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
DNMBP	23268	broad.mit.edu	36	10	101706790	101706790	+	Missense_Mutation	SNP	T	G	G			TCGA-12-1601-01	TCGA-12-1601-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:101706790T>G	uc001kqj.2	-	c.431A>C	c.(430-432)GAA>GCA	p.E144A	NCRNA00093_uc001kqk.1_Non-coding_Transcript	NM_015221	NP_056036	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	144					intracellular signal transduction|regulation of Rho protein signal transduction	cell junction|cytoskeleton|Golgi stack|synapse	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(5)	5		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)										0.533333	22.497383	22.511712	8	7	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	101706790	101706790	4857	10	T	G	G	62	62	DNMBP	G	4	4
OR10A6	390093	broad.mit.edu	36	11	7905902	7905902	+	Missense_Mutation	SNP	C	G	G			TCGA-12-1601-01	TCGA-12-1601-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:7905902C>G	uc001mft.1	-	c.884G>C	c.(883-885)AGT>ACT	p.S295T		NM_001004461	NP_001004461	Q8NH74	O10A6_HUMAN	olfactory receptor, family 10, subfamily A,	295	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)										0.289017	140.37403	147.356839	50	123	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7905902	7905902	11300	11	C	G	G	20	20	OR10A6	G	3	3
NLRP10	338322	broad.mit.edu	36	11	7939162	7939162	+	Silent	SNP	G	T	T			TCGA-12-1601-01	TCGA-12-1601-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:7939162G>T	uc001mfv.1	-	c.573C>A	c.(571-573)GCC>GCA	p.A191A		NM_176821	NP_789791	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	191	NACHT.						ATP binding			lung(4)|ovary(2)|kidney(1)|pancreas(1)	8				Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)						109				0.317073	108.981228	112.640973	39	84	GG		KEEP	---	---	---	---	capture			Silent	SNP	7939162	7939162	10875	11	G	T	T	47	47	NLRP10	T	3	3
LCP1	3936	broad.mit.edu	36	13	45628679	45628679	+	Nonsense_Mutation	SNP	C	T	T			TCGA-12-1601-01	TCGA-12-1601-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:45628679C>T	uc001vaz.2	-	c.386G>A	c.(385-387)TGG>TAG	p.W129*	LCP1_uc001vba.2_Nonsense_Mutation_p.W129*	NM_002298	NP_002289	P13796	PLSL_HUMAN	L-plastin	129	Actin-binding 1.|CH 1.				regulation of intracellular protein transport|T cell activation involved in immune response	cell junction|cytosol|ruffle membrane	calcium ion binding			ovary(2)	2		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.39e-05)						600				0.266968	154.42061	165.264632	59	162	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	45628679	45628679	9015	13	C	T	T	21	21	LCP1	T	5	2
RCBTB2	1102	broad.mit.edu	36	13	47971898	47971898	+	Splice_Site_SNP	SNP	C	T	T			TCGA-12-1601-01	TCGA-12-1601-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:47971898C>T	uc001vch.1	-	c.e13_splice_site			RCBTB2_uc001vci.1_Splice_Site_SNP|RCBTB2_uc001vcj.1_Splice_Site_SNP|RCBTB2_uc010acv.1_Intron	NM_001268	NP_001259			regulator of chromosome condensation and BTB								Ran guanyl-nucleotide exchange factor activity			ovary(2)|lung(2)	4		all_cancers(8;4.86e-71)|all_epithelial(8;2.11e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;2.3e-10)|Lung NSC(96;1.07e-07)|Breast(56;1.53e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.00826)|Myeloproliferative disorder(33;0.0179)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(99;1.8e-09)|LUSC - Lung squamous cell carcinoma(3;0.116)					(JMSU1-Tumor)	264				0.25	46.14356	50.00589	17	51	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	47971898	47971898	13641	13	C	T	T	32	32	RCBTB2	T	5	2
ABCC4	10257	broad.mit.edu	36	13	94659755	94659755	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1601-01	TCGA-12-1601-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:94659755C>T	uc001vmd.2	-	c.719G>A	c.(718-720)GGG>GAG	p.G240E	ABCC4_uc010afk.1_Missense_Mutation_p.G240E|ABCC4_uc001vme.2_Missense_Mutation_p.G240E|ABCC4_uc001vmf.2_Missense_Mutation_p.G197E|ABCC4_uc010afl.1_Missense_Mutation_p.G197E|ABCC4_uc010afm.1_Missense_Mutation_p.G253E	NM_005845	NP_005836	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C, member 4	240	Helical; (Potential).|ABC transmembrane type-1 1.				platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)	3	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)					1222				0.108696	20.220948	48.091175	20	164	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	94659755	94659755	56	13	C	T	T	22	22	ABCC4	T	2	2
RIPK3	11035	broad.mit.edu	36	14	23876186	23876186	+	Silent	SNP	C	T	T			TCGA-12-1601-01	TCGA-12-1601-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:23876186C>T	uc001wpb.1	-	c.1221G>A	c.(1219-1221)CAG>CAA	p.Q407Q	ADCY4_uc001wov.1_5'Flank|ADCY4_uc001wow.1_5'Flank|ADCY4_uc001wox.1_5'Flank|ADCY4_uc001woy.1_5'Flank|ADCY4_uc001woz.2_5'Flank|RIPK3_uc001wpa.1_Silent_p.Q207Q|RIPK3_uc010alq.1_Non-coding_Transcript	NM_006871	NP_006862	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	407					apoptosis|induction of apoptosis by extracellular signals|protein phosphorylation	cytoplasm	ATP binding|protein binding|transcription coactivator activity			central_nervous_system(2)|ovary(1)|lung(1)	4				GBM - Glioblastoma multiforme(265;0.0181)		Pancreas(58;918 1191 4668 13304 15331)				120				0.237288	68.658913	76.090188	28	90	CC		KEEP	---	---	---	---	capture			Silent	SNP	23876186	23876186	13859	14	C	T	T	32	32	RIPK3	T	2	2
TRIP4	9325	broad.mit.edu	36	15	62474758	62474758	+	Missense_Mutation	SNP	T	C	C			TCGA-12-1601-01	TCGA-12-1601-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:62474758T>C	uc002anm.1	+	c.380T>C	c.(379-381)GTT>GCT	p.V127A		NM_016213	NP_057297	Q15650	TRIP4_HUMAN	thyroid hormone receptor interactor 4	127					regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	ligand-dependent nuclear receptor binding|transcription activator activity|transcription coactivator activity|zinc ion binding			ovary(1)|kidney(1)	2														0.294872	68.307064	71.236109	23	55	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	62474758	62474758	17108	15	T	C	C	60	60	TRIP4	C	4	4
ISLR	3671	broad.mit.edu	36	15	72254515	72254515	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1601-01	TCGA-12-1601-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:72254515C>T	uc002axg.1	+	c.263C>T	c.(262-264)ACG>ATG	p.T88M	ISLR_uc002axh.1_Missense_Mutation_p.T88M|ISLR_uc010bjh.1_Missense_Mutation_p.T88M	NM_005545	NP_958934	O14498	ISLR_HUMAN	immunoglobulin superfamily containing	88	LRR 2.				cell adhesion	extracellular region				large_intestine(1)|ovary(1)	2														0.26087	11.974362	13.229106	6	17	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	72254515	72254515	8162	15	C	T	T	19	19	ISLR	T	1	1
KRT32	3882	broad.mit.edu	36	17	36877023	36877023	+	Silent	SNP	G	A	A			TCGA-12-1601-01	TCGA-12-1601-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36877023G>A	uc002hwr.1	-	c.81C>T	c.(79-81)AGC>AGT	p.S27S		NM_002278	NP_002269	Q14532	K1H2_HUMAN	keratin 32	27	Head.				epidermis development	intermediate filament	protein binding|structural molecule activity				0		Breast(137;0.000812)												0.3	8.021732	8.378788	3	7	GG		KEEP	---	---	---	---	capture			Silent	SNP	36877023	36877023	8783	17	G	A	A	38	38	KRT32	A	1	1
WNT3	7473	broad.mit.edu	36	17	42200950	42200950	+	Missense_Mutation	SNP	T	C	C			TCGA-12-1601-01	TCGA-12-1601-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:42200950T>C	uc002ikv.1	-	c.973A>G	c.(973-975)AAG>GAG	p.K325E		NM_030753	NP_110380	P56703	WNT3_HUMAN	wingless-type MMTV integration site family,	325					canonical Wnt receptor signaling pathway involved in mesenchymal stem cell differentiation|canonical Wnt receptor signaling pathway involved in osteoblast differentiation|cellular response to retinoic acid|dorsal/ventral axis specification|embryonic forelimb morphogenesis|embryonic hindlimb morphogenesis|embryonic pattern specification|head morphogenesis|hemopoietic stem cell proliferation|inner ear morphogenesis|limb bud formation|mammary gland epithelium development|mesoderm formation|midbrain-hindbrain boundary development|negative regulation of fat cell differentiation|negative regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of cell proliferation|positive regulation of gene-specific transcription from RNA polymerase II promoter|Spemann organizer formation at the anterior end of the primitive streak|Wnt receptor signaling pathway, calcium modulating pathway	early endosome|extracellular space|late endosome|membrane fraction|membrane raft|plasma membrane|proteinaceous extracellular matrix	frizzled binding|frizzled-2 binding|signal transducer activity				0			BRCA - Breast invasive adenocarcinoma(9;0.0257)											0.189474	34.801734	43.379975	18	77	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42200950	42200950	17962	17	T	C	C	62	62	WNT3	C	4	4
SERPINB4	6318	broad.mit.edu	36	18	59456128	59456128	+	Silent	SNP	A	T	T			TCGA-12-1601-01	TCGA-12-1601-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr18:59456128A>T	uc002ljf.1	-	c.978T>A	c.(976-978)TCT>TCA	p.S326S	SERPINB4_uc002lje.1_Silent_p.S305S|SERPINB4_uc002ljg.1_Silent_p.S326S|SERPINB4_uc002ljh.1_Silent_p.S326S	NM_002974	NP_002965	P48594	SPB4_HUMAN	serine (or cysteine) proteinase inhibitor, clade	326					immune response|regulation of proteolysis	cytoplasm|extracellular region	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)|lung(1)	2										163				0.335404	152.293716	156.156306	54	107	AA		KEEP	---	---	---	---	capture			Silent	SNP	59456128	59456128	14591	18	A	T	T	15	15	SERPINB4	T	4	4
SIN3B	23309	broad.mit.edu	36	19	16835507	16835507	+	Nonsense_Mutation	SNP	G	A	A			TCGA-12-1601-01	TCGA-12-1601-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:16835507G>A	uc002ney.1	+	c.1379G>A	c.(1378-1380)TGG>TAG	p.W460*	SIN3B_uc002nez.1_Nonsense_Mutation_p.W428*	NM_015260	NP_056075	O75182	SIN3B_HUMAN	SIN3 homolog B, transcription regulator	460	Interaction with SDS3 and HDAC1 (By similarity).|Interaction with NCOR1 (By similarity).				cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	protein binding			ovary(2)	2														0.163793	38.466491	50.908887	19	97	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	16835507	16835507	14821	19	G	A	A	47	47	SIN3B	A	5	2
PLVAP	83483	broad.mit.edu	36	19	17348766	17348766	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1601-01	TCGA-12-1601-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:17348766C>T	uc002ngk.1	-	c.332G>A	c.(331-333)CGC>CAC	p.R111H		NM_031310	NP_112600	Q9BX97	PLVAP_HUMAN	plasmalemma vesicle associated protein	111	Extracellular (Potential).					caveola|integral to membrane|perinuclear region of cytoplasm					0														0.2	15.810498	18.736279	7	28	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17348766	17348766	12542	19	C	T	T	27	27	PLVAP	T	1	1
CD22	933	broad.mit.edu	36	19	40524110	40524110	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1601-01	TCGA-12-1601-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:40524110G>A	uc010edt.1	+	c.1532G>A	c.(1531-1533)CGG>CAG	p.R511Q	CD22_uc010edu.1_Missense_Mutation_p.R423Q|CD22_uc010edv.1_Missense_Mutation_p.R511Q|CD22_uc002nzb.2_Missense_Mutation_p.R334Q|CD22_uc010edw.1_Missense_Mutation_p.R339Q|CD22_uc010edx.1_Non-coding_Transcript	NM_001771	NP_001762	P20273	CD22_HUMAN	CD22 molecule	511	Extracellular (Potential).|Ig-like C2-type 5.				cell adhesion		protein binding|sugar binding			ovary(4)	4	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)		OspA lipoprotein(DB00045)	Ovarian(42;1009 1133 23674 26041)								0.428571	19.348787	19.410862	6	8	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40524110	40524110	3112	19	G	A	A	39	39	CD22	A	1	1
ZNF223	7766	broad.mit.edu	36	19	49262713	49262713	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1601-01	TCGA-12-1601-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:49262713C>T	uc002oyf.1	+	c.892C>T	c.(892-894)CGT>TGT	p.R298C	ZNF284_uc010ejd.1_Non-coding_Transcript	NM_013361	NP_037493	Q9UK11	ZN223_HUMAN	zinc finger protein 223	298	C2H2-type 5.			R -> C (in Ref. 1; AAF04105).	regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)												0.384615	300.076283	302.955278	95	152	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49262713	49262713	18368	19	C	T	T	23	23	ZNF223	T	1	1
MBD3L1	85509	broad.mit.edu	36	19	8814699	8814699	+	Silent	SNP	C	T	T			TCGA-12-1601-01	TCGA-12-1601-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8814699C>T	uc002mko.1	+	c.345C>T	c.(343-345)CAC>CAT	p.H115H		NM_145208	NP_660209	Q8WWY6	MB3L1_HUMAN	methyl-CpG binding domain protein 3-like	115					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0														0.414414	141.724269	142.435351	46	65	CC		KEEP	---	---	---	---	capture			Silent	SNP	8814699	8814699	9729	19	C	T	T	20	20	MBD3L1	T	2	2
IFI16	3428	broad.mit.edu	36	1	157254703	157254703	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1601-01	TCGA-12-1601-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:157254703C>T	uc001ftg.1	+	c.610C>T	c.(610-612)CCA>TCA	p.P204S	IFI16_uc001fti.2_Missense_Mutation_p.P204S|IFI16_uc001ftf.1_Missense_Mutation_p.P204S	NM_005531	NP_005522	Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	204	HIN-200 1.				cell proliferation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|monocyte differentiation|regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	cytoplasm|nucleolus|nucleoplasm	double-stranded DNA binding|transcription repressor activity			ovary(1)	1	all_hematologic(112;0.0429)													0.260274	48.390802	52.190357	19	54	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	157254703	157254703	7812	1	C	T	T	22	22	IFI16	T	2	2
LEPR	3953	broad.mit.edu	36	1	65875034	65875034	+	Silent	SNP	C	T	T			TCGA-12-1601-01	TCGA-12-1601-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:65875034C>T	uc001dci.1	+	c.3246C>T	c.(3244-3246)GTC>GTT	p.V1082V	LEPR_uc009waq.1_3'UTR	NM_002303	NP_002294	P48357	LEPR_HUMAN	leptin receptor isoform 1	1082	Cytoplasmic (Potential).				energy reserve metabolic process|multicellular organismal development	extracellular region|integral to membrane|plasma membrane	cytokine receptor activity				0				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)										0.103825	11.792047	40.393259	19	164	CC		KEEP	---	---	---	---	capture			Silent	SNP	65875034	65875034	9052	1	C	T	T	29	29	LEPR	T	2	2
ASXL1	171023	broad.mit.edu	36	20	30487705	30487705	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1601-01	TCGA-12-1601-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:30487705C>T	uc002wxs.1	+	c.3529C>T	c.(3529-3531)CTT>TTT	p.L1177F	ASXL1_uc010gea.1_Missense_Mutation_p.L1177F|ASXL1_uc010geb.1_Missense_Mutation_p.L1068F	NM_015338	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like 1	1177					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	PR-DUB complex	metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(131)|large_intestine(6)|central_nervous_system(2)|ovary(1)	140														0.352941	34.288707	34.937562	12	22	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30487705	30487705	1085	20	C	T	T	32	32	ASXL1	T	2	2
CABIN1	23523	broad.mit.edu	36	22	22839581	22839581	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1601-01	TCGA-12-1601-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:22839581C>T	uc002zzi.1	+	c.4166C>T	c.(4165-4167)ACG>ATG	p.T1389M	CABIN1_uc002zzj.1_Missense_Mutation_p.T1310M|CABIN1_uc002zzl.1_Missense_Mutation_p.T1389M	NM_012295	NP_036427	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	1389					cell surface receptor linked signaling pathway|chromatin modification	nucleus	protein phosphatase inhibitor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.363636	49.190527	49.909335	16	28	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22839581	22839581	2644	22	C	T	T	19	19	CABIN1	T	1	1
COL6A3	1293	broad.mit.edu	36	2	237947884	237947884	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1601-01	TCGA-12-1601-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:237947884C>T	uc002vwl.2	-	c.3589G>A	c.(3589-3591)GTC>ATC	p.V1197I	COL6A3_uc002vwk.2_Missense_Mutation_p.V1197I|COL6A3_uc002vwm.2_Missense_Mutation_p.V996I|COL6A3_uc002vwn.2_Missense_Mutation_p.V997I|COL6A3_uc002vwo.2_Missense_Mutation_p.V991I|COL6A3_uc002vwq.2_Missense_Mutation_p.V991I|COL6A3_uc002vwr.2_Missense_Mutation_p.V790I	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	1197	Nonhelical region.|VWFA 6.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|pancreas(1)	15		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)										0.338028	68.786437	70.429588	24	47	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	237947884	237947884	3839	2	C	T	T	19	19	COL6A3	T	1	1
ZNF80	7634	broad.mit.edu	36	3	115438424	115438424	+	Missense_Mutation	SNP	A	T	T			TCGA-12-1601-01	TCGA-12-1601-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:115438424A>T	uc003ebf.1	-	c.188T>A	c.(187-189)CTC>CAC	p.L63H	ZNF80_uc010hqo.1_Missense_Mutation_p.L63H	NM_007136	NP_009067	P51504	ZNF80_HUMAN	zinc finger protein 80	63	C2H2-type 1.				regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Lung NSC(201;0.0233)|all_neural(597;0.0837)				GBM(23;986 1114 21716)								0.264706	15.45138	17.161085	9	25	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	115438424	115438424	18766	3	A	T	T	11	11	ZNF80	T	4	4
FBXO40	51725	broad.mit.edu	36	3	122824100	122824100	+	Silent	SNP	G	T	T			TCGA-12-1601-01	TCGA-12-1601-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:122824100G>T	uc003eeg.2	+	c.1134G>T	c.(1132-1134)GTG>GTT	p.V378V		NM_016298	NP_057382	Q9UH90	FBX40_HUMAN	F-box protein 40	378						centrosome|nucleus	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(114;0.189)										0.410256	200.966125	202.064795	64	92	GG		KEEP	---	---	---	---	capture			Silent	SNP	122824100	122824100	5986	3	G	T	T	47	47	FBXO40	T	3	3
MSL2	55167	broad.mit.edu	36	3	137396637	137396637	+	Silent	SNP	G	A	A			TCGA-12-1601-01	TCGA-12-1601-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:137396637G>A	uc003eqx.1	-	c.9C>T	c.(7-9)CCC>CCT	p.P3P		NM_018133	NP_060603	Q9HCI7	MSL2_HUMAN	ring finger protein 184 isoform 1	3					histone H4-K16 acetylation	MSL complex	zinc ion binding			central_nervous_system(1)	1														0.194444	17.303001	20.439683	7	29	GG		KEEP	---	---	---	---	capture			Silent	SNP	137396637	137396637	10271	3	G	A	A	39	39	MSL2	A	1	1
SCN11A	11280	broad.mit.edu	36	3	38920593	38920593	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1601-01	TCGA-12-1601-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:38920593C>T	uc010hhm.1	-	c.1609G>A	c.(1609-1611)GAA>AAA	p.E537K		NM_014139	NP_054858	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha	537					response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(1)|pancreas(1)|skin(1)	3				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)									0.14	20.043234	32.652997	14	86	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38920593	38920593	14395	3	C	T	T	32	32	SCN11A	T	2	2
ADH1C	126	broad.mit.edu	36	4	100476946	100476946	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1601-01	TCGA-12-1601-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:100476946C>T	uc003huu.1	-	c.1114G>A	c.(1114-1116)GTC>ATC	p.V372I		NM_000669	NP_000660	P00326	ADH1G_HUMAN	alcohol dehydrogenase 1C, gamma polypeptide	372					ethanol oxidation|xenobiotic metabolic process	cytosol	alcohol dehydrogenase (NAD) activity|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(123;1.08e-07)	Fomepizole(DB01213)|NADH(DB00157)									0.26129	225.444386	241.423502	81	229	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100476946	100476946	310	4	C	T	T	19	19	ADH1C	T	1	1
MARCH1	55016	broad.mit.edu	36	4	164669389	164669389	+	Silent	SNP	T	C	C			TCGA-12-1601-01	TCGA-12-1601-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:164669389T>C	uc003iqs.1	-	c.831A>G	c.(829-831)CCA>CCG	p.P277P	MARCH1_uc003iqr.1_Silent_p.P260P	NM_017923	NP_060393	Q8TCQ1	MARH1_HUMAN	membrane-associated RING-CH protein I	277	Responsible for down-regulation of CD86 and MHC class II cell surface expression (By similarity).					cytoplasmic vesicle membrane|early endosome membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|plasma membrane	ubiquitin-protein ligase activity|zinc ion binding			lung(1)	1	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)												0.222222	32.917973	37.389283	14	49	TT		KEEP	---	---	---	---	capture			Silent	SNP	164669389	164669389	9681	4	T	C	C	51	51	MARCH1	C	4	4
TLL1	7092	broad.mit.edu	36	4	167239890	167239890	+	Nonsense_Mutation	SNP	C	T	T			TCGA-12-1601-01	TCGA-12-1601-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:167239890C>T	uc003irh.1	+	c.2668C>T	c.(2668-2670)CGA>TGA	p.R890*		NM_012464	NP_036596	O43897	TLL1_HUMAN	tolloid-like 1	890	CUB 5.				cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(2)|breast(1)|central_nervous_system(1)	4	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)										0.308824	53.285181	55.541095	21	47	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	167239890	167239890	16475	4	C	T	T	19	19	TLL1	T	5	1
PCDHB8	56128	broad.mit.edu	36	5	140539225	140539225	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1601-01	TCGA-12-1601-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140539225G>A	uc003liu.1	+	c.1426G>A	c.(1426-1428)GCC>ACC	p.A476T	PCDHB16_uc003liv.1_5'Flank|PCDHB16_uc010jfw.1_5'Flank	NM_019120	NP_061993	Q9UN66	PCDB8_HUMAN	protocadherin beta 8 precursor	476	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.333333	34.205755	35.314914	15	30	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	140539225	140539225	11968	5	G	A	A	38	38	PCDHB8	A	1	1
CEP72	55722	broad.mit.edu	36	5	697465	697465	+	Nonsense_Mutation	SNP	A	T	T			TCGA-12-1601-01	TCGA-12-1601-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:697465A>T	uc003jbf.1	+	c.1591A>T	c.(1591-1593)AAA>TAA	p.K531*		NM_018140	NP_060610	Q9P209	CEP72_HUMAN	centrosomal protein 72 kDa	531	Potential.				G2/M transition of mitotic cell cycle|gamma-tubulin complex localization|spindle organization	centrosome|cytosol				ovary(1)	1			Epithelial(17;0.000339)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|Lung(60;0.0863)											0.208333	7.356919	9.254334	5	19	AA		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	697465	697465	3393	5	A	T	T	1	1	CEP72	T	5	4
ZBTB24	9841	broad.mit.edu	36	6	109909599	109909599	+	Missense_Mutation	SNP	T	A	A			TCGA-12-1601-01	TCGA-12-1601-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:109909599T>A	uc003ptl.1	-	c.324A>T	c.(322-324)CAA>CAT	p.Q108H	ZBTB24_uc010kds.1_Missense_Mutation_p.Q108H|ZBTB24_uc010kdt.1_Non-coding_Transcript|ZBTB24_uc003ptm.2_Missense_Mutation_p.Q108H	NM_014797	NP_055612	O43167	ZBT24_HUMAN	zinc finger and BTB domain containing 24	108	BTB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0154)|all cancers(137;0.0216)|OV - Ovarian serous cystadenocarcinoma(136;0.0242)|BRCA - Breast invasive adenocarcinoma(108;0.059)										0.371795	83.751341	84.878785	29	49	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	109909599	109909599	18117	6	T	A	A	64	64	ZBTB24	A	4	4
ENPP3	5169	broad.mit.edu	36	6	132037099	132037099	+	Nonsense_Mutation	SNP	G	A	A			TCGA-12-1601-01	TCGA-12-1601-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:132037099G>A	uc003qcu.2	+	c.747G>A	c.(745-747)TGG>TGA	p.W249*	ENPP3_uc010kfn.1_Non-coding_Transcript|ENPP3_uc010kfo.1_Non-coding_Transcript|ENPP3_uc010kfp.1_Non-coding_Transcript|ENPP3_uc010kfq.1_Non-coding_Transcript|ENPP3_uc003qcv.1_Nonsense_Mutation_p.W249*	NM_005021	NP_005012	O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	249	Extracellular (Potential).|Phosphodiesterase.				immune response|nucleoside triphosphate catabolic process|phosphate metabolic process	extracellular region|integral to plasma membrane|perinuclear region of cytoplasm	metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity			ovary(3)	3	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)										0.300699	116.443114	121.534504	43	100	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	132037099	132037099	5324	6	G	A	A	44	44	ENPP3	A	5	2
MYB	4602	broad.mit.edu	36	6	135552992	135552992	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1601-01	TCGA-12-1601-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:135552992G>A	uc003qfh.1	+	c.341G>A	c.(340-342)CGT>CAT	p.R114H	MYB_uc003qfb.1_Missense_Mutation_p.R114H|MYB_uc003qfc.1_Missense_Mutation_p.R114H|MYB_uc003qfd.1_Non-coding_Transcript|MYB_uc003qfe.1_Non-coding_Transcript|MYB_uc003qff.1_Non-coding_Transcript|MYB_uc003qfg.1_Non-coding_Transcript|MYB_uc003qfi.1_Missense_Mutation_p.R114H|MYB_uc003qfj.1_Non-coding_Transcript|MYB_uc003qfl.1_Non-coding_Transcript|MYB_uc010kgi.1_Missense_Mutation_p.R114H|MYB_uc003qfk.1_Non-coding_Transcript|MYB_uc003qfm.1_Non-coding_Transcript|MYB_uc003qfn.1_Non-coding_Transcript|MYB_uc010kgj.1_Missense_Mutation_p.R114H|MYB_uc003qfo.1_Missense_Mutation_p.R114H|MYB_uc003qfp.1_Non-coding_Transcript|MYB_uc003qfq.1_Missense_Mutation_p.R114H|MYB_uc003qfr.1_Non-coding_Transcript|MYB_uc003qfv.1_Non-coding_Transcript|MYB_uc003qfs.1_Intron|MYB_uc003qft.1_Non-coding_Transcript|MYB_uc003qfu.1_Missense_Mutation_p.R114H|MYB_uc003qfw.1_Intron|MYB_uc003qfx.1_Non-coding_Transcript|MYB_uc003qfy.1_Non-coding_Transcript|MYB_uc003qfz.1_Non-coding_Transcript|MYB_uc003qga.1_Non-coding_Transcript|MYB_uc003qgb.1_Non-coding_Transcript|MYB_uc010kgk.1_Non-coding_Transcript|MYB_uc003qgc.1_Non-coding_Transcript|MYB_uc003qgd.1_5'UTR	NM_005375	NP_005366	P10242	MYB_HUMAN	v-myb myeloblastosis viral oncogene homolog	114	HTH myb-type 2.|Interaction with HIPK2 and NLK (By similarity).				blood coagulation|negative regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of gene-specific transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear matrix	DNA binding|protein binding|specific transcriptional repressor activity|transcription activator activity			lung(1)	1	all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221)	Lung NSC(302;3.08e-05)|Ovarian(999;0.208)		OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117)						299				0.331034	142.661217	146.324288	48	97	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	135552992	135552992	10402	6	G	A	A	40	40	MYB	A	1	1
EYS	346007	broad.mit.edu	36	6	66261339	66261339	+	Missense_Mutation	SNP	A	C	C			TCGA-12-1601-01	TCGA-12-1601-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:66261339A>C	uc003peq.2	-	c.686T>G	c.(685-687)ATT>AGT	p.I229S	EYS_uc003per.1_Missense_Mutation_p.I229S|EYS_uc010kaj.1_Non-coding_Transcript	NM_198283	NP_938024	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 3	229	EGF-like 2.				response to stimulus|visual perception	extracellular region	calcium ion binding			ovary(1)	1														0.357143	9.965017	10.219121	5	9	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	66261339	66261339	5526	6	A	C	C	4	4	EYS	C	4	4
DSP	1832	broad.mit.edu	36	6	7528328	7528328	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1601-01	TCGA-12-1601-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:7528328G>A	uc003mxp.1	+	c.5834G>A	c.(5833-5835)CGC>CAC	p.R1945H	DSP_uc003mxq.1_Missense_Mutation_p.R1346H	NM_004415	NP_004406	P15924	DESP_HUMAN	desmoplakin isoform I	1945	Central fibrous rod domain.|Potential.				cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			central_nervous_system(6)|ovary(2)	8	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)										0.350649	147.145422	150.20073	54	100	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7528328	7528328	4965	6	G	A	A	38	38	DSP	A	1	1
IBTK	25998	broad.mit.edu	36	6	83006859	83006859	+	Missense_Mutation	SNP	G	C	C			TCGA-12-1601-01	TCGA-12-1601-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:83006859G>C	uc003pjl.1	-	c.64C>G	c.(64-66)CTT>GTT	p.L22V	IBTK_uc010kbi.1_5'UTR|IBTK_uc003pjm.1_Missense_Mutation_p.L22V	NM_015525	NP_056340	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton's tyrosine kinase	22					negative regulation of protein phosphorylation|release of sequestered calcium ion into cytosol	cytoplasm|membrane|nucleus	protein kinase binding|protein tyrosine kinase inhibitor activity			ovary(2)|central_nervous_system(2)	4		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)										0.298361	234.842315	245.971535	91	214	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	83006859	83006859	7776	6	G	C	C	35	35	IBTK	C	3	3
C7orf58	79974	broad.mit.edu	36	7	120416957	120416957	+	Nonsense_Mutation	SNP	C	T	T			TCGA-12-1601-01	TCGA-12-1601-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:120416957C>T	uc003vjq.2	+	c.46C>T	c.(46-48)CGA>TGA	p.R16*	C7orf58_uc003vjs.2_Nonsense_Mutation_p.R16*|C7orf58_uc003vjr.1_Nonsense_Mutation_p.R16*	NM_024913	NP_079189	A4D0V7	CG058_HUMAN	hypothetical protein LOC79974 isoform 1	16						endoplasmic reticulum				ovary(4)|large_intestine(2)|pancreas(1)	7	all_neural(327;0.117)													0.22807	63.297474	71.028146	26	88	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	120416957	120416957	2512	7	C	T	T	23	23	C7orf58	T	5	1
PRKAG2	51422	broad.mit.edu	36	7	151003555	151003555	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1601-01	TCGA-12-1601-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:151003555G>A	uc003wkk.1	-	c.568C>T	c.(568-570)CGC>TGC	p.R190C	PRKAG2_uc003wkj.1_Missense_Mutation_p.R146C|PRKAG2_uc010lqe.1_Non-coding_Transcript|PRKAG2_uc003wkm.1_Missense_Mutation_p.R190C	NM_016203	NP_077747	Q9UGJ0	AAKG2_HUMAN	AMP-activated protein kinase gamma2 subunit	190					ATP biosynthetic process|carnitine shuttle|cell cycle arrest|fatty acid biosynthetic process|glycogen metabolic process|insulin receptor signaling pathway|intracellular protein kinase cascade|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein kinase activity|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation|regulation of glucose import|regulation of glycolysis|sterol biosynthetic process	AMP-activated protein kinase complex|cytosol|nucleoplasm	ADP binding|ATP binding|cAMP-dependent protein kinase inhibitor activity|cAMP-dependent protein kinase regulator activity|phosphorylase kinase regulator activity|protein kinase activator activity|protein kinase binding			kidney(1)	1	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)										0.165414	41.883878	56.007743	22	111	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	151003555	151003555	12944	7	G	A	A	37	37	PRKAG2	A	1	1
PTPRN2	5799	broad.mit.edu	36	7	157802355	157802355	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1601-01	TCGA-12-1601-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:157802355G>A	uc003wno.1	-	c.194C>T	c.(193-195)CCG>CTG	p.P65L	PTPRN2_uc003wnp.1_Missense_Mutation_p.P48L|PTPRN2_uc003wnq.1_Missense_Mutation_p.P65L|PTPRN2_uc003wnr.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N	65	Extracellular (Potential).					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)	6	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)										0.292683	35.850314	37.390045	12	29	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	157802355	157802355	13265	7	G	A	A	39	39	PTPRN2	A	1	1
STK31	56164	broad.mit.edu	36	7	23735373	23735373	+	Missense_Mutation	SNP	G	C	C			TCGA-12-1601-01	TCGA-12-1601-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:23735373G>C	uc003sws.2	+	c.463G>C	c.(463-465)GAA>CAA	p.E155Q	STK31_uc003swt.2_Missense_Mutation_p.E132Q|STK31_uc010kuq.1_Missense_Mutation_p.E132Q	NM_031414	NP_116562	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31 isoform a	155					protein phosphorylation		ATP binding|nucleic acid binding|protein serine/threonine kinase activity			ovary(2)|lung(2)	4										598				0.165217	83.905009	108.366834	38	192	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	23735373	23735373	15816	7	G	C	C	33	33	STK31	C	3	3
EGFR	1956	broad.mit.edu	36	7	55177506	55177506	+	Missense_Mutation	SNP	T	G	G			TCGA-12-1601-01	TCGA-12-1601-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55177506T>G	uc003tqk.1	+	c.122T>G	c.(121-123)TTG>TGG	p.L41W	EGFR_uc003tqh.1_Missense_Mutation_p.L41W|EGFR_uc003tqi.1_Missense_Mutation_p.L41W|EGFR_uc003tqj.1_Missense_Mutation_p.L41W|EGFR_uc010kzg.1_Missense_Mutation_p.L41W	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	41	Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.V30_R297>G(5)		lung(8200)|central_nervous_system(103)|upper_aerodigestive_tract(37)|prostate(32)|ovary(31)|thyroid(23)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|stomach(6)|urinary_tract(6)|skin(5)|adrenal_gland(5)|kidney(4)|soft_tissue(4)|bone(3)|NS(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)|pancreas(1)	8515	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8		608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.693291	2229.049813	2260.317059	651	288	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55177506	55177506	5156	7	T	G	G	63	63	EGFR	G	4	4
SAMD9	54809	broad.mit.edu	36	7	92570984	92570984	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1601-01	TCGA-12-1601-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:92570984C>T	uc003umf.1	-	c.2363G>A	c.(2362-2364)CGT>CAT	p.R788H	SAMD9_uc003umg.1_Missense_Mutation_p.R788H|SAMD9_uc010lfa.1_Missense_Mutation_p.R788H	NM_017654	NP_060124	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	788						cytoplasm				ovary(3)|breast(1)|central_nervous_system(1)	5	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)											0.168367	69.363561	89.771244	33	163	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	92570984	92570984	14306	7	C	T	T	19	19	SAMD9	T	1	1
OCM2	4951	broad.mit.edu	36	7	97455690	97455690	+	Silent	SNP	G	A	A			TCGA-12-1601-01	TCGA-12-1601-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:97455690G>A	uc003upc.1	-	c.168C>T	c.(166-168)AGC>AGT	p.S56S		NM_006188	NP_006179	P0CE71	OCM2_HUMAN	oncomodulin-like	56	EF-hand 1.|1 (Potential).						calcium ion binding				0														0.237624	120.43239	133.119519	48	154	GG		KEEP	---	---	---	---	capture			Silent	SNP	97455690	97455690	11227	7	G	A	A	38	38	OCM2	A	1	1
TG	7038	broad.mit.edu	36	8	134215018	134215018	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1601-01	TCGA-12-1601-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:134215018G>A	uc003ytw.1	+	c.8120G>A	c.(8119-8121)CGA>CAA	p.R2707Q	TG_uc010mdw.1_Missense_Mutation_p.R1466Q	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin	2707					hormone biosynthetic process|regulation of synaptic transmission|signal transduction		carboxylesterase activity|hormone activity			ovary(8)|breast(4)|pancreas(1)	13	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)						1778				0.433071	159.299743	159.796317	55	72	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	134215018	134215018	16341	8	G	A	A	37	37	TG	A	1	1
DMRT2	10655	broad.mit.edu	36	9	1046913	1046913	+	Silent	SNP	G	A	A			TCGA-12-1601-01	TCGA-12-1601-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:1046913G>A	uc003zha.1	+	c.1326G>A	c.(1324-1326)ACG>ACA	p.T442T	DMRT2_uc003zgx.2_Silent_p.T209T|DMRT2_uc010mgz.1_Silent_p.T209T|DMRT2_uc003zhb.2_3'UTR|DMRT2_uc003zgy.2_Silent_p.T286T	NM_181872	NP_870987	Q9Y5R5	DMRT2_HUMAN	doublesex and mab-3 related transcription factor	442					male gonad development|regulation of transcription, DNA-dependent|sex determination	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity				0		all_lung(10;1.49e-09)|Lung NSC(10;1.86e-09)		Lung(218;0.0195)|GBM - Glioblastoma multiforme(50;0.0388)										0.328125	181.977593	186.997752	63	129	GG		KEEP	---	---	---	---	capture			Silent	SNP	1046913	1046913	4766	9	G	A	A	39	39	DMRT2	A	1	1
SPAG8	26206	broad.mit.edu	36	9	35800295	35800295	+	Nonsense_Mutation	SNP	G	T	T			TCGA-12-1601-01	TCGA-12-1601-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:35800295G>T	uc003zye.1	-	c.1212C>A	c.(1210-1212)TAC>TAA	p.Y404*	SPAG8_uc003zyf.1_Nonsense_Mutation_p.Y321*|SPAG8_uc003zyg.1_Nonsense_Mutation_p.Y404*	NM_172312	NP_758516	Q99932	SPAG8_HUMAN	sperm associated antigen 8 isoform 2	404						acrosomal vesicle|membrane				ovary(1)	1	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)							7				0.5	6.752833	6.752833	4	4	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	35800295	35800295	15487	9	G	T	T	44	44	SPAG8	T	5	3
POF1B	79983	broad.mit.edu	36	X	84520846	84520846	+	Silent	SNP	G	A	A			TCGA-12-1601-01	TCGA-12-1601-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:84520846G>A	uc004ees.2	-	c.270C>T	c.(268-270)AGC>AGT	p.S90S	POF1B_uc004eer.2_Silent_p.S90S	NM_024921	NP_079197	Q8WVV4	POF1B_HUMAN	premature ovarian failure, 1B	90							actin binding				0														0.68	58.68425	59.40493	17	8	GG		KEEP	---	---	---	---	capture			Silent	SNP	84520846	84520846	12610	23	G	A	A	38	38	POF1B	A	1	1
UTY	7404	broad.mit.edu	36	Y	13924204	13924204	+	Silent	SNP	T	C	C			TCGA-12-1601-01	TCGA-12-1601-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrY:13924204T>C	uc004fsx.1	-	c.3336A>G	c.(3334-3336)GAA>GAG	p.E1112E	UTY_uc004fsw.1_Silent_p.E775E|UTY_uc010nwx.1_Silent_p.E169E|UTY_uc004fsy.1_Silent_p.E1112E	NM_007125	NP_009056	O14607	UTY_HUMAN	tetratricopeptide repeat protein isoform 3	1112	JmjC.				chromatin modification|oxidation-reduction process	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						Colon(103;1740 2135 40732 45171)								0.311111	43.236018	44.664428	14	31	TT		KEEP	---	---	---	---	capture			Silent	SNP	13924204	13924204	17672	24	T	C	C	52	52	UTY	C	4	4
PTEN	5728	broad.mit.edu	36	10	89701888	89701890	+	In_Frame_Del	DEL	TAT	-	-			TCGA-12-1601-01	TCGA-12-1601-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:89701888_89701890delTAT	uc001kfb.1	+	c.526_528delTAT	c.(526-528)TATdel	p.Y178del		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	178	Phosphatase tensin-type.				apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of focal adhesion assembly|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of cyclin-dependent protein kinase activity|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.V166fs*17(3)|p.G165fs*9(3)|p.Y27_N212>Y(2)|p.Y176del(2)|p.G165_K342del(1)|p.G165_*404del(1)|p.Y176*(1)|p.V175fs*3(1)|p.R172fs*5(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)				31		264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.45			54	67				---	---	---	---	capture_indel			In_Frame_Del	DEL	89701888	89701890	13192	10	TAT	-	-	57	57	PTEN	-	5	5
UBE2I	7329	broad.mit.edu	36	16	1310650	1310651	+	Frame_Shift_Ins	INS	-	G	G			TCGA-12-1601-01	TCGA-12-1601-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:1310650_1310651insG	uc002clh.1	+	c.544_545insG	c.(544-546)CGGfs	p.R182fs	UBE2I_uc002clc.1_Intron|UBE2I_uc002cld.1_Intron|UBE2I_uc002clf.1_Intron|UBE2I_uc002clg.1_Intron|UBE2I_uc002cli.1_Frame_Shift_Ins_p.R182fs	NM_194261	NP_919237	P63279	UBC9_HUMAN	ubiquitin-conjugating enzyme E2I	Error:Variant_position_missing_in_P63279_after_alignment					cell division|chromosome segregation|interspecies interaction between organisms|mitosis|negative regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|post-translational protein modification|protein sumoylation	cytoplasm|PML body|synaptonemal complex	ATP binding|enzyme binding|specific transcriptional repressor activity|ubiquitin-protein ligase activity			breast(1)|skin(1)	2		Hepatocellular(780;0.00369)												0.43			3	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	1310650	1310651	17416	16	-	G	G	31	31	UBE2I	G	5	5
IMP5	162540	broad.mit.edu	36	17	41278096	41278102	+	Frame_Shift_Del	DEL	TCATCAG	-	-			TCGA-12-1601-01	TCGA-12-1601-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:41278096_41278102delTCATCAG	uc002ijq.1	+	c.44_50delTCATCAG	c.(43-51)CTCATCAGCfs	p.L15fs	LOC100128977_uc010dat.1_Intron	NM_175882	NP_787078	Q8IUH8	IMP5_HUMAN	intramembrane protease 5	15_17						integral to membrane	aspartic-type endopeptidase activity			pancreas(2)	2	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.148)		NSCLC(24;34 1393 18470)								0.51			64	62				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	41278096	41278102	8022	17	TCATCAG	-	-	54	54	IMP5	-	5	5
TMPRSS9	360200	broad.mit.edu	36	19	2373028	2373029	+	Frame_Shift_Ins	INS	-	C	C			TCGA-12-1601-01	TCGA-12-1601-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:2373028_2373029insC	uc002lvw.1	+	c.2229_2230insC	c.(2227-2232)TCTCCCfs	p.S743fs		NM_182973	NP_892018	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	743_744	Extracellular (Potential).				proteolysis	integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)										0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	2373028	2373029	16794	19	-	C	C	54	54	TMPRSS9	C	5	5
ZNF335	63925	broad.mit.edu	36	20	44022289	44022294	+	In_Frame_Del	DEL	TCCTCT	-	-			TCGA-12-1601-01	TCGA-12-1601-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:44022289_44022294delTCCTCT	uc002xqw.1	-	c.1980_1985delAGAGGA	c.(1978-1986)CGAGAGGAC>CGC	p.ED661del		NM_022095	NP_071378	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	661_662	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(115;0.0122)												0.41			33	47				---	---	---	---	capture_indel			In_Frame_Del	DEL	44022289	44022294	18444	20	TCCTCT	-	-	58	58	ZNF335	-	5	5
CERK	64781	broad.mit.edu	36	22	45466132	45466136	+	Splice_Site_Del	DEL	CCTGG	-	-			TCGA-12-1601-01	TCGA-12-1601-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:45466132_45466136delCCTGG	uc003bia.1	-	c.e11_splice_site			CERK_uc010hae.1_Splice_Site_Del	NM_022766	NP_073603			ceramide kinase						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|ceramide metabolic process	integral to membrane of membrane fraction|membrane|nucleus	ATP binding|ceramide kinase activity|diacylglycerol kinase activity|magnesium ion binding			skin(1)	1		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)|BRCA - Breast invasive adenocarcinoma(115;0.171)										0.36			5	9				---	---	---	---	capture_indel			Splice_Site_Del	DEL	45466132	45466136	3400	22	CCTGG	-	-	18	18	CERK	-	5	5
