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
PLCH2	9651	broad.mit.edu	37	1	2411659	2411659	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr1:2411659G>T	uc001aji.1	+	4	827	c.553G>T	c.(553-555)GGG>TGG	p.G185W	PLCH2_uc010nyz.1_5'UTR|PLCH2_uc009vle.1_5'UTR|PLCH2_uc001ajj.1_5'UTR|PLCH2_uc001ajk.1_5'UTR	NM_014638	NP_055453	O75038	PLCH2_HUMAN	phospholipase C, eta 2	185	Potential.|EF-hand 1.				intracellular signal transduction|lipid catabolic process	cytoplasm|plasma membrane	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			central_nervous_system(3)|ovary(1)|skin(1)	5	all_cancers(77;0.000161)|all_epithelial(69;5.98e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;7.32e-16)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.00832)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.44e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.78e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;4.19e-05)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00034)|BRCA - Breast invasive adenocarcinoma(365;0.00443)|KIRC - Kidney renal clear cell carcinoma(229;0.00548)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.2)		CGACAAGAACGGGGATGGCAG	0.617													36	100	---	---	---	---	PASS
CROCCL2	114819	broad.mit.edu	37	1	16812082	16812082	+	RNA	SNP	A	G	G	rs2418644	by1000genomes	TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr1:16812082A>G	uc001ayt.2	-	7		c.1470T>C			CROCCL2_uc001ays.2_RNA	NR_023386				Homo sapiens mRNA for KIAA1922 protein, partial cds.												0						CAAGCTTCTCAGTGAGGTCCG	0.612													10	14	---	---	---	---	PASS
VAV3	10451	broad.mit.edu	37	1	108247662	108247662	+	Silent	SNP	A	G	G			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr1:108247662A>G	uc001dvk.1	-	16	1578	c.1524T>C	c.(1522-1524)TAT>TAC	p.Y508Y	VAV3_uc010ouw.1_Silent_p.Y508Y|VAV3_uc001dvl.1_Silent_p.Y332Y|VAV3_uc010oux.1_Silent_p.Y508Y	NM_006113	NP_006104	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor isoform	508					angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(5)|lung(2)|breast(2)	9		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		TGGAGTCTGCATAGTCTGGTC	0.403													3	133	---	---	---	---	PASS
HBXIP	10542	broad.mit.edu	37	1	110950282	110950282	+	Silent	SNP	G	A	A	rs143658007	byFrequency	TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr1:110950282G>A	uc001dzr.2	-	1	265	c.207C>T	c.(205-207)GCC>GCT	p.A69A		NM_006402	NP_006393	O43504	HBXIP_HUMAN	hepatitis B virus x-interacting protein	Error:Variant_position_missing_in_O43504_after_alignment					anti-apoptosis|negative regulation of caspase activity|response to virus|viral genome replication	cytosol	protein binding			large_intestine(1)|ovary(1)|pancreas(1)	3		all_cancers(81;4.08e-06)|all_epithelial(167;4.38e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0237)|all cancers(265;0.0675)|Epithelial(280;0.0732)|Colorectal(144;0.102)|LUSC - Lung squamous cell carcinoma(189;0.134)		CCAGCGGCACGGCACGTCCTT	0.632													14	93	---	---	---	---	PASS
MSH6	2956	broad.mit.edu	37	2	48026269	48026269	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr2:48026269A>G	uc002rwd.3	+	4	1299	c.1147A>G	c.(1147-1149)AGG>GGG	p.R383G	MSH6_uc002rwc.2_Missense_Mutation_p.R383G|MSH6_uc010fbj.2_Missense_Mutation_p.R81G|MSH6_uc010yoi.1_Missense_Mutation_p.R253G|MSH6_uc010yoj.1_Missense_Mutation_p.R81G	NM_000179	NP_000170	P52701	MSH6_HUMAN	mutS homolog 6	383					determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes	MutSalpha complex	ATP binding|DNA-dependent ATPase activity|protein binding			large_intestine(53)|central_nervous_system(28)|endometrium(28)|stomach(22)|haematopoietic_and_lymphoid_tissue(9)|lung(7)|skin(6)|urinary_tract(5)|breast(5)|ovary(3)|thyroid(1)|upper_aerodigestive_tract(1)	168		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGATGAGCACAGGAGGAGGCC	0.478			Mis|N|F|S		colorectal	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				47	110	---	---	---	---	PASS
REG1A	5967	broad.mit.edu	37	2	79349167	79349167	+	Silent	SNP	C	T	T			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr2:79349167C>T	uc002snz.2	+	4	340	c.237C>T	c.(235-237)GCC>GCT	p.A79A	REG1A_uc010ffx.1_3'UTR|REG1A_uc010ysd.1_Silent_p.A79A	NM_002909	NP_002900	P05451	REG1A_HUMAN	regenerating islet-derived 1 alpha precursor	79	C-type lectin.				positive regulation of cell proliferation	extracellular region	growth factor activity|sugar binding				0						TCACCCAGGCCGAGGGTGCCT	0.527													73	115	---	---	---	---	PASS
PROM2	150696	broad.mit.edu	37	2	95944760	95944760	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr2:95944760C>A	uc002suh.1	+	10	1275	c.1142C>A	c.(1141-1143)CCG>CAG	p.P381Q	PROM2_uc002sui.2_Missense_Mutation_p.P381Q|PROM2_uc002suj.2_Missense_Mutation_p.P35Q|PROM2_uc002suk.2_Missense_Mutation_p.P381Q|PROM2_uc002sul.2_5'UTR|PROM2_uc002sum.2_5'Flank	NM_144707	NP_653308	Q8N271	PROM2_HUMAN	prominin 2 precursor	381	Extracellular (Potential).					apical plasma membrane|basolateral plasma membrane|cilium membrane|integral to membrane|microvillus membrane				ovary(1)	1						GCCCAGCAGCCGGAAGGGGTG	0.662													3	99	---	---	---	---	PASS
CNTNAP5	129684	broad.mit.edu	37	2	125521571	125521571	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr2:125521571G>A	uc002tno.2	+	16	2741	c.2377G>A	c.(2377-2379)GTC>ATC	p.V793I	CNTNAP5_uc010flu.2_Missense_Mutation_p.V794I	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	793	Laminin G-like 3.|Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		CTGGAACGCCGTCTCATTTTA	0.428													69	118	---	---	---	---	PASS
SSB	6741	broad.mit.edu	37	2	170663358	170663358	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr2:170663358G>T	uc002ufk.2	+	5	516	c.409G>T	c.(409-411)GTA>TTA	p.V137L	SSB_uc002ufl.2_Missense_Mutation_p.V137L|SSB_uc002ufm.2_Missense_Mutation_p.V137L	NM_003142	NP_003133	P05455	LA_HUMAN	autoantigen La	137	RRM.				histone mRNA metabolic process|tRNA modification	nucleus|ribonucleoprotein complex	mRNA binding|nucleotide binding|protein binding|tRNA binding			skin(3)|pancreas(1)	4						TAAAGGTCAAGTACTAAATAT	0.299													5	165	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179472383	179472383	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr2:179472383C>T	uc010zfg.1	-	226	45552	c.45328G>A	c.(45328-45330)GTC>ATC	p.V15110I	uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.V8805I|TTN_uc010zfi.1_Missense_Mutation_p.V8738I|TTN_uc010zfj.1_Missense_Mutation_p.V8613I	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	16037							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)			CCACCCTTGACAGAAACATCC	0.428													79	116	---	---	---	---	PASS
ZDBF2	57683	broad.mit.edu	37	2	207170939	207170939	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr2:207170939C>T	uc002vbp.2	+	5	1937	c.1687C>T	c.(1687-1689)CGG>TGG	p.R563W		NM_020923	NP_065974	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	563							nucleic acid binding|zinc ion binding			ovary(3)	3						AACAAAACTTCGGAAGAAGGC	0.438													27	47	---	---	---	---	PASS
SPHKAP	80309	broad.mit.edu	37	2	228858269	228858269	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr2:228858269G>A	uc002vpq.2	-	9	4749	c.4702C>T	c.(4702-4704)CCA>TCA	p.P1568S	SPHKAP_uc002vpp.2_Intron|SPHKAP_uc010zlx.1_Intron	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	1568						cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		GGAGAAGATGGCATGCTTTCC	0.423													6	14	---	---	---	---	PASS
BRPF1	7862	broad.mit.edu	37	3	9788936	9788936	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr3:9788936A>G	uc003bse.2	+	14	3947	c.3548A>G	c.(3547-3549)AAC>AGC	p.N1183S	BRPF1_uc003bsf.2_Missense_Mutation_p.N1189S|BRPF1_uc003bsg.2_Missense_Mutation_p.N1182S|BRPF1_uc011ati.1_Missense_Mutation_p.N1088S|OGG1_uc003bsh.2_5'Flank|OGG1_uc003bsi.2_5'Flank|OGG1_uc003bsj.2_5'Flank|OGG1_uc003bsk.2_5'Flank|OGG1_uc003bsl.2_5'Flank|OGG1_uc003bsm.2_5'Flank|OGG1_uc003bsn.2_5'Flank|OGG1_uc003bso.2_5'Flank	NM_004634	NP_004625	P55201	BRPF1_HUMAN	bromodomain and PHD finger-containing protein 1	1183					histone H3 acetylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|MOZ/MORF histone acetyltransferase complex|plasma membrane	DNA binding|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Medulloblastoma(99;0.227)					CGCAAGTCCAACATCCGCAAG	0.567													28	124	---	---	---	---	PASS
SLITRK3	22865	broad.mit.edu	37	3	164908014	164908014	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr3:164908014T>C	uc003fej.3	-	2	1049	c.605A>G	c.(604-606)GAC>GGC	p.D202G	SLITRK3_uc003fek.2_Missense_Mutation_p.D202G	NM_014926	NP_055741	O94933	SLIK3_HUMAN	slit and trk like 3 protein precursor	202	Extracellular (Potential).|LRR 6.					integral to membrane				ovary(6)|skin(3)|pancreas(1)	10						TCCACGTAGGTCCAAATGGGT	0.408										HNSCC(40;0.11)			56	117	---	---	---	---	PASS
SDHAP2	727956	broad.mit.edu	37	3	195400728	195400728	+	Silent	SNP	A	G	G	rs12107841	by1000genomes	TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr3:195400728A>G	uc003fuw.2	+	9	1218	c.24A>G	c.(22-24)CCA>CCG	p.P8P	SDHAP2_uc011btb.1_Missense_Mutation_p.S156G|SDHAP2_uc011btc.1_RNA|SDHAP2_uc003fuv.2_RNA					SubName: Full=cDNA FLJ16373 fis, clone THYMU3000269, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (EC 1.3.5.1);												0						GATTGTGCCCAGCCTGTACGC	0.587													5	23	---	---	---	---	PASS
RG9MTD2	93587	broad.mit.edu	37	4	100477359	100477359	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr4:100477359C>T	uc003huy.2	-	5	752	c.439G>A	c.(439-441)GGA>AGA	p.G147R	RG9MTD2_uc003huz.3_Missense_Mutation_p.G147R|RG9MTD2_uc003hva.3_Missense_Mutation_p.G147R	NM_152292	NP_689505	Q8TBZ6	RG9D2_HUMAN	RNA (guanine-9-) methyltransferase domain	147							methyltransferase activity			ovary(2)|breast(1)	3				OV - Ovarian serous cystadenocarcinoma(123;1.7e-08)		AGCTGGCCTCCGTGGCTTGTC	0.313													6	102	---	---	---	---	PASS
PLCXD3	345557	broad.mit.edu	37	5	41382448	41382448	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr5:41382448G>A	uc003jmm.1	-	2	394	c.292C>T	c.(292-294)CGA>TGA	p.R98*		NM_001005473	NP_001005473	Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X	98	PI-PLC X-box.				intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			skin(2)|urinary_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	6						GTGGAAATTCGAAGATCAAAA	0.443													6	186	---	---	---	---	PASS
FNIP1	96459	broad.mit.edu	37	5	131034664	131034664	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr5:131034664G>A	uc003kvs.1	-	11	1290	c.1148C>T	c.(1147-1149)GCC>GTC	p.A383V	RAPGEF6_uc003kvp.1_Intron|FNIP1_uc003kvt.1_Missense_Mutation_p.A355V|FNIP1_uc010jdm.1_Missense_Mutation_p.A338V|FNIP1_uc003kvu.2_Missense_Mutation_p.A383V	NM_133372	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1 isoform 1	383					regulation of protein phosphorylation	cytoplasm	protein binding			pancreas(1)|skin(1)	2		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		TCTCTGACTGGCATCAGCTGA	0.353													7	239	---	---	---	---	PASS
P4HA2	8974	broad.mit.edu	37	5	131531126	131531126	+	Silent	SNP	C	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr5:131531126C>A	uc003kwh.2	-	13	1983	c.1419G>T	c.(1417-1419)GGG>GGT	p.G473G	P4HA2_uc003kwg.2_Silent_p.G471G|P4HA2_uc003kwi.2_Silent_p.G471G|P4HA2_uc003kwk.2_Silent_p.G471G|P4HA2_uc003kwl.2_Silent_p.G473G|P4HA2_uc003kwj.2_Silent_p.G471G	NM_004199	NP_004190	O15460	P4HA2_HUMAN	prolyl 4-hydroxylase, alpha II subunit isoform 1	473	Fe2OG dioxygenase.					endoplasmic reticulum lumen	electron carrier activity|iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 4-dioxygenase activity|protein binding				0		all_cancers(142;0.103)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		L-Proline(DB00172)|Succinic acid(DB00139)	AAATTGCAGCCCCCAGATCAG	0.493													32	79	---	---	---	---	PASS
PCDHGA2	56113	broad.mit.edu	37	5	140719143	140719143	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr5:140719143G>A	uc003ljk.1	+	1	790	c.605G>A	c.(604-606)CGC>CAC	p.R202H	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc011dao.1_Missense_Mutation_p.R202H	NM_018915	NP_061738	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2 isoform 1	202	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTCTGGACCGCGAGGAAGAG	0.592													7	129	---	---	---	---	PASS
TCOF1	6949	broad.mit.edu	37	5	149755319	149755319	+	Silent	SNP	C	T	T			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr5:149755319C>T	uc003lry.2	+	12	1848	c.1740C>T	c.(1738-1740)CCC>CCT	p.P580P	TCOF1_uc003lrw.2_Silent_p.P580P|TCOF1_uc011dch.1_Silent_p.P580P|TCOF1_uc003lrz.2_Silent_p.P580P|TCOF1_uc003lrx.2_Silent_p.P503P|TCOF1_uc003lsa.2_Silent_p.P503P|TCOF1_uc011dci.1_Silent_p.P69P	NM_001135243	NP_001128715	Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	580					skeletal system development	nucleolus	protein binding|transporter activity			ovary(2)|large_intestine(1)	3		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGGCCAAACCCACCTCCAGTC	0.587													51	146	---	---	---	---	PASS
RANBP17	64901	broad.mit.edu	37	5	170395294	170395294	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr5:170395294T>G	uc003mba.2	+	14	1639	c.1623T>G	c.(1621-1623)TGT>TGG	p.C541W	RANBP17_uc003max.1_RNA|RANBP17_uc003may.1_RNA|RANBP17_uc003maz.1_RNA|RANBP17_uc010jjr.1_RNA	NM_022897	NP_075048	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	541					mRNA transport|protein import into nucleus|transmembrane transport	cytoplasm|nuclear pore	GTP binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CTCGATGTTGTAATGAGAAAA	0.343			T	TRD@	ALL								17	187	---	---	---	---	PASS
NKAPL	222698	broad.mit.edu	37	6	28227392	28227392	+	Silent	SNP	C	T	T			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr6:28227392C>T	uc003nkt.2	+	1	295	c.243C>T	c.(241-243)TAC>TAT	p.Y81Y	ZKSCAN4_uc011dlb.1_5'Flank	NM_001007531	NP_001007532	Q5M9Q1	NKAPL_HUMAN	NFKB activating protein-like	81										upper_aerodigestive_tract(1)|ovary(1)	2						TCCGCAACTACGCCTTCGCGT	0.587													39	80	---	---	---	---	PASS
FGD2	221472	broad.mit.edu	37	6	36993625	36993625	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr6:36993625C>A	uc010jwp.1	+	14	1687	c.1516C>A	c.(1516-1518)CCC>ACC	p.P506T	FGD2_uc003ong.2_Missense_Mutation_p.P228T|FGD2_uc011dtv.1_Missense_Mutation_p.P134T|FGD2_uc003onj.1_Missense_Mutation_p.P83T	NM_173558	NP_775829	Q7Z6J4	FGD2_HUMAN	FYVE, RhoGEF and PH domain containing 2	506	FYVE-type.				actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|early endosome membrane|Golgi apparatus|lamellipodium|nucleus|ruffle membrane	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			upper_aerodigestive_tract(1)|lung(1)|pancreas(1)	3						CGACAACAGGCCCAACCGAGT	0.617													5	91	---	---	---	---	PASS
GSTA2	2939	broad.mit.edu	37	6	52616466	52616466	+	Missense_Mutation	SNP	T	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr6:52616466T>A	uc003pay.2	-	6	605	c.455A>T	c.(454-456)AAG>ATG	p.K152M		NM_000846	NP_000837	P09210	GSTA2_HUMAN	glutathione S-transferase alpha 2	152	GST C-terminal.				glutathione metabolic process|xenobiotic metabolic process	cytosol	glutathione transferase activity			ovary(1)	1	Lung NSC(77;0.118)				Aminophenazone(DB01424)|Amsacrine(DB00276)|Busulfan(DB01008)|Chlorambucil(DB00291)|Chloroquine(DB00608)|Cinnarizine(DB00568)|Clofibrate(DB00636)|Ethacrynic acid(DB00903)|Glutathione(DB00143)|Mechlorethamine(DB00888)|Praziquantel(DB01058)|Vitamin E(DB00163)	CCGGCTCAGCTTGTTGCCAAC	0.532													63	146	---	---	---	---	PASS
SIM1	6492	broad.mit.edu	37	6	100841663	100841663	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr6:100841663C>T	uc003pqj.3	-	10	1477	c.1270G>A	c.(1270-1272)GAT>AAT	p.D424N	SIM1_uc010kcu.2_Missense_Mutation_p.D424N	NM_005068	NP_005059	P81133	SIM1_HUMAN	single-minded homolog 1	424	Single-minded C-terminal.				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(4)	4		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		CCAGGCCTATCGGCGGGGTCC	0.597													30	55	---	---	---	---	PASS
PNLDC1	154197	broad.mit.edu	37	6	160237001	160237001	+	Silent	SNP	T	C	C			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr6:160237001T>C	uc003qsx.1	+	13	1134	c.963T>C	c.(961-963)AGT>AGC	p.S321S	PNLDC1_uc003qsy.1_Silent_p.S332S	NM_173516	NP_775787	Q8NA58	PNDC1_HUMAN	poly(A)-specific ribonuclease (PARN)-like domain	321	Cytoplasmic (Potential).					integral to membrane|nucleus	nucleic acid binding				0		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		TTTCCAATAGTGACTTGAATC	0.378													5	126	---	---	---	---	PASS
NFE2L3	9603	broad.mit.edu	37	7	26224957	26224957	+	Missense_Mutation	SNP	A	T	T			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr7:26224957A>T	uc003sxq.2	+	4	1911	c.1639A>T	c.(1639-1641)ATC>TTC	p.I547F		NM_004289	NP_004280	Q9Y4A8	NF2L3_HUMAN	nuclear factor erythroid 2-like 3	547					transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			skin(3)|ovary(1)	4						AGCTTTGCATATCCCTTTTTC	0.413													5	268	---	---	---	---	PASS
HIBADH	11112	broad.mit.edu	37	7	27565971	27565971	+	Silent	SNP	G	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr7:27565971G>A	uc003szf.2	-	8	1068	c.873C>T	c.(871-873)GAC>GAT	p.D291D	HIBADH_uc003szg.2_Silent_p.D242D|HIBADH_uc003szh.2_Silent_p.D190D	NM_152740	NP_689953	P31937	3HIDH_HUMAN	3-hydroxyisobutyrate dehydrogenase precursor	291					branched chain family amino acid catabolic process|pentose-phosphate shunt|valine metabolic process	mitochondrial matrix	3-hydroxyisobutyrate dehydrogenase activity|NAD binding|phosphogluconate dehydrogenase (decarboxylating) activity			ovary(2)	2			GBM - Glioblastoma multiforme(3;0.0368)		NADH(DB00157)	TGGTAGCAGAGTCTTGTGCCA	0.468													13	45	---	---	---	---	PASS
ANLN	54443	broad.mit.edu	37	7	36435954	36435954	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr7:36435954C>G	uc003tff.2	+	2	302	c.98C>G	c.(97-99)TCT>TGT	p.S33C	ANLN_uc011kaz.1_Missense_Mutation_p.S33C|ANLN_uc003tfg.2_Missense_Mutation_p.S33C|ANLN_uc010kxe.2_Missense_Mutation_p.S33C	NM_018685	NP_061155	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	33	Required for ubiquitination.|Nuclear localization.|Interaction with CD2AP.				cytokinesis|mitosis|regulation of exit from mitosis|septin ring assembly	actomyosin contractile ring|nucleus	actin binding			ovary(2)|skin(1)	3						GCTCCAAGGTCTATGACTCAT	0.473													42	77	---	---	---	---	PASS
PHTF2	57157	broad.mit.edu	37	7	77469597	77469597	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr7:77469597A>G	uc003ugs.3	+	1	151	c.25A>G	c.(25-27)ATA>GTA	p.I9V	PHTF2_uc003ugo.3_Missense_Mutation_p.I9V|PHTF2_uc003ugp.2_Missense_Mutation_p.I9V|PHTF2_uc003ugq.3_Missense_Mutation_p.I9V|PHTF2_uc010ldv.2_Missense_Mutation_p.I9V|PHTF2_uc003ugr.3_Missense_Mutation_p.I9V|PHTF2_uc003ugt.3_Missense_Mutation_p.I9V|PHTF2_uc003ugu.3_Missense_Mutation_p.I9V	NM_001127357	NP_001120829	Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	9					regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum|nucleus	DNA binding			ovary(1)	1						CACAGATGCTATAGTCTGGTA	0.318													73	125	---	---	---	---	PASS
RASA4	10156	broad.mit.edu	37	7	102236573	102236573	+	Silent	SNP	G	T	T			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr7:102236573G>T	uc003vae.2	-	9	810	c.741C>A	c.(739-741)GGC>GGA	p.G247G	UPK3BL_uc003uzy.2_Intron|RASA4_uc011kla.1_Silent_p.G175G|RASA4_uc010lig.2_Silent_p.G175G|RASA4_uc003vaf.2_Silent_p.G247G|RASA4_uc011klb.1_Silent_p.G175G|RASA4_uc010lih.2_Silent_p.G55G|RASA4_uc011kld.1_Intron|uc003vag.1_Intron	NM_006989	NP_008920	O43374	RASL2_HUMAN	RAS p21 protein activator 4 isoform 1	247					intracellular signal transduction|negative regulation of Ras protein signal transduction	cytosol|intrinsic to internal side of plasma membrane	metal ion binding|Ras GTPase activator activity				0						AGCCCAGGTTGCCCCTGGAAT	0.657													7	21	---	---	---	---	PASS
ADAM9	8754	broad.mit.edu	37	8	38899534	38899534	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr8:38899534C>A	uc003xmr.2	+	12	1278	c.1200C>A	c.(1198-1200)AAC>AAA	p.N400K	ADAM9_uc011lcf.1_RNA|ADAM9_uc011lcg.1_RNA|ADAM9_uc010lwr.2_RNA	NM_003816	NP_003807	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9 isoform 1	400	Extracellular (Potential).|Peptidase M12B.				activation of MAPKK activity|cell-cell adhesion mediated by integrin|cell-matrix adhesion|keratinocyte differentiation|monocyte activation|PMA-inducible membrane protein ectodomain proteolysis|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell adhesion mediated by integrin|positive regulation of keratinocyte migration|positive regulation of macrophage fusion|positive regulation of membrane protein ectodomain proteolysis|positive regulation of protein secretion|response to calcium ion|response to glucocorticoid stimulus|response to hydrogen peroxide|response to manganese ion|response to tumor necrosis factor|transforming growth factor beta receptor signaling pathway	extracellular space|extracellular space|integral to membrane|intrinsic to external side of plasma membrane	collagen binding|integrin binding|laminin binding|metalloendopeptidase activity|protein kinase C binding|SH3 domain binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)			AAGGAGGAAACTGCCTTCTTA	0.408													7	121	---	---	---	---	PASS
SOX17	64321	broad.mit.edu	37	8	55371662	55371662	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr8:55371662G>A	uc003xsb.3	+	2	556	c.352G>A	c.(352-354)GTG>ATG	p.V118M		NM_022454	NP_071899	Q9H6I2	SOX17_HUMAN	SRY-box 17	118	HMG box.				angiogenesis|cardiac cell fate determination|endocardial cell differentiation|endocardium formation|endoderm formation|heart formation|heart looping|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell growth|outflow tract morphogenesis|positive regulation of transcription, DNA-dependent|protein destabilization|protein stabilization|regulation of embryonic development|renal system development|vasculogenesis|Wnt receptor signaling pathway	transcription factor complex	beta-catenin binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			lung(1)	1		Lung NSC(129;0.109)|all_epithelial(80;0.176)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;1.9e-07)|Epithelial(17;1.7e-05)|all cancers(17;0.000159)			GCGGCCCTTCGTGGAGGAGGC	0.687													4	7	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113657357	113657357	+	Silent	SNP	A	T	T			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr8:113657357A>T	uc003ynu.2	-	20	3450	c.3291T>A	c.(3289-3291)GTT>GTA	p.V1097V	CSMD3_uc003yns.2_Silent_p.V369V|CSMD3_uc003ynt.2_Silent_p.V1057V|CSMD3_uc011lhx.1_Silent_p.V993V	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	1097	Extracellular (Potential).|CUB 6.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						GGGTTACATCAACAGTCCATG	0.363										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			4	112	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	68413635	68413635	+	RNA	SNP	G	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr9:68413635G>A	uc004aex.2	+	1		c.190G>A								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		CATCTAACAGGCTGGAGGTGA	0.637													2	1	---	---	---	---	PASS
GOLM1	51280	broad.mit.edu	37	9	88650293	88650293	+	Silent	SNP	A	G	G			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr9:88650293A>G	uc004aol.2	-	8	1203	c.1005T>C	c.(1003-1005)GCT>GCC	p.A335A	GOLM1_uc004aom.2_Silent_p.A335A	NM_016548	NP_057632	Q8NBJ4	GOLM1_HUMAN	golgi membrane protein 1	335	Lumenal (Potential).					Golgi apparatus|integral to plasma membrane					0						CTTCCCCGGCAGCTTCCTGCT	0.622											OREG0019278	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	180	---	---	---	---	PASS
FAM22F	54754	broad.mit.edu	37	9	97080948	97080948	+	Silent	SNP	A	G	G			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr9:97080948A>G	uc004aup.1	-	7	2091	c.2070T>C	c.(2068-2070)CCT>CCC	p.P690P		NM_017561	NP_060031	A1L443	FA22F_HUMAN	hypothetical protein LOC54754	690											0		Acute lymphoblastic leukemia(62;0.136)				TGGCAGGAGAAGGTGATGGGC	0.622													3	16	---	---	---	---	PASS
FAM22F	54754	broad.mit.edu	37	9	97080953	97080953	+	Missense_Mutation	SNP	A	C	C	rs149638507	by1000genomes	TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr9:97080953A>C	uc004aup.1	-	7	2086	c.2065T>G	c.(2065-2067)TCA>GCA	p.S689A		NM_017561	NP_060031	A1L443	FA22F_HUMAN	hypothetical protein LOC54754	689											0		Acute lymphoblastic leukemia(62;0.136)				GGAGAAGGTGATGGGCTGAGG	0.617													3	18	---	---	---	---	PASS
TBC1D2	55357	broad.mit.edu	37	9	100971252	100971252	+	Silent	SNP	G	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr9:100971252G>A	uc011lvb.1	-	9	2028	c.1848C>T	c.(1846-1848)GCC>GCT	p.A616A	TBC1D2_uc004ayp.2_Silent_p.A156A|TBC1D2_uc004ayq.2_Silent_p.A616A|TBC1D2_uc004ayr.2_Silent_p.A398A|TBC1D2_uc004ayo.3_Silent_p.A616A	NM_018421	NP_060891	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	616						cell junction|cytoplasmic membrane-bounded vesicle|nucleus	Rab GTPase activator activity			ovary(3)	3		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)		GCTTGAGCTCGGCTGAGGGCA	0.667													5	147	---	---	---	---	PASS
KIF12	113220	broad.mit.edu	37	9	116858374	116858374	+	Silent	SNP	C	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr9:116858374C>A	uc004bif.2	-	6	676	c.438G>T	c.(436-438)CTG>CTT	p.L146L	KIF12_uc004big.2_RNA	NM_138424	NP_612433	Q96FN5	KIF12_HUMAN	kinesin family member 12	279	Kinesin-motor.				microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity				0						CCTCAAGCATCAGCTCCCCAC	0.622													33	147	---	---	---	---	PASS
FAM171A1	221061	broad.mit.edu	37	10	15317865	15317865	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr10:15317865G>A	uc001iob.2	-	3	414	c.407C>T	c.(406-408)TCA>TTA	p.S136L		NM_001010924	NP_001010924	Q5VUB5	F1711_HUMAN	hypothetical protein LOC221061 precursor	136	Extracellular (Potential).					integral to membrane				ovary(2)|breast(1)|skin(1)	4						TTGGAATCCTGATACTATTTG	0.269													19	92	---	---	---	---	PASS
NCOA4	8031	broad.mit.edu	37	10	51584845	51584845	+	Missense_Mutation	SNP	G	A	A	rs144343467		TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr10:51584845G>A	uc001jis.3	+	8	1147	c.944G>A	c.(943-945)CGG>CAG	p.R315Q	PARG_uc001jih.2_Intron|uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron|NCOA4_uc009xon.2_Missense_Mutation_p.R331Q|NCOA4_uc010qhd.1_Missense_Mutation_p.R331Q|NCOA4_uc010qhe.1_Missense_Mutation_p.R215Q|NCOA4_uc010qhf.1_Missense_Mutation_p.R149Q|NCOA4_uc001jit.2_Missense_Mutation_p.R315Q|NCOA4_uc009xoo.2_Missense_Mutation_p.R315Q	NM_001145263	NP_001138735	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4 isoform 3	315					androgen receptor signaling pathway|male gonad development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	androgen receptor binding|transcription coactivator activity			central_nervous_system(1)|kidney(1)	2						CATAAGCTGCGGAAGCCTGAG	0.453			T	RET	papillary thyroid 								6	165	---	---	---	---	PASS
NCOA4	8031	broad.mit.edu	37	10	51584846	51584846	+	Silent	SNP	G	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr10:51584846G>A	uc001jis.3	+	8	1148	c.945G>A	c.(943-945)CGG>CGA	p.R315R	PARG_uc001jih.2_Intron|uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron|NCOA4_uc009xon.2_Silent_p.R331R|NCOA4_uc010qhd.1_Silent_p.R331R|NCOA4_uc010qhe.1_Silent_p.R215R|NCOA4_uc010qhf.1_Silent_p.R149R|NCOA4_uc001jit.2_Silent_p.R315R|NCOA4_uc009xoo.2_Silent_p.R315R	NM_001145263	NP_001138735	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4 isoform 3	315					androgen receptor signaling pathway|male gonad development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	androgen receptor binding|transcription coactivator activity			central_nervous_system(1)|kidney(1)	2						ATAAGCTGCGGAAGCCTGAGA	0.453			T	RET	papillary thyroid 								6	164	---	---	---	---	PASS
OR10G8	219869	broad.mit.edu	37	11	123900990	123900990	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr11:123900990G>A	uc001pzp.1	+	1	661	c.661G>A	c.(661-663)GTC>ATC	p.V221I		NM_001004464	NP_001004464	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G,	221	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		TGTGTCCATCGTCTGTTCCAT	0.542													11	183	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	12	8051389	8051389	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr12:8051389G>A	uc001qtp.1	+	4	669	c.589G>A	c.(589-591)GCT>ACT	p.A197T	uc001qtq.1_5'Flank					RecName: Full=Putative homeobox protein NANOG2;																		CTTGGAAGCTGCTGGGGAAGG	0.463													90	116	---	---	---	---	PASS
FGD4	121512	broad.mit.edu	37	12	32764089	32764089	+	Silent	SNP	T	C	C			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr12:32764089T>C	uc001rkz.2	+	10	1687	c.1210T>C	c.(1210-1212)TTA>CTA	p.L404L	FGD4_uc001rlc.2_Silent_p.L489L|FGD4_uc001rky.2_Silent_p.L156L|FGD4_uc001rla.2_Silent_p.L60L|FGD4_uc010ske.1_Silent_p.L516L|FGD4_uc001rlb.1_RNA	NM_139241	NP_640334	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	404					actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|filopodium|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					AAAGAAACTCTTAGAGATTTA	0.353													4	196	---	---	---	---	PASS
SETD8	387893	broad.mit.edu	37	12	123875311	123875311	+	Silent	SNP	C	T	T	rs74356260		TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr12:123875311C>T	uc001uew.2	+	3	309	c.267C>T	c.(265-267)GCC>GCT	p.A89A	SETD8_uc001uex.2_Silent_p.A24A	NM_020382	NP_065115	Q9NQR1	SETD8_HUMAN	SET domain-containing 8	130					cell division|mitosis|negative regulation of transcription from RNA polymerase II promoter|peptidyl-lysine monomethylation|regulation of DNA damage response, signal transduction by p53 class mediator|transcription, DNA-dependent	chromosome|nucleus	histone-lysine N-methyltransferase activity|p53 binding|transcription corepressor activity				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		AACCATTAGCCGGAATCTACA	0.498													5	153	---	---	---	---	PASS
PIWIL1	9271	broad.mit.edu	37	12	130845793	130845793	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr12:130845793T>G	uc001uik.2	+	15	1824	c.1734T>G	c.(1732-1734)GAT>GAG	p.D578E	PIWIL1_uc001uij.1_Missense_Mutation_p.D578E	NM_004764	NP_004755	Q96J94	PIWL1_HUMAN	piwi-like 1	578	RNA-binding (By similarity).|Piwi.				gene silencing by RNA|meiosis|multicellular organismal development|regulation of translation|spermatid development	chromatoid body|P granule	mRNA binding|piRNA binding|protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		TGTGTACAGATTGCCCTACCC	0.433													30	76	---	---	---	---	PASS
LATS2	26524	broad.mit.edu	37	13	21557700	21557700	+	Silent	SNP	G	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr13:21557700G>A	uc009zzs.2	-	5	2510	c.2145C>T	c.(2143-2145)GCC>GCT	p.A715A	LATS2_uc001unr.3_Silent_p.A715A	NM_014572	NP_055387	Q9NRM7	LATS2_HUMAN	LATS, large tumor suppressor, homolog 2	715	Protein kinase.|ATP (By similarity).				cell division|G1/S transition of mitotic cell cycle|hippo signaling cascade|hormone-mediated signaling pathway|intracellular protein kinase cascade|mitosis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity	microtubule organizing center|nucleus|spindle pole	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|central_nervous_system(3)|ovary(2)|breast(1)|pancreas(1)	10		all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000781)|Epithelial(112;0.00144)|OV - Ovarian serous cystadenocarcinoma(117;0.0183)|Lung(94;0.0375)|LUSC - Lung squamous cell carcinoma(192;0.104)		TGTCCCTCTCGGCCTTGACGT	0.532													11	332	---	---	---	---	PASS
NUFIP1	26747	broad.mit.edu	37	13	45523879	45523879	+	Silent	SNP	T	C	C			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr13:45523879T>C	uc001uzp.2	-	8	1158	c.1116A>G	c.(1114-1116)TCA>TCG	p.S372S		NM_012345	NP_036477	Q9UHK0	NUFP1_HUMAN	nuclear fragile X mental retardation protein	372					box C/D snoRNP assembly|positive regulation of transcription from RNA polymerase II promoter|RNA processing	actin cytoskeleton|cytosolic ribosome|nuclear matrix|nucleolus|perichromatin fibrils|pre-snoRNP complex|presynaptic active zone|transcription elongation factor complex	DNA binding|identical protein binding|protein binding, bridging|RNA binding|zinc ion binding				0		Lung NSC(96;8.23e-05)|Breast(139;0.00378)|Prostate(109;0.0107)|all_hematologic(4;0.014)|Lung SC(185;0.0262)|Hepatocellular(98;0.0524)|Acute lymphoblastic leukemia(4;0.143)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000306)|BRCA - Breast invasive adenocarcinoma(63;0.125)		TCTCTGACCCTGAAAGACTGC	0.443													5	201	---	---	---	---	PASS
ABCC4	10257	broad.mit.edu	37	13	95862980	95862980	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr13:95862980T>C	uc001vmd.3	-	5	706	c.587A>G	c.(586-588)AAT>AGT	p.N196S	ABCC4_uc010afk.2_Missense_Mutation_p.N196S|ABCC4_uc001vme.2_Missense_Mutation_p.N196S|ABCC4_uc010tih.1_Missense_Mutation_p.N121S|ABCC4_uc001vmf.2_Missense_Mutation_p.N153S|ABCC4_uc010afl.1_Missense_Mutation_p.N153S|ABCC4_uc010afm.1_Missense_Mutation_p.N209S	NM_005845	NP_005836	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C, member 4	196	ABC transmembrane type-1 1.				platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)	GGACAGCAGATTGACTATCTG	0.408													12	86	---	---	---	---	PASS
HERC1	8925	broad.mit.edu	37	15	63978653	63978653	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr15:63978653G>C	uc002amp.2	-	34	6278	c.6130C>G	c.(6130-6132)CTA>GTA	p.L2044V		NM_003922	NP_003913	Q15751	HERC1_HUMAN	hect domain and RCC1-like domain 1	2044	B30.2/SPRY.				protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(6)|breast(6)|lung(5)|central_nervous_system(2)	19						TTCTCCACTAGGCAACACTGA	0.473													7	439	---	---	---	---	PASS
WDR93	56964	broad.mit.edu	37	15	90258314	90258314	+	Missense_Mutation	SNP	A	C	C	rs75728597		TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr15:90258314A>C	uc002boj.2	+	6	845	c.744A>C	c.(742-744)AGA>AGC	p.R248S	WDR93_uc010bnr.2_Missense_Mutation_p.R248S	NM_020212	NP_064597	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	248					electron transport chain	mitochondrial inner membrane	oxidoreductase activity, acting on NADH or NADPH			ovary(2)	2	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			AAAAAGTCAGACAGCCGCAAC	0.458													9	25	---	---	---	---	PASS
A2BP1	54715	broad.mit.edu	37	16	7657342	7657342	+	Splice_Site	SNP	T	G	G			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr16:7657342T>G	uc002cys.2	+	10	1664	c.676_splice	c.e10+2	p.G226_splice	A2BP1_uc010buf.1_Splice_Site_p.G226_splice|A2BP1_uc002cyr.1_Splice_Site_p.G225_splice|A2BP1_uc002cyt.2_Splice_Site_p.V226_splice|A2BP1_uc010uxz.1_Splice_Site_p.G269_splice|A2BP1_uc010uya.1_Splice_Site_p.G183_splice|A2BP1_uc002cyv.1_Splice_Site_p.G226_splice|A2BP1_uc010uyb.1_Splice_Site_p.G226_splice|A2BP1_uc002cyw.2_Splice_Site_p.G246_splice|A2BP1_uc002cyy.2_Splice_Site_p.G246_splice|A2BP1_uc002cyx.2_Splice_Site_p.G246_splice|A2BP1_uc010uyc.1_Splice_Site_p.V246_splice	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		TCTATGCAGGTACAGAGTTTC	0.368													31	187	---	---	---	---	PASS
TMC7	79905	broad.mit.edu	37	16	19041572	19041572	+	Silent	SNP	T	C	C			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr16:19041572T>C	uc002dfq.2	+	6	868	c.738T>C	c.(736-738)TTT>TTC	p.F246F	TMC7_uc010vao.1_Silent_p.F246F|TMC7_uc002dfp.2_Silent_p.F246F|TMC7_uc010vap.1_Silent_p.F136F	NM_024847	NP_079123	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7 isoform a	246	Extracellular (Potential).					integral to membrane				skin(2)|ovary(1)	3						CTAGCCTCTTTTACGGACATT	0.507													7	283	---	---	---	---	PASS
SLC5A2	6524	broad.mit.edu	37	16	31499068	31499068	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr16:31499068G>A	uc002ecf.3	+	7	892	c.873G>A	c.(871-873)TGG>TGA	p.W291*	SLC5A2_uc010car.2_RNA|C16orf58_uc002ecg.2_RNA	NM_003041	NP_003032	P31639	SC5A2_HUMAN	solute carrier family 5 (sodium/glucose	291	Helical; (Potential).				carbohydrate metabolic process	integral to membrane	low-affinity glucose:sodium symporter activity			ovary(1)	1						GCTGGTACTGGTGCAGCGACC	0.721													10	33	---	---	---	---	PASS
PRPF8	10594	broad.mit.edu	37	17	1559946	1559946	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr17:1559946A>C	uc002fte.2	-	35	5729	c.5615T>G	c.(5614-5616)CTG>CGG	p.L1872R		NM_006445	NP_006436	Q6P2Q9	PRP8_HUMAN	U5 snRNP-specific protein	1872	Involved in interaction with pre-mRNA 5' splice site.					catalytic step 2 spliceosome|nuclear speck|U5 snRNP	protein binding|RNA binding			lung(4)|ovary(2)	6				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		TCTTACCTCCAGTGGGTCCAG	0.552													24	40	---	---	---	---	PASS
RTN4RL1	146760	broad.mit.edu	37	17	1840948	1840948	+	Silent	SNP	G	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr17:1840948G>A	uc002ftp.2	-	2	187	c.168C>T	c.(166-168)AGC>AGT	p.S56S		NM_178568	NP_848663	Q86UN2	R4RL1_HUMAN	reticulon 4 receptor-like 1 precursor	56	LRR 1.				axon regeneration	anchored to plasma membrane	receptor activity				0						AGACGCGCTCGCTGTCCACGG	0.652													4	54	---	---	---	---	PASS
XAF1	54739	broad.mit.edu	37	17	6673970	6673970	+	Silent	SNP	T	C	C			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr17:6673970T>C	uc002gdn.2	+	6	758	c.516T>C	c.(514-516)TGT>TGC	p.C172C	XAF1_uc002gdm.1_Silent_p.C112C|XAF1_uc002gdo.2_Silent_p.C153C|XAF1_uc002gdp.2_Silent_p.C121C|XAF1_uc002gdq.2_Silent_p.C4C|XAF1_uc002gdr.2_Silent_p.C102C	NM_017523	NP_059993	Q6GPH4	XAF1_HUMAN	XIAP associated factor 1 isoform 1	172					apoptosis|type I interferon-mediated signaling pathway	mitochondrion|nucleus	zinc ion binding				0						AGGGTAAATGTTGTCCAGACT	0.289													7	187	---	---	---	---	PASS
TBC1D29	26083	broad.mit.edu	37	17	28890301	28890301	+	Missense_Mutation	SNP	G	A	A	rs80145926	byFrequency	TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr17:28890301G>A	uc002hfh.2	+	5	460	c.311G>A	c.(310-312)AGC>AAC	p.S104N	TBC1D29_uc002hfi.2_RNA	NM_015594	NP_056409	Q9UFV1	TBC29_HUMAN	TBC1 domain family, member 29	104						intracellular	Rab GTPase activator activity				0		Myeloproliferative disorder(56;0.0255)				TCAGAGAGCAGCAGAGGCCCC	0.587													4	85	---	---	---	---	PASS
GH2	2689	broad.mit.edu	37	17	61958402	61958402	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr17:61958402G>A	uc002jco.1	-	3	340	c.278C>T	c.(277-279)ACG>ATG	p.T93M	GH2_uc002jcj.2_Missense_Mutation_p.T93M|CSH2_uc002jck.2_Intron|GH2_uc002jcl.1_Missense_Mutation_p.T93M|GH2_uc002jcm.1_Missense_Mutation_p.T93M|GH2_uc002jcn.1_Missense_Mutation_p.T78M	NM_002059	NP_002050	P01242	SOM2_HUMAN	growth hormone 2 isoform 1	93						extracellular region	hormone activity			upper_aerodigestive_tract(2)|pancreas(1)	3						TTTCTGCTGCGTTTTCACCCT	0.572													82	364	---	---	---	---	PASS
ENGASE	64772	broad.mit.edu	37	17	77073870	77073870	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr17:77073870C>T	uc002jwv.2	+	3	348	c.340C>T	c.(340-342)CGC>TGC	p.R114C	ENGASE_uc002jwu.1_Missense_Mutation_p.R114C|ENGASE_uc010wtz.1_5'UTR|ENGASE_uc002jww.2_5'Flank	NM_001042573	NP_001036038	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	114						cytosol	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity			skin(1)	1						CCTGGCGTGTCGCCAGCCCCC	0.582													44	69	---	---	---	---	PASS
S1PR2	9294	broad.mit.edu	37	19	10335297	10335297	+	Silent	SNP	A	T	T			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr19:10335297A>T	uc002mnl.2	-	2	396	c.285T>A	c.(283-285)TCT>TCA	p.S95S		NM_004230	NP_004221	O95136	S1PR2_HUMAN	endothelial differentiation, sphingolipid	95	Helical; Name=2; (By similarity).				activation of MAPK activity|positive regulation of cell proliferation	integral to membrane|plasma membrane	lipid binding|lysosphingolipid and lysophosphatidic acid receptor activity			lung(1)|central_nervous_system(1)	2						TCAGCGTGACAGAGCCAGAGA	0.612													9	42	---	---	---	---	PASS
ZNF93	81931	broad.mit.edu	37	19	20026167	20026167	+	Silent	SNP	C	T	T			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr19:20026167C>T	uc002non.2	+	2	193	c.82C>T	c.(82-84)CTA>TTA	p.L28L	ZNF93_uc002nom.2_Silent_p.L28L	NM_031218	NP_112495	P35789	ZNF93_HUMAN	zinc finger protein 93	28	KRAB.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)	1						ACAGCGGAATCTATATAGGAA	0.398													8	327	---	---	---	---	PASS
PSG3	5671	broad.mit.edu	37	19	43233960	43233960	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr19:43233960G>A	uc002oue.2	-	4	1090	c.958C>T	c.(958-960)CGC>TGC	p.R320C	PSG3_uc002ouf.2_RNA|PSG1_uc002oug.1_Intron|PSG3_uc010eil.2_Missense_Mutation_p.R342C	NM_021016	NP_066296	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	320	Ig-like C2-type 2.				defense response|female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00682)				GGGTAACTGCGGATGCCACCA	0.488													7	293	---	---	---	---	PASS
VASP	7408	broad.mit.edu	37	19	46020979	46020979	+	Silent	SNP	C	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr19:46020979C>A	uc002pcg.2	+	2	406	c.64C>A	c.(64-66)CGA>AGA	p.R22R	VASP_uc010eki.2_Missense_Mutation_p.S5R|VASP_uc002pci.2_Silent_p.R9R	NM_003370	NP_003361	P50552	VASP_HUMAN	vasodilator-stimulated phosphoprotein	22	WH1.				axon guidance|cell junction assembly|T cell receptor signaling pathway	actin cytoskeleton|cytosol|filopodium membrane|focal adhesion|lamellipodium membrane	actin binding|profilin binding|SH3 domain binding				0		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0145)|GBM - Glioblastoma multiforme(486;0.154)		TGGCAACAAGCGATGGCTCCC	0.617													3	103	---	---	---	---	PASS
LILRA3	11026	broad.mit.edu	37	19	54803046	54803046	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr19:54803046G>C	uc002qfd.2	-	4	696	c.631C>G	c.(631-633)CCC>GCC	p.P211A	LILRA6_uc002qew.1_Intron|LILRA3_uc010erk.2_Intron	NM_006865	NP_006856	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor,	211	Ig-like C2-type 2.				defense response	extracellular region|plasma membrane	antigen binding|receptor activity			ovary(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		AGATCACTGGGTAGAGACCAC	0.617													4	77	---	---	---	---	PASS
PAX1	5075	broad.mit.edu	37	20	21690016	21690016	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr20:21690016G>T	uc002wsj.2	+	4	1270	c.1216G>T	c.(1216-1218)GCC>TCC	p.A406S	PAX1_uc010zsl.1_Missense_Mutation_p.A406S|PAX1_uc010zsm.1_Missense_Mutation_p.A382S	NM_006192	NP_006183	P15863	PAX1_HUMAN	paired box 1	406					regulation of transcription, DNA-dependent|skeletal system development|transcription from RNA polymerase II promoter	nucleus	DNA binding			upper_aerodigestive_tract(1)|kidney(1)	2						GCCCCCCGGGGCCGGCGTAGC	0.731													5	12	---	---	---	---	PASS
FRG1B	284802	broad.mit.edu	37	20	29628300	29628300	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr20:29628300G>A	uc010ztl.1	+	3	244	c.212G>A	c.(211-213)AGT>AAT	p.S71N	FRG1B_uc002wvm.1_RNA|FRG1B_uc010ztj.1_RNA|FRG1B_uc010gdr.1_RNA|FRG1B_uc010ztk.1_Missense_Mutation_p.S23N					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						GAAGCAAAAAGTAAAACAGCA	0.358													6	114	---	---	---	---	PASS
TGM2	7052	broad.mit.edu	37	20	36767850	36767850	+	Missense_Mutation	SNP	G	A	A	rs45629036	byFrequency	TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr20:36767850G>A	uc002xhr.2	-	9	1406	c.1306C>T	c.(1306-1308)CGG>TGG	p.R436W	TGM2_uc010zvx.1_Missense_Mutation_p.R355W|TGM2_uc010zvy.1_Missense_Mutation_p.R376W|TGM2_uc002xhs.1_Missense_Mutation_p.R412W|TGM2_uc002xht.2_Missense_Mutation_p.R436W	NM_004613	NP_004604	P21980	TGM2_HUMAN	transglutaminase 2 isoform a	436					apoptotic cell clearance|peptide cross-linking|positive regulation of cell adhesion		acyltransferase activity|metal ion binding|protein binding|protein-glutamine gamma-glutamyltransferase activity			large_intestine(1)|lung(1)|ovary(1)	3		Myeloproliferative disorder(115;0.00878)			L-Glutamine(DB00130)	ATATCCTCCCGCTCGTCTCGG	0.537													5	122	---	---	---	---	PASS
DIDO1	11083	broad.mit.edu	37	20	61525227	61525227	+	Silent	SNP	G	A	A	rs111520535	byFrequency	TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr20:61525227G>A	uc002ydr.1	-	12	3156	c.2892C>T	c.(2890-2892)TCC>TCT	p.S964S	DIDO1_uc002yds.1_Silent_p.S964S|DIDO1_uc002ydt.1_Silent_p.S964S|DIDO1_uc002ydu.1_Silent_p.S964S	NM_033081	NP_149072	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1 isoform c	964					apoptosis|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(3)|skin(3)	6	Breast(26;5.68e-08)					GGTCCCGGCCGGACACTGTGA	0.687													4	138	---	---	---	---	PASS
B3GALT5	10317	broad.mit.edu	37	21	41032741	41032741	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr21:41032741G>C	uc002yyb.1	+	5	847	c.255G>C	c.(253-255)ATG>ATC	p.M85I	B3GALT5_uc002yye.2_Missense_Mutation_p.M85I|B3GALT5_uc002yyi.1_Missense_Mutation_p.M85I|B3GALT5_uc002yyj.1_Missense_Mutation_p.M85I|B3GALT5_uc002yyk.1_Missense_Mutation_p.M85I|B3GALT5_uc002yyl.1_Missense_Mutation_p.M85I|B3GALT5_uc002yym.1_Missense_Mutation_p.M85I	NM_033173	NP_149363	Q9Y2C3	B3GT5_HUMAN	UDP-Gal:betaGlcNAc beta	85	Lumenal (Potential).				protein glycosylation	endoplasmic reticulum|Golgi membrane|integral to membrane	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity			skin(1)	1		Prostate(19;2.55e-06)				AAGAGAGGATGGTGAAGGGAA	0.602													4	101	---	---	---	---	PASS
HPS4	89781	broad.mit.edu	37	22	26853885	26853885	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr22:26853885G>T	uc003acl.2	-	13	2554	c.1895C>A	c.(1894-1896)GCC>GAC	p.A632D	HPS4_uc003aci.2_Missense_Mutation_p.A627D|HPS4_uc003acj.2_Missense_Mutation_p.A496D|HPS4_uc003ack.2_Missense_Mutation_p.A423D|HPS4_uc003acn.2_Missense_Mutation_p.A478D|HPS4_uc003ach.2_Missense_Mutation_p.A367D	NM_022081	NP_071364	Q9NQG7	HPS4_HUMAN	light ear protein isoform a	632					lysosome organization|positive regulation of eye pigmentation|protein stabilization|protein targeting	lysosome|melanosome|membrane fraction|platelet dense granule	protein homodimerization activity				0						CAGGCTGACGGCCTGGAGGAA	0.592									Hermansky-Pudlak_syndrome				8	70	---	---	---	---	PASS
EFCAB6	64800	broad.mit.edu	37	22	44022442	44022442	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr22:44022442G>A	uc003bdy.1	-	20	2565	c.2350C>T	c.(2350-2352)CGC>TGC	p.R784C	EFCAB6_uc003bdz.1_Missense_Mutation_p.R632C|EFCAB6_uc010gzi.1_Missense_Mutation_p.R632C|EFCAB6_uc010gzj.1_Missense_Mutation_p.R82C|EFCAB6_uc010gzk.1_RNA	NM_022785	NP_073622	Q5THR3	EFCB6_HUMAN	CAP-binding protein complex interacting protein	784					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding	p.R784H(1)		ovary(3)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	7		Ovarian(80;0.0247)|all_neural(38;0.025)				CCAAGGAAGCGCTCAAACTCG	0.438													30	128	---	---	---	---	PASS
SLC25A5	292	broad.mit.edu	37	X	118604367	118604367	+	Silent	SNP	C	T	T	rs80253442	byFrequency	TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chrX:118604367C>T	uc004erh.3	+	3	746	c.630C>T	c.(628-630)ATC>ATT	p.I210I	LOC100303728_uc004ere.1_5'Flank|LOC100303728_uc004erg.1_5'Flank	NM_001152	NP_001143	P05141	ADT2_HUMAN	adenine nucleotide translocator 2	210	Helical; Name=5; (By similarity).				chromosome segregation|energy reserve metabolic process|interspecies interaction between organisms|regulation of insulin secretion|viral reproduction	integral to plasma membrane|mitochondrial inner membrane|mitochondrial nucleoid|MMXD complex	adenine transmembrane transporter activity|protein binding			ovary(1)	1					Clodronate(DB00720)	ACACTCACATCGTCATCAGCT	0.502													4	120	---	---	---	---	PASS
MAGEC3	139081	broad.mit.edu	37	X	140985038	140985038	+	Silent	SNP	C	T	T			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chrX:140985038C>T	uc011mwp.1	+	7	1494	c.1494C>T	c.(1492-1494)TTC>TTT	p.F498F	MAGEC3_uc004fbs.2_Silent_p.F200F|MAGEC3_uc010nsj.2_Silent_p.F200F	NM_138702	NP_619647	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3 isoform 1	498	MAGE 2.									skin(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)					CCATGATCTTCGGGAAAGCCC	0.423													10	180	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	3526	3526	+	RNA	SNP	G	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chrM:3526G>A	uc004cos.3	+	2		c.1819G>A			uc011mfh.1_5'Flank					Homo sapiens mRNA expressed only in placental villi, clone SMAP47.																		TCTACATCACCGCCCCGACCT	0.542													6	19	---	---	---	---	PASS
PKN2	5586	broad.mit.edu	37	1	89206847	89206848	+	Frame_Shift_Ins	INS	-	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr1:89206847_89206848insA	uc001dmn.2	+	2	567_568	c.225_226insA	c.(223-228)GATAAAfs	p.D75fs	PKN2_uc001dmm.1_Frame_Shift_Ins_p.D75fs|PKN2_uc010osp.1_Frame_Shift_Ins_p.D75fs|PKN2_uc010osq.1_Intron|PKN2_uc009wcv.2_Frame_Shift_Ins_p.D75fs	NM_006256	NP_006247	Q16513	PKN2_HUMAN	protein kinase N2	75_76	REM 1.				signal transduction	cytoplasm	ATP binding|histone deacetylase binding|protein kinase C activity			large_intestine(1)|lung(1)|skin(1)	3		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		TCACAACAGATAAAAAAAGTTT	0.307													75	40	---	---	---	---	
INTU	27152	broad.mit.edu	37	4	128577790	128577791	+	Splice_Site	INS	-	GT	GT			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr4:128577790_128577791insGT	uc003ifk.1	+	3	753	c.683_splice	c.e3-1	p.G228_splice	INTU_uc011cgq.1_Splice_Site	NM_015693	NP_056508	Q9ULD6	PDZD6_HUMAN	PDZ domain containing 6											ovary(1)	1						TCTGGTTTCAGGTGATGTCCTT	0.262													114	58	---	---	---	---	
EPB41L4A	64097	broad.mit.edu	37	5	111754715	111754716	+	Frame_Shift_Del	DEL	GA	-	-			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr5:111754715_111754716delGA	uc003kpv.1	-	1	295_296	c.21_22delTC	c.(19-24)GTTCCGfs	p.V7fs	EPB41L4A_uc003kpw.1_Frame_Shift_Del_p.V7fs|FLJ11235_uc003kpx.1_5'Flank	NM_022140	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte protein band 4.1-like 4	7_8						cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		AATTCTTCCGGAACAGCGCAGA	0.594													62	17	---	---	---	---	
MYBL1	4603	broad.mit.edu	37	8	67488452	67488453	+	Frame_Shift_Ins	INS	-	T	T			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr8:67488452_67488453insT	uc003xwj.2	-	10	1666_1667	c.1259_1260insA	c.(1258-1260)AACfs	p.N420fs	MYBL1_uc003xwl.2_Frame_Shift_Ins_p.N420fs|MYBL1_uc003xwk.2_Frame_Shift_Ins_p.N419fs	NM_001080416	NP_001073885	P10243	MYBA_HUMAN	v-myb myeloblastosis viral oncogene homolog	420	Negative regulatory domain (By similarity).				positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)	3			Epithelial(68;0.00211)|all cancers(69;0.00726)|OV - Ovarian serous cystadenocarcinoma(28;0.00989)|BRCA - Breast invasive adenocarcinoma(89;0.0938)			CATTACAAGTGTTTTTTTTCCC	0.406													460	7	---	---	---	---	
RTN3	10313	broad.mit.edu	37	11	63525655	63525656	+	Frame_Shift_Ins	INS	-	A	A			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr11:63525655_63525656insA	uc001nxq.2	+	9	3268_3269	c.3081_3082insA	c.(3079-3084)GCCAAAfs	p.A1027fs	RTN3_uc001nxo.2_Frame_Shift_Ins_p.A231fs|RTN3_uc001nxm.2_Frame_Shift_Ins_p.A250fs|RTN3_uc001nxn.2_Frame_Shift_Ins_p.A1008fs|RTN3_uc001nxp.2_Frame_Shift_Ins_p.Q212fs|RTN3_uc009yov.2_Frame_Shift_Ins_p.A915fs|RTN3_uc010rmt.1_RNA|RTN3_uc010rmu.1_Frame_Shift_Ins_p.P146fs	NM_201428	NP_958831	O95197	RTN3_HUMAN	reticulon 3 isoform b	1027_1028	Interaction with FADD.|Reticulon.				apoptosis|endoplasmic reticulum tubular network organization|interspecies interaction between organisms|response to stress|vesicle-mediated transport	endoplasmic reticulum membrane|extracellular space|Golgi membrane|integral to membrane				ovary(1)	1						CTGGAATCGCCAAAAAAAAGGC	0.337													119	7	---	---	---	---	
HERC2	8924	broad.mit.edu	37	15	28387490	28387490	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr15:28387490delC	uc001zbj.2	-	76	11700	c.11594delG	c.(11593-11595)TGTfs	p.C3865fs		NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	3865					DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CGTCTCGGCACAGCAAGGCAG	0.547													51	8	---	---	---	---	
SRCAP	10847	broad.mit.edu	37	16	30732660	30732666	+	Frame_Shift_Del	DEL	CAGGCTA	-	-			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr16:30732660_30732666delCAGGCTA	uc002dze.1	+	21	3789_3795	c.3404_3410delCAGGCTA	c.(3403-3411)CCAGGCTACfs	p.P1135fs	SRCAP_uc002dzf.2_Intron|SRCAP_uc002dzg.1_Frame_Shift_Del_p.P992fs|SRCAP_uc010bzz.1_Frame_Shift_Del_p.P705fs	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	1135_1137	Pro-rich.				interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)|skin(1)	4			Colorectal(24;0.198)			ACAGTGCCACCAGGCTACACCTTCCCT	0.623													202	10	---	---	---	---	
C19orf53	28974	broad.mit.edu	37	19	13888971	13888971	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CH-5750-01A-11D-1576-08	TCGA-CH-5750-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	e1b169c3-44e0-43e5-9ee3-2df7a678a5ea	69ebe1ab-c416-4473-8d82-91b475b206d4	g.chr19:13888971delA	uc002mxg.2	+	3	294	c.259delA	c.(259-261)AAAfs	p.K87fs		NM_014047	NP_054766	Q9UNZ5	L10K_HUMAN	Leydig cell tumor 10 kDa protein	87										ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(19;7.7e-24)|Epithelial(5;2.53e-19)			AGCCAAGAAGAAAGGGGCAGC	0.597													66	26	---	---	---	---	
