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	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	filter
MTOR	2475	broad.mit.edu	37	1	11188164	11188164	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11188164G>C	uc001asd.2	-	43	6051	c.5930C>G	c.(5929-5931)ACA>AGA	p.T1977R	MTOR_uc001asc.2_Missense_Mutation_p.T182R	NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	1977	FAT.				cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29						AGAAGCCACTGTCAGTGGGTA	0.478													10	112	---	---	---	---	PASS
RPE65	6121	broad.mit.edu	37	1	68906582	68906582	+	Missense_Mutation	SNP	A	T	T	rs141527042		TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68906582A>T	uc001dei.1	-	6	651	c.597T>A	c.(595-597)AAT>AAA	p.N199K		NM_000329	NP_000320	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein	199					visual perception	cytoplasm|plasma membrane	all-trans-retinyl-palmitate hydrolase activity|metal ion binding|retinol isomerase activity			ovary(1)	1						CAATTGAAAAATTTTTTCCAA	0.388													3	102	---	---	---	---	PASS
VAV3	10451	broad.mit.edu	37	1	108307709	108307709	+	Silent	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108307709G>A	uc001dvk.1	-	9	964	c.910C>T	c.(910-912)CTG>TTG	p.L304L	VAV3_uc010ouw.1_Silent_p.L304L|VAV3_uc001dvl.1_Silent_p.L128L|VAV3_uc010oux.1_Silent_p.L304L	NM_006113	NP_006104	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor isoform	304	DH.				angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(5)|lung(2)|breast(2)	9		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		TCTAATTTCAGTTTGACATCT	0.353													40	59	---	---	---	---	PASS
PSRC1	84722	broad.mit.edu	37	1	109824423	109824423	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109824423G>A	uc001dxg.2	-	4	459	c.337C>T	c.(337-339)CGG>TGG	p.R113W	PSRC1_uc001dxb.2_5'UTR|PSRC1_uc001dxc.2_Missense_Mutation_p.R113W|PSRC1_uc001dxd.2_Missense_Mutation_p.R113W|PSRC1_uc001dxe.2_Missense_Mutation_p.R113W|PSRC1_uc001dxf.2_Missense_Mutation_p.R113W|PSRC1_uc001dxh.2_Missense_Mutation_p.R113W|PSRC1_uc001dxi.2_Missense_Mutation_p.R113W|PSRC1_uc001dxj.2_Missense_Mutation_p.R113W	NM_001032290	NP_001027461	Q6PGN9	PSRC1_HUMAN	proline/serine-rich coiled-coil 1 isoform c	113	4 X 4 AA repeats of P-X-X-P.				cell division|microtubule bundle formation|mitotic metaphase plate congression|negative regulation of cell growth|positive regulation of microtubule polymerization|positive regulation of transcription, DNA-dependent|regulation of mitotic spindle organization	cytosol|midbody|spindle pole	microtubule binding				0		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0286)|Lung(183;0.0658)|COAD - Colon adenocarcinoma(174;0.112)|Epithelial(280;0.188)|all cancers(265;0.213)		GTCTCCCGCCGAGGACTGGGC	0.672													38	41	---	---	---	---	PASS
WDR77	79084	broad.mit.edu	37	1	111983947	111983947	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111983947G>C	uc001ebb.2	-	10	973	c.934C>G	c.(934-936)CTG>GTG	p.L312V	WDR77_uc010owd.1_RNA|WDR77_uc010owe.1_Missense_Mutation_p.L248V	NM_024102	NP_077007	Q9BQA1	MEP50_HUMAN	WD repeat domain 77	312					ncRNA metabolic process|spliceosomal snRNP assembly	cytosol|nucleus	ligand-dependent nuclear receptor transcription coactivator activity|protein binding				0		all_cancers(81;0.000902)|all_epithelial(167;0.00056)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0238)|Colorectal(144;0.0296)|all cancers(265;0.0488)|Epithelial(280;0.0732)|COAD - Colon adenocarcinoma(174;0.114)|LUSC - Lung squamous cell carcinoma(189;0.135)		GTGGTAAGCAGGGAGTGATTG	0.537													13	130	---	---	---	---	PASS
AP4B1	10717	broad.mit.edu	37	1	114442814	114442814	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114442814G>A	uc001eeb.2	-	5	969	c.826C>T	c.(826-828)CGG>TGG	p.R276W	uc001edv.1_RNA|AP4B1_uc001eec.2_Missense_Mutation_p.R108W|AP4B1_uc001eed.2_Missense_Mutation_p.R276W|AP4B1_uc010owp.1_Missense_Mutation_p.R177W|AP4B1_uc001eea.1_Missense_Mutation_p.R70W|AP4B1_uc010owq.1_Missense_Mutation_p.R183W	NM_006594	NP_006585	Q9Y6B7	AP4B1_HUMAN	adaptor-related protein complex 4, beta 1	276					intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|soluble fraction|trans-Golgi network	protein binding|protein transporter activity			ovary(3)|central_nervous_system(1)	4	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.1e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CCCTTGACCCGCACAAGGACA	0.483													13	101	---	---	---	---	PASS
NBPF9	400818	broad.mit.edu	37	1	144829067	144829067	+	Intron	SNP	A	G	G			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144829067A>G	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|uc001elr.3_RNA			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						TAGCTACAAAATTCCTCAGGG	0.443													2	7	---	---	---	---	PASS
LCE2D	353141	broad.mit.edu	37	1	152636835	152636835	+	Missense_Mutation	SNP	G	A	A	rs113433987		TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152636835G>A	uc001fag.2	+	2	309	c.254G>A	c.(253-255)CGG>CAG	p.R85Q		NM_178430	NP_848517	Q5TA82	LCE2D_HUMAN	late cornified envelope 2D	85	Cys-rich.				keratinization						0	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CACCGGCGCCGGCACCAGAGC	0.677													35	52	---	---	---	---	PASS
OR10T2	128360	broad.mit.edu	37	1	158368837	158368837	+	Silent	SNP	C	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158368837C>T	uc010pih.1	-	1	420	c.420G>A	c.(418-420)AGG>AGA	p.R140R		NM_001004475	NP_001004475	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T,	140	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3	all_hematologic(112;0.0378)					CCAACCCCAGCCTTTTGTTTA	0.473													7	202	---	---	---	---	PASS
OR6K6	128371	broad.mit.edu	37	1	158725158	158725158	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158725158C>A	uc001fsw.1	+	1	553	c.553C>A	c.(553-555)CTT>ATT	p.L185I		NM_001005184	NP_001005184	Q8NGW6	OR6K6_HUMAN	olfactory receptor, family 6, subfamily K,	185	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	all_hematologic(112;0.0378)					CCTCCTTGTGCTTCCTGAGAT	0.488													7	122	---	---	---	---	PASS
C1orf125	126859	broad.mit.edu	37	1	179452332	179452332	+	Silent	SNP	C	T	T	rs141202947		TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179452332C>T	uc001gmo.2	+	18	2194	c.2067C>T	c.(2065-2067)AAC>AAT	p.N689N	C1orf125_uc009wxg.2_RNA|C1orf125_uc010pnl.1_RNA|C1orf125_uc001gmp.2_Silent_p.N689N	NM_144696	NP_653297	Q5T1B0	AXDN1_HUMAN	hypothetical protein LOC126859 isoform 1	689											0						AAATTAACAACGGTAACATTG	0.348													38	144	---	---	---	---	PASS
C1orf116	79098	broad.mit.edu	37	1	207195320	207195320	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207195320C>T	uc001hfd.2	-	4	2048	c.1789G>A	c.(1789-1791)GGA>AGA	p.G597R	C1orf116_uc009xcb.1_Missense_Mutation_p.G351R	NM_023938	NP_076427	Q9BW04	SARG_HUMAN	specifically androgen-regulated protein isoform	597						cytoplasm|plasma membrane	receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4	Prostate(682;0.19)					TTCAACAGTCCCAGCTTCTTC	0.562													4	106	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237969520	237969520	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237969520C>A	uc001hyl.1	+	99	14355	c.14235C>A	c.(14233-14235)GAC>GAA	p.D4745E	RYR2_uc010pyb.1_Missense_Mutation_p.D178E	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	4745					cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ACCTTCTCGACATTGCTATGG	0.393													27	77	---	---	---	---	PASS
APOB	338	broad.mit.edu	37	2	21229067	21229067	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21229067C>T	uc002red.2	-	26	10801	c.10673G>A	c.(10672-10674)CGC>CAC	p.R3558H		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	3558					cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|skin(9)|central_nervous_system(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)	GGAATATATGCGTTGGAGTGT	0.463													49	90	---	---	---	---	PASS
C2orf71	388939	broad.mit.edu	37	2	29295481	29295481	+	Silent	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29295481G>A	uc002rmt.1	-	1	1647	c.1647C>T	c.(1645-1647)AGC>AGT	p.S549S		NM_001029883	NP_001025054	A6NGG8	CB071_HUMAN	hypothetical protein LOC388939	549					response to stimulus|visual perception	photoreceptor outer segment				skin(1)	1						TGATCCTTTCGCTGATTGACT	0.582													48	101	---	---	---	---	PASS
ITPRIPL1	150771	broad.mit.edu	37	2	96993657	96993657	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96993657C>T	uc002svx.2	+	3	1623	c.1288C>T	c.(1288-1290)CGG>TGG	p.R430W	ITPRIPL1_uc010yuk.1_Missense_Mutation_p.R422W|ITPRIPL1_uc002svy.2_Missense_Mutation_p.R438W|ITPRIPL1_uc010yul.1_Missense_Mutation_p.R422W	NM_001008949	NP_001008949	Q6GPH6	IPIL1_HUMAN	inositol 1,4,5-triphosphate receptor interacting	430	Cytoplasmic (Potential).					integral to membrane				central_nervous_system(2)|ovary(1)	3						TTTAAGTCTCCGGCAGCATCA	0.557													4	183	---	---	---	---	PASS
DDX11L2	84771	broad.mit.edu	37	2	114357543	114357543	+	3'UTR	SNP	T	A	A	rs114684815	by1000genomes	TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114357543T>A	uc010yxx.1	-	3										SubName: Full=DEAD/H box polypeptide 11 like 2;												0						CCTGTCAGGATGAGGCCTACT	0.572													3	15	---	---	---	---	PASS
DDX11L2	84771	broad.mit.edu	37	2	114357557	114357557	+	Nonstop_Mutation	SNP	A	G	G	rs115341812	by1000genomes	TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114357557A>G	uc010yxx.1	-	3	709	c.382T>C	c.(382-384)TAG>CAG	p.*128Q						SubName: Full=DEAD/H box polypeptide 11 like 2;												0						GCCTACTTCTAGTGAAACTGG	0.567													4	18	---	---	---	---	PASS
METTL5	29081	broad.mit.edu	37	2	170677648	170677648	+	Silent	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170677648G>A	uc002ufn.2	-	3	606	c.360C>T	c.(358-360)TTC>TTT	p.F120F	METTL5_uc002ufo.2_Silent_p.F120F|METTL5_uc002ufp.2_Silent_p.F120F|METTL5_uc002ufq.1_Silent_p.F120F	NM_014168	NP_054887	Q9NRN9	METL5_HUMAN	methyltransferase like 5	120							methyltransferase activity|nucleic acid binding			central_nervous_system(1)	1						TTACTGTATCGAATGACTTGG	0.303													4	117	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179486462	179486462	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179486462T>G	uc010zfg.1	-	194	37609	c.37385A>C	c.(37384-37386)GAA>GCA	p.E12462A	TTN_uc010zfh.1_Missense_Mutation_p.E6157A|TTN_uc010zfi.1_Missense_Mutation_p.E6090A|TTN_uc010zfj.1_Missense_Mutation_p.E5965A	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	13389							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			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)			AAAGACAGCTTCTTCTTCTGC	0.353													9	66	---	---	---	---	PASS
COL3A1	1281	broad.mit.edu	37	2	189874962	189874962	+	Silent	SNP	T	C	C			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189874962T>C	uc002uqj.1	+	49	3999	c.3882T>C	c.(3880-3882)TGT>TGC	p.C1294C		NM_000090	NP_000081	P02461	CO3A1_HUMAN	collagen type III alpha 1 preproprotein	1294	Fibrillar collagen NC1.				axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway	collagen type III|extracellular space	extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding			central_nervous_system(7)|ovary(4)|large_intestine(2)	13			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)|Palifermin(DB00039)	AGGTATTCTGTAATATGGAAA	0.403													45	132	---	---	---	---	PASS
SPHKAP	80309	broad.mit.edu	37	2	228890232	228890232	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228890232C>T	uc002vpq.2	-	5	366	c.319G>A	c.(319-321)GTT>ATT	p.V107I	SPHKAP_uc002vpp.2_Missense_Mutation_p.V107I|SPHKAP_uc010zlx.1_Missense_Mutation_p.V107I	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	107						cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		TCTGGTGAAACGTTGACCAGT	0.348													28	151	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195505836	195505836	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195505836G>C	uc011bto.1	-	3	12691	c.12231C>G	c.(12229-12231)CAC>CAG	p.H4077Q	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGGCGTGACCTGTGG	0.597													2	3	---	---	---	---	PASS
SEL1L3	23231	broad.mit.edu	37	4	25783976	25783976	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25783976T>C	uc003gru.3	-	15	2497	c.2345A>G	c.(2344-2346)AAA>AGA	p.K782R	SEL1L3_uc003grv.2_Missense_Mutation_p.K189R	NM_015187	NP_056002	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3	782	Sel1-like 5.					integral to membrane	binding				0						CTTTGCTGCTTTGGCGTAATT	0.418													58	110	---	---	---	---	PASS
PDZD2	23037	broad.mit.edu	37	5	32087621	32087621	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32087621G>A	uc003jhl.2	+	20	4455	c.4067G>A	c.(4066-4068)GGT>GAT	p.G1356D	PDZD2_uc003jhm.2_Missense_Mutation_p.G1356D	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2	1356					cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9						GGAGCTCCAGGTAACCACAGT	0.597													4	29	---	---	---	---	PASS
SLC27A6	28965	broad.mit.edu	37	5	128362928	128362928	+	Missense_Mutation	SNP	T	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128362928T>A	uc003kuy.2	+	8	1754	c.1358T>A	c.(1357-1359)TTT>TAT	p.F453Y	SLC27A6_uc003kuz.2_Missense_Mutation_p.F453Y	NM_014031	NP_054750	Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid	453					long-chain fatty acid transport|transmembrane transport|very long-chain fatty acid metabolic process	integral to membrane|sarcolemma	fatty acid transporter activity|long-chain fatty acid-CoA ligase activity|nucleotide binding				0		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)		TGTGATGTTTTTAAGAAGGGA	0.393													96	222	---	---	---	---	PASS
TTC1	7265	broad.mit.edu	37	5	159492140	159492140	+	3'UTR	SNP	G	C	C			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159492140G>C	uc003lxu.2	+	8						NM_003314	NP_003305	Q99614	TTC1_HUMAN	tetratricopeptide repeat domain 1						protein folding		unfolded protein binding			skin(1)	1	Renal(175;0.00196)	all_hematologic(541;0.00014)|Breast(839;0.0101)|all_neural(177;0.0281)|Medulloblastoma(196;0.0425)|Lung NSC(249;0.119)|all_lung(500;0.163)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	Epithelial(171;8.37e-05)|all cancers(165;0.000694)|OV - Ovarian serous cystadenocarcinoma(192;0.0402)		TAGGGGAAAGGCCCTGCCAAT	0.383													5	58	---	---	---	---	PASS
FBXW11	23291	broad.mit.edu	37	5	171299983	171299983	+	Silent	SNP	C	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171299983C>A	uc003mbm.1	-	9	1541	c.1170G>T	c.(1168-1170)ACG>ACT	p.T390T	FBXW11_uc011dey.1_Silent_p.T358T|FBXW11_uc003mbl.1_Silent_p.T377T|FBXW11_uc003mbn.1_Silent_p.T356T	NM_012300	NP_036432	Q9UKB1	FBW1B_HUMAN	F-box and WD repeat domain containing 11 isoform	390	WD 4.				cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of circadian rhythm|positive regulation of proteolysis|positive regulation of transcription, DNA-dependent|protein dephosphorylation|protein destabilization|protein polyubiquitination|rhythmic process|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	centrosome|cytosol|nucleus|SCF ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(1)|breast(1)	2	Renal(175;0.000159)|Lung NSC(126;0.00384)|all_lung(126;0.00659)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CACAGGTGCTCGTGCTCCAGA	0.418													3	73	---	---	---	---	PASS
BTNL3	10917	broad.mit.edu	37	5	180432367	180432367	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180432367C>T	uc003mmr.2	+	8	1024	c.896C>T	c.(895-897)CCG>CTG	p.P299L	BTNL3_uc010jlp.2_Missense_Mutation_p.P84L	NM_197975	NP_932079	Q6UXE8	BTNL3_HUMAN	butyrophilin-like 3 precursor	299	B30.2/SPRY.|Cytoplasmic (Potential).				lipid metabolic process	integral to membrane					0	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.00336)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)|all_lung(500;0.248)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000272)			ACGGCTCACCCGAAGCTCTGC	0.537													42	101	---	---	---	---	PASS
ZNF187	7741	broad.mit.edu	37	6	28244013	28244013	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28244013A>G	uc011dld.1	+	5	847	c.577A>G	c.(577-579)ACA>GCA	p.T193A	ZNF187_uc011dlc.1_Missense_Mutation_p.T194A|ZNF187_uc003nku.3_Missense_Mutation_p.T59A|ZNF187_uc003nkw.3_Missense_Mutation_p.T40A|ZNF187_uc011dle.1_Missense_Mutation_p.T40A|ZNF187_uc011dlf.1_5'UTR|ZNF187_uc011dlg.1_Missense_Mutation_p.T40A	NM_001111039	NP_001104509	Q16670	ZN187_HUMAN	zinc finger protein 187 isoform b	193					viral reproduction	nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						TATTGTAGTAACAGACTCTTG	0.423													8	80	---	---	---	---	PASS
EHMT2	10919	broad.mit.edu	37	6	31864759	31864759	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31864759G>T	uc003nxz.1	-	2	60	c.50C>A	c.(49-51)GCC>GAC	p.A17D	EHMT2_uc003nxy.1_5'Flank|EHMT2_uc011don.1_Missense_Mutation_p.A74D|EHMT2_uc003nya.1_Missense_Mutation_p.A17D|EHMT2_uc003nyb.1_Missense_Mutation_p.A17D|C2_uc003nyc.2_5'Flank|C2_uc011doo.1_5'Flank	NM_006709	NP_006700	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	17					DNA methylation|peptidyl-lysine dimethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			ovary(1)	1						CTCAGCGGGGGCCTCCCCCTG	0.642													12	123	---	---	---	---	PASS
TNXB	7148	broad.mit.edu	37	6	32053832	32053832	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32053832G>A	uc003nzl.2	-	7	3045	c.2843C>T	c.(2842-2844)ACG>ATG	p.T948M		NM_019105	NP_061978	P22105	TENX_HUMAN	tenascin XB isoform 1 precursor	1035					actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding				0						GGCCCCTTGCGTCGTCGAGGG	0.662													4	5	---	---	---	---	PASS
GABRR2	2570	broad.mit.edu	37	6	89974189	89974189	+	Missense_Mutation	SNP	G	A	A	rs149245573	by1000genomes	TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89974189G>A	uc003pnb.2	-	8	1111	c.1103C>T	c.(1102-1104)GCG>GTG	p.A368V	GABRR2_uc011dzx.1_Missense_Mutation_p.A244V	NM_002043	NP_002034	P28476	GBRR2_HUMAN	gamma-aminobutyric acid (GABA) receptor, rho 2	368	Helical; (Potential).				synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity				0		all_cancers(76;1.67e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.77e-07)|all_epithelial(107;2.51e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0158)		GTTGACAGCCGCATACTCCAG	0.597													3	62	---	---	---	---	PASS
DPY19L1	23333	broad.mit.edu	37	7	34981489	34981489	+	Missense_Mutation	SNP	T	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34981489T>A	uc003tem.3	-	18	1503	c.1358A>T	c.(1357-1359)TAC>TTC	p.Y453F	DPY19L1_uc003ten.1_5'Flank|MIR548N_hsa-mir-548n|MI0006399_5'Flank	NM_015283	NP_056098	Q2PZI1	D19L1_HUMAN	dpy-19-like 1	453	Helical; (Potential).					integral to membrane					0						CAATGCATGGTAAACCAGCTG	0.363													6	203	---	---	---	---	PASS
SPDYE1	285955	broad.mit.edu	37	7	44040598	44040598	+	5'UTR	SNP	T	C	C			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44040598T>C	uc003tjf.2	+	1					POLR2J4_uc003tjc.2_Intron|POLR2J4_uc003tjd.2_Intron|POLR2J4_uc010kxw.2_Intron|POLR2J4_uc003tje.3_Intron	NM_175064	NP_778234	Q8NFV5	SPDE1_HUMAN	Williams Beuren syndrome chromosome region 19											ovary(1)	1						TGGTTTGGGGTTTTGGGTCGG	0.542													12	28	---	---	---	---	PASS
PKD1L1	168507	broad.mit.edu	37	7	47849070	47849070	+	Splice_Site	SNP	C	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47849070C>A	uc003tny.1	-	51	7686	c.7686_splice	c.e51+1	p.E2562_splice	C7orf69_uc003tnz.3_Intron|C7orf69_uc003toa.1_Intron|PKD1L1_uc003tob.2_Missense_Mutation_p.V290L	NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1						cell-cell adhesion	integral to membrane				ovary(8)|upper_aerodigestive_tract(2)|breast(1)	11						AGAGAGGCTACCTCCAGCCAG	0.408													4	11	---	---	---	---	PASS
WBSCR17	64409	broad.mit.edu	37	7	71130409	71130409	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71130409G>A	uc003tvy.2	+	7	1094	c.1094G>A	c.(1093-1095)GGG>GAG	p.G365E	WBSCR17_uc003tvz.2_Missense_Mutation_p.G64E	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide	365	Catalytic subdomain B.|Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				TGGCTCTGTGGGGGCAGCATG	0.512													15	212	---	---	---	---	PASS
FZD1	8321	broad.mit.edu	37	7	90895231	90895231	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90895231C>T	uc003ula.2	+	1	1449	c.1036C>T	c.(1036-1038)CGG>TGG	p.R346W		NM_003505	NP_003496	Q9UP38	FZD1_HUMAN	frizzled 1 precursor	346	Cytoplasmic (Potential).				autocrine signaling|axonogenesis|brain development|canonical Wnt receptor signaling pathway involved in mesenchymal stem cell differentiation|canonical Wnt receptor signaling pathway involved in osteoblast differentiation|embryo development|epithelial cell differentiation|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|lung alveolus development|negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|response to drug|vasculature development|Wnt receptor signaling pathway, calcium modulating pathway	apical part of cell|cell surface|cytoplasm|integral to membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|receptor binding|Wnt receptor activity|Wnt-protein binding				0	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)			GGTGGACATGCGGCGCTTCAG	0.637													5	179	---	---	---	---	PASS
DGKI	9162	broad.mit.edu	37	7	137082144	137082144	+	Nonsense_Mutation	SNP	A	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137082144A>T	uc003vtt.2	-	32	2961	c.2960T>A	c.(2959-2961)TTG>TAG	p.L987*	DGKI_uc003vtu.2_Nonsense_Mutation_p.L656*	NM_004717	NP_004708	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	987	ANK 1.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)|skin(1)	3						TGCCATATCCAATAACTCGGA	0.333													7	165	---	---	---	---	PASS
SGCZ	137868	broad.mit.edu	37	8	14095117	14095117	+	Silent	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14095117G>A	uc003wwq.2	-	4	1068	c.408C>T	c.(406-408)ACC>ACT	p.T136T	SGCZ_uc010lss.2_Silent_p.T89T	NM_139167	NP_631906	Q96LD1	SGCZ_HUMAN	sarcoglycan zeta	123	Extracellular (Potential).				cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		TCAGCTGTCCGGTTAACTGCC	0.338													67	519	---	---	---	---	PASS
ADRA1A	148	broad.mit.edu	37	8	26721617	26721617	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26721617T>G	uc003xfh.1	-	1	1306	c.870A>C	c.(868-870)TTA>TTC	p.L290F	ADRA1A_uc003xfc.1_Missense_Mutation_p.L290F|ADRA1A_uc010lul.1_Missense_Mutation_p.L290F|ADRA1A_uc003xfd.1_RNA|ADRA1A_uc003xfe.1_Missense_Mutation_p.L290F|ADRA1A_uc010lum.1_Missense_Mutation_p.L290F|ADRA1A_uc003xff.1_RNA|ADRA1A_uc003xfg.1_Missense_Mutation_p.L290F	NM_000680	NP_000671	P35348	ADA1A_HUMAN	alpha-1A-adrenergic receptor isoform 1	290	Helical; Name=6; (By similarity).				activation of phospholipase C activity|aging|apoptosis|calcium ion transport into cytosol|cell-cell signaling|intracellular protein kinase cascade|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of synaptic transmission, GABAergic|positive regulation of action potential|positive regulation of cardiac muscle contraction|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase C signaling cascade|positive regulation of vasoconstriction|response to drug|response to hormone stimulus|response to stress|smooth muscle contraction	integral to plasma membrane	alpha1-adrenergic receptor activity			breast(2)|ovary(1)|lung(1)|skin(1)	5		all_cancers(63;0.122)|Ovarian(32;2.61e-05)|all_epithelial(46;0.118)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;4.92e-10)|Colorectal(74;0.0132)|READ - Rectum adenocarcinoma(644;0.115)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amphetamine(DB00182)|Benzphetamine(DB00865)|Bethanidine(DB00217)|Carvedilol(DB01136)|Dapiprazole(DB00298)|Debrisoquin(DB04840)|Dextroamphetamine(DB01576)|Doxazosin(DB00590)|Epinastine(DB00751)|Epinephrine(DB00668)|Ergotamine(DB00696)|Flupenthixol(DB00875)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Labetalol(DB00598)|Lisdexamfetamine(DB01255)|Maprotiline(DB00934)|Mephentermine(DB01365)|Metaraminol(DB00610)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Midodrine(DB00211)|Nefazodone(DB01149)|Nicergoline(DB00699)|Nilutamide(DB00665)|Norepinephrine(DB00368)|Norgestrel(DB00506)|Oxymetazoline(DB00935)|Perphenazine(DB00850)|Phendimetrazine(DB01579)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Prazosin(DB00457)|Promazine(DB00420)|Promethazine(DB01069)|Propericiazine(DB01608)|Propiomazine(DB00777)|Pseudoephedrine(DB00852)|Risperidone(DB00734)|Sertindole(DB06144)|Tamsulosin(DB00706)|Terazosin(DB01162)|Thioridazine(DB00679)|Tolazoline(DB00797)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Ziprasidone(DB00246)	TGGGCATGACTAAGAAAAAAG	0.562													4	39	---	---	---	---	PASS
PCMTD1	115294	broad.mit.edu	37	8	52732843	52732843	+	3'UTR	SNP	C	T	T	rs116069210	by1000genomes	TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52732843C>T	uc003xqx.3	-	6					PCMTD1_uc011ldm.1_3'UTR|PCMTD1_uc003xqw.3_3'UTR|PCMTD1_uc011ldn.1_3'UTR|PCMTD1_uc010lya.2_3'UTR	NM_052937	NP_443169	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate)							cytoplasm	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity				0		Lung NSC(129;0.0795)|all_lung(136;0.144)				TCTCTTTTAACTCCTAACAAA	0.284													3	21	---	---	---	---	PASS
SULF1	23213	broad.mit.edu	37	8	70533358	70533358	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70533358C>T	uc010lza.1	+	14	2183	c.1466C>T	c.(1465-1467)ACG>ATG	p.T489M	SULF1_uc003xyd.2_Missense_Mutation_p.T489M|SULF1_uc003xye.2_Missense_Mutation_p.T489M|SULF1_uc003xyf.2_Missense_Mutation_p.T489M|SULF1_uc003xyg.2_Missense_Mutation_p.T489M|SULF1_uc003xyh.1_RNA	NM_015170	NP_055985	Q8IWU6	SULF1_HUMAN	sulfatase 1 precursor	489					apoptosis|bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			central_nervous_system(3)|ovary(2)|pancreas(1)|skin(1)	7	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			CGGCAGAGCACGCGGAACCTC	0.522													22	85	---	---	---	---	PASS
SLC45A4	57210	broad.mit.edu	37	8	142226017	142226017	+	Silent	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142226017G>A	uc003ywd.1	-	6	1937	c.1629C>T	c.(1627-1629)TAC>TAT	p.Y543Y	SLC45A4_uc003ywc.1_Silent_p.Y543Y|SLC45A4_uc010meq.1_Silent_p.Y541Y	NM_001080431	NP_001073900	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4	594	Helical; (Potential).				transport	integral to membrane				ovary(2)	2	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			TCCCCAGCACGTAGATCACCC	0.602													8	39	---	---	---	---	PASS
SLC39A4	55630	broad.mit.edu	37	8	145639726	145639726	+	Missense_Mutation	SNP	T	C	C	rs2272662	byFrequency	TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145639726T>C	uc003zcq.2	-	6	1169	c.1069A>G	c.(1069-1071)ACC>GCC	p.T357A	SLC39A4_uc003zcm.1_5'Flank|SLC39A4_uc003zcn.2_5'Flank|SLC39A4_uc003zco.2_Missense_Mutation_p.T81A|SLC39A4_uc003zcp.2_Missense_Mutation_p.T332A	NM_130849	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter),	357	Cytoplasmic (Potential).					cytoplasmic membrane-bounded vesicle|integral to membrane|recycling endosome membrane	zinc ion transmembrane transporter activity				0	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;1.12e-40)|all cancers(56;8.17e-36)|BRCA - Breast invasive adenocarcinoma(115;0.0407)|Colorectal(110;0.055)			ATGTAGTGGGTGACCCCCCTG	0.657													4	4	---	---	---	---	PASS
MPDZ	8777	broad.mit.edu	37	9	13190228	13190228	+	Missense_Mutation	SNP	G	A	A	rs147686842	by1000genomes	TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13190228G>A	uc010mia.1	-	15	2096	c.2039C>T	c.(2038-2040)GCG>GTG	p.A680V	MPDZ_uc010mhy.2_Missense_Mutation_p.A680V|MPDZ_uc010mhz.2_Missense_Mutation_p.A680V|MPDZ_uc011lmn.1_Missense_Mutation_p.A680V|MPDZ_uc003zlb.3_Missense_Mutation_p.A680V	NM_003829	NP_003820	O75970	MPDZ_HUMAN	multiple PDZ domain protein	680					interspecies interaction between organisms	apical plasma membrane|dendrite|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	protein C-terminus binding			ovary(5)|central_nervous_system(1)	6				GBM - Glioblastoma multiforme(50;2.03e-06)		ACTCTGACCCGCATCAGTCAT	0.502													3	55	---	---	---	---	PASS
CARD9	64170	broad.mit.edu	37	9	139259649	139259649	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139259649T>C	uc004chg.3	-	11	1544	c.1378A>G	c.(1378-1380)AGC>GGC	p.S460G	DNLZ_uc004chf.1_5'Flank|DNLZ_uc011mdv.1_5'Flank|CARD9_uc011mdw.1_Missense_Mutation_p.S460G	NM_052813	NP_434700	Q9H257	CARD9_HUMAN	caspase recruitment domain protein 9 isoform 1	460					positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of JNK cascade|positive regulation of stress-activated MAPK cascade|regulation of apoptosis	cytoplasm	CARD domain binding|protein homodimerization activity			pancreas(1)|lung(1)|skin(1)	3		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.58e-06)|Epithelial(140;5.65e-06)		TGTTTCGGGCTCCCCCCGCCG	0.682													4	26	---	---	---	---	PASS
GAD2	2572	broad.mit.edu	37	10	26581402	26581402	+	Silent	SNP	C	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26581402C>T	uc001isp.2	+	14	1898	c.1395C>T	c.(1393-1395)ACC>ACT	p.T465T	GAD2_uc001isq.2_Silent_p.T465T	NM_001134366	NP_001127838	Q05329	DCE2_HUMAN	glutamate decarboxylase 2	465					glutamate decarboxylation to succinate|neurotransmitter biosynthetic process|neurotransmitter secretion	cell junction|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|cytosol|Golgi membrane|presynaptic membrane	glutamate decarboxylase activity|protein binding|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					L-Glutamic Acid(DB00142)	AGGGGACTACCGGGTTTGAAG	0.468													34	82	---	---	---	---	PASS
NCOA4	8031	broad.mit.edu	37	10	51584833	51584833	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51584833C>T	uc001jis.3	+	8	1135	c.932C>T	c.(931-933)TCC>TTC	p.S311F	PARG_uc001jih.2_Intron|uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron|NCOA4_uc009xon.2_Missense_Mutation_p.S327F|NCOA4_uc010qhd.1_Missense_Mutation_p.S327F|NCOA4_uc010qhe.1_Missense_Mutation_p.S211F|NCOA4_uc010qhf.1_Missense_Mutation_p.S145F|NCOA4_uc001jit.2_Missense_Mutation_p.S311F|NCOA4_uc009xoo.2_Missense_Mutation_p.S311F	NM_001145263	NP_001138735	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4 isoform 3	311					androgen receptor signaling pathway|male gonad development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	androgen receptor binding|transcription coactivator activity			central_nervous_system(1)|kidney(1)	2						CCCCAGGAATCCCATAAGCTG	0.438			T	RET	papillary thyroid 								43	82	---	---	---	---	PASS
SLIT1	6585	broad.mit.edu	37	10	98762741	98762741	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98762741C>T	uc001kmw.2	-	35	4126	c.3874G>A	c.(3874-3876)GTG>ATG	p.V1292M		NM_003061	NP_003052	O75093	SLIT1_HUMAN	slit homolog 1 precursor	1292	Laminin G-like.				axon extension involved in axon guidance|forebrain morphogenesis|motor axon guidance|negative chemotaxis|negative regulation of synaptogenesis	cytoplasm|extracellular space	calcium ion binding|Roundabout binding			ovary(4)	4		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		TTGACATCCACGGGCATCCCT	0.627													10	159	---	---	---	---	PASS
C10orf78	119392	broad.mit.edu	37	10	105882676	105882676	+	Intron	SNP	T	C	C			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105882676T>C	uc001kxu.2	+						C10orf78_uc001kxs.2_Intron|C10orf78_uc001kxt.2_Intron|C10orf78_uc001kxv.2_Silent_p.Y51Y	NM_001002759	NP_001002759	Q86XK3	SFR1_HUMAN	hypothetical protein LOC119392 isoform a						double-strand break repair via homologous recombination	Swi5-Sfr1 complex	protein binding				0		Colorectal(252;0.102)|Breast(234;0.122)		Epithelial(162;1.31e-09)|all cancers(201;3.84e-08)|BRCA - Breast invasive adenocarcinoma(275;0.014)		AAGTCGACTATAGAGAGGTGT	0.318													14	49	---	---	---	---	PASS
ADAM12	8038	broad.mit.edu	37	10	127737879	127737879	+	Silent	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127737879G>A	uc001ljk.2	-	16	2282	c.1869C>T	c.(1867-1869)GGC>GGT	p.G623G	ADAM12_uc010qul.1_Silent_p.G574G|ADAM12_uc001ljm.2_Silent_p.G623G|ADAM12_uc001ljn.2_Silent_p.G620G|ADAM12_uc001ljl.3_Silent_p.G620G	NM_003474	NP_003465	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12 isoform 1	623	Extracellular (Potential).|Cys-rich.				cell adhesion|epidermal growth factor receptor signaling pathway|myoblast fusion|proteolysis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|protein binding|SH3 domain binding|zinc ion binding			breast(4)|ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	9		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		GCATGTCATCGCCCAAGTACA	0.532													139	266	---	---	---	---	PASS
TTC17	55761	broad.mit.edu	37	11	43418199	43418199	+	Intron	SNP	G	C	C			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43418199G>C	uc001mxi.2	+						TTC17_uc001mxh.2_Intron|TTC17_uc010rfj.1_Intron|TTC17_uc001mxj.2_5'UTR	NM_018259	NP_060729	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17								binding			ovary(5)	5						TGCTCCTTTTGAGTATTCTAA	0.353													13	34	---	---	---	---	PASS
OR5B12	390191	broad.mit.edu	37	11	58206811	58206811	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58206811C>A	uc010rkh.1	-	1	814	c.814G>T	c.(814-816)GCA>TCA	p.A272S		NM_001004733	NP_001004733	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B,	272	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				AACACAGATGCCATTTTGTCT	0.433													6	107	---	---	---	---	PASS
AHNAK	79026	broad.mit.edu	37	11	62286704	62286704	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62286704A>C	uc001ntl.2	-	5	15485	c.15185T>G	c.(15184-15186)GTC>GGC	p.V5062G	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	5062					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)				TGCGATGTTGACATCTACATC	0.463													7	408	---	---	---	---	PASS
B3GAT3	26229	broad.mit.edu	37	11	62389399	62389399	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62389399G>T	uc001ntw.2	-	1	50	c.21C>A	c.(19-21)AAC>AAA	p.N7K	B3GAT3_uc009ynz.2_5'UTR|B3GAT3_uc001ntx.2_RNA|B3GAT3_uc010rlz.1_Missense_Mutation_p.N7K	NM_012200	NP_036332	O94766	B3GA3_HUMAN	beta-1,3-glucuronyltransferase 3	7	Cytoplasmic (Potential).				glycosaminoglycan biosynthetic process	Golgi membrane|integral to membrane	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity|manganese ion binding				0						CGAGAAACACGTTCTTCAGCT	0.453													9	19	---	---	---	---	PASS
MAP6	4135	broad.mit.edu	37	11	75316878	75316878	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75316878T>G	uc001owu.2	-	3	1356	c.1291A>C	c.(1291-1293)AAC>CAC	p.N431H	MAP6_uc001owv.2_Missense_Mutation_p.N431H	NM_033063	NP_149052	Q96JE9	MAP6_HUMAN	microtubule-associated protein 6 isoform 1	431						Golgi apparatus|microtubule|perinuclear region of cytoplasm	calmodulin binding				0	Ovarian(111;0.11)					AGTTTATTGTTCATCTCTTTG	0.488													5	257	---	---	---	---	PASS
LRP1	4035	broad.mit.edu	37	12	57587385	57587385	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57587385G>A	uc001snd.2	+	47	8187	c.7721G>A	c.(7720-7722)AGC>AAC	p.S2574N	MIR1228_hsa-mir-1228|MI0006318_5'Flank	NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	2574	Extracellular (Potential).|LDL-receptor class A 12.				aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2)	22				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CGGCAGTGCAGCAATGGGCGC	0.612													3	48	---	---	---	---	PASS
USP15	9958	broad.mit.edu	37	12	62784708	62784708	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62784708C>A	uc001src.1	+	15	1918	c.1909C>A	c.(1909-1911)CAA>AAA	p.Q637K	USP15_uc001srb.1_Missense_Mutation_p.Q608K	NM_006313	NP_006304	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	637					protein deubiquitination|ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|lung(1)	3			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		CTGTAAGGACCAAAATATTAA	0.348													3	104	---	---	---	---	PASS
POLE	5426	broad.mit.edu	37	12	133249852	133249852	+	Silent	SNP	C	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133249852C>T	uc001uks.1	-	14	1415	c.1371G>A	c.(1369-1371)ACG>ACA	p.T457T	POLE_uc010tbq.1_RNA|POLE_uc009zyu.1_Silent_p.T430T	NM_006231	NP_006222	Q07864	DPOE1_HUMAN	DNA-directed DNA polymerase epsilon	457					base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)		ACACAGAATACGTGGCCAGAG	0.527								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					45	76	---	---	---	---	PASS
FRY	10129	broad.mit.edu	37	13	32759237	32759237	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32759237C>T	uc001utx.2	+	26	3767	c.3271C>T	c.(3271-3273)CGG>TGG	p.R1091W	FRY_uc010tdw.1_RNA	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog	1091					regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		TAAAGATATCCGGGCACATTT	0.428													14	200	---	---	---	---	PASS
RPGRIP1	57096	broad.mit.edu	37	14	21796693	21796693	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21796693C>A	uc001wag.2	+	18	3006	c.3006C>A	c.(3004-3006)TAC>TAA	p.Y1002*	RPGRIP1_uc001wah.2_Nonsense_Mutation_p.Y644*|RPGRIP1_uc001wai.2_Nonsense_Mutation_p.Y328*|RPGRIP1_uc001wak.2_Nonsense_Mutation_p.Y477*|RPGRIP1_uc010aim.2_Nonsense_Mutation_p.Y385*|RPGRIP1_uc001wal.2_Nonsense_Mutation_p.Y361*|RPGRIP1_uc001wam.2_Nonsense_Mutation_p.Y319*	NM_020366	NP_065099	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator	1002	Interaction with RPGR.				response to stimulus|visual perception	cilium				ovary(4)|breast(2)|pancreas(1)	7	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		TTGTGAGCTACTCAAGAAGAA	0.428													3	110	---	---	---	---	PASS
ZFP36L1	677	broad.mit.edu	37	14	69256543	69256543	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69256543T>C	uc001xkh.1	-	2	854	c.724A>G	c.(724-726)ACC>GCC	p.T242A	ZFP36L1_uc001xki.1_Missense_Mutation_p.T242A	NM_004926	NP_004917	Q07352	TISB_HUMAN	butyrate response factor 1	242					regulation of mRNA stability	cytosol|nucleus	DNA binding|mRNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				all cancers(60;0.00203)|BRCA - Breast invasive adenocarcinoma(234;0.00205)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		TCGGGCAGGGTAGGTGAGCCC	0.572											OREG0022753	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	179	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105406624	105406624	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105406624C>G	uc010axc.1	-	7	15284	c.15164G>C	c.(15163-15165)GGG>GCG	p.G5055A	AHNAK2_uc001ypx.2_Missense_Mutation_p.G4955A	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	5055						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			AAAGCTACCCCCTGCTGTGGC	0.547													6	180	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106321713	106321713	+	RNA	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106321713G>A	uc010tyt.1	-	3599		c.55683C>T			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Intron|uc001ysf.2_Intron|uc001ysj.2_Intron|uc001ysk.1_Intron|uc001ysl.1_Intron|uc001ysm.1_Intron|uc001ysn.1_Intron|uc001yso.1_Intron					Parts of antibodies, mostly variable regions.												0						CTTGTAGGTCGTGGGCCCAGA	0.637													6	40	---	---	---	---	PASS
DET1	55070	broad.mit.edu	37	15	89074369	89074369	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89074369C>G	uc002bmr.2	-	2	720	c.568G>C	c.(568-570)GAC>CAC	p.D190H	DET1_uc002bmp.3_RNA|DET1_uc010bnk.2_RNA|DET1_uc002bmq.2_Missense_Mutation_p.D201H	NM_001144074	NP_001137546	Q7L5Y6	DET1_HUMAN	de-etiolated 1 isoform 2	190						nucleus				lung(1)|pancreas(1)	2	Lung NSC(78;0.105)|all_lung(78;0.182)		BRCA - Breast invasive adenocarcinoma(143;0.188)			AGGGAATAGTCTTCTAGAGGG	0.522													23	46	---	---	---	---	PASS
PRSS22	64063	broad.mit.edu	37	16	2903247	2903247	+	Silent	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2903247G>A	uc002cry.1	-	6	867	c.801C>T	c.(799-801)GCC>GCT	p.A267A	PRSS22_uc002crz.1_Silent_p.A157A	NM_022119	NP_071402	Q9GZN4	BSSP4_HUMAN	protease, serine, 22 precursor	267	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			central_nervous_system(1)	1						TGTTGCGCTCGGCACAGCCCT	0.716													4	30	---	---	---	---	PASS
A2BP1	54715	broad.mit.edu	37	16	7645571	7645571	+	Silent	SNP	C	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7645571C>T	uc002cys.2	+	8	1477	c.489C>T	c.(487-489)TTC>TTT	p.F163F	A2BP1_uc010buf.1_Silent_p.F163F|A2BP1_uc002cyr.1_Silent_p.F162F|A2BP1_uc002cyt.2_Silent_p.F163F|A2BP1_uc010uxz.1_Silent_p.F206F|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Silent_p.F163F|A2BP1_uc010uyb.1_Silent_p.F163F|A2BP1_uc002cyw.2_Silent_p.F183F|A2BP1_uc002cyy.2_Silent_p.F183F|A2BP1_uc002cyx.2_Silent_p.F183F|A2BP1_uc010uyc.1_Silent_p.F183F	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4	163	RRM.				mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		TCGTAACTTTCGAAAATAGTG	0.453													89	126	---	---	---	---	PASS
GRIN2A	2903	broad.mit.edu	37	16	9858281	9858281	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9858281C>A	uc002czo.3	-	13	3668	c.3120G>T	c.(3118-3120)GAG>GAT	p.E1040D	GRIN2A_uc010uym.1_Missense_Mutation_p.E1040D|GRIN2A_uc010uyn.1_Missense_Mutation_p.E883D|GRIN2A_uc002czr.3_Missense_Mutation_p.E1040D	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	1040	Cytoplasmic (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	GGGTCCTATTCTCTGCTGTTG	0.532													100	232	---	---	---	---	PASS
ABCC6	368	broad.mit.edu	37	16	16243988	16243988	+	3'UTR	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16243988G>A	uc002den.3	-	31					ABCC6_uc010bvo.2_RNA|ABCC6_uc002dem.2_3'UTR	NM_001171	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C, member 6						response to drug|visual perception	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)		GAGGGTCCTGGCTCAGACCAG	0.627													6	38	---	---	---	---	PASS
DNAH3	55567	broad.mit.edu	37	16	21033374	21033374	+	Missense_Mutation	SNP	G	A	A	rs146618931	by1000genomes	TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21033374G>A	uc010vbe.1	-	40	5695	c.5695C>T	c.(5695-5697)CGC>TGC	p.R1899C		NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1899	AAA 2 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)		CAATGAAGGCGACCAAATTCC	0.458													20	36	---	---	---	---	PASS
ZNF276	92822	broad.mit.edu	37	16	89804607	89804607	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89804607C>T	uc002fos.3	+	11	1895	c.1798C>T	c.(1798-1800)CCC>TCC	p.P600S	ZNF276_uc010ciq.2_Missense_Mutation_p.P386S|ZNF276_uc002fop.2_3'UTR|ZNF276_uc002foq.3_Missense_Mutation_p.P525S|ZNF276_uc010cir.2_RNA|ZNF276_uc002for.3_Missense_Mutation_p.P386S|ZNF276_uc010cis.2_Missense_Mutation_p.P359S|ZNF276_uc002fot.3_RNA|ZNF276_uc010vpm.1_Missense_Mutation_p.P438S|ZNF276_uc010cit.1_3'UTR|FANCA_uc002fou.1_3'UTR|FANCA_uc010vpn.1_3'UTR	NM_001113525	NP_001106997	Q8N554	ZN276_HUMAN	zinc finger protein 276 isoform a	600					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		GCCACCGAGCCCCTCTGTGAC	0.647													3	8	---	---	---	---	PASS
NCOR1	9611	broad.mit.edu	37	17	15976858	15976858	+	Silent	SNP	A	C	C			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15976858A>C	uc002gpo.2	-	28	3936	c.3696T>G	c.(3694-3696)ACT>ACG	p.T1232T	NCOR1_uc002gpn.2_Silent_p.T1248T|NCOR1_uc002gpp.1_Silent_p.T1139T|NCOR1_uc010vwb.1_Intron|NCOR1_uc010coy.2_Silent_p.T140T|NCOR1_uc010vwc.1_Silent_p.T43T	NM_006311	NP_006302	O75376	NCOR1_HUMAN	nuclear receptor co-repressor 1	1232	Interaction with ETO.				cellular lipid metabolic process|chromatin modification|negative regulation of JNK cascade|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	nuclear chromatin|spindle microtubule|transcriptional repressor complex	histone deacetylase binding|transcription corepressor activity|transcription regulatory region DNA binding			upper_aerodigestive_tract(2)|ovary(1)|central_nervous_system(1)|kidney(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		TTGGACTCCTAGTCCCTTCTC	0.393													10	131	---	---	---	---	PASS
MYO15A	51168	broad.mit.edu	37	17	18052094	18052094	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18052094C>T	uc010vxh.1	+	32	7122	c.6784C>T	c.(6784-6786)CGC>TGC	p.R2262C		NM_016239	NP_057323	Q9UKN7	MYO15_HUMAN	myosin XV	2262	Tail.				sensory perception of sound	cytoplasm|myosin complex|stereocilium	actin binding|ATP binding|calmodulin binding|motor activity			skin(4)|ovary(2)|pancreas(1)|breast(1)|central_nervous_system(1)	9	all_neural(463;0.228)					AGATGGCTGGCGCGGCTGGAC	0.602													4	3	---	---	---	---	PASS
KRT25	147183	broad.mit.edu	37	17	38906791	38906791	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38906791G>A	uc002hve.2	-	6	1077	c.1016C>T	c.(1015-1017)GCG>GTG	p.A339V		NM_181534	NP_853512	Q7Z3Z0	K1C25_HUMAN	keratin 25	339	Rod.|Coil 2.					cytoplasm|intermediate filament	structural molecule activity			ovary(2)	2		Breast(137;0.00526)				CTGGATCTGCGCCAGCTGCGC	0.562													7	349	---	---	---	---	PASS
LOC651250	651250	broad.mit.edu	37	17	66122817	66122817	+	RNA	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66122817G>A	uc002jgq.2	+	6		c.1940G>A			LOC651250_uc002kit.2_RNA|LOC651250_uc002jgo.1_Intron	NR_027418				Homo sapiens cDNA FLJ33831 fis, clone CTONG2003937.												0						GGAGCAGTCCGTCTTCAAGGT	0.507													57	89	---	---	---	---	PASS
CD7	924	broad.mit.edu	37	17	80273173	80273173	+	3'UTR	SNP	C	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80273173C>T	uc002kel.1	-	4						NM_006137	NP_006128	P09564	CD7_HUMAN	CD7 antigen precursor						immune response|T cell activation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to membrane|membrane fraction|plasma membrane	receptor activity				0	Breast(20;0.000675)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.249)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0667)			GGACCACAGGCGGGACGTGCA	0.677													10	26	---	---	---	---	PASS
C18orf34	374864	broad.mit.edu	37	18	30517984	30517984	+	Silent	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30517984G>A	uc002kxn.2	-	22	2737	c.2595C>T	c.(2593-2595)AAC>AAT	p.N865N	C18orf34_uc010xbq.1_RNA|C18orf34_uc010dme.1_Silent_p.N329N|C18orf34_uc010xbr.1_Silent_p.N889N|C18orf34_uc010dmf.1_Silent_p.N185N|C18orf34_uc002kxo.2_Silent_p.N827N	NM_001105528	NP_001098998	Q5BJE1	CR034_HUMAN	hypothetical protein LOC374864 isoform 1	865				EESSNLMQHILGFFQTLTDGTCENDG -> NQYDLEKE (in Ref. 3; AAH91517).						ovary(1)	1						CTTAACCATCGTTTTCGCATG	0.368													37	67	---	---	---	---	PASS
CACNA1A	773	broad.mit.edu	37	19	13410024	13410024	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13410024G>A	uc010dze.2	-	19	2662	c.2426C>T	c.(2425-2427)ACG>ATG	p.T809M	CACNA1A_uc010dzc.2_Missense_Mutation_p.T334M|CACNA1A_uc002mwy.3_Missense_Mutation_p.T808M|CACNA1A_uc010xne.1_Missense_Mutation_p.T337M	NM_001127221	NP_001120693	O00555	CAC1A_HUMAN	calcium channel, alpha 1A subunit isoform 3	809	Cytoplasmic (Potential).				cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)	CAGGTGCCGCGTGTAGGCAGC	0.642													3	48	---	---	---	---	PASS
NXNL1	115861	broad.mit.edu	37	19	17571713	17571713	+	Translation_Start_Site	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17571713G>A	uc002ngs.2	-	1	13	c.-34C>T	c.(-36--32)CACGC>CATGC			NM_138454	NP_612463	Q96CM4	NXNL1_HUMAN	nucleoredoxin-like 1						cell redox homeostasis	nuclear outer membrane					0						ACAGCGCGGCGTGTGGTCCCC	0.562													9	27	---	---	---	---	PASS
TSHZ3	57616	broad.mit.edu	37	19	31769517	31769517	+	Silent	SNP	C	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31769517C>T	uc002nsy.3	-	2	1247	c.1182G>A	c.(1180-1182)TCG>TCA	p.S394S		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	394	C2H2-type 3; atypical.				negative regulation of transcription, DNA-dependent|regulation of respiratory gaseous exchange by neurological system process	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(2)|pancreas(1)|lung(1)	8	Esophageal squamous(110;0.226)					GGGTGTCATGCGAGCTCCCAC	0.557													7	222	---	---	---	---	PASS
RABAC1	10567	broad.mit.edu	37	19	42463023	42463023	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42463023C>A	uc002osf.2	-	2	218	c.134G>T	c.(133-135)TGG>TTG	p.W45L		NM_006423	NP_006414	Q9UI14	PRAF1_HUMAN	Rab acceptor 1	45	Required for interaction with prenylated RAB3A and VAMP2 (By similarity).|Cytoplasmic (By similarity).					cell junction|Golgi apparatus|integral to membrane|synaptic vesicle	identical protein binding				0						GAAGGTGCTCCAGGGCCGGAT	0.692													2	3	---	---	---	---	PASS
KLK3	354	broad.mit.edu	37	19	51361384	51361384	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51361384T>G	uc002pts.1	+	3	347	c.306T>G	c.(304-306)GAT>GAG	p.D102E	KLK3_uc010ycj.1_Missense_Mutation_p.D102E|KLK3_uc002ptr.1_Intron|KLK3_uc010eof.1_Intron	NM_001030047	NP_001025218	P07288	KLK3_HUMAN	prostate specific antigen isoform 3	102	Peptidase S1.				negative regulation of angiogenesis|proteolysis	extracellular region	serine-type endopeptidase activity			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00763)|GBM - Glioblastoma multiforme(134;0.0144)		CGCTCTACGATATGAGCCTCC	0.577													27	33	---	---	---	---	PASS
PTPRH	5794	broad.mit.edu	37	19	55707952	55707952	+	Missense_Mutation	SNP	G	A	A	rs138080428	byFrequency	TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55707952G>A	uc002qjq.2	-	10	2268	c.2195C>T	c.(2194-2196)ACG>ATG	p.T732M	PTPRH_uc010esv.2_Missense_Mutation_p.T554M|PTPRH_uc002qjs.2_Missense_Mutation_p.T739M	NM_002842	NP_002833	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	732	Extracellular (Potential).|Fibronectin type-III 8.				apoptosis	cytoplasm|integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(2)|large_intestine(1)|skin(1)	4		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		CCAGATGGTCGTGATGGTGGC	0.632													44	53	---	---	---	---	PASS
PCSK2	5126	broad.mit.edu	37	20	17462414	17462414	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17462414G>A	uc002wpm.2	+	12	1936	c.1616G>A	c.(1615-1617)CGT>CAT	p.R539H	PCSK2_uc002wpl.2_Missense_Mutation_p.R520H|PCSK2_uc010zrm.1_Missense_Mutation_p.R504H|PCSK2_uc002wpn.2_Missense_Mutation_p.R193H	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	539					enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	CTGAGCCGGCGTCCAAGGGAT	0.577													28	38	---	---	---	---	PASS
PROCR	10544	broad.mit.edu	37	20	33762727	33762727	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33762727G>T	uc002xbt.2	+	2	477	c.293G>T	c.(292-294)CGC>CTC	p.R98L	EDEM2_uc010zuv.1_Intron|PROCR_uc010zuw.1_Missense_Mutation_p.R135L	NM_006404	NP_006395	Q9UNN8	EPCR_HUMAN	endothelial protein C receptor precursor	98	Extracellular (Potential).				antigen processing and presentation|blood coagulation|immune response	integral to plasma membrane|MHC class I protein complex	receptor activity				0			BRCA - Breast invasive adenocarcinoma(18;0.0152)		Drotrecogin alfa(DB00055)	GGCCTCGTGCGCCTGGTGCAC	0.498													5	9	---	---	---	---	PASS
GDF5	8200	broad.mit.edu	37	20	34022673	34022673	+	Intron	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34022673G>A	uc010gfc.1	-						uc002xcj.2_3'UTR|GDF5_uc002xck.1_Intron|GDF5_uc010zvc.1_Intron	NM_000557	NP_000548	P43026	GDF5_HUMAN	growth differentiation factor 5 preproprotein						cartilage development|cell-cell signaling|growth|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity				0	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)			CTCTCTCCCCGTCCAGAGAGC	0.542													3	43	---	---	---	---	PASS
SFI1	9814	broad.mit.edu	37	22	31971261	31971261	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31971261T>C	uc003ale.2	+	10	1360	c.967T>C	c.(967-969)TTC>CTC	p.F323L	SFI1_uc003ald.1_Missense_Mutation_p.F299L|SFI1_uc003alf.2_Missense_Mutation_p.F323L|SFI1_uc003alg.2_Missense_Mutation_p.F241L|SFI1_uc011alp.1_Missense_Mutation_p.F241L|SFI1_uc011alq.1_Missense_Mutation_p.F299L|SFI1_uc003alh.2_RNA|SFI1_uc010gwi.2_RNA	NM_001007467	NP_001007468	A8K8P3	SFI1_HUMAN	spindle assembly associated Sfi1 homolog isoform	323					G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1						CCAGATATACTTCTGTGACTG	0.547													3	94	---	---	---	---	PASS
TXN2	25828	broad.mit.edu	37	22	36876770	36876770	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36876770G>A	uc003apk.1	-	2	192	c.115C>T	c.(115-117)CCT>TCT	p.P39S	TXN2_uc003apl.1_RNA	NM_012473	NP_036605	Q99757	THIOM_HUMAN	thioredoxin 2 precursor	39					cell redox homeostasis|electron transport chain|glycerol ether metabolic process|transport	mitochondrion|nucleolus	electron carrier activity				0						AGGCCACCAGGACTGCATTGT	0.552													35	86	---	---	---	---	PASS
C22orf40	150383	broad.mit.edu	37	22	46643050	46643050	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46643050C>T	uc003bhe.2	-	3	223	c.182G>A	c.(181-183)GGC>GAC	p.G61D	C22orf40_uc003bhc.2_Missense_Mutation_p.G61D|C22orf40_uc003bhd.2_Missense_Mutation_p.G61D|C22orf40_uc003bhf.2_RNA	NM_207327	NP_997210	Q6NVV7	CV040_HUMAN	hypothetical protein LOC150383	61											0						GCAGCACGAGCCGAGGACCAG	0.597													3	24	---	---	---	---	PASS
TEX11	56159	broad.mit.edu	37	X	69844762	69844762	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69844762T>C	uc004dyl.2	-	20	1828	c.1666A>G	c.(1666-1668)ATT>GTT	p.I556V	TEX11_uc004dyk.2_Missense_Mutation_p.I231V|TEX11_uc004dym.2_Missense_Mutation_p.I541V	NM_001003811	NP_001003811	Q8IYF3	TEX11_HUMAN	testis expressed sequence 11 isoform 1	556							protein binding			ovary(3)|breast(1)|skin(1)	5	Renal(35;0.156)					TCTGCCACAATTTGTTGTCCA	0.318													4	39	---	---	---	---	PASS
DOCK11	139818	broad.mit.edu	37	X	117700566	117700566	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117700566G>T	uc004eqp.2	+	9	964	c.901G>T	c.(901-903)GAG>TAG	p.E301*	DOCK11_uc004eqq.2_Nonsense_Mutation_p.E67*	NM_144658	NP_653259	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	301					blood coagulation	cytosol	GTP binding			ovary(3)	3						AGGAAAAGCCGAGAACATCAT	0.398													3	40	---	---	---	---	PASS
SMARCA1	6594	broad.mit.edu	37	X	128599698	128599698	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128599698G>T	uc004eun.3	-	23	2942	c.2829C>A	c.(2827-2829)TAC>TAA	p.Y943*	SMARCA1_uc004eup.3_Nonsense_Mutation_p.Y931*|SMARCA1_uc011muk.1_Nonsense_Mutation_p.Y943*|SMARCA1_uc011mul.1_Nonsense_Mutation_p.Y931*	NM_003069	NP_003060	P28370	SMCA1_HUMAN	SWI/SNF-related matrix-associated	943					ATP-dependent chromatin remodeling|brain development|neuron differentiation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	NURF complex	ATP binding|DNA binding|helicase activity|nucleosome binding|protein binding			ovary(3)|skin(1)	4						ATGGAGCCTTGTATCTTGCAA	0.328													69	20	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	38733363	38733364	+	IGR	INS	-	CCTTCCTCCTT	CCTTCCTCCTT	rs142813208	by1000genomes	TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38733363_38733364insCCTTCCTCCTT								POU3F1 (220913 upstream) : RRAGC (571651 downstream)																							tttcctccctcctctctcttcc	0.000													4	3	---	---	---	---	
ASH1L	55870	broad.mit.edu	37	1	155491509	155491510	+	Intron	INS	-	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155491509_155491510insA	uc009wqq.2	-						ASH1L_uc001fkt.2_Intron|ASH1L_uc009wqr.1_Intron	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like						cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			AACAACTACCCAAAAAAAAATC	0.287													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	38456196	38456196	+	IGR	DEL	A	-	-			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38456196delA								C2orf58 (47205 upstream) : ATL2 (65835 downstream)																							tacccaacttaaaaaaaaaaa	0.010													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92119834	92119836	+	IGR	DEL	ATT	-	-			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92119834_92119836delATT								GGT8P (149681 upstream) : FKSG73 (9323 downstream)																							TATGTCTCTCATTATTTTGGTAA	0.187													4	2	---	---	---	---	
SCN3A	6328	broad.mit.edu	37	2	165971746	165971747	+	Intron	INS	-	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165971746_165971747insT	uc002ucx.2	-						SCN3A_uc002ucy.2_Intron|SCN3A_uc002ucz.2_Intron|SCN3A_uc002uda.1_Intron|SCN3A_uc002udb.1_Intron	NM_006922	NP_008853	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha							voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10					Lamotrigine(DB00555)	ttctttctttattttttttttt	0.000													5	4	---	---	---	---	
PLSCR4	57088	broad.mit.edu	37	3	145924591	145924592	+	Intron	INS	-	T	T	rs150172444	by1000genomes	TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145924591_145924592insT	uc010huy.2	-						PLSCR4_uc010huz.2_Intron|PLSCR4_uc003evt.3_Intron|PLSCR4_uc010hva.2_Intron|PLSCR4_uc003evu.3_Intron	NM_001128305	NP_001121777	Q9NRQ2	PLS4_HUMAN	phospholipid scramblase 4 isoform a						blood coagulation|phospholipid scrambling	integral to membrane	calcium ion binding|phospholipid scramblase activity|SH3 domain binding				0						TATTAACACTAAAGTTAGCATA	0.391													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49099688	49099688	+	IGR	DEL	T	-	-			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49099688delT								CWH43 (35595 upstream) : None (None downstream)																							ttccattccattccattccgt	0.000													4	3	---	---	---	---	
SEPT11	55752	broad.mit.edu	37	4	77935815	77935815	+	Intron	DEL	A	-	-	rs35467273		TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77935815delA	uc003hkj.2	+						SEPT11_uc010ijh.1_Intron|SEPT11_uc011cca.1_Intron|SEPT11_uc003hkk.1_5'Flank	NM_018243	NP_060713	Q9NVA2	SEP11_HUMAN	septin 11						cell cycle|cell division|protein heterooligomerization	axon|cell junction|dendritic spine|septin complex|stress fiber|synapse	GTP binding|protein binding				0						TCTCTACCCCAAAAAAAAAAA	0.199													3	3	---	---	---	---	
FRG1	2483	broad.mit.edu	37	4	190874371	190874372	+	Intron	DEL	AG	-	-			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190874371_190874372delAG	uc003izs.2	+							NM_004477	NP_004468	Q14331	FRG1_HUMAN	FSHD region gene 1						rRNA processing	Cajal body|catalytic step 2 spliceosome|nuclear speck|nucleolus					0		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		TTAAGCCCACAGGGTAATTTTG	0.252													5	4	---	---	---	---	
CDH18	1016	broad.mit.edu	37	5	19747498	19747499	+	Intron	INS	-	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19747498_19747499insT	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)					CTTTTCTGCAGTTTTTTTTTTT	0.287													5	4	---	---	---	---	
MTMR12	54545	broad.mit.edu	37	5	32263538	32263539	+	Intron	INS	-	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32263538_32263539insT	uc003jhq.2	-						MTMR12_uc010iuk.2_Intron|MTMR12_uc010iul.2_Intron	NM_001040446	NP_001035536	Q9C0I1	MTMRC_HUMAN	myotubularin related protein 12							cytoplasm	phosphatase activity			ovary(1)	1						GACTGAGTCTCttttttttttt	0.173													4	2	---	---	---	---	
AP3B1	8546	broad.mit.edu	37	5	77458455	77458455	+	Intron	DEL	A	-	-			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77458455delA	uc003kfj.2	-							NM_003664	NP_003655	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1						endocytosis|melanosome organization	clathrin coated vesicle membrane|Golgi apparatus|membrane coat	protein phosphatase binding|protein transporter activity			central_nervous_system(1)	1		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		CTATTTTACTAAAAAAAAAAG	0.294									Hermansky-Pudlak_syndrome				4	2	---	---	---	---	
AQPEP	206338	broad.mit.edu	37	5	115339285	115339285	+	Intron	DEL	T	-	-	rs149550375		TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115339285delT	uc003kro.2	+						AQPEP_uc003krp.2_Intron|AQPEP_uc003krq.2_Intron|AQPEP_uc003krr.2_Intron|AQPEP_uc003krs.2_Intron	NM_173800	NP_776161	Q6Q4G3	AMPQ_HUMAN	laeverin						proteolysis	integral to membrane	metallopeptidase activity|zinc ion binding				0						gttttttttgttttttttttt	0.144													4	2	---	---	---	---	
TTYH3	80727	broad.mit.edu	37	7	2687414	2687415	+	Intron	INS	-	G	G			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2687414_2687415insG	uc003smp.2	+						TTYH3_uc010ksn.2_Intron|TTYH3_uc003smq.2_5'UTR	NM_025250	NP_079526	Q9C0H2	TTYH3_HUMAN	tweety 3							chloride channel complex|plasma membrane	chloride channel activity				0		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.04e-14)		AGGCAGTGGCTGGAGTTCCCCT	0.604													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	22867823	22867826	+	IGR	DEL	AGGA	-	-	rs58682948		TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22867823_22867826delAGGA								TOMM7 (5402 upstream) : SNORD93 (28406 downstream)																							ggaggaagggaggaaggaaggaag	0.108													6	3	---	---	---	---	
BBS9	27241	broad.mit.edu	37	7	33312723	33312723	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33312723delT	uc003tdn.1	+	8	1315	c.802delT	c.(802-804)TTTfs	p.F268fs	BBS9_uc003tdo.1_Frame_Shift_Del_p.F268fs|BBS9_uc003tdp.1_Frame_Shift_Del_p.F268fs|BBS9_uc003tdq.1_Frame_Shift_Del_p.F268fs|BBS9_uc010kwn.1_RNA|BBS9_uc011kan.1_Frame_Shift_Del_p.F268fs|BBS9_uc011kao.1_Frame_Shift_Del_p.F146fs	NM_198428	NP_940820	Q3SYG4	PTHB1_HUMAN	parathyroid hormone-responsive B1 isoform 2	268					fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)			TGAGAGAAACTTTTTTTGCCT	0.393									Bardet-Biedl_syndrome				458	8	---	---	---	---	
GGH	8836	broad.mit.edu	37	8	63928200	63928201	+	Intron	INS	-	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63928200_63928201insA	uc003xuw.2	-							NM_003878	NP_003869	Q92820	GGH_HUMAN	gamma-glutamyl hydrolase precursor						glutamine metabolic process	extracellular space|lysosome|melanosome	gamma-glutamyl-peptidase activity				0	Breast(64;0.0716)	all_cancers(86;0.189)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.131)			Folic Acid(DB00158)|L-Glutamic Acid(DB00142)	acttactttcCAAAAAAAAAAA	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	11704259	11704260	+	IGR	INS	-	GAAAGAAA	GAAAGAAA	rs113401656		TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11704259_11704260insGAAAGAAA								USP6NL (50580 upstream) : ECHDC3 (80096 downstream)																							aaggaaggaagggaaggaagga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42385465	42385474	+	IGR	DEL	GAATGGAATA	-	-	rs67030057		TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42385465_42385474delGAATGGAATA								None (None upstream) : LOC441666 (441841 downstream)																							aatcatcattgaatggaatagaatggaatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	48917192	48917193	+	IGR	INS	-	AA	AA			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48917192_48917193insAA								FRMPD2L1 (53560 upstream) : FRMPD2 (447415 downstream)																							CAACTAAGAATAAAAAAAAAAA	0.272													4	2	---	---	---	---	
IDE	3416	broad.mit.edu	37	10	94239368	94239369	+	Intron	DEL	GT	-	-	rs3831274		TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94239368_94239369delGT	uc001kia.2	-						IDE_uc010qnp.1_Intron|IDE_uc001khz.2_Intron	NM_004969	NP_004960	P14735	IDE_HUMAN	insulin-degrading enzyme isoform 1 precursor						beta-amyloid metabolic process|bradykinin catabolic process|interspecies interaction between organisms|sex differentiation	cell surface|extracellular space|soluble fraction	ATP binding|metalloendopeptidase activity|protein homodimerization activity|signal transducer activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3					Bacitracin(DB00626)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	gtgtgtgtgagtgtgtgtgtgt	0.317													4	2	---	---	---	---	
NT5C2	22978	broad.mit.edu	37	10	104851106	104851107	+	Intron	INS	-	T	T			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104851106_104851107insT	uc001kwo.2	-						NT5C2_uc010qqp.1_Intron|NT5C2_uc001kwq.2_Intron|NT5C2_uc001kwp.2_Intron	NM_012229	NP_036361	P49902	5NTC_HUMAN	5'-nucleotidase, cytosolic II						purine base metabolic process|purine nucleotide catabolic process	cytosol	5'-nucleotidase activity|metal ion binding|nucleotide binding|protein binding				0		all_hematologic(284;0.176)|Colorectal(252;0.178)		Epithelial(162;1.33e-08)|all cancers(201;1.04e-07)|BRCA - Breast invasive adenocarcinoma(275;0.159)	Adenosine triphosphate(DB00171)|Ribavirin(DB00811)	cTGGAAAGAACttttttttttt	0.020													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	134206066	134206068	+	IGR	DEL	TGG	-	-	rs72458419		TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134206066_134206068delTGG								LRRC27 (11056 upstream) : PWWP2B (4634 downstream)																							gtggtggtaatggtgatgatggt	0.000													3	5	---	---	---	---	
OR8H2	390151	broad.mit.edu	37	11	55872323	55872324	+	5'Flank	INS	-	T	T	rs113669153		TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55872323_55872324insT	uc010riy.1	+							NM_001005200	NP_001005200	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	Esophageal squamous(21;0.00693)					Gtttttttttgtttgttttttg	0.109										HNSCC(53;0.14)			4	2	---	---	---	---	
GOLGA6L10	647042	broad.mit.edu	37	15	83014189	83014190	+	Intron	DEL	AA	-	-			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83014189_83014190delAA	uc010unt.1	-						uc002bhl.2_Intron|uc002bhm.2_Intron|GOLGA6L10_uc010uny.1_Intron|GOLGA6L10_uc002bia.1_5'Flank			A6NI86	GG6LA_HUMAN	Homo sapiens cDNA FLJ40113 fis, clone TESTI2008621.												0						CTGGATTCTCAAAAAAAAAAAA	0.515													4	2	---	---	---	---	
LPCAT2	54947	broad.mit.edu	37	16	55571303	55571304	+	Intron	INS	-	AA	AA	rs113975796		TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55571303_55571304insAA	uc002eie.3	+						LPCAT2_uc002eic.2_Intron	NM_017839	NP_060309	Q7L5N7	PCAT2_HUMAN	lysophosphatidylcholine acyltransferase 2						cellular membrane organization|platelet activating factor biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|Golgi stack|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity|1-alkylglycerophosphocholine O-acetyltransferase activity|calcium ion binding				0						accctgtccccaaaaaaaaaaa	0.149													3	4	---	---	---	---	
CNTNAP4	85445	broad.mit.edu	37	16	76569770	76569771	+	Intron	INS	-	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76569770_76569771insA	uc002feu.1	+						CNTNAP4_uc002fev.1_Intron|CNTNAP4_uc010chb.1_Intron|CNTNAP4_uc002fex.1_Intron	NM_033401	NP_207837	Q9C0A0	CNTP4_HUMAN	cell recognition protein CASPR4 isoform 1						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2						CTATTTGAAACAAAAAAAATTC	0.337													7	4	---	---	---	---	
DNAH9	1770	broad.mit.edu	37	17	11597927	11597930	+	Intron	DEL	CTTT	-	-	rs12946303		TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11597927_11597930delCTTT	uc002gne.2	+						DNAH9_uc010coo.2_Intron	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2						cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		AGctttcttgctttcttgctttct	0.245													9	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25754047	25754047	+	Intron	DEL	T	-	-			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25754047delT	uc002gzg.2	+											Homo sapiens similar to ubiquitin specific protease 6, mRNA (cDNA clone IMAGE:5168266), with apparent retained intron.																		GACGCTGTTCTTttttttttt	0.274													4	2	---	---	---	---	
ITGB3	3690	broad.mit.edu	37	17	45377704	45377705	+	Intron	INS	-	GT	GT	rs145406552		TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45377704_45377705insGT	uc002ilj.2	+						ITGB3_uc010wkr.1_Intron	NM_000212	NP_000203	P05106	ITB3_HUMAN	integrin beta chain, beta 3 precursor						activation of protein kinase activity|angiogenesis involved in wound healing|axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte migration|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|platelet activation|platelet degranulation|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway|regulation of bone resorption|smooth muscle cell migration|tube development	alphav-beta3 integrin-vitronectin complex|integrin complex|platelet alpha granule membrane	cell adhesion molecule binding|identical protein binding|platelet-derived growth factor receptor binding|receptor activity|vascular endothelial growth factor receptor 2 binding			central_nervous_system(5)|large_intestine(1)	6					Abciximab(DB00054)|Tirofiban(DB00775)	CTTACAGGCGCGCGCGCGCgtg	0.520													5	4	---	---	---	---	
NXPH3	11248	broad.mit.edu	37	17	47655757	47655757	+	Intron	DEL	G	-	-	rs36092852		TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47655757delG	uc002ipa.2	+						NXPH3_uc010wlw.1_Intron	NM_007225	NP_009156	O95157	NXPH3_HUMAN	neurexophilin 3 precursor						neuropeptide signaling pathway	extracellular region				pancreas(1)|skin(1)	2	all_cancers(4;7.45e-14)|Breast(4;1.08e-27)|all_epithelial(4;2.27e-17)					AAAGGACAATGGGGGGGGGGG	0.532													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	65267562	65267562	+	IGR	DEL	A	-	-			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65267562delA								HELZ (26243 upstream) : PSMD12 (69058 downstream)																							accctgtttcaaaaaaaaaaa	0.184													4	3	---	---	---	---	
KIAA1632	57724	broad.mit.edu	37	18	43432246	43432247	+	3'UTR	DEL	AC	-	-			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43432246_43432247delAC	uc002lbm.2	-	44						NM_020964	NP_066015	Q9HCE0	EPG5_HUMAN	hypothetical protein LOC57724						autophagy						0						AGCTAAGAAAacacacacacac	0.356													4	2	---	---	---	---	
MED16	10025	broad.mit.edu	37	19	873324	873341	+	Intron	DEL	TAGGGGCGGGACTCCAAC	-	-	rs56920346	by1000genomes	TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:873324_873341delTAGGGGCGGGACTCCAAC	uc002lqd.1	-						MED16_uc010drw.1_Intron|MED16_uc002lqe.2_Intron|MED16_uc002lqf.2_Intron	NM_005481	NP_005472	Q9Y2X0	MED16_HUMAN	mediator complex subunit 16						androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	receptor activity|thyroid hormone receptor binding|thyroid hormone receptor coactivator activity|vitamin D receptor binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		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)		GGACTCCAAGTAGGGGCGGGACTCCAACTAGGGGCGGG	0.683													4	3	---	---	---	---	
ABCA7	10347	broad.mit.edu	37	19	1050008	1050009	+	Intron	INS	-	AA	AA			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1050008_1050009insAA	uc002lqw.3	+						ABCA7_uc010dsb.1_Intron	NM_019112	NP_061985	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A, member 7						phagocytosis|transmembrane transport	ATP-binding cassette (ABC) transporter complex|endosome membrane|Golgi membrane|integral to membrane|plasma membrane	ATP binding|ATPase activity|transporter activity			pancreas(7)|ovary(1)|central_nervous_system(1)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		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)		GTGAGCCCCCCACCACTTCCTC	0.470													4	2	---	---	---	---	
AES	166	broad.mit.edu	37	19	3055889	3055890	+	Intron	INS	-	C	C			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3055889_3055890insC	uc002lwy.1	-						AES_uc002lwx.1_Intron|AES_uc002lwz.1_Intron|AES_uc002lxa.1_Intron|AES_uc002lxb.1_Intron|AES_uc002lxc.2_Intron	NM_001130	NP_001121	Q08117	AES_HUMAN	amino-terminal enhancer of split isoform b						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of protein binding|negative regulation of response to cytokine stimulus|negative regulation of transcription from RNA polymerase II promoter|organ morphogenesis|response to interleukin-1|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|transcription corepressor activity				0		Hepatocellular(1079;0.137)		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)		GGGCCCGAGGGCAGCCAGTCAG	0.663													4	3	---	---	---	---	
UBXN6	80700	broad.mit.edu	37	19	4452145	4452146	+	Intron	INS	-	A	A			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4452145_4452146insA	uc002man.1	-						UBXN6_uc010dty.1_Intron|UBXN6_uc002mam.1_Intron	NM_025241	NP_079517	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6							microtubule organizing center|nucleus	protein binding				0						gactccatctcaaaaaaaaaaa	0.208													4	2	---	---	---	---	
GRWD1	83743	broad.mit.edu	37	19	48950328	48950330	+	Intron	DEL	ATT	-	-	rs57416905		TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48950328_48950330delATT	uc002pjd.2	+							NM_031485	NP_113673	Q9BQ67	GRWD1_HUMAN	glutamate-rich WD repeat containing 1							nucleolus				ovary(1)	1		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000206)|all cancers(93;0.000207)|Epithelial(262;0.0125)|GBM - Glioblastoma multiforme(486;0.0222)		tgcctggccCAtttttttttttt	0.005													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16915279	16915280	+	IGR	INS	-	TT	TT	rs5746975		TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16915279_16915280insTT								OR11H1 (465475 upstream) : CCT8L2 (156368 downstream)																							TCTCCCTCACCAtttttttttt	0.129													3	3	---	---	---	---	
LOC91316	91316	broad.mit.edu	37	22	23991795	23991795	+	Intron	DEL	G	-	-			TCGA-CH-5768-01	TCGA-CH-5768-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23991795delG	uc002zxh.3	-						LOC91316_uc002zxi.3_Intron|LOC91316_uc002zxk.3_Intron|LOC91316_uc010gua.2_Intron|LOC91316_uc002zxl.3_Intron|LOC91316_uc011aiz.1_Intron					Homo sapiens cDNA FLJ32313 fis, clone PROST2003232, weakly similar to BETA-GLUCURONIDASE PRECURSOR (EC 3.2.1.31).												0						CCTGCACCCTGtttttttttt	0.308													7	4	---	---	---	---	
