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	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
WASH7P	653635	broad.mit.edu	37	1	14976	14976	+	RNA	SNP	G	A	A			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr1:14976G>A	uc009vis.2	-	3		c.369C>T			WASH7P_uc009vit.2_RNA|WASH7P_uc001aae.3_RNA|WASH7P_uc009viu.2_RNA|WASH7P_uc001aab.3_RNA|WASH7P_uc001aah.3_RNA|WASH7P_uc009vir.2_RNA|WASH7P_uc009viq.2_Intron|WASH7P_uc001aac.3_RNA|WASH7P_uc009viv.2_RNA|WASH7P_uc009viw.2_RNA					Homo sapiens cDNA FLJ31670 fis, clone NT2RI2004984.												0						CTACCCTTGCGCCTCATGACC	0.582000													3	15					0	0	1	0	0
FUCA1	2517	broad.mit.edu	37	1	24194728	24194728	+	Missense_Mutation	SNP	G	C	C			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr1:24194728G>C	uc001bie.2	-	1	94	c.49C>G	c.(49-51)CTG>GTG	p.L17V	FUCA1_uc009vqt.1_RNA|FUCA1_uc010oed.1_RNA	NM_000147	NP_000138	P04066	FUCO_HUMAN	fucosidase, alpha-L-1, tissue precursor	17					fucose metabolic process|glycosaminoglycan catabolic process	lysosome	alpha-L-fucosidase activity|cation binding			breast(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144)		AGCAGCAGCAGCAACAGCGCG	0.746000													2	2					0	0	1	0	0
ABCA4	24	broad.mit.edu	37	1	94528252	94528252	+	Silent	SNP	G	T	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr1:94528252G>T	uc001dqh.2	-	13	1922	c.1818C>A	c.(1816-1818)GGC>GGA	p.G606G	ABCA4_uc010otn.1_Silent_p.G606G	NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	606	Extracellular.				phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		AGGCAAACCCGCCCCAGATGT	0.562000													10	30					0.000442599	0.000442599	1	1	0
LOC650623	650623	broad.mit.edu	37	10	81444193	81444193	+	RNA	SNP	T	C	C			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr10:81444193T>C	uc010qlu.1	+	1		c.1463T>C				NR_027512				Homo sapiens BEN domain containing 3 pseudogene (LOC650623), non-coding RNA.												0						ACGACAAGCTTCAGGGCCTGG	0.627000													2	12					0	0	1	0	0
COMMD9	29099	broad.mit.edu	37	11	36293264	36293264	+	RNA	SNP	G	A	A			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr11:36293264G>A	uc009yki.1	-	2		c.308C>T						Q9P000	COMD9_HUMAN	Homo sapiens cDNA FLJ45212 fis, clone BRCAN2018667.											ovary(1)	1	all_lung(20;0.211)	all_hematologic(20;0.107)				CAGGTACCAAGATTTTCTCAT	0.418000													9	36					0	0	1	0	0
ANKK1	255239	broad.mit.edu	37	11	113267965	113267965	+	Silent	SNP	C	T	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr11:113267965C>T	uc001pny.2	+	6	952	c.858C>T	c.(856-858)GAC>GAT	p.D286D		NM_178510	NP_848605	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	286	Protein kinase.						ATP binding|protein serine/threonine kinase activity			lung(5)|stomach(1)|ovary(1)|breast(1)	8		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		TCGAGACAGACATACTGCTGT	0.582000													10	37					0	0	1	0	0
FMNL3	91010	broad.mit.edu	37	12	50043069	50043069	+	Silent	SNP	A	G	G			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr12:50043069A>G	uc001ruv.1	-	20	2592	c.2358T>C	c.(2356-2358)TAT>TAC	p.Y786Y	FMNL3_uc001ruw.1_Silent_p.Y735Y|FMNL3_uc001rut.1_Silent_p.Y352Y|FMNL3_uc001ruu.1_Silent_p.Y636Y	NM_175736	NP_783863	Q8IVF7	FMNL3_HUMAN	formin-like 3 isoform 1	786	FH2.				actin cytoskeleton organization		actin binding|Rho GTPase binding			breast(2)|pancreas(2)	4						GCTTGAAGCCATACACAGCTC	0.572000													14	94					0	0	1	0	0
PTPN11	5781	broad.mit.edu	37	12	112888197	112888197	+	Missense_Mutation	SNP	T	A	A			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr12:112888197T>A	uc001ttx.2	+	3	593	c.213T>A	c.(211-213)TTT>TTA	p.F71L	PTPN11_uc001ttw.1_Missense_Mutation_p.F71L	NM_002834	NP_002825	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type	71	SH2 1.		F -> K (in acute myeloid leukemia; requires 2 nucleotide substitutions).|F -> L (in myelodysplastic syndrome).		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.F71L(5)|p.F71K(2)		haematopoietic_and_lymphoid_tissue(375)|lung(6)|autonomic_ganglia(2)|soft_tissue(2)|central_nervous_system(2)|large_intestine(1)|skin(1)|ovary(1)|NS(1)|kidney(1)	392						GGGAGAAATTTGCCACTTTGG	0.418000			Mis		JMML|AML|MDS		Noonan Syndrome		Noonan_syndrome				50	97					0	0	1	0	0
C15orf2	23742	broad.mit.edu	37	15	24921605	24921605	+	Silent	SNP	C	T	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr15:24921605C>T	uc001ywo.2	+	1	1065	c.591C>T	c.(589-591)GAC>GAT	p.D197D		NM_018958	NP_061831	Q9NZP6	CO002_HUMAN	hypothetical protein LOC23742	197					cell differentiation|multicellular organismal development|spermatogenesis					ovary(2)|large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1)	8		all_cancers(20;2.14e-21)|all_epithelial(15;4.77e-19)|Lung NSC(15;1.43e-14)|all_lung(15;9.57e-14)|Breast(32;0.00086)		all cancers(64;3.19e-24)|Epithelial(43;2.67e-17)|GBM - Glioblastoma multiforme(186;7.36e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000273)|Lung(196;0.229)		CCCAGGGAGACGTGGCCTCCT	0.592000													6	44					0	0	1	0	0
C15orf21	283651	broad.mit.edu	37	15	45848224	45848224	+	RNA	SNP	G	T	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr15:45848224G>T	uc010beg.1	+	6		c.1219G>T			C15orf21_uc010beh.1_RNA|C15orf21_uc010bei.1_RNA|C15orf21_uc010bej.1_RNA|C15orf21_uc001zvm.1_RNA|C15orf21_uc001zvn.1_RNA					Homo sapiens cDNA FLJ39426 fis, clone PROST2000505.												0		Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;3.03e-17)|GBM - Glioblastoma multiforme(94;7.36e-07)		TGCAGATTTTGTTTAGCTTTT	0.318000			T	ETV1	prostate								8	19					1.76689e-08	1.84721e-08	1	1	0
KLHL25	64410	broad.mit.edu	37	15	86311637	86311637	+	Missense_Mutation	SNP	C	T	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr15:86311637C>T	uc002bly.2	-	2	1608	c.1405G>A	c.(1405-1407)GAG>AAG	p.E469K		NM_022480	NP_071925	Q9H0H3	ENC2_HUMAN	BTB/POZ KELCH domain protein	469	Kelch 4.					cytoplasm				ovary(2)	2						CACCTGTTCTCCGAGGGGTCA	0.602000													18	137					0	0	1	0	0
C16orf7	9605	broad.mit.edu	37	16	89785502	89785502	+	Silent	SNP	G	A	A			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr16:89785502G>A	uc002fom.1	-	2	233	c.108C>T	c.(106-108)TAC>TAT	p.Y36Y	C16orf7_uc002fol.1_5'UTR|ZNF276_uc010ciq.2_5'Flank|ZNF276_uc002fop.2_5'Flank|ZNF276_uc002foq.3_5'Flank|ZNF276_uc010cir.2_5'Flank|ZNF276_uc002for.3_5'Flank|ZNF276_uc010cis.2_5'Flank|ZNF276_uc002fos.3_5'Flank|ZNF276_uc002fot.3_5'Flank	NM_004913	NP_004904	Q9Y2B5	CP007_HUMAN	chromosome 16 open reading frame 7	36					ATP synthesis coupled proton transport		GTPase activator activity|transporter activity				0		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0273)		GGTATTCCGTGTATGCCTCCT	0.473000													17	107					0	0	1	0	0
NF1	4763	broad.mit.edu	37	17	29576001	29576001	+	Splice_Site	SNP	G	A	A			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr17:29576001G>A	uc002hgg.2	+	30	4308	c.3975_splice	c.e30-1	p.R1325_splice	NF1_uc002hgh.2_Splice_Site_p.R1325_splice|NF1_uc010csn.1_Splice_Site_p.R1185_splice|NF1_uc002hgi.1_Splice_Site_p.R358_splice	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1						actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(2)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TTTTTTTGTAGGTTAGAACCA	0.368000			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			48	36					0	0	1	0	0
Unknown	0	broad.mit.edu	37	17	39296466	39296466	+	RNA	SNP	G	A	A	rs35985080	by1000genomes	TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr17:39296466G>A	uc010cxk.1	-	1		c.238C>T								Homo sapiens partial mRNA for keratin associated protein 4.6 (KRTAP4.6 gene).																		CAGCACTGGGGTCTGCAGCAG	0.542000													6	70					0	0	1	0	0
APOC1P1	342	broad.mit.edu	37	19	45430280	45430280	+	RNA	SNP	C	G	G	rs5112	by1000genomes	TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr19:45430280C>G	uc010eju.2	+	1		c.220C>G								Homo sapiens clone DKFZp781C1677 mRNA sequence.												0						TTCTGTCGATCGTCTTGGAAG	0.607000													3	13					0	0	1	0	0
C19orf63	284361	broad.mit.edu	37	19	50981247	50981247	+	Nonsense_Mutation	SNP	C	G	G			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr19:50981247C>G	uc002psl.2	+	2	242	c.176C>G	c.(175-177)TCA>TGA	p.S59*	FAM71E1_uc002psg.2_5'Flank|FAM71E1_uc002psh.2_5'Flank|FAM71E1_uc002psi.2_5'Flank|C19orf63_uc002psj.2_Nonsense_Mutation_p.S59*|C19orf63_uc002psk.2_Nonsense_Mutation_p.S59*	NM_206538	NP_996261	Q5UCC4	INM02_HUMAN	hematopoietic signal peptide-containing isoform	59	Extracellular (Potential).					extracellular region|integral to membrane					0		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00733)|GBM - Glioblastoma multiforme(134;0.0252)		CTGGAGCACTCATTTGAGATC	0.607000													3	34					0	0	1	0	0
Unknown	0	broad.mit.edu	37	21	15399864	15399864	+	RNA	SNP	T	C	C	rs2298673	by1000genomes	TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr21:15399864T>C	uc002yjk.2	+	1		c.123T>C			uc002yjl.2_RNA					Homo sapiens, clone IMAGE:4102980, mRNA.																		TGTGACCTGCTGGCATTGAAT	0.587000													4	49					0	0	1	0	0
LOC348926	348926	broad.mit.edu	37	4	3948570	3948570	+	RNA	SNP	G	A	A			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr4:3948570G>A	uc011bvu.1	-	5		c.1765C>T			LOC348926_uc003ghn.2_Intron	NR_024253				Homo sapiens hypothetical protein LOC348926, mRNA (cDNA clone IMAGE:4546485), partial cds.												0						GGAGCCCGCTGGTGCTCCCGG	0.622000													4	53					0	0	1	0	0
TET2	54790	broad.mit.edu	37	4	106155166	106155166	+	Missense_Mutation	SNP	C	T	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr4:106155166C>T	uc003hxk.2	+	3	453	c.67C>T	c.(67-69)CCC>TCC	p.P23S	TET2_uc011cez.1_Missense_Mutation_p.P44S|TET2_uc003hxj.2_RNA|TET2_uc010ilp.1_Missense_Mutation_p.P23S|TET2_uc003hxi.1_Missense_Mutation_p.P23S	NM_001127208	NP_001120680	Q6N021	TET2_HUMAN	tet oncogene family member 2 isoform a	23					cell cycle|myeloid cell differentiation		metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			haematopoietic_and_lymphoid_tissue(732)|pancreas(1)	733		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		ACCATCACCTCCCATTTGCCA	0.527000			Mis N|F		MDS								11	43					0	0	1	0	0
NAA15	80155	broad.mit.edu	37	4	140262069	140262069	+	Nonsense_Mutation	SNP	G	A	A			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr4:140262069G>A	uc003ihu.1	+	4	504	c.248G>A	c.(247-249)TGG>TAG	p.W83*		NM_057175	NP_476516	Q9BXJ9	NAA15_HUMAN	NMDA receptor regulated 1	83	TPR 2.				angiogenesis|cell differentiation|N-terminal protein amino acid acetylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|transcription factor complex	protein binding			ovary(1)|skin(1)	2						TCTTTAGGTTGGCACGTTTAT	0.363000													26	51					0	0	1	0	0
DUSP22	56940	broad.mit.edu	37	6	348272	348272	+	Nonsense_Mutation	SNP	C	T	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr6:348272C>T	uc003msx.2	+	6	872	c.433C>T	c.(433-435)CAG>TAG	p.Q145*	DUSP22_uc011dhn.1_Nonsense_Mutation_p.Q145*|DUSP22_uc003msy.1_Nonsense_Mutation_p.Q102*	NM_020185	NP_064570	Q9NRW4	DUS22_HUMAN	dual specificity phosphatase 22	145					apoptosis|cell proliferation|inactivation of MAPK activity|multicellular organismal development|positive regulation of JNK cascade|regulation of cell proliferation|transforming growth factor beta receptor signaling pathway	cytoplasm|nucleus	protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	all_hematologic(77;0.228)	Breast(5;0.0249)|all_hematologic(90;0.0489)		OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669)		TGAGGTCCATCAGGTAAGCAG	0.577000													14	132					0	0	1	0	0
OR10C1	442194	broad.mit.edu	37	6	29407957	29407957	+	Missense_Mutation	SNP	G	T	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr6:29407957G>T	uc011dlp.1	+	1	165	c.165G>T	c.(163-165)CAG>CAT	p.Q55H	OR11A1_uc010jrh.1_Intron	NM_013941	NP_039229	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C,	55	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						CTGCCCTCCAGTCCCCTATGT	0.567000													20	159					5.35267e-07	5.47161e-07	1	1	0
DNAH8	1769	broad.mit.edu	37	6	38810444	38810444	+	Missense_Mutation	SNP	G	A	A			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr6:38810444G>A	uc003ooe.1	+	33	4559	c.3959G>A	c.(3958-3960)CGT>CAT	p.R1320H		NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						GAAAGATGTCGTAAACTTCCA	0.323000													24	67					0	0	1	0	0
POU6F2	11281	broad.mit.edu	37	7	39500263	39500263	+	Missense_Mutation	SNP	A	C	C			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr7:39500263A>C	uc003thb.1	+	9	1562	c.1520A>C	c.(1519-1521)CAG>CCG	p.Q507P		NM_007252	NP_009183	P78424	PO6F2_HUMAN	POU class 6 homeobox 2 isoform 1	507	POU-specific.				central nervous system development|ganglion mother cell fate determination|transcription from RNA polymerase II promoter|visual perception		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1						CAGGTGGGACAGGCTCTCAGT	0.602000													6	11					0	0	1	0	0
EXOC4	60412	broad.mit.edu	37	7	133749244	133749244	+	Missense_Mutation	SNP	A	G	G			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr7:133749244A>G	uc003vrk.2	+	18	2923	c.2888A>G	c.(2887-2889)AAG>AGG	p.K963R	EXOC4_uc011kpo.1_Missense_Mutation_p.K862R|EXOC4_uc003vrl.2_Missense_Mutation_p.K573R|EXOC4_uc011kpp.1_Missense_Mutation_p.K495R|EXOC4_uc011kpq.1_Missense_Mutation_p.K251R	NM_021807	NP_068579	Q96A65	EXOC4_HUMAN	SEC8 protein isoform a	963					vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)				GCTGCCATCAAGCAAGCCACC	0.572000													21	68					0	0	1	0	0
UBR5	51366	broad.mit.edu	37	8	103266680	103266680	+	Silent	SNP	G	A	A			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr8:103266680G>A	uc003ykr.1	-	59	8283	c.8250C>T	c.(8248-8250)CCC>CCT	p.P2750P	UBR5_uc003yks.1_Silent_p.P2749P|UBR5_uc003ykq.2_Silent_p.P261P	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	2750	Pro-rich.|HECT.				cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			TTGTGATTGAGGGCATAGGCT	0.408000													10	68					0	0	1	0	0
APEX2	27301	broad.mit.edu	37	X	55033116	55033116	+	Missense_Mutation	SNP	C	T	T	rs145122391		TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chrX:55033116C>T	uc004dtz.2	+	6	881	c.805C>T	c.(805-807)CAT>TAT	p.H269Y	APEX2_uc011mom.1_Missense_Mutation_p.H98Y	NM_014481	NP_055296	Q9UBZ4	APEX2_HUMAN	apurinic/apyrimidinic endonuclease 2	269			H -> Y (identified in a patient with mtDNA maintenance disorders).	H->A: Abolishes AP endodeoxyribonuclease, 3'-5' exonuclease activity and 3'- phosphodiesterase activities.	cell cycle|DNA recombination|DNA repair	nucleus	DNA binding|DNA-(apurinic or apyrimidinic site) lyase activity|endonuclease activity|exonuclease activity|zinc ion binding			breast(1)	1						TGGCGCCCGCCATCTCAACTA	0.597000								Other_BER_factors					3	22					0	0	1	0	0
ST8SIA6	338596	broad.mit.edu	37	10	17495614	17495614	+	Frame_Shift_Del	DEL	G	-	-			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr10:17495614delG	uc001ipd.2	-	2	144	c.144delC	c.(142-144)CCCfs	p.P48fs	ST8SIA6_uc010qce.1_RNA	NM_001004470	NP_001004470	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide	48	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(1)	1						TCAGCGCTGCGGGGGTGCCGT	0.697													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	16	53403273	53403273	+	RNA	DEL	A	-	-			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr16:53403273delA	uc002ehh.2	-	2		c.1186delT								Homo sapiens mRNA; cDNA DKFZp313P036 (from clone DKFZp313P036).																		actccatctcaaaaaaaaaag	0.129													3	5	---	---	---	---					
PLA2G15	23659	broad.mit.edu	37	16	68293167	68293171	+	Frame_Shift_Del	DEL	CGTGC	-	-	rs142263893		TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr16:68293167_68293171delCGTGC	uc002evr.2	+	6	929_933	c.846_850delCGTGC	c.(844-852)TTCGTGCAGfs	p.F282fs	PLA2G15_uc010vld.1_3'UTR|PLA2G15_uc010vle.1_Frame_Shift_Del_p.F188fs|PLA2G15_uc010vlf.1_Frame_Shift_Del_p.F82fs|PLA2G15_uc002evs.2_Frame_Shift_Del_p.F103fs	NM_012320	NP_036452	Q8NCC3	PAG15_HUMAN	lysophospholipase 3 (lysosomal phospholipase A2)	282_284					fatty acid catabolic process	extracellular region|lysosome	lysophospholipase activity|phosphatidylcholine-sterol O-acyltransferase activity|phospholipid binding			ovary(1)	1						AGAAGGTGTTCGTGCAGACACCCAC	0.580													16	67	---	---	---	---					
PSME4	23198	broad.mit.edu	37	2	54148047	54148049	+	In_Frame_Del	DEL	AGG	-	-			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr2:54148047_54148049delAGG	uc002rxp.2	-	18	2295_2297	c.2239_2241delCCT	c.(2239-2241)CCTdel	p.P747del	PSME4_uc010yop.1_In_Frame_Del_p.P633del|PSME4_uc010yoq.1_RNA|PSME4_uc010fbu.1_In_Frame_Del_p.P122del|PSME4_uc010fbv.1_Intron	NM_014614	NP_055429	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator	747					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			ovary(2)|breast(2)|pancreas(1)	5			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			AGTATTCAGAAGGAGGCTTGTCA	0.374													22	75	---	---	---	---					
C4orf17	84103	broad.mit.edu	37	4	100443784	100443785	+	Frame_Shift_Ins	INS	-	G	G	rs61732380	byFrequency	TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr4:100443784_100443785insG	uc003huw.2	+	3	578_579	c.255_256insG	c.(253-258)CCGAGCfs	p.P85fs	C4orf17_uc003hux.2_RNA	NM_032149	NP_115525	Q53FE4	CD017_HUMAN	hypothetical protein LOC84103	85_86											0				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)		GTTACCCCTCCAGCACTGCAGT	0.500													7	93	---	---	---	---					
ATRX	546	broad.mit.edu	37	X	76814303	76814306	+	Frame_Shift_Del	DEL	ATAA	-	-			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chrX:76814303_76814306delATAA	uc004ecp.3	-	29	6570_6573	c.6338_6341delTTAT	c.(6337-6342)TTTATCfs	p.F2113fs	ATRX_uc004ecq.3_Frame_Shift_Del_p.F2075fs|ATRX_uc004eco.3_Frame_Shift_Del_p.F1898fs	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	2113_2114	Helicase C-terminal.				DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding	p.F2113fs*9(1)		haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	AGTAGAAATGATAAATAATCGTCC	0.289			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						18	68	---	---	---	---					
