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
CALHM2	51063	broad.mit.edu	36	10	105199437	105199437	+	Silent	SNP	G	A	A			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:105199437G>A	uc001kwz.1	-	c.252C>T	c.(250-252)GCC>GCT	p.A84A	CALHM2_uc001kxa.1_Silent_p.A84A|CALHM2_uc001kxc.1_Silent_p.A84A|CALHM2_uc001kxb.1_Silent_p.A84A|CALHM2_uc001kxd.1_Silent_p.A84A	NM_015916	NP_057000	Q9HA72	CAHM2_HUMAN	calcium homeostasis modulator 2	84						integral to membrane					0														0.6125	161.886565	162.775097	49	31	GG		KEEP	---	---	---	---	capture			Silent	SNP	105199437	105199437	2699	10	G	A	A	39	39	CALHM2	A	1	1
JAKMIP3	282973	broad.mit.edu	36	10	133804033	133804033	+	Missense_Mutation	SNP	C	T	T			TCGA-41-2571-01	TCGA-41-2571-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:133804033C>T	uc009yaz.1	+	c.1433C>T	c.(1432-1434)ACG>ATG	p.T478M	JAKMIP3_uc001lkx.2_5'Flank	NM_001105521	NP_001098991			janus kinase and microtubule interacting protein											breast(1)	1		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)												0.64	51.206032	51.637563	16	9	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)	Missense_Mutation	SNP	133804033	133804033	8246	10	C	T	T	19	19	JAKMIP3	T	1	1
PTEN	5728	broad.mit.edu	36	10	89707652	89707652	+	Nonsense_Mutation	SNP	C	T	T			TCGA-41-2571-01	TCGA-41-2571-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89707652C>T	uc001kfb.1	+	c.697C>T	c.(697-699)CGA>TGA	p.R233*		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	233	C2 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.R233*(61)|p.R233fs*10(3)|p.R233fs*12(1)|p.R233fs*23(1)|p.R233fs*25(1)|p.R233fs*20(1)|p.R233R(1)|p.G165_*404del(1)|p.G165_K342del(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)					R233*(JHUEM1_ENDOMETRIUM)|R233*(SW1783_CENTRAL_NERVOUS_SYSTEM)|R233*(NCIH1155_LUNG)|R233*(SF295_CENTRAL_NERVOUS_SYSTEM)|R233*(HEC59_ENDOMETRIUM)	31	p.R233*(JHUEM1-Tumor)|p.R233*(SW1783-Tumor)|p.R233*(SF295-Tumor)|p.T232fs(P31FUJ-Tumor)	264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.693878	218.231454	221.526031	68	30	CC		KEEP	---	---	---	---	capture	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)	Nonsense_Mutation	SNP	89707652	89707652	13192	10	C	T	T	19	19	PTEN	T	5	1
EIF3M	10480	broad.mit.edu	36	11	32572022	32572022	+	Missense_Mutation	SNP	G	A	A			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:32572022G>A	uc001mtu.1	+	c.568G>A	c.(568-570)GGA>AGA	p.G190R		NM_006360	NP_006351	Q7L2H7	EIF3M_HUMAN	eukaryotic translation initiation factor 3,	190						eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			ovary(1)|breast(1)	2	Breast(20;0.109)													0.40708	147.931811	148.7836	46	67	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32572022	32572022	5214	11	G	A	A	39	39	EIF3M	A	1	1
USP35	57558	broad.mit.edu	36	11	77585029	77585029	+	Silent	SNP	G	C	C			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:77585029G>C	uc009yva.1	+	c.90G>C	c.(88-90)CGG>CGC	p.R30R	USP35_uc001oze.2_Intron|USP35_uc001ozc.2_Intron|USP35_uc001ozd.2_5'UTR|USP35_uc001ozf.2_5'Flank	NM_020798	NP_065849	Q9P2H5	UBP35_HUMAN	ubiquitin specific protease 35	30					ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|lung(1)	2	all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)													0.470588	12.085724	12.11236	8	9	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(8;1.04e-25)		Silent	SNP	77585029	77585029	17630	11	G	C	C	42	42	USP35	C	3	3
HEPHL1	341208	broad.mit.edu	36	11	93436372	93436372	+	Missense_Mutation	SNP	G	T	T			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:93436372G>T	uc001pep.2	+	c.466G>T	c.(466-468)GTT>TTT	p.V156F		NM_001098672	NP_001092142	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	156	Plastocyanin-like 1.|Extracellular (Potential).				copper ion transport|oxidation-reduction process	integral to membrane	copper ion binding|oxidoreductase activity			ovary(3)	3		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)												0.292683	30.080944	31.660487	12	29	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	93436372	93436372	7338	11	G	T	T	44	44	HEPHL1	T	3	3
PIWIL4	143689	broad.mit.edu	36	11	93974704	93974704	+	Silent	SNP	C	T	T			TCGA-41-2571-01	TCGA-41-2571-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:93974704C>T	uc001pfa.1	+	c.1476C>T	c.(1474-1476)AGC>AGT	p.S492S	PIWIL4_uc009ywk.1_Non-coding_Transcript	NM_152431	NP_689644	Q7Z3Z4	PIWL4_HUMAN	piwi-like 4	492					cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|meiosis|multicellular organismal development|piRNA metabolic process|regulation of translation|spermatogenesis	nucleus|piP-body	piRNA binding				0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)												0.336842	266.711915	273.422948	96	189	CC		KEEP	---	---	---	---	capture			Silent	SNP	93974704	93974704	12384	11	C	T	T	27	27	PIWIL4	T	1	1
RNF34	80196	broad.mit.edu	36	12	120345608	120345608	+	Missense_Mutation	SNP	A	C	C			TCGA-41-2571-01	TCGA-41-2571-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:120345608A>C	uc001uam.1	+	c.965A>C	c.(964-966)GAC>GCC	p.D322A	RNF34_uc001uak.1_Missense_Mutation_p.D323A|RNF34_uc001ual.1_Missense_Mutation_p.D322A	NM_025126	NP_079402	Q969K3	RNF34_HUMAN	ring finger protein 34 isoform 2	322					apoptosis	endomembrane system|membrane|nuclear speck	ligase activity|zinc ion binding				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)													0.333333	7.390191	7.688308	4	8	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;0.000432)|Epithelial(86;0.00233)	Missense_Mutation	SNP	120345608	120345608	13968	12	A	C	C	10	10	RNF34	C	4	4
ANO2	57101	broad.mit.edu	36	12	5778977	5778977	+	Missense_Mutation	SNP	G	A	A			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:5778977G>A	uc001qnm.1	-	c.1003C>T	c.(1003-1005)CGC>TGC	p.R335C		NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2	339	Cytoplasmic (Potential).					chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7														0.269231	36.252358	38.735525	14	38	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5778977	5778977	705	12	G	A	A	38	38	ANO2	A	1	1
VWF	7450	broad.mit.edu	36	12	5998620	5998620	+	Missense_Mutation	SNP	C	T	T			TCGA-41-2571-01	TCGA-41-2571-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:5998620C>T	uc001qnn.1	-	c.4225G>A	c.(4225-4227)GTC>ATC	p.V1409I		NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein	1409	VWFA 1; binding site for platelet glycoprotein Ib.				blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			ovary(3)|pancreas(2)|breast(1)|central_nervous_system(1)	7					Antihemophilic Factor(DB00025)									0.390071	157.314425	158.799057	55	86	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5998620	5998620	17818	12	C	T	T	18	18	VWF	T	2	2
ELK3	2004	broad.mit.edu	36	12	95165211	95165211	+	Silent	SNP	C	T	T			TCGA-41-2571-01	TCGA-41-2571-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:95165211C>T	uc001teo.1	+	c.570C>T	c.(568-570)ACC>ACT	p.T190T		NM_005230	NP_005221	P41970	ELK3_HUMAN	ELK3 protein	190					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)													0.353741	156.259133	159.030394	52	95	CC		KEEP	---	---	---	---	capture			Silent	SNP	95165211	95165211	5252	12	C	T	T	23	23	ELK3	T	1	1
AHNAK2	113146	broad.mit.edu	36	14	104489190	104489190	+	Missense_Mutation	SNP	G	A	A			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:104489190G>A	uc010axc.1	-	c.3643C>T	c.(3643-3645)CCC>TCC	p.P1215S	AHNAK2_uc001ypx.2_Missense_Mutation_p.P1115S	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1215						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)												0.5	8.524262	8.524262	3	3	GG		KEEP	---	---	---	---	capture	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)		Missense_Mutation	SNP	104489190	104489190	418	14	G	A	A	42	42	AHNAK2	A	2	2
SLC28A1	9154	broad.mit.edu	36	15	83279403	83279403	+	Missense_Mutation	SNP	G	A	A			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:83279403G>A	uc002blg.1	+	c.1357G>A	c.(1357-1359)GTG>ATG	p.V453M	SLC28A1_uc010bnb.1_Missense_Mutation_p.V453M	NM_004213	NP_004204	O00337	S28A1_HUMAN	solute carrier family 28 (sodium-coupled	453					nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding			ovary(1)	1														0.407767	119.527813	120.293986	42	61	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(143;0.0587)		Missense_Mutation	SNP	83279403	83279403	15028	15	G	A	A	44	44	SLC28A1	A	2	2
APOB48R	55911	broad.mit.edu	36	16	28414887	28414887	+	Missense_Mutation	SNP	G	A	A			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:28414887G>A	uc002dqb.1	+	c.1024G>A	c.(1024-1026)GGC>AGC	p.G342S	APOB48R_uc010byg.1_5'UTR	NM_018690	NP_061160	Q0VD83	APOBR_HUMAN	apolipoprotein B48 receptor	342	Glu-rich.				cholesterol metabolic process|lipid transport	chylomicron|low-density lipoprotein particle|plasma membrane|very-low-density lipoprotein particle					0														0.470588	24.898592	24.911407	8	9	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	28414887	28414887	797	16	G	A	A	35	35	APOB48R	A	2	2
ALDOA	226	broad.mit.edu	36	16	29988485	29988485	+	Silent	SNP	C	T	T			TCGA-41-2571-01	TCGA-41-2571-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:29988485C>T	uc002dwd.1	+	c.801C>T	c.(799-801)CCC>CCT	p.P267P	BOLA2_uc010bzb.1_Intron|BOLA2_uc010bzc.1_Intron|ALDOA_uc002dvw.1_Silent_p.P263P|ALDOA_uc002dvx.1_Silent_p.P263P|ALDOA_uc002dvy.1_Silent_p.P263P|ALDOA_uc002dvz.1_Silent_p.P263P|ALDOA_uc002dwa.2_Silent_p.P263P|ALDOA_uc002dwb.1_Silent_p.P263P|ALDOA_uc002dwc.1_Silent_p.P263P	NM_184043	NP_908932	P04075	ALDOA_HUMAN	fructose-bisphosphate aldolase A	263					actin filament organization|ATP biosynthetic process|fructose 1,6-bisphosphate metabolic process|gluconeogenesis|glycolysis|muscle cell homeostasis|platelet activation|platelet degranulation|protein homotetramerization|regulation of cell shape|striated muscle contraction	actin cytoskeleton|cytosol|extracellular vesicular exosome|I band|platelet alpha granule lumen	actin binding|fructose binding|fructose-bisphosphate aldolase activity|identical protein binding|tubulin binding			lung(1)	1														0.351852	53.800748	54.849395	19	35	CC		KEEP	---	---	---	---	capture			Silent	SNP	29988485	29988485	510	16	C	T	T	23	23	ALDOA	T	1	1
MYO15A	51168	broad.mit.edu	36	17	17993350	17993350	+	Missense_Mutation	SNP	G	C	C			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:17993350G>C	uc010cpt.1	+	c.7052G>C	c.(7051-7053)AGC>ACC	p.S2351T	MYO15A_uc010cpu.1_Missense_Mutation_p.S2351T	NM_016239	NP_057323	Q9UKN7	MYO15_HUMAN	myosin XV	2351	Tail.				sensory perception of sound	cytoplasm|myosin complex|stereocilium	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|pancreas(1)|breast(1)|central_nervous_system(1)|skin(1)	6	all_neural(463;0.228)													0.285714	6.783317	7.368873	4	10	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17993350	17993350	10458	17	G	C	C	34	34	MYO15A	C	3	3
MNT	4335	broad.mit.edu	36	17	2237261	2237261	+	Missense_Mutation	SNP	G	A	A			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:2237261G>A	uc002fur.1	-	c.1433C>T	c.(1432-1434)GCG>GTG	p.A478V		NM_020310	NP_064706	Q99583	MNT_HUMAN	MAX binding protein	478					multicellular organismal development|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|transcription regulator activity				0														0.375	8.327562	8.435474	3	5	GG		KEEP	---	---	---	---	capture		Colorectal(2;1.37e-05)|READ - Rectum adenocarcinoma(2;8.68e-05)	Missense_Mutation	SNP	2237261	2237261	10069	17	G	A	A	38	38	MNT	A	1	1
RARA	5914	broad.mit.edu	36	17	35741165	35741165	+	Missense_Mutation	SNP	T	C	C			TCGA-41-2571-01	TCGA-41-2571-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:35741165T>C	uc002hum.1	+	c.169T>C	c.(169-171)TCC>CCC	p.S57P	RARA_uc002huk.1_Missense_Mutation_p.S57P|RARA_uc002hul.2_Missense_Mutation_p.S57P	NM_000964	NP_000955	P10276	RARA_HUMAN	retinoic acid receptor, alpha isoform 1	57	Modulating.				apoptotic cell clearance|cellular response to estrogen stimulus|cellular response to retinoic acid|estrogen receptor signaling pathway|negative regulation of gene-specific transcription|negative regulation of granulocyte differentiation|negative regulation of interferon-gamma production|negative regulation of tumor necrosis factor production|positive regulation of binding|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene-specific transcription|positive regulation of interleukin-13 production|positive regulation of interleukin-4 production|positive regulation of interleukin-5 production|positive regulation of T-helper 2 cell differentiation|positive regulation of transcription from RNA polymerase II promoter|protein phosphorylation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	cell surface|cytoplasm|nucleoplasm	chromatin DNA binding|enzyme binding|protein domain specific binding|protein heterodimerization activity|receptor binding|retinoic acid binding|retinoic acid receptor activity|retinoic acid-responsive element binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription activator activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)	2		Breast(137;0.00328)			Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Isotretinoin(DB00982)|Tamibarotene(DB04942)|Tazarotene(DB00799)					272				0.230769	7.620206	9.384114	6	20	TT		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(5;0.00143)		Missense_Mutation	SNP	35741165	35741165	13512	17	T	C	C	50	50	RARA	C	4	4
COL1A1	1277	broad.mit.edu	36	17	45623237	45623237	+	Silent	SNP	G	T	T			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:45623237G>T	uc002iqm.1	-	c.2283C>A	c.(2281-2283)GGC>GGA	p.G761G		NM_000088	NP_000079	P02452	CO1A1_HUMAN	alpha 1 type I collagen preproprotein	761	Triple-helical region.				axon guidance|blood vessel development|collagen biosynthetic process|collagen fibril organization|embryonic skeletal system development|leukocyte migration|platelet activation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|protein localization to nucleus|sensory perception of sound|skin morphogenesis|tooth mineralization|visual perception	collagen type I|extracellular space|plasma membrane	identical protein binding|platelet-derived growth factor binding|transcription activator activity		COL1A1/PDGFB(372)	soft_tissue(372)|central_nervous_system(7)|breast(1)|pancreas(1)	381					Collagenase(DB00048)|Palifermin(DB00039)					504				0.408451	86.251508	86.773762	29	42	GG		KEEP	---	---	---	---	capture			Silent	SNP	45623237	45623237	3815	17	G	T	T	38	38	COL1A1	T	3	3
GPR142	350383	broad.mit.edu	36	17	69879582	69879582	+	Missense_Mutation	SNP	G	A	A			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:69879582G>A	uc010dfq.1	+	c.628G>A	c.(628-630)GCG>ACG	p.A210T	GPR142_uc002jko.1_Missense_Mutation_p.A213T	NM_181790	NP_861455	Q7Z601	GP142_HUMAN	G protein-coupled receptor 142	213	Helical; Name=2; (Potential).					cell junction|cytoplasm|integral to membrane	G-protein coupled receptor activity			ovary(2)|central_nervous_system(1)	3														0.354167	43.868208	44.764592	17	31	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69879582	69879582	6924	17	G	A	A	38	38	GPR142	A	1	1
ABR	29	broad.mit.edu	36	17	860810	860810	+	Silent	SNP	G	A	A			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:860810G>A	uc002fsd.1	-	c.2145C>T	c.(2143-2145)AAC>AAT	p.N715N	ABR_uc002fsg.1_Silent_p.N678N|ABR_uc002fse.1_Silent_p.N669N|ABR_uc002fsh.1_Silent_p.N323N|ABR_uc002fsf.1_Silent_p.N252N	NM_021962	NP_068781	Q12979	ABR_HUMAN	active breakpoint cluster region-related	715	Rho-GAP.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity				0						Esophageal Squamous(197;2016 2115 4129 29033 46447)								0.25625	100.611848	109.224866	41	119	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)	Silent	SNP	860810	860810	100	17	G	A	A	40	40	ABR	A	1	1
SLC14A2	8170	broad.mit.edu	36	18	41459720	41459720	+	Silent	SNP	C	T	T			TCGA-41-2571-01	TCGA-41-2571-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:41459720C>T	uc010dnj.1	+	c.225C>T	c.(223-225)GAC>GAT	p.D75D	SLC14A2_uc002lbb.2_Silent_p.D75D|SLC14A2_uc002lbe.1_Silent_p.D75D	NM_007163	NP_009094	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter),	75						apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2														0.32	41.379395	42.820432	16	34	CC		KEEP	---	---	---	---	capture			Silent	SNP	41459720	41459720	14892	18	C	T	T	19	19	SLC14A2	T	1	1
ARMC6	93436	broad.mit.edu	36	19	19027113	19027113	+	Missense_Mutation	SNP	G	T	T			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:19027113G>T	uc002nld.1	+	c.1063G>T	c.(1063-1065)GCA>TCA	p.A355S	ARMC6_uc002nlc.1_Missense_Mutation_p.A330S|ARMC6_uc002nle.1_Missense_Mutation_p.A330S	NM_033415	NP_219483	Q6NXE6	ARMC6_HUMAN	armadillo repeat containing 6	355	ARM 3.						protein binding				0														0.20438	66.927785	78.033563	28	109	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(5;5.66e-06)|Epithelial(12;0.000391)		Missense_Mutation	SNP	19027113	19027113	973	19	G	T	T	38	38	ARMC6	T	3	3
PSG8	440533	broad.mit.edu	36	19	47951010	47951010	+	Missense_Mutation	SNP	G	A	A			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:47951010G>A	uc002ouo.1	-	c.958C>T	c.(958-960)CGC>TGC	p.R320C	PSG3_uc002ouf.1_Intron|PSG1_uc002oug.1_Intron|PSG8_uc002ouj.2_Missense_Mutation_p.R102C|PSG8_uc002ouk.2_Missense_Mutation_p.R159C|PSG8_uc002oul.2_Missense_Mutation_p.R320C|PSG8_uc002oum.2_Missense_Mutation_p.R227C|PSG1_uc002oun.1_Intron|PSG8_uc002oup.2_Missense_Mutation_p.R227C|PSG8_uc010eim.1_Intron|PSG8_uc002ouh.1_Missense_Mutation_p.R320C|PSG8_uc010ein.1_Missense_Mutation_p.R198C|PSG8_uc002oui.1_Missense_Mutation_p.R159C	NM_182707	NP_874366	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8 isoform	320	Ig-like C2-type 2.					extracellular region					0		Prostate(69;0.00899)												0.446078	277.801447	278.317401	91	113	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47951010	47951010	13114	19	G	A	A	39	39	PSG8	A	1	1
SIX5	147912	broad.mit.edu	36	19	50960722	50960722	+	Silent	SNP	G	A	A			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:50960722G>A	uc002pdb.1	-	c.2097C>T	c.(2095-2097)CCC>CCT	p.P699P	SIX5_uc002pdc.1_3'UTR	NM_175875	NP_787071	Q8N196	SIX5_HUMAN	sine oculis homeobox homolog 5	699					regulation of transcription, DNA-dependent	cytoplasm|nucleus	protein binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(1)	1		Ovarian(192;0.0308)|all_neural(266;0.112)												0.465116	184.28889	184.425362	60	69	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00783)|GBM - Glioblastoma multiforme(486;0.0802)|Epithelial(262;0.235)	Silent	SNP	50960722	50960722	14845	19	G	A	A	39	39	SIX5	A	1	1
RSPH6A	81492	broad.mit.edu	36	19	50999767	50999767	+	Silent	SNP	G	A	A			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:50999767G>A	uc002pdm.1	-	c.1236C>T	c.(1234-1236)CCC>CCT	p.P412P	RSPH6A_uc002pdl.1_Silent_p.P148P	NM_030785	NP_110412	Q9H0K4	RSH6A_HUMAN	radial spokehead-like 1	412						intracellular				ovary(1)|central_nervous_system(1)	2														0.369231	68.279819	69.257677	24	41	GG		KEEP	---	---	---	---	capture			Silent	SNP	50999767	50999767	14187	19	G	A	A	39	39	RSPH6A	A	1	1
DUS3L	56931	broad.mit.edu	36	19	5736666	5736666	+	Missense_Mutation	SNP	C	T	T			TCGA-41-2571-01	TCGA-41-2571-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:5736666C>T	uc002mdc.1	-	c.1699G>A	c.(1699-1701)GGC>AGC	p.G567S	PRR22_uc002mdb.1_5'Flank|DUS3L_uc002mdd.1_Missense_Mutation_p.G325S|DUS3L_uc010duk.1_Missense_Mutation_p.G232S	NM_020175	NP_064560	Q96G46	DUS3L_HUMAN	dihydrouridine synthase 3-like	567					oxidation-reduction process|tRNA processing		flavin adenine dinucleotide binding|nucleic acid binding|tRNA dihydrouridine synthase activity|zinc ion binding				0														0.333333	45.218531	46.382744	16	32	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5736666	5736666	4992	19	C	T	T	22	22	DUS3L	T	2	2
CD209	30835	broad.mit.edu	36	19	7715880	7715880	+	Missense_Mutation	SNP	C	T	T			TCGA-41-2571-01	TCGA-41-2571-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:7715880C>T	uc002mht.1	-	c.847G>A	c.(847-849)GCC>ACC	p.A283T	CD209_uc010dvp.1_Missense_Mutation_p.A259T|CD209_uc002mhs.1_Missense_Mutation_p.A213T|CD209_uc002mhq.1_Missense_Mutation_p.A283T|CD209_uc002mhr.1_Missense_Mutation_p.A259T|CD209_uc002mhu.1_Missense_Mutation_p.A191T|CD209_uc010dvq.1_Missense_Mutation_p.A283T|CD209_uc002mhv.1_Missense_Mutation_p.A259T|CD209_uc002mhw.1_Missense_Mutation_p.A147T|CD209_uc002mhx.1_Missense_Mutation_p.A239T|CD209_uc010dvr.1_Intron	NM_021155	NP_066978	Q9NNX6	CD209_HUMAN	CD209 molecule isoform 1	283	Extracellular (Probable).|C-type lectin.				cell-cell recognition|endocytosis|heterophilic cell-cell adhesion|innate immune response|intracellular signal transduction|intracellular virion transport|leukocyte cell-cell adhesion|peptide antigen transport|viral genome replication|virion attachment to host cell surface receptor	cytoplasm|extracellular region|integral to membrane|plasma membrane	mannose binding|metal ion binding|peptide antigen binding|receptor activity|virion binding				0														0.25641	68.460561	74.789379	30	87	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7715880	7715880	3111	19	C	T	T	27	27	CD209	T	1	1
SPTA1	6708	broad.mit.edu	36	1	156893016	156893016	+	Missense_Mutation	SNP	T	A	A			TCGA-41-2571-01	TCGA-41-2571-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:156893016T>A	uc001fst.1	-	c.2860A>T	c.(2860-2862)AGT>TGT	p.S954C		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	954	Spectrin 10.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.301948	271.057993	281.844113	93	215	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	156893016	156893016	15630	1	T	A	A	55	55	SPTA1	A	4	4
LY9	4063	broad.mit.edu	36	1	159060101	159060101	+	Missense_Mutation	SNP	A	G	G			TCGA-41-2571-01	TCGA-41-2571-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:159060101A>G	uc001fwu.1	+	c.1721A>G	c.(1720-1722)GAC>GGC	p.D574G	LY9_uc001fwv.1_Missense_Mutation_p.D560G|LY9_uc001fww.1_Missense_Mutation_p.D484G|LY9_uc001fwx.1_Missense_Mutation_p.D484G|LY9_uc001fwy.1_Missense_Mutation_p.D372G|LY9_uc001fwz.1_Missense_Mutation_p.D212G	NM_002348	NP_002339	Q9HBG7	LY9_HUMAN	lymphocyte antigen 9 isoform a	574	Cytoplasmic (Potential).				cell adhesion|immunoglobulin mediated immune response	integral to membrane				ovary(1)	1	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)													0.177419	121.973259	152.656854	55	255	AA		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(70;0.00737)		Missense_Mutation	SNP	159060101	159060101	9478	1	A	G	G	10	10	LY9	G	4	4
CEP350	9857	broad.mit.edu	36	1	178238978	178238978	+	Silent	SNP	G	A	A			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:178238978G>A	uc001gnt.1	+	c.1065G>A	c.(1063-1065)GTG>GTA	p.V355V	CEP350_uc001gnu.1_Silent_p.V189V	NM_014810	NP_055625	Q5VT06	CE350_HUMAN	centrosome-associated protein 350	355						centrosome|nucleus|spindle				ovary(4)	4														0.454545	44.320098	44.379644	15	18	GG		KEEP	---	---	---	---	capture			Silent	SNP	178238978	178238978	3387	1	G	A	A	48	48	CEP350	A	2	2
PLA2G2F	64600	broad.mit.edu	36	1	20342609	20342609	+	Missense_Mutation	SNP	G	A	A			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:20342609G>A	uc009vpp.1	+	c.253G>A	c.(253-255)GTG>ATG	p.V85M		NM_022819	NP_073730	Q9BZM2	PA2GF_HUMAN	phospholipase A2, group IIF	42					lipid catabolic process|phospholipid metabolic process	extracellular region	calcium ion binding|phospholipase A2 activity			ovary(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000247)|Lung NSC(340;0.000285)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)												0.325397	112.440445	115.844175	41	85	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.000524)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)	Missense_Mutation	SNP	20342609	20342609	12425	1	G	A	A	40	40	PLA2G2F	A	1	1
FMN2	56776	broad.mit.edu	36	1	238437834	238437834	+	Silent	SNP	G	T	T			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:238437834G>T	uc009xgl.1	+	c.3540G>T	c.(3538-3540)CCG>CCT	p.P1180P		NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	1033	Pro-rich.|FH1.				actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|large_intestine(1)|central_nervous_system(1)	9	Ovarian(103;0.127)	all_cancers(173;0.013)								1289				0.375	7.521994	7.632052	3	5	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0106)		Silent	SNP	238437834	238437834	6192	1	G	T	T	38	38	FMN2	T	3	3
OR2T12	127064	broad.mit.edu	36	1	246524542	246524542	+	Silent	SNP	C	T	T			TCGA-41-2571-01	TCGA-41-2571-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246524542C>T	uc001iee.1	-	c.962G>A	c.(961-963)TGA>TAA	p.*321*		NM_001004692	NP_001004692	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T,	321					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(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)													0.272109	206.457857	220.23148	80	214	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0201)		Silent	SNP	246524542	246524542	11425	1	C	T	T	29	29	OR2T12	T	2	2
JAG1	182	broad.mit.edu	36	20	10601470	10601470	+	Missense_Mutation	SNP	C	T	T			TCGA-41-2571-01	TCGA-41-2571-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:10601470C>T	uc002wnw.2	-	c.266G>A	c.(265-267)GGG>GAG	p.G89E		NM_000214	NP_000205	P78504	JAG1_HUMAN	jagged 1 precursor	89	Extracellular (Potential).				angiogenesis|cell communication|cell fate determination|endothelial cell differentiation|hemopoiesis|keratinocyte differentiation|myoblast differentiation|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation	extracellular region|integral to plasma membrane	calcium ion binding|growth factor activity|Notch binding|structural molecule activity			lung(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5										587				0.268293	83.533139	89.486941	33	90	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10601470	10601470	8238	20	C	T	T	22	22	JAG1	T	2	2
C22orf43	51233	broad.mit.edu	36	22	22304205	22304205	+	Silent	SNP	C	T	T			TCGA-41-2571-01	TCGA-41-2571-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:22304205C>T	uc002zxf.1	-	c.6G>A	c.(4-6)GGG>GGA	p.G2G		NM_016449	NP_057533	Q6PGQ1	CV043_HUMAN	hypothetical protein LOC51233	2											0														0.423913	109.402791	109.865756	39	53	CC		KEEP	---	---	---	---	capture			Silent	SNP	22304205	22304205	2232	22	C	T	T	30	30	C22orf43	T	2	2
RRP7A	27341	broad.mit.edu	36	22	41242085	41242085	+	Missense_Mutation	SNP	T	C	C			TCGA-41-2571-01	TCGA-41-2571-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:41242085T>C	uc003bcp.1	-	c.287A>G	c.(286-288)GAG>GGG	p.E96G	RRP7A_uc003bcq.1_Missense_Mutation_p.E73G	NM_015703	NP_056518	Q9Y3A4	RRP7A_HUMAN	ribosomal RNA processing 7 homolog A	73	RRM.						nucleotide binding|RNA binding			central_nervous_system(1)	1														0.368421	6.760702	7.147814	7	12	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41242085	41242085	14169	22	T	C	C	54	54	RRP7A	C	4	4
FAM118A	55007	broad.mit.edu	36	22	44102462	44102462	+	Missense_Mutation	SNP	C	T	T			TCGA-41-2571-01	TCGA-41-2571-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:44102462C>T	uc003bfz.2	+	c.376C>T	c.(376-378)CGG>TGG	p.R126W	FAM118A_uc003bga.2_Missense_Mutation_p.R126W	NM_001104595	NP_060381	Q9NWS6	F118A_HUMAN	hypothetical protein LOC55007	126						integral to membrane					0		Ovarian(80;0.00965)|all_neural(38;0.0416)							p.R126W(ISTMES1-Tumor)	952				0.393443	71.389265	71.994765	24	37	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)	Missense_Mutation	SNP	44102462	44102462	5608	22	C	T	T	23	23	FAM118A	T	1	1
CRYGD	1421	broad.mit.edu	36	2	208694717	208694717	+	Missense_Mutation	SNP	G	C	C			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:208694717G>C	uc002vcn.2	-	c.450C>G	c.(448-450)GAC>GAG	p.D150E		NM_006891	NP_008822	P07320	CRGD_HUMAN	crystallin, gamma D	150	Beta/gamma crystallin 'Greek key' 4.				cellular response to reactive oxygen species|visual perception	soluble fraction	protein binding|structural constituent of eye lens				0														0.252033	89.876114	96.738132	31	92	GG		KEEP	---	---	---	---	capture		LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.0858)|Lung(261;0.133)	Missense_Mutation	SNP	208694717	208694717	4056	2	G	C	C	36	36	CRYGD	C	3	3
OBSL1	23363	broad.mit.edu	36	2	220131398	220131398	+	Missense_Mutation	SNP	G	T	T			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:220131398G>T	uc010fwk.1	-	c.3254C>A	c.(3253-3255)GCA>GAA	p.A1085E	OBSL1_uc002vmh.1_Missense_Mutation_p.A76E|OBSL1_uc010fwl.1_Missense_Mutation_p.A560E	NM_015311	NP_056126	O75147	OBSL1_HUMAN	obscurin-like 1	1085	Ig-like 9.				cardiac myofibril assembly	intercalated disc|M band|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity				0		Renal(207;0.0376)												0.363636	8.006113	8.181915	4	7	GG		KEEP	---	---	---	---	capture		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)	Missense_Mutation	SNP	220131398	220131398	11218	2	G	T	T	46	46	OBSL1	T	3	3
SRBD1	55133	broad.mit.edu	36	2	45627374	45627374	+	Splice_Site_SNP	SNP	C	A	A			TCGA-41-2571-01	TCGA-41-2571-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:45627374C>A	uc002rus.1	-	c.1874_splice	c.e14+1	p.C625_splice		NM_018079	NP_060549			S1 RNA binding domain 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		hydrolase activity, acting on ester bonds|RNA binding				0		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)												0.39604	129.280073	130.235099	40	61	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)		Splice_Site_SNP	SNP	45627374	45627374	15647	2	C	A	A	18	18	SRBD1	A	5	3
CD96	10225	broad.mit.edu	36	3	112839673	112839673	+	Missense_Mutation	SNP	G	A	A			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:112839673G>A	uc003dxw.1	+	c.1493G>A	c.(1492-1494)GGA>GAA	p.G498E	CD96_uc003dxx.1_Missense_Mutation_p.G482E|CD96_uc010hpy.1_Missense_Mutation_p.G481E	NM_198196	NP_937839	P40200	TACT_HUMAN	CD96 antigen isoform 1 precursor	498	Extracellular (Potential).|Pro/Ser/Thr-rich.				cell adhesion|immune response|regulation of immune response	integral to plasma membrane				central_nervous_system(1)	1														0.340659	178.788537	182.875546	62	120	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	112839673	112839673	3176	3	G	A	A	41	41	CD96	A	2	2
HPS3	84343	broad.mit.edu	36	3	150340585	150340585	+	Missense_Mutation	SNP	A	C	C			TCGA-41-2571-01	TCGA-41-2571-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:150340585A>C	uc003ewu.1	+	c.322A>C	c.(322-324)ATG>CTG	p.M108L	HPS3_uc003ewt.1_Missense_Mutation_p.M108L	NM_032383	NP_115759	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3 protein	108						cytoplasm				ovary(5)|large_intestine(1)	6														0.34359	218.467486	222.680728	67	128	AA		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Missense_Mutation	SNP	150340585	150340585	7632	3	A	C	C	4	4	HPS3	C	4	4
CPN2	1370	broad.mit.edu	36	3	195543782	195543782	+	Missense_Mutation	SNP	G	A	A			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:195543782G>A	uc003fts.1	-	c.1345C>T	c.(1345-1347)CGG>TGG	p.R449W	CPN2_uc010hzj.1_Missense_Mutation_p.R449W	NM_001080513	NP_001073982	P22792	CPN2_HUMAN	carboxypeptidase N, polypeptide 2, 83kD	449					protein stabilization	extracellular region	enzyme regulator activity			ovary(5)	5	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)													0.366013	165.06722	167.47865	56	97	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.65e-05)	Missense_Mutation	SNP	195543782	195543782	3948	3	G	A	A	39	39	CPN2	A	1	1
CCR4	1233	broad.mit.edu	36	3	32970892	32970892	+	Missense_Mutation	SNP	T	A	A			TCGA-41-2571-01	TCGA-41-2571-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:32970892T>A	uc003cfg.1	+	c.974T>A	c.(973-975)CTT>CAT	p.L325H	CCR4_uc010hfx.1_Missense_Mutation_p.L325H	NM_005508	NP_005499	P51679	CCR4_HUMAN	chemokine (C-C motif) receptor 4	325	Cytoplasmic (Potential).				chemotaxis|elevation of cytosolic calcium ion concentration|immune response|inflammatory response	integral to plasma membrane					0										38				0.416667	139.288516	140.024322	50	70	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32970892	32970892	3070	3	T	A	A	56	56	CCR4	A	4	4
DCP1A	55802	broad.mit.edu	36	3	53351339	53351339	+	Splice_Site_SNP	SNP	C	A	A			TCGA-41-2571-01	TCGA-41-2571-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:53351339C>A	uc003dgs.2	-	c.177_splice	c.e3-1	p.R59_splice	DCP1A_uc003dgt.2_Splice_Site_SNP	NM_018403	NP_060873			DCP1 decapping enzyme homolog A						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasmic mRNA processing body|cytosol|nucleus	hydrolase activity|protein binding				0														0.391304	25.868733	26.107097	9	14	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;0.000164)|KIRC - Kidney renal clear cell carcinoma(197;0.00525)|Kidney(197;0.00579)|OV - Ovarian serous cystadenocarcinoma(275;0.0647)	Splice_Site_SNP	SNP	53351339	53351339	4469	3	C	A	A	24	24	DCP1A	A	5	3
TLR1	7096	broad.mit.edu	36	4	38474996	38474996	+	Nonsense_Mutation	SNP	G	A	A			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:38474996G>A	uc003gtl.1	-	c.1852C>T	c.(1852-1854)CAG>TAG	p.Q618*	TLR1_uc010iff.1_Nonsense_Mutation_p.Q618*	NM_003263	NP_003254	Q15399	TLR1_HUMAN	toll-like receptor 1	618	Cytoplasmic (Potential).				cellular response to triacyl bacterial lipopeptide|detection of triacyl bacterial lipopeptide|inflammatory response|innate immune response|macrophage activation|positive regulation of interleukin-6 biosynthetic process|positive regulation of tumor necrosis factor biosynthetic process	integral to plasma membrane|phagocytic vesicle membrane|Toll-like receptor 1-Toll-like receptor 2 protein complex	protein heterodimerization activity|transmembrane receptor activity				0						GBM(5;216 373 40795 46382)								0.379888	198.446835	200.71565	68	111	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	38474996	38474996	16479	4	G	A	A	47	47	TLR1	A	5	2
SMR3B	10879	broad.mit.edu	36	4	71284829	71284829	+	Missense_Mutation	SNP	A	T	T			TCGA-41-2571-01	TCGA-41-2571-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:71284829A>T	uc003hfh.1	+	c.13A>T	c.(13-15)ACT>TCT	p.T5S		NM_006685	NP_006676	P02814	SMR3B_HUMAN	submaxillary gland androgen regulated protein 3	5						extracellular space				skin(1)	1		all_hematologic(202;0.196)												0.379747	87.731204	88.733304	30	49	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71284829	71284829	15312	4	A	T	T	10	10	SMR3B	T	4	4
CCDC158	339965	broad.mit.edu	36	4	77507553	77507553	+	Missense_Mutation	SNP	C	T	T			TCGA-41-2571-01	TCGA-41-2571-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:77507553C>T	uc003hkb.2	-	c.1748G>A	c.(1747-1749)CGA>CAA	p.R583Q	CCDC158_uc010ijg.1_Intron	NM_001042784	NP_001036249	Q5M9N0	CD158_HUMAN	hypothetical protein LOC339965	583	Potential.									ovary(2)|pancreas(1)	3														0.407895	184.82534	185.950719	62	90	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	77507553	77507553	2912	4	C	T	T	31	31	CCDC158	T	1	1
PCDHGA7	56108	broad.mit.edu	36	5	140743243	140743243	+	Missense_Mutation	SNP	G	A	A			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140743243G>A	uc003lka.1	+	c.593G>A	c.(592-594)CGG>CAG	p.R198Q	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003ljz.1_Missense_Mutation_p.R198Q	NM_018920	NP_061743	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7 isoform 1	198	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.382353	38.569045	38.980924	13	21	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140743243	140743243	11979	5	G	A	A	39	39	PCDHGA7	A	1	1
TBP	6908	broad.mit.edu	36	6	170720761	170720761	+	Missense_Mutation	SNP	G	T	T			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:170720761G>T	uc003qxt.1	+	c.814G>T	c.(814-816)GGC>TGC	p.G272C	TBP_uc003qxu.1_Missense_Mutation_p.G272C	NM_003194	NP_003185	P20226	TBP_HUMAN	TATA box binding protein	272	2.				cell death|general transcription from RNA polymerase II promoter|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	transcription factor TFIIA complex|transcription factor TFIID complex	general RNA polymerase II transcription factor activity|promoter binding|repressing transcription factor binding			ovary(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)												0.267606	48.28959	51.754496	19	52	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)	Missense_Mutation	SNP	170720761	170720761	16170	6	G	T	T	35	35	TBP	T	3	3
HLA-E	3133	broad.mit.edu	36	6	30566909	30566909	+	Silent	SNP	C	T	T			TCGA-41-2571-01	TCGA-41-2571-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:30566909C>T	uc003nqg.1	+	c.627C>T	c.(625-627)CAC>CAT	p.H209H		NM_005516	NP_005507	P13747	HLAE_HUMAN	major histocompatibility complex, class I, E	209	Ig-like C1-type.|Alpha-3.|Extracellular (Potential).				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			central_nervous_system(4)|ovary(1)	5														0.381643	224.58359	227.123414	79	128	CC		KEEP	---	---	---	---	capture			Silent	SNP	30566909	30566909	7501	6	C	T	T	19	19	HLA-E	T	1	1
DST	667	broad.mit.edu	36	6	56464994	56464994	+	Missense_Mutation	SNP	C	G	G			TCGA-41-2571-01	TCGA-41-2571-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:56464994C>G	uc003pcz.2	-	c.13856G>C	c.(13855-13857)AGA>ACA	p.R4619T	DST_uc003pcy.2_Missense_Mutation_p.R4293T|DST_uc003pda.2_5'UTR	NM_183380	NP_899236	Q03001	DYST_HUMAN	dystonin isoform 1	6705	Spectrin 18.				cell adhesion|cell cycle arrest|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization	basement membrane|cytoplasmic membrane-bounded vesicle|hemidesmosome|microtubule plus end|nucleus	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein C-terminus binding			ovary(7)|central_nervous_system(6)	13	Lung NSC(77;0.103)									2498				0.402062	138.208269	139.021337	39	58	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)		Missense_Mutation	SNP	56464994	56464994	4967	6	C	G	G	32	32	DST	G	3	3
COL19A1	1310	broad.mit.edu	36	6	70934825	70934825	+	Silent	SNP	T	A	A			TCGA-41-2571-01	TCGA-41-2571-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:70934825T>A	uc003pfc.1	+	c.2538T>A	c.(2536-2538)CCT>CCA	p.P846P		NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor	846	Triple-helical region 5 (COL5).				cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4														0.428571	96.960589	97.303651	33	44	TT		KEEP	---	---	---	---	capture			Silent	SNP	70934825	70934825	3814	6	T	A	A	54	54	COL19A1	A	4	4
PPP1R3A	5506	broad.mit.edu	36	7	113346140	113346140	+	Missense_Mutation	SNP	C	T	T			TCGA-41-2571-01	TCGA-41-2571-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:113346140C>T	uc010ljy.1	-	c.148G>A	c.(148-150)GAA>AAA	p.E50K		NM_002711	NP_002702	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory (inhibitor)	50					glycogen metabolic process	integral to membrane				ovary(9)|pancreas(7)|skin(2)|breast(2)|lung(1)	21										235				0.184906	98.903127	123.58996	49	216	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	113346140	113346140	12806	7	C	T	T	29	29	PPP1R3A	T	2	2
TBXAS1	6916	broad.mit.edu	36	7	139301830	139301830	+	Missense_Mutation	SNP	C	T	T			TCGA-41-2571-01	TCGA-41-2571-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:139301830C>T	uc003vvh.1	+	c.646C>T	c.(646-648)CGT>TGT	p.R216C	TBXAS1_uc010lne.1_Missense_Mutation_p.R148C|TBXAS1_uc003vvi.1_Missense_Mutation_p.R216C|TBXAS1_uc003vvj.1_Missense_Mutation_p.R216C	NM_001061	NP_001052	P24557	THAS_HUMAN	thromboxane A synthase 1 isoform TXS-I	215	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)													0.186235	91.200945	113.996289	46	201	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	139301830	139301830	16190	7	C	T	T	27	27	TBXAS1	T	1	1
C7orf65	401335	broad.mit.edu	36	7	47665276	47665276	+	Missense_Mutation	SNP	G	T	T			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:47665276G>T	uc010kyp.1	+	c.381G>T	c.(379-381)AAG>AAT	p.K127N		NM_001123065	NP_001116537	Q6ZTY9	CG065_HUMAN	hypothetical protein LOC401335	127											0														0.172897	72.833726	94.46791	37	177	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47665276	47665276	2518	7	G	T	T	35	35	C7orf65	T	3	3
KANK1	23189	broad.mit.edu	36	9	722407	722407	+	Missense_Mutation	SNP	G	T	T			TCGA-41-2571-01	TCGA-41-2571-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:722407G>T	uc003zgl.1	+	c.3035G>T	c.(3034-3036)AGC>ATC	p.S1012I	KANK1_uc003zgm.2_3'UTR|KANK1_uc003zgn.1_Missense_Mutation_p.S1012I|KANK1_uc003zgs.1_Missense_Mutation_p.S854I|KANK1_uc010mgx.1_5'UTR|KANK1_uc010mgy.1_5'UTR|KANK1_uc003zgt.1_5'Flank	NM_015158	NP_055973	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1 isoform a	1012					negative regulation of actin filament polymerization	cytoplasm				ovary(2)|central_nervous_system(1)|pancreas(1)	4		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)												0.313559	98.725679	102.379757	37	81	GG		KEEP	---	---	---	---	capture		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)	Missense_Mutation	SNP	722407	722407	8280	9	G	T	T	34	34	KANK1	T	3	3
HEPH	9843	broad.mit.edu	36	X	65308930	65308930	+	Missense_Mutation	SNP	C	T	T			TCGA-41-2571-01	TCGA-41-2571-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:65308930C>T	uc004dwn.1	+	c.185C>T	c.(184-186)TCC>TTC	p.S62F	HEPH_uc004dwm.1_Missense_Mutation_p.S59F|HEPH_uc004dwo.1_5'UTR|HEPH_uc010nkr.1_Missense_Mutation_p.S62F|HEPH_uc004dwp.1_Missense_Mutation_p.S59F	NM_138737	NP_620074	Q9BQS7	HEPH_HUMAN	hephaestin isoform a	59	Extracellular (Potential).|Plastocyanin-like 1.				cellular iron ion homeostasis|copper ion transport|oxidation-reduction process|transmembrane transport	integral to membrane|plasma membrane	copper ion binding|oxidoreductase activity			lung(5)|ovary(4)	9									p.S62F(OE33-Tumor)	386				0.333333	8.247521	8.740572	6	12	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65308930	65308930	7337	23	C	T	T	30	30	HEPH	T	2	2
MAP2K1	5604	broad.mit.edu	36	15	64466760	64466760	+	Frame_Shift_Del	DEL	G	-	-			TCGA-41-2571-01	TCGA-41-2571-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:64466760_64466760delG	uc010bhq.1	+	c.21_21delG	c.(19-21)ACGfs	p.T7fs		NM_002755	NP_002746	Q02750	MP2K1_HUMAN	mitogen-activated protein kinase kinase 1	7					activation of MAPK activity|activation of MAPKK activity|axon guidance|cell cycle arrest|cellular senescence|epidermal growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of cell proliferation|nerve growth factor receptor signaling pathway|Ras protein signal transduction|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|plasma membrane	ATP binding|MAP kinase kinase activity|protein serine/threonine kinase activity|protein tyrosine kinase activity				0										667				0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	64466760	64466760	9619	15	G	-	-	38	38	MAP2K1	-	5	5
KIAA0182	23199	broad.mit.edu	36	16	84259369	84259369	+	Frame_Shift_Del	DEL	C	-	-			TCGA-41-2571-01	TCGA-41-2571-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:84259369_84259369delC	uc002fix.1	+	c.3253_3253delC	c.(3253-3255)CCCfs	p.P1085fs	KIAA0182_uc002fiw.1_Frame_Shift_Del_p.P981fs|KIAA0182_uc002fiy.1_Frame_Shift_Del_p.P1012fs|KIAA0182_uc002fiz.1_Frame_Shift_Del_p.P227fs|KIAA0182_uc010cho.1_Frame_Shift_Del_p.P265fs	NM_014615	NP_055430	Q14687	GSE1_HUMAN	genetic suppressor element 1 isoform 1	1085							protein binding			large_intestine(3)|ovary(1)|skin(1)	5														0.35			56	103				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	84259369	84259369	8466	16	C	-	-	26	26	KIAA0182	-	5	5
