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
DCLRE1A	9937	broad.mit.edu	36	10	115600381	115600381	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1749-01	TCGA-28-1749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:115600381C>T	uc001law.1	-	c.473G>A	c.(472-474)GGT>GAT	p.G158D		NM_014881	NP_055696	Q6PJP8	DCR1A_HUMAN	DNA cross-link repair 1A	158	Nuclear localization region.				cell division|mitosis	nucleus	hydrolase activity			skin(1)	1				Epithelial(162;0.0157)|all cancers(201;0.0171)										0.77907	217.858957	224.019568	67	19	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	115600381	115600381	4465	10	C	T	T	18	18	DCLRE1A	T	2	2
MMP27	64066	broad.mit.edu	36	11	102080607	102080607	+	Missense_Mutation	SNP	C	A	A			TCGA-28-1749-01	TCGA-28-1749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:102080607C>A	uc001phd.1	-	c.212G>T	c.(211-213)GGA>GTA	p.G71V		NM_022122	NP_071405	Q9H306	MMP27_HUMAN	matrix metalloproteinase 27	71					collagen catabolic process|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(2)	2	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)										0.5	11.398175	11.398175	4	4	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102080607	102080607	10055	11	C	A	A	30	30	MMP27	A	3	3
SPI1	6688	broad.mit.edu	36	11	47337978	47337978	+	Splice_Site_SNP	SNP	A	T	T			TCGA-28-1749-01	TCGA-28-1749-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:47337978A>T	uc001nfb.1	-	c.e3_splice_site			SPI1_uc001nfc.1_Splice_Site_SNP|SLC39A13_uc001nfd.2_Intron|SPI1_uc009ylp.1_Splice_Site_SNP	NM_001080547	NP_001074016			hematopoietic transcription factor PU.1 isoform						negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene-specific transcription|regulation of erythrocyte differentiation	nucleus	protein binding|RNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			lung(1)|central_nervous_system(1)	2				Lung(87;0.0967)										0.392857	31.319401	31.600573	11	17	AA		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	47337978	47337978	15561	11	A	T	T	6	6	SPI1	T	5	4
OR51T1	401665	broad.mit.edu	36	11	4859914	4859914	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1749-01	TCGA-28-1749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:4859914C>T	uc001lzp.1	+	c.290C>T	c.(289-291)GCT>GTT	p.A97V		NM_001004759	NP_001004759	Q8NGJ9	O51T1_HUMAN	olfactory receptor, family 51, subfamily T,	70	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|large_intestine(1)	3		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)										0.411765	358.751562	360.720655	119	170	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	4859914	4859914	11516	11	C	T	T	28	28	OR51T1	T	2	2
OR51A2	401667	broad.mit.edu	36	11	4932739	4932739	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1749-01	TCGA-28-1749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:4932739C>T	uc001lzu.1	-	c.781G>A	c.(781-783)GTT>ATT	p.V261I		NM_001004748	NP_001004748	Q8NGJ7	O51A2_HUMAN	olfactory receptor, family 51, subfamily A,	261	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)										0.288288	92.359196	96.817289	32	79	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	4932739	4932739	11496	11	C	T	T	19	19	OR51A2	T	1	1
SCYL1	57410	broad.mit.edu	36	11	65055641	65055641	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1749-01	TCGA-28-1749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:65055641G>A	uc001oea.1	+	c.1027G>A	c.(1027-1029)GCT>ACT	p.A343T	SCYL1_uc009yqk.1_Missense_Mutation_p.A343T|SCYL1_uc001oeb.1_Missense_Mutation_p.A343T|SCYL1_uc001oec.1_Missense_Mutation_p.A343T|SCYL1_uc001oed.1_Missense_Mutation_p.A200T|SCYL1_uc001oee.1_5'UTR	NM_020680	NP_065731	Q96KG9	NTKL_HUMAN	SCY1-like 1 isoform A	343					protein phosphorylation|regulation of transcription, DNA-dependent|retrograde vesicle-mediated transport, Golgi to ER|transcription, DNA-dependent	cis-Golgi network|COPI vesicle coat|ER-Golgi intermediate compartment|microtubule organizing center|nucleus	ATP binding|DNA binding|protein tyrosine kinase activity			skin(1)	1										387				0.446154	92.168405	92.332266	29	36	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65055641	65055641	14432	11	G	A	A	38	38	SCYL1	A	1	1
ANO4	121601	broad.mit.edu	36	12	100044915	100044915	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1749-01	TCGA-28-1749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:100044915G>A	uc001thx.1	+	c.2804G>A	c.(2803-2805)CGT>CAT	p.R935H	ANO4_uc001thw.1_Missense_Mutation_p.R900H|ANO4_uc001thy.1_Missense_Mutation_p.R455H	NM_178826	NP_849148	Q32M45	ANO4_HUMAN	anoctamin 4	935	Extracellular (Potential).					chloride channel complex	chloride channel activity			ovary(4)	4														0.333333	33.516018	34.32683	11	22	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100044915	100044915	707	12	G	A	A	40	40	ANO4	A	1	1
ATP8A2	51761	broad.mit.edu	36	13	25023643	25023643	+	Splice_Site_SNP	SNP	T	A	A			TCGA-28-1749-01	TCGA-28-1749-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr13:25023643T>A	uc001uqk.1	+	c.e11_splice_site			ATP8A2_uc001uql.1_Splice_Site_SNP	NM_016529	NP_057613			ATPase, aminophospholipid transporter-like,						ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)	3		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)										0.413969	710.222923	714.01306	243	344	TT		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	25023643	25023643	1212	13	T	A	A	57	57	ATP8A2	A	5	4
PCDH20	64881	broad.mit.edu	36	13	60884320	60884320	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1749-01	TCGA-28-1749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:60884320C>T	uc001vid.2	-	c.1913G>A	c.(1912-1914)CGG>CAG	p.R638Q	PCDH20_uc001vie.1_Missense_Mutation_p.R611Q	NM_022843	NP_073754	Q8N6Y1	PCD20_HUMAN	protocadherin 20	611	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|breast(1)|central_nervous_system(1)	6		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)										0.119342	39.604	74.167048	29	214	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	60884320	60884320	11935	13	C	T	T	23	23	PCDH20	T	1	1
PRTG	283659	broad.mit.edu	36	15	53708335	53708335	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1749-01	TCGA-28-1749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:53708335C>T	uc002adg.1	-	c.2783G>A	c.(2782-2784)CGT>CAT	p.R928H		NM_173814	NP_776175	Q2VWP7	PRTG_HUMAN	protogenin	928					multicellular organismal development	integral to membrane				large_intestine(1)|ovary(1)	2				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)										0.352941	56.638417	57.609415	18	33	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53708335	53708335	13089	15	C	T	T	19	19	PRTG	T	1	1
SNUPN	10073	broad.mit.edu	36	15	73689327	73689327	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1749-01	TCGA-28-1749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:73689327C>T	uc002bap.1	-	c.493G>A	c.(493-495)GTG>ATG	p.V165M	SNUPN_uc002ban.1_Missense_Mutation_p.V123M|SNUPN_uc002bao.1_Missense_Mutation_p.V123M|SNUPN_uc002baq.1_Missense_Mutation_p.V123M|SNUPN_uc002bar.1_Missense_Mutation_p.V123M|SNUPN_uc002bas.1_Missense_Mutation_p.V123M	NM_005701	NP_005692	O95149	SPN1_HUMAN	snurportin 1	123	Necessary for interaction with XPO1.				ncRNA metabolic process|protein import into nucleus|spliceosomal snRNP assembly	cytosol|nuclear pore	protein transporter activity|RNA cap binding			pancreas(1)	1														0.32967	89.423867	91.761615	30	61	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73689327	73689327	15377	15	C	T	T	19	19	SNUPN	T	1	1
ALDH1A3	220	broad.mit.edu	36	15	99264890	99264890	+	Silent	SNP	C	T	T			TCGA-28-1749-01	TCGA-28-1749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:99264890C>T	uc002bwn.2	+	c.1275C>T	c.(1273-1275)ATC>ATT	p.I425I	ALDH1A3_uc010bpb.1_Silent_p.I318I	NM_000693	NP_000684	P47895	AL1A3_HUMAN	aldehyde dehydrogenase 1A3	425					oxidation-reduction process|retinal metabolic process	cytoplasm	protein homodimerization activity			central_nervous_system(2)|lung(1)|pancreas(1)	4	Lung NSC(78;0.00144)|all_lung(78;0.0018)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)		NADH(DB00157)|Vitamin A(DB00162)									0.345455	104.116723	106.436534	38	72	CC		KEEP	---	---	---	---	capture			Silent	SNP	99264890	99264890	495	15	C	T	T	31	31	ALDH1A3	T	1	1
KIF2B	84643	broad.mit.edu	36	17	49256382	49256382	+	Missense_Mutation	SNP	C	A	A			TCGA-28-1749-01	TCGA-28-1749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:49256382C>A	uc002iua.2	+	c.989C>A	c.(988-990)GCT>GAT	p.A330D		NM_032559	NP_115948	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	330	Kinesin-motor.				blood coagulation|cell division|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|microtubule|microtubule organizing center|nucleolus|spindle	ATP binding|microtubule motor activity			ovary(5)	5														0.40146	162.194842	163.358606	55	82	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49256382	49256382	8609	17	C	A	A	28	28	KIF2B	A	3	3
CLEC10A	10462	broad.mit.edu	36	17	6919827	6919827	+	Missense_Mutation	SNP	A	C	C			TCGA-28-1749-01	TCGA-28-1749-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:6919827A>C	uc002gek.1	-	c.622T>G	c.(622-624)TAC>GAC	p.Y208D	CLEC10A_uc002gej.1_Missense_Mutation_p.Y184D|CLEC10A_uc002gel.1_Missense_Mutation_p.Y181D|CLEC10A_uc010clv.1_Missense_Mutation_p.Y181D	NM_182906	NP_878910	Q8IUN9	CLC10_HUMAN	C-type lectin, superfamily member 14 isoform 1	208	C-type lectin.|Extracellular (Potential).				endocytosis|innate immune response	integral to membrane|plasma membrane	sugar binding				0														0.30303	63.081695	65.3633	20	46	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6919827	6919827	3632	17	A	C	C	14	14	CLEC10A	C	4	4
NUP85	79902	broad.mit.edu	36	17	70717543	70717543	+	Missense_Mutation	SNP	T	G	G			TCGA-28-1749-01	TCGA-28-1749-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:70717543T>G	uc002jng.1	+	c.158T>G	c.(157-159)TTT>TGT	p.F53C	NUP85_uc010dgd.1_Missense_Mutation_p.F53C	NM_024844	NP_079120	Q9BW27	NUP85_HUMAN	nucleoporin 85	53					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|nuclear membrane|Nup107-160 complex|spindle	protein binding			ovary(1)	1	all_lung(278;0.14)|Lung NSC(278;0.168)		all cancers(21;3.45e-06)											0.416667	84.166502	84.5297	25	35	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70717543	70717543	11175	17	T	G	G	64	64	NUP85	G	4	4
DNAH2	146754	broad.mit.edu	36	17	7663100	7663100	+	Silent	SNP	G	A	A			TCGA-28-1749-01	TCGA-28-1749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7663100G>A	uc002giu.1	+	c.10809G>A	c.(10807-10809)GCG>GCA	p.A3603A	DNAH2_uc010cnm.1_Silent_p.A541A	NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	3603					ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|central_nervous_system(1)	7		all_cancers(10;4.66e-07)|Prostate(122;0.081)												0.529412	26.372427	26.384999	9	8	GG		KEEP	---	---	---	---	capture			Silent	SNP	7663100	7663100	4785	17	G	A	A	38	38	DNAH2	A	1	1
DSG3	1830	broad.mit.edu	36	18	27298098	27298098	+	Silent	SNP	C	T	T			TCGA-28-1749-01	TCGA-28-1749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:27298098C>T	uc002kws.1	+	c.1026C>T	c.(1024-1026)AGC>AGT	p.S342S		NM_001944	NP_001935	P32926	DSG3_HUMAN	desmoglein 3 preproprotein	342	Cadherin 3.|Extracellular (Potential).				cellular component disassembly involved in apoptosis|homophilic cell adhesion	cytosol|desmosome|integral to membrane	calcium ion binding			ovary(3)|lung(1)|central_nervous_system(1)	5			OV - Ovarian serous cystadenocarcinoma(10;0.00504)											0.5	31.949759	31.949759	10	10	CC		KEEP	---	---	---	---	capture			Silent	SNP	27298098	27298098	4962	18	C	T	T	27	27	DSG3	T	1	1
CCBE1	147372	broad.mit.edu	36	18	55257960	55257960	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1749-01	TCGA-28-1749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:55257960G>A	uc002lib.1	-	c.844C>T	c.(844-846)CGG>TGG	p.R282W	CCBE1_uc010dpq.1_Intron|CCBE1_uc002lia.1_Missense_Mutation_p.R135W	NM_133459	NP_597716	Q6UXH8	CCBE1_HUMAN	collagen and calcium binding EGF domains 1	282	Collagen-like 1.				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)								0.368421	17.618787	17.90829	7	12	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55257960	55257960	2851	18	G	A	A	40	40	CCBE1	A	1	1
PSG1	5669	broad.mit.edu	36	19	48074043	48074043	+	Nonsense_Mutation	SNP	G	A	A			TCGA-28-1749-01	TCGA-28-1749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:48074043G>A	uc010eio.1	-	c.292C>T	c.(292-294)CGA>TGA	p.R98*	PSG10_uc002ouv.1_Intron|PSG3_uc002ouf.1_Intron|PSG1_uc002oug.1_Nonsense_Mutation_p.R98*|PSG1_uc002oun.1_Non-coding_Transcript|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG11_uc002ouw.1_Intron|PSG1_uc002our.1_Nonsense_Mutation_p.R98*|PSG1_uc002oux.1_Nonsense_Mutation_p.R27*|PSG1_uc002ouy.1_Nonsense_Mutation_p.R98*|PSG1_uc002ouz.1_Nonsense_Mutation_p.R98*|PSG1_uc002ova.1_Nonsense_Mutation_p.R98*|PSG1_uc002ovb.2_Nonsense_Mutation_p.R98*|PSG1_uc002ovc.2_Nonsense_Mutation_p.R98*|PSG1_uc002ovd.1_Nonsense_Mutation_p.R98*	NM_006905	NP_008836	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	98	Ig-like V-type.				female pregnancy	extracellular region				ovary(2)	2		Prostate(69;0.00682)												0.305606	464.784651	483.415215	169	384	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	48074043	48074043	13106	19	G	A	A	40	40	PSG1	A	5	1
ERCC2	2068	broad.mit.edu	36	19	50559977	50559977	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1749-01	TCGA-28-1749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:50559977G>A	uc002pbj.1	-	c.553C>T	c.(553-555)CGG>TGG	p.R185W	ERCC2_uc002pbi.1_5'Flank|ERCC2_uc010ejz.1_Intron|ERCC2_uc002pbk.1_Missense_Mutation_p.R161W|ERCC2_uc002pbl.2_Missense_Mutation_p.R161W	NM_000400	NP_000391	P18074	ERCC2_HUMAN	excision repair cross-complementing rodent	185	Helicase ATP-binding.				cell cycle checkpoint|chromosome segregation|hair cell differentiation|induction of apoptosis|interspecies interaction between organisms|mRNA capping|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|response to oxidative stress|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|UV protection|viral reproduction	cytoplasm|holo TFIIH complex|MMXD complex	5'-3' DNA helicase activity|ATP binding|ATP-dependent DNA helicase activity|DNA binding|iron-sulfur cluster binding|metal ion binding|protein C-terminus binding|protein N-terminus binding			lung(1)|pancreas(1)	2		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)						447				0.346154	50.832574	51.919959	18	34	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	50559977	50559977	5406	19	G	A	A	38	38	ERCC2	A	1	1
KLK15	55554	broad.mit.edu	36	19	56022128	56022128	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1749-01	TCGA-28-1749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:56022128G>A	uc002ptl.1	-	c.299C>T	c.(298-300)GCG>GTG	p.A100V	KLK15_uc002ptn.1_Missense_Mutation_p.A100V|KLK15_uc002ptm.1_Missense_Mutation_p.A100V|KLK15_uc002pto.1_Missense_Mutation_p.A99V|KLK15_uc010eod.1_Non-coding_Transcript	NM_017509	NP_059979	Q9H2R5	KLK15_HUMAN	kallikrein-related peptidase 15 isoform 4	100	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			lung(1)|breast(1)	2		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00758)|GBM - Glioblastoma multiforme(134;0.0143)		Pancreas(140;10 2513 7143 9246)								0.313953	63.200891	65.847483	27	59	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56022128	56022128	8717	19	G	A	A	38	38	KLK15	A	1	1
CHIA	27159	broad.mit.edu	36	1	111663531	111663531	+	Missense_Mutation	SNP	T	A	A			TCGA-28-1749-01	TCGA-28-1749-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:111663531T>A	uc001eas.1	+	c.1095T>A	c.(1093-1095)GAT>GAA	p.D365E	CHIA_uc001ear.1_Missense_Mutation_p.D257E|CHIA_uc001eaq.1_Missense_Mutation_p.D257E|CHIA_uc009wgc.1_Missense_Mutation_p.D257E|CHIA_uc001eat.1_Missense_Mutation_p.D204E|CHIA_uc001eav.1_Missense_Mutation_p.D204E|CHIA_uc001eau.1_Missense_Mutation_p.D204E|CHIA_uc009wgd.1_Missense_Mutation_p.D204E	NM_201653	NP_068569	Q9BZP6	CHIA_HUMAN	chitinase, acidic isoform c	365					apoptosis|cell wall chitin metabolic process|chitin catabolic process|digestion|immune response|positive regulation of chemokine secretion|production of molecular mediator involved in inflammatory response|response to acid|response to fungus	cytoplasm|extracellular space	cation binding|chitin binding|chitinase activity|kinase binding|lysozyme activity|sugar binding			ovary(1)	1		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)										0.421818	378.960208	380.425706	116	159	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	111663531	111663531	3476	1	T	A	A	51	51	CHIA	A	4	4
RPTN	126638	broad.mit.edu	36	1	150394279	150394279	+	Silent	SNP	G	A	A			TCGA-28-1749-01	TCGA-28-1749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150394279G>A	uc001ezs.1	-	c.1920C>T	c.(1918-1920)GAC>GAT	p.D640D		NM_001122965	NP_001116437	Q6XPR3	RPTN_HUMAN	repetin	640	Gln-rich.					proteinaceous extracellular matrix	calcium ion binding				0														0.434426	318.004869	318.920724	106	138	GG		KEEP	---	---	---	---	capture			Silent	SNP	150394279	150394279	14144	1	G	A	A	36	36	RPTN	A	2	2
FLG2	388698	broad.mit.edu	36	1	150592345	150592345	+	Missense_Mutation	SNP	G	C	C			TCGA-28-1749-01	TCGA-28-1749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150592345G>C	uc001ezw.2	-	c.4541C>G	c.(4540-4542)TCG>TGG	p.S1514W		NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	1514							calcium ion binding|structural molecule activity			ovary(9)|breast(1)	10	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.430693	589.003985	590.692562	174	230	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	150592345	150592345	6161	1	G	C	C	37	37	FLG2	C	3	3
HMCN1	83872	broad.mit.edu	36	1	184363946	184363946	+	Silent	SNP	C	T	T			TCGA-28-1749-01	TCGA-28-1749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:184363946C>T	uc001grq.1	+	c.12804C>T	c.(12802-12804)GAC>GAT	p.D4268D	HMCN1_uc001grs.1_De_novo_Start_OutOfFrame	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1	4268	Ig-like C2-type 42.				bioluminescence|protein-chromophore linkage|response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)	22														0.419492	298.390664	299.723024	99	137	CC		KEEP	---	---	---	---	capture			Silent	SNP	184363946	184363946	7511	1	C	T	T	19	19	HMCN1	T	1	1
OBSCN	84033	broad.mit.edu	36	1	226522936	226522936	+	Silent	SNP	C	T	T			TCGA-28-1749-01	TCGA-28-1749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:226522936C>T	uc009xez.1	+	c.4944C>T	c.(4942-4944)TGC>TGT	p.C1648C	OBSCN_uc001hsn.1_Silent_p.C1648C|OBSCN_uc001hso.2_Silent_p.C94C	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	1648	Ig-like 17.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			large_intestine(7)|breast(5)|ovary(4)|skin(2)|stomach(1)|central_nervous_system(1)|pancreas(1)	21		Prostate(94;0.0405)							p.C1648C(PF382-Tumor)	4006				0.45	26.272654	26.316041	9	11	CC		KEEP	---	---	---	---	capture			Silent	SNP	226522936	226522936	11217	1	C	T	T	27	27	OBSCN	T	1	1
OR2T11	127077	broad.mit.edu	36	1	246856535	246856535	+	Missense_Mutation	SNP	T	A	A			TCGA-28-1749-01	TCGA-28-1749-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246856535T>A	uc001ier.1	-	c.518A>T	c.(517-519)CAT>CTT	p.H173L		NM_001001964	NP_001001964	Q8NH01	O2T11_HUMAN	olfactory receptor, family 2, subfamily T,	173	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			lung(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)											0.103896	10.690034	34.754376	16	138	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	246856535	246856535	11424	1	T	A	A	51	51	OR2T11	A	4	4
CSMD2	114784	broad.mit.edu	36	1	33815577	33815577	+	Silent	SNP	G	A	A			TCGA-28-1749-01	TCGA-28-1749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:33815577G>A	uc001bxm.1	-	c.7482C>T	c.(7480-7482)AAC>AAT	p.N2494N	CSMD2_uc001bxn.1_Silent_p.N2496N	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2496	Sushi 14.|Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(5)|pancreas(1)	6		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)												0.509091	84.796975	84.800875	28	27	GG		KEEP	---	---	---	---	capture			Silent	SNP	33815577	33815577	4086	1	G	A	A	40	40	CSMD2	A	1	1
SLC1A7	6512	broad.mit.edu	36	1	53328904	53328904	+	Silent	SNP	G	A	A			TCGA-28-1749-01	TCGA-28-1749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:53328904G>A	uc001cuy.1	-	c.1194C>T	c.(1192-1194)TAC>TAT	p.Y398Y	SLC1A7_uc001cux.1_De_novo_Start_OutOfFrame	NM_006671	NP_006662	O00341	EAA5_HUMAN	solute carrier family 1 (glutamate transporter),	398						integral to membrane|plasma membrane	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity			ovary(2)|large_intestine(1)	3				Colorectal(1306;0.234)	L-Glutamic Acid(DB00142)	NSCLC(128;80 1811 21245 38490 51715)								0.428571	28.071888	28.165281	9	12	GG		KEEP	---	---	---	---	capture			Silent	SNP	53328904	53328904	14933	1	G	A	A	40	40	SLC1A7	A	1	1
LHX8	431707	broad.mit.edu	36	1	75395300	75395300	+	Silent	SNP	C	T	T			TCGA-28-1749-01	TCGA-28-1749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:75395300C>T	uc001dgo.1	+	c.945C>T	c.(943-945)TAC>TAT	p.Y315Y	LHX8_uc001dgq.1_Silent_p.Y254Y	NM_001001933	NP_001001933	Q68G74	LHX8_HUMAN	LIM homeobox 8	315					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			ovary(3)	3														0.175879	76.40666	96.112441	35	164	CC		KEEP	---	---	---	---	capture			Silent	SNP	75395300	75395300	9102	1	C	T	T	19	19	LHX8	T	1	1
SLC4A10	57282	broad.mit.edu	36	2	162468799	162468799	+	Silent	SNP	T	G	G			TCGA-28-1749-01	TCGA-28-1749-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:162468799T>G	uc002ubx.2	+	c.1482T>G	c.(1480-1482)GCT>GCG	p.A494A	SLC4A10_uc002uby.2_Silent_p.A464A	NM_022058	NP_071341	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate	494	Cytoplasmic (Potential).				bicarbonate transport|chloride transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity|symporter activity			ovary(2)|lung(2)|pancreas(1)	5														0.416667	193.740506	194.687395	65	91	TT		KEEP	---	---	---	---	capture			Silent	SNP	162468799	162468799	15148	2	T	G	G	54	54	SLC4A10	G	4	4
DYSF	8291	broad.mit.edu	36	2	71596278	71596278	+	Silent	SNP	C	T	T			TCGA-28-1749-01	TCGA-28-1749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:71596278C>T	uc010fen.1	+	c.777C>T	c.(775-777)ATC>ATT	p.I259I	DYSF_uc002sie.1_Silent_p.I227I|DYSF_uc002sig.2_Silent_p.I227I|DYSF_uc010fee.1_Silent_p.I227I|DYSF_uc010fef.1_Silent_p.I258I|DYSF_uc010feg.1_Silent_p.I258I|DYSF_uc010feh.1_Silent_p.I227I|DYSF_uc010fei.1_Silent_p.I258I|DYSF_uc010fej.1_Silent_p.I228I|DYSF_uc002sif.1_Silent_p.I228I|DYSF_uc010fek.1_Silent_p.I259I|DYSF_uc010fel.1_Silent_p.I228I|DYSF_uc010fem.1_Silent_p.I228I|DYSF_uc010feo.1_Silent_p.I259I	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8	227	Cytoplasmic (Potential).|C2 2.					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)	6														0.459459	102.389466	102.488417	34	40	CC		KEEP	---	---	---	---	capture			Silent	SNP	71596278	71596278	5045	2	C	T	T	31	31	DYSF	T	1	1
ALCAM	214	broad.mit.edu	36	3	106746868	106746868	+	Missense_Mutation	SNP	A	C	C			TCGA-28-1749-01	TCGA-28-1749-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:106746868A>C	uc003dvx.1	+	c.1103A>C	c.(1102-1104)AAA>ACA	p.K368T	ALCAM_uc003dvw.1_Missense_Mutation_p.K368T|ALCAM_uc003dvy.1_Missense_Mutation_p.K368T|ALCAM_uc010hpp.1_Missense_Mutation_p.K90T|ALCAM_uc003dvz.1_Missense_Mutation_p.K2T	NM_001627	NP_001618	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	368	Extracellular (Potential).|Ig-like C2-type 2.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(2)|breast(1)	3														0.494737	659.511355	659.520125	188	192	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	106746868	106746868	490	3	A	C	C	1	1	ALCAM	C	4	4
COL7A1	1294	broad.mit.edu	36	3	48601792	48601792	+	Silent	SNP	C	G	G			TCGA-28-1749-01	TCGA-28-1749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:48601792C>G	uc003ctz.2	-	c.2286G>C	c.(2284-2286)GGG>GGC	p.G762G		NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor	762	Nonhelical region (NC1).|Fibronectin type-III 6.				cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(2)	9				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)										0.285714	8.892683	9.471125	4	10	CC		KEEP	---	---	---	---	capture			Silent	SNP	48601792	48601792	3842	3	C	G	G	26	26	COL7A1	G	3	3
KDR	3791	broad.mit.edu	36	4	55668762	55668762	+	Silent	SNP	G	A	A			TCGA-28-1749-01	TCGA-28-1749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:55668762G>A	uc003has.1	-	c.1311C>T	c.(1309-1311)TAC>TAT	p.Y437Y	KDR_uc003hat.1_Silent_p.Y437Y	NM_002253	NP_002244	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III	437	Ig-like C2-type 5.|Extracellular (Potential).				angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|protein phosphorylation|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(9)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|ovary(2)|kidney(1)	22	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Sorafenib(DB00398)|Sunitinib(DB01268)					1022	TSP Lung(20;0.16)			0.43125	1079.127939	1082.428333	345	455	GG		KEEP	---	---	---	---	capture			Silent	SNP	55668762	55668762	8445	4	G	A	A	40	40	KDR	A	1	1
NPFFR2	10886	broad.mit.edu	36	4	73116732	73116732	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1749-01	TCGA-28-1749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:73116732C>T	uc003hgg.1	+	c.250C>T	c.(250-252)CGG>TGG	p.R84W	NPFFR2_uc010iig.1_De_novo_Start_OutOfFrame	NM_004885	NP_444264	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2 isoform 1	84	Extracellular (Potential).				detection of abiotic stimulus	actin cytoskeleton|integral to plasma membrane	neuropeptide receptor activity			ovary(2)|central_nervous_system(1)	3			Lung(101;0.0935)|LUSC - Lung squamous cell carcinoma(112;0.138)											0.4375	18.51515	18.570282	7	9	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73116732	73116732	10982	4	C	T	T	19	19	NPFFR2	T	1	1
RPL26L1	51121	broad.mit.edu	36	5	172329058	172329058	+	Missense_Mutation	SNP	A	C	C			TCGA-28-1749-01	TCGA-28-1749-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:172329058A>C	uc003mcc.1	+	c.346A>C	c.(346-348)AAA>CAA	p.K116Q		NM_001093761	NP_001087230	Q9UNX3	RL26L_HUMAN	hypothetical protein LOC653147	116					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|large ribosomal subunit	structural constituent of ribosome				0	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)											0.132075	8.993617	15.961914	7	46	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	172329058	172329058	14053	5	A	C	C	9	9	RPL26L1	C	4	4
PAX4	5078	broad.mit.edu	36	7	127042342	127042342	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1749-01	TCGA-28-1749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:127042342C>T	uc010lld.1	-	c.164G>A	c.(163-165)CGC>CAC	p.R55H	PAX4_uc003vmf.2_Missense_Mutation_p.R53H|PAX4_uc003vmg.1_Missense_Mutation_p.R55H|PAX4_uc003vmh.2_Missense_Mutation_p.R53H	NM_006193	NP_006184	O43316	PAX4_HUMAN	paired box 4	63	Paired.				cell differentiation|endocrine pancreas development|organ morphogenesis|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(1)	1						Ovarian(113;737 1605 7858 27720 34092)								0.320755	48.357597	49.869608	17	36	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	127042342	127042342	11901	7	C	T	T	27	27	PAX4	T	1	1
TBXAS1	6916	broad.mit.edu	36	7	139366322	139366322	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1749-01	TCGA-28-1749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:139366322C>T	uc003vvh.1	+	c.1559C>T	c.(1558-1560)GCC>GTC	p.A520V	TBXAS1_uc010lne.1_Missense_Mutation_p.A452V|TBXAS1_uc003vvi.1_Missense_Mutation_p.A520V|TBXAS1_uc003vvj.1_3'UTR	NM_001061	NP_001052	P24557	THAS_HUMAN	thromboxane A synthase 1 isoform TXS-I	519	Cytoplasmic (Potential).				hormone biosynthetic process|oxidation-reduction process|prostaglandin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|thromboxane-A synthase activity			ovary(2)|breast(1)	3	Melanoma(164;0.0142)													0.1875	36.708049	45.478344	18	78	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	139366322	139366322	16190	7	C	T	T	26	26	TBXAS1	T	2	2
DPP6	1804	broad.mit.edu	36	7	154229645	154229645	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1749-01	TCGA-28-1749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:154229645C>T	uc003wlk.1	+	c.1556C>T	c.(1555-1557)ACG>ATG	p.T519M	DPP6_uc003wli.1_Missense_Mutation_p.T455M|DPP6_uc003wlm.1_Missense_Mutation_p.T457M	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1	519	Extracellular (Potential).				cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			NSCLC(125;1384 1783 2490 7422 34254)								0.294118	55.071456	57.652205	20	48	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	154229645	154229645	4914	7	C	T	T	19	19	DPP6	T	1	1
DNAH11	8701	broad.mit.edu	36	7	21621315	21621315	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1749-01	TCGA-28-1749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:21621315G>A	uc003svc.1	+	c.3911G>A	c.(3910-3912)CGT>CAT	p.R1304H		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1304	Potential.|Stem (By similarity).				microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														0.242366	324.32507	356.001162	127	397	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21621315	21621315	4781	7	G	A	A	40	40	DNAH11	A	1	1
SDK1	221935	broad.mit.edu	36	7	4151990	4151990	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1749-01	TCGA-28-1749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:4151990G>A	uc003smx.1	+	c.4339G>A	c.(4339-4341)GCA>ACA	p.A1447T	SDK1_uc010kso.1_Missense_Mutation_p.A723T|SDK1_uc003smy.1_5'UTR	NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 isoform 1	1447	Fibronectin type-III 8.				cell adhesion	integral to membrane				large_intestine(3)|ovary(2)	5		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)										0.333333	12.268276	12.638149	5	10	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	4151990	4151990	14454	7	G	A	A	38	38	SDK1	A	1	1
EGFR	1956	broad.mit.edu	36	7	55191801	55191801	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1749-01	TCGA-28-1749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55191801C>T	uc003tqk.1	+	c.1088C>T	c.(1087-1089)ACC>ATC	p.T363I	EGFR_uc003tqh.1_Missense_Mutation_p.T363I|EGFR_uc003tqi.1_Missense_Mutation_p.T363I|EGFR_uc003tqj.1_Missense_Mutation_p.T363I|EGFR_uc010kzg.1_Missense_Mutation_p.T318I	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	363	Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(8200)|central_nervous_system(103)|upper_aerodigestive_tract(37)|prostate(32)|ovary(31)|thyroid(23)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|stomach(6)|urinary_tract(6)|skin(5)|adrenal_gland(5)|kidney(4)|soft_tissue(4)|bone(3)|NS(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)|pancreas(1)	8515	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8		608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.251925	474.371777	525.26706	229	680	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55191801	55191801	5156	7	C	T	T	18	18	EGFR	T	2	2
PMS2	5395	broad.mit.edu	36	7	6009933	6009933	+	Silent	SNP	T	C	C			TCGA-28-1749-01	TCGA-28-1749-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:6009933T>C	uc003spl.1	-	c.267A>G	c.(265-267)ACA>ACG	p.T89T	PMS2_uc003spj.1_Intron|PMS2_uc003spk.1_5'UTR|PMS2_uc010kte.1_Silent_p.T89T|PMS2_uc010ktf.1_Silent_p.T89T|PMS2_uc010ktg.1_Silent_p.T89T	NM_000535	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 isoform	89					mismatch repair|reciprocal meiotic recombination|somatic hypermutation of immunoglobulin genes	MutLalpha complex	ATP binding|ATPase activity|endonuclease activity|protein binding|single base insertion or deletion binding			central_nervous_system(1)	1		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)						812				0.319728	263.536758	272.031582	94	200	TT		KEEP	---	---	---	---	capture			Silent	SNP	6009933	6009933	12569	7	T	C	C	51	51	PMS2	C	4	4
MSR1	4481	broad.mit.edu	36	8	16066013	16066013	+	Missense_Mutation	SNP	A	G	G			TCGA-28-1749-01	TCGA-28-1749-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:16066013A>G	uc010lsu.1	-	c.803T>C	c.(802-804)ATC>ACC	p.I268T	MSR1_uc003wwz.1_Missense_Mutation_p.I250T|MSR1_uc003wxa.1_Missense_Mutation_p.I250T|MSR1_uc003wxb.1_Missense_Mutation_p.I250T	NM_138715	NP_619729	P21757	MSRE_HUMAN	macrophage scavenger receptor 1 isoform type 1	250	Potential.|Extracellular (Potential).				cholesterol transport|plasma lipoprotein particle clearance|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis	collagen|integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|protein binding|scavenger receptor activity			ovary(1)	1				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)										0.444444	70.296652	70.417331	20	25	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16066013	16066013	10279	8	A	G	G	12	12	MSR1	G	4	4
PSKH2	85481	broad.mit.edu	36	8	87145635	87145635	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1749-01	TCGA-28-1749-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:87145635G>A	uc003ydo.1	-	c.527C>T	c.(526-528)GCG>GTG	p.A176V		NM_033126	NP_149117	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	176	Protein kinase.				protein phosphorylation		ATP binding|protein serine/threonine kinase activity			lung(2)|ovary(1)	3			STAD - Stomach adenocarcinoma(118;0.129)							100				0.413146	266.56009	267.963061	88	125	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	87145635	87145635	13118	8	G	A	A	38	38	PSKH2	A	1	1
SLC7A13	157724	broad.mit.edu	36	8	87298852	87298852	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1749-01	TCGA-28-1749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:87298852C>T	uc003ydq.1	-	c.1142G>A	c.(1141-1143)CGG>CAG	p.R381Q	SLC7A13_uc003ydr.1_Missense_Mutation_p.R372Q	NM_138817	NP_620172	Q8TCU3	S7A13_HUMAN	solute carrier family 7, (cationic amino acid	381	Cytoplasmic (Potential).					integral to membrane	amino acid transmembrane transporter activity			central_nervous_system(1)	1														0.357143	13.971598	14.223008	5	9	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	87298852	87298852	15192	8	C	T	T	23	23	SLC7A13	T	1	1
FAM47B	170062	broad.mit.edu	36	X	34872143	34872143	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1749-01	TCGA-28-1749-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:34872143C>T	uc004ddi.1	+	c.1274C>T	c.(1273-1275)CCG>CTG	p.P425L		NM_152631	NP_689844	Q8NA70	FA47B_HUMAN	hypothetical protein LOC170062	425										ovary(3)|breast(1)	4														0.854839	182.807277	190.321862	53	9	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	34872143	34872143	5791	23	C	T	T	23	23	FAM47B	T	1	1
PTEN	5728	broad.mit.edu	36	10	89614273	89614273	+	Frame_Shift_Del	DEL	T	-	-			TCGA-28-1749-01	TCGA-28-1749-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:89614273_89614273delT	uc001kfb.1	+	c.67_67delT	c.(67-69)TTAfs	p.L23fs	KILLIN_uc009xti.1_5'Flank	NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	23	Phosphatase tensin-type.				apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of focal adhesion assembly|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of cyclin-dependent protein kinase activity|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.0?(12)|p.L23V(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)				31		264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.78			29	8				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	89614273	89614273	13192	10	T	-	-	56	56	PTEN	-	5	5
KIAA0664	23277	broad.mit.edu	36	17	2548443	2548454	+	In_Frame_Del	DEL	CGCCACGTAGGC	-	-			TCGA-28-1749-01	TCGA-28-1749-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:2548443_2548454delCGCCACGTAGGC	uc002fuy.1	-	c.1333_1344delGCCTACGTGGCG	c.(1333-1344)GCCTACGTGGCGdel	p.AYVA445del	KIAA0664_uc002fux.1_In_Frame_Del_p.AYVA377del	NM_015229	NP_056044	O75153	K0664_HUMAN	hypothetical protein LOC23277	445_448							binding			breast(2)	2														0.32			6	13				---	---	---	---	capture_indel			In_Frame_Del	DEL	2548443	2548454	8496	17	CGCCACGTAGGC	-	-	27	27	KIAA0664	-	5	5
ACACA	31	broad.mit.edu	36	17	32708110	32708110	+	Frame_Shift_Del	DEL	G	-	-			TCGA-28-1749-01	TCGA-28-1749-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:32708110_32708110delG	uc002hno.1	-	c.731_731delC	c.(730-732)GCTfs	p.A244fs	ACACA_uc002hnk.1_Frame_Shift_Del_p.A129fs|ACACA_uc002hnl.1_Frame_Shift_Del_p.A149fs|ACACA_uc002hnm.1_Frame_Shift_Del_p.A207fs|ACACA_uc002hnn.1_Frame_Shift_Del_p.A207fs|ACACA_uc010cuz.1_Frame_Shift_Del_p.A207fs|ACACA_uc002hnq.2_Frame_Shift_Del_p.A129fs	NM_198834	NP_942135	Q13085	ACACA_HUMAN	acetyl-Coenzyme A carboxylase alpha isoform 1	207	Biotin carboxylation.				acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)				742				0.36			103	184				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	32708110	32708110	107	17	G	-	-	34	34	ACACA	-	5	5
CC2D1A	54862	broad.mit.edu	36	19	13890729	13890730	+	Frame_Shift_Ins	INS	-	C	C			TCGA-28-1749-01	TCGA-28-1749-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:13890729_13890730insC	uc002mxo.1	+	c.1023_1024insC	c.(1021-1026)GTGCCCfs	p.V341fs	CC2D1A_uc002mxp.1_Frame_Shift_Ins_p.V341fs|CC2D1A_uc010dzh.1_5'UTR|CC2D1A_uc002mxq.1_5'UTR|CC2D1A_uc002mxn.1_Frame_Shift_Ins_p.V240fs	NM_017721	NP_060191	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	341_342	Pro-rich.				positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus|plasma membrane	DNA binding|signal transducer activity				0			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)											0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	13890729	13890730	2846	19	-	C	C	46	46	CC2D1A	C	5	5
FRRS1	391059	broad.mit.edu	36	1	99986832	99986832	+	Frame_Shift_Del	DEL	T	-	-			TCGA-28-1749-01	TCGA-28-1749-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:99986832_99986832delT	uc001dsh.1	-	c.81_81delA	c.(79-81)AAAfs	p.K27fs		NM_001013660	NP_001013682	Q6ZNA5	FRRS1_HUMAN	stromal cell derived factor receptor 2 homolog	27	Reelin.				electron transport chain|transport	integral to membrane	ferric-chelate reductase activity|metal ion binding				0		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)										0.34			28	55				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	99986832	99986832	6310	1	T	-	-	56	56	FRRS1	-	5	5
ZFHX4	79776	broad.mit.edu	36	8	77927854	77927859	+	In_Frame_Del	DEL	CCTCCT	-	-			TCGA-28-1749-01	TCGA-28-1749-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:77927854_77927859delCCTCCT	uc003yav.1	+	c.6007_6012delCCTCCT	c.(6007-6012)CCTCCTdel	p.PP2015del	ZFHX4_uc003yau.1_In_Frame_Del_p.PP2060del|ZFHX4_uc003yaw.1_In_Frame_Del_p.PP2015del	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	2015_2016	Pro-rich.				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)											0.33			2	4				---	---	---	---	capture_indel			In_Frame_Del	DEL	77927854	77927859	18223	8	CCTCCT	-	-	18	18	ZFHX4	-	5	5
