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
PTPN11	5781	broad.mit.edu	36	12	111395220	111395220	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0171-01	TCGA-06-0171-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:111395220C>G	uc001ttx.1	+	c.846C>G	c.(844-846)ATC>ATG	p.I282M	PTPN11_uc001ttw.1_Missense_Mutation_p.I282M	NM_002834	NP_002825	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type	282	Tyrosine-protein phosphatase.		I -> V (in NS1).		axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol	non-membrane spanning protein tyrosine phosphatase activity|protein binding	p.I282M(1)		haematopoietic_and_lymphoid_tissue(372)|lung(6)|autonomic_ganglia(2)|soft_tissue(2)|central_nervous_system(2)|large_intestine(1)|ovary(1)|NS(1)|kidney(1)	388										372				0.231405	80.83839	88.833614	28	93	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	111395220	111395220	13235	12	C	G	G	30	30	PTPN11	G	3	3
DDX11	1663	broad.mit.edu	36	12	31129189	31129189	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:31129189G>C	uc001rjt.1	+	c.500G>C	c.(499-501)AGA>ACA	p.R167T	DDX11_uc001rjr.1_Missense_Mutation_p.R167T|DDX11_uc001rjs.1_Missense_Mutation_p.R167T|DDX11_uc001rju.1_5'UTR|DDX11_uc001rjv.1_Missense_Mutation_p.R167T|DDX11_uc001rjw.1_Missense_Mutation_p.R141T|DDX11_uc001rjx.1_5'Flank	NM_152438	NP_689651	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11	167	Glu-rich.|Helicase ATP-binding.				G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitotic sister chromatid segregation|positive regulation of cell proliferation|S phase of mitotic cell cycle|sister chromatid cohesion	midbody|nuclear chromatin|nucleolus|spindle pole	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|RNA binding			breast(3)	3	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)										Multiple Myeloma(12;0.14)			0.142857	7.187201	10.623735	4	24	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31129189	31129189	4514	12	G	C	C	33	33	DDX11	C	3	3
NRL	4901	broad.mit.edu	36	14	23620536	23620536	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0171-01	TCGA-06-0171-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:23620536C>G	uc001wlo.1	-	c.463G>C	c.(463-465)GAC>CAC	p.D155H	NRL_uc001wlp.1_Missense_Mutation_p.D155H|NRL_uc001wlq.1_Missense_Mutation_p.D155H	NM_006177	NP_006168	P54845	NRL_HUMAN	neural retina leucine zipper	155					response to stimulus|transcription from RNA polymerase II promoter|visual perception	nucleus	sequence-specific DNA binding|specific RNA polymerase II transcription factor activity				0														0.25	8.619204	9.300906	3	9	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(265;0.0181)	Missense_Mutation	SNP	23620536	23620536	11061	14	C	G	G	31	31	NRL	G	3	3
CSPG4	1464	broad.mit.edu	36	15	73769488	73769488	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0171-01	TCGA-06-0171-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:73769488C>T	uc002baw.1	-	c.973G>A	c.(973-975)GGG>AGG	p.G325R		NM_001897	NP_001888	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	325	Extracellular (Potential).|Neurite growth inhibition (By similarity).|Globular or compact configuration stabilized by disulfide bonds.|Laminin G-like 2.				angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling	apical plasma membrane|cell surface|integral to plasma membrane|lamellipodium membrane	protein kinase binding|signal transducer activity			ovary(2)|pancreas(1)	3										549				0.423077	34.52111	34.655267	11	15	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73769488	73769488	4101	15	C	T	T	23	23	CSPG4	T	1	1
AKAP13	11214	broad.mit.edu	36	15	83877979	83877979	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0171-01	TCGA-06-0171-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:83877979C>A	uc002blu.1	+	c.342C>A	c.(340-342)AAC>AAA	p.N114K	AKAP13_uc002blt.1_Missense_Mutation_p.N114K|AKAP13_uc002blv.1_Missense_Mutation_p.N114K|AKAP13_uc002bls.2_Missense_Mutation_p.N114K	NM_006738	NP_006729	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 1	114					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|ovary(1)|liver(1)	8						Melanoma(94;603 1453 3280 32295 32951)								0.194737	78.856253	95.377805	37	153	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	83877979	83877979	452	15	C	A	A	20	20	AKAP13	A	3	3
FAM169B	283777	broad.mit.edu	36	15	96841521	96841521	+	Silent	SNP	C	T	T			TCGA-06-0171-01	TCGA-06-0171-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:96841521C>T	uc002buk.1	-	c.15G>A	c.(13-15)TCG>TCA	p.S5S		NM_182562	NP_872368	Q8N8A8	F169B_HUMAN	hypothetical protein LOC283777	5											0														0.3	41.332706	43.104242	15	35	CC		KEEP	---	---	---	---	capture			Silent	SNP	96841521	96841521	5692	15	C	T	T	19	19	FAM169B	T	1	1
INPP5K	51763	broad.mit.edu	36	17	1364014	1364014	+	Silent	SNP	G	A	A			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:1364014G>A	uc002fsr.1	-	c.54C>T	c.(52-54)GTC>GTT	p.V18V	INPP5K_uc002fsq.1_5'UTR|INPP5K_uc002fss.1_5'UTR|INPP5K_uc010cjr.1_5'UTR|INPP5K_uc010cjs.1_Silent_p.V18V	NM_016532	NP_570122	Q9BT40	INP5K_HUMAN	inositol polyphosphate-5-phosphatase K isoform	18	Catalytic (Potential).				actin cytoskeleton organization	cytosol|endoplasmic reticulum|membrane fraction|neuron projection|ruffle	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol bisphosphate phosphatase activity|inositol bisphosphate phosphatase activity|inositol trisphosphate phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|lipid phosphatase activity|protein binding				0														0.298969	78.433153	81.938971	29	68	GG		KEEP	---	---	---	---	capture			Silent	SNP	1364014	1364014	8061	17	G	A	A	37	37	INPP5K	A	1	1
RPTOR	57521	broad.mit.edu	36	17	76552655	76552655	+	Splice_Site_SNP	SNP	A	G	G			TCGA-06-0171-01	TCGA-06-0171-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:76552655A>G	uc002jyt.1	+	c.3940_splice	c.e34-2	p.P1314_splice	RPTOR_uc002jyu.1_Splice_Site_SNP_p.P207_splice	NM_020761	NP_065812			raptor						cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)	5										1368				0.27619	67.921487	72.663999	29	76	AA		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	76552655	76552655	14145	17	A	G	G	7	7	RPTOR	G	5	4
DSC2	1824	broad.mit.edu	36	18	26925089	26925089	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:26925089G>T	uc002kwl.2	-	c.374C>A	c.(373-375)ACT>AAT	p.T125N	DSC2_uc002kwk.2_Missense_Mutation_p.T125N	NM_024422	NP_077740	Q02487	DSC2_HUMAN	desmocollin 2 isoform Dsc2a preproprotein	125					homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			ovary(1)	1														0.329412	82.569863	84.763139	28	57	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(10;0.0241)		Missense_Mutation	SNP	26925089	26925089	4950	18	G	T	T	36	36	DSC2	T	3	3
ONECUT2	9480	broad.mit.edu	36	18	53294846	53294846	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:53294846G>A	uc002lgo.1	+	c.1408G>A	c.(1408-1410)GTC>ATC	p.V470I		NM_004852	NP_004843	O95948	ONEC2_HUMAN	one cut domain, family member 2	470	Homeobox.				organ morphogenesis	nucleus	RNA polymerase II transcription factor activity|sequence-specific DNA binding	p.V470I(1)		ovary(2)|central_nervous_system(1)	3		Colorectal(73;0.234)												0.27907	93.043388	98.707345	36	93	GG		KEEP	---	---	---	---	capture		READ - Rectum adenocarcinoma(59;0.227)|Colorectal(16;0.245)	Missense_Mutation	SNP	53294846	53294846	11274	18	G	A	A	40	40	ONECUT2	A	1	1
SERPINB13	5275	broad.mit.edu	36	18	59407892	59407892	+	Missense_Mutation	SNP	C	T	T	rs61733412	unknown	TCGA-06-0171-01	TCGA-06-0171-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:59407892C>T	uc002ljc.1	+	c.188C>T	c.(187-189)ACG>ATG	p.T63M	SERPINB13_uc002ljd.1_De_novo_Start_InFrame	NM_012397	NP_036529	Q9UIV8	SPB13_HUMAN	serine (or cysteine) proteinase inhibitor, clade	63					regulation of proteolysis|response to UV	cytoplasm|extracellular region	serine-type endopeptidase inhibitor activity			ovary(1)	1														0.211538	24.794378	28.796855	11	41	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59407892	59407892	14588	18	C	T	T	19	19	SERPINB13	T	1	1
ZNF407	55628	broad.mit.edu	36	18	70904711	70904711	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:70904711G>A	uc002llw.2	+	c.6046G>A	c.(6046-6048)GCC>ACC	p.A2016T		NM_017757	NP_060227	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	2016					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Esophageal squamous(42;0.131)|Prostate(75;0.173)												0.433333	38.276806	38.391508	13	17	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(31;0.184)	Missense_Mutation	SNP	70904711	70904711	18480	18	G	A	A	38	38	ZNF407	A	1	1
LPHN1	22859	broad.mit.edu	36	19	14133186	14133186	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0171-01	TCGA-06-0171-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:14133186A>C	uc002myg.1	-	c.1463T>G	c.(1462-1464)GTC>GGC	p.V488G	LPHN1_uc002myh.1_Missense_Mutation_p.V483G	NM_001008701	NP_001008701	O94910	LPHN1_HUMAN	latrophilin 1 isoform 1 precursor	488	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(1)|central_nervous_system(1)	2														0.266667	8.494161	9.232213	4	11	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	14133186	14133186	9288	19	A	C	C	10	10	LPHN1	C	4	4
WIZ	58525	broad.mit.edu	36	19	15396741	15396741	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0171-01	TCGA-06-0171-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:15396741C>T	uc002nba.2	-	c.1835G>A	c.(1834-1836)TGG>TAG	p.W612*	WIZ_uc002nbb.2_Nonsense_Mutation_p.W571*	NM_021241	NP_067064	O95785	WIZ_HUMAN	widely-interspaced zinc finger motifs	1428						nucleus	zinc ion binding				0														0.16	7.284288	10.036233	4	21	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	15396741	15396741	17949	19	C	T	T	21	21	WIZ	T	5	2
KHSRP	8570	broad.mit.edu	36	19	6369513	6369513	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0171-01	TCGA-06-0171-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:6369513C>T	uc002mer.2	-	c.860G>A	c.(859-861)GGG>GAG	p.G287E		NM_003685	NP_003676	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein (FUSE	287	Gly-rich.|KH 2.				mRNA processing|mRNA transport|regulation of transcription, DNA-dependent|RNA splicing, via transesterification reactions|transcription, DNA-dependent	cytosol|nucleus	DNA binding|protein binding|RNA binding			skin(1)	1						Colon(55;593 1006 2067 9135 22980)								0.18	20.14428	24.959274	9	41	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6369513	6369513	8457	19	C	T	T	22	22	KHSRP	T	2	2
SPRR4	163778	broad.mit.edu	36	1	151211200	151211200	+	Silent	SNP	C	T	T			TCGA-06-0171-01	TCGA-06-0171-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:151211200C>T	uc001fav.1	+	c.210C>T	c.(208-210)GCC>GCT	p.A70A	SPRR4_uc009wnt.1_Silent_p.A70A	NM_173080	NP_775103	Q96PI1	SPRR4_HUMAN	small proline-rich protein 4	70	Gln-rich.				keratinization	cell cortex					0	Lung NSC(65;1.46e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)													0.272727	76.106717	81.754256	33	88	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.171)		Silent	SNP	151211200	151211200	15618	1	C	T	T	22	22	SPRR4	T	2	2
ARHGAP30	257106	broad.mit.edu	36	1	159288114	159288114	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0171-01	TCGA-06-0171-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:159288114A>C	uc001fxl.1	-	c.1034T>G	c.(1033-1035)GTG>GGG	p.V345G	ARHGAP30_uc001fxk.1_Missense_Mutation_p.V345G|ARHGAP30_uc001fxm.1_Missense_Mutation_p.V191G|ARHGAP30_uc009wtx.1_Missense_Mutation_p.V18G|ARHGAP30_uc001fxn.1_Missense_Mutation_p.V191G	NM_001025598	NP_001020769	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30 isoform 1	345					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(2)	2	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)													0.294118	8.998374	10.458801	10	24	AA		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(70;0.00122)		Missense_Mutation	SNP	159288114	159288114	891	1	A	C	C	6	6	ARHGAP30	C	4	4
KCNH1	3756	broad.mit.edu	36	1	209159845	209159845	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0171-01	TCGA-06-0171-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:209159845C>T	uc001hib.1	-	c.1222G>A	c.(1222-1224)GAG>AAG	p.E408K	KCNH1_uc001hic.1_Missense_Mutation_p.E381K	NM_172362	NP_758872	O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H,	408	Extracellular (Potential).				myoblast fusion|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	calmodulin binding|delayed rectifier potassium channel activity|two-component sensor activity			ovary(4)|central_nervous_system(1)	5														0.241206	114.140511	126.273633	48	151	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)	Missense_Mutation	SNP	209159845	209159845	8336	1	C	T	T	31	31	KCNH1	T	1	1
HFM1	164045	broad.mit.edu	36	1	91557459	91557459	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:91557459G>A	uc001doa.2	-	c.2659C>T	c.(2659-2661)CAT>TAT	p.H887Y	HFM1_uc009wdb.1_Non-coding_Transcript|HFM1_uc001dob.2_Missense_Mutation_p.H119Y	NM_001017975	NP_001017975	A2PYH4	HFM1_HUMAN	HFM1 protein	887	SEC63.						ATP binding|ATP-dependent helicase activity|nucleic acid binding				0		all_lung(203;0.00961)|Lung NSC(277;0.0351)												0.192308	50.290445	61.793018	25	105	GG		KEEP	---	---	---	---	capture		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)	Missense_Mutation	SNP	91557459	91557459	7366	1	G	A	A	48	48	HFM1	A	2	2
PDYN	5173	broad.mit.edu	36	20	1909118	1909118	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:1909118G>A	uc010gaj.1	-	c.616C>T	c.(616-618)CGC>TGC	p.R206C	PDYN_uc002wfv.1_Missense_Mutation_p.R206C	NM_024411	NP_077722	P01213	PDYN_HUMAN	beta-neoendorphin-dynorphin preproprotein	206					cell death|neuropeptide signaling pathway|synaptic transmission	extracellular region|plasma membrane	opioid peptide activity			ovary(1)	1														0.230769	174.208506	196.643039	78	260	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1909118	1909118	12120	20	G	A	A	40	40	PDYN	A	1	1
RBPJL	11317	broad.mit.edu	36	20	43373692	43373692	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:43373692G>A	uc002xns.1	+	c.307G>A	c.(307-309)GTG>ATG	p.V103M	RBPJL_uc002xnt.1_Missense_Mutation_p.V103M	NM_014276	NP_055091	Q9UBG7	RBPJL_HUMAN	recombining binding protein L	103					regulation of transcription, DNA-dependent|signal transduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)										OREG0025979	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.215054	40.282202	47.341069	20	73	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43373692	43373692	13631	20	G	A	A	44	44	RBPJL	A	2	2
POTED	317754	broad.mit.edu	36	21	13904804	13904804	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0171-01	TCGA-06-0171-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:13904804C>A	uc002yjb.1	+	c.384C>A	c.(382-384)TTC>TTA	p.F128L		NM_174981	NP_778146	Q86YR6	POTED_HUMAN	pote protein	128						plasma membrane				ovary(3)	3														0.322034	147.609494	152.589877	57	120	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	13904804	13904804	12693	21	C	A	A	29	29	POTED	A	3	3
KRTAP13-1	140258	broad.mit.edu	36	21	30690704	30690704	+	Silent	SNP	C	T	T			TCGA-06-0171-01	TCGA-06-0171-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:30690704C>T	uc002yoa.1	+	c.429C>T	c.(427-429)GGC>GGT	p.G143G		NM_181599	NP_853630	Q8IUC0	KR131_HUMAN	keratin associated protein 13-1	143						intermediate filament				ovary(1)	1														0.315068	61.905976	64.123094	23	50	CC		KEEP	---	---	---	---	capture			Silent	SNP	30690704	30690704	8837	21	C	T	T	27	27	KRTAP13-1	T	1	1
COL6A3	1293	broad.mit.edu	36	2	237917925	237917925	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:237917925G>A	uc002vwl.2	-	c.7475C>T	c.(7474-7476)TCG>TTG	p.S2492L	COL6A3_uc002vwj.2_5'Flank|COL6A3_uc002vwk.2_Missense_Mutation_p.S2325L|COL6A3_uc002vwm.2_Missense_Mutation_p.S2291L|COL6A3_uc002vwn.2_Missense_Mutation_p.S2292L|COL6A3_uc002vwo.2_Missense_Mutation_p.S2286L|COL6A3_uc002vwp.1_Missense_Mutation_p.S313L	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	2492	VWFA 11.|Nonhelical region.				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)												0.313131	172.376339	178.531368	62	136	GG		KEEP	---	---	---	---	capture		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)	Missense_Mutation	SNP	237917925	237917925	3839	2	G	A	A	37	37	COL6A3	A	1	1
FAM98A	25940	broad.mit.edu	36	2	33666930	33666930	+	Silent	SNP	T	C	C			TCGA-06-0171-01	TCGA-06-0171-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:33666930T>C	uc002rpa.1	-	c.498A>G	c.(496-498)CAA>CAG	p.Q166Q	FAM98A_uc002roz.1_Silent_p.Q43Q	NM_015475	NP_056290	Q8NCA5	FA98A_HUMAN	hypothetical protein LOC25940	166										ovary(1)	1	all_hematologic(175;0.115)													0.328125	341.675681	350.052709	105	215	TT		KEEP	---	---	---	---	capture			Silent	SNP	33666930	33666930	5892	2	T	C	C	52	52	FAM98A	C	4	4
COL6A6	131873	broad.mit.edu	36	3	131769893	131769893	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:131769893G>A	uc010htl.1	+	c.2156G>A	c.(2155-2157)CGG>CAG	p.R719Q		NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6	719	Nonhelical region.|VWFA 4.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8														0.374302	207.990415	210.469939	67	112	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	131769893	131769893	3841	3	G	A	A	39	39	COL6A6	A	1	1
HLTF	6596	broad.mit.edu	36	3	150285301	150285301	+	Nonsense_Mutation	SNP	G	C	C			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:150285301G>C	uc003ewq.1	-	c.86C>G	c.(85-87)TCA>TGA	p.S29*	HLTF_uc003ewr.1_Nonsense_Mutation_p.S29*|HLTF_uc003ews.1_Nonsense_Mutation_p.S29*|HLTF_uc010hve.1_Nonsense_Mutation_p.S29*	NM_139048	NP_620636	Q14527	HLTF_HUMAN	helicase-like transcription factor	29					chromatin modification|transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding				0														0.311927	115.510328	118.942806	34	75	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Nonsense_Mutation	SNP	150285301	150285301	7506	3	G	C	C	45	45	HLTF	C	5	3
PIK3CA	5290	broad.mit.edu	36	3	180434766	180434766	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0171-01	TCGA-06-0171-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:180434766A>G	uc003fjk.1	+	c.3127A>G	c.(3127-3129)ATG>GTG	p.M1043V		NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha	1043	PI3K/PI4K.		M -> I (in cancer; shows an increase in lipid kinase activity).		epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity	p.M1043V(13)		breast(1506)|large_intestine(749)|endometrium(244)|urinary_tract(195)|ovary(136)|skin(112)|stomach(89)|thyroid(77)|central_nervous_system(69)|lung(61)|upper_aerodigestive_tract(48)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|kidney(2)|prostate(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3437	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)					Colon(199;1504 1750 3362 26421 31210 32040)		57		621	TCGA GBM(8;5.49e-07)			0.360656	149.870533	151.954179	44	78	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Missense_Mutation	SNP	180434766	180434766	12337	3	A	G	G	4	4	PIK3CA	G	4	4
RNF168	165918	broad.mit.edu	36	3	197684040	197684040	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0171-01	TCGA-06-0171-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:197684040C>T	uc003fwq.1	-	c.763G>A	c.(763-765)GAC>AAC	p.D255N	RNF168_uc010iah.1_Missense_Mutation_p.D88N	NM_152617	NP_689830	Q8IYW5	RN168_HUMAN	ring finger protein 168	255					double-strand break repair|histone H2A K63-linked ubiquitination|positive regulation of DNA repair|response to ionizing radiation	nucleus|ubiquitin ligase complex	chromatin binding|histone binding|ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding				0	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)													0.3375	77.897842	79.767445	27	53	CC		KEEP	---	---	---	---	capture	Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)	Missense_Mutation	SNP	197684040	197684040	13936	3	C	T	T	30	30	RNF168	T	2	2
SLC4A7	9497	broad.mit.edu	36	3	27393282	27393282	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0171-01	TCGA-06-0171-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:27393282C>T	uc003cdv.1	-	c.3622G>A	c.(3622-3624)GTG>ATG	p.V1208M	SLC4A7_uc010hfl.1_Missense_Mutation_p.V794M|SLC4A7_uc003cdw.1_Missense_Mutation_p.V1084M|SLC4A7_uc003cdu.2_Missense_Mutation_p.V1125M	NM_003615	NP_003606	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate	1208	Cytoplasmic (Potential).					apical plasma membrane|basolateral plasma membrane|integral to membrane|stereocilium	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|central_nervous_system(1)	4														0.243902	50.159186	55.060188	20	62	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27393282	27393282	15155	3	C	T	T	19	19	SLC4A7	T	1	1
PXK	54899	broad.mit.edu	36	3	58360145	58360145	+	Splice_Site_SNP	SNP	G	A	A			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:58360145G>A	uc003djz.1	+	c.1181_splice	c.e12+1	p.P394_splice	PXK_uc003djx.1_Splice_Site_SNP_p.P394_splice|PXK_uc003djy.1_Splice_Site_SNP_p.P377_splice|PXK_uc003dka.1_Splice_Site_SNP_p.P394_splice|PXK_uc003dkb.1_Splice_Site_SNP_p.P311_splice|PXK_uc003dkc.1_Splice_Site_SNP_p.P377_splice|PXK_uc010hnj.1_Splice_Site_SNP_p.P361_splice|PXK_uc003dkd.1_Splice_Site_SNP_p.P257_splice|PXK_uc010hnk.1_Splice_Site_SNP_p.P168_splice	NM_017771	NP_060241			PX domain containing serine/threonine kinase						cell communication|inflammatory response|negative regulation of ATPase activity|negative regulation of ion transport|protein phosphorylation|regulation of synaptic transmission	centrosome|cytoplasm|nucleus|plasma membrane	actin binding|ATP binding|phosphatidylinositol binding|phosphatidylinositol binding|protein C-terminus binding|protein kinase activity			ovary(1)	1										508				0.372881	61.831777	62.670344	22	37	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22)	Splice_Site_SNP	SNP	58360145	58360145	13307	3	G	A	A	40	40	PXK	A	5	1
TRIML2	205860	broad.mit.edu	36	4	189249891	189249891	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0171-01	TCGA-06-0171-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:189249891C>A	uc003izl.1	-	c.794G>T	c.(793-795)AGG>ATG	p.R265M	TRIML2_uc003izj.1_Missense_Mutation_p.R93M|TRIML2_uc003izk.1_Missense_Mutation_p.R73M	NM_173553	NP_775824	Q8N7C3	TRIMM_HUMAN	tripartite motif family-like 2	265	B30.2/SPRY.						ligase activity			central_nervous_system(2)	2		all_cancers(14;3.11e-44)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|all_hematologic(60;0.0202)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)												0.32	316.092776	326.930333	120	255	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(60;1.79e-11)|BRCA - Breast invasive adenocarcinoma(30;4.52e-06)|GBM - Glioblastoma multiforme(59;1.62e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.0091)|READ - Rectum adenocarcinoma(43;0.163)	Missense_Mutation	SNP	189249891	189249891	17101	4	C	A	A	24	24	TRIML2	A	3	3
RBM47	54502	broad.mit.edu	36	4	40135388	40135388	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0171-01	TCGA-06-0171-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:40135388C>T	uc003gvc.2	-	c.280G>A	c.(280-282)GTG>ATG	p.V94M	RBM47_uc003gve.2_Non-coding_Transcript|RBM47_uc003gvd.2_Missense_Mutation_p.V94M|RBM47_uc003gvg.1_Missense_Mutation_p.V94M	NM_001098634	NP_001092104	A0AV96	RBM47_HUMAN	RNA binding motif protein 47 isoform a	94	RRM 1.					nucleus	nucleotide binding|RNA binding			breast(3)	3														0.347826	109.968149	112.317201	40	75	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40135388	40135388	13603	4	C	T	T	19	19	RBM47	T	1	1
DNAH5	1767	broad.mit.edu	36	5	13780679	13780679	+	Silent	SNP	A	G	G			TCGA-06-0171-01	TCGA-06-0171-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:13780679A>G	uc003jfd.2	-	c.11970T>C	c.(11968-11970)TCT>TCC	p.S3990S	DNAH5_uc003jfc.2_Silent_p.S158S	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3990					microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|breast(1)|central_nervous_system(1)|pancreas(1)	17	Lung NSC(4;0.00476)													0.264463	102.948671	109.013648	32	89	AA		KEEP	---	---	---	---	capture			Silent	SNP	13780679	13780679	4787	5	A	G	G	11	11	DNAH5	G	4	4
DNAH5	1767	broad.mit.edu	36	5	13822686	13822686	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0171-01	TCGA-06-0171-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:13822686T>A	uc003jfd.2	-	c.9644A>T	c.(9643-9645)GAG>GTG	p.E3215V	DNAH5_uc003jfc.2_5'Flank	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3215	Stalk (By similarity).|Potential.				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|breast(1)|central_nervous_system(1)|pancreas(1)	17	Lung NSC(4;0.00476)													0.096677	16.64822	70.623064	32	299	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	13822686	13822686	4787	5	T	A	A	54	54	DNAH5	A	4	4
ANKHD1-EIF4EBP3	404734	broad.mit.edu	36	5	139885803	139885803	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0171-01	TCGA-06-0171-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:139885803A>G	uc003lfs.1	+	c.4531A>G	c.(4531-4533)ACC>GCC	p.T1511A	ANKHD1_uc003lfr.1_Missense_Mutation_p.T1511A|ANKHD1_uc003lfu.1_Missense_Mutation_p.T991A|ANKHD1_uc003lfw.1_Missense_Mutation_p.T149A|ANKHD1_uc010jfl.1_5'UTR|ANKHD1-EIF4EBP3_uc003lfx.1_5'Flank	NM_020690	NP_065741	Q8IWZ2	Q8IWZ2_HUMAN	ANKHD1-EIF4EBP3 protein	1511						cytoplasm|nucleus	RNA binding			ovary(6)	6														0.327273	140.283378	144.654706	54	111	AA		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	139885803	139885803	632	5	A	G	G	6	6	ANKHD1-EIF4EBP3	G	4	4
CAMK2A	815	broad.mit.edu	36	5	149588000	149588000	+	Silent	SNP	G	A	A			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:149588000G>A	uc003lrt.1	-	c.1185C>T	c.(1183-1185)GCC>GCT	p.A395A	CAMK2A_uc003lrs.1_Silent_p.A95A|CAMK2A_uc003lru.1_Silent_p.A384A	NM_015981	NP_057065	Q9UQM7	KCC2A_HUMAN	calcium/calmodulin-dependent protein kinase II	384					interferon-gamma-mediated signaling pathway|positive regulation of NF-kappaB transcription factor activity|protein phosphorylation|synaptic transmission	cell junction|cytosol|endocytic vesicle membrane|nucleoplasm|presynaptic membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			large_intestine(1)	1		all_hematologic(541;0.224)								161				0.404494	112.788046	113.496035	36	53	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Silent	SNP	149588000	149588000	2716	5	G	A	A	43	43	CAMK2A	A	2	2
GALNT10	55568	broad.mit.edu	36	5	153740374	153740374	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:153740374G>T	uc003lvh.1	+	c.928G>T	c.(928-930)GAC>TAC	p.D310Y	GALNT10_uc003lvg.1_Missense_Mutation_p.D310Y|GALNT10_uc010jic.1_Non-coding_Transcript|GALNT10_uc010jid.1_Missense_Mutation_p.D151Y	NM_198321	NP_938080	Q86SR1	GLT10_HUMAN	GalNAc transferase 10 isoform a	310	Lumenal (Potential).					Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)												0.240506	43.682809	48.540077	19	60	GG		KEEP	---	---	---	---	capture	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)		Missense_Mutation	SNP	153740374	153740374	6472	5	G	T	T	37	37	GALNT10	T	3	3
HAVCR1	26762	broad.mit.edu	36	5	156415068	156415068	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0171-01	TCGA-06-0171-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:156415068A>G	uc010jij.1	-	c.101T>C	c.(100-102)CTA>CCA	p.L34P	HAVCR1_uc003lwi.2_Missense_Mutation_p.L34P	NM_001099414	NP_036338	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	34	Extracellular (Potential).|Ig-like V-type.				interspecies interaction between organisms	integral to membrane	receptor activity			ovary(1)	1	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)												0.333333	14.138277	14.756259	8	16	AA		KEEP	---	---	---	---	capture	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		Missense_Mutation	SNP	156415068	156415068	7255	5	A	G	G	15	15	HAVCR1	G	4	4
SAMD3	154075	broad.mit.edu	36	6	130546998	130546998	+	Silent	SNP	G	A	A			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:130546998G>A	uc003qbv.1	-	c.597C>T	c.(595-597)GAC>GAT	p.D199D	SAMD3_uc003qbw.1_Silent_p.D199D|SAMD3_uc003qbx.1_Silent_p.D199D|SAMD3_uc010kfg.1_Silent_p.D199D|SAMD3_uc003qby.1_Silent_p.D199D|SAMD3_uc003qbz.1_Silent_p.D158D	NM_001017373	NP_001017373	Q8N6K7	SAMD3_HUMAN	sterile alpha motif domain containing 3 isoform	199										ovary(1)	1														0.41791	82.807409	83.196157	28	39	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(226;0.00594)|OV - Ovarian serous cystadenocarcinoma(155;0.128)	Silent	SNP	130546998	130546998	14300	6	G	A	A	40	40	SAMD3	A	1	1
TCF21	6943	broad.mit.edu	36	6	134252302	134252302	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0171-01	TCGA-06-0171-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:134252302T>C	uc003qei.2	+	c.74T>C	c.(73-75)ATG>ACG	p.M25T	TCF21_uc010kgf.1_Missense_Mutation_p.M25T|TCF21_uc003qej.1_Missense_Mutation_p.M25T	NM_198392	NP_938206	O43680	TCF21_HUMAN	transcription factor 21	25					branching involved in ureteric bud morphogenesis|mesoderm development|negative regulation of androgen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus	androgen receptor binding|E-box binding|protein dimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0	Colorectal(23;0.221)|Breast(56;0.247)									20				0.439655	152.60893	152.976896	51	65	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(68;0.00518)|OV - Ovarian serous cystadenocarcinoma(155;0.00783)	Missense_Mutation	SNP	134252302	134252302	16217	6	T	C	C	51	51	TCF21	C	4	4
MDC1	9656	broad.mit.edu	36	6	30783700	30783700	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0171-01	TCGA-06-0171-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:30783700C>G	uc003nrg.2	-	c.2635G>C	c.(2635-2637)GAA>CAA	p.E879Q	MDC1_uc003nrf.2_Intron	NM_014641	NP_055456	Q14676	MDC1_HUMAN	mediator of DNA damage checkpoint 1	879				Missing (in Ref. 2; CAH18685).	cell cycle|double-strand break repair via homologous recombination|intra-S DNA damage checkpoint	focal adhesion|nucleoplasm	FHA domain binding|protein C-terminus binding			breast(2)|ovary(1)|kidney(1)	4														0.295726	572.849051	594.680441	173	412	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30783700	30783700	9792	6	C	G	G	30	30	MDC1	G	3	3
PKHD1	5314	broad.mit.edu	36	6	51907023	51907023	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:51907023G>A	uc003pah.1	-	c.5965C>T	c.(5965-5967)CTT>TTT	p.L1989F	PKHD1_uc010jzn.1_Missense_Mutation_p.L14F|PKHD1_uc003pai.1_Missense_Mutation_p.L1989F	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	1989	Extracellular (Potential).|G8 1.				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			ovary(12)|large_intestine(5)|central_nervous_system(3)	20	Lung NSC(77;0.0605)									1537		OREG0017491	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.284916	150.980521	158.395032	51	128	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51907023	51907023	12396	6	G	A	A	35	35	PKHD1	A	2	2
TRIM24	8805	broad.mit.edu	36	7	137886376	137886376	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:137886376G>A	uc003vuc.1	+	c.1172G>A	c.(1171-1173)CGT>CAT	p.R391H	TRIM24_uc003vub.1_Missense_Mutation_p.R391H	NM_015905	NP_056989	O15164	TIF1A_HUMAN	transcriptional intermediary factor 1 alpha	391					cellular response to estrogen stimulus|protein catabolic process|regulation of apoptosis|regulation of protein stability|transcription from RNA polymerase II promoter	cytoplasm	chromatin binding|estrogen response element binding|histone acetyl-lysine binding|p53 binding|transcription coactivator activity|ubiquitin-protein ligase activity|zinc ion binding	p.R391H(1)		central_nervous_system(2)|ovary(1)|breast(1)	4						Pancreas(179;936 2074 16128 47811 50326)|Colon(136;168 1735 9344 12243 52014)				258				0.276498	157.611372	167.365907	60	157	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	137886376	137886376	17042	7	G	A	A	40	40	TRIM24	A	1	1
TRPV6	55503	broad.mit.edu	36	7	142283343	142283343	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0171-01	TCGA-06-0171-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:142283343C>A	uc003wbx.1	-	c.1122G>T	c.(1120-1122)CAG>CAT	p.Q374H	TRPV6_uc003wbw.1_Missense_Mutation_p.Q160H|TRPV6_uc010lou.1_Missense_Mutation_p.Q245H	NM_018646	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel,	374	Extracellular (Potential).				regulation of calcium ion-dependent exocytosis	integral to plasma membrane	calcium channel activity|calmodulin binding			ovary(1)	1	Melanoma(164;0.059)													0.253521	90.329218	98.162856	36	106	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	142283343	142283343	17151	7	C	A	A	24	24	TRPV6	A	3	3
NOS3	4846	broad.mit.edu	36	7	150334923	150334923	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0171-01	TCGA-06-0171-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:150334923C>T	uc003wif.1	+	c.1834C>T	c.(1834-1836)CGC>TGC	p.R612C		NM_000603	NP_000594	P29474	NOS3_HUMAN	nitric oxide synthase 3 (endothelial cell)	612	Flavodoxin-like.				anti-apoptosis|arginine catabolic process|blood vessel remodeling|endothelial cell migration|mitochondrion organization|negative regulation of muscle hyperplasia|negative regulation of platelet activation|nitric oxide biosynthetic process|oxidation-reduction process|platelet activation|positive regulation of angiogenesis|positive regulation of guanylate cyclase activity|positive regulation of vasodilation|regulation of blood vessel size|regulation of nitric-oxide synthase activity|regulation of systemic arterial blood pressure by endothelin|response to fluid shear stress|response to heat|smooth muscle hyperplasia	caveola|cytoskeleton|cytosol|Golgi membrane	actin monomer binding|arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			central_nervous_system(5)|large_intestine(2)	7	all_neural(206;0.219)				L-Arginine(DB00125)|L-Citrulline(DB00155)|Rosuvastatin(DB01098)|Tetrahydrobiopterin(DB00360)					755				0.114286	24.478053	50.143625	20	155	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Missense_Mutation	SNP	150334923	150334923	10947	7	C	T	T	23	23	NOS3	T	1	1
TMEM184A	202915	broad.mit.edu	36	7	1554787	1554787	+	Silent	SNP	G	A	A			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:1554787G>A	uc003skv.2	-	c.708C>T	c.(706-708)TAC>TAT	p.Y236Y	TMEM184A_uc003skt.2_Silent_p.Y215Y|TMEM184A_uc003skw.2_Silent_p.Y41Y	NM_001097620	NP_001091089	Q6ZMB5	T184A_HUMAN	transmembrane protein 184A	236	Helical; (Potential).					integral to membrane					0		Ovarian(82;0.0253)												0.255208	115.778268	126.221348	49	143	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;5.88e-15)	Silent	SNP	1554787	1554787	16638	7	G	A	A	40	40	TMEM184A	A	1	1
CCDC129	223075	broad.mit.edu	36	7	31658948	31658948	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:31658948G>T	uc003tcj.1	+	c.3115G>T	c.(3115-3117)GAT>TAT	p.D1039Y	CCDC129_uc003tci.1_Missense_Mutation_p.D890Y|CCDC129_uc003tck.1_Missense_Mutation_p.D947Y	NM_194300	NP_919276	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	1039											0														0.189189	83.407563	103.482825	42	180	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31658948	31658948	2884	7	G	T	T	41	41	CCDC129	T	3	3
RIMS2	9699	broad.mit.edu	36	8	105070789	105070789	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:105070789G>A	uc003yls.2	+	c.2342G>A	c.(2341-2343)CGT>CAT	p.R781H	RIMS2_uc003ylp.2_Missense_Mutation_p.R1003H|RIMS2_uc003ylw.2_Missense_Mutation_p.R795H|RIMS2_uc003ylq.2_Missense_Mutation_p.R795H|RIMS2_uc003ylr.2_Missense_Mutation_p.R842H	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	1065					intracellular protein transport	cell junction|presynaptic membrane	Rab GTPase binding|zinc ion binding			ovary(6)|lung(2)|breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)|pancreas(1)	14										728				0.189024	65.925818	80.766533	31	133	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)		Missense_Mutation	SNP	105070789	105070789	13845	8	G	A	A	40	40	RIMS2	A	1	1
PCMTD1	115294	broad.mit.edu	36	8	52936161	52936161	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:52936161G>A	uc003xqx.2	-	c.104C>T	c.(103-105)GCG>GTG	p.A35V	PCMTD1_uc003xqw.2_Missense_Mutation_p.A35V|PCMTD1_uc010lya.1_Intron	NM_052937	NP_443169	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate)	35						cytoplasm	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity				0		Lung NSC(129;0.0795)|all_lung(136;0.144)												0.106557	8.182828	26.939943	13	109	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	52936161	52936161	12006	8	G	A	A	38	38	PCMTD1	A	1	1
PPP3R2	5535	broad.mit.edu	36	9	103396727	103396727	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0171-01	TCGA-06-0171-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:103396727C>T	uc004bbr.1	-	c.307G>A	c.(307-309)GAC>AAC	p.D103N	GRIN3A_uc004bbp.1_Intron|GRIN3A_uc004bbq.1_Intron|PPP3R2_uc010mtf.1_Non-coding_Transcript	NM_147180	NP_671709	Q96LZ3	CANB2_HUMAN	protein phosphatase 3 regulatory subunit B, beta	100	EF-hand 3.|3.						calcium ion binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(62;0.0527)			Cyclosporine(DB00091)					16				0.333333	175.760757	180.410897	63	126	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	103396727	103396727	12837	9	C	T	T	31	31	PPP3R2	T	1	1
SOHLH1	402381	broad.mit.edu	36	9	137728455	137728455	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:137728455G>A	uc010nbe.1	-	c.485C>T	c.(484-486)GCG>GTG	p.A162V	SOHLH1_uc004cgl.1_Missense_Mutation_p.A162V	NM_001101677	NP_001095147	Q5JUK2	SOLH1_HUMAN	spermatogenesis and oogenesis specific basic	162					cell differentiation|multicellular organismal development|oogenesis|regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|transcription regulator activity			breast(1)|central_nervous_system(1)	2		Myeloproliferative disorder(178;0.0511)												0.244186	47.830027	52.961131	21	65	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;1.66e-07)|Epithelial(140;1.11e-06)|all cancers(34;6.45e-05)	Missense_Mutation	SNP	137728455	137728455	15423	9	G	A	A	38	38	SOHLH1	A	1	1
MAMDC4	158056	broad.mit.edu	36	9	138871822	138871822	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:138871822G>A	uc004cjs.1	+	c.2289G>A	c.(2287-2289)TGG>TGA	p.W763*		NM_206920	NP_996803	Q6UXC1	AEGP_HUMAN	apical early endosomal glycoprotein precursor	842	MAM 5.|Extracellular (Potential).				protein transport	integral to membrane				breast(4)	4	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0511)								290				0.40625	120.368728	121.087343	39	57	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)	Nonsense_Mutation	SNP	138871822	138871822	9587	9	G	A	A	43	43	MAMDC4	A	5	2
GPC4	2239	broad.mit.edu	36	X	132376642	132376642	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0171-01	TCGA-06-0171-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:132376642C>A	uc004exc.1	-	c.18G>T	c.(16-18)TTG>TTT	p.L6F		NM_001448	NP_001439	O75487	GPC4_HUMAN	glypican 4	6					anatomical structure morphogenesis|cell proliferation	anchored to membrane|external side of plasma membrane|extracellular space|insoluble fraction|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	Acute lymphoblastic leukemia(192;0.000127)													0.368421	9.581223	9.921937	7	12	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	132376642	132376642	6874	23	C	A	A	25	25	GPC4	A	3	3
ZMYM3	9203	broad.mit.edu	36	X	70389578	70389578	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0171-01	TCGA-06-0171-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:70389578G>C	uc004dzh.1	-	c.253C>G	c.(253-255)CTG>GTG	p.L85V	ZMYM3_uc004dzi.1_Missense_Mutation_p.L85V|ZMYM3_uc004dzj.1_Missense_Mutation_p.L85V|ZMYM3_uc004dzk.2_Missense_Mutation_p.L85V|ZMYM3_uc004dzl.2_Missense_Mutation_p.L85V|ZMYM3_uc004dzm.2_Missense_Mutation_p.L85V	NM_201599	NP_963893	Q14202	ZMYM3_HUMAN	zinc finger protein 261	85					multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Renal(35;0.156)													0.190476	8.890993	10.769327	4	17	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70389578	70389578	18292	23	G	C	C	34	34	ZMYM3	C	3	3
MTHFR	4524	broad.mit.edu	36	1	11773367	11773367	+	Frame_Shift_Del	DEL	A	-	-			TCGA-06-0171-01	TCGA-06-0171-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:11773367_11773367delA	uc001atb.1	-	c.1997_1997delT	c.(1996-1998)CTCfs	p.L666fs	MTHFR_uc001atc.1_Frame_Shift_Del_p.L643fs	NM_005957	NP_005948	P42898	MTHR_HUMAN	5,10-methylenetetrahydrofolate reductase	643					blood circulation|folic acid metabolic process|oxidation-reduction process	cytosol	methylenetetrahydrofolate reductase (NADPH) activity|protein binding				0	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|Raltitrexed(DB00293)|Riboflavin(DB00140)|S-Adenosylmethionine(DB00118)|Tetrahydrofolic acid(DB00116)									0.49			36	38				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	11773367	11773367	10324	1	A	-	-	11	11	MTHFR	-	5	5
TTN	7273	broad.mit.edu	36	2	179250812	179250812	+	Frame_Shift_Del	DEL	C	-	-			TCGA-06-0171-01	TCGA-06-0171-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179250812_179250812delC	uc002umr.1	-	c.30340_30340delG	c.(30340-30342)GTTfs	p.V10114fs	TTN_uc002ums.1_Intron|TTN_uc010frc.1_Intron|TTN_uc010frd.1_Intron|TTN_uc002umz.1_Frame_Shift_Del_p.V6775fs|TTN_uc010fre.1_Intron|TTN_uc002una.1_Non-coding_Transcript|TTN_uc010frf.1_Non-coding_Transcript	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	11041										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)							8722				0.30			83	190				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	179250812	179250812	17290	2	C	-	-	17	17	TTN	-	5	5
FZD5	7855	broad.mit.edu	36	2	208340106	208340107	+	Frame_Shift_Ins	INS	-	G	G			TCGA-06-0171-01	TCGA-06-0171-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:208340106_208340107insG	uc002vcj.1	-	c.1602_1603insC	c.(1600-1605)ACCAGCfs	p.T534fs	FZD5_uc010ful.1_Frame_Shift_Ins_p.T534fs	NM_003468	NP_003459	Q13467	FZD5_HUMAN	frizzled 5 precursor	534_535	Cytoplasmic (Potential).				angiogenesis|anterior/posterior axis specification, embryo|axonogenesis|brain development|canonical Wnt receptor signaling pathway|cellular response to molecule of bacterial origin|embryonic camera-type eye development|gonad development|labyrinthine layer blood vessel development|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of interferon-gamma production|post-embryonic camera-type eye development|Spemann organizer formation|T cell differentiation in thymus|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	cell projection|cell surface|Golgi membrane|integral to membrane|plasma membrane	G-protein coupled receptor activity|PDZ domain binding|protein kinase binding|Wnt receptor activity|Wnt-protein binding			ovary(2)	2				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.13)|Lung(261;0.134)										0.50			3	3				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	208340106	208340107	6384	2	-	G	G	55	55	FZD5	G	5	5
FRG2	448831	broad.mit.edu	36	4	191183747	191183749	+	In_Frame_Del	DEL	GTT	-	-			TCGA-06-0171-01	TCGA-06-0171-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:191183747_191183749delGTT	uc003izv.1	-	c.798_800delAAC	c.(796-801)ATAACT>ATT	p.T267del		NM_001005217	NP_001005217	Q64ET8	FRG2_HUMAN	FSHD region gene 2	267						nucleus				ovary(1)	1		all_cancers(14;1.01e-50)|all_epithelial(14;6.7e-35)|all_lung(41;2.17e-14)|Lung NSC(41;4.95e-14)|Breast(6;3.4e-05)|Melanoma(20;0.000539)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|all_hematologic(60;0.0489)|Prostate(90;0.0513)		all cancers(3;3.83e-31)|Epithelial(3;1.36e-30)|OV - Ovarian serous cystadenocarcinoma(60;1.99e-15)|BRCA - Breast invasive adenocarcinoma(30;8.54e-06)|Lung(3;3.23e-05)|STAD - Stomach adenocarcinoma(60;8.24e-05)|LUSC - Lung squamous cell carcinoma(40;0.000184)|GBM - Glioblastoma multiforme(59;0.00831)|READ - Rectum adenocarcinoma(43;0.155)										0.50			3	3				---	---	---	---	capture_indel			In_Frame_Del	DEL	191183747	191183749	6295	4	GTT	-	-	36	36	FRG2	-	5	5
