.372881	63.938012	64.774177	22	37	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	120085765	120085765	11992	2	C	T	T	19	19	PCDP1	T	1	1
LRP1B	53353	broad.mit.edu	36	2	140788976	140788976	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0122-01	TCGA-06-0122-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:140788976A>G	uc002tvj.1	-	c.12803T>C	c.(12802-12804)CTA>CCA	p.L4268P		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	4268	Extracellular (Potential).|EGF-like 11.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|ovary(10)|pancreas(3)|central_nervous_system(2)|liver(1)|kidney(1)	34		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)				Colon(99;50 2074 2507 20106)				2546	TSP Lung(27;0.18)			0.373333	91.786441	92.841247	28	47	AA		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)	Missense_Mutation	SNP	140788976	140788976	9328	2	A	G	G	15	15	LRP1B	G	4	4
COBLL1	22837	broad.mit.edu	36	2	165286947	165286947	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:165286947G>A	uc002ucp.1	-	c.880C>T	c.(880-882)CGG>TGG	p.R294W	COBLL1_uc002uco.1_Missense_Mutation_p.R63W|COBLL1_uc002ucq.1_Missense_Mutation_p.R294W|COBLL1_uc002ucr.1_Missense_Mutation_p.R332W|COBLL1_uc002ucs.1_Non-coding_Transcript	NM_014900	NP_055715	Q53SF7	COBL1_HUMAN	COBL-like 1	332	KKRRAP 1.									ovary(2)|pancreas(1)	3														0.377358	108.289673	109.682366	40	66	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	165286947	165286947	3792	2	G	A	A	38	38	COBLL1	A	1	1
SCN1A	6323	broad.mit.edu	36	2	166559093	166559093	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0122-01	TCGA-06-0122-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:166559093T>C	uc010fpj.1	-	c.4628A>G	c.(4627-4629)AAC>AGC	p.N1543S		NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha	1554	Helical; Name=S1 of repeat IV; (By similarity).|IV.					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|large_intestine(1)	7					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)									0.306667	71.799914	74.297721	23	52	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	166559093	166559093	14396	2	T	C	C	60	60	SCN1A	C	4	4
TTN	7273	broad.mit.edu	36	2	179185120	179185120	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179185120G>C	uc002umr.1	-	c.42559C>G	c.(42559-42561)CCC>GCC	p.P14187A	TTN_uc002ums.1_Missense_Mutation_p.P7882A|TTN_uc010frc.1_Missense_Mutation_p.P7815A|TTN_uc010frd.1_Missense_Mutation_p.P7690A	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	15114										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153										8722				0.37037	32.243635	32.642108	10	17	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179185120	179185120	17290	2	G	C	C	44	44	TTN	C	3	3
TTN	7273	broad.mit.edu	36	2	179306022	179306022	+	Silent	SNP	G	A	A	rs72648936	unknown	TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179306022G>A	uc002umr.1	-	c.12394C>T	c.(12394-12396)CTG>TTG	p.L4132L	TTN_uc002ums.1_Intron|TTN_uc010frc.1_Intron|TTN_uc010frd.1_Intron|TTN_uc002umz.1_Silent_p.L793L	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	5059										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153									p.L4132V(SNGM-Tumor)	8722				0.317073	34.455696	35.678234	13	28	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Silent	SNP	179306022	179306022	17290	2	G	A	A	36	36	TTN	A	2	2
TTN	7273	broad.mit.edu	36	2	179307488	179307488	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179307488G>A	uc002umr.1	-	c.11576C>T	c.(11575-11577)CCA>CTA	p.P3859L	TTN_uc002ums.1_Intron|TTN_uc010frc.1_Intron|TTN_uc010frd.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.P520L	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	4786										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153										8722				0.308271	106.91989	111.280769	41	92	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179307488	179307488	17290	2	G	A	A	47	47	TTN	A	2	2
IHH	3549	broad.mit.edu	36	2	219628806	219628806	+	Silent	SNP	G	A	A			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:219628806G>A	uc002vjo.1	-	c.603C>T	c.(601-603)GGC>GGT	p.G201G		NM_002181	NP_002172	Q14623	IHH_HUMAN	Indian hedgehog homolog	201					cell-cell signaling|intein-mediated protein splicing|proteolysis	extracellular space|plasma membrane	cholesterol binding|patched binding|peptidase activity				0		Renal(207;0.0915)												0.25641	21.628223	23.729885	10	29	GG		KEEP	---	---	---	---	capture		Epithelial(149;1.13e-06)|all cancers(144;0.000188)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Silent	SNP	219628806	219628806	7908	2	G	A	A	38	38	IHH	A	1	1
ACCN4	55515	broad.mit.edu	36	2	220105043	220105043	+	Silent	SNP	G	C	C			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:220105043G>C	uc002vlz.1	+	c.1185G>C	c.(1183-1185)GGG>GGC	p.G395G	ACCN4_uc010fwi.1_Silent_p.G395G|ACCN4_uc010fwj.1_Silent_p.G395G|ACCN4_uc002vly.1_Silent_p.G395G|ACCN4_uc002vma.1_Silent_p.G395G|ACCN4_uc002vmb.2_Silent_p.G49G	NM_018674	NP_061144	Q96FT7	ACCN4_HUMAN	amiloride-sensitive cation channel 4 isoform 1	395	Extracellular (Potential).					integral to plasma membrane	sodium channel activity|sodium ion transmembrane transporter activity			ovary(2)	2		Renal(207;0.0183)												0.328571	136.003224	139.650568	46	94	GG		KEEP	---	---	---	---	capture		Epithelial(149;5.47e-10)|all cancers(144;9e-08)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.0086)|READ - Rectum adenocarcinoma(5;0.156)	Silent	SNP	220105043	220105043	132	2	G	C	C	44	44	ACCN4	C	3	3
UGT1A6	54578	broad.mit.edu	36	2	234267011	234267011	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:234267011C>T	uc002vuv.2	+	c.622C>T	c.(622-624)CGA>TGA	p.R208*	UGT1A8_uc002vup.1_Intron|UGT1A10_uc002vuq.2_Intron|UGT1A10_uc002vur.1_Intron|UGT1A9_uc002vus.1_Intron|UGT1A7_uc002vut.1_Intron|UGT1A6_uc002vuu.1_Intron	NM_001072	NP_001063	P19224	UD16_HUMAN	UDP glycosyltransferase 1 family, polypeptide A6	208					xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	enzyme binding|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity				0		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)												0.382353	219.20191	221.677396	78	126	CC		KEEP	---	---	---	---	capture		Epithelial(121;5.86e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000384)|Lung(119;0.00306)|LUSC - Lung squamous cell carcinoma(224;0.00702)	Nonsense_Mutation	SNP	234267011	234267011	17507	2	C	T	T	19	19	UGT1A6	T	5	1
ALLC	55821	broad.mit.edu	36	2	3707143	3707143	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:3707143G>C	uc010ewt.1	+	c.343G>C	c.(343-345)GCA>CCA	p.A115P		NM_018436	NP_060906	Q8N6M5	ALLC_HUMAN	allantoicase isoform a	134							allantoicase activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)												0.333333	7.120739	7.342775	3	6	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)	Missense_Mutation	SNP	3707143	3707143	537	2	G	C	C	46	46	ALLC	C	3	3
PRKD3	23683	broad.mit.edu	36	2	37370082	37370082	+	Nonsense_Mutation	SNP	G	C	C			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:37370082G>C	uc002rqd.1	-	c.638C>G	c.(637-639)TCA>TGA	p.S213*	PRKD3_uc002rqf.1_Nonsense_Mutation_p.S213*	NM_005813	NP_005804	O94806	KPCD3_HUMAN	protein kinase D3	213					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|protein phosphorylation	cytoplasm|membrane|nucleus	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(2)|ovary(1)|central_nervous_system(1)	4		all_hematologic(82;0.21)				Melanoma(80;621 1355 8613 11814 51767)				569				0.366667	106.15226	107.558797	33	57	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	37370082	37370082	12963	2	G	C	C	45	45	PRKD3	C	5	3
RTP1	132112	broad.mit.edu	36	3	188400348	188400348	+	Silent	SNP	G	A	A			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:188400348G>A	uc003frg.1	+	c.588G>A	c.(586-588)GAG>GAA	p.E196E		NM_153708	NP_714919	P59025	RTP1_HUMAN	receptor transporting protein 1	196	Cytoplasmic (Potential).				protein insertion into membrane	cell surface|integral to membrane|plasma membrane	olfactory receptor binding			ovary(2)|breast(1)	3	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)													0.265306	34.154927	36.592698	13	36	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)	Silent	SNP	188400348	188400348	14213	3	G	A	A	35	35	RTP1	A	2	2
OR5K3	403277	broad.mit.edu	36	3	99592546	99592546	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:99592546C>T	uc003dsl.1	+	c.347C>T	c.(346-348)GCG>GTG	p.A116V		NM_001005516	NP_001005516	A6NET4	OR5K3_HUMAN	olfactory receptor, family 5, subfamily K,	116	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.325243	178.210872	183.764049	67	139	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99592546	99592546	11578	3	C	T	T	27	27	OR5K3	T	1	1
HCN1	348980	broad.mit.edu	36	5	45497842	45497842	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:45497842C>G	uc003jok.1	-	c.874G>C	c.(874-876)GCC>CCC	p.A292P		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	292	Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1														0.205882	14.505254	17.370912	7	27	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45497842	45497842	7278	5	C	G	G	27	27	HCN1	G	3	3
ADAMTS16	170690	broad.mit.edu	36	5	5315831	5315831	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:5315831C>A	uc003jdl.1	+	c.2724C>A	c.(2722-2724)TTC>TTA	p.F908L	ADAMTS16_uc003jdk.1_Missense_Mutation_p.F908L	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1	908	TSP type-1 2.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8														0.430233	105.15863	105.524165	37	49	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5315831	5315831	262	5	C	A	A	32	32	ADAMTS16	A	3	3
EZR	7430	broad.mit.edu	36	6	159126591	159126591	+	Nonsense_Mutation	SNP	C	A	A			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:159126591C>A	uc003qrt.2	-	c.205G>T	c.(205-207)GAG>TAG	p.E69*	EZR_uc003qru.2_Nonsense_Mutation_p.E69*	NM_003379	NP_003370	P15311	EZRI_HUMAN	ezrin	69	FERM.				actin filament bundle assembly|axon guidance|cytoskeletal anchoring at plasma membrane|leukocyte cell-cell adhesion|membrane to membrane docking|regulation of cell shape	actin filament|apical plasma membrane|basolateral plasma membrane|cortical cytoskeleton|cytosol|extrinsic to membrane|filopodium|microvillus membrane|nucleolus|ruffle membrane	actin filament binding|cell adhesion molecule binding			ovary(1)	1		Breast(66;0.000776)|Ovarian(120;0.0303)												0.394737	41.517073	41.88544	15	23	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(65;2.16e-17)|BRCA - Breast invasive adenocarcinoma(81;6.58e-06)	Nonsense_Mutation	SNP	159126591	159126591	5529	6	C	A	A	30	30	EZR	A	5	3
TFEC	22797	broad.mit.edu	36	7	115401464	115401464	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:115401464C>T	uc003vhj.1	-	c.263G>A	c.(262-264)AGA>AAA	p.R88K	TFEC_uc003vhk.1_Intron|TFEC_uc003vhl.2_Intron	NM_012252	NP_036384	O14948	TFEC_HUMAN	transcription factor EC isoform a	88	Necessary for transcriptional transactivation.				regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|transcription regulator activity			large_intestine(1)	1														0.298507	53.371623	55.804255	20	47	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(10;0.00878)		Missense_Mutation	SNP	115401464	115401464	16330	7	C	T	T	32	32	TFEC	T	2	2
EPHA1	2041	broad.mit.edu	36	7	142807013	142807013	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0122-01	TCGA-06-0122-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:142807013T>C	uc003wcz.1	-	c.688A>G	c.(688-690)ACC>GCC	p.T230A		NM_005232	NP_005223	P21709	EPHA1_HUMAN	ephrin receptor EphA1	230	Extracellular (Potential).|Cys-rich.				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|ephrin receptor activity			ovary(3)|lung(1)|breast(1)	5	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)								379				0.5	7.622336	7.622336	3	3	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	142807013	142807013	5358	7	T	C	C	58	58	EPHA1	C	4	4
CNTNAP2	26047	broad.mit.edu	36	7	146890249	146890249	+	Silent	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:146890249C>T	uc003weu.1	+	c.1864C>T	c.(1864-1866)CTG>TTG	p.L622L		NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor	622	Extracellular (Potential).|Fibrinogen C-terminal.				behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)												0.25	62.997264	68.908082	26	78	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.0319)		Silent	SNP	146890249	146890249	3785	7	C	T	T	32	32	CNTNAP2	T	2	2
PCLO	27445	broad.mit.edu	36	7	82228661	82228661	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0122-01	TCGA-06-0122-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:82228661A>G	uc003uhx.2	-	c.15092T>C	c.(15091-15093)CTC>CCC	p.L5031P		NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	4954	C2 2.				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity|zinc ion binding			ovary(7)	7														0.482759	49.253883	49.261075	14	15	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	82228661	82228661	12003	7	A	G	G	11	11	PCLO	G	4	4
PCLO	27445	broad.mit.edu	36	7	82424117	82424117	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:82424117G>A	uc003uhx.2	-	c.4088C>T	c.(4087-4089)ACG>ATG	p.T1363M	PCLO_uc003uhv.2_Missense_Mutation_p.T1363M	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	1294					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity|zinc ion binding			ovary(7)	7														0.298701	59.994239	62.783423	23	54	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	82424117	82424117	12003	7	G	A	A	40	40	PCLO	A	1	1
DEFB135	613209	broad.mit.edu	36	8	11879427	11879427	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:11879427C>G	uc003wuw.1	+	c.153C>G	c.(151-153)AAC>AAG	p.N51K		NM_001033017	NP_001028189	Q30KP9	DB135_HUMAN	beta-defensin 136	51					defense response to bacterium	extracellular region					0														0.282759	119.961428	126.154111	41	104	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11879427	11879427	4598	8	C	G	G	19	19	DEFB135	G	3	3
COL22A1	169044	broad.mit.edu	36	8	139959310	139959310	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:139959310C>T	uc003yvd.1	-	c.523G>A	c.(523-525)GTG>ATG	p.V175M		NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	175	VWFA.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(10)|pancreas(1)	11	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)													0.291667	16.719384	17.650201	7	17	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(115;0.0517)		Missense_Mutation	SNP	139959310	139959310	3819	8	C	T	T	19	19	COL22A1	T	1	1
SLCO5A1	81796	broad.mit.edu	36	8	70830375	70830375	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0122-01	TCGA-06-0122-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:70830375A>T	uc003xyl.1	-	c.1096T>A	c.(1096-1098)TTT>ATT	p.F366I	SLCO5A1_uc010lzb.1_Missense_Mutation_p.F366I|SLCO5A1_uc003xyk.1_Missense_Mutation_p.F366I|SLCO5A1_uc010lzc.1_Missense_Mutation_p.F366I	NM_030958	NP_112220	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family,	366	Helical; Name=6; (Potential).					integral to membrane|plasma membrane	transporter activity			ovary(3)	3	Breast(64;0.0654)													0.431373	65.443065	65.652263	22	29	AA		KEEP	---	---	---	---	capture	Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)		Missense_Mutation	SNP	70830375	70830375	15228	8	A	T	T	2	2	SLCO5A1	T	4	4
KCNB2	9312	broad.mit.edu	36	8	74011030	74011030	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:74011030G>A	uc003xzb.1	+	c.886G>A	c.(886-888)GTG>ATG	p.V296M		NM_004770	NP_004761	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related	296					regulation of smooth muscle contraction	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|protein binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|pancreas(1)	4	Breast(64;0.137)													0.6	81.91773	82.308668	27	18	GG		KEEP	---	---	---	---	capture	Epithelial(68;0.105)		Missense_Mutation	SNP	74011030	74011030	8318	8	G	A	A	40	40	KCNB2	A	1	1
MCART6	401612	broad.mit.edu	36	X	103235703	103235703	+	Silent	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:103235703C>T	uc004elu.1	-	c.894G>A	c.(892-894)TCG>TCA	p.S298S	MCART6_uc010npb.1_Silent_p.S298S	NM_001012755	NP_001012773	Q5H9E4	MCAR6_HUMAN	mitochondrial carrier triple repeat 6	298	Solcar 3.				transport	integral to membrane|mitochondrial inner membrane					0														0.283951	58.489519	61.886	23	58	CC		KEEP	---	---	---	---	capture			Silent	SNP	103235703	103235703	9760	23	C	T	T	27	27	MCART6	T	1	1
KLHL13	90293	broad.mit.edu	36	X	116917206	116917206	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0122-01	TCGA-06-0122-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:116917206A>T	uc004eql.1	-	c.1661T>A	c.(1660-1662)GTC>GAC	p.V554D	KLHL13_uc004eqk.1_Missense_Mutation_p.V503D|KLHL13_uc004eqm.1_Missense_Mutation_p.V503D	NM_033495	NP_277030	Q9P2N7	KLH13_HUMAN	kelch-like 13	554	Kelch 5.				cytokinesis|mitosis|protein ubiquitination	Cul3-RING ubiquitin ligase complex				kidney(1)	1														0.356322	333.996841	340.327409	124	224	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	116917206	116917206	8681	23	A	T	T	10	10	KLHL13	T	4	4
THOC2	57187	broad.mit.edu	36	X	122648165	122648165	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0122-01	TCGA-06-0122-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:122648165A>G	uc004etu.1	-	c.682T>C	c.(682-684)TTT>CTT	p.F228L	THOC2_uc004ett.1_Missense_Mutation_p.F113L	NM_001081550	NP_001075019	Q8NI27	THOC2_HUMAN	THO complex 2 isoform 1	228					intronless viral mRNA export from host nucleus|mRNA processing|RNA splicing	THO complex part of transcription export complex	protein binding|RNA binding			ovary(3)	3														0.344	136.388745	139.074933	43	82	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	122648165	122648165	16393	23	A	G	G	3	3	THOC2	G	4	4
PRPS2	5634	broad.mit.edu	36	X	12727407	12727407	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:12727407G>A	uc004cva.1	+	c.283G>A	c.(283-285)GCC>ACC	p.A95T	PRPS2_uc004cvb.1_Missense_Mutation_p.A95T|PRPS2_uc010nec.1_Missense_Mutation_p.A28T	NM_001039091	NP_001034180	P11908	PRPS2_HUMAN	phosphoribosyl pyrophosphate synthetase 2	95					nucleoside metabolic process|ribonucleoside monophosphate biosynthetic process		ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity				0														0.327731	98.877946	102.013083	39	80	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12727407	12727407	13023	23	G	A	A	38	38	PRPS2	A	1	1
PPP1R3F	89801	broad.mit.edu	36	X	49029356	49029356	+	Silent	SNP	C	G	G			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:49029356C>G	uc004dnh.1	+	c.1260C>G	c.(1258-1260)TCC>TCG	p.S420S	PPP1R3F_uc004dni.1_Silent_p.S74S|PPP1R3F_uc004dnj.1_Silent_p.S74S	NM_033215	NP_149992	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory (inhibitor)	420	Extracellular (Potential).					integral to membrane				ovary(2)	2	Ovarian(276;0.236)													0.346154	26.467037	27.01042	9	17	CC		KEEP	---	---	---	---	capture			Silent	SNP	49029356	49029356	12810	23	C	G	G	24	24	PPP1R3F	G	3	3
AWAT2	158835	broad.mit.edu	36	X	69178922	69178922	+	Silent	SNP	G	A	A			TCGA-06-0122-01	TCGA-06-0122-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:69178922G>A	uc004dxt.1	-	c.687C>T	c.(685-687)GAC>GAT	p.D229D		NM_001002254	NP_001002254	Q6E213	AWAT2_HUMAN	diacylglycerol O-acyltransferase 2-like 4	229						endoplasmic reticulum membrane|integral to membrane	long-chain-alcohol O-fatty-acyltransferase activity				0						NSCLC(80;1334 1436 9350 24214 26427)								0.345455	49.701629	50.864635	19	36	GG		KEEP	---	---	---	---	capture			Silent	SNP	69178922	69178922	1256	23	G	A	A	44	44	AWAT2	A	2	2
KLHL4	56062	broad.mit.edu	36	X	86759659	86759659	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0122-01	TCGA-06-0122-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:86759659C>T	uc004efa.1	+	c.796C>T	c.(796-798)CAG>TAG	p.Q266*	KLHL4_uc004efb.1_Nonsense_Mutation_p.Q266*	NM_057162	NP_476503	Q9C0H6	KLHL4_HUMAN	kelch-like 4 isoform 2	266						cytoplasm|microtubule cytoskeleton|nucleolus	actin binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5														0.410256	88.887727	89.435528	32	46	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	86759659	86759659	8705	23	C	T	T	29	29	KLHL4	T	5	2
ARHGAP22	58504	broad.mit.edu	36	10	49328970	49328970	+	Frame_Shift_Del	DEL	A	-	-			TCGA-06-0122-01	TCGA-06-0122-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:49328970_49328970delA	uc001jgu.1	-	c.1256_1256delT	c.(1255-1257)GTGfs	p.V419fs	ARHGAP22_uc001jgt.1_Frame_Shift_Del_p.V403fs|ARHGAP22_uc001jgv.1_Frame_Shift_Del_p.V101fs|ARHGAP22_uc001jgr.1_Frame_Shift_Del_p.V120fs|ARHGAP22_uc001jgs.1_Frame_Shift_Del_p.V313fs	NM_021226	NP_067049	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 2	403					angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol|nucleus	GTPase activator activity			ovary(1)	1														0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	49328970	49328970	883	10	A	-	-	6	6	ARHGAP22	-	5	5
KANK3	256949	broad.mit.edu	36	19	8304950	8304961	+	In_Frame_Del	DEL	TCGCTGTCGCCA	-	-			TCGA-06-0122-01	TCGA-06-0122-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:8304950_8304961delTCGCTGTCGCCA	uc010dwa.1	-	c.1467_1478delTGGCGACAGCGA	c.(1465-1479)GATGGCGACAGCGAG>GAG	p.DGDS489del	KANK3_uc002mjp.1_In_Frame_Del_p.MATA1del	NM_198471	NP_940873	Q6NY19	KANK3_HUMAN	ankyrin repeat domain 47	489_492											0														0.33			2	4				---	---	---	---	capture_indel			In_Frame_Del	DEL	8304950	8304961	8282	19	TCGCTGTCGCCA	-	-	54	54	KANK3	-	5	5
PAPD7	11044	broad.mit.edu	36	5	6790716	6790717	+	Frame_Shift_Del	DEL	TG	-	-			TCGA-06-0122-01	TCGA-06-0122-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:6790716_6790717delTG	uc003jdx.1	+	c.60_61delTG	c.(58-63)ACTGTGfs	p.T20fs		NM_006999	NP_008930	Q5XG87	PAPD7_HUMAN	DNA polymerase sigma	20_21					cell division|DNA replication|double-strand break repair|mitotic chromosome condensation|response to drug|sister chromatid cohesion	nucleus	DNA binding|DNA-directed DNA polymerase activity|SMC protein binding			ovary(1)	1						NSCLC(7;212 333 5667 23379 46547)								0.43			22	29				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	6790716	6790717	11843	5	TG	-	-	55	55	PAPD7	-	5	5
IRF5	3663	broad.mit.edu	36	7	128374603	128374617	+	Splice_Site_Del	DEL	ACTCTGCGGCCGCCT	-	-			TCGA-06-0122-01	TCGA-06-0122-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:128374603_128374617delACTCTGCGGCCGCCT	uc003vog.1	+	c.e7_splice_site			IRF5_uc010llr.1_In_Frame_Del_p.LCGRL162del|IRF5_uc010lls.1_In_Frame_Del_p.LCGRL162del|IRF5_uc003voh.1_Splice_Site_Del|IRF5_uc010llt.1_Intron|IRF5_uc003voi.1_Splice_Site_Del|IRF5_uc003vok.2_3'UTR|IRF5_uc010llu.1_In_Frame_Del_p.LCGRL162del|IRF5_uc003voj.2_Splice_Site_Del|IRF5_uc010llv.1_3'UTR|IRF5_uc010llw.1_In_Frame_Del_p.LCGRL162del	NM_002200	NP_002191			interferon regulatory factor 5 isoform a						interferon-gamma-mediated signaling pathway|regulation of transcription, DNA-dependent|type I interferon-mediated signaling pathway	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0														0.76			16	5				---	---	---	---	capture_indel			Splice_Site_Del	DEL	128374603	128374617	8136	7	ACTCTGCGGCCGCCT	-	-	6	6	IRF5	-	5	5
