Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
MTHFR	4524	broad.mit.edu	37	1	11855381	11855381	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr1:11855381C>T	uc001atc.1	-	6	989	c.805G>A	c.(805-807)GTG>ATG	p.V269M	MTHFR_uc001atb.1_Missense_Mutation_p.V292M	NM_005957	NP_005948	P42898	MTHR_HUMAN	5,10-methylenetetrahydrofolate reductase	269					blood circulation|folic acid metabolic process	cytosol	methylenetetrahydrofolate reductase (NADPH) activity|protein binding				0	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|Raltitrexed(DB00293)|Riboflavin(DB00140)|S-Adenosylmethionine(DB00118)|Tetrahydrofolic acid(DB00116)	GACAGCTTCACAAGCTGCCGA	0.582													19	44	---	---	---	---	PASS
C1orf109	54955	broad.mit.edu	37	1	38155401	38155401	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr1:38155401G>T	uc001cbp.2	-	2	342	c.152C>A	c.(151-153)GCC>GAC	p.A51D	C1orf109_uc010oig.1_Missense_Mutation_p.A114D|C1orf109_uc001cbo.2_Missense_Mutation_p.A113D|C1orf109_uc001cbq.1_Missense_Mutation_p.A51D|CDCA8_uc001cbr.2_5'Flank|CDCA8_uc001cbs.2_5'Flank	NM_017850	NP_060320	Q9NX04	CA109_HUMAN	hypothetical protein LOC54955	51											0		Myeloproliferative disorder(586;0.0393)				GTTCTGTGCGGCCTGCAGCTG	0.647													7	112	---	---	---	---	PASS
PROX1	5629	broad.mit.edu	37	1	214171237	214171237	+	Silent	SNP	C	T	T			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr1:214171237C>T	uc001hkh.2	+	2	1631	c.1359C>T	c.(1357-1359)TCC>TCT	p.S453S	PROX1_uc001hkg.1_Silent_p.S453S	NM_002763	NP_002754	Q92786	PROX1_HUMAN	prospero homeobox 1	453					aorta smooth muscle tissue morphogenesis|atrial cardiac muscle tissue morphogenesis|brain development|dorsal spinal cord development|embryonic retina morphogenesis in camera-type eye|endocardium formation|hepatocyte differentiation|kidney development|lens fiber cell morphogenesis|lung development|lymphangiogenesis|negative regulation of bile acid biosynthetic process|negative regulation of cell proliferation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of viral genome replication|neural tube development|olfactory placode formation|optic placode formation involved in camera-type eye formation|otic placode formation|pancreas development|positive regulation of cyclin-dependent protein kinase activity|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of heart growth|positive regulation of S phase of mitotic cell cycle|positive regulation of sarcomere organization|positive regulation of transcription, DNA-dependent|regulation of transcription involved in lymphatic endothelial cell fate commitment|skeletal muscle thin filament assembly|venous blood vessel morphogenesis|ventricular cardiac muscle tissue morphogenesis|ventricular cardiac myofibril development|ventricular septum morphogenesis	cytoplasm|nucleus	DBD domain binding|LBD domain binding|ligand-dependent nuclear receptor binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription corepressor activity|transcription regulatory region DNA binding			ovary(3)|lung(1)|central_nervous_system(1)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219)		AGTCTGCCTCCGGCCCTGCCG	0.647													27	85	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	215848631	215848631	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr1:215848631C>T	uc001hku.1	-	63	13009	c.12622G>A	c.(12622-12624)GAC>AAC	p.D4208N		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	4208	Extracellular (Potential).|Fibronectin type-III 27.				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)		ATTTTCTCGTCGGCCTGGATT	0.393										HNSCC(13;0.011)			44	126	---	---	---	---	PASS
LRRTM4	80059	broad.mit.edu	37	2	76975914	76975914	+	Silent	SNP	G	A	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr2:76975914G>A	uc002snr.2	-	4	2095	c.1680C>T	c.(1678-1680)AGC>AGT	p.S560S	LRRTM4_uc002snq.2_Silent_p.S560S	NM_001134745	NP_001128217	Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	560	Cytoplasmic (Potential).					integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)		CCAGGCCGGGGCTTTCGTCCT	0.587													54	165	---	---	---	---	PASS
PTCD3	55037	broad.mit.edu	37	2	86360495	86360495	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr2:86360495G>A	uc002sqw.2	+	19	1545	c.1479G>A	c.(1477-1479)ATG>ATA	p.M493I	PTCD3_uc002sqx.1_Missense_Mutation_p.M83I|SNORD94_uc010fgr.1_5'Flank	NM_017952	NP_060422	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3 precursor	493	PPR 9.					mitochondrion	protein binding			ovary(1)	1						CCCAAACAATGATACATCTTC	0.373													16	309	---	---	---	---	PASS
EFHB	151651	broad.mit.edu	37	3	19924217	19924217	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr3:19924217G>C	uc003cbl.3	-	12	2349	c.2153C>G	c.(2152-2154)CCC>CGC	p.P718R	EFHB_uc003cbm.2_Missense_Mutation_p.P588R	NM_144715	NP_653316	Q8N7U6	EFHB_HUMAN	EF hand domain family, member B	718					signal transduction	proteinaceous extracellular matrix	calcium ion binding				0						ACCACAAATGGGGTAACCTAG	0.313													11	31	---	---	---	---	PASS
BSN	8927	broad.mit.edu	37	3	49698154	49698154	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr3:49698154G>A	uc003cxe.3	+	6	8990	c.8876G>A	c.(8875-8877)CGC>CAC	p.R2959H		NM_003458	NP_003449	Q9UPA5	BSN_HUMAN	bassoon protein	2959	Potential.				synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	metal ion binding			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		ACCAAACTGCGCAAGAAGCAG	0.602													4	31	---	---	---	---	PASS
SSR3	6747	broad.mit.edu	37	3	156266713	156266713	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr3:156266713G>A	uc003fau.2	-	3	397	c.340C>T	c.(340-342)CGG>TGG	p.R114W	SSR3_uc011bop.1_Missense_Mutation_p.R114W	NM_007107	NP_009038	Q9UNL2	SSRG_HUMAN	signal sequence receptor gamma subunit	114	Lumenal (Potential).				cotranslational protein targeting to membrane	integral to endoplasmic reticulum membrane|microsome|Sec61 translocon complex	protein binding|signal sequence binding				0			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			TTCTCCTTCCGAGACATCTTT	0.363													24	82	---	---	---	---	PASS
PIK3CA	5290	broad.mit.edu	37	3	178927980	178927980	+	Missense_Mutation	SNP	T	C	C	rs121913272		TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr3:178927980T>C	uc003fjk.2	+	8	1415	c.1258T>C	c.(1258-1260)TGT>CGT	p.C420R		NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha	420	C2 PI3K-type.		C -> R (in cancer; shows an increase in lipid kinase activity; may increase the affinity for lipid membranes).		epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity	p.C420R(26)		breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)			TAAGGAACACTGTCCATTGGC	0.328	C420R(EFM192A_BREAST)|C420R(OVISE_OVARY)|C420R(HEC151_ENDOMETRIUM)|C420R(CCK81_LARGE_INTESTINE)	57	Mis		colorectal|gastric|gliobastoma|breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			5	205	---	---	---	---	PASS
C1QTNF7	114905	broad.mit.edu	37	4	15444073	15444073	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr4:15444073G>A	uc011bxb.1	+	3	747	c.520G>A	c.(520-522)GAG>AAG	p.E174K	C1QTNF7_uc003gno.2_Missense_Mutation_p.E181K|C1QTNF7_uc003gnp.2_Missense_Mutation_p.E174K	NM_001135171	NP_001128643	Q9BXJ2	C1QT7_HUMAN	C1q and tumor necrosis factor related protein 7	174	C1q.					collagen					0						CCTCTTCAACGAGGGAGAGCA	0.443													15	486	---	---	---	---	PASS
LOC100133050	100133050	broad.mit.edu	37	5	99715528	99715528	+	RNA	SNP	C	T	T			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr5:99715528C>T	uc011cuw.1	-	4		c.382G>A				NR_027503				Homo sapiens glucuronidase, beta pseudogene (LOC100133050), non-coding RNA.												0						AGCGGACAGTCGAAGCCCTTC	0.607													5	13	---	---	---	---	PASS
RREB1	6239	broad.mit.edu	37	6	7230059	7230059	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr6:7230059G>A	uc003mxc.2	+	10	2117	c.1727G>A	c.(1726-1728)CGG>CAG	p.R576Q	RREB1_uc003mxb.2_Missense_Mutation_p.R576Q|RREB1_uc010jnx.2_Missense_Mutation_p.R576Q	NM_001003698	NP_001003698	Q92766	RREB1_HUMAN	ras responsive element binding protein 1 isoform	576					multicellular organismal development|positive regulation of transcription, DNA-dependent|Ras protein signal transduction|transcription from RNA polymerase II promoter	cytoplasm|nuclear speck	DNA binding|zinc ion binding			ovary(4)|large_intestine(2)|pancreas(2)|skin(2)|breast(1)	11	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				GCGGCCACGCGGCTCTCCCTG	0.711													4	13	---	---	---	---	PASS
RBM24	221662	broad.mit.edu	37	6	17292224	17292224	+	Nonsense_Mutation	SNP	C	A	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr6:17292224C>A	uc003nbz.3	+	4	589	c.585C>A	c.(583-585)TAC>TAA	p.Y195*	RBM24_uc003nby.3_3'UTR|RBM24_uc011dix.1_Nonsense_Mutation_p.Y137*|RBM24_uc003nca.2_Nonsense_Mutation_p.Y150*|RBM24_uc011diy.1_Missense_Mutation_p.T109K|RBM24_uc011diz.1_Missense_Mutation_p.T94K	NM_001143942	NP_001137414	Q9BX46	RBM24_HUMAN	RNA binding motif protein 24 isoform 1	195	Ala-rich.				cell differentiation|regulation of mRNA stability|regulation of myotube differentiation	cytoplasm|nucleus	mRNA 3'-UTR binding|nucleotide binding			ovary(1)|skin(1)	2	Breast(50;0.0615)|Ovarian(93;0.0733)	all_hematologic(90;0.062)	all cancers(50;0.131)|Epithelial(50;0.15)			GCTATGGCTACGCAGTCCAGC	0.393													4	32	---	---	---	---	PASS
COL21A1	81578	broad.mit.edu	37	6	55924962	55924962	+	Missense_Mutation	SNP	A	G	G	rs12209452	by1000genomes	TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr6:55924962A>G	uc003pcs.2	-	28	2694	c.2462T>C	c.(2461-2463)CTG>CCG	p.L821P	COL21A1_uc010jzz.2_Missense_Mutation_p.L206P|COL21A1_uc011dxg.1_Missense_Mutation_p.L194P|COL21A1_uc011dxh.1_Intron|COL21A1_uc003pcr.2_Missense_Mutation_p.L178P	NM_030820	NP_110447	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1 precursor	821					cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(2)	2	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			ATGTTGGGACAGGCAATGATC	0.493													3	61	---	---	---	---	PASS
TBX18	9096	broad.mit.edu	37	6	85473758	85473758	+	Missense_Mutation	SNP	C	T	T	rs172562	by1000genomes	TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr6:85473758C>T	uc003pkl.1	-	1	142	c.142G>A	c.(142-144)GGG>AGG	p.G48R	TBX18_uc010kbq.1_5'Flank	NM_001080508	NP_001073977	O95935	TBX18_HUMAN	T-box 18	48					multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|pancreas(2)|lung(1)	5		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		tccacggcccccgccgccTCT	0.478													4	1	---	---	---	---	PASS
URGCP	55665	broad.mit.edu	37	7	43918497	43918497	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr7:43918497C>A	uc003tiw.2	-	6	622	c.565G>T	c.(565-567)GCC>TCC	p.A189S	URGCP_uc003tiu.2_Missense_Mutation_p.A146S|URGCP_uc003tiv.2_Missense_Mutation_p.A114S|URGCP_uc003tix.2_Missense_Mutation_p.A180S|URGCP_uc003tiy.2_Missense_Mutation_p.A146S|URGCP_uc003tiz.2_Missense_Mutation_p.A146S|URGCP_uc011kbj.1_Missense_Mutation_p.A146S	NM_001077663	NP_001071131	Q8TCY9	URGCP_HUMAN	up-regulated gene 4 isoform 3	189					cell cycle	centrosome|nucleus	GTP binding			ovary(2)|liver(1)|skin(1)	4						AGCAGCAGGGCACAGAGAAGG	0.532													21	54	---	---	---	---	PASS
ZNF680	340252	broad.mit.edu	37	7	63981563	63981563	+	Silent	SNP	A	G	G	rs10243954	byFrequency	TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr7:63981563A>G	uc003tta.2	-	4	1742	c.1569T>C	c.(1567-1569)TGT>TGC	p.C523C	ZNF680_uc010kzr.2_Silent_p.C450C	NM_178558	NP_848653	Q8NEM1	ZN680_HUMAN	zinc finger protein 680 isoform 1	523					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(55;0.118)|all_lung(88;0.243)				AATTATTGTCACATTTTTCAG	0.338													4	165	---	---	---	---	PASS
RORB	6096	broad.mit.edu	37	9	77280437	77280437	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr9:77280437G>A	uc004aji.2	+	7	1008	c.959G>A	c.(958-960)CGT>CAT	p.R320H	RORB_uc004ajh.2_Missense_Mutation_p.R309H	NM_006914	NP_008845	Q92753	RORB_HUMAN	RAR-related orphan receptor B	320	Ligand-binding (Potential).				eye photoreceptor cell development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|visual perception	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(2)|lung(1)|skin(1)	4						AGAATGTGCCGTGCCTTCAAC	0.313													54	130	---	---	---	---	PASS
LCN2	3934	broad.mit.edu	37	9	130914560	130914560	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr9:130914560A>G	uc004bto.1	+	5	647	c.574A>G	c.(574-576)ATC>GTC	p.I192V	LCN2_uc011map.1_Missense_Mutation_p.I192V	NM_005564	NP_005555	P80188	NGAL_HUMAN	lipocalin 2 precursor	192					apoptosis|innate immune response|regulation of apoptosis|siderophore transport		iron ion binding|transporter activity				0						CCCTGTCCCAATCGGTAATGG	0.562													23	48	---	---	---	---	PASS
TMEM141	85014	broad.mit.edu	37	9	139686405	139686405	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr9:139686405G>A	uc004cje.3	+	3	174	c.128G>A	c.(127-129)GGC>GAC	p.G43D	TMEM141_uc011meg.1_Missense_Mutation_p.G43D	NM_032928	NP_116317	Q96I45	TM141_HUMAN	transmembrane protein 141	43	Helical; (Potential).					integral to membrane					0	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.67e-06)|Epithelial(140;0.000112)		GCAGGCACCGGCATGGCCTTT	0.637											OREG0019622	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	272	---	---	---	---	PASS
CCDC3	83643	broad.mit.edu	37	10	12940424	12940424	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr10:12940424G>A	uc001ilq.1	-	3	939	c.805C>T	c.(805-807)CGG>TGG	p.R269W	CCDC3_uc009xjb.1_RNA|CCDC3_uc001ilr.2_RNA|CCDC3_uc009xjc.1_RNA	NM_031455	NP_113643	Q9BQI4	CCDC3_HUMAN	coiled-coil domain containing 3 precursor	269						endoplasmic reticulum|extracellular region				ovary(1)	1		Ovarian(717;0.0822)	BRCA - Breast invasive adenocarcinoma(52;0.163)			CGTTACCCCCGCAGGTAGGGG	0.637													10	54	---	---	---	---	PASS
JMJD1C	221037	broad.mit.edu	37	10	64927823	64927823	+	Missense_Mutation	SNP	C	G	G	rs1935	by1000genomes	TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr10:64927823C>G	uc001jmn.2	-	26	7905	c.7605G>C	c.(7603-7605)GAG>GAC	p.E2535D	JMJD1C_uc001jml.2_Missense_Mutation_p.E2298D|JMJD1C_uc001jmm.2_Missense_Mutation_p.E2247D|JMJD1C_uc010qiq.1_Missense_Mutation_p.E2353D|JMJD1C_uc009xpi.2_Missense_Mutation_p.E2353D|JMJD1C_uc009xpj.1_RNA|JMJD1C_uc001jmk.2_RNA	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a	2535					blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)					CTTCCATATCCTCTACTTCAT	0.333													7	301	---	---	---	---	PASS
OR52A1	23538	broad.mit.edu	37	11	5172911	5172911	+	Missense_Mutation	SNP	C	T	T	rs149615083		TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr11:5172911C>T	uc010qyy.1	-	1	689	c.689G>A	c.(688-690)CGT>CAT	p.R230H		NM_012375	NP_036507	Q9UKL2	O52A1_HUMAN	olfactory receptor, family 52, subfamily A,	230	Cytoplasmic (Potential).				sensory perception of smell	integral to plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2		Medulloblastoma(188;0.00106)|Breast(177;0.0155)|all_neural(188;0.0189)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTGGGGCAAACGAAAAACTGT	0.428													30	121	---	---	---	---	PASS
ACER3	55331	broad.mit.edu	37	11	76730798	76730798	+	Missense_Mutation	SNP	T	G	G			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr11:76730798T>G	uc009yum.1	+	10	832	c.728T>G	c.(727-729)CTG>CGG	p.L243R	ACER3_uc001oxu.2_RNA|ACER3_uc009yun.1_Missense_Mutation_p.L201R|ACER3_uc009yuo.1_Missense_Mutation_p.L148R|ACER3_uc010rsh.1_Missense_Mutation_p.L206R|ACER3_uc010rsi.1_Missense_Mutation_p.L148R|ACER3_uc010rsj.1_Missense_Mutation_p.L148R	NM_018367	NP_060837	Q9NUN7	ACER3_HUMAN	phytoceramidase, alkaline	243					ceramide metabolic process|phytosphingosine biosynthetic process|positive regulation of cell proliferation|sphingosine biosynthetic process	integral to endoplasmic reticulum membrane|integral to Golgi membrane	phytoceramidase activity				0						ACACTTTACCTGAGATATAGG	0.423													35	193	---	---	---	---	PASS
FAT3	120114	broad.mit.edu	37	11	92533734	92533734	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr11:92533734C>G	uc001pdj.3	+	9	7572	c.7555C>G	c.(7555-7557)CGA>GGA	p.R2519G		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	2519	Cadherin 23.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				AATTCATGTTCGAGCCACAGA	0.493										TCGA Ovarian(4;0.039)			4	28	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	12	92920	92920	+	Missense_Mutation	SNP	C	G	G	rs145563795	by1000genomes	TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr12:92920C>G	uc010sdi.1	-	1	99	c.71G>C	c.(70-72)AGT>ACT	p.S24T	uc010sdj.1_RNA					SubName: Full=DEAD/H box polypeptide 11 like 11;																		ACTCACAAGACTGTGATCCAA	0.622													2	3	---	---	---	---	PASS
PTGER2	5732	broad.mit.edu	37	14	52781424	52781424	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr14:52781424A>G	uc001wzr.2	+	1	409	c.158A>G	c.(157-159)GAC>GGC	p.D53G		NM_000956	NP_000947	P43116	PE2R2_HUMAN	prostaglandin E receptor 2 (subtype EP2), 53kDa	53	Cytoplasmic (Potential).					integral to plasma membrane	prostaglandin E receptor activity			lung(1)|breast(1)	2	Breast(41;0.0639)|all_epithelial(31;0.0729)				Alprostadil(DB00770)|Iloprost(DB01088)	TGGCGGGGGGACGTGGGGTGC	0.697													4	25	---	---	---	---	PASS
RBPMS2	348093	broad.mit.edu	37	15	65041630	65041630	+	Silent	SNP	G	A	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr15:65041630G>A	uc002anq.2	-	4	519	c.267C>T	c.(265-267)AAC>AAT	p.N89N		NM_194272	NP_919248	Q6ZRY4	RBPS2_HUMAN	RNA binding protein with multiple splicing 2	89	RRM.						nucleic acid binding|nucleotide binding				0						ACCTACTCACGTTCAGCGCAT	0.512													30	113	---	---	---	---	PASS
ULK3	25989	broad.mit.edu	37	15	75131661	75131661	+	Silent	SNP	A	G	G	rs4886615	by1000genomes	TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr15:75131661A>G	uc010bkf.1	-	8	1012	c.906T>C	c.(904-906)GCT>GCC	p.A302A	ULK3_uc010ulp.1_Silent_p.A212A|ULK3_uc010ulq.1_Silent_p.A313A|ULK3_uc010ulr.1_Silent_p.A185A|ULK3_uc002ayv.2_Silent_p.A302A|ULK3_uc010uls.1_Silent_p.A185A	NM_001099436	NP_001092906	Q6PHR2	ULK3_HUMAN	unc-51-like kinase 3	302	MIT 1.					cytoplasm	ATP binding|protein serine/threonine kinase activity			breast(2)	2						GTGATAAGGCAGCTGCTGAAT	0.612													3	5	---	---	---	---	PASS
GLIS2	84662	broad.mit.edu	37	16	4384871	4384871	+	Missense_Mutation	SNP	G	A	A	rs147175353	byFrequency	TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr16:4384871G>A	uc002cwc.1	+	3	472	c.415G>A	c.(415-417)GGG>AGG	p.G139R		NM_032575	NP_115964	Q9BZE0	GLIS2_HUMAN	GLIS family zinc finger 2	139	Interaction with CTNND1 (By similarity).				cell differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development	cytoplasm|nuclear speck	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|transcription regulatory region DNA binding|zinc ion binding				0						CCTCGGCTCCGGGGGGGCCCT	0.657													21	87	---	---	---	---	PASS
OSGIN1	29948	broad.mit.edu	37	16	83999180	83999180	+	Silent	SNP	C	T	T			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr16:83999180C>T	uc002fha.2	+	7	1634	c.1251C>T	c.(1249-1251)TAC>TAT	p.Y417Y	OSGIN1_uc002fhb.2_Silent_p.Y334Y|OSGIN1_uc002fhc.2_Silent_p.Y334Y	NM_013370	NP_037502	Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	417					cell differentiation|multicellular organismal development|negative regulation of cell growth		growth factor activity				0						AGATGCTGTACCCCGAGTACC	0.637													22	62	---	---	---	---	PASS
BANP	54971	broad.mit.edu	37	16	88061088	88061088	+	Splice_Site	SNP	G	C	C			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr16:88061088G>C	uc002fkr.2	+	8	1093	c.869_splice	c.e8-1	p.C290_splice	BANP_uc002fkp.2_Splice_Site_p.C260_splice|BANP_uc002fkq.2_Splice_Site_p.C260_splice|BANP_uc010vow.1_Splice_Site_p.C298_splice|BANP_uc002fks.3_Splice_Site_p.C259_splice|BANP_uc002fko.1_Splice_Site_p.C196_splice|BANP_uc010vov.1_Splice_Site_p.C265_splice	NM_079837	NP_524576	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein isoform b						cell cycle|chromatin modification|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0				BRCA - Breast invasive adenocarcinoma(80;0.00551)		TGTCCTTCCAGGTCACCTTTT	0.612													10	111	---	---	---	---	PASS
CBFA2T3	863	broad.mit.edu	37	16	88967911	88967911	+	Splice_Site	SNP	C	A	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr16:88967911C>A	uc002fmm.1	-	2	490	c.304_splice	c.e2+1	p.H102_splice	CBFA2T3_uc002fml.1_Splice_Site_p.L41_splice|CBFA2T3_uc010cif.1_Splice_Site_p.H41_splice|CBFA2T3_uc002fmn.1_Splice_Site_p.L102_splice	NM_005187	NP_005178	O75081	MTG16_HUMAN	myeloid translocation gene on chromosome 16						cell proliferation|granulocyte differentiation	Golgi membrane|nucleolus|nucleoplasm	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(3)|ovary(1)	4				BRCA - Breast invasive adenocarcinoma(80;0.0275)		GGGCTACTTACGTGTGTGTGG	0.677			T	RUNX1	AML								10	40	---	---	---	---	PASS
PPP4R1	9989	broad.mit.edu	37	18	9547949	9547949	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr18:9547949G>C	uc002koe.1	-	20	2809	c.2691C>G	c.(2689-2691)GAC>GAG	p.D897E	PPP4R1_uc002kof.2_Missense_Mutation_p.D314E|PPP4R1_uc010wzo.1_Missense_Mutation_p.D743E|PPP4R1_uc002kod.1_Missense_Mutation_p.D880E	NM_001042388	NP_001035847	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1	897	HEAT 14.				protein phosphorylation|signal transduction	protein phosphatase 4 complex	protein binding|protein phosphatase type 4 regulator activity			skin(1)	1						CCAAGAAATAGTCTGGAAATG	0.478													24	41	---	---	---	---	PASS
FAM38B	63895	broad.mit.edu	37	18	10671739	10671739	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr18:10671739C>T	uc002kor.3	-	14	2055	c.1915G>A	c.(1915-1917)GGG>AGG	p.G639R	FAM38B_uc002koq.2_Missense_Mutation_p.G474R	NM_022068	NP_071351	Q9H5I5	PIEZ2_HUMAN	family with sequence similarity 38, member B	2682	Helical; (Potential).					integral to membrane	ion channel activity			ovary(1)	1						ACAAATTTCCCAATCACAAGG	0.333													42	132	---	---	---	---	PASS
COMP	1311	broad.mit.edu	37	19	18898325	18898325	+	Silent	SNP	C	G	G			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr19:18898325C>G	uc002nke.2	-	10	1146	c.1110G>C	c.(1108-1110)GCG>GCC	p.A370A	COMP_uc002nkd.2_Silent_p.A337A|COMP_uc010xqj.1_Silent_p.A317A	NM_000095	NP_000086	P49747	COMP_HUMAN	cartilage oligomeric matrix protein precursor	370	TSP type-3 4.				anti-apoptosis|apoptosis|cell adhesion|limb development	extracellular space|proteinaceous extracellular matrix	calcium ion binding|collagen binding|extracellular matrix structural constituent|heparan sulfate proteoglycan binding|heparin binding				0						CGTCGTCGCACGCATCGCCCC	0.697													39	149	---	---	---	---	PASS
CYP2A6	1548	broad.mit.edu	37	19	41354198	41354198	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr19:41354198T>C	uc002opl.3	-	4	601	c.580A>G	c.(580-582)AAG>GAG	p.K194E	CYP2A6_uc010ehe.1_Translation_Start_Site|CYP2A6_uc010ehf.1_RNA	NM_000762	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A,	194			K -> E (in allele CYP2A6*15).		coumarin catabolic process|exogenous drug catabolic process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|coumarin 7-hydroxylase activity|electron carrier activity|enzyme binding|heme binding			ovary(2)	2			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Chlorzoxazone(DB00356)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Ethinyl Estradiol(DB00977)|Formoterol(DB00983)|Halothane(DB01159)|Letrozole(DB01006)|Methoxsalen(DB00553)|Metyrapone(DB01011)|Nicotine(DB00184)|Pilocarpine(DB01085)|Tolbutamide(DB01124)|Tranylcypromine(DB00752)	TCTTTGTCCTTATAGTCAAAG	0.557													45	189	---	---	---	---	PASS
JPH2	57158	broad.mit.edu	37	20	42788455	42788455	+	Silent	SNP	G	A	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr20:42788455G>A	uc002xli.1	-	2	1845	c.972C>T	c.(970-972)CAC>CAT	p.H324H		NM_020433	NP_065166	Q9BR39	JPH2_HUMAN	junctophilin 2 isoform 1	324	MORN 8.|Cytoplasmic (Potential).				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane					0		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			AGCCATAGCCGTGGCGCAGGT	0.662													4	13	---	---	---	---	PASS
SAMSN1	64092	broad.mit.edu	37	21	15884893	15884893	+	Missense_Mutation	SNP	T	A	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr21:15884893T>A	uc002yju.1	-	4	363	c.281A>T	c.(280-282)GAT>GTT	p.D94V	SAMSN1_uc010gky.1_Intron|SAMSN1_uc002yjv.1_Missense_Mutation_p.D162V	NM_022136	NP_071419	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization	94					negative regulation of adaptive immune response|negative regulation of B cell activation|negative regulation of peptidyl-tyrosine phosphorylation	cytoplasm|nucleus|ruffle	phosphotyrosine binding			ovary(3)|pancreas(1)	4				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		ATCTTCCTCATCCTTCAGAAA	0.413													55	146	---	---	---	---	PASS
MYO18B	84700	broad.mit.edu	37	22	26299697	26299697	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr22:26299697G>A	uc003abz.1	+	31	5297	c.5047G>A	c.(5047-5049)GTT>ATT	p.V1683I	MYO18B_uc003aca.1_Missense_Mutation_p.V1564I|MYO18B_uc010guy.1_Missense_Mutation_p.V1565I|MYO18B_uc010guz.1_Missense_Mutation_p.V1563I|MYO18B_uc011aka.1_Missense_Mutation_p.V837I|MYO18B_uc011akb.1_Missense_Mutation_p.V1196I	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1683	Potential.|Tail.|Gln-rich.					nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						GGAAAATTGCGTTGCTGGCTT	0.552													11	13	---	---	---	---	PASS
FAM47B	170062	broad.mit.edu	37	X	34961794	34961794	+	Silent	SNP	T	C	C			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chrX:34961794T>C	uc004ddi.1	+	1	864	c.846T>C	c.(844-846)CAT>CAC	p.H282H		NM_152631	NP_689844	Q8NA70	FA47B_HUMAN	hypothetical protein LOC170062	282	Pro-rich.									ovary(3)|breast(1)	4						GAGCGTCCCATCTCTGCCCGG	0.622													32	25	---	---	---	---	PASS
XK	7504	broad.mit.edu	37	X	37553558	37553558	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chrX:37553558A>G	uc004ddq.2	+	2	347	c.265A>G	c.(265-267)ATC>GTC	p.I89V		NM_021083	NP_066569	P51811	XK_HUMAN	membrane transport protein XK	89	Helical; (Potential).				amino acid transport	integral to membrane	protein binding|transporter activity				0		all_lung(315;0.175)				AGTCTTCTGCATCTACTTTCA	0.408													19	26	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	13711	13711	+	RNA	SNP	G	A	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chrM:13711G>A	uc004cox.3	+	1		c.1375G>A			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		AACGCCTGGCAGCCGGAAGCC	0.483													3	3	---	---	---	---	PASS
IL6ST	3572	broad.mit.edu	37	5	55250760	55250772	+	Frame_Shift_Del	DEL	CATTCCACCCAAA	-	-			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr5:55250760_55250772delCATTCCACCCAAA	uc003jqq.2	-	11	1571_1583	c.1316_1328delTTTGGGTGGAATG	c.(1315-1329)CTTTGGGTGGAATGGfs	p.L439fs	IL6ST_uc010iwb.2_Intron|IL6ST_uc010iwc.2_Intron|IL6ST_uc010iwd.2_Intron|IL6ST_uc011cqk.1_Frame_Shift_Del_p.L150fs|IL6ST_uc003jqr.2_3'UTR	NM_002184	NP_002175	P40189	IL6RB_HUMAN	interleukin 6 signal transducer isoform 1	439_443	Extracellular (Potential).|Fibronectin type-III 4.				interleukin-6-mediated signaling pathway|leukemia inhibitory factor signaling pathway|negative regulation of interleukin-6-mediated signaling pathway|positive regulation of anti-apoptosis|positive regulation of cardiac muscle hypertrophy|positive regulation of osteoblast differentiation|positive regulation of T cell proliferation|positive regulation of tyrosine phosphorylation of Stat1 protein|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation vascular endothelial growth factor production	ciliary neurotrophic factor receptor complex|extracellular region|extracellular space|interleukin-6 receptor complex|oncostatin-M receptor complex	ciliary neurotrophic factor receptor activity|ciliary neurotrophic factor receptor binding|growth factor binding|protein homodimerization activity			large_intestine(1)|ovary(1)	2		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				TGGAGTAGTCCATTCCACCCAAAGCATGTTATC	0.347			O		hepatocellular ca								290	45	---	---	---	---	
BAT2	7916	broad.mit.edu	37	6	31590596	31590598	+	In_Frame_Del	DEL	GGG	-	-			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr6:31590596_31590598delGGG	uc003nvb.3	+	2	279_281	c.30_32delGGG	c.(28-33)AAGGGA>AAA	p.G11del	BAT2_uc011dnv.1_RNA|BAT2_uc003nvc.3_In_Frame_Del_p.G11del|SNORA38_uc003nvd.2_5'Flank|BAT2_uc003nve.2_5'Flank	NM_080686	NP_542417	P48634	PRC2A_HUMAN	HLA-B associated transcript-2	11						cytoplasm|nucleus	protein binding				0						CGACTGCCAAGGGAAAGGATGGA	0.547													298	46	---	---	---	---	
PLEKHA2	59339	broad.mit.edu	37	8	38793568	38793569	+	Splice_Site	DEL	GG	-	-			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr8:38793568_38793569delGG	uc003xmi.3	+	3	432	c.198_splice	c.e3+1	p.K66_splice	PLEKHA2_uc011lce.1_Splice_Site_p.K16_splice	NM_021623	NP_067636	Q9HB19	PKHA2_HUMAN	pleckstrin homology domain containing, family A						positive regulation of cell-matrix adhesion	cytoplasm|nucleus|plasma membrane|protein complex	fibronectin binding|laminin binding				0		all_lung(54;0.0413)|Lung NSC(58;0.115)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;4.68e-08)|COAD - Colon adenocarcinoma(9;0.235)			ACATCTCGAAGGTAATGTTGAC	0.426													203	24	---	---	---	---	
PLIN3	10226	broad.mit.edu	37	19	4847750	4847750	+	Frame_Shift_Del	DEL	G	-	-			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr19:4847750delG	uc002mbj.2	-	6	964	c.787delC	c.(787-789)CAGfs	p.Q263fs	PLIN3_uc002mbk.2_Frame_Shift_Del_p.Q251fs|PLIN3_uc002mbl.3_Frame_Shift_Del_p.Q263fs	NM_005817	NP_005808	O60664	PLIN3_HUMAN	mannose 6 phosphate receptor binding protein 1	263					vesicle-mediated transport	endosome membrane|Golgi apparatus|lipid particle	protein binding				0					Galsulfase(DB01279)|Idursulfase(DB01271)	TGTGCCCTCTGCTTGGTGGCT	0.662													16	9	---	---	---	---	
