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
WDR11	55717	broad.mit.edu	36	10	122600996	122600996	+	Missense_Mutation	SNP	C	A	A			TCGA-27-2524-01	TCGA-27-2524-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:122600996C>A	uc009xzm.1	+	c.74C>A	c.(73-75)GCG>GAG	p.A25E	WDR11_uc001lfd.1_5'Flank	NM_018117	NP_060587	Q9BZH6	WDR11_HUMAN	bromodomain and WD repeat domain containing 2	25						integral to membrane					0														0.272727	6.71821	7.231994	3	8	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	122600996	122600996	17846	10	C	A	A	27	27	WDR11	A	3	3
PTEN	5728	broad.mit.edu	36	10	89682884	89682884	+	Nonsense_Mutation	SNP	C	T	T			TCGA-27-2524-01	TCGA-27-2524-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89682884C>T	uc001kfb.1	+	c.388C>T	c.(388-390)CGA>TGA	p.R130*		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	130	Phosphatase tensin-type.		R -> L (in CD and endometrial hyperplasia; loss of phosphatase activity towards Ins(1,3,4,5)P4; retains ability to bind phospholipid membranes).|R -> Q (in CD; loss of phosphatase activity towards Ins(1,3,4,5)P4; retains ability to bind phospholipid membranes).|R -> G (loss of phosphatase activity towards Ins(1,3,4,5)P4 and PtdIns(3,4,5)P3).	R->M: Does not affect the ability to inhibit AKT/PKB activation.	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.R130G(64)|p.R130*(60)|p.K128_R130del(3)|p.R130Q(2)|p.Y27_N212>Y(2)|p.K128fs*47(1)|p.R130R(1)|p.A121_F145del(1)|p.F56fs*2(1)|p.G129fs*50(1)|p.G129fs*51(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)					R130G(OV56_OVARY)|R130G(KMBC2_URINARY_TRACT)	31	p.R130G(OV56-Tumor)|p.KGR128del(A2780-Tumor)|p.R130G(KMBC2-Tumor)|p.G129fs(U937-Tumor)	264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.587302	244.074715	244.914974	74	52	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	89682884	89682884	13192	10	C	T	T	19	19	PTEN	T	5	1
SLC17A6	57084	broad.mit.edu	36	11	22319825	22319825	+	Missense_Mutation	SNP	C	A	A			TCGA-27-2524-01	TCGA-27-2524-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:22319825C>A	uc001mqk.1	+	c.262C>A	c.(262-264)CGC>AGC	p.R88S		NM_020346	NP_065079	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (sodium-dependent	88	Helical; (Potential).				sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)|breast(1)	4														0.413793	111.786035	112.350212	36	51	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22319825	22319825	14917	11	C	A	A	23	23	SLC17A6	A	3	3
OR52D1	390066	broad.mit.edu	36	11	5467361	5467361	+	Silent	SNP	C	G	G			TCGA-27-2524-01	TCGA-27-2524-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:5467361C>G	uc001max.1	+	c.849C>G	c.(847-849)CTC>CTG	p.L283L	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron|OR51B5_uc001maq.1_Intron	NM_001005163	NP_001005163	Q9H346	O52D1_HUMAN	olfactory receptor, family 52, subfamily D,	283	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)												0.418367	137.321275	137.898904	41	57	CC		KEEP	---	---	---	---	capture		Epithelial(150;3.46e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	Silent	SNP	5467361	5467361	11524	11	C	G	G	32	32	OR52D1	G	3	3
CD5	921	broad.mit.edu	36	11	60642520	60642520	+	Missense_Mutation	SNP	C	A	A			TCGA-27-2524-01	TCGA-27-2524-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:60642520C>A	uc009ynk.1	+	c.392C>A	c.(391-393)ACC>AAC	p.T131N		NM_014207	NP_055022	P06127	CD5_HUMAN	CD5 molecule	131	Extracellular (Potential).|SRCR 1.				cell proliferation|cell recognition	integral to plasma membrane	scavenger receptor activity			ovary(1)	1		all_lung(304;5.94e-05)|Lung NSC(402;7.26e-05)												0.37037	136.316322	138.308661	50	85	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.000946)|Lung(977;0.0086)|LUSC - Lung squamous cell carcinoma(625;0.0528)	Missense_Mutation	SNP	60642520	60642520	3149	11	C	A	A	18	18	CD5	A	3	3
ERP27	121506	broad.mit.edu	36	12	14965220	14965220	+	Silent	SNP	G	A	A			TCGA-27-2524-01	TCGA-27-2524-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:14965220G>A	uc001rco.1	-	c.363C>T	c.(361-363)GAC>GAT	p.D121D		NM_152321	NP_689534	Q96DN0	ERP27_HUMAN	endoplasmic reticulum protein 27 kDa	121	Thioredoxin.					endoplasmic reticulum lumen				breast(1)	1														0.333333	147.004032	150.924615	53	106	GG		KEEP	---	---	---	---	capture			Silent	SNP	14965220	14965220	5434	12	G	A	A	40	40	ERP27	A	1	1
LST-3TM12	338821	broad.mit.edu	36	12	21067151	21067151	+	Silent	SNP	T	C	C			TCGA-27-2524-01	TCGA-27-2524-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:21067151T>C	uc001ren.1	+	c.582T>C	c.(580-582)TCT>TCC	p.S194S	SLCO1B3_uc001rem.1_Intron|LST-3TM12_uc001rep.1_Silent_p.S147S	NM_001009562	NP_001009562	Q71QF0	Q71QF0_HUMAN	liver-specific organic anion transporter 3TM12	147						membrane	transporter activity				0														0.398649	201.460313	202.799247	59	89	TT		KEEP	---	---	---	---	capture			Silent	SNP	21067151	21067151	9442	12	T	C	C	56	56	LST-3TM12	C	4	4
AMHR2	269	broad.mit.edu	36	12	52109594	52109594	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2524-01	TCGA-27-2524-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:52109594G>A	uc001scx.1	+	c.1058G>A	c.(1057-1059)GGC>GAC	p.G353D	AMHR2_uc009zmy.1_Missense_Mutation_p.G353D	NM_020547	NP_065434	Q16671	AMHR2_HUMAN	anti-Mullerian hormone receptor, type II	353	Cytoplasmic (Potential).|Protein kinase.				Mullerian duct regression|protein phosphorylation		ATP binding|hormone binding|metal ion binding			ovary(1)	1					Adenosine triphosphate(DB00171)					136				0.420168	138.963193	139.614305	50	69	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	52109594	52109594	576	12	G	A	A	42	42	AMHR2	A	2	2
LUM	4060	broad.mit.edu	36	12	90022102	90022102	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2524-01	TCGA-27-2524-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:90022102G>A	uc001tbm.1	-	c.988C>T	c.(988-990)CGT>TGT	p.R330C	LUM_uc001tbn.1_Non-coding_Transcript	NM_002345	NP_002336	P51884	LUM_HUMAN	lumican precursor	330					collagen fibril organization|visual perception	extracellular space|fibrillar collagen	collagen binding|extracellular matrix structural constituent			central_nervous_system(2)	2														0.291045	106.777652	112.015144	39	95	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	90022102	90022102	9461	12	G	A	A	40	40	LUM	A	1	1
MGA	23269	broad.mit.edu	36	15	39834052	39834052	+	Missense_Mutation	SNP	A	C	C			TCGA-27-2524-01	TCGA-27-2524-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:39834052A>C	uc001zoh.1	+	c.7281A>C	c.(7279-7281)AAA>AAC	p.K2427N		NM_001080541	NP_001074010	Q8IWI9	MGAP_HUMAN	MAX gene associated	2339	Basic motif.				regulation of transcription, DNA-dependent	MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|skin(1)	11		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)								606				0.3	8.323491	9.120509	6	14	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Missense_Mutation	SNP	39834052	39834052	9930	15	A	C	C	2	2	MGA	C	4	4
SPTBN5	51332	broad.mit.edu	36	15	39933120	39933120	+	Missense_Mutation	SNP	G	C	C			TCGA-27-2524-01	TCGA-27-2524-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:39933120G>C	uc001zos.1	-	c.9827C>G	c.(9826-9828)GCG>GGG	p.A3276G		NM_016642	NP_057726	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	3311	Spectrin 29.				actin cytoskeleton organization|actin filament capping|axon guidance	cytosol|membrane|spectrin				ovary(1)|central_nervous_system(1)	2		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)												0.272727	7.31869	8.365593	6	16	GG		KEEP	---	---	---	---	capture		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)	Missense_Mutation	SNP	39933120	39933120	15636	15	G	C	C	38	38	SPTBN5	C	3	3
CHD9	80205	broad.mit.edu	36	16	51888373	51888373	+	Missense_Mutation	SNP	A	G	G			TCGA-27-2524-01	TCGA-27-2524-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:51888373A>G	uc002ehb.1	+	c.5515A>G	c.(5515-5517)ACA>GCA	p.T1839A	CHD9_uc002egy.1_Missense_Mutation_p.T1839A|CHD9_uc002ehc.1_Missense_Mutation_p.T1839A|CHD9_uc002ehf.1_Missense_Mutation_p.T953A|CHD9_uc010cbw.1_Missense_Mutation_p.T207A	NM_025134	NP_079410	Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	1839					cellular lipid metabolic process|chromatin assembly or disassembly|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|cytoplasm|nucleoplasm	ATP binding|chromatin binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)								1157				0.11875	33.028569	55.849187	19	141	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51888373	51888373	3466	16	A	G	G	10	10	CHD9	G	4	4
ZFHX3	463	broad.mit.edu	36	16	71384868	71384868	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2524-01	TCGA-27-2524-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:71384868C>T	uc002fck.1	-	c.9214G>A	c.(9214-9216)GTA>ATA	p.V3072I	ZFHX3_uc002fcl.1_Missense_Mutation_p.V2158I	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	AT-binding transcription factor 1	3072					muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription repressor activity|transcription repressor activity|zinc ion binding			ovary(2)	2		Ovarian(137;0.13)												0.089928	10.470097	57.549685	25	253	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71384868	71384868	18222	16	C	T	T	19	19	ZFHX3	T	1	1
RFWD3	55159	broad.mit.edu	36	16	73215447	73215447	+	Silent	SNP	C	G	G			TCGA-27-2524-01	TCGA-27-2524-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:73215447C>G	uc002fda.1	-	c.2205G>C	c.(2203-2205)TCG>TCC	p.S735S	RFWD3_uc010cgq.1_Silent_p.S735S	NM_018124	NP_060594	Q6PCD5	RFWD3_HUMAN	ring finger and WD repeat domain 3	735					DNA repair|mitotic cell cycle G1/S transition DNA damage checkpoint|response to ionizing radiation	nucleus	MDM2 binding|p53 binding|ubiquitin-protein ligase activity|zinc ion binding				0														0.352941	13.836779	14.164381	6	11	CC		KEEP	---	---	---	---	capture			Silent	SNP	73215447	73215447	13733	16	C	G	G	19	19	RFWD3	G	3	3
CPD	1362	broad.mit.edu	36	17	25794949	25794949	+	Missense_Mutation	SNP	C	A	A			TCGA-27-2524-01	TCGA-27-2524-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:25794949C>A	uc002hfb.1	+	c.2377C>A	c.(2377-2379)CAT>AAT	p.H793N		NM_001304	NP_001295	O75976	CBPD_HUMAN	carboxypeptidase D precursor	793	Extracellular (Potential).|Carboxypeptidase-like 2.				proteolysis	integral to membrane	metallocarboxypeptidase activity|serine-type carboxypeptidase activity|zinc ion binding			liver(1)	1														0.368	258.520909	262.355301	92	158	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	25794949	25794949	3936	17	C	A	A	29	29	CPD	A	3	3
SLC4A1	6521	broad.mit.edu	36	17	39693334	39693334	+	Missense_Mutation	SNP	C	T	T	rs55735880	unknown	TCGA-27-2524-01	TCGA-27-2524-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:39693334C>T	uc002igf.2	-	c.449G>A	c.(448-450)CGA>CAA	p.R150Q	SLC4A1_uc002igg.2_Missense_Mutation_p.R150Q	NM_000342	NP_000333	P02730	B3AT_HUMAN	solute carrier family 4, anion exchanger, member	150	Cytoplasmic.				bicarbonate transport|cellular ion homeostasis	basolateral plasma membrane|cortical cytoskeleton|integral to plasma membrane|Z disc	ankyrin binding|chloride transmembrane transporter activity|inorganic anion exchanger activity|protein anchor|protein homodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(137;0.014)|Prostate(33;0.0181)												0.295455	32.556329	34.204261	13	31	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(366;0.115)	Missense_Mutation	SNP	39693334	39693334	15147	17	C	T	T	31	31	SLC4A1	T	1	1
FMNL1	752	broad.mit.edu	36	17	40678523	40678523	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2524-01	TCGA-27-2524-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:40678523C>T	uc002iin.1	+	c.2849C>T	c.(2848-2850)TCG>TTG	p.S950L	FMNL1_uc002iiq.1_Missense_Mutation_p.S528L|FMNL1_uc010dag.1_Non-coding_Transcript|LOC100133991_uc010dah.1_5'Flank	NM_005892	NP_005883	O95466	FMNL_HUMAN	formin-like 1	950	FH2.				actin cytoskeleton organization		actin binding|Rho GTPase binding			pancreas(1)	1						GBM(164;1247 1997 8702 11086 51972)								0.341667	112.041536	114.698354	41	79	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40678523	40678523	6193	17	C	T	T	31	31	FMNL1	T	1	1
C17orf47	284083	broad.mit.edu	36	17	53976326	53976326	+	Missense_Mutation	SNP	T	A	A			TCGA-27-2524-01	TCGA-27-2524-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:53976326T>A	uc002iwq.1	-	c.221A>T	c.(220-222)CAG>CTG	p.Q74L		NM_001038704	NP_001033793	Q8NEP4	CQ047_HUMAN	hypothetical protein LOC284083	74										breast(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)													0.290076	103.190379	108.3683	38	93	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53976326	53976326	1914	17	T	A	A	55	55	C17orf47	A	4	4
GAA	2548	broad.mit.edu	36	17	75696234	75696234	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2524-01	TCGA-27-2524-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:75696234C>T	uc002jxo.1	+	c.899C>T	c.(898-900)GCG>GTG	p.A300V	GAA_uc002jxp.1_Missense_Mutation_p.A300V|GAA_uc002jxq.1_Missense_Mutation_p.A300V	NM_001079803	NP_001073272	P10253	LYAG_HUMAN	acid alpha-glucosidase preproprotein	300					cardiac muscle contraction|diaphragm contraction|glucose metabolic process|glycogen catabolic process|lysosome organization|maltose metabolic process|sucrose metabolic process|tongue morphogenesis|vacuolar sequestering|ventricular cardiac muscle tissue morphogenesis	lysosomal membrane	carbohydrate binding|maltose alpha-glucosidase activity			ovary(1)	1	all_neural(118;0.117)				Acarbose(DB00284)									0.361111	36.473993	37.081368	13	23	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)		Missense_Mutation	SNP	75696234	75696234	6398	17	C	T	T	27	27	GAA	T	1	1
ATG4D	84971	broad.mit.edu	36	19	10518719	10518719	+	Missense_Mutation	SNP	T	G	G			TCGA-27-2524-01	TCGA-27-2524-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:10518719T>G	uc002mov.1	+	c.698T>G	c.(697-699)GTG>GGG	p.V233G	ATG4D_uc010dxh.1_Non-coding_Transcript|ATG4D_uc010dxi.1_Intron|ATG4D_uc010dxj.1_Intron	NM_032885	NP_116274	Q86TL0	ATG4D_HUMAN	APG4 autophagy 4 homolog D	233					autophagy|protein transport	cytoplasm	cysteine-type endopeptidase activity				0														0.363636	9.896489	10.07658	4	7	TT		KEEP	---	---	---	---	capture	Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)		Missense_Mutation	SNP	10518719	10518719	1118	19	T	G	G	59	59	ATG4D	G	4	4
GADD45GIP1	90480	broad.mit.edu	36	19	12928795	12928795	+	Missense_Mutation	SNP	A	C	C			TCGA-27-2524-01	TCGA-27-2524-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:12928795A>C	uc002mwb.1	-	c.232T>G	c.(232-234)TCG>GCG	p.S78A		NM_052850	NP_443082	Q8TAE8	G45IP_HUMAN	growth arrest and DNA-damage-inducible, gamma	78					cell cycle|interspecies interaction between organisms	nucleus	protein binding			ovary(1)	1														0.26087	6.533885	7.822982	6	17	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12928795	12928795	6435	19	A	C	C	10	10	GADD45GIP1	C	4	4
LPHN1	22859	broad.mit.edu	36	19	14122999	14122999	+	Missense_Mutation	SNP	T	G	G			TCGA-27-2524-01	TCGA-27-2524-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:14122999T>G	uc002myg.1	-	c.4111A>C	c.(4111-4113)ACC>CCC	p.T1371P	LPHN1_uc002myh.1_Missense_Mutation_p.T1366P	NM_001008701	NP_001008701	O94910	LPHN1_HUMAN	latrophilin 1 isoform 1 precursor	1371	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(1)|central_nervous_system(1)	2														0.3125	6.907742	7.446163	5	11	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	14122999	14122999	9288	19	T	G	G	59	59	LPHN1	G	4	4
FAM129C	199786	broad.mit.edu	36	19	17509320	17509320	+	Missense_Mutation	SNP	C	G	G			TCGA-27-2524-01	TCGA-27-2524-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:17509320C>G	uc010eav.1	+	c.656C>G	c.(655-657)GCC>GGC	p.A219G	FAM129C_uc010eau.1_Missense_Mutation_p.A219G|FAM129C_uc002ngy.2_5'Flank|FAM129C_uc002ngz.2_5'Flank|FAM129C_uc010eaw.1_5'Flank|FAM129C_uc002nhb.2_5'Flank	NM_173544	NP_775815	Q86XR2	NIBL2_HUMAN	B-cell novel protein 1 isoform a	219											0														0.160584	22.651302	37.764988	22	115	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17509320	17509320	5635	19	C	G	G	26	26	FAM129C	G	3	3
MUC16	94025	broad.mit.edu	36	19	8917586	8917586	+	Missense_Mutation	SNP	G	T	T			TCGA-27-2524-01	TCGA-27-2524-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8917586G>T	uc002mkp.1	-	c.30860C>A	c.(30859-30861)ACT>AAT	p.T10287N		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	10289	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.108108	19.659348	47.843682	20	165	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8917586	8917586	10367	19	G	T	T	36	36	MUC16	T	3	3
RPTN	126638	broad.mit.edu	36	1	150394275	150394275	+	Nonsense_Mutation	SNP	G	A	A			TCGA-27-2524-01	TCGA-27-2524-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150394275G>A	uc001ezs.1	-	c.1924C>T	c.(1924-1926)CAG>TAG	p.Q642*		NM_001122965	NP_001116437	Q6XPR3	RPTN_HUMAN	repetin	642	Gln-rich.					proteinaceous extracellular matrix	calcium ion binding				0														0.199153	93.745211	113.685544	47	189	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	150394275	150394275	14144	1	G	A	A	48	48	RPTN	A	5	2
DCST2	127579	broad.mit.edu	36	1	153270838	153270838	+	Missense_Mutation	SNP	A	G	G			TCGA-27-2524-01	TCGA-27-2524-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:153270838A>G	uc001fgm.1	-	c.575T>C	c.(574-576)CTG>CCG	p.L192P	DCST2_uc009wpb.1_Non-coding_Transcript|DCST1_uc001fgn.1_5'Flank	NM_144622	NP_653223	Q5T1A1	DCST2_HUMAN	DC-STAMP domain containing 2	192	Cytoplasmic (Potential).					integral to membrane				ovary(2)|central_nervous_system(1)	3	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)													0.16	6.385299	9.137357	4	21	AA		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(34;0.00034)		Missense_Mutation	SNP	153270838	153270838	4474	1	A	G	G	7	7	DCST2	G	4	4
GNPAT	8443	broad.mit.edu	36	1	229478534	229478534	+	Missense_Mutation	SNP	A	C	C			TCGA-27-2524-01	TCGA-27-2524-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:229478534A>C	uc001hup.2	+	c.1968A>C	c.(1966-1968)GAA>GAC	p.E656D		NM_014236	NP_055051	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase	656					ether lipid biosynthetic process|fatty acid metabolic process|organ morphogenesis	peroxisomal matrix|peroxisomal membrane	glycerone-phosphate O-acyltransferase activity			ovary(3)|breast(1)	4	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)												0.235294	9.09025	10.180673	4	13	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	229478534	229478534	6810	1	A	C	C	2	2	GNPAT	C	4	4
KIAA0754	643314	broad.mit.edu	36	1	39651642	39651642	+	Missense_Mutation	SNP	A	G	G			TCGA-27-2524-01	TCGA-27-2524-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:39651642A>G	uc009vvt.1	+	c.3118A>G	c.(3118-3120)ACC>GCC	p.T1040A	MACF1_uc009vvo.1_Intron|MACF1_uc009vvp.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc009vvr.1_Intron|MACF1_uc009vvs.1_Intron	NM_015038	NP_055853	O94854	K0754_HUMAN	hypothetical protein LOC643314	904	Ala-rich.|3.										0	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)												0.4	6.552625	6.651546	4	6	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)		Missense_Mutation	SNP	39651642	39651642	8499	1	A	G	G	6	6	KIAA0754	G	4	4
PABPC4	8761	broad.mit.edu	36	1	39801961	39801961	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2524-01	TCGA-27-2524-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:39801961G>A	uc001cdl.1	-	c.1580C>T	c.(1579-1581)GCT>GTT	p.A527V	PABPC4_uc001cdm.1_Missense_Mutation_p.A498V|PABPC4_uc001cdn.1_Missense_Mutation_p.A511V	NM_003819	NP_003810	Q13310	PABP4_HUMAN	poly A binding protein, cytoplasmic 4 isoform 2	511	Poly-Ala.				blood coagulation|RNA catabolic process|RNA processing|translation	cytoplasm|ribonucleoprotein complex	nucleotide binding|poly(A) RNA binding|poly(U) RNA binding|protein binding				0	Lung NSC(20;1.55e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)												0.322034	106.92392	110.234811	38	80	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(33;2.89e-18)|Epithelial(16;6.17e-17)|all cancers(16;1.18e-15)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)		Missense_Mutation	SNP	39801961	39801961	11781	1	G	A	A	34	34	PABPC4	A	2	2
SIM2	6493	broad.mit.edu	36	21	37035984	37035984	+	Missense_Mutation	SNP	A	C	C			TCGA-27-2524-01	TCGA-27-2524-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr21:37035984A>C	uc002yvr.1	+	c.947A>C	c.(946-948)AAC>ACC	p.N316T	SIM2_uc002yvq.1_Missense_Mutation_p.N316T	NM_005069	NP_005060	Q14190	SIM2_HUMAN	single-minded homolog 2 long isoform	316	PAC.				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(1)	1														0.444444	11.893418	11.968747	8	10	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37035984	37035984	14819	21	A	C	C	2	2	SIM2	C	4	4
ELFN2	114794	broad.mit.edu	36	22	36099118	36099118	+	Silent	SNP	G	A	A			TCGA-27-2524-01	TCGA-27-2524-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:36099118G>A	uc003asq.2	-	c.2403C>T	c.(2401-2403)GAC>GAT	p.D801D	ELFN2_uc010gxg.1_Silent_p.D801D	NM_052906	NP_443138	Q5R3F8	LRFN6_HUMAN	leucine rich repeat containing 62	801	Cytoplasmic (Potential).					cell surface|integral to membrane				ovary(1)	1	Melanoma(58;0.0574)													0.370079	137.699281	139.579971	47	80	GG		KEEP	---	---	---	---	capture			Silent	SNP	36099118	36099118	5250	22	G	A	A	40	40	ELFN2	A	1	1
RANGAP1	5905	broad.mit.edu	36	22	39972591	39972591	+	Missense_Mutation	SNP	C	G	G			TCGA-27-2524-01	TCGA-27-2524-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:39972591C>G	uc003azs.1	-	c.1726G>C	c.(1726-1728)GCC>CCC	p.A576P	RANGAP1_uc003azr.1_Missense_Mutation_p.A89P|RANGAP1_uc010gyk.1_Missense_Mutation_p.A79P|RANGAP1_uc003azt.1_Missense_Mutation_p.A576P|RANGAP1_uc003azu.1_Missense_Mutation_p.A576P	NM_002883	NP_002874	P46060	RAGP1_HUMAN	Ran GTPase activating protein 1	576					mitotic prometaphase|signal transduction	condensed chromosome kinetochore|cytosol|nuclear membrane|nuclear pore|soluble fraction|spindle pole	protein binding|Ran GTPase activator activity				0														0.363636	7.288667	7.471757	4	7	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	39972591	39972591	13493	22	C	G	G	27	27	RANGAP1	G	3	3
CLASP1	23332	broad.mit.edu	36	2	121932887	121932887	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2524-01	TCGA-27-2524-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:121932887C>T	uc002tnc.1	-	c.1313G>A	c.(1312-1314)CGG>CAG	p.R438Q	CLASP1_uc002tna.1_5'Flank|CLASP1_uc002tnb.1_Non-coding_Transcript|CLASP1_uc002tnd.1_Non-coding_Transcript|CLASP1_uc002tne.1_Non-coding_Transcript|CLASP1_uc002tng.1_Missense_Mutation_p.R438Q	NM_015282	NP_056097	Q7Z460	CLAP1_HUMAN	CLIP-associating protein 1 isoform 1	438	HEAT 3.				axon guidance|cell division|establishment or maintenance of cell polarity|exit from mitosis|G2/M transition of mitotic cell cycle|microtubule anchoring|microtubule bundle formation|microtubule nucleation|microtubule organizing center organization|mitotic prometaphase|negative regulation of microtubule depolymerization	centrosomal corona|condensed chromosome kinetochore|cortical microtubule cytoskeleton|cytoplasmic microtubule|cytosol|Golgi apparatus|kinetochore microtubule	kinetochore binding|microtubule plus-end binding			ovary(1)|central_nervous_system(1)	2	Renal(3;0.0496)													0.379032	151.018818	152.601906	47	77	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	121932887	121932887	3590	2	C	T	T	23	23	CLASP1	T	1	1
ACVR2A	92	broad.mit.edu	36	2	148392613	148392613	+	Missense_Mutation	SNP	A	C	C			TCGA-27-2524-01	TCGA-27-2524-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:148392613A>C	uc002twg.1	+	c.944A>C	c.(943-945)AAA>ACA	p.K315T	ACVR2A_uc002twh.1_Missense_Mutation_p.K315T	NM_001616	NP_001607	P27037	AVR2A_HUMAN	activin A receptor, type IIA precursor	315	Cytoplasmic (Potential).|Protein kinase.				activin receptor signaling pathway|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of erythrocyte differentiation|positive regulation of osteoblast differentiation|positive regulation of protein phosphorylation|protein phosphorylation	cytoplasm|inhibin-betaglycan-ActRII complex|integral to plasma membrane	ATP binding|coreceptor activity|inhibin beta-A binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity			stomach(8)|large_intestine(2)|kidney(1)	11										196				0.155556	6.356745	11.539659	7	38	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.0969)	Missense_Mutation	SNP	148392613	148392613	224	2	A	C	C	1	1	ACVR2A	C	4	4
MBD5	55777	broad.mit.edu	36	2	148936676	148936676	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2524-01	TCGA-27-2524-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:148936676G>A	uc002twm.2	+	c.169G>A	c.(169-171)GAT>AAT	p.D57N	MBD5_uc010fns.1_Missense_Mutation_p.D57N	NM_018328	NP_060798	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	57	MBD.					chromosome|nucleus	chromatin binding|DNA binding			ovary(2)	2														0.392405	183.909551	185.513125	62	96	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.0569)	Missense_Mutation	SNP	148936676	148936676	9735	2	G	A	A	45	45	MBD5	A	2	2
DYTN	391475	broad.mit.edu	36	2	207238940	207238940	+	Nonsense_Mutation	SNP	G	A	A			TCGA-27-2524-01	TCGA-27-2524-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:207238940G>A	uc002vbr.1	-	c.1039C>T	c.(1039-1041)CAG>TAG	p.Q347*		NM_001093730	NP_001087199	A2CJ06	DYTN_HUMAN	dystrotelin	347	Potential.					plasma membrane	zinc ion binding			ovary(1)	1														0.286624	119.002676	125.4203	45	112	GG		KEEP	---	---	---	---	capture		LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)	Nonsense_Mutation	SNP	207238940	207238940	5047	2	G	A	A	47	47	DYTN	A	5	2
WNT10A	80326	broad.mit.edu	36	2	219454073	219454073	+	Missense_Mutation	SNP	A	T	T			TCGA-27-2524-01	TCGA-27-2524-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:219454073A>T	uc002vjd.1	+	c.112A>T	c.(112-114)AGG>TGG	p.R38W		NM_025216	NP_079492	Q9GZT5	WN10A_HUMAN	wingless-type MMTV integration site family,	38					anterior/posterior pattern formation|axis specification|canonical Wnt receptor signaling pathway|cellular response to transforming growth factor beta stimulus|female gonad development|hair follicle morphogenesis|negative regulation of gene-specific transcription from RNA polymerase II promoter|odontogenesis|positive regulation of gene-specific transcription from RNA polymerase II promoter|regulation of odontogenesis of dentine-containing tooth|sebaceous gland development|skin development|tongue development|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	G-protein-coupled receptor binding|signal transducer activity				0		Renal(207;0.0474)												0.333333	8.82214	9.043476	3	6	AA		KEEP	---	---	---	---	capture		Epithelial(149;4.26e-07)|all cancers(144;8.8e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Missense_Mutation	SNP	219454073	219454073	17956	2	A	T	T	7	7	WNT10A	T	4	4
EPHB1	2047	broad.mit.edu	36	3	136127375	136127375	+	Missense_Mutation	SNP	C	A	A			TCGA-27-2524-01	TCGA-27-2524-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:136127375C>A	uc003eqt.1	+	c.86C>A	c.(85-87)ACT>AAT	p.T29N	EPHB1_uc010htz.1_Non-coding_Transcript	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor	29	Extracellular (Potential).				transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(7)|ovary(4)|stomach(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	18										376				0.333333	7.038992	7.251976	3	6	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	136127375	136127375	5367	3	C	A	A	20	20	EPHB1	A	3	3
CACNA1D	776	broad.mit.edu	36	3	53814066	53814066	+	Missense_Mutation	SNP	T	A	A			TCGA-27-2524-01	TCGA-27-2524-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:53814066T>A	uc003dgu.2	+	c.5662T>A	c.(5662-5664)TAC>AAC	p.Y1888N	CACNA1D_uc003dgv.2_Missense_Mutation_p.Y1868N|CACNA1D_uc003dgy.2_Missense_Mutation_p.Y1844N|CACNA1D_uc003dgw.2_Missense_Mutation_p.Y1535N	NM_000720	NP_000711	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type,	1868	Cytoplasmic (Potential).				axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|liver(1)	7					Verapamil(DB00661)									0.236364	12.345596	16.178967	13	42	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Missense_Mutation	SNP	53814066	53814066	2657	3	T	A	A	53	53	CACNA1D	A	4	4
SLC7A11	23657	broad.mit.edu	36	4	139319876	139319876	+	Silent	SNP	C	A	A			TCGA-27-2524-01	TCGA-27-2524-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:139319876C>A	uc010iof.1	-	c.1389G>T	c.(1387-1389)GCG>GCT	p.A463A		NM_014331	NP_055146	Q9UPY5	XCT_HUMAN	solute carrier family 7, (cationic amino acid	463	Helical; (Potential).				blood coagulation|cellular nitrogen compound metabolic process|leukocyte migration|response to toxin	integral to membrane|plasma membrane	cystine:glutamate antiporter activity|protein binding				0	all_hematologic(180;0.166)				L-Cystine(DB00138)|L-Glutamic Acid(DB00142)|Sulfasalazine(DB00795)									0.405594	183.73358	184.843798	58	85	CC		KEEP	---	---	---	---	capture			Silent	SNP	139319876	139319876	15191	4	C	A	A	19	19	SLC7A11	A	3	3
HAVCR1	26762	broad.mit.edu	36	5	156415068	156415068	+	Missense_Mutation	SNP	A	G	G			TCGA-27-2524-01	TCGA-27-2524-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:156415068A>G	uc010jij.1	-	c.101T>C	c.(100-102)CTA>CCA	p.L34P	HAVCR1_uc003lwi.2_Missense_Mutation_p.L34P	NM_001099414	NP_036338	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	34	Extracellular (Potential).|Ig-like V-type.				interspecies interaction between organisms	integral to membrane	receptor activity			ovary(1)	1	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)												0.227273	9.363047	10.866375	5	17	AA		KEEP	---	---	---	---	capture	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		Missense_Mutation	SNP	156415068	156415068	7255	5	A	G	G	15	15	HAVCR1	G	4	4
CARD6	84674	broad.mit.edu	36	5	40879100	40879100	+	Missense_Mutation	SNP	C	A	A			TCGA-27-2524-01	TCGA-27-2524-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:40879100C>A	uc003jmg.1	+	c.373C>A	c.(373-375)CCT>ACT	p.P125T		NM_032587	NP_115976	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	125					apoptosis|regulation of apoptosis	intracellular				ovary(2)|skin(2)|lung(1)	5														0.234483	80.095148	89.436266	34	111	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40879100	40879100	2769	5	C	A	A	26	26	CARD6	A	3	3
TDP2	51567	broad.mit.edu	36	6	24766094	24766094	+	Missense_Mutation	SNP	T	C	C			TCGA-27-2524-01	TCGA-27-2524-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:24766094T>C	uc003nej.1	-	c.442A>G	c.(442-444)ATA>GTA	p.I148V	TDP2_uc003nei.1_Missense_Mutation_p.I36V|TDP2_uc010jpu.1_Missense_Mutation_p.I148V	NM_016614	NP_057698	O95551	TYDP2_HUMAN	TRAF and TNF receptor-associated protein	148					cell surface receptor linked signaling pathway|double-strand break repair	PML body	5'-tyrosyl-DNA phosphodiesterase activity|magnesium ion binding|nuclease activity|protein binding|transcription corepressor activity			ovary(1)	1														0.377483	193.344272	195.331085	57	94	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	24766094	24766094	16255	6	T	C	C	50	50	TDP2	C	4	4
DST	667	broad.mit.edu	36	6	56674650	56674650	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2524-01	TCGA-27-2524-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:56674650G>A	uc003pcz.2	-	c.316C>T	c.(316-318)CGC>TGC	p.R106C		NM_183380	NP_899236	Q03001	DYST_HUMAN	dystonin isoform 1	106	CH 1.|Actin-binding.				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				0.338462	63.430023	64.92985	22	43	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)		Missense_Mutation	SNP	56674650	56674650	4967	6	G	A	A	40	40	DST	A	1	1
RREB1	6239	broad.mit.edu	36	6	7174250	7174250	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2524-01	TCGA-27-2524-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:7174250C>T	uc003mxb.1	+	c.919C>T	c.(919-921)CGG>TGG	p.R307W	RREB1_uc003mxc.1_Missense_Mutation_p.R307W|RREB1_uc010jnx.1_Missense_Mutation_p.R307W|RREB1_uc003mxe.1_Missense_Mutation_p.R307W	NM_001003699	NP_001003699	Q92766	RREB1_HUMAN	ras responsive element binding protein 1 isoform	307					multicellular organismal development|Ras protein signal transduction|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nuclear speck	DNA binding|transcription activator activity|zinc ion binding			ovary(4)|large_intestine(2)|pancreas(2)|breast(1)	9	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)												0.53125	51.484426	51.513061	17	15	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7174250	7174250	14159	6	C	T	T	27	27	RREB1	T	1	1
TRPV5	56302	broad.mit.edu	36	7	142319947	142319947	+	Silent	SNP	A	G	G			TCGA-27-2524-01	TCGA-27-2524-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:142319947A>G	uc003wby.1	-	c.1611T>C	c.(1609-1611)TTT>TTC	p.F537F		NM_019841	NP_062815	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel,	537					protein tetramerization	apical plasma membrane|integral to plasma membrane	calcium channel activity			ovary(3)|central_nervous_system(2)	5	Melanoma(164;0.059)													0.222798	116.779196	130.37785	43	150	AA		KEEP	---	---	---	---	capture			Silent	SNP	142319947	142319947	17150	7	A	G	G	9	9	TRPV5	G	4	4
BAT2L1	84726	broad.mit.edu	36	9	133342992	133342992	+	Missense_Mutation	SNP	A	G	G			TCGA-27-2524-01	TCGA-27-2524-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:133342992A>G	uc004can.2	+	c.4447A>G	c.(4447-4449)AGC>GGC	p.S1483G	BAT2L1_uc004cao.2_Missense_Mutation_p.S841G	NM_013318	NP_037450	Q5JSZ5	PRC2B_HUMAN	HLA-B associated transcript 2-like	1483							protein binding				0														0.5	6.338793	6.338793	5	5	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	133342992	133342992	1341	9	A	G	G	7	7	BAT2L1	G	4	4
RIBC1	158787	broad.mit.edu	36	X	53472074	53472074	+	Silent	SNP	G	A	A			TCGA-27-2524-01	TCGA-27-2524-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:53472074G>A	uc004dsk.1	+	c.318G>A	c.(316-318)AAG>AAA	p.K106K	RIBC1_uc004dsj.1_Silent_p.K106K	NM_001031745	NP_001026915	Q8N443	RIBC1_HUMAN	RIB43A domain with coiled-coils 1 isoform 1	106	Potential.										0														0.666667	95.813287	96.846124	28	14	GG		KEEP	---	---	---	---	capture			Silent	SNP	53472074	53472074	13827	23	G	A	A	33	33	RIBC1	A	2	2
LAMB3	3914	broad.mit.edu	36	1	207863567	207863573	+	Frame_Shift_Del	DEL	TGCCGCA	-	-			TCGA-27-2524-01	TCGA-27-2524-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:207863567_207863573delTGCCGCA	uc001hhg.1	-	c.2258_2264delTGCGGCA	c.(2257-2265)GTGCGGCAGfs	p.V753fs	LAMB3_uc009xco.1_Frame_Shift_Del_p.V753fs|LAMB3_uc001hhh.1_Frame_Shift_Del_p.V753fs	NM_001017402	NP_001121113	Q13751	LAMB3_HUMAN	laminin, beta 3 precursor	753_755	Potential.|Domain II.				cell adhesion|epidermis development|hemidesmosome assembly		structural molecule activity			central_nervous_system(2)|large_intestine(1)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(81;0.0519)										0.33			19	38				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	207863567	207863573	8935	1	TGCCGCA	-	-	55	55	LAMB3	-	5	5
