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
CLSTN1	22883	broad.mit.edu	37	1	9795231	9795231	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr1:9795231A>C	uc001aqh.2	-	14	2644	c.1885T>G	c.(1885-1887)TGT>GGT	p.C629G	CLSTN1_uc001aqi.2_Missense_Mutation_p.C619G|CLSTN1_uc010oag.1_Missense_Mutation_p.C610G|CLSTN1_uc001aqf.2_5'Flank	NM_001009566	NP_001009566	O94985	CSTN1_HUMAN	calsyntenin 1 isoform 1	629	Extracellular (Potential).				homophilic cell adhesion	cell junction|cell projection|endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nucleus|postsynaptic membrane	calcium ion binding			skin(1)	1	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		TCGTTAAAACACCTGCCAGCA	0.587													18	89	---	---	---	---	PASS
CROCCL1	84809	broad.mit.edu	37	1	16946368	16946368	+	RNA	SNP	A	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr1:16946368A>G	uc010ocf.1	-	3		c.530T>C			CROCCL1_uc009vov.1_RNA|CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						GGCCAGGAGGAGGCCCTCGTC	0.562													2	16	---	---	---	---	PASS
ZNF683	257101	broad.mit.edu	37	1	26691329	26691329	+	Silent	SNP	C	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr1:26691329C>A	uc001bmg.1	-	4	826	c.708G>T	c.(706-708)CTG>CTT	p.L236L	ZNF683_uc001bmh.1_Silent_p.L236L|ZNF683_uc009vsj.1_Silent_p.L236L	NM_173574	NP_775845	Q8IZ20	ZN683_HUMAN	zinc finger protein 683	236					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(24;2.39e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.76e-26)|Colorectal(126;1.38e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00793)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.159)|LUSC - Lung squamous cell carcinoma(448;0.233)		CCATCATCAGCAGGCTAGGCA	0.632													13	119	---	---	---	---	PASS
CACHD1	57685	broad.mit.edu	37	1	65130209	65130209	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr1:65130209C>A	uc001dbo.1	+	15	2075	c.1970C>A	c.(1969-1971)ACC>AAC	p.T657N	CACHD1_uc001dbp.1_Missense_Mutation_p.T412N|CACHD1_uc001dbq.1_Missense_Mutation_p.T412N|CACHD1_uc010opa.1_5'Flank	NM_020925	NP_065976	Q5VU97	CAHD1_HUMAN	cache domain containing 1	708	Extracellular (Potential).				calcium ion transport	integral to membrane				ovary(2)	2						GTAATGGCTACCAGCCACGTC	0.463													10	91	---	---	---	---	PASS
CYR61	3491	broad.mit.edu	37	1	86048170	86048170	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr1:86048170T>C	uc001dle.2	+	4	930	c.706T>C	c.(706-708)TGG>CGG	p.W236R	CYR61_uc001dlg.2_Missense_Mutation_p.W65R|CYR61_uc009wcp.1_5'Flank	NM_001554	NP_001545	O00622	CYR61_HUMAN	cysteine-rich, angiogenic inducer, 61 precursor	236	TSP type-1.				cell proliferation|chemotaxis|positive regulation of BMP signaling pathway|positive regulation of cell migration|positive regulation of osteoblast differentiation|positive regulation of osteoblast proliferation|positive regulation of protein kinase activity|positive regulation of protein phosphorylation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell growth|regulation of ERK1 and ERK2 cascade|wound healing, spreading of cells	extracellular region	heparin binding|insulin-like growth factor binding			central_nervous_system(1)	1				all cancers(265;0.0216)|Epithelial(280;0.0441)		AACAACTTCATGGTCCCAGTG	0.458											OREG0013583	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	13	110	---	---	---	---	PASS
WDR3	10885	broad.mit.edu	37	1	118502003	118502003	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr1:118502003C>T	uc010oxe.1	+	27	2831	c.2765C>T	c.(2764-2766)ACT>ATT	p.T922I	WDR3_uc001ehi.2_Intron|SPAG17_uc001ehk.2_Intron	NM_006784	NP_006775	Q9UNX4	WDR3_HUMAN	WD repeat-containing protein 3	922						nuclear membrane|nucleolus				upper_aerodigestive_tract(1)	1	Esophageal squamous(2;0.162)	all_cancers(81;2.72e-05)|Acute lymphoblastic leukemia(138;1e-08)|all_epithelial(167;4.4e-07)|all_lung(203;1.7e-06)|Lung NSC(69;1.98e-05)|Prostate(1639;0.00955)|Breast(1374;0.244)		OV - Ovarian serous cystadenocarcinoma(397;1.39e-08)|Epithelial(280;1.82e-07)|all cancers(265;2.04e-05)|Lung(183;0.0525)|BRCA - Breast invasive adenocarcinoma(282;0.0695)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.185)		GCTGATGCTACTAGCCACTTG	0.318													20	55	---	---	---	---	PASS
HIST3H3	8290	broad.mit.edu	37	1	228612642	228612642	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr1:228612642G>A	uc001hsx.1	-	1	385	c.385C>T	c.(385-387)CGC>TGC	p.R129C		NM_003493	NP_003484	Q16695	H31T_HUMAN	histone cluster 3, H3	129					nucleosome assembly|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding				0		Prostate(94;0.0724)				CGGATACGGCGTGCCAGCTGG	0.602													6	85	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152474946	152474946	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr2:152474946A>C	uc010fnx.2	-	70	10381	c.10190T>G	c.(10189-10191)GTT>GGT	p.V3397G		NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	3397	Nebulin 93.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		ATCAATCGGAACCCAGCCAAT	0.393													16	69	---	---	---	---	PASS
PDK1	5163	broad.mit.edu	37	2	173457705	173457705	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr2:173457705C>A	uc002uhr.2	+	10	1199	c.1099C>A	c.(1099-1101)CAA>AAA	p.Q367K	PDK1_uc010zdz.1_Missense_Mutation_p.Q212K|PDK1_uc010zea.1_RNA|PDK1_uc002uhq.1_Missense_Mutation_p.Q387K|PDK1_uc002uhs.2_Missense_Mutation_p.Q367K|PDK1_uc010zeb.1_Missense_Mutation_p.Q387K	NM_002610	NP_002601	Q15118	PDK1_HUMAN	pyruvate dehydrogenase kinase 1 precursor	367	Histidine kinase.				glucose metabolic process|peptidyl-histidine phosphorylation|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate|small GTPase mediated signal transduction	mitochondrial matrix	ATP binding|pyruvate dehydrogenase (acetyl-transferring) kinase activity|two-component sensor activity			lung(3)|central_nervous_system(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.12)			TCTTTACGCACAATACTTCCA	0.378									Autosomal_Dominant_Polycystic_Kidney_Disease				4	160	---	---	---	---	PASS
ALS2	57679	broad.mit.edu	37	2	202591577	202591577	+	Silent	SNP	G	T	T	rs121908137		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr2:202591577G>T	uc002uyo.2	-	18	3348	c.2992C>A	c.(2992-2994)CGA>AGA	p.R998R	ALS2_uc002uyp.3_Silent_p.R998R|ALS2_uc010ftl.2_RNA	NM_020919	NP_065970	Q96Q42	ALS2_HUMAN	alsin isoform 1	998	PH.				cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size	centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle	protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity			skin(5)|lung(1)|breast(1)	7						CTTATAGCTCGTAGCCACTTT	0.433													4	23	---	---	---	---	PASS
CHPF	79586	broad.mit.edu	37	2	220406592	220406592	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr2:220406592G>T	uc002vmc.3	-	2	861	c.634C>A	c.(634-636)CTA>ATA	p.L212I	CHPF_uc010zlh.1_Missense_Mutation_p.L50I|CHPF_uc002vmd.3_Missense_Mutation_p.L212I|TMEM198_uc002vme.2_5'Flank|TMEM198_uc002vmf.2_5'Flank	NM_024536	NP_078812	Q8IZ52	CHSS2_HUMAN	chondroitin polymerizing factor	212	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity|protein binding				0		Renal(207;0.0183)		Epithelial(149;3.02e-08)|all cancers(144;3.41e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		TGGCCAGTTAGGCGTGCCAGG	0.706											OREG0015229	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	30	---	---	---	---	PASS
CSPG5	10675	broad.mit.edu	37	3	47618408	47618408	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr3:47618408A>G	uc003crp.3	-	2	1284	c.1108T>C	c.(1108-1110)TGC>CGC	p.C370R	CSPG5_uc003crn.2_Missense_Mutation_p.C232R|CSPG5_uc003cro.3_Missense_Mutation_p.C370R|CSPG5_uc011bbb.1_Missense_Mutation_p.C232R	NM_006574	NP_006565	O95196	CSPG5_HUMAN	chondroitin sulfate proteoglycan 5 (neuroglycan	370	Extracellular (Potential).				cell differentiation|intracellular transport|nervous system development|regulation of growth	endoplasmic reticulum membrane|Golgi-associated vesicle membrane|integral to plasma membrane|membrane fraction	growth factor activity			ovary(1)|central_nervous_system(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000266)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		ACTGACCGGCAGGAGCCGTTA	0.617													9	76	---	---	---	---	PASS
HLTF	6596	broad.mit.edu	37	3	148786108	148786108	+	Silent	SNP	C	T	T	rs812249	byFrequency	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr3:148786108C>T	uc003ewq.1	-	8	1127	c.909G>A	c.(907-909)ACG>ACA	p.T303T	HLTF_uc003ewr.1_Silent_p.T303T|HLTF_uc003ews.1_Silent_p.T303T|HLTF_uc010hve.1_Silent_p.T303T	NM_139048	NP_620636	Q14527	HLTF_HUMAN	helicase-like transcription factor	303					chromatin modification|transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			CTGCAATGGCCGTAAGAGTTT	0.353													5	346	---	---	---	---	PASS
CRIPAK	285464	broad.mit.edu	37	4	1389063	1389063	+	Missense_Mutation	SNP	G	C	C	rs148588369	byFrequency	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr4:1389063G>C	uc003gdf.2	+	1	3724	c.764G>C	c.(763-765)CGA>CCA	p.R255P		NM_175918	NP_787114	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	255	7.				ER-nucleus signaling pathway|negative regulation of protein kinase activity|regulation of cytoskeleton organization|response to estrogen stimulus	endoplasmic reticulum|nucleus|plasma membrane	protein binding				0			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CTCACGTGCCGATGTGGAGTG	0.682													4	141	---	---	---	---	PASS
FAM13A	10144	broad.mit.edu	37	4	89660254	89660254	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr4:89660254A>C	uc003hse.1	-	20	2697	c.2489T>G	c.(2488-2490)GTG>GGG	p.V830G	FAM13A_uc011cdp.1_5'Flank|FAM13A_uc003hsa.1_Missense_Mutation_p.V301G|FAM13A_uc003hsb.1_Missense_Mutation_p.V504G|FAM13A_uc003hsd.1_Missense_Mutation_p.V504G|FAM13A_uc003hsc.1_Missense_Mutation_p.V490G|FAM13A_uc011cdq.1_Missense_Mutation_p.V476G|FAM13A_uc003hsf.1_Missense_Mutation_p.V416G|FAM13A_uc003hsg.1_Missense_Mutation_p.V301G	NM_014883	NP_055698	O94988	FA13A_HUMAN	family with sequence similarity 13, member A1	830					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)|liver(1)	2						TGGCTTCATCACCTGCCGTTC	0.512													12	20	---	---	---	---	PASS
NDUFS4	4724	broad.mit.edu	37	5	52979037	52979037	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr5:52979037G>T	uc003jpe.2	+	5	542	c.514G>T	c.(514-516)GTA>TTA	p.V172L		NM_002495	NP_002486	O43181	NDUS4_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 4	172					brain development|cAMP-mediated signaling|mitochondrial electron transport, NADH to ubiquinone|mitochondrial respiratory chain complex I assembly|positive regulation of fibroblast proliferation|reactive oxygen species metabolic process|regulation of protein phosphorylation|response to cAMP|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity			central_nervous_system(1)	1		Lung NSC(810;8.27e-05)|Breast(144;0.0848)			NADH(DB00157)	AAGAACAAGAGTATCCACAAA	0.378													8	67	---	---	---	---	PASS
LOC100133050	100133050	broad.mit.edu	37	5	99715528	99715528	+	RNA	SNP	C	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	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													3	19	---	---	---	---	PASS
PHF15	23338	broad.mit.edu	37	5	133914476	133914476	+	Silent	SNP	G	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr5:133914476G>A	uc003kzo.1	+	11	2021	c.1842G>A	c.(1840-1842)GGG>GGA	p.G614G	PHF15_uc011cxt.1_Silent_p.G658G|PHF15_uc003kzk.2_Silent_p.G674G|PHF15_uc003kzm.2_Silent_p.G615G|PHF15_uc003kzn.2_3'UTR	NM_015288	NP_056103	Q9NQC1	JADE2_HUMAN	PHD finger protein 15	614	Pro-rich.				histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CGCAGGACGGGCCTGGTTCAC	0.672													5	48	---	---	---	---	PASS
PCDHB9	56127	broad.mit.edu	37	5	140568817	140568817	+	Silent	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr5:140568817G>T	uc003liw.1	+	3	1926	c.1926G>T	c.(1924-1926)GTG>GTT	p.V642V		NM_019119	NP_061992	Q9Y5E1	PCDB9_HUMAN	protocadherin beta 9 precursor	642	Extracellular (Potential).|Cadherin 6.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGCTGGTGGTGCTTGTCAAGG	0.697													4	63	---	---	---	---	PASS
GCM2	9247	broad.mit.edu	37	6	10881950	10881950	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr6:10881950G>T	uc003mzn.3	-	1	149	c.77C>A	c.(76-78)CCG>CAG	p.P26Q	SYCP2L_uc011dim.1_Intron	NM_004752	NP_004743	O75603	GCM2_HUMAN	glial cells missing homolog 2	26	GCM.				cellular calcium ion homeostasis|cellular phosphate ion homeostasis|parathyroid gland development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|sequence-specific DNA binding			ovary(2)|central_nervous_system(1)	3	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)				AGGCATCTGCGGATCGTTGAT	0.642													3	68	---	---	---	---	PASS
SLC26A8	116369	broad.mit.edu	37	6	35930384	35930384	+	Silent	SNP	A	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr6:35930384A>C	uc003olm.2	-	12	1491	c.1380T>G	c.(1378-1380)GGT>GGG	p.G460G	SLC26A8_uc010jwa.2_RNA|SLC26A8_uc003olk.2_Silent_p.G42G|SLC26A8_uc003oln.2_Silent_p.G460G|SLC26A8_uc003oll.2_Silent_p.G355G	NM_052961	NP_443193	Q96RN1	S26A8_HUMAN	solute carrier family 26, member 8 isoform a	460	Helical; (Potential).				cell differentiation|meiosis|multicellular organismal development|spermatogenesis	integral to membrane|plasma membrane	anion:anion antiporter activity|chloride channel activity|oxalate transmembrane transporter activity|protein binding|sulfate transmembrane transporter activity			ovary(2)	2						TCAGAATAATACCAGCCAGCA	0.463													12	25	---	---	---	---	PASS
CUL9	23113	broad.mit.edu	37	6	43183065	43183065	+	Splice_Site	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr6:43183065G>T	uc003ouk.2	+	30	6011	c.5936_splice	c.e30+1	p.S1979_splice	CUL9_uc003oul.2_Splice_Site_p.S1951_splice|CUL9_uc010jyk.2_Splice_Site_p.S1131_splice|CUL9_uc003oun.2_Splice_Site	NM_015089	NP_055904	Q8IWT3	CUL9_HUMAN	p53-associated parkin-like cytoplasmic protein						ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex|cytoplasm	ATP binding|ubiquitin protein ligase binding|zinc ion binding			ovary(5)|lung(3)|skin(2)|breast(1)|central_nervous_system(1)	12						CCAAGCCCAGGTAGCCACTGC	0.587													7	26	---	---	---	---	PASS
TBX18	9096	broad.mit.edu	37	6	85448257	85448257	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr6:85448257G>A	uc003pkl.1	-	7	1057	c.1057C>T	c.(1057-1059)CGG>TGG	p.R353W	TBX18_uc010kbq.1_Missense_Mutation_p.R195W	NM_001080508	NP_001073977	O95935	TBX18_HUMAN	T-box 18	353					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)		GTCAGAGTCCGTAGTGATGGT	0.468													93	398	---	---	---	---	PASS
SHPRH	257218	broad.mit.edu	37	6	146240560	146240560	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr6:146240560G>T	uc003qlf.2	-	22	4475	c.4076C>A	c.(4075-4077)ACA>AAA	p.T1359K	SHPRH_uc003qld.2_Missense_Mutation_p.T1363K|SHPRH_uc003qle.2_Missense_Mutation_p.T1363K|SHPRH_uc003qlg.1_Missense_Mutation_p.T915K|SHPRH_uc003qlh.2_Missense_Mutation_p.T284K|SHPRH_uc003qli.1_Missense_Mutation_p.T284K	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a	1359					DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)|central_nervous_system(1)	3		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		TAGTCGTTCTGTAGCCATTGC	0.428													10	185	---	---	---	---	PASS
GPR141	353345	broad.mit.edu	37	7	37780909	37780909	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr7:37780909G>T	uc003tfm.1	+	1	914	c.914G>T	c.(913-915)CGT>CTT	p.R305L	uc003tfl.2_Intron	NM_181791	NP_861456	Q7Z602	GP141_HUMAN	G protein-coupled receptor 141	305	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity	p.R305H(1)		ovary(3)	3						GTTTTGTGCCGTTAGCCACAA	0.363													6	78	---	---	---	---	PASS
POM121	9883	broad.mit.edu	37	7	72413243	72413243	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr7:72413243A>C	uc003twk.2	+	11	2711	c.2711A>C	c.(2710-2712)CAC>CCC	p.H904P	POM121_uc003twj.2_Missense_Mutation_p.H639P|POM121_uc010lam.1_Missense_Mutation_p.H639P	NM_172020	NP_742017	Q96HA1	P121A_HUMAN	nuclear pore membrane protein 121	904	Thr-rich.|Pore side (Potential).			H -> P (in Ref. 3; BAB14097).	carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore					0		Lung NSC(55;0.163)				CAGTCCCTGCACACTGCCGTG	0.647													7	167	---	---	---	---	PASS
DEFA1B	728358	broad.mit.edu	37	8	6873603	6873603	+	Missense_Mutation	SNP	T	G	G	rs145076681	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr8:6873603T>G	uc003wqz.1	-	3	279	c.194A>C	c.(193-195)GAC>GCC	p.D65A		NM_005217	NP_005208	P59665	DEF1_HUMAN	defensin, alpha 3 preproprotein	65					chemotaxis|defense response to bacterium|defense response to fungus|immune response|killing of cells of other organism|response to virus	extracellular space					0						GCAATAGCAGTCCATGTTTTT	0.498													3	110	---	---	---	---	PASS
TNFRSF10C	8794	broad.mit.edu	37	8	22974405	22974405	+	Missense_Mutation	SNP	C	A	A	rs61736406	byFrequency	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr8:22974405C>A	uc003xcy.2	+	5	842	c.641C>A	c.(640-642)ACC>AAC	p.T214N	TNFRSF10C_uc011kzr.1_RNA	NM_003841	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily,	214	TAPE 4.				apoptosis	anchored to membrane|integral to plasma membrane	TRAIL binding|transmembrane receptor activity				0		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		GAGACAATGACCACCAGCCCG	0.612													9	166	---	---	---	---	PASS
TNFRSF10C	8794	broad.mit.edu	37	8	22974415	22974415	+	Silent	SNP	G	A	A	rs11780526	byFrequency	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr8:22974415G>A	uc003xcy.2	+	5	852	c.651G>A	c.(649-651)CCG>CCA	p.P217P	TNFRSF10C_uc011kzr.1_RNA	NM_003841	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily,	217	TAPE 4.				apoptosis	anchored to membrane|integral to plasma membrane	TRAIL binding|transmembrane receptor activity				0		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		CCACCAGCCCGGGGACTCCTG	0.607													9	142	---	---	---	---	PASS
DPYSL2	1808	broad.mit.edu	37	8	26484737	26484737	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr8:26484737G>A	uc003xfb.1	+	6	897	c.547G>A	c.(547-549)GAA>AAA	p.E183K	DPYSL2_uc003xfa.2_Missense_Mutation_p.E288K|DPYSL2_uc011lag.1_Missense_Mutation_p.E183K|DPYSL2_uc010luk.1_RNA|DPYSL2_uc011lah.1_Missense_Mutation_p.E147K	NM_001386	NP_001377	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2	183					axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	dihydropyrimidinase activity|protein binding			large_intestine(1)	1		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)		TCAGATTTATGAAGTACTGAG	0.483													14	55	---	---	---	---	PASS
CPNE3	8895	broad.mit.edu	37	8	87563330	87563330	+	Splice_Site	SNP	T	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr8:87563330T>G	uc003ydv.2	+	13	1230	c.1068_splice	c.e13+2	p.Q356_splice	CPNE3_uc003ydw.1_Splice_Site_p.Q72_splice	NM_003909	NP_003900	O75131	CPNE3_HUMAN	copine III						lipid metabolic process|vesicle-mediated transport	cytosol	calcium-dependent phospholipid binding|protein serine/threonine kinase activity|transporter activity			ovary(1)|skin(1)	2						CAGTGGCAGGTAAGAGGAAAT	0.368													13	18	---	---	---	---	PASS
EPPK1	83481	broad.mit.edu	37	8	144945349	144945349	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr8:144945349G>T	uc003zaa.1	-	1	2086	c.2073C>A	c.(2071-2073)TAC>TAA	p.Y691*		NM_031308	NP_112598	P58107	EPIPL_HUMAN	epiplakin 1	691	Plectin 13.					cytoplasm|cytoskeleton	protein binding|structural molecule activity			pancreas(1)|skin(1)	2	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			AGGGGTCAGTGTAGCCAGTGA	0.637													4	44	---	---	---	---	PASS
CTNNAL1	8727	broad.mit.edu	37	9	111718091	111718091	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr9:111718091G>T	uc004bdo.1	-	12	1650	c.1608C>A	c.(1606-1608)TAC>TAA	p.Y536*	CTNNAL1_uc010mts.1_Nonsense_Mutation_p.Y188*|CTNNAL1_uc010mtt.1_Nonsense_Mutation_p.Y536*|CTNNAL1_uc004bdp.1_Nonsense_Mutation_p.Y536*|CTNNAL1_uc004bdq.1_Nonsense_Mutation_p.Y22*	NM_003798	NP_003789	Q9UBT7	CTNL1_HUMAN	catenin, alpha-like 1	536					cell adhesion|Rho protein signal transduction	actin cytoskeleton|cytosol|plasma membrane	cadherin binding|structural molecule activity			ovary(1)	1				STAD - Stomach adenocarcinoma(157;0.0768)		GAAGTGAAAGGTAGCCATACT	0.244													8	47	---	---	---	---	PASS
SPTAN1	6709	broad.mit.edu	37	9	131339198	131339198	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr9:131339198A>G	uc004bvl.3	+	6	861	c.748A>G	c.(748-750)AAG>GAG	p.K250E	SPTAN1_uc011mbg.1_Missense_Mutation_p.K250E|SPTAN1_uc011mbh.1_Missense_Mutation_p.K262E|SPTAN1_uc004bvm.3_Missense_Mutation_p.K250E|SPTAN1_uc004bvn.3_Missense_Mutation_p.K250E	NM_003127	NP_003118	Q13813	SPTA2_HUMAN	spectrin, alpha, non-erythrocytic 1	250	Spectrin 3.				actin filament capping|axon guidance|cellular component disassembly involved in apoptosis	cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin	actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton			breast(5)|ovary(4)|pancreas(1)	10						GAGGCAGGGGAAGCTCTTTGG	0.567													4	33	---	---	---	---	PASS
BRD3	8019	broad.mit.edu	37	9	136899859	136899859	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr9:136899859C>T	uc004cew.2	-	11	2217	c.2029G>A	c.(2029-2031)GGG>AGG	p.G677R		NM_007371	NP_031397	Q15059	BRD3_HUMAN	bromodomain containing protein 3	677	Potential.|Ser-rich.					nucleus	protein binding		BRD3/C15orf55(3)	stomach(4)|midline_organs(3)|kidney(1)	8				OV - Ovarian serous cystadenocarcinoma(145;1.43e-08)|Epithelial(140;8.41e-08)|all cancers(34;5.21e-07)		CTCAGCTGCCCGCTGACATCC	0.617			T	NUT|C15orf55	lethal midline carcinoma of young people								4	181	---	---	---	---	PASS
PHYH	5264	broad.mit.edu	37	10	13330436	13330436	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr10:13330436C>T	uc001imf.2	-	6	690	c.602G>A	c.(601-603)CGG>CAG	p.R201Q	PHYH_uc001ime.2_Missense_Mutation_p.R101Q|PHYH_uc001img.2_Missense_Mutation_p.R184Q	NM_006214	NP_006205	O14832	PAHX_HUMAN	phytanoyl-CoA 2-hydroxylase isoform a precursor	201					fatty acid alpha-oxidation|nervous system development	peroxisomal matrix	electron carrier activity|L-ascorbic acid binding|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|phytanoyl-CoA dioxygenase activity|protein binding				0		Ovarian(717;0.0448)			Antihemophilic Factor(DB00025)|Vitamin C(DB00126)	GCCGTTGTTCCGGCTGATGTG	0.627													3	88	---	---	---	---	PASS
HSD17B7P2	158160	broad.mit.edu	37	10	38654432	38654432	+	Missense_Mutation	SNP	A	G	G	rs2257765		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr10:38654432A>G	uc010qex.1	+	5	599	c.524A>G	c.(523-525)AAT>AGT	p.N175S	HSD17B7P2_uc001izq.2_RNA|HSD17B7P2_uc001izo.1_RNA|HSD17B7P2_uc001izp.1_Missense_Mutation_p.N173S					SubName: Full=cDNA FLJ60462, highly similar to 3-keto-steroid reductase (EC 1.1.1.270);												0						TCATCTCGCAATGCAAGGAAA	0.453													3	118	---	---	---	---	PASS
LOC441666	441666	broad.mit.edu	37	10	42832122	42832122	+	RNA	SNP	C	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr10:42832122C>T	uc010qey.1	-	3		c.1853G>A				NR_024380				Homo sapiens noncoding mRNA sequence.												0						CAGTAAAAGGCTTTGCCACAT	0.348													3	20	---	---	---	---	PASS
LOC441666	441666	broad.mit.edu	37	10	42832147	42832147	+	RNA	SNP	G	T	T	rs144592176	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr10:42832147G>T	uc010qey.1	-	3		c.1828C>A				NR_024380				Homo sapiens noncoding mRNA sequence.												0						CACAATTGTAGGGTTTCTCTC	0.353													3	18	---	---	---	---	PASS
INA	9118	broad.mit.edu	37	10	105048298	105048298	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr10:105048298G>T	uc001kws.2	+	3	1421	c.1372G>T	c.(1372-1374)GTA>TTA	p.V458L		NM_032727	NP_116116	Q16352	AINX_HUMAN	internexin neuronal intermediate filament	458	Tail.				cell differentiation|nervous system development	neurofilament	structural constituent of cytoskeleton			ovary(1)|breast(1)	2				Epithelial(162;3.45e-09)|all cancers(201;9.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)		GGCATCTAAGGTAGCCTCTAA	0.423													10	136	---	---	---	---	PASS
NRAP	4892	broad.mit.edu	37	10	115422474	115422474	+	Silent	SNP	A	G	G	rs3127122	byFrequency	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr10:115422474A>G	uc001laj.2	-	3	383	c.219T>C	c.(217-219)AAT>AAC	p.N73N	NRAP_uc001lak.2_Silent_p.N73N|NRAP_uc001lal.3_Silent_p.N73N	NM_198060	NP_932326	Q86VF7	NRAP_HUMAN	nebulin-related anchoring protein isoform S	73	Nebulin 1.					fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)|upper_aerodigestive_tract(1)	10		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		TCACATTTAGATTTAATGGAG	0.259													5	175	---	---	---	---	PASS
CNGA4	1262	broad.mit.edu	37	11	6261464	6261464	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr11:6261464C>T	uc001mco.2	+	4	547	c.440C>T	c.(439-441)GCG>GTG	p.A147V	CNGA4_uc010raa.1_Intron|CNGA4_uc001mcn.2_Missense_Mutation_p.A107V	NM_001037329	NP_001032406	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	147	Extracellular (Potential).				response to stimulus|sensory perception of smell		cAMP binding			skin(1)	1		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTTCTCCGCGCGCCCCGCCTC	0.587													5	205	---	---	---	---	PASS
MRVI1	10335	broad.mit.edu	37	11	10622488	10622488	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr11:10622488G>T	uc010rcc.1	-	15	2380	c.1994C>A	c.(1993-1995)TCA>TAA	p.S665*	MRVI1_uc001miw.2_Nonsense_Mutation_p.S656*|MRVI1_uc010rcb.1_Nonsense_Mutation_p.S657*|MRVI1_uc009ygb.1_Nonsense_Mutation_p.S350*|MRVI1_uc001mix.2_Nonsense_Mutation_p.S350*|MRVI1_uc001miz.2_Nonsense_Mutation_p.S574*|MRVI1_uc009ygc.1_Nonsense_Mutation_p.S574*|MRVI1_uc010rcd.1_Nonsense_Mutation_p.S459*|MRVI1_uc009ygd.1_Nonsense_Mutation_p.S350*|MRVI1_uc010rce.1_RNA	NM_001100167	NP_001093637	Q9Y6F6	MRVI1_HUMAN	JAW1-related protein isoform c	638					platelet activation	endoplasmic reticulum membrane|integral to membrane|perinuclear region of cytoplasm|platelet dense tubular network membrane|sarcoplasmic reticulum				ovary(2)|central_nervous_system(1)	3				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)		GCTGCGGCTTGAATTCTGATT	0.507													6	93	---	---	---	---	PASS
SLC2A14	144195	broad.mit.edu	37	12	7982567	7982567	+	Missense_Mutation	SNP	G	A	A	rs145793375	byFrequency	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr12:7982567G>A	uc001qtk.2	-	10	1170	c.377C>T	c.(376-378)GCC>GTC	p.A126V	SLC2A14_uc001qtl.2_Missense_Mutation_p.A103V|SLC2A14_uc001qtm.2_Missense_Mutation_p.A103V|SLC2A14_uc010sgg.1_Missense_Mutation_p.A17V|SLC2A14_uc001qtn.2_Missense_Mutation_p.A126V|SLC2A14_uc001qto.2_Intron|SLC2A14_uc010sgh.1_Missense_Mutation_p.A141V	NM_153449	NP_703150	Q8TDB8	GTR14_HUMAN	glucose transporter 14	126	Helical; Name=3; (Potential).				cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane	glucose transmembrane transporter activity			ovary(1)	1				Kidney(36;0.0883)		GCCACCAGTGGCAGCCAACAG	0.478													3	69	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	12	9723393	9723393	+	RNA	SNP	G	A	A	rs141653604	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr12:9723393G>A	uc001qwb.1	+	8		c.6073G>A								Homo sapiens mRNA; cDNA DKFZp686A1124 (from clone DKFZp686A1124).																		CCAGGTTAACGGTCATAACCG	0.473													13	52	---	---	---	---	PASS
SLCO1B1	10599	broad.mit.edu	37	12	21350054	21350054	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr12:21350054C>A	uc001req.3	+	8	1006	c.902C>A	c.(901-903)ACA>AAA	p.T301K		NM_006446	NP_006437	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family,	301	Cytoplasmic (Potential).				bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|integral to plasma membrane|membrane fraction	bile acid transmembrane transporter activity|sodium-independent organic anion transmembrane transporter activity|thyroid hormone transmembrane transporter activity			ovary(3)|skin(3)|pancreas(1)|central_nervous_system(1)	8					Digoxin(DB00390)|Gemfibrozil(DB01241)|Pravastatin(DB00175)	GTGCTGGAAACAAATGATGAA	0.328													30	122	---	---	---	---	PASS
GALNT4	8693	broad.mit.edu	37	12	89917323	89917323	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr12:89917323C>G	uc001tbd.2	-	1	1213	c.1004G>C	c.(1003-1005)GGA>GCA	p.G335A	POC1B_uc001tba.2_Intron|POC1B_uc001tbb.2_Intron|POC1B_uc001tbc.2_Intron|POC1B_uc010sun.1_Intron|GALNT4_uc001tbe.2_Missense_Mutation_p.G332A|GALNT4_uc010suo.1_Missense_Mutation_p.G27A	NM_003774	NP_003765	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	335	Catalytic subdomain B.|Lumenal (Potential).				carbohydrate metabolic process	Golgi membrane|integral to membrane|perinuclear region of cytoplasm	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0						GTTTTCACCTCCCCACACTTC	0.522													42	257	---	---	---	---	PASS
SFRS9	8683	broad.mit.edu	37	12	120899912	120899912	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr12:120899912G>T	uc001tyi.2	-	4	722	c.576C>A	c.(574-576)TAC>TAA	p.Y192*		NM_003769	NP_003760	Q13242	SRSF9_HUMAN	splicing factor, arginine/serine-rich 9	192	Interacts with SAFB1.|Arg/Ser-rich (RS domain).				mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|RNA binding				0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GAGACCGTGAGTAGCCATAGC	0.483													6	26	---	---	---	---	PASS
CLMN	79789	broad.mit.edu	37	14	95670748	95670748	+	Missense_Mutation	SNP	C	T	T	rs145924471		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr14:95670748C>T	uc001yef.2	-	9	1054	c.938G>A	c.(937-939)CGC>CAC	p.R313H		NM_024734	NP_079010	Q96JQ2	CLMN_HUMAN	calmin	313						integral to membrane	actin binding				0				Epithelial(152;0.193)		TTCTTTGATGCGAACAAAAGT	0.338													4	174	---	---	---	---	PASS
MIR409	574413	broad.mit.edu	37	14	101531657	101531657	+	RNA	SNP	C	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr14:101531657C>A	hsa-mir-409|MI0001735	+			c.21C>A			MIR412_hsa-mir-412|MI0002464_5'Flank|uc010txp.1_5'Flank|MIR369_hsa-mir-369|MI0000777_5'Flank|MIR410_hsa-mir-410|MI0002465_5'Flank|MIR656_hsa-mir-656|MI0003678_5'Flank																	0						GGAGAGGTTACCCGAGCAACT	0.587													6	44	---	---	---	---	PASS
SECISBP2L	9728	broad.mit.edu	37	15	49305008	49305008	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr15:49305008G>T	uc001zxe.1	-	12	1702	c.1568C>A	c.(1567-1569)ACT>AAT	p.T523N	SECISBP2L_uc001zxd.1_Missense_Mutation_p.T478N|SECISBP2L_uc010bep.1_Missense_Mutation_p.T285N	NM_014701	NP_055516	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	523										breast(1)|skin(1)	2						AGAAGCTGCAGTAACCACTAA	0.363													5	57	---	---	---	---	PASS
NOX5	79400	broad.mit.edu	37	15	69348910	69348910	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr15:69348910C>A	uc002ars.1	+	16	2192	c.2172C>A	c.(2170-2172)TTC>TTA	p.F724L	NOX5_uc002arp.1_Missense_Mutation_p.F706L|NOX5_uc002arq.1_Missense_Mutation_p.F678L|NOX5_uc010bid.1_Missense_Mutation_p.F689L|NOX5_uc002arr.1_Missense_Mutation_p.F696L|NOX5_uc010bie.1_Missense_Mutation_p.F524L|NOX5_uc010bif.1_RNA	NM_024505	NP_078781	Q96PH1	NOX5_HUMAN	NADPH oxidase, EF-hand calcium binding domain 5	724	Extracellular (Potential).				angiogenesis|angiogenesis|cytokine secretion|cytokinesis|electron transport chain|endothelial cell proliferation|induction of apoptosis|positive regulation of reactive oxygen species metabolic process|regulation of fusion of sperm to egg plasma membrane|regulation of proton transport|superoxide anion generation	endoplasmic reticulum|endoplasmic reticulum|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|hydrogen ion channel activity|NADP binding|superoxide-generating NADPH oxidase activity			breast(1)|pancreas(1)	2						TCCAGGTGTTCCAGAAAGTGG	0.557													26	145	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	102292811	102292811	+	Silent	SNP	C	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr15:102292811C>A	uc010usj.1	+	4	458	c.399C>A	c.(397-399)CGC>CGA	p.R133R	uc002bxo.2_RNA|uc002bxp.3_5'Flank|uc002bxt.2_5'Flank|uc002bxz.3_5'Flank|uc002byd.2_5'Flank|uc002bye.2_5'Flank|uc002byf.1_5'Flank|uc002byg.2_5'Flank|uc002byi.2_5'Flank|uc002byk.2_5'Flank|uc002bym.2_5'Flank|uc002byn.2_5'Flank|uc010usm.1_5'Flank|uc002byr.2_5'Flank					RecName: Full=Uncharacterized protein C15orf51.; Flags: Fragment;																		CCTGCACTCGCGTGGGAACGA	0.607													4	19	---	---	---	---	PASS
C16orf62	57020	broad.mit.edu	37	16	19661780	19661780	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr16:19661780G>A	uc002dgn.1	+	25	2117	c.2105G>A	c.(2104-2106)CGG>CAG	p.R702Q	C16orf62_uc002dgo.1_Intron|C16orf62_uc002dgp.1_Missense_Mutation_p.R451Q	NM_020314	NP_064710	Q7Z3J2	CP062_HUMAN	hypothetical protein LOC57020	702						integral to membrane				ovary(1)	1						GCATTTGTCCGGGTATGTTCT	0.378													4	186	---	---	---	---	PASS
SRCAP	10847	broad.mit.edu	37	16	30731617	30731617	+	Silent	SNP	A	C	C	rs145842115	byFrequency	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr16:30731617A>C	uc002dze.1	+	19	3337	c.2952A>C	c.(2950-2952)CCA>CCC	p.P984P	SRCAP_uc002dzf.2_RNA|SRCAP_uc002dzg.1_Silent_p.P841P|SRCAP_uc010bzz.1_Silent_p.P554P	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	984	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)			CTGACCCCCCACCCCGGCCCA	0.572													36	77	---	---	---	---	PASS
LRRC36	55282	broad.mit.edu	37	16	67375899	67375899	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr16:67375899G>A	uc002esv.2	+	2	129	c.110G>A	c.(109-111)GGC>GAC	p.G37D	LRRC36_uc002esw.2_RNA	NM_018296	NP_060766	Q1X8D7	LRC36_HUMAN	leucine rich repeat containing 36 isoform 1	37											0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0669)|Epithelial(162;0.161)		TCTTATGCTGGCAAAATCCAT	0.378													4	159	---	---	---	---	PASS
KRT27	342574	broad.mit.edu	37	17	38938611	38938611	+	Silent	SNP	G	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr17:38938611G>A	uc002hvg.2	-	1	176	c.135C>T	c.(133-135)TTC>TTT	p.F45F		NM_181537	NP_853515	Q7Z3Y8	K1C27_HUMAN	keratin 27	45	Head.|Gly-rich.					cytoplasm|intermediate filament	structural molecule activity				0		Breast(137;0.000812)				AAGCACAAGAGAAGCCACTTC	0.617													3	11	---	---	---	---	PASS
CDC27	996	broad.mit.edu	37	17	45219282	45219282	+	Silent	SNP	G	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr17:45219282G>A	uc002ild.3	-	12	1615	c.1488C>T	c.(1486-1488)TAC>TAT	p.Y496Y	CDC27_uc002ile.3_Silent_p.Y502Y|CDC27_uc002ilf.3_Silent_p.Y495Y|CDC27_uc010wkp.1_Silent_p.Y435Y|CDC27_uc010wkq.1_Intron	NM_001256	NP_001247	P30260	CDC27_HUMAN	cell division cycle protein 27 isoform 2	496					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding			lung(2)|breast(2)|ovary(1)	5						AACCAGTATTGTAGTGGTGAG	0.378													18	477	---	---	---	---	PASS
MYOM1	8736	broad.mit.edu	37	18	3075746	3075746	+	Silent	SNP	G	A	A	rs16944353	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr18:3075746G>A	uc002klp.2	-	35	4996	c.4662C>T	c.(4660-4662)GCC>GCT	p.A1554A	MYOM1_uc002klq.2_Silent_p.A1458A	NM_003803	NP_003794	P52179	MYOM1_HUMAN	myomesin 1 isoform a	1554						striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5						ATTCAGCATAGGCCTCATCGT	0.443													10	16	---	---	---	---	PASS
PRKCSH	5589	broad.mit.edu	37	19	11558391	11558391	+	Silent	SNP	G	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr19:11558391G>A	uc002mrt.2	+	11	1323	c.987G>A	c.(985-987)GAG>GAA	p.E329E	PRKCSH_uc002mru.2_Silent_p.E329E|PRKCSH_uc010xlz.1_Silent_p.E329E|PRKCSH_uc010dya.2_Silent_p.E111E|PRKCSH_uc002mrv.1_Silent_p.E329E|PRKCSH_uc010dyb.2_Silent_p.E329E	NM_002743	NP_002734	P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H isoform 1	329	Glu-rich (acidic).				innate immune response|intracellular protein kinase cascade|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen	calcium ion binding|protein kinase C binding				0						ctgaagaagaggaggaggagg	0.438													3	11	---	---	---	---	PASS
ZNF676	163223	broad.mit.edu	37	19	22363643	22363643	+	Silent	SNP	C	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr19:22363643C>T	uc002nqs.1	-	3	1194	c.876G>A	c.(874-876)TCG>TCA	p.S292S		NM_001001411	NP_001001411	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	292	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				GCTTTGAGGACGAGTTGGAAG	0.438													6	277	---	---	---	---	PASS
ZNF492	57615	broad.mit.edu	37	19	22836805	22836805	+	Missense_Mutation	SNP	G	A	A	rs139107317	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr19:22836805G>A	uc002nqw.3	+	3	362	c.118G>A	c.(118-120)GCT>ACT	p.A40T		NM_020855	NP_065906	Q9P255	ZN492_HUMAN	zinc finger protein 492	40	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				TGAGATGGTAGCTGAACCCCC	0.408													4	189	---	---	---	---	PASS
ZNF99	7652	broad.mit.edu	37	19	22940373	22940373	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr19:22940373T>C	uc010xrh.1	-	5	2065	c.2065A>G	c.(2065-2067)AAG>GAG	p.K689E		NM_001080409	NP_001073878			zinc finger protein 99											ovary(1)|skin(1)	2		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TGAATTATCTTATGTTTTCTA	0.343													4	172	---	---	---	---	PASS
HRC	3270	broad.mit.edu	37	19	49656664	49656664	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr19:49656664C>A	uc002pmv.2	-	1	2018	c.1831G>T	c.(1831-1833)GGT>TGT	p.G611C		NM_002152	NP_002143	P23327	SRCH_HUMAN	histidine rich calcium binding protein	611					muscle contraction	sarcoplasmic reticulum lumen	calcium ion binding			ovary(1)	1		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		GGCCACTTACCTGTGTCCTCA	0.597													3	72	---	---	---	---	PASS
NCAM2	4685	broad.mit.edu	37	21	22849736	22849736	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr21:22849736A>G	uc002yld.1	+	15	2270	c.2021A>G	c.(2020-2022)TAT>TGT	p.Y674C	NCAM2_uc011acb.1_Missense_Mutation_p.Y532C	NM_004540	NP_004531	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2 precursor	674	Fibronectin type-III 2.|Extracellular (Potential).				neuron cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)	4		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		AGATTGGGATATTCTGAACCG	0.368													21	129	---	---	---	---	PASS
FTCD	10841	broad.mit.edu	37	21	47558836	47558836	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr21:47558836T>C	uc002zif.2	-	11	1306	c.1262A>G	c.(1261-1263)GAA>GGA	p.E421G	FTCD_uc002zie.2_Intron|FTCD_uc002zig.2_Missense_Mutation_p.E421G|FTCD_uc002zih.2_Missense_Mutation_p.E421G|FTCD_uc010gqf.2_Intron|FTCD_uc010gqg.1_Missense_Mutation_p.E290G	NM_006657	NP_006648	O95954	FTCD_HUMAN	formiminotransferase cyclodeaminase	421	Cyclodeaminase/cyclohydrolase (By similarity).				folic acid-containing compound metabolic process|histidine catabolic process	centriole|cytosol|Golgi apparatus	folic acid binding|formimidoyltetrahydrofolate cyclodeaminase activity|glutamate formimidoyltransferase activity			pancreas(1)|skin(1)	2	Breast(49;0.214)			Colorectal(79;0.235)	L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Tetrahydrofolic acid(DB00116)	CCTCATTGCTTCCTGCCATAA	0.627													4	26	---	---	---	---	PASS
GGT5	2687	broad.mit.edu	37	22	24622217	24622217	+	Silent	SNP	C	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr22:24622217C>A	uc002zzo.3	-	8	1473	c.1056G>T	c.(1054-1056)CTG>CTT	p.L352L	GGT5_uc002zzp.3_Silent_p.L352L|GGT5_uc002zzr.3_Silent_p.L320L|GGT5_uc002zzq.3_Silent_p.L320L|GGT5_uc011ajm.1_Silent_p.L275L|GGT5_uc011ajn.1_RNA	NM_004121	NP_004112	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5 isoform b	352	Extracellular (Potential).				glutathione biosynthetic process|hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process	integral to membrane|plasma membrane	acyltransferase activity|gamma-glutamyltransferase activity			ovary(2)|skin(1)	3						TCTCCCCCAGCAGGTCCCGGG	0.682													3	52	---	---	---	---	PASS
COL9A2	1298	broad.mit.edu	37	1	40769637	40769637	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr1:40769637delG	uc001cfh.1	-	26	1401	c.1331delC	c.(1330-1332)CCAfs	p.P444fs	COL9A2_uc001cfi.1_Frame_Shift_Del_p.P263fs	NM_001852	NP_001843	Q14055	CO9A2_HUMAN	alpha 2 type IX collagen precursor	444	Triple-helical region 3 (COL3).				axon guidance|skeletal system development	collagen type IX				ovary(2)	2	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.08e-17)			GGCCACCCCTGGGTCACCCTG	0.736													4	2	---	---	---	---	
SFRS11	9295	broad.mit.edu	37	1	70687370	70687371	+	Frame_Shift_Ins	INS	-	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr1:70687370_70687371insG	uc001des.2	+	2	175_176	c.51_52insG	c.(49-54)GGCGGGfs	p.G17fs	SFRS11_uc009wbi.2_Frame_Shift_Ins_p.G17fs|SFRS11_uc009wbj.1_Frame_Shift_Ins_p.G17fs|SFRS11_uc010oqo.1_Frame_Shift_Ins_p.G17fs|SFRS11_uc001det.2_Frame_Shift_Ins_p.G17fs|SFRS11_uc001deu.2_Frame_Shift_Ins_p.G17fs	NM_004768	NP_004759	Q05519	SRS11_HUMAN	splicing factor, arginine/serine-rich 11	17_18	Poly-Gly.				mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|protein binding|RNA binding				0						GCCCCAGCGGCGGGCCcggtgg	0.495													253	7	---	---	---	---	
NID1	4811	broad.mit.edu	37	1	236228307	236228308	+	Frame_Shift_Ins	INS	-	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr1:236228307_236228308insC	uc001hxo.2	-	1	174_175	c.72_73insG	c.(70-75)GGGCCTfs	p.G24fs	NID1_uc009xgd.2_Frame_Shift_Ins_p.G24fs|uc001hxp.1_Frame_Shift_Ins_p.A150fs	NM_002508	NP_002499	P14543	NID1_HUMAN	nidogen 1 precursor	24_25					cell-matrix adhesion	basement membrane	calcium ion binding			large_intestine(1)|pancreas(1)	2	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Becaplermin(DB00102)|Urokinase(DB00013)	CAGCCCACAGGCCCCGCCAGCA	0.708													4	2	---	---	---	---	
REEP4	80346	broad.mit.edu	37	8	21996234	21996235	+	Frame_Shift_Ins	INS	-	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr8:21996234_21996235insG	uc003xau.1	-	7	1078_1079	c.625_626insC	c.(625-627)CGGfs	p.R209fs	REEP4_uc010ltt.1_Frame_Shift_Ins_p.P163fs	NM_025232	NP_079508	Q9H6H4	REEP4_HUMAN	receptor accessory protein 4	209						integral to membrane				skin(1)	1				Colorectal(74;0.00187)|COAD - Colon adenocarcinoma(73;0.061)|READ - Rectum adenocarcinoma(644;0.0993)		GGCTGGCGCCCGGGGGACTGCC	0.663													253	11	---	---	---	---	
PALM2-AKAP2	445815	broad.mit.edu	37	9	112900482	112900483	+	Frame_Shift_Ins	INS	-	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr9:112900482_112900483insC	uc004bei.2	+	9	3546_3547	c.3354_3355insC	c.(3352-3357)GGGCCCfs	p.G1118fs	PALM2-AKAP2_uc004bek.3_Frame_Shift_Ins_p.G886fs|PALM2-AKAP2_uc004bej.3_Frame_Shift_Ins_p.G886fs|PALM2-AKAP2_uc004bel.1_Frame_Shift_Ins_p.G696fs|AKAP2_uc011lwi.1_Frame_Shift_Ins_p.G744fs|AKAP2_uc004bem.2_Frame_Shift_Ins_p.G744fs|PALM2-AKAP2_uc010mtw.1_Frame_Shift_Ins_p.G704fs|AKAP2_uc011lwj.1_Frame_Shift_Ins_p.G655fs|PALM2-AKAP2_uc004ben.2_Frame_Shift_Ins_p.G655fs	NM_001136562	NP_001130034	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2 isoform 2	655_656							enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6						GGGAAAGGGGGCCCCCCCAGCC	0.564													36	11	---	---	---	---	
DDX10	1662	broad.mit.edu	37	11	108788635	108788637	+	In_Frame_Del	DEL	TGA	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr11:108788635_108788637delTGA	uc001pkm.2	+	17	2405_2407	c.2340_2342delTGA	c.(2338-2343)AGTGAT>AGT	p.D788del	DDX10_uc001pkl.1_In_Frame_Del_p.D788del	NM_004398	NP_004389	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	788							ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity			breast(2)|lung(1)|prostate(1)	4		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		TGGATTGGAGtgatgatgatgat	0.310			T	NUP98	AML*								207	9	---	---	---	---	
SIP1	8487	broad.mit.edu	37	14	39601187	39601188	+	Frame_Shift_Ins	INS	-	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr14:39601187_39601188insT	uc001wuq.2	+	8	681_682	c.659_660insT	c.(658-660)GCTfs	p.A220fs	SIP1_uc001wur.2_Frame_Shift_Ins_p.A220fs|SIP1_uc001wus.2_Frame_Shift_Ins_p.A205fs|SIP1_uc010amx.2_RNA	NM_003616	NP_003607	O14893	GEMI2_HUMAN	SMN-interacting protein 1 isoform alpha	220					ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly	Cajal body|cytosol|spliceosomal complex	protein binding				0	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0121)		GCTTTATTGGCTTGTCTTGAAA	0.347													381	11	---	---	---	---	
FOXF1	2294	broad.mit.edu	37	16	86545125	86545126	+	Frame_Shift_Ins	INS	-	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr16:86545125_86545126insC	uc002fjl.2	+	1	993_994	c.950_951insC	c.(949-951)AACfs	p.N317fs	uc002fjk.1_5'Flank	NM_001451	NP_001442	Q12946	FOXF1_HUMAN	forkhead box F1	317					branching involved in open tracheal system development|cardiac left ventricle morphogenesis|embryonic ectodermal digestive tract morphogenesis|endocardial cushion development|in utero embryonic development|lung vasculature development|midgut development|pancreas development|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|ureter development|venous blood vessel development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding				0						CTGCACCAGAACAGCCACAACG	0.683													5	5	---	---	---	---	
RNF43	54894	broad.mit.edu	37	17	56435501	56435502	+	Frame_Shift_Ins	INS	-	G	G	rs144487242	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr17:56435501_56435502insG	uc002iwf.2	-	8	3591_3592	c.1635_1636insC	c.(1633-1638)TCCAGCfs	p.S545fs	RNF43_uc010wnv.1_Frame_Shift_Ins_p.S504fs|RNF43_uc002iwh.3_Frame_Shift_Ins_p.S545fs|RNF43_uc002iwg.3_Frame_Shift_Ins_p.S545fs|RNF43_uc010dcw.2_Frame_Shift_Ins_p.S418fs	NM_017763	NP_060233	Q68DV7	RNF43_HUMAN	ring finger protein 43 precursor	545_546	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane|nuclear envelope	ligase activity|protein binding|zinc ion binding			ovary(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TGGACATGGCTGGAAACCTGGG	0.624													195	7	---	---	---	---	
