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
FOXRED1	55572	broad.mit.edu	36	11	125651501	125651501	+	Missense_Mutation	SNP	A	G	G			TCGA-26-5139-01	TCGA-26-5139-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:125651501A>G	uc001qdi.1	+	c.974A>G	c.(973-975)TAT>TGT	p.Y325C	FOXRED1_uc001qdj.1_Missense_Mutation_p.Y114C|FOXRED1_uc001qdk.1_Missense_Mutation_p.Y114C	NM_017547	NP_060017	Q96CU9	FXRD1_HUMAN	FAD-dependent oxidoreductase domain containing	325					oxidation-reduction process	integral to membrane|mitochondrion	oxidoreductase activity|protein binding				0	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.224)												0.15493	14.990235	23.067512	11	60	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0729)	Missense_Mutation	SNP	125651501	125651501	6279	11	A	G	G	16	16	FOXRED1	G	4	4
OR4C46	119749	broad.mit.edu	36	11	51372585	51372585	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5139-01	TCGA-26-5139-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:51372585C>T	uc001nhj.1	+	c.728C>T	c.(727-729)ACG>ATG	p.T243M		NM_001004703	NP_001004703	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C,	243	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.38326	203.333336	206.056957	87	140	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51372585	51372585	11458	11	C	T	T	19	19	OR4C46	T	1	1
CCDC60	160777	broad.mit.edu	36	12	118257422	118257422	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5139-01	TCGA-26-5139-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:118257422C>T	uc001txe.1	+	c.58C>T	c.(58-60)CGG>TGG	p.R20W		NM_178499	NP_848594	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	20										ovary(2)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)													0.34104	146.451402	150.324412	59	114	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(302;0.207)	Missense_Mutation	SNP	118257422	118257422	2954	12	C	T	T	23	23	CCDC60	T	1	1
ADAMTS20	80070	broad.mit.edu	36	12	42109750	42109750	+	Silent	SNP	G	A	A			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:42109750G>A	uc001rnn.1	-	c.3426C>T	c.(3424-3426)ACC>ACT	p.T1142T	ADAMTS20_uc001rno.1_Intron|ADAMTS20_uc001rnp.1_Silent_p.T296T	NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	1142						proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)								2149				0.24	13.335972	14.879923	6	19	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(48;0.0473)	Silent	SNP	42109750	42109750	267	12	G	A	A	39	39	ADAMTS20	A	1	1
LRRC23	10233	broad.mit.edu	36	12	6892244	6892244	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5139-01	TCGA-26-5139-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:6892244C>T	uc001qrp.1	+	c.848C>T	c.(847-849)ACG>ATG	p.T283M	LRRC23_uc001qrq.1_Intron|LRRC23_uc001qrr.1_Missense_Mutation_p.T232M|LRRC23_uc001qrs.1_Intron|LRRC23_uc001qrt.2_Missense_Mutation_p.T283M|LRRC23_uc009zfh.1_Intron|ENO2_uc001qru.1_5'Flank|ENO2_uc009zfi.1_5'Flank|ENO2_uc001qrv.1_5'Flank	NM_201650	NP_964013	Q53EV4	LRC23_HUMAN	leucine rich repeat containing 23 isoform a	283	LRRCT.									ovary(1)	1														0.370892	180.229475	183.362797	79	134	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6892244	6892244	9352	12	C	T	T	19	19	LRRC23	T	1	1
PTPN6	5777	broad.mit.edu	36	12	6931485	6931485	+	Silent	SNP	G	A	A			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:6931485G>A	uc009zfl.1	+	c.210G>A	c.(208-210)GCG>GCA	p.A70A	PTPN6_uc001qsa.1_Silent_p.A72A|PTPN6_uc001qsb.2_Silent_p.A70A	NM_080549	NP_536859	P29350	PTN6_HUMAN	protein tyrosine phosphatase, non-receptor type	70	SH2 1.				apoptosis|cell junction assembly|G-protein coupled receptor protein signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|negative regulation of peptidyl-tyrosine phosphorylation|platelet activation|positive regulation of cell proliferation|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of G1/S transition of mitotic cell cycle|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol|membrane|nucleus	protein binding|protein tyrosine phosphatase activity			breast(1)	1														0.41954	170.002518	170.993389	73	101	GG		KEEP	---	---	---	---	capture			Silent	SNP	6931485	6931485	13249	12	G	A	A	37	37	PTPN6	A	1	1
GALNT4	8693	broad.mit.edu	36	12	88441888	88441888	+	Silent	SNP	G	T	T			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:88441888G>T	uc001tbd.1	-	c.570C>A	c.(568-570)ATC>ATA	p.I190I	POC1B_uc001tba.1_Intron|POC1B_uc001tbb.1_Intron|POC1B_uc001tbc.1_Intron|GALNT4_uc001tbe.2_Silent_p.I187I	NM_003774	NP_003765	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	190	Lumenal (Potential).|Catalytic subdomain A.				carbohydrate metabolic process	Golgi membrane|integral to membrane|perinuclear region of cytoplasm	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0												OREG0022018	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.482955	215.325241	215.371182	85	91	GG		KEEP	---	---	---	---	capture			Silent	SNP	88441888	88441888	6479	12	G	T	T	45	45	GALNT4	T	3	3
ELK3	2004	broad.mit.edu	36	12	95165036	95165036	+	Missense_Mutation	SNP	C	G	G			TCGA-26-5139-01	TCGA-26-5139-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:95165036C>G	uc001teo.1	+	c.395C>G	c.(394-396)ACG>AGG	p.T132R		NM_005230	NP_005221	P41970	ELK3_HUMAN	ELK3 protein	132					negative regulation of transcription, DNA-dependent|signal transduction	mitochondrion|nucleus	protein binding|purine-rich negative regulatory element binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	all_cancers(2;0.00173)													0.148148	6.481662	9.691139	4	23	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	95165036	95165036	5252	12	C	G	G	19	19	ELK3	G	3	3
ULK3	25989	broad.mit.edu	36	15	72917723	72917723	+	Missense_Mutation	SNP	C	A	A			TCGA-26-5139-01	TCGA-26-5139-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:72917723C>A	uc010bkf.1	-	c.1183G>T	c.(1183-1185)GGG>TGG	p.G395W	ULK3_uc002ayv.2_Missense_Mutation_p.G395W	NM_001099436	NP_001092906	Q6PHR2	ULK3_HUMAN	unc-51-like kinase 3	395	MIT 2.				protein phosphorylation	cytoplasm	ATP binding|protein serine/threonine kinase activity			breast(2)	2										352				0.375	6.621041	6.731438	3	5	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	72917723	72917723	17535	15	C	A	A	23	23	ULK3	A	3	3
PKD1L2	114780	broad.mit.edu	36	16	79732595	79732595	+	Missense_Mutation	SNP	C	G	G			TCGA-26-5139-01	TCGA-26-5139-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:79732595C>G	uc002fgh.1	-	c.5225G>C	c.(5224-5226)AGT>ACT	p.S1742T	PKD1L2_uc002fgg.1_Non-coding_Transcript	NM_052892	NP_443124	Q7Z442	PK1L2_HUMAN	polycystin 1-like 2 isoform a	1742	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.25	16.437933	17.801682	6	18	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	79732595	79732595	12389	16	C	G	G	20	20	PKD1L2	G	3	3
COG1	9382	broad.mit.edu	36	17	68714524	68714524	+	Missense_Mutation	SNP	T	C	C			TCGA-26-5139-01	TCGA-26-5139-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:68714524T>C	uc002jjg.1	+	c.2702T>C	c.(2701-2703)ATC>ACC	p.I901T	COG1_uc002jjf.1_Missense_Mutation_p.I901T|COG1_uc002jjh.1_Missense_Mutation_p.I901T	NM_018714	NP_061184	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	901					Golgi organization|intra-Golgi vesicle-mediated transport|protein transport	Golgi membrane|Golgi transport complex	protein binding			ovary(1)	1														0.225806	8.459804	10.674881	7	24	TT		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(166;0.197)		Missense_Mutation	SNP	68714524	68714524	3795	17	T	C	C	50	50	COG1	C	4	4
AZI1	22994	broad.mit.edu	36	17	76779148	76779148	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5139-01	TCGA-26-5139-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:76779148C>T	uc002jzp.1	-	c.3002G>A	c.(3001-3003)CGC>CAC	p.R1001H	AZI1_uc002jzn.1_Missense_Mutation_p.R998H|AZI1_uc002jzo.1_Missense_Mutation_p.R962H|AZI1_uc002jzm.1_Missense_Mutation_p.R433H|AZI1_uc002jzq.2_Missense_Mutation_p.R149H	NM_014984	NP_055799	Q9UPN4	AZI1_HUMAN	5-azacytidine induced 1 isoform a	1001					cell differentiation|G2/M transition of mitotic cell cycle|multicellular organismal development|spermatogenesis	centrosome|cytosol|intracellular membrane-bounded organelle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_neural(118;0.0804)|Melanoma(429;0.242)													0.236842	14.951142	17.362853	9	29	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)		Missense_Mutation	SNP	76779148	76779148	1261	17	C	T	T	27	27	AZI1	T	1	1
DSG4	147409	broad.mit.edu	36	18	27243412	27243412	+	Splice_Site_SNP	SNP	G	A	A			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:27243412G>A	uc002kwr.1	+	c.1934_splice	c.e13-1	p.L645_splice	DSG4_uc002kwq.1_Splice_Site_SNP_p.L645_splice	NM_177986	NP_817123			desmoglein 4 isoform 2						homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			central_nervous_system(5)|ovary(3)	8														0.396552	312.131911	314.856467	115	175	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(10;0.00504)		Splice_Site_SNP	SNP	27243412	27243412	4963	18	G	A	A	36	36	DSG4	A	5	2
C18orf34	374864	broad.mit.edu	36	18	29204072	29204072	+	Silent	SNP	G	C	C			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:29204072G>C	uc002kxn.2	-	c.288C>G	c.(286-288)GTC>GTG	p.V96V	C18orf34_uc010dmf.1_Silent_p.V96V|C18orf34_uc002kxo.2_Silent_p.V96V|C18orf34_uc002kxp.2_Silent_p.V96V	NM_001105528	NP_001098998	Q5BJE1	CR034_HUMAN	hypothetical protein LOC374864 isoform 1	96										ovary(1)	1														0.389937	219.019943	220.705691	62	97	GG		KEEP	---	---	---	---	capture			Silent	SNP	29204072	29204072	1963	18	G	C	C	45	45	C18orf34	C	3	3
SERPINB13	5275	broad.mit.edu	36	18	59413377	59413377	+	Silent	SNP	C	T	T			TCGA-26-5139-01	TCGA-26-5139-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:59413377C>T	uc002ljc.1	+	c.750C>T	c.(748-750)AAC>AAT	p.N250N	SERPINB13_uc002ljd.1_Silent_p.N114N	NM_012397	NP_036529	Q9UIV8	SPB13_HUMAN	serine (or cysteine) proteinase inhibitor, clade	250					regulation of proteolysis|response to UV	cytoplasm|extracellular region	serine-type endopeptidase inhibitor activity			ovary(1)	1														0.369176	234.393415	238.610788	103	176	CC		KEEP	---	---	---	---	capture			Silent	SNP	59413377	59413377	14588	18	C	T	T	19	19	SERPINB13	T	1	1
TJP3	27134	broad.mit.edu	36	19	3679405	3679405	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5139-01	TCGA-26-5139-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:3679405C>T	uc002lym.1	+	c.32C>T	c.(31-33)CCC>CTC	p.P11L	TJP3_uc002lyk.1_Intron|TJP3_uc002lyl.1_Intron|TJP3_uc002lyn.1_5'UTR	NM_014428	NP_055243	O95049	ZO3_HUMAN	tight junction protein 3	Error:Variant_position_missing_in_O95049_after_alignment						tight junction	protein binding			ovary(1)|central_nervous_system(1)	2														0.311111	72.16277	75.024954	28	62	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	3679405	3679405	16460	19	C	T	T	22	22	TJP3	T	2	2
FCGBP	8857	broad.mit.edu	36	19	45087830	45087830	+	Silent	SNP	G	A	A			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:45087830G>A	uc002omp.2	-	c.7407C>T	c.(7405-7407)TTC>TTT	p.F2469F		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2469	VWFD 6.					extracellular region	protein binding			ovary(4)|central_nervous_system(1)	5	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)													0.104545	6.560101	40.813255	23	197	GG		KEEP	---	---	---	---	capture	Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)		Silent	SNP	45087830	45087830	6015	19	G	A	A	37	37	FCGBP	A	1	1
PRR12	57479	broad.mit.edu	36	19	54796922	54796922	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:54796922G>A	uc002poo.2	+	c.4708G>A	c.(4708-4710)GGA>AGA	p.G1570R		NM_020719	NP_065770	Q9ULL5	PRR12_HUMAN	proline rich 12	749							DNA binding			central_nervous_system(1)|pancreas(1)	2		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)												0.304348	31.130544	32.703371	14	32	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)	Missense_Mutation	SNP	54796922	54796922	13027	19	G	A	A	39	39	PRR12	A	1	1
CD70	970	broad.mit.edu	36	19	6537314	6537314	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5139-01	TCGA-26-5139-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:6537314C>T	uc002mfi.1	-	c.299G>A	c.(298-300)CGT>CAT	p.R100H		NM_001252	NP_001243	P32970	CD70_HUMAN	tumor necrosis factor ligand superfamily, member	100	Extracellular (Potential).				cell proliferation|cell-cell signaling|immune response|induction of apoptosis|signal transduction	extracellular space|integral to membrane of membrane fraction|integral to plasma membrane	cytokine activity|protease binding|tumor necrosis factor receptor binding				0						Pancreas(183;2617 2876 10173 34193)								0.268908	61.529645	67.281172	32	87	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6537314	6537314	3161	19	C	T	T	19	19	CD70	T	1	1
RETN	56729	broad.mit.edu	36	19	7640784	7640784	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:7640784G>A	uc002mhf.1	+	c.196G>A	c.(196-198)GGC>AGC	p.G66S	RETN_uc002mhg.1_Missense_Mutation_p.G66S|RETN_uc010dvm.1_Intron	NM_020415	NP_065148	Q9HD89	RETN_HUMAN	resistin	66							hormone activity			ovary(1)	1														0.306818	70.888282	73.818937	27	61	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7640784	7640784	13706	19	G	A	A	35	35	RETN	A	2	2
VPS72	6944	broad.mit.edu	36	1	149415804	149415804	+	Silent	SNP	A	T	T			TCGA-26-5139-01	TCGA-26-5139-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:149415804A>T	uc001exe.1	-	c.1035T>A	c.(1033-1035)CCT>CCA	p.P345P	TMOD4_uc001exd.1_5'Flank|TMOD4_uc001exc.2_5'Flank	NM_005997	NP_005988	Q15906	VPS72_HUMAN	transcription factor-like 1	345	Poly-Pro.|Pro-rich.				chromatin modification|negative regulation of transcription from RNA polymerase II promoter	nucleus|protein complex	DNA binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding transcription factor activity			breast(1)|pancreas(1)	2	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)					Pancreas(109;1131 2287 3209 24201)								0.391941	230.975437	233.790045	107	166	AA		KEEP	---	---	---	---	capture	UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)		Silent	SNP	149415804	149415804	17784	1	A	T	T	11	11	VPS72	T	4	4
YY1AP1	55249	broad.mit.edu	36	1	153913102	153913102	+	Missense_Mutation	SNP	A	G	G			TCGA-26-5139-01	TCGA-26-5139-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:153913102A>G	uc001flh.1	-	c.599T>C	c.(598-600)TTT>TCT	p.F200S	YY1AP1_uc009wqt.1_Missense_Mutation_p.F51S|YY1AP1_uc009wqu.1_5'UTR|YY1AP1_uc001fll.1_Missense_Mutation_p.F62S|YY1AP1_uc009wqv.1_5'UTR|YY1AP1_uc001flm.1_Missense_Mutation_p.F51S|YY1AP1_uc001fli.1_Missense_Mutation_p.F62S|YY1AP1_uc009wqw.1_Missense_Mutation_p.F51S|YY1AP1_uc001flj.1_Missense_Mutation_p.F62S|YY1AP1_uc001flk.1_Missense_Mutation_p.F51S|YY1AP1_uc001flo.1_5'UTR|YY1AP1_uc001flp.1_Missense_Mutation_p.F62S|YY1AP1_uc001fln.1_Missense_Mutation_p.F128S|YY1AP1_uc009wqx.1_Missense_Mutation_p.F200S	NM_139118	NP_620829	Q9H869	YYAP1_HUMAN	YY1-associated protein isoform 2	128					regulation of cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding			ovary(2)	2	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)													0.37551	303.861121	307.186125	92	153	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153913102	153913102	18091	1	A	G	G	1	1	YY1AP1	G	4	4
PEAR1	375033	broad.mit.edu	36	1	155141762	155141762	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5139-01	TCGA-26-5139-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:155141762C>T	uc001fqj.1	+	c.229C>T	c.(229-231)CGT>TGT	p.R77C	PEAR1_uc009wsl.1_5'Flank|PEAR1_uc001fqk.1_5'Flank	NM_001080471	NP_001073940	Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	77	EMI.					integral to membrane				ovary(2)|central_nervous_system(1)	3	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)													0.333333	42.182401	43.364032	16	32	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	155141762	155141762	12133	1	C	T	T	23	23	PEAR1	T	1	1
CD5L	922	broad.mit.edu	36	1	156071068	156071068	+	Silent	SNP	G	A	A			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:156071068G>A	uc001frk.2	-	c.471C>T	c.(469-471)AAC>AAT	p.N157N		NM_005894	NP_005885	O43866	CD5L_HUMAN	CD5 molecule-like	157	SRCR 2.				apoptosis|cellular defense response	extracellular space|membrane	scavenger receptor activity			ovary(1)	1	all_hematologic(112;0.0378)													0.366667	211.902274	215.664973	88	152	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.24)		Silent	SNP	156071068	156071068	3155	1	G	A	A	44	44	CD5L	A	2	2
SNAP25	6616	broad.mit.edu	36	20	10204146	10204146	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:10204146G>A	uc002wnq.1	+	c.7G>A	c.(7-9)GAA>AAA	p.E3K	SNAP25_uc002wnr.1_Missense_Mutation_p.E3K|SNAP25_uc002wns.1_5'UTR|SNAP25_uc010gca.1_Missense_Mutation_p.E3K|SNAP25_uc010gcb.1_5'UTR|SNAP25_uc010gcc.1_5'UTR	NM_130811	NP_570824	P60880	SNP25_HUMAN	synaptosomal-associated protein 25 isoform	3	Interaction with CENPF (By similarity).				energy reserve metabolic process|glutamate secretion|neurotransmitter uptake|synaptic vesicle docking involved in exocytosis	cell junction|growth cone|perinuclear region of cytoplasm|synapse|synaptosome					0					Botulinum Toxin Type A(DB00083)									0.290323	17.856205	19.081991	9	22	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10204146	10204146	15330	20	G	A	A	37	37	SNAP25	A	1	1
TMPRSS6	164656	broad.mit.edu	36	22	35812338	35812338	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5139-01	TCGA-26-5139-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:35812338C>T	uc003aqt.1	-	c.904G>A	c.(904-906)GTC>ATC	p.V302I	TMPRSS6_uc003aqs.1_Missense_Mutation_p.V311I|TMPRSS6_uc003aqu.2_Missense_Mutation_p.V302I	NM_153609	NP_705837	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	311	CUB 1.|Extracellular (Potential).				angiogenesis|extracellular matrix organization|fibrinolysis|intracellular signal transduction|proteolysis	integral to membrane|plasma membrane	serine-type endopeptidase activity			breast(4)|ovary(1)	5														0.407407	22.50779	22.71118	11	16	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35812338	35812338	16792	22	C	T	T	19	19	TMPRSS6	T	1	1
MYT1L	23040	broad.mit.edu	36	2	1905972	1905972	+	Silent	SNP	G	A	A			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:1905972G>A	uc002qxe.1	-	c.576C>T	c.(574-576)GAC>GAT	p.D192D	MYT1L_uc002qxd.1_Silent_p.D192D|MYT1L_uc010ewl.1_Non-coding_Transcript	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	192					cell differentiation|nervous system development|regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)												0.408451	65.538462	66.06371	29	42	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)	Silent	SNP	1905972	1905972	10502	2	G	A	A	40	40	MYT1L	A	1	1
XDH	7498	broad.mit.edu	36	2	31474058	31474058	+	Missense_Mutation	SNP	C	A	A			TCGA-26-5139-01	TCGA-26-5139-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:31474058C>A	uc002rnv.1	-	c.475G>T	c.(475-477)GGC>TGC	p.G159C		NM_000379	NP_000370	P47989	XDH_HUMAN	xanthine dehydrogenase	159					oxidation-reduction process|purine nucleotide catabolic process|xanthine catabolic process	cytosol|extracellular region|peroxisome	2 iron, 2 sulfur cluster binding|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|molybdopterin cofactor binding|protein homodimerization activity|xanthine dehydrogenase activity|xanthine oxidase activity			breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	5	Acute lymphoblastic leukemia(172;0.155)				Allopurinol(DB00437)|Carvedilol(DB01136)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Desflurane(DB01189)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|NADH(DB00157)|Nitrofurazone(DB00336)|Papaverine(DB01113)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Rasburicase(DB00049)|Spermine(DB00127)|Trifluoperazine(DB00831)|Vitamin E(DB00163)	Colon(66;682 1445 30109 40147)								0.295082	178.78406	190.278674	90	215	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31474058	31474058	18007	2	C	A	A	22	22	XDH	A	3	3
TMEM45A	55076	broad.mit.edu	36	3	101758306	101758306	+	Missense_Mutation	SNP	A	G	G			TCGA-26-5139-01	TCGA-26-5139-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:101758306A>G	uc003dua.1	+	c.251A>G	c.(250-252)GAG>GGG	p.E84G	TMEM45A_uc003dtz.1_Missense_Mutation_p.E68G	NM_018004	NP_060474	Q9NWC5	TM45A_HUMAN	transmembrane protein 45A	68	Helical; (Potential).					integral to membrane				ovary(1)	1														0.296296	10.810424	11.867986	8	19	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	101758306	101758306	16708	3	A	G	G	11	11	TMEM45A	G	4	4
STXBP5L	9515	broad.mit.edu	36	3	122316571	122316571	+	Missense_Mutation	SNP	A	G	G			TCGA-26-5139-01	TCGA-26-5139-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:122316571A>G	uc003eec.2	+	c.580A>G	c.(580-582)ATC>GTC	p.I194V		NM_014980	NP_055795	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	194	WD 3.				exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)	7														0.352941	208.39941	211.618923	60	110	AA		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(114;0.0694)	Missense_Mutation	SNP	122316571	122316571	15877	3	A	G	G	16	16	STXBP5L	G	4	4
FGD5	152273	broad.mit.edu	36	3	14836543	14836543	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:14836543G>A	uc003bzc.1	+	c.238G>A	c.(238-240)GCC>ACC	p.A80T		NM_152536	NP_689749	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	321	Glu-rich.				actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(3)|kidney(1)|pancreas(1)	5														0.377193	93.869639	95.387053	43	71	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	14836543	14836543	6073	3	G	A	A	38	38	FGD5	A	1	1
SI	6476	broad.mit.edu	36	3	166213481	166213481	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:166213481G>A	uc003fei.1	-	c.4043C>T	c.(4042-4044)ACG>ATG	p.T1348M		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	1348	Sucrase.|Lumenal.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|pancreas(1)	8		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)									0.327645	209.053033	216.796468	96	197	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	166213481	166213481	14792	3	G	A	A	40	40	SI	A	1	1
CHL1	10752	broad.mit.edu	36	3	415026	415026	+	Missense_Mutation	SNP	A	T	T			TCGA-26-5139-01	TCGA-26-5139-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:415026A>T	uc003bot.1	+	c.3211A>T	c.(3211-3213)AAT>TAT	p.N1071Y	CHL1_uc003bou.1_Missense_Mutation_p.N1055Y|CHL1_uc003bow.1_Missense_Mutation_p.N1055Y	NM_006614	NP_006605	O00533	CHL1_HUMAN	cell adhesion molecule with homology to L1CAM	1055	Extracellular (Potential).				axon guidance|cell adhesion|signal transduction	integral to membrane|plasma membrane|proteinaceous extracellular matrix				central_nervous_system(4)|large_intestine(2)|ovary(1)	7		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)								659				0.333333	134.767513	139.121078	59	118	AA		KEEP	---	---	---	---	capture		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)	Missense_Mutation	SNP	415026	415026	3483	3	A	T	T	13	13	CHL1	T	4	4
NPRL2	10641	broad.mit.edu	36	3	50360759	50360759	+	Silent	SNP	G	A	A			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:50360759G>A	uc003daj.1	-	c.807C>T	c.(805-807)ACC>ACT	p.T269T	ZMYND10_uc003dag.1_5'Flank|ZMYND10_uc010hll.1_5'Flank|ZMYND10_uc003dah.1_5'Flank|ZMYND10_uc010hlm.1_5'Flank|NPRL2_uc003dai.1_Silent_p.T149T|CYB561D2_uc003dak.1_5'Flank|CYB561D2_uc003dal.1_5'Flank|CYB561D2_uc003dam.1_5'Flank	NM_006545	NP_006536	Q8WTW4	NPRL2_HUMAN	tumor suppressor candidate 4	269					negative regulation of kinase activity		protein binding|protein kinase activity			lung(1)	1										248				0.359223	92.331404	94.134779	37	66	GG		KEEP	---	---	---	---	capture			Silent	SNP	50360759	50360759	11002	3	G	A	A	47	47	NPRL2	A	2	2
FAT4	79633	broad.mit.edu	36	4	126591511	126591511	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:126591511G>A	uc003ifj.2	+	c.9890G>A	c.(9889-9891)CGT>CAT	p.R3297H	FAT4_uc003ifh.2_Missense_Mutation_p.R3297H|FAT4_uc003ifi.1_Missense_Mutation_p.R775H	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4	3297	Cadherin 31.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(8)|pancreas(2)	10														0.356322	139.668409	142.845917	62	112	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	126591511	126591511	5928	4	G	A	A	40	40	FAT4	A	1	1
DCHS2	54798	broad.mit.edu	36	4	155461330	155461330	+	Silent	SNP	C	T	T			TCGA-26-5139-01	TCGA-26-5139-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:155461330C>T	uc003inw.1	-	c.3306G>A	c.(3304-3306)ACG>ACA	p.T1102T		NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1	1102	Cadherin 9.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)												0.411504	447.091762	450.197735	186	266	CC		KEEP	---	---	---	---	capture		LUSC - Lung squamous cell carcinoma(193;0.107)	Silent	SNP	155461330	155461330	4459	4	C	T	T	31	31	DCHS2	T	1	1
KIAA1430	57587	broad.mit.edu	36	4	186348558	186348558	+	Missense_Mutation	SNP	T	C	C			TCGA-26-5139-01	TCGA-26-5139-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:186348558T>C	uc003ixf.2	-	c.787A>G	c.(787-789)ATT>GTT	p.I263V	KIAA1430_uc003ixg.2_Missense_Mutation_p.I263V	NM_020827	NP_065878	Q9P2B7	K1430_HUMAN	hypothetical protein LOC57587	263											0		all_lung(41;1.19e-13)|Lung NSC(41;3.16e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00872)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)												0.436364	79.101872	79.29394	24	31	TT		KEEP	---	---	---	---	capture		all cancers(43;9.44e-26)|Epithelial(43;2.64e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.66e-11)|Colorectal(24;6.03e-05)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000331)|COAD - Colon adenocarcinoma(29;0.000427)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00924)|READ - Rectum adenocarcinoma(43;0.165)	Missense_Mutation	SNP	186348558	186348558	8541	4	T	C	C	51	51	KIAA1430	C	4	4
PTTG2	10744	broad.mit.edu	36	4	37638458	37638458	+	Missense_Mutation	SNP	C	A	A			TCGA-26-5139-01	TCGA-26-5139-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:37638458C>A	uc003gtc.1	+	c.8C>A	c.(7-9)ACT>AAT	p.T3N	TBC1D1_uc003gtb.1_Intron|TBC1D1_uc010ifd.1_Intron	NM_006607	NP_006598	Q9NZH5	PTTG2_HUMAN	pituitary tumor-transforming 2	3					chromosome organization|DNA metabolic process	cytoplasm|nucleus	SH3 domain binding				0														0.176471	6.737663	10.094399	6	28	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37638458	37638458	13279	4	C	A	A	20	20	PTTG2	A	3	3
PRKG2	5593	broad.mit.edu	36	4	82275440	82275440	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5139-01	TCGA-26-5139-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:82275440C>T	uc003hmh.1	-	c.1669G>A	c.(1669-1671)GTT>ATT	p.V557I		NM_006259	NP_006250	Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	557	Protein kinase.				platelet activation|protein phosphorylation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			breast(3)|central_nervous_system(2)|ovary(1)|large_intestine(1)	7									p.V557I(SNU466-Tumor)	728				0.35567	151.175979	154.754385	69	125	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	82275440	82275440	12966	4	C	T	T	19	19	PRKG2	T	1	1
FAM13B	51306	broad.mit.edu	36	5	137303897	137303897	+	Silent	SNP	C	T	T			TCGA-26-5139-01	TCGA-26-5139-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:137303897C>T	uc003lbz.2	-	c.2664G>A	c.(2662-2664)GAG>GAA	p.E888E	FAM13B_uc003lcb.2_Silent_p.E764E|FAM13B_uc003lca.2_Silent_p.E860E|PKD2L2_uc003lbw.1_3'UTR|PKD2L2_uc003lbx.2_3'UTR|PKD2L2_uc003lby.2_Intron	NM_016603	NP_057687	Q9NYF5	FA13B_HUMAN	hypothetical protein LOC51306 isoform 1	888					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0														0.386076	166.221839	168.024285	61	97	CC		KEEP	---	---	---	---	capture			Silent	SNP	137303897	137303897	5650	5	C	T	T	20	20	FAM13B	T	2	2
CDH18	1016	broad.mit.edu	36	5	19579789	19579789	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:19579789G>A	uc003jgc.1	-	c.1336C>T	c.(1336-1338)CTC>TTC	p.L446F	CDH18_uc003jgd.1_Missense_Mutation_p.L446F|CDH18_uc010iua.1_Missense_Mutation_p.L446F|CDH18_uc010itz.1_Missense_Mutation_p.L446F	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	446	Extracellular (Potential).|Cadherin 4.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)	6	Lung NSC(1;0.00734)|all_lung(1;0.0197)													0.410526	210.695427	212.028537	78	112	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19579789	19579789	3232	5	G	A	A	33	33	CDH18	A	2	2
PREP	5550	broad.mit.edu	36	6	105907639	105907639	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5139-01	TCGA-26-5139-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:105907639C>T	uc003prc.1	-	c.724G>A	c.(724-726)GAT>AAT	p.D242N		NM_002726	NP_002717	P48147	PPCE_HUMAN	prolyl endopeptidase	242					proteolysis		serine-type endopeptidase activity			ovary(3)	3		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)									0.366197	231.039311	235.542132	104	180	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	105907639	105907639	12917	6	C	T	T	29	29	PREP	T	2	2
DNAH11	8701	broad.mit.edu	36	7	21607579	21607579	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:21607579G>A	uc003svc.1	+	c.3466G>A	c.(3466-3468)GGA>AGA	p.G1156R		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1156	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														0.269006	103.984438	112.215619	46	125	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21607579	21607579	4781	7	G	A	A	39	39	DNAH11	A	1	1
EGFR	1956	broad.mit.edu	36	7	55206364	55206364	+	Missense_Mutation	SNP	G	T	T			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55206364G>T	uc003tqk.1	+	c.1883G>T	c.(1882-1884)TGC>TTC	p.C628F	EGFR_uc010kzg.1_Missense_Mutation_p.C583F	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	628	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)				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)			0.825314	2366.431168	2461.782351	789	167	GG		KEEP	---	---	---	---	capture	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)		Missense_Mutation	SNP	55206364	55206364	5156	7	G	T	T	46	46	EGFR	T	3	3
KCNV1	27012	broad.mit.edu	36	8	111053736	111053736	+	Silent	SNP	G	A	A			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:111053736G>A	uc003ynr.2	-	c.918C>T	c.(916-918)AAC>AAT	p.N306N	KCNV1_uc010mcw.1_Silent_p.N306N	NM_014379	NP_055194	Q6PIU1	KCNV1_HUMAN	potassium channel, subfamily V, member 1	306	Extracellular (Potential).					voltage-gated potassium channel complex	ion channel inhibitor activity|potassium channel regulator activity|voltage-gated potassium channel activity			lung(1)|kidney(1)	2	all_neural(195;0.219)													0.340426	68.356733	70.479125	32	62	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(57;5.35e-13)		Silent	SNP	111053736	111053736	8399	8	G	A	A	40	40	KCNV1	A	1	1
MYOM2	9172	broad.mit.edu	36	8	1992977	1992977	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:1992977G>A	uc003wpx.2	+	c.368G>A	c.(367-369)CGC>CAC	p.R123H		NM_003970	NP_003961	P54296	MYOM2_HUMAN	myomesin 2	123					muscle contraction	myosin filament	structural constituent of muscle			ovary(4)|central_nervous_system(1)	5		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)												0.361111	29.057573	29.671713	13	23	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)	Missense_Mutation	SNP	1992977	1992977	10487	8	G	A	A	38	38	MYOM2	A	1	1
BTK	695	broad.mit.edu	36	X	100497876	100497876	+	Silent	SNP	G	A	A			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:100497876G>A	uc010nno.1	-	c.1488C>T	c.(1486-1488)GGC>GGT	p.G496G	BTK_uc004ehf.1_Intron|BTK_uc010nnh.1_Intron|BTK_uc010nni.1_Intron|BTK_uc004ehe.1_Intron|BTK_uc010nnj.1_Non-coding_Transcript|BTK_uc010nnk.1_Intron|BTK_uc010nnl.1_Intron|BTK_uc010nnm.1_Silent_p.G32G|BTK_uc004ehg.1_Silent_p.G462G|BTK_uc010nnn.1_Intron|BTK_uc004ehh.1_Intron|BTK_uc004ehi.1_Silent_p.G462G	NM_000061	NP_000052	Q06187	BTK_HUMAN	Bruton agammaglobulinemia tyrosine kinase	462	Protein kinase.		G -> D (in XLA).|G -> V (in XLA).		calcium-mediated signaling|induction of apoptosis by extracellular signals|mesoderm development	cytosol|membrane raft|nucleus|plasma membrane	ATP binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|phosphatidylinositol-3,4,5-trisphosphate binding			central_nervous_system(2)|ovary(1)|lung(1)	4										247				0.358696	71.022819	72.650949	33	59	GG		KEEP	---	---	---	---	capture			Silent	SNP	100497876	100497876	1591	23	G	A	A	38	38	BTK	A	1	1
SOX3	6658	broad.mit.edu	36	X	139414400	139414400	+	Missense_Mutation	SNP	C	G	G			TCGA-26-5139-01	TCGA-26-5139-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:139414400C>G	uc004fbd.1	-	c.492G>C	c.(490-492)ATG>ATC	p.M164I		NM_005634	NP_005625	P41225	SOX3_HUMAN	SRY (sex determining region Y)-box 3	164	HMG box.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			pancreas(1)	1	Acute lymphoblastic leukemia(192;7.65e-05)													0.346405	168.927117	172.114648	53	100	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	139414400	139414400	15451	23	C	G	G	25	25	SOX3	G	3	3
PNMA5	114824	broad.mit.edu	36	X	151910162	151910162	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:151910162G>A	uc010ntw.1	-	c.637C>T	c.(637-639)CGG>TGG	p.R213W	PNMA5_uc004fha.2_Missense_Mutation_p.R213W|PNMA5_uc010ntx.1_Missense_Mutation_p.R213W|PNMA5_uc004fgy.2_Missense_Mutation_p.R213W|PNMA5_uc010nty.1_Missense_Mutation_p.R213W	NM_001103151	NP_443158	Q96PV4	PNMA5_HUMAN	paraneoplastic antigen like 5	213					apoptosis					ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(192;6.56e-05)													0.331967	173.869634	179.985154	81	163	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	151910162	151910162	12582	23	G	A	A	38	38	PNMA5	A	1	1
F8	2157	broad.mit.edu	36	X	153838632	153838632	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:153838632G>A	uc004fmt.1	-	c.1546C>T	c.(1546-1548)CAT>TAT	p.H516Y		NM_000132	NP_000123	P00451	FA8_HUMAN	coagulation factor VIII isoform a precursor	516	F5/8 type A 2.|Plastocyanin-like 3.				acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|oxidation-reduction process|platelet activation|platelet degranulation	extracellular space|plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity|protein binding			ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	11	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)					359				0.419811	212.803483	213.998836	89	123	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153838632	153838632	5544	23	G	A	A	48	48	F8	A	2	2
WNK3	65267	broad.mit.edu	36	X	54336406	54336406	+	Silent	SNP	T	C	C			TCGA-26-5139-01	TCGA-26-5139-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:54336406T>C	uc004dtc.1	-	c.1773A>G	c.(1771-1773)TCA>TCG	p.S591S	WNK3_uc004dtd.1_Silent_p.S591S	NM_020922	NP_065973	Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3 isoform 1	591					intracellular protein kinase cascade|protein phosphorylation		ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(3)|kidney(2)|central_nervous_system(2)	11										290				0.339286	177.545982	181.371427	57	111	TT		KEEP	---	---	---	---	capture			Silent	SNP	54336406	54336406	17953	23	T	C	C	63	63	WNK3	C	4	4
LAS1L	81887	broad.mit.edu	36	X	64660777	64660777	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5139-01	TCGA-26-5139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:64660777G>A	uc004dwa.1	-	c.1184C>T	c.(1183-1185)ACG>ATG	p.T395M	LAS1L_uc004dwc.1_Missense_Mutation_p.T378M|LAS1L_uc004dwd.1_Missense_Mutation_p.T336M	NM_031206	NP_112483	Q9Y4W2	LAS1L_HUMAN	LAS1-like	395						MLL1 complex|nucleolus	protein binding			ovary(3)|large_intestine(1)	4														0.378378	62.053338	63.022835	28	46	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	64660777	64660777	8959	23	G	A	A	40	40	LAS1L	A	1	1
KRTAP5-5	439915	broad.mit.edu	36	11	1608162	1608191	+	In_Frame_Del	DEL	CTGCTGCCAGTCCAGCTGCTGTAAGCCTTA	-	-			TCGA-26-5139-01	TCGA-26-5139-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:1608162_1608191delCTGCTGCCAGTCCAGCTGCTGTAAGCCTTA	uc001lty.1	+	c.516_545delCTGCTGCCAGTCCAGCTGCTGTAAGCCTTA	c.(514-546)TCCTGCTGCCAGTCCAGCTGCTGTAAGCCTTAC>TCC	p.CCQSSCCKPY183del		NM_001001480	NP_001001480	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	183_192	8 X 4 AA repeats of C-C-X-P.					keratin filament				lung(1)	1		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)										0.30			66	153				---	---	---	---	capture_indel			In_Frame_Del	DEL	1608162	1608191	8886	11	CTGCTGCCAGTCCAGCTGCTGTAAGCCTTA	-	-	24	24	KRTAP5-5	-	5	5
RIC8B	55188	broad.mit.edu	36	12	105701943	105701944	+	Frame_Shift_Ins	INS	-	A	A			TCGA-26-5139-01	TCGA-26-5139-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:105701943_105701944insA	uc001tlw.2	+	c.123_124insA	c.(121-126)GATAAAfs	p.D41fs	RIC8B_uc001tlx.1_Frame_Shift_Ins_p.D41fs|RIC8B_uc001tly.1_5'UTR|RIC8B_uc001tlz.1_Non-coding_Transcript	NM_018157	NP_060627	Q9NVN3	RIC8B_HUMAN	resistance to inhibitors of cholinesterase 8	41_42					regulation of G-protein coupled receptor protein signaling pathway	cell cortex|cytosol|plasma membrane	G-protein alpha-subunit binding|guanyl-nucleotide exchange factor activity			ovary(1)	1														0.32			63	137				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	105701943	105701944	13831	12	-	A	A	49	49	RIC8B	A	5	5
POLR2A	5430	broad.mit.edu	36	17	7357941	7357941	+	Frame_Shift_Del	DEL	T	-	-			TCGA-26-5139-01	TCGA-26-5139-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7357941_7357941delT	uc002ghf.2	+	c.5634_5634delT	c.(5632-5634)AGTfs	p.S1878fs		NM_000937	NP_000928	P24928	RPB1_HUMAN	DNA directed RNA polymerase II polypeptide A	1878	41.|52 X 7 AA approximate tandem repeats of Y-[ST]-P-[STQ]-[ST]-P-[SRTEVKGN].				mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|RNA-directed RNA polymerase activity|ubiquitin protein ligase binding			pancreas(1)	1		Prostate(122;0.173)												0.41			83	118				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	7357941	7357941	12642	17	T	-	-	58	58	POLR2A	-	5	5
PIK3R1	5295	broad.mit.edu	36	5	67627003	67627005	+	Splice_Site_Del	DEL	GGT	-	-			TCGA-26-5139-01	TCGA-26-5139-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:67627003_67627005delGGT	uc003jva.1	+	c.e14_splice_site			PIK3R1_uc003jvb.1_Splice_Site_Del|PIK3R1_uc003jvc.1_Splice_Site_Del|PIK3R1_uc003jvd.1_Splice_Site_Del|PIK3R1_uc003jve.1_Splice_Site_Del	NM_181523	NP_852664			phosphoinositide-3-kinase, regulatory subunit 1						epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex	1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding	p.M582_D605>I(4)|p.?(3)|p.Y580fs*1(1)		endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(5)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1)	99		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoproterenol(DB01064)					370	TCGA GBM(4;<1E-8)			0.38			48	79				---	---	---	---	capture_indel			Splice_Site_Del	DEL	67627003	67627005	12342	5	GGT	-	-	35	35	PIK3R1	-	5	5
