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	TCGAscape_Amplification_Peaks	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_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	Oncotatorv0393GAF20hg19Feb2011dbSNPbuild132UniProtRelease2011_6	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	newbase	context_orig	context65	gene_name	categ	categ_ignoring_null_categ
LARP4B	23185	broad.mit.edu	37	10	876909	876909	+	Missense_Mutation	SNP	T	G	G			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:876909T>G	uc001ifs.1	-	c.759A>C	c.(757-759)GAA>GAC	p.E253D		NM_015155	NP_055970	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	253	RRM.						nucleotide binding|RNA binding			ovary(2)|central_nervous_system(1)	3														0.081081	1.494699	8.110361	3	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	876909	876909	8954	10	T	G	G	G	725	56	LARP4B	4	4
TECTA	7007	broad.mit.edu	37	11	120996044	120996044	+	Missense_Mutation	SNP	T	G	G			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:120996044T>G	uc010rzo.1	+	c.1237T>G	c.(1237-1239)TTA>GTA	p.L413V		NM_005422	NP_005413	O75443	TECTA_HUMAN	tectorin alpha precursor	413	VWFD 1.				cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix				breast(6)|ovary(2)	8	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)										0.103797	26.885817	88.628798	41	354	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	120996044	120996044	16274	11	T	G	G	G	725	56	TECTA	4	4
ZNF408	79797	broad.mit.edu	37	11	46726804	46726804	+	Silent	SNP	C	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:46726804C>T	uc001nde.1	+	c.1554C>T	c.(1552-1554)CAC>CAT	p.H518H	ZNF408_uc010rgw.1_Silent_p.H510H	NM_024741	NP_079017	Q9H9D4	ZN408_HUMAN	zinc finger protein 408	518	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|identical protein binding|zinc ion binding				0						Pancreas(79;698 1390 6545 18745 34127)|Esophageal Squamous(120;1014 1625 12837 24601 49525)								0.097222	3.440935	26.85392	14	130	KEEP	---	---	---	---	capture		Silent	SNP	46726804	46726804	18481	11	C	T	T	T	220	17	ZNF408	2	2
AHNAK	79026	broad.mit.edu	37	11	62289394	62289394	+	Silent	SNP	G	A	A			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:62289394G>A	uc001ntl.2	-	c.12495C>T	c.(12493-12495)ATC>ATT	p.I4165I	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	4165					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)	14		Melanoma(852;0.155)												0.129231	48.583905	92.180571	42	283	KEEP	---	---	---	---	capture		Silent	SNP	62289394	62289394	417	11	G	A	A	A	577	45	AHNAK	2	2
PTPRB	5787	broad.mit.edu	37	12	70938424	70938424	+	Missense_Mutation	SNP	T	C	C			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:70938424T>C	uc001swc.3	-	c.5407A>G	c.(5407-5409)ACA>GCA	p.T1803A	PTPRB_uc001swb.3_Missense_Mutation_p.T1585A|PTPRB_uc010sto.1_Missense_Mutation_p.T1495A|PTPRB_uc010stp.1_Missense_Mutation_p.T1495A|PTPRB_uc001swa.3_Missense_Mutation_p.T1715A	NM_001109754	NP_001103224	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1585	Extracellular (Potential).				angiogenesis	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(2)|skin(1)	3	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)											0.129032	8.682183	12.832436	4	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70938424	70938424	13253	12	T	C	C	C	741	57	PTPRB	4	4
CEP290	80184	broad.mit.edu	37	12	88486598	88486598	+	Silent	SNP	G	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:88486598G>T	uc001tar.2	-	c.3321C>A	c.(3319-3321)ATC>ATA	p.I1107I	CEP290_uc001taq.2_Silent_p.I167I	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa	1107	Potential.				cell projection organization|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding|transcription activator activity	p.I1109I(1)		ovary(5)|breast(1)|pancreas(1)	7														0.158879	27.79808	39.672267	17	90	KEEP	---	---	---	---	capture		Silent	SNP	88486598	88486598	3386	12	G	T	T	T	577	45	CEP290	2	2
PPIB	5479	broad.mit.edu	37	15	64455120	64455120	+	Silent	SNP	G	C	C			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:64455120G>C	uc002and.2	-	c.66C>G	c.(64-66)GTC>GTG	p.V22V	PPIB_uc010bgx.1_Silent_p.V14V	NM_000942	NP_000933	P23284	PPIB_HUMAN	peptidylprolyl isomerase B precursor	22					protein folding	endoplasmic reticulum lumen|melanosome	peptide binding|peptidyl-prolyl cis-trans isomerase activity|unfolded protein binding				0					L-Proline(DB00172)	GBM(105;399 1481 32889 33051 36637)								0.102564	5.271683	11.408662	4	35	KEEP	---	---	---	---	capture		Silent	SNP	64455120	64455120	12754	15	G	C	C	C	418	33	PPIB	3	3
KIAA1024	23251	broad.mit.edu	37	15	79749775	79749775	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:79749775C>A	uc002bew.1	+	c.1286C>A	c.(1285-1287)GCG>GAG	p.A429E	KIAA1024_uc010unk.1_Missense_Mutation_p.A429E	NM_015206	NP_056021	Q9UPX6	K1024_HUMAN	hypothetical protein LOC23251	429						integral to membrane				pancreas(2)|ovary(1)|central_nervous_system(1)	4														0.122807	29.853305	53.664944	21	150	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79749775	79749775	8512	15	C	A	A	A	351	27	KIAA1024	1	1
KIAA1199	57214	broad.mit.edu	37	15	81235319	81235319	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:81235319G>A	uc002bfw.1	+	c.3733G>A	c.(3733-3735)GGC>AGC	p.G1245S	KIAA1199_uc010unn.1_Missense_Mutation_p.G1245S	NM_018689	NP_061159	Q8WUJ3	K1199_HUMAN	KIAA1199 precursor	1245										ovary(1)	1														0.124841	101.666635	209.70228	98	687	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	81235319	81235319	8521	15	G	A	A	A	611	47	KIAA1199	2	2
SLC5A2	6524	broad.mit.edu	37	16	31499014	31499014	+	Silent	SNP	T	C	C			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:31499014T>C	uc002ecf.3	+	c.819T>C	c.(817-819)GAT>GAC	p.D273D	SLC5A2_uc010car.2_Non-coding_Transcript|C16orf58_uc002ecg.2_Non-coding_Transcript	NM_003041	NP_003032	P31639	SC5A2_HUMAN	solute carrier family 5 (sodium/glucose	273	Helical; (Potential).				carbohydrate metabolic process	integral to membrane	low-affinity glucose:sodium symporter activity			ovary(1)	1														0.169231	23.300732	30.019647	11	54	KEEP	---	---	---	---	capture		Silent	SNP	31499014	31499014	15162	16	T	C	C	C	647	50	SLC5A2	4	4
TRIM16	10626	broad.mit.edu	37	17	15535856	15535856	+	Missense_Mutation	SNP	A	G	G			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:15535856A>G	uc002gox.2	-	c.982T>C	c.(982-984)TAT>CAT	p.Y328H	TRIM16_uc002gor.1_Missense_Mutation_p.Y328H|TRIM16_uc002gow.2_Missense_Mutation_p.Y112H|TRIM16_uc002goy.2_Missense_Mutation_p.Y198H	NM_006470	NP_006461	O95361	TRI16_HUMAN	tripartite motif-containing 16	328	Potential.				histone H3 acetylation|histone H4 acetylation|positive regulation of gene-specific transcription|positive regulation of interleukin-1 beta secretion|positive regulation of keratinocyte differentiation|positive regulation of retinoic acid receptor signaling pathway|response to growth hormone stimulus|response to organophosphorus|response to retinoic acid	cytoplasm|plasma membrane|PML body	DNA binding|interleukin-1 binding|NACHT domain binding|transcription activator activity|zinc ion binding			ovary(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (92;0.0839)|Epithelial(1;8.4e-29)|all cancers(1;3.06e-28)|Colorectal(1;1.57e-19)|OV - Ovarian serous cystadenocarcinoma(1;6.1e-17)|COAD - Colon adenocarcinoma(1;3.38e-12)|READ - Rectum adenocarcinoma(2;1.46e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0559)										0.143519	72.79034	99.213406	31	185	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15535856	15535856	17035	17	A	G	G	G	195	15	TRIM16	4	4
SHMT1	6470	broad.mit.edu	37	17	18250892	18250892	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:18250892C>T	uc002gta.2	-	c.437G>A	c.(436-438)GGG>GAG	p.G146E	SHMT1_uc002gtb.2_Missense_Mutation_p.G146E|SHMT1_uc010cqb.2_Missense_Mutation_p.G146E|SHMT1_uc010vxt.1_Missense_Mutation_p.G8E|SHMT1_uc002gtd.1_Missense_Mutation_p.G146E|SHMT1_uc010vxu.1_Missense_Mutation_p.G146E	NM_004169	NP_004160	P34896	GLYC_HUMAN	serine hydroxymethyltransferase 1 (soluble)	146					carnitine biosynthetic process|folic acid metabolic process|L-serine catabolic process|one-carbon metabolic process|purine base biosynthetic process	cytosol|nucleus	glycine hydroxymethyltransferase activity|protein homodimerization activity|pyridoxal phosphate binding			ovary(1)	1					Glycine(DB00145)|Mimosine(DB01055)|Pyridoxal Phosphate(DB00114)|Tetrahydrofolic acid(DB00116)									0.234513	128.815606	143.352274	53	173	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18250892	18250892	14780	17	C	T	T	T	286	22	SHMT1	2	2
MYO18A	399687	broad.mit.edu	37	17	27448618	27448618	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:27448618G>C	uc002hdt.1	-	c.1318C>G	c.(1318-1320)CCC>GCC	p.P440A	MYO18A_uc010wbc.1_5'UTR|MYO18A_uc002hds.2_5'UTR|MYO18A_uc010csa.1_Missense_Mutation_p.P440A|MYO18A_uc002hdu.1_Missense_Mutation_p.P440A|MYO18A_uc010wbd.1_Missense_Mutation_p.P109A	NM_078471	NP_510880	Q92614	MY18A_HUMAN	myosin 18A isoform a	440	Myosin head-like.				anti-apoptosis|DNA metabolic process	ER-Golgi intermediate compartment|myosin complex	ATP binding|DNA binding|DNA-dependent ATPase activity|identical protein binding|motor activity				0			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			Esophageal Squamous(182;472 2015 7001 15270 22562)								0.157895	5.111308	7.233372	3	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27448618	27448618	10460	17	G	C	C	C	559	43	MYO18A	3	3
STAT5A	6776	broad.mit.edu	37	17	40441527	40441527	+	Missense_Mutation	SNP	A	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:40441527A>T	uc002hzj.1	+	c.98A>T	c.(97-99)TAC>TTC	p.Y33F	STAT5A_uc010cya.1_Missense_Mutation_p.Y33F|STAT5A_uc010cyb.1_Missense_Mutation_p.Y33F|STAT5A_uc010cyc.1_Missense_Mutation_p.Y33F	NM_003152	NP_003143	P42229	STA5A_HUMAN	signal transducer and activator of transcription	33					2-oxoglutarate metabolic process|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|fatty acid metabolic process|isoleucine metabolic process|oxaloacetate metabolic process|succinate metabolic process|taurine metabolic process|valine metabolic process	cytosol|nucleoplasm	calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(1)	1		all_cancers(22;1.56e-06)|all_epithelial(22;3.17e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)						465				0.142857	19.929373	31.940568	14	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40441527	40441527	15788	17	A	T	T	T	182	14	STAT5A	3	3
MRPL10	124995	broad.mit.edu	37	17	45901636	45901636	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:45901636G>A	uc002ilz.2	-	c.721C>T	c.(721-723)CGC>TGC	p.R241C	OSBPL7_uc002ilx.1_5'Flank|MRPL10_uc010wky.1_Missense_Mutation_p.R202C|MRPL10_uc002ily.2_Missense_Mutation_p.R251C	NM_145255	NP_660298	Q7Z7H8	RM10_HUMAN	mitochondrial ribosomal protein L10 precursor	241					ribosome biogenesis|translation	mitochondrial large ribosomal subunit	structural constituent of ribosome			ovary(1)	1														0.07438	-5.097931	17.40015	9	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45901636	45901636	10168	17	G	A	A	A	520	40	MRPL10	1	1
ST6GALNAC1	55808	broad.mit.edu	37	17	74625395	74625395	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:74625395G>T	uc002jsh.2	-	c.530C>A	c.(529-531)TCC>TAC	p.S177Y	ST6GALNAC1_uc002jsi.2_Missense_Mutation_p.S45Y|ST6GALNAC1_uc002jsj.2_Non-coding_Transcript	NM_018414	NP_060884	Q9NSC7	SIA7A_HUMAN	sialyltransferase 7A	177	Lumenal (Potential).				protein glycosylation	integral to Golgi membrane	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity				0														0.032911	-74.647739	19.439601	13	382	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74625395	74625395	15741	17	G	T	T	T	533	41	ST6GALNAC1	2	2
CDKN2D	1032	broad.mit.edu	37	19	10677773	10677773	+	Silent	SNP	G	A	A			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:10677773G>A	uc002mpa.2	-	c.462C>T	c.(460-462)CTC>CTT	p.L154L	KRI1_uc002mox.1_5'Flank|KRI1_uc002moy.1_5'Flank|CDKN2D_uc002mpb.2_Silent_p.L154L	NM_001800	NP_001791	P55273	CDN2D_HUMAN	cyclin-dependent kinase inhibitor 2D	154	ANK 4.				anti-apoptosis|autophagic cell death|cell cycle arrest|DNA synthesis involved in DNA repair|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|negative regulation of caspase activity|negative regulation of cell growth|negative regulation of cell proliferation|regulation of cyclin-dependent protein kinase activity|response to retinoic acid|response to UV|response to vitamin D	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|protein kinase binding				0			Epithelial(33;1.58e-05)|all cancers(31;6.36e-05)							14				0.115108	15.401858	35.692928	16	123	KEEP	---	---	---	---	capture		Silent	SNP	10677773	10677773	3295	19	G	A	A	A	470	37	CDKN2D	1	1
EMR2	30817	broad.mit.edu	37	19	14866619	14866619	+	Silent	SNP	C	A	A			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:14866619C>A	uc002mzp.1	-	c.1263G>T	c.(1261-1263)CTG>CTT	p.L421L	EMR2_uc010dzs.1_Intron|EMR2_uc010xnw.1_Silent_p.L421L|EMR2_uc002mzo.1_Silent_p.L410L|EMR2_uc002mzq.1_Silent_p.L361L|EMR2_uc002mzr.1_Silent_p.L372L|EMR2_uc002mzs.1_Silent_p.L279L|EMR2_uc002mzt.1_Silent_p.L317L|EMR2_uc002mzu.1_Silent_p.L328L|EMR2_uc010xnx.1_Intron|EMR2_uc010xny.1_Intron	NM_013447	NP_038475	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone	421	Extracellular (Potential).				cell adhesion|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(1)	1														0.125	10.992643	23.064758	11	77	KEEP	---	---	---	---	capture		Silent	SNP	14866619	14866619	5298	19	C	A	A	A	262	21	EMR2	2	2
GMIP	51291	broad.mit.edu	37	19	19751158	19751158	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:19751158C>T	uc002nnd.2	-	c.376G>A	c.(376-378)GCT>ACT	p.A126T	GMIP_uc010xrb.1_Missense_Mutation_p.A126T|GMIP_uc010xrc.1_Missense_Mutation_p.A126T	NM_016573	NP_057657	Q9P107	GMIP_HUMAN	GEM interacting protein	126					negative regulation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	metal ion binding|protein binding|Rho GTPase activator activity			ovary(1)	1														0.148515	39.259409	63.335227	30	172	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19751158	19751158	6760	19	C	T	T	T	325	25	GMIP	2	2
PLEKHF1	79156	broad.mit.edu	37	19	30164791	30164791	+	Silent	SNP	C	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:30164791C>T	uc002nsi.3	+	c.300C>T	c.(298-300)ATC>ATT	p.I100I	PLEKHF1_uc002nsh.3_Silent_p.I15I	NM_024310	NP_077286	Q96S99	PKHF1_HUMAN	apoptosis-inducing protein D	15					apoptosis	lysosome|nucleus|perinuclear region of cytoplasm	zinc ion binding				0	Ovarian(5;0.000567)|Breast(6;0.0602)|Esophageal squamous(110;0.239)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|STAD - Stomach adenocarcinoma(5;1.7e-06)|Lung(7;0.0623)|LUAD - Lung adenocarcinoma(5;0.0989)|BRCA - Breast invasive adenocarcinoma(6;0.225)											0.166667	24.671469	34.158831	15	75	KEEP	---	---	---	---	capture		Silent	SNP	30164791	30164791	12492	19	C	T	T	T	395	31	PLEKHF1	1	1
ZNF585B	92285	broad.mit.edu	37	19	37676879	37676879	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:37676879C>A	uc002ofq.2	-	c.1560G>T	c.(1558-1560)AAG>AAT	p.K520N	ZNF585B_uc002ofr.1_Missense_Mutation_p.K334N	NM_152279	NP_689492	Q52M93	Z585B_HUMAN	zinc finger protein 585B	520					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			Melanoma(93;882 1454 18863 28917 48427)								0.059524	-7.298981	9.760852	5	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37676879	37676879	18613	19	C	A	A	A	363	28	ZNF585B	2	2
ATP1A3	478	broad.mit.edu	37	19	42472957	42472957	+	Silent	SNP	C	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:42472957C>T	uc010xwh.1	-	c.2838G>A	c.(2836-2838)TCG>TCA	p.S946S	ATP1A3_uc010xwf.1_Silent_p.S944S|ATP1A3_uc010xwg.1_Silent_p.S903S|ATP1A3_uc002osg.2_Silent_p.S933S|ATP1A3_uc002osh.2_Silent_p.S933S	NM_152296	NP_689509	P13637	AT1A3_HUMAN	Na+/K+ -ATPase alpha 3 subunit	933	Cytoplasmic (Potential).				ATP biosynthetic process	endoplasmic reticulum|Golgi apparatus|sodium:potassium-exchanging ATPase complex	ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			ovary(1)|pancreas(1)	2														0.14433	23.882983	35.697312	14	83	KEEP	---	---	---	---	capture		Silent	SNP	42472957	42472957	1149	19	C	T	T	T	288	23	ATP1A3	1	1
GPR4	2828	broad.mit.edu	37	19	46094725	46094725	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:46094725C>A	uc002pcm.2	-	c.400G>T	c.(400-402)GCC>TCC	p.A134S	OPA3_uc010xxk.1_Intron	NM_005282	NP_005273	P46093	GPR4_HUMAN	G protein-coupled receptor 4	134	Helical; Name=4; (Potential).					integral to plasma membrane	G-protein coupled receptor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(262;0.0071)|GBM - Glioblastoma multiforme(486;0.128)|Epithelial(262;0.223)		Esophageal Squamous(117;181 1612 1673 14956 42937)								0.110092	12.426835	28.82046	12	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46094725	46094725	6969	19	C	A	A	A	351	27	GPR4	1	1
GPR108	56927	broad.mit.edu	37	19	6733061	6733061	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:6733061G>T	uc002mfp.2	-	c.870C>A	c.(868-870)TTC>TTA	p.F290L	GPR108_uc010duv.2_5'Flank|GPR108_uc002mfn.2_Intron|GPR108_uc002mfo.3_Missense_Mutation_p.F48L|GPR108_uc010duw.2_Non-coding_Transcript	NM_001080452	NP_001073921	Q9NPR9	GP108_HUMAN	G protein-coupled receptor 108 isoform 1	290						integral to membrane					0														0.078947	-0.406196	6.47593	3	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6733061	6733061	6898	19	G	T	T	T	581	45	GPR108	2	2
FAM5C	339479	broad.mit.edu	37	1	190067976	190067976	+	Silent	SNP	G	A	A			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:190067976G>A	uc001gse.1	-	c.1473C>T	c.(1471-1473)GAC>GAT	p.D491D	FAM5C_uc010pot.1_Silent_p.D389D	NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C	491						extracellular region				lung(2)|ovary(1)|kidney(1)	4	Prostate(682;0.198)													0.094828	15.801637	73.178539	33	315	KEEP	---	---	---	---	capture		Silent	SNP	190067976	190067976	5817	1	G	A	A	A	568	44	FAM5C	2	2
FAM58B	339521	broad.mit.edu	37	1	200182895	200182895	+	Silent	SNP	G	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:200182895G>T	uc009wzi.1	+	c.204G>T	c.(202-204)CTG>CTT	p.L68L		NM_001105517	NP_001098987	P0C7Q3	FA58B_HUMAN	family with sequence similarity 58 member B	68											0	Prostate(682;0.19)													0.037975	-50.989985	21.995725	12	304	KEEP	---	---	---	---	capture		Silent	SNP	200182895	200182895	5813	1	G	T	T	T	600	47	FAM58B	2	2
C1orf106	55765	broad.mit.edu	37	1	200868613	200868613	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:200868613C>T	uc001gvo.2	+	c.323C>T	c.(322-324)CCG>CTG	p.P108L	C1orf106_uc010ppm.1_Missense_Mutation_p.P23L	NM_018265	NP_060735	Q3KP66	CA106_HUMAN	hypothetical protein LOC55765 isoform 1	108										ovary(1)	1														0.150442	28.50004	41.738828	17	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	200868613	200868613	2047	1	C	T	T	T	299	23	C1orf106	1	1
DUSP10	11221	broad.mit.edu	37	1	221875902	221875902	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:221875902G>A	uc001hmy.1	-	c.1301C>T	c.(1300-1302)GCT>GTT	p.A434V	DUSP10_uc001hmx.1_Missense_Mutation_p.A92V|DUSP10_uc001hmz.1_Missense_Mutation_p.A92V	NM_007207	NP_009138	Q9Y6W6	DUS10_HUMAN	dual specificity phosphatase 10 isoform a	434	Tyrosine-protein phosphatase.				inactivation of MAPK activity|JNK cascade|negative regulation of JNK cascade|negative regulation of JUN kinase activity|negative regulation of stress-activated MAPK cascade	Golgi apparatus|nucleus	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity				0				GBM - Glioblastoma multiforme(131;0.0103)										0.100629	10.980087	36.302088	16	143	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	221875902	221875902	4995	1	G	A	A	A	442	34	DUSP10	2	2
OR6F1	343169	broad.mit.edu	37	1	247875225	247875225	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247875225T>A	uc001idj.1	-	c.833A>T	c.(832-834)AAC>ATC	p.N278I		NM_001005286	NP_001005286	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F,	278	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0168)											0.161458	52.897956	73.842746	31	161	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	247875225	247875225	11611	1	T	A	A	A	780	60	OR6F1	3	3
SLC6A9	6536	broad.mit.edu	37	1	44474144	44474144	+	Silent	SNP	G	A	A			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:44474144G>A	uc001cll.2	-	c.690C>T	c.(688-690)GCC>GCT	p.A230A	SLC6A9_uc009vxe.2_Silent_p.A86A|SLC6A9_uc010okm.1_Silent_p.A157A|SLC6A9_uc001clm.2_Silent_p.A176A|SLC6A9_uc009vxd.2_Non-coding_Transcript|SLC6A9_uc010okn.1_Silent_p.A161A|SLC6A9_uc001cln.2_Silent_p.A157A|SLC6A9_uc010oko.1_Silent_p.A46A|SLC6A9_uc010okp.1_Non-coding_Transcript	NM_201649	NP_964012	P48067	SC6A9_HUMAN	solute carrier family 6 member 9 isoform 2	230	Extracellular (Potential).					integral to plasma membrane|membrane fraction	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity				0	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			Glycine(DB00145)									0.111702	24.151124	52.149233	21	167	KEEP	---	---	---	---	capture		Silent	SNP	44474144	44474144	15188	1	G	A	A	A	496	39	SLC6A9	1	1
ZNF133	7692	broad.mit.edu	37	20	18295923	18295923	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:18295923C>T	uc010zrv.1	+	c.437C>T	c.(436-438)GCA>GTA	p.A146V	ZNF133_uc010gcq.2_Missense_Mutation_p.A143V|ZNF133_uc010zrw.1_Missense_Mutation_p.A80V|ZNF133_uc010gcr.2_Missense_Mutation_p.A143V|ZNF133_uc010zrx.1_Missense_Mutation_p.A48V|ZNF133_uc002wql.3_Missense_Mutation_p.A142V|ZNF133_uc010gcs.2_Missense_Mutation_p.A142V|ZNF133_uc010zry.1_Missense_Mutation_p.A48V|ZNF133_uc002wqm.2_Missense_Mutation_p.A143V	NM_003434	NP_003425	P52736	ZN133_HUMAN	zinc finger protein 133	143					regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|pancreas(1)	2														0.113793	25.36743	68.0538	33	257	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18295923	18295923	18314	20	C	T	T	T	325	25	ZNF133	2	2
APOL5	80831	broad.mit.edu	37	22	36122633	36122633	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:36122633G>C	uc003aof.2	+	c.518G>C	c.(517-519)GGG>GCG	p.G173A		NM_030642	NP_085145	Q9BWW9	APOL5_HUMAN	apolipoprotein L5	173					lipid metabolic process|lipid transport|lipoprotein metabolic process	cytoplasm|extracellular region	high-density lipoprotein particle binding|lipid binding|protein binding				0														0.118182	37.316787	68.82381	26	194	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36122633	36122633	820	22	G	C	C	C	559	43	APOL5	3	3
LRP1B	53353	broad.mit.edu	37	2	141598530	141598530	+	Nonsense_Mutation	SNP	C	A	A			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141598530C>A	uc002tvj.1	-	c.5071G>T	c.(5071-5073)GGA>TGA	p.G1691*		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	1691	Extracellular (Potential).|LDL-receptor class B 15.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|ovary(10)|pancreas(3)|central_nervous_system(2)|liver(1)|kidney(1)	34		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		Colon(99;50 2074 2507 20106)				2546	TSP Lung(27;0.18)			0.078947	-0.106448	6.775369	3	35	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	141598530	141598530	9328	2	C	A	A	A	273	21	LRP1B	5	2
NLGN1	22871	broad.mit.edu	37	3	173997033	173997033	+	Silent	SNP	T	C	C			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:173997033T>C	uc003fio.1	+	c.1242T>C	c.(1240-1242)GCT>GCC	p.A414A	NLGN1_uc010hww.1_Silent_p.A454A|NLGN1_uc003fip.1_Silent_p.A414A	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	431	Extracellular (Potential).				calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of excitatory postsynaptic membrane potential|regulation of N-methyl-D-aspartate selective glutamate receptor activity|regulation of synaptic transmission|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	carboxylesterase activity|cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|pancreas(1)	6	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)											0.109091	6.011221	14.336366	6	49	KEEP	---	---	---	---	capture		Silent	SNP	173997033	173997033	10864	3	T	C	C	C	704	55	NLGN1	4	4
ABCF3	55324	broad.mit.edu	37	3	183909004	183909004	+	Silent	SNP	C	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:183909004C>T	uc003fmz.2	+	c.1530C>T	c.(1528-1530)CGC>CGT	p.R510R	ABCF3_uc003fna.2_Silent_p.R504R|ABCF3_uc003fnb.2_Silent_p.R191R	NM_018358	NP_060828	Q9NUQ8	ABCF3_HUMAN	ATP-binding cassette, sub-family F (GCN20),	510	ABC transporter 2.						ATP binding|ATPase activity			ovary(3)|lung(1)	4	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.35e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)											0.143836	58.906311	94.694527	42	250	KEEP	---	---	---	---	capture		Silent	SNP	183909004	183909004	68	3	C	T	T	T	327	26	ABCF3	2	2
DNAH1	25981	broad.mit.edu	37	3	52429049	52429049	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:52429049C>G	uc011bef.1	+	c.10942C>G	c.(10942-10944)CTG>GTG	p.L3648V	DNAH1_uc003ddv.2_Missense_Mutation_p.L506V	NM_015512	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	3713	AAA 6 (By similarity).				ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			large_intestine(3)	3				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)										0.25	20.111727	21.70219	7	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52429049	52429049	4779	3	C	G	G	G	311	24	DNAH1	3	3
KIAA0922	23240	broad.mit.edu	37	4	154555427	154555427	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:154555427C>T	uc010ipp.2	+	c.4412C>T	c.(4411-4413)CCA>CTA	p.P1471L	KIAA0922_uc003inm.3_Missense_Mutation_p.P1470L|KIAA0922_uc010ipq.2_Missense_Mutation_p.P1239L	NM_001131007	NP_001124479	A2VDJ0	T131L_HUMAN	hypothetical protein LOC23240 isoform 1	1470	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1	all_hematologic(180;0.093)	Renal(120;0.118)												0.108974	11.347488	34.998593	17	139	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	154555427	154555427	8508	4	C	T	T	T	273	21	KIAA0922	2	2
PITX1	5307	broad.mit.edu	37	5	134364489	134364489	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:134364489C>T	uc010jea.2	-	c.925G>A	c.(925-927)GCG>ACG	p.A309T	PITX1_uc011cxy.1_Missense_Mutation_p.A309T	NM_002653	NP_002644	P78337	PITX1_HUMAN	paired-like homeodomain transcription factor 1	309						nucleolus	sequence-specific DNA binding|transcription regulator activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	READ - Rectum adenocarcinoma(2;0.0607)										0.176471	10.328372	13.684048	6	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	134364489	134364489	12378	5	C	T	T	T	351	27	PITX1	1	1
PCDHA2	56146	broad.mit.edu	37	5	140174709	140174709	+	Silent	SNP	C	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140174709C>T	uc003lhd.2	+	c.160C>T	c.(160-162)CTG>TTG	p.L54L	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhc.1_Silent_p.L54L|PCDHA2_uc011czy.1_Silent_p.L54L	NM_018905	NP_061728	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2 isoform 1 precursor	54	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.06383	-14.354981	22.8705	12	176	KEEP	---	---	---	---	capture		Silent	SNP	140174709	140174709	11944	5	C	T	T	T	363	28	PCDHA2	2	2
PCDHGA1	56114	broad.mit.edu	37	5	140712646	140712646	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140712646G>C	uc003lji.1	+	c.2395G>C	c.(2395-2397)GAA>CAA	p.E799Q	PCDHGA1_uc011dan.1_Missense_Mutation_p.E799Q	NM_018912	NP_061735	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1 isoform 1	799	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|breast(1)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.040816	-20.203763	13.366074	6	141	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140712646	140712646	11970	5	G	C	C	C	585	45	PCDHGA1	3	3
G3BP1	10146	broad.mit.edu	37	5	151166212	151166212	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:151166212G>T	uc003lun.2	+	c.31G>T	c.(31-33)GTC>TTC	p.V11F	G3BP1_uc010jhy.1_Missense_Mutation_p.V11F|G3BP1_uc003lum.2_Missense_Mutation_p.V11F|G3BP1_uc011dcu.1_5'UTR|G3BP1_uc010jhz.2_5'UTR	NM_005754	NP_005745	Q13283	G3BP1_HUMAN	Ras-GTPase-activating protein SH3-domain-binding	11	NTF2.				Ras protein signal transduction|transport	cytosol|nucleus|plasma membrane	ATP binding|ATP-dependent DNA helicase activity|ATP-dependent RNA helicase activity|DNA binding|endonuclease activity|protein binding|RNA binding			ovary(1)	1		all_hematologic(541;0.0338)|Medulloblastoma(196;0.091)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)											0.151316	42.063861	59.734639	23	129	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151166212	151166212	6392	5	G	T	T	T	572	44	G3BP1	2	2
SPEF2	79925	broad.mit.edu	37	5	35727857	35727857	+	Missense_Mutation	SNP	G	T	T	rs115170604	by1000genomes	TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:35727857G>T	uc003jjo.2	+	c.2995G>T	c.(2995-2997)GCA>TCA	p.A999S	SPEF2_uc003jjp.1_Missense_Mutation_p.A485S	NM_024867	NP_079143	Q9C093	SPEF2_HUMAN	KPL2 protein isoform 1	999					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity			ovary(1)|central_nervous_system(1)	2	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)											0.077922	-0.715668	13.315601	6	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35727857	35727857	15547	5	G	T	T	T	598	46	SPEF2	2	2
GPR98	84059	broad.mit.edu	37	5	90136558	90136558	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:90136558C>G	uc003kju.2	+	c.16775C>G	c.(16774-16776)CCT>CGT	p.P5592R	GPR98_uc003kjt.2_Missense_Mutation_p.P3298R|GPR98_uc003kjw.2_Missense_Mutation_p.P1253R	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	5592	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)										0.096154	13.703167	39.216813	15	141	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	90136558	90136558	6997	5	C	G	G	G	312	24	GPR98	3	3
HIST1H1C	3006	broad.mit.edu	37	6	26056605	26056605	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:26056605C>G	uc003nfw.2	-	c.52G>C	c.(52-54)GCC>CCC	p.A18P		NM_005319	NP_005310	P16403	H12_HUMAN	histone cluster 1, H1c	18					nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(3)	3														0.056452	-11.137208	14.468127	7	117	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26056605	26056605	7409	6	C	G	G	G	338	26	HIST1H1C	3	3
ASL	435	broad.mit.edu	37	7	65546942	65546942	+	Silent	SNP	C	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:65546942C>T	uc003tuo.2	+	c.165C>T	c.(163-165)CTC>CTT	p.L55L	ASL_uc011kdu.1_Silent_p.L55L|ASL_uc010kzx.1_Silent_p.L55L|ASL_uc011kdv.1_Silent_p.L55L|ASL_uc003tup.2_Silent_p.L55L|ASL_uc003tur.2_Silent_p.L55L|ASL_uc003tuq.2_Silent_p.L55L	NM_000048	NP_000039	P04424	ARLY_HUMAN	argininosuccinate lyase isoform 1	55					arginine biosynthetic process via ornithine|arginine catabolic process|urea cycle	cytosol	argininosuccinate lyase activity			breast(2)	2					L-Arginine(DB00125)									0.12766	6.114581	12.471891	6	41	KEEP	---	---	---	---	capture		Silent	SNP	65546942	65546942	1063	7	C	T	T	T	366	29	ASL	2	2
WRN	7486	broad.mit.edu	37	8	30977835	30977835	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:30977835C>T	uc003xio.3	+	c.2525C>T	c.(2524-2526)CCT>CTT	p.P842L	WRN_uc010lvk.2_Missense_Mutation_p.P309L	NM_000553	NP_000544	Q14191	WRN_HUMAN	Werner syndrome protein	842	Helicase C-terminal.				base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance	centrosome|nucleolus|nucleoplasm	3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding			ovary(2)|kidney(2)|large_intestine(1)	5		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		Ovarian(18;161 598 2706 14834 27543)				832				0.146067	24.311036	35.032448	13	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30977835	30977835	17976	8	C	T	T	T	312	24	WRN	2	2
TEK	7010	broad.mit.edu	37	9	27204929	27204929	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:27204929G>A	uc003zqi.3	+	c.2230G>A	c.(2230-2232)GGG>AGG	p.G744R	TEK_uc011lno.1_Missense_Mutation_p.G701R|TEK_uc011lnp.1_Missense_Mutation_p.G597R|TEK_uc003zqj.1_Missense_Mutation_p.G678R	NM_000459	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial precursor	744	Extracellular (Potential).				angiogenesis|blood coagulation|cell-cell signaling|leukocyte migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase B signaling cascade|protein oligomerization|protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	apical plasma membrane|basolateral plasma membrane|cell surface|integral to plasma membrane|membrane raft|microvillus	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			ovary(3)|central_nervous_system(3)|breast(3)|lung(2)|kidney(1)	12		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)						493				0.084615	3.13007	25.889231	11	119	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27204929	27204929	16278	9	G	A	A	A	559	43	TEK	2	2
C9orf11	54586	broad.mit.edu	37	9	27289707	27289707	+	Silent	SNP	G	A	A			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:27289707G>A	uc003zql.2	-	c.444C>T	c.(442-444)GTC>GTT	p.V148V	C9orf11_uc011lnq.1_Silent_p.V119V	NM_020641	NP_065692	Q9NQ60	AFAF_HUMAN	Acr formation associated factor isoform 1	148	Vesicular (Potential).					acrosomal membrane|integral to membrane				ovary(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(39;7.39e-08)|Lung(218;1.26e-05)|LUSC - Lung squamous cell carcinoma(38;0.000106)										0.136364	4.108949	6.927066	3	19	KEEP	---	---	---	---	capture		Silent	SNP	27289707	27289707	2561	9	G	A	A	A	574	45	C9orf11	2	2
VPS13A	23230	broad.mit.edu	37	9	79946995	79946995	+	Nonsense_Mutation	SNP	G	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:79946995G>T	uc004akr.2	+	c.6061G>T	c.(6061-6063)GAA>TAA	p.E2021*	VPS13A_uc004akp.3_Nonsense_Mutation_p.E2021*|VPS13A_uc004akq.3_Nonsense_Mutation_p.E2021*|VPS13A_uc004aks.2_Nonsense_Mutation_p.E1982*|VPS13A_uc004akt.2_Nonsense_Mutation_p.E361*	NM_033305	NP_150648	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13A isoform A	2021	TPR 6.				Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	7														0.081081	-0.103708	6.512471	3	34	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	79946995	79946995	17756	9	G	T	T	T	585	45	VPS13A	5	2
ARSD	414	broad.mit.edu	37	X	2825346	2825346	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:2825346C>T	uc004cqy.2	-	c.1748G>A	c.(1747-1749)TGT>TAT	p.C583Y	ARSD_uc004cqz.1_Non-coding_Transcript	NM_001669	NP_001660	P51689	ARSD_HUMAN	arylsulfatase D isoform a precursor	583						lysosome	arylsulfatase activity|metal ion binding				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)												0.158537	21.118608	30.236543	13	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2825346	2825346	1007	23	C	T	T	T	221	17	ARSD	2	2
KDM6A	7403	broad.mit.edu	37	X	44938572	44938572	+	Silent	SNP	C	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:44938572C>T	uc011mkz.1	+	c.3276C>T	c.(3274-3276)GCC>GCT	p.A1092A	KDM6A_uc010nhk.2_Silent_p.A1006A|KDM6A_uc004dge.3_Silent_p.A1040A|KDM6A_uc011mla.1_Silent_p.A995A|KDM6A_uc011mlb.1_Silent_p.A1047A|KDM6A_uc011mlc.1_Silent_p.A744A|KDM6A_uc011mld.1_Silent_p.A679A	NM_021140	NP_066963	O15550	KDM6A_HUMAN	ubiquitously transcribed tetratricopeptide	1040					histone H3-K4 methylation|oxidation-reduction process		metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2)	84						Colon(129;1273 1667 15230 27352 52914)				372				0.180328	24.685418	30.549279	11	50	KEEP	---	---	---	---	capture		Silent	SNP	44938572	44938572	8443	23	C	T	T	T	301	24	KDM6A	2	2
CXCR3	2833	broad.mit.edu	37	X	70836739	70836739	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:70836739C>T	uc011mpx.1	-	c.724G>A	c.(724-726)GAC>AAC	p.D242N	BCYRN1_uc011mpt.1_Intron|CXCR3_uc004eaf.2_Missense_Mutation_p.D195N	NM_001142797	NP_001136269	P49682	CXCR3_HUMAN	chemokine (C-X-C motif) receptor 3 isoform B	195	Extracellular (Potential).				cell adhesion|cellular component movement|chemotaxis|elevation of cytosolic calcium ion concentration	cytoplasm|integral to plasma membrane	C-X-C chemokine receptor activity			ovary(2)|central_nervous_system(1)	3	Renal(35;0.156)													0.172414	9.3636	12.299296	5	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70836739	70836739	4252	23	C	T	T	T	403	31	CXCR3	1	1
MAP3K9	4293	broad.mit.edu	37	14	71275774	71275776	+	In_Frame_Del	DEL	CCT	-	-			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:71275774_71275776delCCT	uc001xml.2	-	c.113_115delAGG	c.(112-117)GAGGCG>GCG	p.E38del	MAP3K9_uc001xmm.2_In_Frame_Del_p.E38del	NM_033141	NP_149132	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase	38	Ala-rich.|Poly-Glu.				activation of JUN kinase activity|protein autophosphorylation		ATP binding|JUN kinase kinase kinase activity|MAP kinase kinase activity|protein homodimerization activity			stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	4				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		GBM(114;411 1587 13539 28235 50070)				190				0.67			4	2		---	---	---	---	capture_indel		In_Frame_Del	DEL	71275774	71275776	9640	14	CCT	-	-	-	338	26	MAP3K9	5	5
PGLS	25796	broad.mit.edu	37	19	17622663	17622663	+	Frame_Shift_Del	DEL	C	-	-			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:17622663_17622663delC	uc002ngw.2	+	c.182_182delC	c.(181-183)GCCfs	p.A61fs		NM_012088	NP_036220	O95336	6PGL_HUMAN	6-phosphogluconolactonase	61						cytosol	6-phosphogluconolactonase activity				0														0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	17622663	17622663	12215	19	C	-	-	-	338	26	PGLS	5	5
FAM46A	55603	broad.mit.edu	37	6	82461884	82461884	+	Frame_Shift_Del	DEL	C	-	-			TCGA-44-2661-01	TCGA-44-2661-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:82461884_82461884delC	uc003pjf.2	-	c.32_32delG	c.(31-33)GGCfs	p.G11fs	FAM46A_uc003pjg.2_5'UTR|FAM46A_uc003pjh.1_5'UTR	NM_017633	NP_060103	Q96IP4	FA46A_HUMAN	hypothetical protein LOC55603	Error:Variant_position_missing_in_Q96IP4_after_alignment											0		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)		BRCA - Breast invasive adenocarcinoma(397;0.0428)										0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	82461884	82461884	5786	6	C	-	-	-	326	26	FAM46A	5	5
