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
PTCHD2	57540	broad.mit.edu	37	1	11594491	11594491	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11594491G>T	uc001ash.3	+	18	3567	c.3429G>T	c.(3427-3429)TGG>TGT	p.W1143C		NM_020780	NP_065831	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	1143	Extracellular (Potential).				cholesterol homeostasis|regulation of lipid transport|smoothened signaling pathway	endoplasmic reticulum|integral to membrane|nuclear membrane	hedgehog receptor activity			skin(3)|ovary(2)|pancreas(1)|breast(1)	7	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		ACCTGCGCTGGGAGAGCTTCC	0.607													19	38	---	---	---	---	PASS
UBR4	23352	broad.mit.edu	37	1	19482023	19482023	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19482023T>C	uc001bbi.2	-	43	6216	c.6212A>G	c.(6211-6213)TAT>TGT	p.Y2071C	UBR4_uc001bbl.1_Missense_Mutation_p.Y8C|UBR4_uc001bbm.1_Missense_Mutation_p.Y1282C	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	2071					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		AAGCTGAGTATAGATGTACCC	0.433													48	98	---	---	---	---	PASS
HIVEP3	59269	broad.mit.edu	37	1	42045713	42045713	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42045713C>T	uc001cgz.3	-	4	5969	c.4756G>A	c.(4756-4758)GGT>AGT	p.G1586S	HIVEP3_uc001cha.3_Missense_Mutation_p.G1586S|HIVEP3_uc001cgy.2_RNA	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer	1586					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				GAGTCCGTACCTTCTTGTGAC	0.493													87	174	---	---	---	---	PASS
MCOLN3	55283	broad.mit.edu	37	1	85491737	85491737	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85491737T>C	uc001dkp.2	-	9	1073	c.980A>G	c.(979-981)AAG>AGG	p.K327R	MCOLN3_uc001dko.2_5'Flank|MCOLN3_uc001dkq.2_Missense_Mutation_p.K271R|MCOLN3_uc001dkr.2_3'UTR|MCOLN3_uc001dks.3_Missense_Mutation_p.K172R	NM_018298	NP_060768	Q8TDD5	MCLN3_HUMAN	mucolipin 3	327						integral to membrane	ion channel activity			skin(1)	1				all cancers(265;0.00957)|Epithelial(280;0.0254)		AGAAACTTCCTTCTTATAATG	0.343													14	51	---	---	---	---	PASS
COL24A1	255631	broad.mit.edu	37	1	86591494	86591494	+	Silent	SNP	G	C	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86591494G>C	uc001dlj.2	-	3	567	c.525C>G	c.(523-525)GTC>GTG	p.V175V	COL24A1_uc010osd.1_5'UTR|COL24A1_uc001dlk.2_RNA|COL24A1_uc010ose.1_RNA|COL24A1_uc010osf.1_RNA|COL24A1_uc009wcq.2_Silent_p.V175V	NM_152890	NP_690850	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1 precursor	175	TSP N-terminal.|Laminin G-like.				cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)		CAAACATTGAGACACTTTGGT	0.363													5	90	---	---	---	---	PASS
DPYD	1806	broad.mit.edu	37	1	98186381	98186381	+	Intron	SNP	C	G	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98186381C>G	uc001drv.2	-						DPYD_uc010oub.1_Intron|DPYD_uc001drw.2_3'UTR	NM_000110	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase isoform 1						'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)	GGGAATTAACCTGCTTGTTGA	0.358													13	18	---	---	---	---	PASS
PHTF1	10745	broad.mit.edu	37	1	114243424	114243424	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114243424T>A	uc009wgp.1	-	15	2490	c.2038A>T	c.(2038-2040)ACA>TCA	p.T680S	PHTF1_uc001edm.2_Missense_Mutation_p.T437S	NM_006608	NP_006599	Q9UMS5	PHTF1_HUMAN	putative homeodomain transcription factor 1	680						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-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)		ACCTGTTCTGTAAGTAATATT	0.269													4	114	---	---	---	---	PASS
NOTCH2	4853	broad.mit.edu	37	1	120464896	120464896	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120464896G>A	uc001eik.2	-	28	5432	c.5176C>T	c.(5176-5178)CGT>TGT	p.R1726C		NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein	1726	Cytoplasmic (Potential).				anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		GGCTCACGACGCTTGTGATTG	0.488			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				7	76	---	---	---	---	PASS
NR1I3	9970	broad.mit.edu	37	1	161200669	161200669	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161200669A>T	uc001fzx.2	-	8	1066	c.863T>A	c.(862-864)CTG>CAG	p.L288Q	TOMM40L_uc009wuf.1_Intron|NR1I3_uc001fzf.2_Missense_Mutation_p.L289Q|NR1I3_uc001fzg.2_Missense_Mutation_p.L260Q|NR1I3_uc001fzh.2_Missense_Mutation_p.L260Q|NR1I3_uc001fzi.2_Missense_Mutation_p.L255Q|NR1I3_uc001fzj.2_Missense_Mutation_p.L255Q|NR1I3_uc001fzk.2_Missense_Mutation_p.L216Q|NR1I3_uc001fzl.2_Missense_Mutation_p.L216Q|NR1I3_uc001fzm.2_Missense_Mutation_p.L209Q|NR1I3_uc001fzn.2_Missense_Mutation_p.L78Q|NR1I3_uc009wug.2_Missense_Mutation_p.L122Q|NR1I3_uc001fzp.2_Missense_Mutation_p.L293Q|NR1I3_uc001fzo.2_Missense_Mutation_p.L117Q|NR1I3_uc001fzq.2_Missense_Mutation_p.C142S|NR1I3_uc001fzr.2_Missense_Mutation_p.C142S|NR1I3_uc001fzs.2_Missense_Mutation_p.L78Q|NR1I3_uc001fzt.2_Missense_Mutation_p.L78Q|NR1I3_uc001fzu.2_Missense_Mutation_p.C113S|NR1I3_uc001fzv.2_Missense_Mutation_p.C113S|NR1I3_uc001fzw.2_Missense_Mutation_p.L288Q|NR1I3_uc001fzy.2_Missense_Mutation_p.L284Q|NR1I3_uc001fzz.2_Missense_Mutation_p.L250Q|NR1I3_uc001gaa.2_Missense_Mutation_p.L245Q|NR1I3_uc001gab.2_Missense_Mutation_p.L245Q|NR1I3_uc001gac.2_Missense_Mutation_p.L264Q|NR1I3_uc010pkm.1_Missense_Mutation_p.L255Q	NM_001077480	NP_001070948	Q14994	NR1I3_HUMAN	constitutive androstane receptor isoform 2	288					regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	androgen receptor activity|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|thyroid hormone receptor activity|transcription coactivator activity|zinc ion binding			ovary(1)|skin(1)	2	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			CTCCTCTTGCAGCTGATCAAT	0.602													34	50	---	---	---	---	PASS
C1orf114	57821	broad.mit.edu	37	1	169391258	169391258	+	Silent	SNP	A	G	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169391258A>G	uc001gga.1	-	3	579	c.411T>C	c.(409-411)CTT>CTC	p.L137L	C1orf114_uc001gfz.1_Silent_p.L137L|C1orf114_uc009wvq.1_Silent_p.L137L|C1orf114_uc001ggb.2_Silent_p.L137L|C1orf114_uc001ggc.1_Silent_p.L137L	NM_021179	NP_067002	Q5TID7	CA114_HUMAN	hypothetical protein LOC57821	137											0	all_hematologic(923;0.208)					GATTCTGTAGAAGCTTGTTAG	0.398													45	194	---	---	---	---	PASS
RNASEL	6041	broad.mit.edu	37	1	182551344	182551344	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182551344A>G	uc001gpj.1	-	3	1783	c.1616T>C	c.(1615-1617)TTT>TCT	p.F539S	RNASEL_uc009wxz.1_Missense_Mutation_p.F539S|RNASEL_uc001gpk.2_Missense_Mutation_p.F539S|RNASEL_uc009wya.1_Silent_p.I510I	NM_021133	NP_066956	Q05823	RN5A_HUMAN	ribonuclease L	539	Protein kinase.				mRNA processing|response to virus|type I interferon-mediated signaling pathway	mitochondrion	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|metal ion binding|protein kinase activity|RNA binding			ovary(4)|stomach(1)	5						CAGATCCTCAAATGAGATGCT	0.353									Hereditary_Prostate_Cancer				107	229	---	---	---	---	PASS
LAMC2	3918	broad.mit.edu	37	1	183194784	183194784	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183194784G>C	uc001gqa.2	+	8	1309	c.995G>C	c.(994-996)AGT>ACT	p.S332T	LAMC2_uc001gpz.3_Missense_Mutation_p.S332T|LAMC2_uc010poa.1_Missense_Mutation_p.S32T	NM_005562	NP_005553	Q13753	LAMC2_HUMAN	laminin, gamma 2 isoform a precursor	332	Laminin IV type A.				cell adhesion|epidermis development|hemidesmosome assembly		heparin binding			skin(2)|ovary(1)	3						CCCCAGCTGAGTTACTTTGAG	0.398													82	167	---	---	---	---	PASS
PLXNA2	5362	broad.mit.edu	37	1	208390748	208390748	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208390748G>A	uc001hgz.2	-	2	1278	c.520C>T	c.(520-522)CGC>TGC	p.R174C	PLXNA2_uc001hha.3_Missense_Mutation_p.R228C	NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2 precursor	174	Extracellular (Potential).|Sema.				axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)		CCCTCAGAGCGCACAATCACC	0.602													4	290	---	---	---	---	PASS
SERTAD4	56256	broad.mit.edu	37	1	210412917	210412917	+	Silent	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210412917G>A	uc001hhy.2	+	3	434	c.255G>A	c.(253-255)GAG>GAA	p.E85E	SERTAD4_uc009xcw.2_Silent_p.E85E	NM_019605	NP_062551	Q9NUC0	SRTD4_HUMAN	SERTA domain containing 4	85							protein binding			ovary(1)|pancreas(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0237)|all cancers(67;0.127)		TGGAAGAAGAGGATTTTCACC	0.328													27	37	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	216595423	216595423	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216595423G>T	uc001hku.1	-	2	643	c.256C>A	c.(256-258)CAG>AAG	p.Q86K	USH2A_uc001hkv.2_Missense_Mutation_p.Q86K	NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	86	Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GGGCAATCCTGAATACAAAAC	0.493										HNSCC(13;0.011)			7	73	---	---	---	---	PASS
ITPKB	3707	broad.mit.edu	37	1	226829707	226829707	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226829707C>T	uc010pvo.1	-	5	2706	c.2366G>A	c.(2365-2367)CGG>CAG	p.R789Q		NM_002221	NP_002212	P27987	IP3KB_HUMAN	1D-myo-inositol-trisphosphate 3-kinase B	789							ATP binding|calmodulin binding|inositol trisphosphate 3-kinase activity			ovary(4)|central_nervous_system(1)	5		Prostate(94;0.0773)				GGTCACAGCCCGCTGTGCTTT	0.632													14	187	---	---	---	---	PASS
GJC2	57165	broad.mit.edu	37	1	228346349	228346349	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228346349C>T	uc001hsk.2	+	2	1065	c.890C>T	c.(889-891)GCG>GTG	p.A297V		NM_020435	NP_065168	Q5T442	CXG2_HUMAN	gap junction protein, gamma 2, 47kDa	297	Cytoplasmic (Potential).				cell death	connexon complex|integral to membrane					0		Prostate(94;0.0405)				GCGCAGGACGCGGTGCGCGGC	0.562													3	13	---	---	---	---	PASS
CPSF3	51692	broad.mit.edu	37	2	9588441	9588441	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9588441G>A	uc002qzo.1	+	11	1392	c.1357G>A	c.(1357-1359)GCA>ACA	p.A453T	CPSF3_uc010ewx.1_Missense_Mutation_p.A404T|CPSF3_uc002qzp.1_Missense_Mutation_p.A416T|CPSF3_uc002qzq.1_Missense_Mutation_p.A30T	NM_016207	NP_057291	Q9UKF6	CPSF3_HUMAN	cleavage and polyadenylation specific factor 3,	453					histone mRNA 3'-end processing|mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex|ribonucleoprotein complex	5'-3' exonuclease activity|endoribonuclease activity|metal ion binding|protein binding|RNA binding			breast(2)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;2.39e-25)|all_epithelial(98;8.75e-19)|Lung NSC(108;2.38e-06)|Ovarian(717;0.0308)		all cancers(51;2.2e-40)|Epithelial(75;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(76;4.35e-21)|STAD - Stomach adenocarcinoma(1183;0.00644)		GAATACAGAAGCAGTGACCTT	0.393													27	70	---	---	---	---	PASS
EHBP1	23301	broad.mit.edu	37	2	62998585	62998585	+	Intron	SNP	T	C	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62998585T>C	uc002sby.2	+						EHBP1_uc010fcp.2_Intron|EHBP1_uc010fcq.1_Intron|EHBP1_uc002sbx.2_Intron|EHBP1_uc002sbz.2_Intron|EHBP1_uc002scb.2_Intron|EHBP1_uc002sca.2_3'UTR	NM_015252	NP_056067	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1 isoform 1							cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			TATGCATTATTAAGGTACATT	0.303									Hereditary_Prostate_Cancer				26	57	---	---	---	---	PASS
LOXL3	84695	broad.mit.edu	37	2	74763177	74763177	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74763177A>C	uc002smp.1	-	7	1266	c.1194T>G	c.(1192-1194)CAT>CAG	p.H398Q	LOXL3_uc002smo.1_Missense_Mutation_p.H37Q|LOXL3_uc010ffm.1_Missense_Mutation_p.H398Q|LOXL3_uc002smq.1_Missense_Mutation_p.H253Q|LOXL3_uc010ffn.1_Missense_Mutation_p.H253Q	NM_032603	NP_115992	P58215	LOXL3_HUMAN	lysyl oxidase-like 3 precursor	398	SRCR 3.					extracellular space|membrane	copper ion binding|protein-lysine 6-oxidase activity|scavenger receptor activity				0						CATCCTGGCTATGTGAACAAT	0.557													33	93	---	---	---	---	PASS
RAB3GAP1	22930	broad.mit.edu	37	2	135926185	135926185	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135926185C>A	uc002tuj.2	+	24	2805	c.2780C>A	c.(2779-2781)TCC>TAC	p.S927Y	RAB3GAP1_uc010fnf.2_Missense_Mutation_p.S934Y|RAB3GAP1_uc010fng.2_Missense_Mutation_p.S752Y|RAB3GAP1_uc010fnh.1_RNA	NM_012233	NP_036365	Q15042	RB3GP_HUMAN	RAB3 GTPase-activating protein	927						centrosome|nucleus|soluble fraction	Rab GTPase activator activity|Rab GTPase binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.117)		AGGCAGAACTCCGTGTCAGAC	0.542													57	102	---	---	---	---	PASS
BBS5	129880	broad.mit.edu	37	2	170361179	170361179	+	3'UTR	SNP	T	C	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170361179T>C	uc002uet.2	+	12					BBS5_uc010fpw.2_3'UTR|KBTBD10_uc010zdh.1_Intron	NM_152384	NP_689597	Q8N3I7	BBS5_HUMAN	Bardet-Biedl syndrome 5						cilium assembly|flagellum assembly|heart looping|melanosome transport|response to stimulus|visual perception	BBSome|cilium membrane|microtubule basal body	phosphatidylinositol-3-phosphate binding|protein binding				0						GAATAGTTTTTATATTTACAG	0.318									Bardet-Biedl_syndrome				7	11	---	---	---	---	PASS
EVX2	344191	broad.mit.edu	37	2	176948341	176948341	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176948341G>A	uc010zeu.1	-	1	350	c.164C>T	c.(163-165)TCT>TTT	p.S55F		NM_001080458	NP_001073927	Q03828	EVX2_HUMAN	even-skipped homeobox 2	55						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	READ - Rectum adenocarcinoma(9;0.0678)|Colorectal(32;0.115)		CAGGGGGGCAGACGGCAGGCG	0.602													16	43	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179441300	179441300	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179441300G>A	uc010zfg.1	-	274	62191	c.61967C>T	c.(61966-61968)CCA>CTA	p.P20656L	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.P14351L|TTN_uc010zfi.1_Missense_Mutation_p.P14284L|TTN_uc010zfj.1_Missense_Mutation_p.P14159L|uc002umv.1_5'Flank	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	21583							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)			CTCACTGGGTGGACCAATTCC	0.428													21	240	---	---	---	---	PASS
CRYGB	1419	broad.mit.edu	37	2	209007477	209007477	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209007477G>C	uc002vcp.3	-	3	446	c.413C>G	c.(412-414)CCC>CGC	p.P138R		NM_005210	NP_005201	P07316	CRGB_HUMAN	crystallin, gamma B	138	Beta/gamma crystallin 'Greek key' 4.				visual perception		structural constituent of eye lens				0				Epithelial(149;0.0641)|LUSC - Lung squamous cell carcinoma(261;0.0703)|Lung(261;0.132)		CCTGTAGTTGGGCATCTCATA	0.547													79	156	---	---	---	---	PASS
FARSB	10056	broad.mit.edu	37	2	223489068	223489068	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223489068C>A	uc002vne.1	-	12	1128	c.1093G>T	c.(1093-1095)GTA>TTA	p.V365L	FARSB_uc010zlq.1_Missense_Mutation_p.V385L|FARSB_uc002vnf.1_Missense_Mutation_p.V266L	NM_005687	NP_005678	Q9NSD9	SYFB_HUMAN	phenylalanyl-tRNA synthetase, beta subunit	365	B5.				phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|RNA binding			ovary(1)	1		Renal(207;0.0183)		Epithelial(121;3.47e-10)|all cancers(144;1.86e-07)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.011)	L-Phenylalanine(DB00120)	GCATCTTCTACAATATCACAT	0.373													4	266	---	---	---	---	PASS
PASK	23178	broad.mit.edu	37	2	242063382	242063382	+	Silent	SNP	G	C	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242063382G>C	uc002wao.1	-	11	2978	c.2886C>G	c.(2884-2886)ACC>ACG	p.T962T	PASK_uc010zol.1_Silent_p.T776T|PASK_uc010zom.1_Silent_p.T927T|PASK_uc010fzl.1_Silent_p.T962T|PASK_uc010zon.1_Silent_p.T743T|PASK_uc002wap.2_Silent_p.T505T|PASK_uc002waq.2_Silent_p.T962T	NM_015148	NP_055963	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	962					regulation of transcription, DNA-dependent	Golgi apparatus	ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(4)|lung(1)|skin(1)	6		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		GGCTGGGTCCGGTGAGCTCAG	0.587													18	42	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10188210	10188210	+	Missense_Mutation	SNP	T	C	C	rs5030830		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188210T>C	uc003bvc.2	+	2	566	c.353T>C	c.(352-354)CTC>CCC	p.L118P	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	118	Involved in binding to CCT complex.		L -> R (in VHLD).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.L118P(4)|p.W117fs*40(1)|p.L118fs*14(1)|p.L118H(1)|p.?(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CACCTTTGGCTCTTCAGAGAT	0.353		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				82	104	---	---	---	---	PASS
ALS2CL	259173	broad.mit.edu	37	3	46721931	46721931	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46721931C>A	uc003cqa.1	-	14	1727	c.1537G>T	c.(1537-1539)GAC>TAC	p.D513Y	ALS2CL_uc003cpz.1_Missense_Mutation_p.D28Y|ALS2CL_uc003cqb.1_Missense_Mutation_p.D513Y|ALS2CL_uc003cqc.1_RNA	NM_147129	NP_667340	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like isoform 1	513	MORN 7.				endosome organization|regulation of Rho protein signal transduction		GTPase activator activity|identical protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)|central_nervous_system(2)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		ACCGTCTTGTCCGCCTGGAAG	0.642													45	55	---	---	---	---	PASS
CLDN18	51208	broad.mit.edu	37	3	137717885	137717885	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137717885G>T	uc003ero.1	+	1	228	c.175G>T	c.(175-177)GGC>TGC	p.G59C		NM_001002026	NP_001002026	P56856	CLD18_HUMAN	claudin 18 isoform 2	59	Extracellular (Potential).				calcium-independent cell-cell adhesion|tight junction assembly	integral to membrane|tight junction	identical protein binding|structural molecule activity			upper_aerodigestive_tract(1)|ovary(1)	2						AGAGAGCTCTGGCTTCACCGA	0.602													7	157	---	---	---	---	PASS
ZBBX	79740	broad.mit.edu	37	3	166958709	166958709	+	Intron	SNP	T	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166958709T>A	uc003fep.2	-						ZBBX_uc011bpc.1_Intron|ZBBX_uc003feq.2_Intron	NM_024687	NP_078963	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing							intracellular	zinc ion binding			ovary(2)	2						CCAGAACAGCTGAAAATACAT	0.383													37	92	---	---	---	---	PASS
ATP13A4	84239	broad.mit.edu	37	3	193188726	193188726	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193188726T>C	uc003ftd.2	-	9	973	c.865A>G	c.(865-867)ACA>GCA	p.T289A	ATP13A4_uc003fte.1_Missense_Mutation_p.T289A|ATP13A4_uc011bsr.1_5'UTR|ATP13A4_uc003ftf.3_5'UTR	NM_032279	NP_115655	Q4VNC1	AT134_HUMAN	ATPase type 13A4	289	Extracellular (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(2)	2	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		TTGTTCCCTGTCAAAATTAAT	0.488													4	327	---	---	---	---	PASS
ACOX3	8310	broad.mit.edu	37	4	8394072	8394072	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8394072C>T	uc010idk.2	-	11	1433	c.1288G>A	c.(1288-1290)GGC>AGC	p.G430S	ACOX3_uc003glc.3_Missense_Mutation_p.G430S|ACOX3_uc003gld.3_Missense_Mutation_p.G430S|ACOX3_uc003gle.1_Missense_Mutation_p.G335S	NM_003501	NP_003492	O15254	ACOX3_HUMAN	acyl-Coenzyme A oxidase 3 isoform a	430					bile acid metabolic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|pristanoyl-CoA oxidase activity			central_nervous_system(1)	1						GCCAGATAGCCGTGTCCTCCA	0.517													109	202	---	---	---	---	PASS
TLR6	10333	broad.mit.edu	37	4	38830418	38830418	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38830418G>T	uc003gtm.2	-	1	743	c.677C>A	c.(676-678)ACT>AAT	p.T226N	TLR6_uc010ifg.1_Missense_Mutation_p.T226N	NM_006068	NP_006059	Q9Y2C9	TLR6_HUMAN	toll-like receptor 6 precursor	226	Extracellular (Potential).				activation of NF-kappaB-inducing kinase activity|cellular response to diacyl bacterial lipopeptide|defense response to bacterium|detection of diacyl bacterial lipopeptide|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-6 biosynthetic process|positive regulation of JUN kinase activity|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	integral to plasma membrane|phagocytic vesicle membrane	lipopeptide binding|transmembrane receptor activity			ovary(2)	2						TTTAATATTAGTCAGTTGTAA	0.333													36	93	---	---	---	---	PASS
RUFY3	22902	broad.mit.edu	37	4	71634345	71634345	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71634345T>G	uc003hfq.2	+	5	1258	c.663T>G	c.(661-663)AAT>AAG	p.N221K	RUFY3_uc003hfp.3_Missense_Mutation_p.N281K|RUFY3_uc011cax.1_Missense_Mutation_p.N239K|RUFY3_uc003hfr.2_Missense_Mutation_p.N221K|RUFY3_uc011cay.1_Missense_Mutation_p.N157K	NM_014961	NP_055776	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3 isoform 2	221	RUN.				negative regulation of axonogenesis	filopodium|growth cone					0		all_hematologic(202;0.248)	Lung(101;0.235)			TTGATGCCAATTTCTGTATGA	0.443													79	170	---	---	---	---	PASS
CAMK2D	817	broad.mit.edu	37	4	114378530	114378530	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114378530A>C	uc003ibi.2	-	17	2253	c.1394T>G	c.(1393-1395)GTT>GGT	p.V465G	CAMK2D_uc003ibj.2_Missense_Mutation_p.V465G|CAMK2D_uc003ibk.2_Missense_Mutation_p.V465G|CAMK2D_uc003ibo.3_Missense_Mutation_p.V499G|CAMK2D_uc003ibm.2_Missense_Mutation_p.V479G|CAMK2D_uc003ibn.2_Missense_Mutation_p.V476G|CAMK2D_uc003ibl.2_Missense_Mutation_p.V465G	NM_001221	NP_001212	Q13557	KCC2D_HUMAN	calcium/calmodulin-dependent protein kinase II	465					interferon-gamma-mediated signaling pathway|regulation of cell growth|synaptic transmission	calcium- and calmodulin-dependent protein kinase complex|cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)	1		Ovarian(17;0.00369)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000271)		ATGAAAATGAACATTCTGCCA	0.478													4	171	---	---	---	---	PASS
DMGDH	29958	broad.mit.edu	37	5	78359437	78359437	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78359437G>T	uc003kfs.2	-	2	281	c.275C>A	c.(274-276)GCA>GAA	p.A92E	DMGDH_uc011ctf.1_Silent_p.R47R|DMGDH_uc011ctg.1_Missense_Mutation_p.Q18K	NM_013391	NP_037523	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase precursor	92					choline metabolic process|glycine catabolic process	mitochondrial matrix	aminomethyltransferase activity|dimethylglycine dehydrogenase activity|electron carrier activity			ovary(2)|liver(1)|skin(1)	4		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)		TTTTCTTACTGCGTGCCAGGT	0.493													62	176	---	---	---	---	PASS
VCAN	1462	broad.mit.edu	37	5	82849280	82849280	+	Silent	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82849280C>T	uc003kii.3	+	11	9947	c.9591C>T	c.(9589-9591)TGC>TGT	p.C3197C	VCAN_uc003kij.3_Silent_p.C2210C|VCAN_uc010jau.2_Silent_p.C1443C|VCAN_uc003kik.3_Silent_p.C456C|VCAN_uc003kil.3_Silent_p.C1861C	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	3197	C-type lectin.				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(6)|lung(2)|central_nervous_system(1)	16		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)		AACGGGAATGCCGTCTGCAGG	0.478													5	234	---	---	---	---	PASS
RASA1	5921	broad.mit.edu	37	5	86674302	86674302	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86674302C>T	uc003kiw.2	+	18	2552	c.2434C>T	c.(2434-2436)CAT>TAT	p.H812Y	RASA1_uc010jav.2_RNA|RASA1_uc003kix.2_Missense_Mutation_p.H635Y|RASA1_uc011ctv.1_Missense_Mutation_p.H645Y|RASA1_uc011ctw.1_Missense_Mutation_p.H646Y|RASA1_uc010jaw.2_Missense_Mutation_p.H634Y	NM_002890	NP_002881	P20936	RASA1_HUMAN	RAS p21 protein activator 1 isoform 1	812	Ras-GAP.				cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis	cytosol|intrinsic to internal side of plasma membrane	glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding			upper_aerodigestive_tract(3)|ovary(1)|lung(1)	5		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		GTTTGTTCATCATGCTTTGAA	0.348													19	155	---	---	---	---	PASS
PCDHB10	56126	broad.mit.edu	37	5	140572477	140572477	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140572477C>T	uc003lix.2	+	1	526	c.352C>T	c.(352-354)CGG>TGG	p.R118W		NM_018930	NP_061753	Q9UN67	PCDBA_HUMAN	protocadherin beta 10 precursor	118	Extracellular (Potential).|Cadherin 1.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCAGATTTACCGGGCTGAGCT	0.433													4	183	---	---	---	---	PASS
HIST1H4H	8365	broad.mit.edu	37	6	26285406	26285406	+	3'UTR	SNP	A	G	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26285406A>G	uc003nhm.2	-	1					HIST1H4H_uc003nhl.1_RNA	NM_003543	NP_003534	P62805	H4_HUMAN	histone cluster 1, H4h						CenH3-containing nucleosome assembly at centromere|negative regulation of megakaryocyte differentiation|phosphatidylinositol-mediated signaling|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(2)	2						GAGTGCAGCAAGCAGGAGCCT	0.502										HNSCC(76;0.23)			13	47	---	---	---	---	PASS
C6orf47	57827	broad.mit.edu	37	6	31627421	31627421	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31627421C>A	uc003nvm.1	-	1	1129	c.304G>T	c.(304-306)GAG>TAG	p.E102*		NM_021184	NP_067007	O95873	CF047_HUMAN	G4 protein	102										ovary(1)	1						CTCCCAGACTCTTGAGTGCTA	0.582													4	76	---	---	---	---	PASS
DST	667	broad.mit.edu	37	6	56484745	56484745	+	Intron	SNP	C	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56484745C>A	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron|DST_uc003pdb.2_Intron|DST_uc003pdc.3_Nonsense_Mutation_p.E1363*	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TGTTTGAGTTCTTCTGCTTTC	0.453													45	132	---	---	---	---	PASS
DOPEY1	23033	broad.mit.edu	37	6	83838711	83838711	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83838711C>G	uc003pjs.1	+	16	2085	c.1825C>G	c.(1825-1827)CAA>GAA	p.Q609E	DOPEY1_uc011dyy.1_Missense_Mutation_p.Q600E|DOPEY1_uc010kbl.1_Missense_Mutation_p.Q600E	NM_015018	NP_055833	Q5JWR5	DOP1_HUMAN	dopey family member 1	609					protein transport					ovary(2)|breast(1)|central_nervous_system(1)	4		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		TATACAATATCAAGCAGACCG	0.443													71	121	---	---	---	---	PASS
T	6862	broad.mit.edu	37	6	166579294	166579294	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166579294C>T	uc003quu.1	-	4	999	c.506G>A	c.(505-507)CGA>CAA	p.R169Q	T_uc003qut.1_Missense_Mutation_p.R169Q|T_uc003quv.1_Missense_Mutation_p.R169Q	NM_003181	NP_003172	O15178	BRAC_HUMAN	transcription factor T	169	T-box.				anterior/posterior axis specification, embryo|mesoderm development|primitive streak formation	nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)|pancreas(1)	2		Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559)		OV - Ovarian serous cystadenocarcinoma(33;1.09e-113)|GBM - Glioblastoma multiforme(31;1.51e-108)|BRCA - Breast invasive adenocarcinoma(81;8.45e-09)|LUAD - Lung adenocarcinoma(999;0.0407)		TATGTGGATTCGAGGCTCATA	0.502									Chordoma_Familial_Clustering_of				24	382	---	---	---	---	PASS
THBS2	7058	broad.mit.edu	37	6	169634969	169634969	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169634969G>A	uc003qwt.2	-	11	1759	c.1511C>T	c.(1510-1512)TCG>TTG	p.S504L		NM_003247	NP_003238	P35442	TSP2_HUMAN	thrombospondin 2 precursor	504	TSP type-1 3.				cell adhesion	extracellular region	calcium ion binding|heparin binding|protein binding|structural molecule activity			ovary(5)	5		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		AGTGCAGGCCGACCACGGGGA	0.682													8	56	---	---	---	---	PASS
DFNA5	1687	broad.mit.edu	37	7	24758693	24758693	+	Silent	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24758693G>A	uc010kus.1	-	4	637	c.549C>T	c.(547-549)ATC>ATT	p.I183I	DFNA5_uc003swz.2_Silent_p.I19I|DFNA5_uc003sxa.1_Silent_p.I183I|DFNA5_uc010kut.1_Silent_p.I19I|DFNA5_uc003sxb.2_Silent_p.I183I	NM_001127453	NP_001120925	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5 protein isoform	183					sensory perception of sound					ovary(1)	1						GGATGCCCACGATGCCACCAC	0.577													50	203	---	---	---	---	PASS
CRCP	27297	broad.mit.edu	37	7	65592713	65592713	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65592713C>A	uc003tus.2	+	2	176	c.31C>A	c.(31-33)CTC>ATC	p.L11I	CRCP_uc003tuv.2_RNA|CRCP_uc011kdw.1_Missense_Mutation_p.L37I|CRCP_uc003tut.2_Missense_Mutation_p.L11I|CRCP_uc003tuu.2_Intron	NM_014478	NP_055293	O75575	RPC9_HUMAN	calcitonin gene-related peptide-receptor	11					acrosome reaction|innate immune response|response to virus|transcription from RNA polymerase III promoter	DNA polymerase III complex|nucleus|plasma membrane	calcitonin receptor activity|DNA-directed RNA polymerase activity|nucleotide binding				0						TTCTGCGCTTCTCAGTAACTA	0.393													5	328	---	---	---	---	PASS
GRM3	2913	broad.mit.edu	37	7	86416315	86416315	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86416315G>T	uc003uid.2	+	3	2306	c.1207G>T	c.(1207-1209)GCT>TCT	p.A403S	GRM3_uc010lef.2_Missense_Mutation_p.A401S|GRM3_uc010leg.2_Missense_Mutation_p.A275S|GRM3_uc010leh.2_Intron	NM_000840	NP_000831	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3 precursor	403	Extracellular (Potential).				synaptic transmission	integral to plasma membrane				lung(4)|ovary(3)|central_nervous_system(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)	13	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)				Acamprosate(DB00659)|Nicotine(DB00184)	CATGGCCCACGCTTTGCACAA	0.522													7	297	---	---	---	---	PASS
CDK14	5218	broad.mit.edu	37	7	90355879	90355879	+	Splice_Site	SNP	A	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90355879A>T	uc003uky.2	+	3	346	c.124_splice	c.e3-2	p.I42_splice	CDK14_uc003ukt.1_Splice_Site|CDK14_uc003ukv.1_Splice_Site|CDK14_uc003uku.1_Splice_Site|CDK14_uc003ukx.1_Intron|CDK14_uc003ukz.1_Splice_Site_p.I24_splice|CDK14_uc010les.1_Splice_Site|CDK14_uc011khl.1_Splice_Site	NM_012395	NP_036527	O94921	CDK14_HUMAN	PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4						TTCTTTTCTCAGATATGTGTC	0.378													17	82	---	---	---	---	PASS
SLC25A13	10165	broad.mit.edu	37	7	95776002	95776002	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95776002C>T	uc003uof.3	-	14	1509	c.1318G>A	c.(1318-1320)GGC>AGC	p.G440S	SLC25A13_uc003uog.3_Missense_Mutation_p.G441S|SLC25A13_uc011kik.1_Missense_Mutation_p.G332S	NM_014251	NP_055066	Q9UJS0	CMC2_HUMAN	solute carrier family 25, member 13 isoform 2	440	Solcar 2.|Helical; Name=3; (Potential).				ATP biosynthetic process|gluconeogenesis|malate-aspartate shuttle|response to calcium ion	integral to plasma membrane|mitochondrial inner membrane	calcium ion binding|L-aspartate transmembrane transporter activity|L-glutamate transmembrane transporter activity			central_nervous_system(3)|skin(1)	4	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)	ACCTGGGAGCCTCCAGCCTAA	0.408													76	209	---	---	---	---	PASS
ZNF789	285989	broad.mit.edu	37	7	99084805	99084805	+	Silent	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99084805G>A	uc003uqq.1	+	5	1191	c.972G>A	c.(970-972)CGG>CGA	p.R324R	ZNF789_uc010lfw.1_Silent_p.R229R|ZNF789_uc003uqr.1_Silent_p.R266R	NM_213603	NP_998768	Q5FWF6	ZN789_HUMAN	zinc finger protein 789 isoform 1	324	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					CCTTTGGCCGGCATTCAACCC	0.423													4	165	---	---	---	---	PASS
MYL10	93408	broad.mit.edu	37	7	101256829	101256829	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101256829G>A	uc003uyr.2	-	8	785	c.607C>T	c.(607-609)CCC>TCC	p.P203S		NM_138403	NP_612412	Q9BUA6	MYL10_HUMAN	myosin, light chain 10, regulatory	203	EF-hand 3.					mitochondrion	calcium ion binding			ovary(1)|breast(1)	2						ACATCTGGGGGAAATGCTGCA	0.557													59	166	---	---	---	---	PASS
DPY19L2P2	349152	broad.mit.edu	37	7	102912264	102912264	+	5'UTR	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102912264C>T	uc003vbh.3	-	6					DPY19L2P2_uc003vbg.3_RNA|DPY19L2P2_uc010lit.2_RNA	NR_003561				RecName: Full=Protein dpy-19 homolog 2-like 2; AltName: Full=Dpy-19-like protein 2 pseudogene 2;												0						CCACAGTCCTCCCAAAAATGA	0.308													4	175	---	---	---	---	PASS
CHRM2	1129	broad.mit.edu	37	7	136700642	136700642	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136700642G>A	uc003vtf.1	+	4	1653	c.1030G>A	c.(1030-1032)GTG>ATG	p.V344M	CHRM2_uc003vtg.1_Missense_Mutation_p.V344M|CHRM2_uc003vtj.1_Missense_Mutation_p.V344M|CHRM2_uc003vtk.1_Missense_Mutation_p.V344M|CHRM2_uc003vtl.1_Missense_Mutation_p.V344M|CHRM2_uc003vtm.1_Missense_Mutation_p.V344M|CHRM2_uc003vti.1_Missense_Mutation_p.V344M|CHRM2_uc003vto.1_Missense_Mutation_p.V344M|CHRM2_uc003vtn.1_Missense_Mutation_p.V344M|uc003vtp.1_Intron	NM_001006630	NP_001006631	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	344	Cytoplasmic (By similarity).				activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|nervous system development|regulation of heart contraction|response to virus	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|protein binding			ovary(4)|central_nervous_system(1)	5					Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Carbachol(DB00411)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Desipramine(DB01151)|Diphenidol(DB01231)|Doxacurium(DB01334)|Doxacurium chloride(DB01135)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Ipratropium(DB00332)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pilocarpine(DB01085)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Rocuronium(DB00728)|Thiethylperazine(DB00372)|Tolterodine(DB01036)|Tridihexethyl(DB00505)|Triflupromazine(DB00508)	TAATACCACCGTGGAGGTAGT	0.463													35	161	---	---	---	---	PASS
ENTPD4	9583	broad.mit.edu	37	8	23291703	23291703	+	Intron	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23291703C>T	uc003xdl.2	-						ENTPD4_uc011kzu.1_Intron|ENTPD4_uc003xdm.2_Intron|ENTPD4_uc011kzv.1_3'UTR	NM_004901	NP_004892	Q9Y227	ENTP4_HUMAN	ectonucleoside triphosphate diphosphohydrolase 4						UDP catabolic process	autophagic vacuole membrane|cytoplasmic vesicle|integral to Golgi membrane	uridine-diphosphatase activity			ovary(1)|kidney(1)	2		Prostate(55;0.114)		Colorectal(74;0.0161)|COAD - Colon adenocarcinoma(73;0.0649)		CGTCACTGTCCCTACAATTCT	0.537													15	8	---	---	---	---	PASS
CDCA2	157313	broad.mit.edu	37	8	25317954	25317954	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25317954C>T	uc003xep.1	+	3	595	c.116C>T	c.(115-117)GCC>GTC	p.A39V	PPP2R2A_uc003xek.2_Intron|KCTD9_uc003xeo.2_5'Flank|CDCA2_uc011lae.1_Missense_Mutation_p.A39V|CDCA2_uc003xeq.1_Missense_Mutation_p.A24V	NM_152562	NP_689775	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	39					cell division|mitosis	cytoplasm|nucleus					0		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)		CAGAAGCATGCCGAATTACCT	0.428													4	194	---	---	---	---	PASS
WHSC1L1	54904	broad.mit.edu	37	8	38187059	38187059	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38187059G>A	uc003xli.2	-	6	1936	c.1418C>T	c.(1417-1419)GCG>GTG	p.A473V	WHSC1L1_uc011lbm.1_Missense_Mutation_p.A473V|WHSC1L1_uc010lwe.2_Missense_Mutation_p.A473V|WHSC1L1_uc003xlj.2_Missense_Mutation_p.A473V	NM_023034	NP_075447	Q9BZ95	NSD3_HUMAN	WHSC1L1 protein isoform long	473					cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome	histone-lysine N-methyltransferase activity|zinc ion binding			breast(1)	1	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			CCTTGCTGCCGCAGTTTTCCA	0.483			T	NUP98	AML								4	146	---	---	---	---	PASS
XKR4	114786	broad.mit.edu	37	8	56436707	56436707	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56436707G>A	uc003xsf.2	+	3	1906	c.1874G>A	c.(1873-1875)TGT>TAT	p.C625Y		NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related	625						integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)			GCTTTTGAATGTTCCCCATCT	0.448													39	91	---	---	---	---	PASS
HNF4G	3174	broad.mit.edu	37	8	76465297	76465297	+	Silent	SNP	G	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76465297G>T	uc003yaq.2	+	6	639	c.369G>T	c.(367-369)GGG>GGT	p.G123G	HNF4G_uc003yar.2_Silent_p.G160G	NM_004133	NP_004124	Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma	123					endocrine pancreas development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1	Breast(64;0.0448)		BRCA - Breast invasive adenocarcinoma(89;0.161)			CAAGCCCTGGGTCAAGCACTG	0.343													4	103	---	---	---	---	PASS
RALYL	138046	broad.mit.edu	37	8	85774642	85774642	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85774642G>A	uc003ycq.3	+	7	941	c.525G>A	c.(523-525)ATG>ATA	p.M175I	RALYL_uc003ycr.3_Missense_Mutation_p.M175I|RALYL_uc003ycs.3_Missense_Mutation_p.M175I|RALYL_uc010lzy.2_Missense_Mutation_p.M164I|RALYL_uc003yct.3_Missense_Mutation_p.M188I|RALYL_uc003ycu.3_Missense_Mutation_p.M102I|RALYL_uc003ycv.3_Missense_Mutation_p.M87I	NM_001100392	NP_001093862	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like isoform 2	175							identical protein binding|nucleotide binding|RNA binding			ovary(1)	1						TCTTTTCCATGAAAGGTGGAT	0.488													6	33	---	---	---	---	PASS
VPS13B	157680	broad.mit.edu	37	8	100515083	100515083	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100515083A>T	uc003yiv.2	+	27	4173	c.4062A>T	c.(4060-4062)GAA>GAT	p.E1354D	VPS13B_uc003yiw.2_Missense_Mutation_p.E1354D|VPS13B_uc003yiu.1_Missense_Mutation_p.E1354D|VPS13B_uc003yix.1_Missense_Mutation_p.E824D	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	1354					protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			TGGTCAGTGAACTAGAAGATC	0.318													91	264	---	---	---	---	PASS
PKHD1L1	93035	broad.mit.edu	37	8	110502193	110502193	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110502193T>G	uc003yne.2	+	60	9997	c.9893T>G	c.(9892-9894)ATA>AGA	p.I3298R		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	3298	Extracellular (Potential).|PbH1 5.				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			AATGCAAGAATAAGTAATGTG	0.333										HNSCC(38;0.096)			7	51	---	---	---	---	PASS
ERMP1	79956	broad.mit.edu	37	9	5801287	5801287	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5801287C>A	uc003zjm.1	-	11	2010	c.1956G>T	c.(1954-1956)ATG>ATT	p.M652I	ERMP1_uc011lme.1_RNA|ERMP1_uc010mhs.1_Missense_Mutation_p.M266I	NM_024896	NP_079172	Q7Z2K6	ERMP1_HUMAN	aminopeptidase Fxna	652	Helical; (Potential).				proteolysis	endoplasmic reticulum membrane|integral to membrane	metal ion binding|metallopeptidase activity			ovary(1)	1		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)		TTAAAGTTAGCATGGTTTTTT	0.373													3	67	---	---	---	---	PASS
RANBP6	26953	broad.mit.edu	37	9	6012658	6012658	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6012658T>G	uc003zjr.2	-	1	2961	c.2950A>C	c.(2950-2952)ATA>CTA	p.I984L	RANBP6_uc011lmf.1_Missense_Mutation_p.I632L|RANBP6_uc003zjs.2_Missense_Mutation_p.I572L	NM_012416	NP_036548	O60518	RNBP6_HUMAN	RAN binding protein 6	984	HEAT 7.				protein transport	cytoplasm|nucleus	binding			ovary(3)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		ATCTTCCCTATTGCTGAGATA	0.363													3	125	---	---	---	---	PASS
AQP7	364	broad.mit.edu	37	9	33385545	33385545	+	Intron	SNP	A	T	T	rs114344786	by1000genomes	TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33385545A>T	uc003zst.2	-						SUGT1P1_uc010mjq.1_Intron|AQP7_uc003zsu.1_Intron|AQP7_uc010mjs.2_3'UTR|AQP7_uc010mjt.2_3'UTR|AQP7_uc011lnx.1_3'UTR|AQP7_uc011lny.1_3'UTR|AQP7_uc003zss.3_3'UTR|AQP7_uc011lnz.1_3'UTR|AQP7_uc011loa.1_3'UTR	NM_001170	NP_001161	O14520	AQP7_HUMAN	aquaporin 7						excretion|generation of precursor metabolites and energy	cell-cell junction|cytoplasm|integral to plasma membrane	glycerol channel activity|water channel activity				0			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		CTGGGGGCTCAGCAGGACCCT	0.607													3	20	---	---	---	---	PASS
LOC442421	442421	broad.mit.edu	37	9	66500794	66500794	+	RNA	SNP	T	C	C	rs7866420	by1000genomes	TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66500794T>C	uc004aed.1	+	3		c.887T>C								Homo sapiens similar to prostaglandin E receptor 4, subtype EP4; PGE receptor, EP4 subtype; prostaglandin E2 receptor, mRNA (cDNA clone IMAGE:5288780).												0						TTAAAGACTTTGGACCACCTA	0.647													6	12	---	---	---	---	PASS
AMBP	259	broad.mit.edu	37	9	116840415	116840415	+	Silent	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116840415C>T	uc004bie.3	-	1	338	c.75G>A	c.(73-75)CCG>CCA	p.P25P	AMBP_uc011lxk.1_5'Flank|AMBP_uc010mvc.1_RNA	NM_001633	NP_001624	P02760	AMBP_HUMAN	alpha-1-microglobulin/bikunin preproprotein	25					cell adhesion|female pregnancy|heme catabolic process|interspecies interaction between organisms|negative regulation of immune response|negative regulation of JNK cascade|protein-chromophore linkage	extracellular region|plasma membrane	calcium channel inhibitor activity|calcium oxalate binding|heme binding|IgA binding|protein homodimerization activity|serine-type endopeptidase inhibitor activity|transporter activity			skin(1)	1					Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064)	TGTTGTCGGGCGGCGTTGGCA	0.617													44	54	---	---	---	---	PASS
SLC34A3	142680	broad.mit.edu	37	9	140129157	140129157	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140129157G>A	uc004cmf.1	+	12	1495	c.1309G>A	c.(1309-1311)GCA>ACA	p.A437T	SLC34A3_uc011met.1_Missense_Mutation_p.A437T	NM_080877	NP_543153	Q8N130	NPT2C_HUMAN	solute carrier family 34 (sodium phosphate),	437	Extracellular (Potential).				cellular phosphate ion homeostasis	apical plasma membrane|integral to membrane	sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity				0	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		GGCCAGCCCCGCAGACAGGAT	0.662													9	11	---	---	---	---	PASS
TUBBP5	643224	broad.mit.edu	37	9	141071110	141071110	+	Silent	SNP	A	G	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:141071110A>G	uc004com.2	+	4	774	c.513A>G	c.(511-513)CCA>CCG	p.P171P	TUBBP5_uc010ncq.2_3'UTR					RecName: Full=Putative tubulin beta-4q chain;												0						TGCGCTTCCCAGGCCAGCTGA	0.597													11	42	---	---	---	---	PASS
C10orf129	142827	broad.mit.edu	37	10	96967148	96967148	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96967148G>A	uc001kke.2	+	4	712	c.587G>A	c.(586-588)TGG>TAG	p.W196*	C10orf129_uc009xuu.1_Nonsense_Mutation_p.W106*	NM_207321	NP_997204	Q6P461	ACSM6_HUMAN	acyl-coenzyme A synthetase ACSM6, mitochondrial	196					fatty acid metabolic process	mitochondrion	ATP binding|butyrate-CoA ligase activity|GTP binding|metal ion binding				0		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)		TATGATGGGTGGTTGGATTTC	0.423													40	119	---	---	---	---	PASS
ODF3	113746	broad.mit.edu	37	11	199997	199997	+	Silent	SNP	T	C	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:199997T>C	uc001lob.2	+	7	1023	c.729T>C	c.(727-729)TCT>TCC	p.S243S	ODF3_uc010qvk.1_Silent_p.S196S|ODF3_uc001loc.2_3'UTR	NM_053280	NP_444510	Q96PU9	ODF3A_HUMAN	outer dense fiber of sperm tails 3	243					cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm				ovary(1)	1		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;3.95e-27)|Epithelial(43;2.66e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.55e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		TCAAACACTCTGATTACATGA	0.607													14	47	---	---	---	---	PASS
OR52B4	143496	broad.mit.edu	37	11	4389154	4389154	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4389154G>C	uc010qye.1	-	1	372	c.372C>G	c.(370-372)CAC>CAG	p.H124Q		NM_001005161	NP_001005161	Q8NGK2	O52B4_HUMAN	olfactory receptor, family 52, subfamily B,	124	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|Breast(177;0.0249)|all_neural(188;0.0577)		Epithelial(150;1.57e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0826)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGGCAATATAGTGGTCAAAGG	0.458													27	113	---	---	---	---	PASS
OR52J3	119679	broad.mit.edu	37	11	5068411	5068411	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5068411A>G	uc010qyv.1	+	1	656	c.656A>G	c.(655-657)TAT>TGT	p.Y219C		NM_001001916	NP_001001916	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J,	219	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|lung(1)|skin(1)	3		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)		GGCATCTCGTATGTTTACATT	0.443													7	370	---	---	---	---	PASS
NR1H3	10062	broad.mit.edu	37	11	47283271	47283271	+	Silent	SNP	G	C	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47283271G>C	uc009ylm.2	+	6	1103	c.882G>C	c.(880-882)GCG>GCC	p.A294A	NR1H3_uc009yll.1_Silent_p.A300A|NR1H3_uc010rhk.1_Silent_p.A300A|NR1H3_uc001nek.2_Silent_p.A249A|NR1H3_uc001nej.2_Intron|NR1H3_uc001nel.2_Silent_p.A249A|NR1H3_uc001nen.3_Intron|NR1H3_uc001nem.2_Silent_p.A294A|NR1H3_uc001nep.2_Intron	NM_005693	NP_005684	Q13133	NR1H3_HUMAN	nuclear receptor subfamily 1, group H, member 3	294	Ligand-binding (Potential).				apoptotic cell clearance|cellular response to lipopolysaccharide|cholesterol homeostasis|negative regulation of cholesterol storage|negative regulation of inflammatory response|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of lipid transport|negative regulation of macrophage activation|negative regulation of pancreatic juice secretion|negative regulation of pinocytosis|negative regulation of secretion of lysosomal enzymes|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cellular protein metabolic process|positive regulation of cholesterol efflux|positive regulation of cholesterol homeostasis|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of receptor biosynthetic process|positive regulation of toll-like receptor 4 signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of triglyceride biosynthetic process|regulation of circadian rhythm|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to progesterone stimulus|triglyceride homeostasis	nuclear chromatin|nucleoplasm	cholesterol binding|steroid hormone receptor activity|sterol response element binding|transcription coactivator activity|zinc ion binding			ovary(2)|lung(1)	3						AGACCTCTGCGATCGAGGTGG	0.577													7	62	---	---	---	---	PASS
C1QTNF4	114900	broad.mit.edu	37	11	47611595	47611595	+	Silent	SNP	G	C	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47611595G>C	uc001ngc.2	-	2	1035	c.768C>G	c.(766-768)GCC>GCG	p.A256A		NM_031909	NP_114115	Q9BXJ3	C1QT4_HUMAN	C1q and tumor necrosis factor related protein 4	256	C1q 2.					extracellular region					0						CGTAAATCATGGCCTGCACCT	0.672													11	32	---	---	---	---	PASS
SYT7	9066	broad.mit.edu	37	11	61295625	61295625	+	Silent	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61295625G>A	uc001nrv.2	-	5	390	c.384C>T	c.(382-384)CAC>CAT	p.H128H	SYT7_uc009ynr.2_Silent_p.H203H	NM_004200	NP_004191	O43581	SYT7_HUMAN	synaptotagmin VII	128	Cytoplasmic (Potential).					cell junction|integral to membrane|synaptic vesicle membrane	transporter activity			ovary(3)|pancreas(1)	4						TGCAACCCTCGTGGGCCTCAT	0.652													26	58	---	---	---	---	PASS
BEST1	7439	broad.mit.edu	37	11	61727371	61727371	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61727371T>C	uc001nss.2	+	9	1536	c.956T>C	c.(955-957)CTG>CCG	p.L319P	BEST1_uc010rlq.1_Missense_Mutation_p.C327R|BEST1_uc010rlr.1_Intron|BEST1_uc010rls.1_Intron|BEST1_uc001nsr.2_Missense_Mutation_p.L259P|BEST1_uc009ynt.2_RNA|BEST1_uc010rlt.1_Missense_Mutation_p.L259P|BEST1_uc001nst.2_Missense_Mutation_p.L232P|BEST1_uc010rlu.1_Missense_Mutation_p.C281R|BEST1_uc010rlv.1_Missense_Mutation_p.L213P	NM_004183	NP_004174	O76090	BEST1_HUMAN	bestrophin 1 isoform 1	319	Cytoplasmic (Potential).				response to stimulus|transepithelial chloride transport|visual perception	basolateral plasma membrane|chloride channel complex|cytosol|membrane fraction	chloride channel activity			central_nervous_system(1)	1						CAGGTGTCCCTGTTGGCTGTG	0.517													17	25	---	---	---	---	PASS
SUV420H1	51111	broad.mit.edu	37	11	67926348	67926348	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67926348G>A	uc001onm.1	-	11	1721	c.1465C>T	c.(1465-1467)CCC>TCC	p.P489S	SUV420H1_uc009yse.1_Missense_Mutation_p.P75S|SUV420H1_uc001onn.1_Missense_Mutation_p.P317S|SUV420H1_uc009ysf.2_Missense_Mutation_p.P249S	NM_017635	NP_060105	Q4FZB7	SV421_HUMAN	suppressor of variegation 4-20 homolog 1 isoform	489					regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			ovary(2)|kidney(1)	3						TTTTTAATGGGCAAATTTTTA	0.458													4	163	---	---	---	---	PASS
NARS2	79731	broad.mit.edu	37	11	78285406	78285406	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78285406C>T	uc001ozi.2	-	1	504	c.128G>A	c.(127-129)CGC>CAC	p.R43H	NARS2_uc010rsq.1_Intron	NM_024678	NP_078954	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial	43					asparaginyl-tRNA aminoacylation	mitochondrial matrix	asparagine-tRNA ligase activity|ATP binding|nucleic acid binding			ovary(2)	2	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	GATCTTAATGCGCTCCCCACT	0.542													4	315	---	---	---	---	PASS
ODZ4	26011	broad.mit.edu	37	11	78380861	78380861	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78380861C>G	uc001ozl.3	-	32	6992	c.6529G>C	c.(6529-6531)GTG>CTG	p.V2177L	ODZ4_uc001ozk.3_Missense_Mutation_p.V402L|ODZ4_uc009yvb.1_Missense_Mutation_p.V761L	NM_001098816	NP_001092286	Q6N022	TEN4_HUMAN	odz, odd Oz/ten-m homolog 4	2177	YD 17.|Extracellular (Potential).				signal transduction	integral to membrane				ovary(2)|pancreas(2)	4						TCCTTCTTCACTACTCGCCCC	0.498													20	29	---	---	---	---	PASS
CBL	867	broad.mit.edu	37	11	119168096	119168096	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119168096C>T	uc001pwe.2	+	14	2294	c.2156C>T	c.(2155-2157)GCA>GTA	p.A719V		NM_005188	NP_005179	P22681	CBL_HUMAN	Cas-Br-M (murine) ecotropic retroviral	719	Interaction with CD2AP.|Asp/Glu-rich (acidic).				epidermal growth factor receptor signaling pathway|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of receptor-mediated endocytosis	cytosol|nucleus	calcium ion binding|sequence-specific DNA binding transcription factor activity|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(135)|lung(10)|central_nervous_system(2)|ovary(1)|breast(1)	149		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		TGGTTCAGAGCATGTGATTGC	0.398									CBL_gene-associated_Juvenile_Myelomonocytic_Leukemia_and_Developmental_Anomalies|Noonan_syndrome				37	77	---	---	---	---	PASS
TECTA	7007	broad.mit.edu	37	11	121016494	121016494	+	Silent	SNP	G	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121016494G>T	uc010rzo.1	+	11	3774	c.3774G>T	c.(3772-3774)CTG>CTT	p.L1258L		NM_005422	NP_005413	O75443	TECTA_HUMAN	tectorin alpha precursor	1258	VWFD 3.				cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix				breast(6)|ovary(2)|skin(2)	10	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		CCATGGGTCTGCTTGCATCGA	0.592													6	139	---	---	---	---	PASS
KDM5A	5927	broad.mit.edu	37	12	442697	442697	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:442697C>T	uc001qif.1	-	12	1972	c.1609G>A	c.(1609-1611)GTT>ATT	p.V537I	KDM5A_uc001qie.1_Missense_Mutation_p.V537I|KDM5A_uc010sdn.1_Missense_Mutation_p.V496I|KDM5A_uc010sdo.1_Missense_Mutation_p.V156I	NM_001042603	NP_001036068	P29375	KDM5A_HUMAN	retinoblastoma binding protein 2 isoform 1	537	JmjC.				chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3						ATGATGGTAACTAACTGATGC	0.433			T 	NUP98	AML								91	82	---	---	---	---	PASS
SCNN1A	6337	broad.mit.edu	37	12	6463640	6463640	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6463640C>T	uc001qnx.2	-	8	1613	c.1324G>A	c.(1324-1326)GTG>ATG	p.V442M	SCNN1A_uc001qnv.2_Missense_Mutation_p.V142M|SCNN1A_uc001qnw.2_Missense_Mutation_p.V501M|SCNN1A_uc010sfb.1_Missense_Mutation_p.V465M	NM_001038	NP_001029	P37088	SCNNA_HUMAN	sodium channel, nonvoltage-gated 1 alpha isoform	442	Extracellular (By similarity).				excretion|response to stimulus|sensory perception of taste	apical plasma membrane	WW domain binding				0					Amiloride(DB00594)|Triamterene(DB00384)	CAGTACTCCACGTTCTGGGGC	0.577													25	145	---	---	---	---	PASS
RIMKLB	57494	broad.mit.edu	37	12	8902521	8902521	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8902521C>T	uc001quu.2	+	3	490	c.239C>T	c.(238-240)ACC>ATC	p.T80I	RIMKLB_uc009zgf.1_RNA|RIMKLB_uc001qux.2_Missense_Mutation_p.T80I|RIMKLB_uc010sgl.1_Missense_Mutation_p.T80I|RIMKLB_uc001quw.2_Missense_Mutation_p.T80I	NM_020734	NP_065785	Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family	80					protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0						AGAGTACCAACCCCTTGGGTG	0.463													11	76	---	---	---	---	PASS
KIAA1467	57613	broad.mit.edu	37	12	13233561	13233561	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13233561C>G	uc001rbi.2	+	13	1889	c.1866C>G	c.(1864-1866)ATC>ATG	p.I622M	KIAA1467_uc009zhx.1_RNA	NM_020853	NP_065904	A2RU67	K1467_HUMAN	hypothetical protein LOC57613	622						integral to membrane				central_nervous_system(2)|skin(1)	3		Prostate(47;0.184)		BRCA - Breast invasive adenocarcinoma(232;0.157)		TTCCATAGATCTAATCTGATG	0.363													22	116	---	---	---	---	PASS
CTDSP2	10106	broad.mit.edu	37	12	58217389	58217389	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58217389G>T	uc001sqm.2	-	8	1341	c.812C>A	c.(811-813)CCT>CAT	p.P271H	CTDSP2_uc010ssg.1_Missense_Mutation_p.P145H|CTDSP2_uc009zqf.2_Missense_Mutation_p.P119H|CTDSP2_uc009zqg.2_Missense_Mutation_p.P98H	NM_005730	NP_005721	O14595	CTDS2_HUMAN	nuclear LIM interactor-interacting factor 2	271					protein dephosphorylation	nucleus|soluble fraction	CTD phosphatase activity|metal ion binding			central_nervous_system(1)	1	all_neural(12;0.00559)|Glioma(12;0.0143)|Melanoma(17;0.122)					GGCAGGCTAAGGGGCCCGCAG	0.582													20	27	---	---	---	---	PASS
LIN7A	8825	broad.mit.edu	37	12	81239638	81239638	+	Silent	SNP	A	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81239638A>T	uc001szj.1	-	4	547	c.354T>A	c.(352-354)CTT>CTA	p.L118L	LIN7A_uc001szk.1_RNA	NM_004664	NP_004655	O14910	LIN7A_HUMAN	lin-7 homolog A	118	PDZ.				exocytosis|protein complex assembly|protein transport	basolateral plasma membrane|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	L27 domain binding			ovary(1)|skin(1)	2						CATTAAAACCAAGGCCTTCAT	0.458													40	106	---	---	---	---	PASS
KDM2B	84678	broad.mit.edu	37	12	121932322	121932322	+	Intron	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121932322C>T	uc001uat.2	-						KDM2B_uc001uar.2_Intron|KDM2B_uc001uas.2_Intron|KDM2B_uc001uau.2_Intron|KDM2B_uc001uav.3_Silent_p.*508*	NM_032590	NP_115979	Q8NHM5	KDM2B_HUMAN	F-box and leucine-rich repeat protein 10 isoform						embryonic camera-type eye morphogenesis|fourth ventricle development|histone H2A monoubiquitination|initiation of neural tube closure|lateral ventricle development|midbrain development|midbrain-hindbrain boundary morphogenesis|negative regulation of neural precursor cell proliferation|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|spermatogenesis|third ventricle development|transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding			ovary(1)|skin(1)	2						GCTGTTCACCCTACAGGAGGT	0.552											OREG0022202	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	4	---	---	---	---	PASS
DNAH10	196385	broad.mit.edu	37	12	124325980	124325980	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124325980C>T	uc001uft.3	+	29	4919	c.4894C>T	c.(4894-4896)CGG>TGG	p.R1632W		NM_207437	NP_997320	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1632	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GAAGATCTTGCGGGCTGAAGG	0.453													5	325	---	---	---	---	PASS
ANKLE2	23141	broad.mit.edu	37	12	133331594	133331594	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133331594C>G	uc001ukx.2	-	2	374	c.307G>C	c.(307-309)GAG>CAG	p.E103Q	ANKLE2_uc001uky.3_Missense_Mutation_p.E41Q	NM_015114	NP_055929	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	103	LEM.					cytoplasm|integral to membrane|nuclear envelope					0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		AATTTTTTCTCAAAAATGAAC	0.458													59	210	---	---	---	---	PASS
LOC284232	284232	broad.mit.edu	37	13	19415641	19415641	+	RNA	SNP	A	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19415641A>T	uc010tcj.1	-	1		c.30469T>A				NR_027995				Homo sapiens ankyrin repeat domain 20 family, member A2 pseudogene (LOC284232), non-coding RNA.												0						aaaaaaaaaaaaacccaaaca	0.169													4	23	---	---	---	---	PASS
RALGAPA1	253959	broad.mit.edu	37	14	36104763	36104763	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36104763C>G	uc001wti.2	-	31	4591	c.4200G>C	c.(4198-4200)ATG>ATC	p.M1400I	RALGAPA1_uc010amp.2_RNA|RALGAPA1_uc001wtj.2_Missense_Mutation_p.M1400I|RALGAPA1_uc010tpv.1_Missense_Mutation_p.M1413I|RALGAPA1_uc010tpw.1_Missense_Mutation_p.M1447I	NM_014990	NP_055805	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1	1400	Minimal domain that binds to TCF3/E12 (By similarity).				activation of Ral GTPase activity	cytosol|mitochondrion|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(3)|breast(1)	4						GAGGTAAGGCCATGATCCAGT	0.343													26	27	---	---	---	---	PASS
SYNE2	23224	broad.mit.edu	37	14	64568741	64568741	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64568741C>T	uc001xgm.2	+	64	12703	c.12473C>T	c.(12472-12474)TCC>TTC	p.S4158F	SYNE2_uc001xgl.2_Missense_Mutation_p.S4158F|SYNE2_uc010apy.2_Missense_Mutation_p.S543F|SYNE2_uc010apz.1_Missense_Mutation_p.S50F	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4158	Cytoplasmic (Potential).			S -> F (in Ref. 2; AAL33802 and 3).	centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GCTTCCTCATCCTCTGGAACA	0.517													21	22	---	---	---	---	PASS
C14orf169	79697	broad.mit.edu	37	14	73959721	73959721	+	3'UTR	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73959721C>T	uc001xok.1	+	3					HEATR4_uc010tua.1_Intron	NM_024644	NP_078920	Q9H6W3	NO66_HUMAN	chromosome 14 open reading frame 169						negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|nucleoplasm	histone demethylase activity (H3-K36 specific)|histone demethylase activity (H3-K4 specific)|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0				BRCA - Breast invasive adenocarcinoma(234;0.0033)|OV - Ovarian serous cystadenocarcinoma(108;0.215)		TTTTTTTTTCCTTAAACTCAC	0.408													7	60	---	---	---	---	PASS
VPS18	57617	broad.mit.edu	37	15	41194909	41194909	+	Silent	SNP	G	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41194909G>T	uc001zne.2	+	5	2631	c.2292G>T	c.(2290-2292)GTG>GTT	p.V764V		NM_020857	NP_065908	Q9P253	VPS18_HUMAN	vacuolar protein sorting 18	764	Clathrin.				endosome organization|lysosome organization|protein transport	HOPS complex|late endosome membrane|lysosomal membrane	metal ion binding|protein binding			ovary(2)|large_intestine(1)	3		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.07e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.164)		GGCACGTGGTGCAGGAAGAGG	0.562													10	37	---	---	---	---	PASS
ZSCAN2	54993	broad.mit.edu	37	15	85164527	85164527	+	Silent	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85164527C>T	uc002bkr.2	+	3	1327	c.1101C>T	c.(1099-1101)TGC>TGT	p.C367C	ZSCAN2_uc010bmz.1_Silent_p.C365C|ZSCAN2_uc010bna.2_Silent_p.C217C|ZSCAN2_uc010uox.1_Intron|ZSCAN2_uc010uoy.1_Intron|ZSCAN2_uc010uoz.1_Intron	NM_181877	NP_870992	Q7Z7L9	ZSCA2_HUMAN	zinc finger protein 29 isoform 1	367	C2H2-type 6.				cell differentiation|multicellular organismal development|spermatogenesis|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (272;0.168)|all cancers(203;5.43e-22)		GTAAAGAATGCGGCGAAAGCT	0.502													5	259	---	---	---	---	PASS
WASH3P	374666	broad.mit.edu	37	15	102516424	102516424	+	Silent	SNP	G	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102516424G>T	uc002cdi.2	+	11	2170	c.750G>T	c.(748-750)CCG>CCT	p.P250P	WASH3P_uc002cdl.2_Silent_p.P250P|WASH3P_uc002cdk.2_RNA|WASH3P_uc002cdp.2_Silent_p.P250P|WASH3P_uc010bpo.2_RNA|WASH3P_uc002cdq.2_RNA|WASH3P_uc002cdr.2_RNA	NR_003659				RecName: Full=WAS protein family homolog 2; AltName: Full=Protein FAM39B; AltName: Full=CXYorf1-like protein on chromosome 2;												0						TGCCGCCACCGCAGCAGCCAC	0.647													5	24	---	---	---	---	PASS
TELO2	9894	broad.mit.edu	37	16	1557648	1557648	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1557648A>C	uc002cly.2	+	20	2629	c.2338A>C	c.(2338-2340)AGC>CGC	p.S780R		NM_016111	NP_057195	Q9Y4R8	TELO2_HUMAN	TEL2, telomere maintenance 2, homolog	780						chromosome, telomeric region|cytoplasm|membrane|nucleus	protein binding				0		Hepatocellular(780;0.219)				CGTCCTGCTCAGCCTGCCTGC	0.697													3	8	---	---	---	---	PASS
C16orf75	116028	broad.mit.edu	37	16	11444604	11444604	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11444604T>C	uc002daw.1	+	2	419	c.401T>C	c.(400-402)ATG>ACG	p.M134T	C16orf75_uc002daq.1_RNA	NM_152308	NP_689521	Q96E14	RMI2_HUMAN	RecQ-mediated genome instability protein 2	134					DNA replication	nucleus	DNA binding				0						CATGAAAGTATGTGGGAACTG	0.443			T	CIITA	PMBL|Hodgkin Lymphona|								60	116	---	---	---	---	PASS
TMEM159	57146	broad.mit.edu	37	16	21172478	21172478	+	5'UTR	SNP	C	G	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21172478C>G	uc002dif.3	+	2					DNAH3_uc010vbe.1_5'Flank|TMEM159_uc002dig.3_RNA|TMEM159_uc010vbf.1_5'UTR|TMEM159_uc002dih.3_5'UTR	NM_020422	NP_065155	Q96B96	TM159_HUMAN	transmembrane protein 159							integral to membrane				ovary(1)	1				GBM - Glioblastoma multiforme(48;0.0972)		TAATTCATCCCTAAAGAGATT	0.478													17	72	---	---	---	---	PASS
RRN3P1	730092	broad.mit.edu	37	16	21817457	21817457	+	Silent	SNP	G	A	A	rs150520281	by1000genomes	TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21817457G>A	uc010vbl.1	-	7	603	c.106C>T	c.(106-108)CTG>TTG	p.L36L	uc002diq.3_Intron	NR_003370				SubName: Full=Putative uncharacterized protein ENSP00000219758;												0						CTTACATCCAGCTTGAGTAGT	0.254													3	38	---	---	---	---	PASS
CACNG3	10368	broad.mit.edu	37	16	24268131	24268131	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24268131C>T	uc002dmf.2	+	1	1256	c.56C>T	c.(55-57)GCC>GTC	p.A19V		NM_006539	NP_006530	O60359	CCG3_HUMAN	voltage-dependent calcium channel gamma-3	19	Helical; (Potential).				regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex	voltage-gated calcium channel activity				0				GBM - Glioblastoma multiforme(48;0.0809)		GGAGCCTTTGCCGCTTTTAGT	0.483													4	247	---	---	---	---	PASS
ATXN2L	11273	broad.mit.edu	37	16	28847661	28847661	+	3'UTR	SNP	A	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28847661A>T	uc002drc.2	+	22					uc010vct.1_Intron|ATXN2L_uc002drb.2_Intron|ATXN2L_uc002dqy.2_Nonsense_Mutation_p.R1052*|ATXN2L_uc002dra.2_Intron|ATXN2L_uc002dqz.2_Intron|ATXN2L_uc010vdb.1_Intron|ATXN2L_uc002dre.2_Intron|ATXN2L_uc002drf.2_3'UTR|ATXN2L_uc002drg.2_3'UTR	NM_007245	NP_009176	Q8WWM7	ATX2L_HUMAN	ataxin 2 related protein isoform A							membrane				upper_aerodigestive_tract(1)|ovary(1)	2						TAGGGTGGGCAGAAGCCACAG	0.662													10	29	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	32077407	32077407	+	RNA	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32077407G>A	uc010vft.1	+	1		c.22G>A			uc010vfu.1_5'Flank					Homo sapiens IGH mRNA for immunoglobulin heavy chain VHDJ region, partial cds, clone:aims0058h.																		GGTGGAGTCTGGAGGAGGCTT	0.562													27	261	---	---	---	---	PASS
GNAO1	2775	broad.mit.edu	37	16	56309956	56309956	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56309956G>A	uc002eit.3	+	3	1172	c.275G>A	c.(274-276)GGC>GAC	p.G92D	GNAO1_uc002eiu.3_Missense_Mutation_p.G92D	NM_138736	NP_620073	P09471	GNAO_HUMAN	guanine nucleotide binding protein, alpha	92					dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|muscle contraction	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|metabotropic serotonin receptor binding|signal transducer activity			lung(1)|breast(1)	2		all_neural(199;0.159)				GACACTTTGGGCATCGAATAT	0.522													24	65	---	---	---	---	PASS
NLRP1	22861	broad.mit.edu	37	17	5425107	5425107	+	Splice_Site	SNP	C	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5425107C>A	uc002gci.2	-	13	4076	c.3521_splice	c.e13-1	p.G1174_splice	NLRP1_uc002gcg.1_Splice_Site_p.G1178_splice|NLRP1_uc002gck.2_Splice_Site_p.G1174_splice|NLRP1_uc002gcj.2_Splice_Site_p.G1144_splice|NLRP1_uc002gcl.2_Splice_Site_p.G1144_splice|NLRP1_uc002gch.3_Splice_Site_p.G1174_splice	NM_033004	NP_127497	Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1 isoform 1						defense response to bacterium|induction of apoptosis|neuron apoptosis|positive regulation of interleukin-1 beta secretion|response to muramyl dipeptide	cytoplasm|NALP1 inflammasome complex|nucleus	ATP binding|caspase activator activity|enzyme binding|protein domain specific binding			lung(4)|breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	9		Colorectal(1115;3.48e-05)				ACATGGCCCCCTGTAAAAGAA	0.343													4	72	---	---	---	---	PASS
TEX19	400629	broad.mit.edu	37	17	80320495	80320495	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80320495C>A	uc002keq.2	+	2	778	c.469C>A	c.(469-471)CAC>AAC	p.H157N		NM_207459	NP_997342	Q8NA77	TEX19_HUMAN	testis expressed 19	157						nucleus					0						TACCTGCTCACACTGGCCAAG	0.592													7	113	---	---	---	---	PASS
C18orf8	29919	broad.mit.edu	37	18	21084363	21084363	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21084363C>T	uc010xax.1	+	2	252	c.131C>T	c.(130-132)ACT>ATT	p.T44I	C18orf8_uc010xau.1_5'UTR|C18orf8_uc010xav.1_Missense_Mutation_p.T44I|C18orf8_uc010xaw.1_5'UTR|C18orf8_uc002kul.2_RNA	NM_013326	NP_037458	Q96DM3	MIC1_HUMAN	colon cancer-associated protein Mic1	44										ovary(1)	1	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)					GGTGGAGCTACTGGCGTGGTA	0.433													112	214	---	---	---	---	PASS
AQP4	361	broad.mit.edu	37	18	24436258	24436258	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24436258C>A	uc002kwa.2	-	5	952	c.889G>T	c.(889-891)GGA>TGA	p.G297*	AQP4_uc002kvz.2_Nonsense_Mutation_p.G275*	NM_001650	NP_001641	P55087	AQP4_HUMAN	aquaporin 4 isoform a	297	Cytoplasmic (Potential).				cellular response to interferon-gamma|excretion|nervous system development	cytoplasm|external side of plasma membrane|integral to plasma membrane	water channel activity				0	all_cancers(21;0.0172)|Lung NSC(5;0.00299)|all_lung(6;0.00747)|Ovarian(20;0.124)					TGCACCACTCCAGGTTTTAGA	0.493													6	580	---	---	---	---	PASS
ABCA7	10347	broad.mit.edu	37	19	1048966	1048966	+	Missense_Mutation	SNP	A	T	T	rs145106069		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1048966A>T	uc002lqw.3	+	17	2573	c.2342A>T	c.(2341-2343)AAG>ATG	p.K781M	ABCA7_uc010dsb.1_Missense_Mutation_p.K643M	NM_019112	NP_061985	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A, member 7	781					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)		CGGCCCCCCAAGAGTCCAGCC	0.607													6	26	---	---	---	---	PASS
NCLN	56926	broad.mit.edu	37	19	3192504	3192504	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3192504C>T	uc002lxi.2	+	2	375	c.221C>T	c.(220-222)ACG>ATG	p.T74M	NCLN_uc002lxh.1_RNA	NM_020170	NP_064555	Q969V3	NCLN_HUMAN	nicalin precursor	74	Lumenal (Potential).				proteolysis|regulation of signal transduction	endoplasmic reticulum membrane|integral to membrane|nucleus	peptidase activity|protein binding				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.83e-113)|Epithelial(107;1.65e-111)|all cancers(105;1.53e-103)|BRCA - Breast invasive adenocarcinoma(158;0.00139)|STAD - Stomach adenocarcinoma(1328;0.18)		GAGGCGCGCACGATGGCGGCG	0.706													7	13	---	---	---	---	PASS
INSR	3643	broad.mit.edu	37	19	7152929	7152929	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7152929A>G	uc002mgd.1	-	10	2148	c.2039T>C	c.(2038-2040)CTG>CCG	p.L680P	INSR_uc002mge.1_Missense_Mutation_p.L680P|INSR_uc002mgf.2_Missense_Mutation_p.L680P	NM_000208	NP_000199	P06213	INSR_HUMAN	insulin receptor isoform Long precursor	680	Fibronectin type-III 1.				activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	CCTCGAGGGCAGCTTCAGCCC	0.428													47	73	---	---	---	---	PASS
GDF15	9518	broad.mit.edu	37	19	18499472	18499472	+	Silent	SNP	G	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18499472G>T	uc002niv.2	+	2	686	c.654G>T	c.(652-654)GCG>GCT	p.A218A		NM_004864	NP_004855	Q99988	GDF15_HUMAN	growth differentiation factor 15	218					cell-cell signaling|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity			central_nervous_system(1)	1						CGGTCCGCGCGTCGCTGGAAG	0.736											OREG0025363	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	41	---	---	---	---	PASS
PRX	57716	broad.mit.edu	37	19	40900919	40900919	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40900919C>A	uc002onr.2	-	7	3609	c.3340G>T	c.(3340-3342)GGG>TGG	p.G1114W	PRX_uc002onq.2_Missense_Mutation_p.G975W|PRX_uc002ons.2_3'UTR	NM_181882	NP_870998	Q9BXM0	PRAX_HUMAN	periaxin isoform 2	1114	Glu-rich (acidic).				axon ensheathment	cytoplasm|nucleus|plasma membrane	protein binding			ovary(2)	2			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GCCACAGCCCCCTCTGCCCTC	0.672													28	83	---	---	---	---	PASS
B3GNT8	374907	broad.mit.edu	37	19	41931921	41931921	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41931921C>T	uc002oqs.2	-	3	1217	c.763G>A	c.(763-765)GCC>ACC	p.A255T	CYP2F1_uc010xvw.1_Intron|B3GNT8_uc002oqt.1_Intron	NM_198540	NP_940942	Q7Z7M8	B3GN8_HUMAN	UDP-GlcNAc:betaGal	255	Lumenal (Potential).				poly-N-acetyllactosamine biosynthetic process|protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity|protein N-acetylglucosaminyltransferase activity				0						GCCAGCAGGGCAGGGGTGTGT	0.657													38	48	---	---	---	---	PASS
FLRT3	23767	broad.mit.edu	37	20	14306094	14306094	+	3'UTR	SNP	T	C	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14306094T>C	uc002wov.1	-	3					MACROD2_uc002wot.2_Intron|MACROD2_uc002wou.2_Intron|FLRT3_uc002wow.1_3'UTR	NM_198391	NP_938205	Q9NZU0	FLRT3_HUMAN	fibronectin leucine rich transmembrane protein 3						cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity			kidney(1)	1		Colorectal(1;0.0464)	COAD - Colon adenocarcinoma(2;0.129)	Colorectal(1;0.0393)		AGTACATTGCTTTTTTTCAGT	0.358													20	33	---	---	---	---	PASS
FAM182B	728882	broad.mit.edu	37	20	25848606	25848606	+	RNA	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25848606G>A	uc002wvd.1	-	1		c.181C>T								Homo sapiens cDNA FLJ30282 fis, clone BRACE2002803.												0						atcaccgtccgggcaggcctg	0.000													3	6	---	---	---	---	PASS
C20orf191	149934	broad.mit.edu	37	20	26084295	26084295	+	Missense_Mutation	SNP	C	T	T	rs76611503	by1000genomes	TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26084295C>T	uc002wvj.3	-	2	176	c.121G>A	c.(121-123)GGA>AGA	p.G41R		NR_003678				SubName: Full=Putative uncharacterized protein ENSP00000323172;												0						TGTTTGCCTCCAAATGCTGGA	0.373													4	187	---	---	---	---	PASS
C20orf191	149934	broad.mit.edu	37	20	26084296	26084296	+	Silent	SNP	A	G	G	rs61752037	by1000genomes	TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26084296A>G	uc002wvj.3	-	2	175	c.120T>C	c.(118-120)TTT>TTC	p.F40F		NR_003678				SubName: Full=Putative uncharacterized protein ENSP00000323172;												0						GTTTGCCTCCAAATGCTGGAT	0.378													4	185	---	---	---	---	PASS
MANBAL	63905	broad.mit.edu	37	20	35944852	35944852	+	3'UTR	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35944852G>A	uc002xgu.2	+	4					MANBAL_uc002xgv.2_3'UTR|MANBAL_uc002xgw.2_RNA|MANBAL_uc010gfx.2_RNA|MANBAL_uc010gfy.2_RNA	NM_022077	NP_071360	Q9NQG1	MANBL_HUMAN	mannosidase, beta A, lysosomal-like							integral to membrane					0		Myeloproliferative disorder(115;0.00878)				CGGGCAGGGAGAGGGTCTTGG	0.587													22	25	---	---	---	---	PASS
MAFB	9935	broad.mit.edu	37	20	39317054	39317054	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39317054G>A	uc002xji.2	-	1	823	c.437C>T	c.(436-438)CCG>CTG	p.P146L		NM_005461	NP_005452	Q9Y5Q3	MAFB_HUMAN	transcription factor MAFB	146					negative regulation of erythrocyte differentiation		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding				0		Myeloproliferative disorder(115;0.00878)				GCCGGCGCCCGGGTACGCgtg	0.587			T	IGH@	MM								14	13	---	---	---	---	PASS
ZNFX1	57169	broad.mit.edu	37	20	47886935	47886935	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47886935T>C	uc002xui.2	-	3	1661	c.1414A>G	c.(1414-1416)AGG>GGG	p.R472G		NM_021035	NP_066363	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	472							metal ion binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			TCCTGCTCCCTGTTAGATACG	0.488													42	193	---	---	---	---	PASS
GNAS	2778	broad.mit.edu	37	20	57470663	57470663	+	Intron	SNP	C	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57470663C>A	uc002xzw.2	+						GNAS_uc002xzt.2_Intron|GNAS_uc002xzu.3_Intron|GNAS_uc010gjq.2_Intron|GNAS_uc002xzv.2_Intron|GNAS_uc002xzx.2_Intron|GNAS_uc010gjr.2_Intron|GNAS_uc002xzy.2_Intron|GNAS_uc002yaa.2_Intron|GNAS_uc010zzt.1_Intron|GNAS_uc002yab.2_Intron|GNAS_uc002yac.1_RNA|GNAS_uc002yad.2_5'Flank	NM_080425	NP_536350	P63092	GNAS2_HUMAN	GNAS complex locus XLas						activation of adenylate cyclase activity|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|intracellular transport|platelet activation|regulation of insulin secretion|sensory perception of smell|transmembrane transport|water transport	heterotrimeric G-protein complex|intrinsic to membrane|trans-Golgi network membrane	adenylate cyclase activity|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|identical protein binding|signal transducer activity			pituitary(201)|thyroid(35)|ovary(15)|adrenal_gland(9)|liver(7)|large_intestine(5)|parathyroid(5)|kidney(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|testis(1)|stomach(1)|small_intestine(1)|autonomic_ganglia(1)|pancreas(1)	292	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			CTTTCATTTTCTAGGTGCTGG	0.423			Mis		pituitary adenoma		McCune-Albright syndrome; pseudohypoparathyroidism|type IA		3-Methylglutaconic_Aciduria_and_Myelodysplasia|McCune-Albright_syndrome|Mazabraud_syndrome	TSP Lung(22;0.16)			7	103	---	---	---	---	PASS
BCR	613	broad.mit.edu	37	22	23605880	23605880	+	Intron	SNP	C	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23605880C>T	uc002zww.2	+						BCR_uc002zwx.2_Intron|BCR_uc011aiy.1_Intron|BCR_uc010gtx.1_Intron|uc010gty.2_RNA	NM_004327	NP_004318	P11274	BCR_HUMAN	breakpoint cluster region isoform 1						regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	ATP binding|GTPase activator activity|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity		BCR/JAK2(6)	haematopoietic_and_lymphoid_tissue(6)|central_nervous_system(3)|urinary_tract(1)|lung(1)|skin(1)	12						ATTCACAGCACCTTCGCTGCC	0.542			T	ABL1| FGFR1|JAK2 	CML|ALL|AML								33	47	---	---	---	---	PASS
KLHDC7B	113730	broad.mit.edu	37	22	50987493	50987493	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50987493C>A	uc003bmi.2	+	1	1032	c.898C>A	c.(898-900)CCC>ACC	p.P300T		NM_138433	NP_612442	Q96G42	KLD7B_HUMAN	kelch domain containing 7B	300										central_nervous_system(1)	1		all_cancers(38;1.53e-10)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		OV - Ovarian serous cystadenocarcinoma(4;7.49e-69)|all cancers(3;9.79e-66)|Epithelial(4;1.3e-63)|GBM - Glioblastoma multiforme(4;0.000399)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CTCAGGGCTCCCCAGGGGCCC	0.741													19	25	---	---	---	---	PASS
KDM5C	8242	broad.mit.edu	37	X	53227796	53227796	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53227796C>A	uc004drz.2	-	17	2925	c.2392G>T	c.(2392-2394)GAG>TAG	p.E798*	KDM5C_uc011moc.1_RNA|KDM5C_uc011mod.1_Nonsense_Mutation_p.E731*|KDM5C_uc004dsa.2_Nonsense_Mutation_p.E797*	NM_004187	NP_004178	P41229	KDM5C_HUMAN	jumonji, AT rich interactive domain 1C isoform	798					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			kidney(9)|ovary(5)|salivary_gland(1)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|oesophagus(1)	18						GCTTCAGACTCTAGTGCCCTC	0.527			N|F|S		clear cell renal carcinoma								20	4	---	---	---	---	PASS
AIFM1	9131	broad.mit.edu	37	X	129265667	129265667	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129265667G>T	uc004evg.2	-	14	1734	c.1556C>A	c.(1555-1557)TCT>TAT	p.S519Y	AIFM1_uc011mur.1_Missense_Mutation_p.S167Y|AIFM1_uc011mus.1_3'UTR|AIFM1_uc004evh.2_Missense_Mutation_p.S515Y|AIFM1_uc004evi.2_Missense_Mutation_p.S232Y|AIFM1_uc004evk.2_RNA	NM_004208	NP_004199	O95831	AIFM1_HUMAN	programmed cell death 8 isoform 1	519					activation of caspase activity|apoptosis in response to endoplasmic reticulum stress|cell redox homeostasis|DNA damage response, signal transduction resulting in induction of apoptosis|DNA fragmentation involved in apoptotic nuclear change	cytosol|mitochondrial inner membrane|mitochondrial intermembrane space|nucleus|perinuclear region of cytoplasm	DNA binding|electron carrier activity|flavin adenine dinucleotide binding|oxidoreductase activity|protein binding			ovary(4)|central_nervous_system(1)	5						CTCTGTGGCAGATTTGGGGTT	0.488													76	193	---	---	---	---	PASS
PASD1	139135	broad.mit.edu	37	X	150840969	150840969	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150840969G>C	uc004fev.3	+	14	2084	c.1752G>C	c.(1750-1752)CAG>CAC	p.Q584H		NM_173493	NP_775764	Q8IV76	PASD1_HUMAN	PAS domain containing 1	584						nucleus	signal transducer activity			ovary(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)					AGAGGGTGCAGATATGCCTGC	0.333													5	71	---	---	---	---	PASS
TARDBP	23435	broad.mit.edu	37	1	11077260	11077260	+	Intron	DEL	T	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11077260delT	uc001art.2	+						TARDBP_uc010oap.1_Intron	NM_007375	NP_031401	Q13148	TADBP_HUMAN	TAR DNA binding protein						3'-UTR-mediated mRNA stabilization|cell death|mRNA processing|negative regulation by host of viral transcription|RNA splicing|transcription from RNA polymerase II promoter	nucleus	double-stranded DNA binding|mRNA 3'-UTR binding|nucleotide binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	Ovarian(185;0.249)	Lung NSC(185;1.04e-05)|all_lung(284;1.31e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0578)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.37e-07)|COAD - Colon adenocarcinoma(227;7.38e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|Kidney(185;0.000754)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)		GTTACCtttcttttttttttt	0.025													6	3	---	---	---	---	
MCOLN3	55283	broad.mit.edu	37	1	85485035	85485035	+	Intron	DEL	T	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85485035delT	uc001dkp.2	-						MCOLN3_uc001dko.2_Intron|MCOLN3_uc001dkq.2_Intron	NM_018298	NP_060768	Q8TDD5	MCLN3_HUMAN	mucolipin 3							integral to membrane	ion channel activity			skin(1)	1				all cancers(265;0.00957)|Epithelial(280;0.0254)		AGGGAGGGGGTTTTCTAGAGA	0.413													28	17	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	91123544	91123548	+	IGR	DEL	AAGAG	-	-	rs34570318		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91123544_91123548delAAGAG								ZNF326 (629450 upstream) : BARHL2 (54032 downstream)																							AAAAAAAAAAAAGAGAGAGAGTCGC	0.244													6	3	---	---	---	---	
SOX13	9580	broad.mit.edu	37	1	204081655	204081656	+	Intron	INS	-	CACACT	CACACT	rs112691572	by1000genomes	TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204081655_204081656insCACACT	uc001ham.2	+						SOX13_uc001hal.2_Intron|SOX13_uc010pqp.1_5'Flank	NM_005686	NP_005677	Q9UN79	SOX13_HUMAN	SRY-box 13						anatomical structure morphogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|central_nervous_system(1)	2	all_cancers(21;0.0754)|Breast(84;0.116)|all_epithelial(62;0.189)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)			acacacacacacTTTCTCTCTC	0.287													4	2	---	---	---	---	
RYR2	6262	broad.mit.edu	37	1	237905571	237905571	+	Intron	DEL	T	-	-	rs71656371		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237905571delT	uc001hyl.1	+						RYR2_uc010pya.1_Intron	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						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)			TCCTGTCTCCttttttttttt	0.308													5	6	---	---	---	---	
GGCX	2677	broad.mit.edu	37	2	85787729	85787730	+	Intron	INS	-	A	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85787729_85787730insA	uc002sps.2	-						GGCX_uc010yss.1_5'Flank|GGCX_uc010yst.1_Intron	NM_000821	NP_000812	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase isoform 1						blood coagulation|peptidyl-glutamic acid carboxylation|post-translational protein modification	endoplasmic reticulum membrane|integral to membrane|membrane fraction	gamma-glutamyl carboxylase activity			ovary(1)	1					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|L-Glutamic Acid(DB00142)|Menadione(DB00170)|Phytonadione(DB01022)	tccgtctaaggaaaaaaaaaaa	0.173													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91902877	91902878	+	IGR	DEL	AT	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91902877_91902878delAT								LOC654342 (54902 upstream) : GGT8P (60490 downstream)																							AAATGCAAACATATGGAAATTT	0.317													2	5	---	---	---	---	
CNOT10	25904	broad.mit.edu	37	3	32769472	32769483	+	Intron	DEL	TTTATTTATTTA	-	-	rs71695725		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32769472_32769483delTTTATTTATTTA	uc003cfc.1	+						CNOT10_uc011axi.1_Intron|CNOT10_uc003cfd.1_Intron|CNOT10_uc003cfe.1_Intron|CNOT10_uc010hfv.1_Intron|CNOT10_uc011axj.1_Intron|CNOT10_uc010hfw.1_Intron	NM_015442	NP_056257	Q9H9A5	CNOTA_HUMAN	CCR4-NOT transcription complex, subunit 10						nuclear-transcribed mRNA poly(A) tail shortening	cytosol	protein binding			central_nervous_system(1)|skin(1)	2						CATTTCTCTTtttatttatttatttatttatt	0.151													4	4	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52588877	52588877	+	Frame_Shift_Del	DEL	G	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52588877delG	uc003des.2	-	27	4484	c.4472delC	c.(4471-4473)CCGfs	p.P1491fs	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Intron|PBRM1_uc003der.2_Frame_Shift_Del_p.P1404fs|PBRM1_uc003det.2_Intron|PBRM1_uc003deu.2_Intron|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.P1436fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.P1411fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.P1384fs|PBRM1_uc003dez.1_Frame_Shift_Del_p.P1435fs	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1491	Pro-rich.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding	p.P1491fs*14(1)		kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		AAGGCCTGGCGGATAGCCACC	0.537			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								20	29	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	140526651	140526658	+	IGR	DEL	TTGTGTGT	-	-	rs140533582	by1000genomes	TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140526651_140526658delTTGTGTGT								TRIM42 (106660 upstream) : SLC25A36 (134004 downstream)																							aataccttgATtgtgtgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
HPS3	84343	broad.mit.edu	37	3	148859306	148859307	+	Intron	INS	-	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148859306_148859307insT	uc003ewu.1	+						HPS3_uc003ewt.1_Intron|HPS3_uc011bnq.1_Intron	NM_032383	NP_115759	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3 protein							cytoplasm				ovary(5)|large_intestine(1)	6			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			CTTTAACAAAGttttttttttt	0.248									Hermansky-Pudlak_syndrome				7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	25042989	25042989	+	IGR	DEL	T	-	-	rs35642561		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25042989delT								LGI2 (10575 upstream) : SEPSECS (78639 downstream)																							tctttcttgcttttttttttt	0.000													5	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49241350	49241350	+	IGR	DEL	G	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49241350delG								CWH43 (177257 upstream) : None (None downstream)																							AGTTAAACAAGAAACATTATC	0.269													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	40263280	40263281	+	IGR	DEL	GA	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40263280_40263281delGA								DAB2 (837945 upstream) : PTGER4 (416751 downstream)																							aggaaggaaggagagagaagaa	0.050													2	5	---	---	---	---	
TNPO1	3842	broad.mit.edu	37	5	72182819	72182819	+	Intron	DEL	A	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72182819delA	uc003kck.3	+						TNPO1_uc011csj.1_Intron|TNPO1_uc003kch.2_Intron|TNPO1_uc003kci.3_Intron|TNPO1_uc003kcg.3_Intron	NM_002270	NP_002261	Q92973	TNPO1_HUMAN	transportin 1 isoform 1						interspecies interaction between organisms|mRNA metabolic process|protein import into nucleus, translocation	cytosol|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			skin(3)|urinary_tract(1)|ovary(1)|kidney(1)|central_nervous_system(1)	7		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		AGATACGAATAAAATGTTACA	0.244													18	17	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	87232931	87232934	+	IGR	DEL	CTTC	-	-	rs72449897		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87232931_87232934delCTTC								CCNH (524095 upstream) : TMEM161B (258090 downstream)																							ttctttctttcttccttccttcct	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	14383214	14383221	+	IGR	DEL	TCCTTCCT	-	-	rs58552935		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14383214_14383221delTCCTTCCT								CD83 (246068 upstream) : JARID2 (862513 downstream)																							ccttccttcctccttccttccttccttc	0.159													3	5	---	---	---	---	
ABCF1	23	broad.mit.edu	37	6	30545058	30545059	+	Intron	DEL	TT	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30545058_30545059delTT	uc003nql.2	+						ABCF1_uc003nqk.2_Intron|ABCF1_uc003nqm.2_Intron|ABCF1_uc010jsb.2_Intron	NM_001025091	NP_001020262	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F, member 1						inflammatory response|translational initiation	nuclear envelope|nuclear envelope|nucleoplasm|nucleoplasm|polysomal ribosome	ATP binding|ATP binding|ATPase activity|protein binding|ribosome binding|translation activator activity|translation factor activity, nucleic acid binding			ovary(2)	2						AGTACAAATATTTAAGGAGTGA	0.277													4	2	---	---	---	---	
TINAG	27283	broad.mit.edu	37	6	54208331	54208332	+	Intron	INS	-	T	T	rs3836940		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54208331_54208332insT	uc003pcj.2	+						TINAG_uc010jzt.2_Intron	NM_014464	NP_055279	Q9UJW2	TINAG_HUMAN	tubulointerstitial nephritis antigen						cell adhesion|immune response|Malpighian tubule morphogenesis|proteolysis	basement membrane	cysteine-type endopeptidase activity|nucleotide binding|polysaccharide binding|scavenger receptor activity			ovary(3)|central_nervous_system(1)	4	Lung NSC(77;0.0518)		LUSC - Lung squamous cell carcinoma(124;0.246)			TAGTCTAAAAGTTTTTTTTTTT	0.228													3	3	---	---	---	---	
ECHDC1	55862	broad.mit.edu	37	6	127652297	127652297	+	Intron	DEL	T	-	-	rs66884305		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127652297delT	uc003qax.2	-						ECHDC1_uc003qaz.3_Intron|ECHDC1_uc010key.2_Intron|ECHDC1_uc003qay.3_Intron|ECHDC1_uc010kez.2_Intron|ECHDC1_uc010kex.2_5'Flank	NM_001139510	NP_001132982	Q9NTX5	ECHD1_HUMAN	enoyl Coenzyme A hydratase domain containing 1								catalytic activity				0				GBM - Glioblastoma multiforme(226;0.0423)|all cancers(137;0.156)		TCCCCAtttcttttttttttt	0.189													5	3	---	---	---	---	
SERAC1	84947	broad.mit.edu	37	6	158564368	158564389	+	Intron	DEL	TCTCTCTCTCTCTATATATATA	-	-	rs61058694		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158564368_158564389delTCTCTCTCTCTCTATATATATA	uc003qrc.2	-						SERAC1_uc003qrb.2_Intron	NM_032861	NP_116250	Q96JX3	SRAC1_HUMAN	serine active site containing 1						GPI anchor metabolic process|intracellular protein transport	integral to membrane|intrinsic to endoplasmic reticulum membrane	binding|hydrolase activity, acting on ester bonds				0		Breast(66;0.00519)|Ovarian(120;0.123)|Prostate(117;0.178)		OV - Ovarian serous cystadenocarcinoma(65;1.37e-18)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)		tctctctctctctctctctctctatatatatatatatatata	0.185													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	1429845	1429845	+	IGR	DEL	G	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1429845delG								UNCX (153233 upstream) : MICALL2 (44151 downstream)																							aaggaaggaagggagAGAGAA	0.040													5	4	---	---	---	---	
MAD1L1	8379	broad.mit.edu	37	7	2041500	2041500	+	Intron	DEL	G	-	-	rs939940	by1000genomes	TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2041500delG	uc003slh.1	-						MAD1L1_uc003sle.1_Intron|MAD1L1_uc003slf.1_Intron|MAD1L1_uc003slg.1_Intron|MAD1L1_uc010ksh.1_Intron|MAD1L1_uc003sli.1_Intron|MAD1L1_uc010ksi.1_Intron|MAD1L1_uc010ksj.2_Intron	NM_001013836	NP_001013858	Q9Y6D9	MD1L1_HUMAN	MAD1-like 1 protein						cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		TGTGCTCCCCGCCGGCGCATG	0.647													10	8	---	---	---	---	
AHR	196	broad.mit.edu	37	7	17367496	17367496	+	Intron	DEL	T	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17367496delT	uc011jxz.1	+						AHR_uc003stt.3_Intron	NM_001621	NP_001612	P35869	AHR_HUMAN	aryl hydrocarbon receptor precursor						apoptosis|blood vessel development|cell cycle|regulation of B cell proliferation|response to stress|transcription from RNA polymerase II promoter|xenobiotic metabolic process	cytosolic aryl hydrocarbon receptor complex|transcription factor complex	Hsp90 protein binding|ligand-dependent nuclear receptor activity|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			urinary_tract(1)|kidney(1)|pancreas(1)	3	Lung NSC(10;0.0392)|all_lung(11;0.0754)					atttatatcatttatattatt	0.244													55	25	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	48782123	48782124	+	IGR	DEL	TG	-	-	rs113189810	by1000genomes	TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48782123_48782124delTG								ABCA13 (95032 upstream) : CDC14C (182033 downstream)																							CCTTGAGGGCtgtgtgtgtgtg	0.287													2	4	---	---	---	---	
GTF2IRD1	9569	broad.mit.edu	37	7	74004033	74004033	+	Intron	DEL	A	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74004033delA	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_Intron|GTF2IRD1_uc003uar.1_Intron	NM_016328	NP_057412	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1 isoform 1							nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4						tctcaaaaggaaaaaaaaaaa	0.244													6	3	---	---	---	---	
STAG3L2	442582	broad.mit.edu	37	7	74300557	74300564	+	Frame_Shift_Del	DEL	AGAGCTCC	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74300557_74300564delAGAGCTCC	uc003ubj.3	-	5	625_632	c.243_250delGGAGCTCT	c.(241-252)CTGGAGCTCTTCfs	p.L81fs	STAG3L2_uc011kfj.1_RNA	NM_001025202	NP_001020373	P0CL84	ST3L2_HUMAN	STAG3-like	81_84	SCD.					nucleus	binding				0						CGGCCAGTGAAGAGCTCCAGGCGTGCGG	0.572													6	5	---	---	---	---	
ZNF804B	219578	broad.mit.edu	37	7	88411417	88411418	+	Intron	DEL	GT	-	-	rs146369984		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88411417_88411418delGT	uc011khi.1	+							NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B							intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			gtgtgagtgcgtgtgtgtgtgt	0.322										HNSCC(36;0.09)			4	2	---	---	---	---	
MYOM2	9172	broad.mit.edu	37	8	2033648	2033649	+	Intron	DEL	CC	-	-	rs67333717		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2033648_2033649delCC	uc003wpx.3	+						MYOM2_uc011kwi.1_Intron	NM_003970	NP_003961	P54296	MYOM2_HUMAN	myomesin 2						muscle contraction	myosin filament	structural constituent of muscle			ovary(4)|central_nervous_system(1)|skin(1)	6		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		CTCTGCGTGGCCCCCCACTGTT	0.594													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	93872675	93872676	+	Intron	DEL	AC	-	-	rs34010842		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93872675_93872676delAC	uc003yfj.1	-											Homo sapiens cDNA FLJ46284 fis, clone TESTI4031818.																		acacacacatacacacacacac	0.228													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	138016448	138016451	+	IGR	DEL	AAGA	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138016448_138016451delAAGA								OLFM1 (3417 upstream) : KIAA0649 (355197 downstream)																							ggaaggaaggaagaaagaaagaaa	0.000													4	3	---	---	---	---	
FAM13C	220965	broad.mit.edu	37	10	61084019	61084019	+	Intron	DEL	A	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61084019delA	uc001jkn.2	-						FAM13C_uc001jko.2_Intron|FAM13C_uc010qid.1_Intron|FAM13C_uc010qie.1_Intron|FAM13C_uc010qif.1_Intron|FAM13C_uc001jkp.2_Intron	NM_198215	NP_937858	Q8NE31	FA13C_HUMAN	hypothetical protein LOC220965 isoform 1											ovary(2)	2						TCACTGGTCCAAAATTTTAAA	0.358													11	14	---	---	---	---	
C10orf58	84293	broad.mit.edu	37	10	82186899	82186899	+	Intron	DEL	A	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82186899delA	uc001kcc.3	+						C10orf58_uc001kcd.3_Intron|C10orf58_uc001kce.3_Intron|C10orf58_uc001kcf.3_Intron	NM_032333	NP_115709	Q9BRX8	CJ058_HUMAN	hypothetical protein LOC84293 precursor							extracellular region					0			Colorectal(32;0.229)			actccatctcaaaaaaaaaaa	0.219													4	2	---	---	---	---	
FAM22D	728130	broad.mit.edu	37	10	89117852	89117854	+	5'UTR	DEL	AGA	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89117852_89117854delAGA	uc001kes.2	+	1					FAM22D_uc009xte.1_5'UTR	NM_001009610	NP_001009610	Q5VT03	FA22D_HUMAN	hypothetical protein LOC728130												0						GCTGTGAGTCAGAAGGACAATTT	0.483													9	4	---	---	---	---	
TUBGCP2	10844	broad.mit.edu	37	10	135097228	135097228	+	Intron	DEL	G	-	-	rs67681147		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135097228delG	uc001lmg.1	-						TUBGCP2_uc001lmf.1_Intron|TUBGCP2_uc010qvc.1_Intron|TUBGCP2_uc009ybk.1_Intron|TUBGCP2_uc010qvd.1_Intron|TUBGCP2_uc001lmh.1_Intron	NM_006659	NP_006650	Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2						G2/M transition of mitotic cell cycle|microtubule nucleation|protein complex assembly	centrosome|cytoplasmic microtubule|cytosol|spindle pole	protein binding				0		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		tgcctctcccgcactccctgc	0.055													9	8	---	---	---	---	
ZDHHC13	54503	broad.mit.edu	37	11	19167707	19167708	+	Intron	INS	-	T	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19167707_19167708insT	uc001mpi.2	+						ZDHHC13_uc001mpj.2_Intron	NM_019028	NP_061901	Q8IUH4	ZDH13_HUMAN	zinc finger, DHHC domain containing 13 isoform						positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi-associated vesicle membrane|integral to membrane	magnesium ion transmembrane transporter activity|palmitoyltransferase activity|signal transducer activity|zinc ion binding				0						ATCAATTATGCTTTTTTTTTTC	0.297													12	9	---	---	---	---	
MACROD1	28992	broad.mit.edu	37	11	63920011	63920011	+	Intron	DEL	G	-	-	rs77547365		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63920011delG	uc001nyh.2	-							NM_014067	NP_054786	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1												0						CAGGCATGCTGGGGAAACCTC	0.323													3	3	---	---	---	---	
DDX11	1663	broad.mit.edu	37	12	31231624	31231624	+	Intron	DEL	T	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31231624delT	uc001rjt.1	+						DDX11_uc010sjw.1_Intron|DDX11_uc010sjx.1_Intron|DDX11_uc001rjr.1_Intron|DDX11_uc001rjs.1_Intron|DDX11_uc001rju.1_Intron|DDX11_uc001rjv.1_Intron|DDX11_uc001rjw.1_Intron	NM_152438	NP_689651	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11						G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitotic sister chromatid segregation|positive regulation of cell proliferation|S phase of mitotic cell cycle|sister chromatid cohesion	midbody|nuclear chromatin|nucleolus|spindle pole	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|RNA binding			breast(3)	3	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					TATTAAAGtcttttttttttt	0.184										Multiple Myeloma(12;0.14)			9	6	---	---	---	---	
SYT1	6857	broad.mit.edu	37	12	79325081	79325082	+	Intron	INS	-	G	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79325081_79325082insG	uc001sys.2	+						SYT1_uc001syt.2_Intron|SYT1_uc001syu.2_Intron	NM_001135805	NP_001129277	P21579	SYT1_HUMAN	synaptotagmin I						detection of calcium ion|glutamate secretion|neurotransmitter secretion|protein homooligomerization	cell junction|chromaffin granule membrane|clathrin sculpted acetylcholine transport vesicle membrane|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|clathrin sculpted glutamate transport vesicle membrane|clathrin sculpted monoamine transport vesicle membrane|endocytic vesicle membrane|integral to membrane|synaptic vesicle membrane	1-phosphatidylinositol binding|low-density lipoprotein particle receptor binding|metal ion binding|syntaxin-1 binding|transporter activity			skin(3)|pancreas(2)|ovary(1)	6						gaaggaaggaaggaaggagagg	0.000													4	2	---	---	---	---	
SOCS2	8835	broad.mit.edu	37	12	93968379	93968379	+	Intron	DEL	T	-	-	rs35259505		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93968379delT	uc001tcw.1	+						uc001tcv.1_5'Flank|uc001tcu.2_5'Flank|SOCS2_uc001tcx.1_Intron|SOCS2_uc009zsu.2_3'UTR|SOCS2_uc001tcy.1_Intron|SOCS2_uc001tcz.2_3'UTR	NM_003877	NP_003868	O14508	SOCS2_HUMAN	suppressor of cytokine signaling-2						anti-apoptosis|growth hormone receptor signaling pathway|JAK-STAT cascade|negative regulation of signal transduction|regulation of cell growth|response to estradiol stimulus	cytoplasm	growth hormone receptor binding|insulin-like growth factor receptor binding|JAK pathway signal transduction adaptor activity|prolactin receptor binding|SH3/SH2 adaptor activity			lung(1)	1						ACACACCACCTTTTTTTTTTT	0.328													4	3	---	---	---	---	
DNAH10	196385	broad.mit.edu	37	12	124315343	124315343	+	Intron	DEL	T	-	-	rs7976816		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124315343delT	uc001uft.3	+							NM_207437	NP_997320	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		aaaaaaaaaattagctgagcg	0.100													4	3	---	---	---	---	
TRPC4	7223	broad.mit.edu	37	13	38213330	38213330	+	Intron	DEL	T	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38213330delT	uc001uws.2	-						TRPC4_uc010abv.2_Intron|TRPC4_uc001uwt.2_Intron|TRPC4_uc010tey.1_Intron|TRPC4_uc010abw.2_Intron|TRPC4_uc010abx.2_Intron|TRPC4_uc010aby.2_Intron	NM_016179	NP_057263	Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel,						axon guidance|calcium ion import	basolateral plasma membrane|calcium channel complex|cell surface|cortical cytoskeleton	beta-catenin binding|cadherin binding|store-operated calcium channel activity			ovary(3)|skin(2)|breast(1)	6				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		CCTGAGTCAGTTCTGAAGGGG	0.388													87	82	---	---	---	---	
HEATR5A	25938	broad.mit.edu	37	14	31819967	31819970	+	Intron	DEL	TTTG	-	-	rs72055697		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31819967_31819970delTTTG	uc001wrf.3	-						HEATR5A_uc010ami.2_Intron|HEATR5A_uc001wrg.1_Intron|HEATR5A_uc010tpk.1_Intron	NM_015473	NP_056288	Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A								binding			ovary(1)	1	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		TAGGTAAGTTtttgtttgtttgtt	0.176													3	6	---	---	---	---	
GABRG3	2567	broad.mit.edu	37	15	27633288	27633299	+	Intron	DEL	GTAAGGAAGGAA	-	-	rs145752625	by1000genomes	TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27633288_27633299delGTAAGGAAGGAA	uc001zbg.1	+						GABRG3_uc001zbf.2_Intron	NM_033223	NP_150092	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)		gggagggagggtaaggaaggaaggaagaaagg	0.000													7	4	---	---	---	---	
ZFYVE19	84936	broad.mit.edu	37	15	41104758	41104759	+	Intron	DEL	AG	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41104758_41104759delAG	uc001zmt.1	+						ZFYVE19_uc001zmu.1_Intron|ZFYVE19_uc001zmv.1_Intron|ZFYVE19_uc001zmw.1_Intron|ZFYVE19_uc001zmx.1_Intron|ZFYVE19_uc010bcc.1_Intron	NM_001077268	NP_001070736	Q96K21	ZFY19_HUMAN	zinc finger, FYVE domain containing 19								zinc ion binding				0		all_cancers(109;3.31e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.76e-05)|COAD - Colon adenocarcinoma(120;0.151)|BRCA - Breast invasive adenocarcinoma(123;0.164)		aaaaaaaaaaagaaagaaagaa	0.099													4	2	---	---	---	---	
BNIP2	663	broad.mit.edu	37	15	59960942	59960943	+	Intron	DEL	CT	-	-	rs6151566		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59960942_59960943delCT	uc010uhc.1	-						BNIP2_uc002agi.3_Intron|BNIP2_uc010uhb.1_Intron	NM_004330	NP_004321	Q12982	BNIP2_HUMAN	BCL2/adenovirus E1B 19kD interacting protein 2						anti-apoptosis|apoptosis|positive regulation of muscle cell differentiation	nuclear envelope|perinuclear region of cytoplasm	calcium ion binding|GTPase activator activity|protein binding			ovary(1)	1						TGGCTTCTTCCTCTTTTTCTTT	0.381													1	6	---	---	---	---	
PKM2	5315	broad.mit.edu	37	15	72492163	72492164	+	Intron	INS	-	C	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72492163_72492164insC	uc002atx.1	-						GRAMD2_uc002atq.2_5'Flank|GRAMD2_uc010bis.2_5'Flank|PKM2_uc002atr.1_Intron|PKM2_uc002ats.1_Intron|PKM2_uc002att.1_Intron|PKM2_uc002atu.1_Intron|PKM2_uc010bit.1_Intron|PKM2_uc010uki.1_Intron|PKM2_uc002atv.1_Intron|PKM2_uc002atw.1_Intron|PKM2_uc002aty.1_Intron|PKM2_uc010ukj.1_Intron|PKM2_uc010ukk.1_Intron	NM_182471	NP_872271	P14618	KPYM_HUMAN	pyruvate kinase, muscle isoform M1						glycolysis|programmed cell death	cytosol|nucleus|plasma membrane	ATP binding|magnesium ion binding|potassium ion binding|protein binding|pyruvate kinase activity			breast(1)	1					Pyruvic acid(DB00119)	CTGGGCAGCTGCCCCATAGCCT	0.574											OREG0023252	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	78279107	78279108	+	IGR	INS	-	ACCCAGG	ACCCAGG			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78279107_78279108insACCCAGG								LOC645752 (59919 upstream) : LOC91450 (6468 downstream)																							GCCTGCCCTGAACCCAGGACCC	0.663													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32177847	32177850	+	IGR	DEL	TTGA	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32177847_32177850delTTGA								HERC2P4 (13973 upstream) : TP53TG3B (506991 downstream)																							GATGCAATTGTTGACTCACCAAGC	0.368													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	51074929	51074930	+	IGR	INS	-	GGAG	GGAG	rs145692350	by1000genomes	TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51074929_51074930insGGAG								CYLD (239083 upstream) : SALL1 (94956 downstream)																							ggagggagggaggaaggaggga	0.000													4	3	---	---	---	---	
CIRH1A	84916	broad.mit.edu	37	16	69190057	69190058	+	Intron	INS	-	TTT	TTT	rs72463058		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69190057_69190058insTTT	uc002ews.3	+						CIRH1A_uc002ewr.2_Intron|CIRH1A_uc002ewt.3_Intron|CIRH1A_uc010cfi.2_Intron	NM_032830	NP_116219	Q969X6	CIR1A_HUMAN	cirhin							nucleolus	protein binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.125)		ttctttctttcttttttttttt	0.158													9	8	---	---	---	---	
ZCCHC14	23174	broad.mit.edu	37	16	87500652	87500652	+	Intron	DEL	T	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87500652delT	uc002fjz.1	-						ZCCHC14_uc002fka.1_Intron	NM_015144	NP_055959	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14						cell communication		nucleic acid binding|phosphatidylinositol binding|zinc ion binding			upper_aerodigestive_tract(1)|breast(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0285)		AAAAAAATTGTtttttttttt	0.229													4	2	---	---	---	---	
MYH8	4626	broad.mit.edu	37	17	10302312	10302313	+	Intron	DEL	TA	-	-	rs35772133		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10302312_10302313delTA	uc002gmm.2	-						uc002gml.1_Intron	NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,						muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			skin(6)|ovary(3)|breast(2)	11						tgtgtgtgtgtatatatatata	0.074									Trismus-Pseudocamptodactyly_Syndrome_with_Cardiac_Myxoma_and_Freckling				4	2	---	---	---	---	
TMEM220	388335	broad.mit.edu	37	17	10619317	10619318	+	Intron	INS	-	GATA	GATA	rs146093202	by1000genomes	TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10619317_10619318insGATA	uc002gmx.2	-						TMEM220_uc002gmy.2_Intron	NM_001004313	NP_001004313	Q6QAJ8	TM220_HUMAN	transmembrane protein 220							integral to membrane					0						tataCTGCCCTGACACAAAATG	0.203													4	3	---	---	---	---	
HS3ST3B1	9953	broad.mit.edu	37	17	14233868	14233869	+	Intron	DEL	GT	-	-	rs72046773		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14233868_14233869delGT	uc002goh.1	+							NM_006041	NP_006032	Q9Y662	HS3SB_HUMAN	heparan sulfate D-glucosaminyl						heparan sulfate proteoglycan biosynthetic process, enzymatic modification	Golgi membrane|integral to plasma membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity|[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity				0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0887)		TGGTTTCCCGgtgtgtgtgtgt	0.297													4	2	---	---	---	---	
SLFN12	55106	broad.mit.edu	37	17	33761383	33761383	+	5'Flank	DEL	A	-	-	rs71375409		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33761383delA	uc002hji.3	-						SLFN12_uc002hjj.3_5'Flank|SLFN12_uc010cts.2_5'Flank	NM_018042	NP_060512	Q8IYM2	SLN12_HUMAN	schlafen family member 12								ATP binding			skin(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		agagagagagaaaggaaggaa	0.000													3	3	---	---	---	---	
FOXK2	3607	broad.mit.edu	37	17	80525803	80525808	+	Intron	DEL	TTTTTT	-	-	rs5822539		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80525803_80525808delTTTTTT	uc002kfn.2	+						FOXK2_uc002kfm.1_Intron|FOXK2_uc010diu.2_Intron	NM_004514	NP_004505	Q01167	FOXK2_HUMAN	forkhead box K2						embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			ATTCTCTTCCtttttttttttttttt	0.325													9	4	---	---	---	---	
SAFB2	9667	broad.mit.edu	37	19	5605123	5605123	+	Intron	DEL	T	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5605123delT	uc002mcd.2	-							NM_014649	NP_055464	Q14151	SAFB2_HUMAN	scaffold attachment factor B2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|nucleotide binding|protein binding|RNA binding				0				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		ATACAATTGCttttttttttt	0.169													5	3	---	---	---	---	
TPM4	7171	broad.mit.edu	37	19	16176846	16176847	+	5'Flank	INS	-	GTGT	GTGT	rs143863545	by1000genomes	TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16176846_16176847insGTGT	uc002ndi.2	+							NM_001145160	NP_001138632	P67936	TPM4_HUMAN	tropomyosin 4 isoform 1						cellular component movement|muscle filament sliding|response to oxidative stress	cytosol|muscle thin filament tropomyosin|stress fiber	actin binding|calcium ion binding|structural constituent of muscle		TPM4/ALK(12)	soft_tissue(10)|haematopoietic_and_lymphoid_tissue(2)|breast(1)	13						taggcagCGAAgtgtgtgtgtg	0.069			T	ALK	ALCL								3	3	---	---	---	---	
NWD1	284434	broad.mit.edu	37	19	16872615	16872616	+	Intron	INS	-	A	A	rs141486324	by1000genomes	TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16872615_16872616insA	uc002neu.3	+						NWD1_uc002net.3_Intron|NWD1_uc002nev.3_Intron			Q149M9	NWD1_HUMAN	RecName: Full=NACHT and WD repeat domain-containing protein 1;								ATP binding			skin(3)|ovary(2)|pancreas(2)	7						TTGATGTAAGGAAAAAAAAAAC	0.267													4	3	---	---	---	---	
UNC13A	23025	broad.mit.edu	37	19	17741883	17741886	+	Intron	DEL	TCCT	-	-	rs145348480		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17741883_17741886delTCCT	uc002nhd.2	-							NM_001080421	NP_001073890	Q9UPW8	UN13A_HUMAN	unc-13 homolog A						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3						cctccctccctccttccttccttc	0.284													4	2	---	---	---	---	
FCHO1	23149	broad.mit.edu	37	19	17888847	17888848	+	Intron	INS	-	A	A	rs34991275		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17888847_17888848insA	uc010ebb.2	+						FCHO1_uc002nhg.3_Intron|FCHO1_uc002nhh.2_Intron|FCHO1_uc010xpw.1_Intron|FCHO1_uc002nhi.2_5'Flank|FCHO1_uc002nhj.2_5'Flank	NM_001161358	NP_001154830	O14526	FCHO1_HUMAN	FCH domain only 1 isoform b											breast(1)	1						gactccgtctcaaaaaaaaaaa	0.109													2	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29881445	29881446	+	Intron	INS	-	AGGAAGGA	AGGAAGGA			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29881445_29881446insAGGAAGGA	uc002nse.1	-											Homo sapiens cDNA FLJ37474 fis, clone BRAWH2012619.																		ggaagaaaggcaggaaggaagg	0.000													4	2	---	---	---	---	
MAP3K10	4294	broad.mit.edu	37	19	40715309	40715309	+	Intron	DEL	T	-	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40715309delT	uc002ona.2	+						MAP3K10_uc002onb.2_Intron	NM_002446	NP_002437	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|induction of apoptosis|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of JNK cascade|protein autophosphorylation|smoothened signaling pathway	cytoplasm	ATP binding|bHLH transcription factor binding|JUN kinase kinase kinase activity|protein homodimerization activity|transcription corepressor activity			ovary(2)|lung(2)|skin(1)|pancreas(1)	6						ggataatttcttttttttttt	0.000													4	2	---	---	---	---	
PLCB4	5332	broad.mit.edu	37	20	9195208	9195209	+	Intron	DEL	AC	-	-	rs71861168		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9195208_9195209delAC	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Intron	NM_182797	NP_877949	Q15147	PLCB4_HUMAN	phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15						AACACCCCAGacacacacacac	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	49068601	49068602	+	IGR	DEL	AA	-	-	rs71338418		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49068601_49068602delAA								CEBPB (259389 upstream) : PTPN1 (58289 downstream)																							agaaagaaagaaaaagaaagaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	23823953	23823956	+	IGR	DEL	TTCG	-	-	rs28541799	by1000genomes	TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23823953_23823956delTTCG								NCAM2 (912739 upstream) : None (None downstream)																							ccttccttccttcgttccttcctt	0.000													4	2	---	---	---	---	
TTC28	23331	broad.mit.edu	37	22	28462291	28462298	+	Intron	DEL	TGGTGTGT	-	-	rs147007029	by1000genomes	TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28462291_28462298delTGGTGTGT	uc003adp.3	-							NM_001145418	NP_001138890	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28								binding				0						tgtgtgtgtgtggtgtgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
