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
PRAMEF2	65122	broad.mit.edu	37	1	12919064	12919064	+	Missense_Mutation	SNP	T	G	G	rs3204790	byFrequency	TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr1:12919064T>G	uc001aum.1	+	2	287	c.200T>G	c.(199-201)GTA>GGA	p.V67G		NM_023014	NP_075390	O60811	PRAM2_HUMAN	PRAME family member 2	67											0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CTCCCTCTGGTATCGCTGATG	0.557													3	41	---	---	---	---	PASS
PRAMEF4	400735	broad.mit.edu	37	1	12939664	12939664	+	Missense_Mutation	SNP	A	T	T	rs78455617	byFrequency	TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr1:12939664A>T	uc001aun.2	-	4	1209	c.1138T>A	c.(1138-1140)TTT>ATT	p.F380I		NM_001009611	NP_001009611	O60810	PRAM4_HUMAN	PRAME family member 4	380										ovary(1)	1	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TTGAGCTCAAAGCAGCGGCTC	0.507													5	93	---	---	---	---	PASS
PRAMEF4	400735	broad.mit.edu	37	1	12939674	12939674	+	Silent	SNP	C	G	G	rs72474510	byFrequency	TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr1:12939674C>G	uc001aun.2	-	4	1199	c.1128G>C	c.(1126-1128)CTG>CTC	p.L376L		NM_001009611	NP_001009611	O60810	PRAM4_HUMAN	PRAME family member 4	376										ovary(1)	1	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AGCAGCGGCTCAGGGCAGGCA	0.498													5	107	---	---	---	---	PASS
LCE5A	254910	broad.mit.edu	37	1	152484310	152484310	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr1:152484310C>G	uc001ezy.2	+	2	476	c.300C>G	c.(298-300)AGC>AGG	p.S100R	CRCT1_uc001ezz.2_5'Flank	NM_178438	NP_848525	Q5TCM9	LCE5A_HUMAN	late cornified envelope 5A	100	Cys-rich.				keratinization					ovary(1)	1	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGGGCTCCAGCTGCTGCCACA	0.682													4	9	---	---	---	---	PASS
CFHR5	81494	broad.mit.edu	37	1	196971637	196971637	+	Silent	SNP	G	A	A			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr1:196971637G>A	uc001gts.3	+	8	1301	c.1173G>A	c.(1171-1173)CCG>CCA	p.P391P		NM_030787	NP_110414	Q9BXR6	FHR5_HUMAN	complement factor H-related 5 precursor	391	Sushi 7.				complement activation, alternative pathway	extracellular region				breast(1)|skin(1)	2						TCTGCCCACCGCCACCTCAGA	0.348													7	79	---	---	---	---	PASS
GALNT2	2590	broad.mit.edu	37	1	230338965	230338965	+	Silent	SNP	C	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr1:230338965C>T	uc010pwa.1	+	3	375	c.303C>T	c.(301-303)CGC>CGT	p.R101R	GALNT2_uc010pvy.1_Silent_p.R63R|GALNT2_uc010pvz.1_RNA	NM_004481	NP_004472	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	101	Lumenal (Potential).				immunoglobulin biosynthetic process|protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane|perinuclear region of cytoplasm	manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				CTTACGCCCGCAACAAGTTCA	0.552													6	224	---	---	---	---	PASS
CLIP4	79745	broad.mit.edu	37	2	29354154	29354154	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr2:29354154C>T	uc002rmv.2	+	3	403	c.164C>T	c.(163-165)TCA>TTA	p.S55L	CLIP4_uc002rmu.2_Missense_Mutation_p.S55L|CLIP4_uc010ezm.1_Missense_Mutation_p.S55L|CLIP4_uc002rmw.2_RNA|CLIP4_uc010ymn.1_Missense_Mutation_p.S37L	NM_024692	NP_078968	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family,	55										ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)					AATGATGCATCATGCCAGGAA	0.249													42	99	---	---	---	---	PASS
CEBPZ	10153	broad.mit.edu	37	2	37441066	37441066	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr2:37441066C>T	uc002rpz.2	-	10	2516	c.2486G>A	c.(2485-2487)CGG>CAG	p.R829Q		NM_005760	NP_005751	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein zeta	829					regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding			pancreas(1)	1		all_hematologic(82;0.21)				ATCTGCATCCCGTTTTTGTTT	0.269													9	42	---	---	---	---	PASS
THSD7B	80731	broad.mit.edu	37	2	137814268	137814268	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr2:137814268C>A	uc002tva.1	+	2	325	c.325C>A	c.(325-327)CAC>AAC	p.H109N	THSD7B_uc010zbj.1_RNA|THSD7B_uc002tvb.2_5'UTR	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		TGGACTGCAGCACCGGATGGT	0.547													11	123	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141460073	141460073	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr2:141460073G>T	uc002tvj.1	-	38	7045	c.6073C>A	c.(6073-6075)CGC>AGC	p.R2025S		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	2025	Extracellular (Potential).|LDL-receptor class B 21.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CCATCCAAGCGAGCCTTTCCA	0.408										TSP Lung(27;0.18)			51	86	---	---	---	---	PASS
RAPH1	65059	broad.mit.edu	37	2	204304794	204304794	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr2:204304794A>G	uc002vad.2	-	14	3344	c.3119T>C	c.(3118-3120)GTT>GCT	p.V1040A		NM_213589	NP_998754	Q70E73	RAPH1_HUMAN	Ras association and pleckstrin homology domains	1040					cell-matrix adhesion|signal transduction	cytoplasm|cytoskeleton|filopodium|lamellipodium|nucleus|plasma membrane				ovary(3)|breast(3)|central_nervous_system(2)|lung(1)|skin(1)	10						TTGTTGGAGAACTCCAGGAAG	0.537													53	100	---	---	---	---	PASS
COL4A3	1285	broad.mit.edu	37	2	228155518	228155518	+	Silent	SNP	C	A	A			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr2:228155518C>A	uc002vom.1	+	37	3288	c.3126C>A	c.(3124-3126)GGC>GGA	p.G1042G	COL4A3_uc002von.1_Silent_p.G1042G|COL4A3_uc002voo.1_Silent_p.G1042G|COL4A3_uc002vop.1_Silent_p.G1042G|uc002voq.1_Intron|uc002vor.1_Intron	NM_000091	NP_000082	Q01955	CO4A3_HUMAN	alpha 3 type IV collagen isoform 1 precursor	1042	Triple-helical region.				activation of caspase activity|axon guidance|blood circulation|cell adhesion|cell proliferation|cell surface receptor linked signaling pathway|glomerular basement membrane development|induction of apoptosis|negative regulation of angiogenesis|negative regulation of cell proliferation|sensory perception of sound	collagen type IV	extracellular matrix structural constituent|integrin binding|metalloendopeptidase inhibitor activity			skin(2)|ovary(1)	3		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		GAAGACCAGGCCTCCCAGGTA	0.488													3	61	---	---	---	---	PASS
PID1	55022	broad.mit.edu	37	2	229890759	229890759	+	Silent	SNP	T	A	A			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr2:229890759T>A	uc002vpr.3	-	3	380	c.342A>T	c.(340-342)CCA>CCT	p.P114P	PID1_uc002vps.3_Silent_p.P112P|PID1_uc002vpt.3_Silent_p.P81P|PID1_uc002vpu.3_Silent_p.P32P	NM_001100818	NP_001094288	Q7Z2X4	PCLI1_HUMAN	phosphotyrosine interaction domain containing 1	114	PID.					cytoplasm				breast(3)|skin(1)	4		Renal(207;0.0112)|all_lung(227;0.0191)|Lung NSC(271;0.0851)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.171)		Epithelial(121;3.08e-11)|all cancers(144;2.28e-08)|LUSC - Lung squamous cell carcinoma(224;0.0145)|Lung(261;0.0189)		GCTCAATGACTGGCTTTTCTG	0.532													10	88	---	---	---	---	PASS
SCN5A	6331	broad.mit.edu	37	3	38640517	38640517	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr3:38640517C>A	uc003cio.2	-	13	2109	c.1915G>T	c.(1915-1917)GGG>TGG	p.G639W	SCN5A_uc003cin.2_Missense_Mutation_p.G639W|SCN5A_uc003cil.3_Missense_Mutation_p.G639W|SCN5A_uc010hhi.2_Missense_Mutation_p.G639W|SCN5A_uc010hhk.2_Missense_Mutation_p.G639W|SCN5A_uc011ayr.1_Missense_Mutation_p.G639W|SCN5A_uc010hhj.1_Missense_Mutation_p.G250W	NM_198056	NP_932173	Q14524	SCN5A_HUMAN	voltage-gated sodium channel type V alpha	639			G -> R (in LQT3).		blood circulation|cellular response to calcium ion|muscle contraction|regulation of heart contraction	sarcolemma|voltage-gated sodium channel complex	protein binding|voltage-gated sodium channel activity			ovary(4)|pancreas(2)|skin(2)|central_nervous_system(1)	9	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Benzonatate(DB00868)|Bepridil(DB01244)|Carbamazepine(DB00564)|Cocaine(DB00907)|Dibucaine(DB00527)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lamotrigine(DB00555)|Lidocaine(DB00281)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mibefradil(DB01388)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine(DB00908)|Riluzole(DB00740)|Tocainide(DB01056)|Verapamil(DB00661)	ATCTGGGGCCCGCCTGGCTCC	0.667													3	60	---	---	---	---	PASS
KLHL18	23276	broad.mit.edu	37	3	47376266	47376266	+	Silent	SNP	C	A	A			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr3:47376266C>A	uc003crd.2	+	6	981	c.855C>A	c.(853-855)TCC>TCA	p.S285S	KLHL18_uc003crc.2_Silent_p.S285S|KLHL18_uc011bav.1_Silent_p.S173S|KLHL18_uc010hjq.1_Silent_p.S136S	NM_025010	NP_079286	O94889	KLH18_HUMAN	kelch-like 18	285											0		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00645)|Kidney(197;0.00741)		GCTGCACATCCATCGCTGGAC	0.582													3	54	---	---	---	---	PASS
IL17RB	55540	broad.mit.edu	37	3	53886921	53886921	+	Silent	SNP	C	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr3:53886921C>T	uc003dha.2	+	5	417	c.378C>T	c.(376-378)TTC>TTT	p.F126F		NM_018725	NP_061195	Q9NRM6	I17RB_HUMAN	interleukin 17B receptor precursor	126	Extracellular (Potential).				defense response|regulation of cell growth	extracellular region|integral to plasma membrane	cytokine receptor activity			ovary(2)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)		ACATCGGCTTCCCTGTAGAGC	0.428													10	159	---	---	---	---	PASS
FILIP1L	11259	broad.mit.edu	37	3	99568295	99568295	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr3:99568295T>G	uc003dtm.2	-	5	2688	c.2225A>C	c.(2224-2226)GAT>GCT	p.D742A	C3orf26_uc003dtk.1_Intron|C3orf26_uc003dtl.2_Intron|FILIP1L_uc003dto.2_Missense_Mutation_p.D742A|FILIP1L_uc010hpf.2_Missense_Mutation_p.D318A|FILIP1L_uc010hpg.2_Missense_Mutation_p.D502A|FILIP1L_uc003dtn.2_Missense_Mutation_p.D502A|FILIP1L_uc003dtp.1_Missense_Mutation_p.D502A	NM_182909	NP_878913	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like isoform 1	742	Potential.					cytoplasm|membrane|myosin complex|nucleus				ovary(1)	1						GACTGAGTGATCTCCCTGGAG	0.408													10	393	---	---	---	---	PASS
BCL6	604	broad.mit.edu	37	3	187447645	187447645	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr3:187447645C>T	uc003frp.3	-	5	1005	c.548G>A	c.(547-549)AGC>AAC	p.S183N	BCL6_uc011bsf.1_Missense_Mutation_p.S183N|BCL6_uc010hza.2_Missense_Mutation_p.S81N|BCL6_uc003frq.1_Missense_Mutation_p.S183N	NM_001130845	NP_001124317	P41182	BCL6_HUMAN	B-cell lymphoma 6 protein isoform 1	183					negative regulation of B cell apoptosis|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|protein import into nucleus, translocation|regulation of germinal center formation|response to DNA damage stimulus	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|lung(2)|central_nervous_system(1)	5	all_cancers(143;9.45e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0141)		ACTGTACAGGCTGGGGGCAAA	0.602			T|Mis	IG loci|ZNFN1A1|LCP1|PIM1|TFRC|MHC2TA|NACA|HSPCB|HSPCA|HIST1H4I|IL21R| POU2AF1|ARHH|EIF4A2|SFRS3	NHL|CLL								30	38	---	---	---	---	PASS
GRXCR1	389207	broad.mit.edu	37	4	42895345	42895345	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr4:42895345C>T	uc003gwt.2	+	1	62	c.62C>T	c.(61-63)GCG>GTG	p.A21V		NM_001080476	NP_001073945	A8MXD5	GRCR1_HUMAN	glutaredoxin, cysteine rich 1	21					cell redox homeostasis|inner ear receptor stereocilium organization|sensory perception of sound|vestibular receptor cell development	kinocilium|stereocilium	electron carrier activity|protein disulfide oxidoreductase activity			ovary(1)	1						TTTCGGATCGCGTCCTCTCAC	0.507													45	103	---	---	---	---	PASS
PPEF2	5470	broad.mit.edu	37	4	76813087	76813087	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr4:76813087C>T	uc003hix.2	-	3	457	c.100G>A	c.(100-102)GTG>ATG	p.V34M	PPEF2_uc003hiy.2_RNA|PPEF2_uc003hiz.1_Missense_Mutation_p.V34M	NM_006239	NP_006230	O14830	PPE2_HUMAN	serine/threonine protein phosphatase with	34	IQ.				detection of stimulus involved in sensory perception|negative regulation of MAPKKK cascade|negative regulation of peptidyl-threonine phosphorylation|protein dephosphorylation|visual perception	cytoplasm|photoreceptor inner segment|photoreceptor outer segment	calcium ion binding|Hsp70 protein binding|Hsp90 protein binding|iron ion binding|manganese ion binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine phosphatase activity			ovary(2)|lung(1)|central_nervous_system(1)	4			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			AGGCGGGCCACGTAGCGCCGG	0.582													22	79	---	---	---	---	PASS
FRAS1	80144	broad.mit.edu	37	4	79343065	79343065	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr4:79343065C>T	uc003hlb.2	+	34	5029	c.4589C>T	c.(4588-4590)ACG>ATG	p.T1530M	FRAS1_uc003hkw.2_Missense_Mutation_p.T1530M|FRAS1_uc010ijj.1_Intron	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	1529	CSPG 4.|Extracellular (Potential).				cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						CGGTATTTCACGCAAGAGGAT	0.547													93	226	---	---	---	---	PASS
PLG	5340	broad.mit.edu	37	6	161139389	161139389	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr6:161139389G>A	uc003qtm.3	+	8	914	c.851G>A	c.(850-852)CGC>CAC	p.R284H		NM_000301	NP_000292	P00747	PLMN_HUMAN	plasminogen	284	Kringle 3.				extracellular matrix disassembly|fibrinolysis|negative regulation of cell proliferation|negative regulation of cell-substrate adhesion|negative regulation of fibrinolysis|platelet activation|platelet degranulation|positive regulation of fibrinolysis|proteolysis|tissue remodeling	extracellular space|extrinsic to external side of plasma membrane|platelet alpha granule lumen	apolipoprotein binding|cell surface binding|serine-type endopeptidase activity			skin(3)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Aminocaproic Acid(DB00513)|Streptokinase(DB00086)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	GAAAACTATCGCGGGAATGTG	0.493													40	170	---	---	---	---	PASS
DNAH11	8701	broad.mit.edu	37	7	21939032	21939032	+	Silent	SNP	C	A	A	rs56333627	by1000genomes	TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr7:21939032C>A	uc003svc.2	+	81	13180	c.13149C>A	c.(13147-13149)CTC>CTA	p.L4383L		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	4383					microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15						TCGTGTGGCTCTCCGGCTTCT	0.557									Kartagener_syndrome				6	272	---	---	---	---	PASS
CLK2P	1197	broad.mit.edu	37	7	23624896	23624896	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr7:23624896G>A	uc003swk.2	-	1	1251	c.601C>T	c.(601-603)CGC>TGC	p.R201C		NR_002711				SubName: Full=cDNA FLJ61616, highly similar to Dual specificity protein kinase CLK2 (EC 2.7.12.1); SubName: Full=CDC-like kinase 2, isoform CRA_c; SubName: Full=Putative uncharacterized protein CLK2;												0						CGAACATAGCGTCCAGCTGAT	0.498													58	125	---	---	---	---	PASS
INHBA	3624	broad.mit.edu	37	7	41739653	41739653	+	Missense_Mutation	SNP	A	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr7:41739653A>T	uc003thq.2	-	1	555	c.320T>A	c.(319-321)ATT>AAT	p.I107N	LOC285954_uc003tht.3_Intron|INHBA_uc003thr.2_Missense_Mutation_p.I107N|LOC285954_uc003ths.2_Intron	NM_002192	NP_002183	P08476	INHBA_HUMAN	inhibin beta A precursor	107					cell cycle arrest|cell surface receptor linked signaling pathway|defense response|erythrocyte differentiation|eyelid development in camera-type eye|G1/S transition of mitotic cell cycle|growth|hair follicle development|hemoglobin biosynthetic process|hemopoietic progenitor cell differentiation|induction of apoptosis|male gonad development|negative regulation of B cell differentiation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of follicle-stimulating hormone secretion|negative regulation of interferon-gamma biosynthetic process|negative regulation of macrophage differentiation|negative regulation of phosphorylation|nervous system development|odontogenesis|ovarian follicle development|palate development|positive regulation of erythrocyte differentiation|positive regulation of follicle-stimulating hormone secretion|positive regulation of ovulation|positive regulation of transcription from RNA polymerase II promoter|progesterone secretion|regulation of activin receptor signaling pathway	activin A complex|inhibin A complex	cytokine activity|follistatin binding|growth factor activity|hormone activity|identical protein binding|signal transducer activity			lung(5)|ovary(1)	6						CCTCCTTCCAATGTCATCCTC	0.562										TSP Lung(11;0.080)			19	758	---	---	---	---	PASS
ZKSCAN5	23660	broad.mit.edu	37	7	99110202	99110202	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr7:99110202C>G	uc003uqv.2	+	3	665	c.541C>G	c.(541-543)CTG>GTG	p.L181V	ZKSCAN5_uc010lfx.2_Missense_Mutation_p.L181V|ZKSCAN5_uc003uqw.2_Missense_Mutation_p.L181V|ZKSCAN5_uc003uqx.2_Missense_Mutation_p.L181V|ZKSCAN5_uc003uqy.2_5'UTR	NM_145102	NP_659570	Q9Y2L8	ZKSC5_HUMAN	zinc finger with KRAB and SCAN domains 5	181					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					GCCTCGTCTCCTGGAGGAAAA	0.587													20	35	---	---	---	---	PASS
SSPO	23145	broad.mit.edu	37	7	149526028	149526028	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr7:149526028G>A	uc010lpk.2	+	109	15082	c.15082G>A	c.(15082-15084)GAG>AAG	p.E5028K	SSPO_uc003wgh.2_RNA	NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	5028	VWFC 3.				cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			TCTGCAGGGCGAGGAGATGGT	0.667													8	6	---	---	---	---	PASS
FLJ10661	286042	broad.mit.edu	37	8	8095990	8095990	+	RNA	SNP	C	G	G			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr8:8095990C>G	uc011kwt.1	+	8		c.1185C>G			FLJ10661_uc010lrq.2_Intron|FLJ10661_uc003wsf.3_Intron	NR_024362				Homo sapiens cDNA FLJ60033 complete cds, highly similar to Protein FAM86A.												0						CCAGGAGCCCCGAGACCTGCA	0.647													2	4	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77764257	77764257	+	Silent	SNP	C	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr8:77764257C>T	uc003yav.2	+	10	5352	c.4965C>T	c.(4963-4965)CAC>CAT	p.H1655H	ZFHX4_uc003yau.1_Silent_p.H1700H|ZFHX4_uc003yaw.1_Silent_p.H1655H	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1655	Gln-rich.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AACTACAGCACGAATTACAAC	0.443										HNSCC(33;0.089)			24	96	---	---	---	---	PASS
KCNQ3	3786	broad.mit.edu	37	8	133196585	133196585	+	Silent	SNP	G	A	A			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr8:133196585G>A	uc003ytj.2	-	3	732	c.507C>T	c.(505-507)GCC>GCT	p.A169A	KCNQ3_uc010mdt.2_Silent_p.A169A	NM_004519	NP_004510	O43525	KCNQ3_HUMAN	potassium voltage-gated channel KQT-like protein	169	Helical; Name=Segment S2; (Potential).				axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)			AAGCAAACTCGGCTCCAAAGA	0.512													49	80	---	---	---	---	PASS
FANCG	2189	broad.mit.edu	37	9	35076446	35076446	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr9:35076446C>A	uc003zwb.1	-	8	1551	c.1059G>T	c.(1057-1059)AGG>AGT	p.R353S	FANCG_uc003zwa.1_Missense_Mutation_p.R95S|FANCG_uc010mkj.1_Missense_Mutation_p.R95S|FANCG_uc011lot.1_Missense_Mutation_p.R353S	NM_004629	NP_004620	O15287	FANCG_HUMAN	Fanconi anemia, complementation group G	353	TPR 2.				cell cycle checkpoint|DNA repair|mitochondrion organization	mitochondrion|nucleoplasm	damaged DNA binding|protein binding			ovary(2)|large_intestine(1)|lung(1)	4			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			TCTGTAGGCACCTGCTTGCTA	0.532			Mis|N|F|S			AML|leukemia		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				9	105	---	---	---	---	PASS
NPR2	4882	broad.mit.edu	37	9	35809214	35809214	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr9:35809214G>T	uc003zyd.2	+	21	3048	c.3048G>T	c.(3046-3048)CAG>CAT	p.Q1016H	NPR2_uc010mlb.2_Missense_Mutation_p.Q992H|SPAG8_uc003zye.2_Intron	NM_003995	NP_003986	P20594	ANPRB_HUMAN	natriuretic peptide receptor B precursor	1016	Cytoplasmic (Potential).				intracellular signal transduction|ossification|receptor guanylyl cyclase signaling pathway|regulation of blood pressure	integral to membrane|plasma membrane	GTP binding|guanylate cyclase activity|natriuretic peptide receptor activity|protein kinase activity|transmembrane receptor activity			ovary(2)|stomach(1)	3	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	GATGCTTCCAGCTAGAGCTTC	0.547													11	211	---	---	---	---	PASS
SMC2	10592	broad.mit.edu	37	9	106889711	106889711	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr9:106889711G>A	uc004bbv.2	+	20	3028	c.2740G>A	c.(2740-2742)GAC>AAC	p.D914N	SMC2_uc004bbw.2_Missense_Mutation_p.D914N|SMC2_uc011lvl.1_Missense_Mutation_p.D914N|SMC2_uc004bbx.2_Missense_Mutation_p.D914N|SMC2_uc004bby.2_RNA	NM_001042551	NP_001036016	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	914	Potential.				cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism	condensin complex|cytoplasm|nuclear chromosome	ATP binding|protein heterodimerization activity			ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1)	9						TAAGGAATTAGACCACAACAT	0.363													53	82	---	---	---	---	PASS
COL5A1	1289	broad.mit.edu	37	9	137707834	137707834	+	Silent	SNP	G	A	A	rs3827848	byFrequency	TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr9:137707834G>A	uc004cfe.2	+	52	4504	c.4122G>A	c.(4120-4122)ACG>ACA	p.T1374T		NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein	1374	Triple-helical region.				axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CCGGGCAGACGGTGAGTCCAC	0.552													4	99	---	---	---	---	PASS
UBAC1	10422	broad.mit.edu	37	9	138837764	138837764	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr9:138837764G>C	uc004cgt.2	-	6	842	c.624C>G	c.(622-624)AAC>AAG	p.N208K	UBAC1_uc004cgs.1_Missense_Mutation_p.N208K|UBAC1_uc004cgu.2_RNA	NM_016172	NP_057256	Q9BSL1	UBAC1_HUMAN	ubiquitin associated domain containing 1	208	UBA 1.					Golgi apparatus|plasma membrane	protein binding			skin(2)	2		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.1e-06)|Epithelial(140;7.79e-06)		TGGTGGCTCTGTTCTCCGGAA	0.662													14	46	---	---	---	---	PASS
ZNF485	220992	broad.mit.edu	37	10	44104090	44104090	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr10:44104090T>G	uc010qfc.1	+	3	247	c.53T>G	c.(52-54)GTG>GGG	p.V18G	ZNF485_uc010qfd.1_Intron	NM_145312	NP_660355	Q8NCK3	ZN485_HUMAN	zinc finger protein 485	18	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GATGTGGCTGTGGCCTTTACC	0.562													11	17	---	---	---	---	PASS
PTEN	5728	broad.mit.edu	37	10	89690802	89690802	+	Splice_Site	SNP	G	A	A			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr10:89690802G>A	uc001kfb.2	+	5	1241	c.210_splice	c.e5-1	p.L70_splice		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog						activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.R55fs*1(4)|p.?(4)|p.L70fs*7(2)|p.Y27fs*1(2)|p.F56fs*2(1)		endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TTTTCTTTTAGTTGTGCTGAA	0.254		31	D|Mis|N|F|S		glioma| prostate|endometrial	harmartoma|glioma| prostate|endometrial			Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)			32	23	---	---	---	---	PASS
CRTAC1	55118	broad.mit.edu	37	10	99642555	99642555	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr10:99642555C>A	uc001kou.1	-	13	2019	c.1663G>T	c.(1663-1665)GGC>TGC	p.G555C	CRTAC1_uc001kov.2_Missense_Mutation_p.G544C|CRTAC1_uc001kot.1_Intron	NM_018058	NP_060528	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1 precursor	555						proteinaceous extracellular matrix	calcium ion binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		ATGCAATGGCCATTTTCCTGC	0.577													17	33	---	---	---	---	PASS
ENTPD7	57089	broad.mit.edu	37	10	101455823	101455823	+	Silent	SNP	C	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr10:101455823C>T	uc001kqa.3	+	9	1132	c.954C>T	c.(952-954)AAC>AAT	p.N318N	ENTPD7_uc009xwl.2_Silent_p.N320N	NM_020354	NP_065087	Q9NQZ7	ENTP7_HUMAN	ectonucleoside triphosphate diphosphohydrolase	318	Vesicular (Potential).					cytoplasmic vesicle membrane|integral to membrane	hydrolase activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.75e-08)		TCGGAGGCAACTTTGCCCGGC	0.453													11	169	---	---	---	---	PASS
TLX1	3195	broad.mit.edu	37	10	102896459	102896459	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr10:102896459C>G	uc001ksw.2	+	3	1020	c.782C>G	c.(781-783)GCG>GGG	p.A261G		NM_005521	NP_005512	P31314	TLX1_HUMAN	T-cell leukemia homeobox 1	261						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)	1				Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		CGGCAGACTGCGGAGGAACGG	0.652			T	TRB@|TRD@	T-ALL								5	64	---	---	---	---	PASS
ADAM12	8038	broad.mit.edu	37	10	128019025	128019025	+	Missense_Mutation	SNP	C	G	G	rs3740199	byFrequency	TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr10:128019025C>G	uc001ljk.2	-	2	555	c.142G>C	c.(142-144)GGG>CGG	p.G48R	ADAM12_uc010qul.1_Missense_Mutation_p.G48R|ADAM12_uc001ljm.2_Missense_Mutation_p.G48R|ADAM12_uc001ljn.2_Missense_Mutation_p.G48R|ADAM12_uc001ljl.3_Missense_Mutation_p.G48R	NM_003474	NP_003465	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12 isoform 1	48					cell adhesion|epidermal growth factor receptor signaling pathway|myoblast fusion|proteolysis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|protein binding|SH3 domain binding|zinc ion binding			breast(4)|ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	9		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		TCCCCACTCCCAACAGAGGCA	0.468													4	174	---	---	---	---	PASS
NAV2	89797	broad.mit.edu	37	11	20101630	20101630	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr11:20101630G>T	uc010rdm.1	+	27	5729	c.5368G>T	c.(5368-5370)GCA>TCA	p.A1790S	NAV2_uc001mpp.2_Missense_Mutation_p.A1670S|NAV2_uc001mpr.3_Missense_Mutation_p.A1734S|NAV2_uc001mpt.2_Missense_Mutation_p.A783S|NAV2_uc009yhx.2_Missense_Mutation_p.A798S|NAV2_uc009yhy.1_Missense_Mutation_p.A696S|NAV2_uc009yhz.2_Missense_Mutation_p.A379S|NAV2_uc001mpu.2_Missense_Mutation_p.A172S	NM_145117	NP_660093	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 2	1790						nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6						TGCCCAGTCTGCAGACCTCCG	0.562													13	39	---	---	---	---	PASS
TCN1	6947	broad.mit.edu	37	11	59633903	59633903	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr11:59633903A>G	uc001noj.2	-	1	139	c.41T>C	c.(40-42)CTG>CCG	p.L14P		NM_001062	NP_001053	P20061	TCO1_HUMAN	transcobalamin I precursor	14					cobalamin metabolic process|cobalamin transport|cobalt ion transport	extracellular region	cobalamin binding			ovary(2)	2		all_epithelial(135;0.198)			Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AAAAGAAAACAGTAAGAGCCC	0.413													49	109	---	---	---	---	PASS
EML3	256364	broad.mit.edu	37	11	62378665	62378665	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr11:62378665G>A	uc001ntu.1	-	3	654	c.346C>T	c.(346-348)CCT>TCT	p.P116S	EML3_uc001ntr.1_Missense_Mutation_p.P88S|EML3_uc001nts.1_Missense_Mutation_p.P88S|EML3_uc001ntt.1_Silent_p.S12S|EML3_uc010rly.1_Missense_Mutation_p.P116S|EML3_uc009yny.1_5'UTR|ROM1_uc001ntv.2_5'Flank	NM_153265	NP_694997	Q32P44	EMAL3_HUMAN	echinoderm microtubule associated protein like	116						cytoplasm|microtubule	protein binding			ovary(1)	1						GTCCCGCTAGGCTCTTCGCTG	0.697													4	30	---	---	---	---	PASS
MAML2	84441	broad.mit.edu	37	11	95712225	95712225	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr11:95712225G>A	uc001pfw.1	-	5	4643	c.3358C>T	c.(3358-3360)CCT>TCT	p.P1120S		NM_032427	NP_115803	Q8IZL2	MAML2_HUMAN	mastermind-like 2	1120					Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity		CRTC1/MAML2(516)|CRTC3/MAML2(26)	salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1)	546		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				TTTAGGGCAGGGCCCATGTTA	0.423			T	MECT1|CRTC3	salivary gland mucoepidermoid								27	133	---	---	---	---	PASS
MMP12	4321	broad.mit.edu	37	11	102737090	102737090	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr11:102737090G>T	uc001phk.2	-	8	1046	c.1001C>A	c.(1000-1002)GCT>GAT	p.A334D		NM_002426	NP_002417	P39900	MMP12_HUMAN	matrix metalloproteinase 12 preproprotein	334	Hemopexin-like 2.				positive regulation of epithelial cell proliferation involved in wound healing|proteolysis|wound healing, spreading of epidermal cells	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding				0		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.014)	Acetohydroxamic Acid(DB00551)	TTCATAAGCAGCTTCAATGCC	0.353													3	22	---	---	---	---	PASS
SIDT2	51092	broad.mit.edu	37	11	117052139	117052139	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr11:117052139G>C	uc001pqh.1	+	2	232	c.191G>C	c.(190-192)GGC>GCC	p.G64A	SIDT2_uc010rxe.1_Missense_Mutation_p.G64A|SIDT2_uc001pqg.2_Missense_Mutation_p.G64A|SIDT2_uc001pqi.1_Missense_Mutation_p.G64A	NM_001040455	NP_001035545	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2 precursor	64	Extracellular (Potential).					integral to membrane|lysosomal membrane					0	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000219)|all cancers(92;0.00144)		CAGACAGAGGGCGTGCGTGTG	0.597											OREG0021368	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	42	---	---	---	---	PASS
CCDC15	80071	broad.mit.edu	37	11	124857794	124857794	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr11:124857794C>T	uc001qbm.3	+	8	1931	c.1672C>T	c.(1672-1674)CAG>TAG	p.Q558*		NM_025004	NP_079280	Q0P6D6	CCD15_HUMAN	coiled-coil domain containing 15	558						centrosome				ovary(1)|central_nervous_system(1)	2	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.68e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0413)		ACCCAAATGTCAGGACCAGGA	0.433													16	481	---	---	---	---	PASS
SLC37A2	219855	broad.mit.edu	37	11	124947149	124947149	+	Silent	SNP	G	A	A	rs12276567	byFrequency	TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr11:124947149G>A	uc001qbn.2	+	3	416	c.165G>A	c.(163-165)TCG>TCA	p.S55S	SLC37A2_uc010sau.1_Silent_p.S55S	NM_001145290	NP_001138762	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glycerol-3-phosphate	55					carbohydrate transport|transmembrane transport	integral to membrane				ovary(2)	2	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)		AGAACTGCTCGGAGCAGATCA	0.542													5	274	---	---	---	---	PASS
FGFR1OP2	26127	broad.mit.edu	37	12	27107226	27107226	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr12:27107226G>T	uc001rhm.2	+	2	477	c.135G>T	c.(133-135)CAG>CAT	p.Q45H	FGFR1OP2_uc001rhl.2_Missense_Mutation_p.Q45H|FGFR1OP2_uc001rhn.2_Missense_Mutation_p.Q45H	NM_015633	NP_056448	Q9NVK5	FGOP2_HUMAN	FGFR1 oncogene partner 2	45	Potential.					cytoplasm					0	Colorectal(261;0.0847)					CCATGAAACAGGTTTGATTTT	0.348													3	65	---	---	---	---	PASS
ZNF641	121274	broad.mit.edu	37	12	48737263	48737263	+	Silent	SNP	C	A	A			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr12:48737263C>A	uc001rrn.1	-	6	975	c.810G>T	c.(808-810)GGG>GGT	p.G270G	ZNF641_uc001rro.1_Silent_p.G256G|ZNF641_uc010sls.1_Silent_p.G247G	NM_152320	NP_689533	Q96N77	ZN641_HUMAN	zinc finger protein 641	270	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2						CAAACTGTTTCCCACACTGGG	0.527													6	123	---	---	---	---	PASS
INHBC	3626	broad.mit.edu	37	12	57843267	57843267	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr12:57843267C>T	uc001snv.1	+	2	648	c.521C>T	c.(520-522)GCC>GTC	p.A174V		NM_005538	NP_005529	P55103	INHBC_HUMAN	inhibin beta C chain preproprotein	174					growth	extracellular region	growth factor activity|hormone activity|transforming growth factor beta receptor binding				0						GAGGTGGATGCCAGTGGCTGG	0.577													4	124	---	---	---	---	PASS
ANO4	121601	broad.mit.edu	37	12	101433785	101433785	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr12:101433785G>A	uc010svm.1	+	11	1522	c.950G>A	c.(949-951)CGA>CAA	p.R317Q	ANO4_uc001thw.2_Missense_Mutation_p.R282Q|ANO4_uc001thx.2_Missense_Mutation_p.R317Q	NM_178826	NP_849148	Q32M45	ANO4_HUMAN	anoctamin 4	317	Extracellular (Potential).					chloride channel complex	chloride channel activity			ovary(4)|skin(2)	6						GAAAACCACCGACATCTACTC	0.438										HNSCC(74;0.22)			104	249	---	---	---	---	PASS
DAO	1610	broad.mit.edu	37	12	109290787	109290787	+	Silent	SNP	C	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr12:109290787C>T	uc001tnr.3	+	8	771	c.618C>T	c.(616-618)GAC>GAT	p.D206D	DAO_uc001tnq.3_Silent_p.D140D|DAO_uc009zvb.2_RNA|DAO_uc001tns.3_Intron	NM_001917	NP_001908	P14920	OXDA_HUMAN	D-amino-acid oxidase	206					glyoxylate metabolic process	peroxisomal matrix	binding|D-amino-acid oxidase activity			ovary(1)|skin(1)	2						AACAGGTGGACGCCCCTTGGA	0.547													34	55	---	---	---	---	PASS
GCN1L1	10985	broad.mit.edu	37	12	120615277	120615277	+	Silent	SNP	G	A	A			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr12:120615277G>A	uc001txo.2	-	9	824	c.811C>T	c.(811-813)CTG>TTG	p.L271L		NM_006836	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis	271	HEAT 1.				regulation of translation	ribosome	protein binding|translation factor activity, nucleic acid binding			ovary(4)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GGACTCCTCAGTAAGGACTTC	0.448													19	66	---	---	---	---	PASS
GPR133	283383	broad.mit.edu	37	12	131593399	131593399	+	Missense_Mutation	SNP	G	A	A	rs141128784		TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr12:131593399G>A	uc001uit.3	+	18	2577	c.2018G>A	c.(2017-2019)CGT>CAT	p.R673H	GPR133_uc010tbm.1_Missense_Mutation_p.R705H|GPR133_uc009zyo.2_Intron|GPR133_uc001uiv.1_Missense_Mutation_p.R192H|GPR133_uc009zyp.2_RNA	NM_198827	NP_942122	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133 precursor	673	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)|skin(2)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		AGCAAGCACCGTTACTACTat	0.299													26	163	---	---	---	---	PASS
GOLGA3	2802	broad.mit.edu	37	12	133357412	133357412	+	Missense_Mutation	SNP	T	C	C	rs2291260	byFrequency	TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr12:133357412T>C	uc001ukz.1	-	18	4113	c.3554A>G	c.(3553-3555)AAG>AGG	p.K1185R	GOLGA3_uc001ula.1_Missense_Mutation_p.K1185R	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3	1185	Potential.				intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		CACCTTCTCCTTCTCCTTCTC	0.557													4	149	---	---	---	---	PASS
METTL3	56339	broad.mit.edu	37	14	21971365	21971365	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr14:21971365A>C	uc001wbc.2	-	3	766	c.674T>G	c.(673-675)ATA>AGA	p.I225R	METTL3_uc001wbb.2_Missense_Mutation_p.I70R|METTL3_uc010tlw.1_RNA|METTL3_uc010tlx.1_Missense_Mutation_p.I225R|METTL3_uc001wbd.1_Missense_Mutation_p.I225R	NM_019852	NP_062826	Q86U44	MTA70_HUMAN	methyltransferase like 3	225					gene expression	nuclear speck	mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity|RNA binding			pancreas(1)|skin(1)	2	all_cancers(95;0.000628)		Epithelial(56;6.61e-06)	GBM - Glioblastoma multiforme(265;0.0146)		AAGGCTCTCTATCTCCAGATC	0.443													97	210	---	---	---	---	PASS
LRRC16B	90668	broad.mit.edu	37	14	24530760	24530760	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr14:24530760C>T	uc001wlj.2	+	27	2516	c.2359C>T	c.(2359-2361)CGG>TGG	p.R787W	LRRC16B_uc001wlk.2_5'Flank	NM_138360	NP_612369	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	787										ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(265;0.019)		TGTGGCCATGCGGGTGGCCGA	0.612													3	62	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	23114213	23114213	+	RNA	SNP	C	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr15:23114213C>T	uc001yvf.2	-	2		c.218G>A								Homo sapiens cDNA clone IMAGE:5275816.																		TTCAACCATTCGGTGTCAAGG	0.433													4	58	---	---	---	---	PASS
SPSB3	90864	broad.mit.edu	37	16	1831441	1831441	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr16:1831441A>G	uc002cmr.2	-	1	77	c.44T>C	c.(43-45)CTG>CCG	p.L15P	NUBP2_uc002cmw.3_5'Flank|NUBP2_uc002cmx.3_5'Flank|NUBP2_uc010brx.2_5'Flank|SPSB3_uc002cms.2_5'UTR|SPSB3_uc002cmt.2_5'UTR|SPSB3_uc002cmu.2_Missense_Mutation_p.L15P|SPSB3_uc002cmv.2_5'UTR|SPSB3_uc010uvm.1_Missense_Mutation_p.L15P	NM_080861	NP_543137	Q6PJ21	SPSB3_HUMAN	splA/ryanodine receptor domain and SOCS box	15					intracellular signal transduction						0						GGCTGCACTCAGGACGAAGTG	0.617													16	19	---	---	---	---	PASS
GRIN2A	2903	broad.mit.edu	37	16	9892213	9892213	+	Silent	SNP	G	T	T	rs148846694	byFrequency	TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr16:9892213G>T	uc002czo.3	-	11	2825	c.2277C>A	c.(2275-2277)ACC>ACA	p.T759T	GRIN2A_uc010uym.1_Silent_p.T759T|GRIN2A_uc010uyn.1_Silent_p.T602T|GRIN2A_uc002czr.3_Silent_p.T759T	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	759	Extracellular (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	TTCCATAACCGGTGGTGGCAA	0.547													3	86	---	---	---	---	PASS
CCDC135	84229	broad.mit.edu	37	16	57756742	57756742	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr16:57756742A>G	uc002emi.2	+	10	1486	c.1397A>G	c.(1396-1398)GAG>GGG	p.E466G	CCDC135_uc002emj.2_Missense_Mutation_p.E466G|CCDC135_uc002emk.2_Missense_Mutation_p.E401G	NM_032269	NP_115645	Q8IY82	CC135_HUMAN	coiled-coil domain containing 135	466						cytoplasm				central_nervous_system(1)	1						ACCACCTATGAGGACTTGCAG	0.597													3	75	---	---	---	---	PASS
GOT2	2806	broad.mit.edu	37	16	58750604	58750604	+	Silent	SNP	G	A	A	rs1058192	byFrequency	TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr16:58750604G>A	uc002eof.1	-	7	930	c.816C>T	c.(814-816)TGC>TGT	p.C272C	GOT2_uc010vim.1_Silent_p.C229C	NM_002080	NP_002071	P00505	AATM_HUMAN	aspartate aminotransferase 2 precursor	272					aspartate catabolic process|fatty acid transport|gluconeogenesis|response to ethanol	mitochondrial matrix|plasma membrane	L-aspartate:2-oxoglutarate aminotransferase activity|protein binding|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					L-Aspartic Acid(DB00128)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)	ATTGGCAGAGGCAAACATTAA	0.502													4	67	---	---	---	---	PASS
ZZEF1	23140	broad.mit.edu	37	17	3992020	3992020	+	Silent	SNP	C	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr17:3992020C>T	uc002fxe.2	-	13	2257	c.2193G>A	c.(2191-2193)ACG>ACA	p.T731T	ZZEF1_uc002fxk.1_Silent_p.T731T	NM_015113	NP_055928	O43149	ZZEF1_HUMAN	zinc finger, ZZ type with EF hand domain 1	731							calcium ion binding|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4						TGAGGAGCAACGTGGCCCCAC	0.547													8	57	---	---	---	---	PASS
GAS2L2	246176	broad.mit.edu	37	17	34072555	34072555	+	Missense_Mutation	SNP	G	A	A	rs3744374	byFrequency	TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr17:34072555G>A	uc002hjv.1	-	6	1989	c.1961C>T	c.(1960-1962)GCC>GTC	p.A654V		NM_139285	NP_644814	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	654					cell cycle arrest	cytoplasm|cytoskeleton				ovary(1)|skin(1)	2		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TTCTTGGATGGCTTTGTCATA	0.627													5	189	---	---	---	---	PASS
SYNRG	11276	broad.mit.edu	37	17	35937637	35937637	+	Missense_Mutation	SNP	T	C	C	rs12602536	byFrequency	TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr17:35937637T>C	uc002hoa.2	-	7	747	c.664A>G	c.(664-666)ACT>GCT	p.T222A	SYNRG_uc010wde.1_Intron|SYNRG_uc010wdf.1_Intron|SYNRG_uc002hoc.2_Intron|SYNRG_uc002hoe.2_Intron|SYNRG_uc002hod.2_Intron|SYNRG_uc010wdg.1_Intron|SYNRG_uc002hob.2_Missense_Mutation_p.T222A|SYNRG_uc002hof.2_5'Flank|SYNRG_uc010cvd.1_Intron|SYNRG_uc002hog.1_Missense_Mutation_p.T356A|SYNRG_uc010wdh.1_Missense_Mutation_p.T323A	NM_007247	NP_009178	Q9UMZ2	SYNRG_HUMAN	synergin, gamma isoform 1	222					endocytosis|intracellular protein transport	AP-1 adaptor complex	calcium ion binding			ovary(2)	2						ACTTCAGAAGTATTTAATTTA	0.428													6	353	---	---	---	---	PASS
AFG3L2	10939	broad.mit.edu	37	18	12340252	12340252	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr18:12340252G>T	uc002kqz.1	-	15	2041	c.1928C>A	c.(1927-1929)ACA>AAA	p.T643K		NM_006796	NP_006787	Q9Y4W6	AFG32_HUMAN	AFG3 ATPase family gene 3-like 2	643					cell death|protein catabolic process|proteolysis	integral to membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding				0					Adenosine triphosphate(DB00171)	AGCACCAGTTGTAATTCTTCC	0.393													10	272	---	---	---	---	PASS
SLC5A5	6528	broad.mit.edu	37	19	18001748	18001748	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr19:18001748C>T	uc002nhr.3	+	14	2052	c.1705C>T	c.(1705-1707)CGG>TGG	p.R569W		NM_000453	NP_000444	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium iodide	569	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process|cellular response to cAMP|cellular response to gonadotropin stimulus|hormone biosynthetic process	integral to membrane|nucleus|plasma membrane	iodide transmembrane transporter activity|sodium:iodide symporter activity			skin(2)|ovary(1)|central_nervous_system(1)	4						GGACCTCGCACGGCAGACAGC	0.602													76	154	---	---	---	---	PASS
ZNF257	113835	broad.mit.edu	37	19	22271812	22271812	+	Silent	SNP	G	A	A			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr19:22271812G>A	uc010ecx.2	+	4	1429	c.1260G>A	c.(1258-1260)CAG>CAA	p.Q420Q	ZNF257_uc010ecy.2_Silent_p.Q388Q	NM_033468	NP_258429	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	420	C2H2-type 9; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_lung(12;0.0961)|Lung NSC(12;0.103)				CCCTTACTCAGCATAAGATAA	0.363													3	71	---	---	---	---	PASS
ZNF257	113835	broad.mit.edu	37	19	22271820	22271820	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr19:22271820T>G	uc010ecx.2	+	4	1437	c.1268T>G	c.(1267-1269)ATA>AGA	p.I423R	ZNF257_uc010ecy.2_Missense_Mutation_p.I391R	NM_033468	NP_258429	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	423	C2H2-type 9; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_lung(12;0.0961)|Lung NSC(12;0.103)				CAGCATAAGATAATTCATACT	0.383													3	72	---	---	---	---	PASS
ZNF492	57615	broad.mit.edu	37	19	22836805	22836805	+	Missense_Mutation	SNP	G	A	A	rs139107317	by1000genomes	TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	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													6	189	---	---	---	---	PASS
SIGLEC1	6614	broad.mit.edu	37	20	3672817	3672817	+	Missense_Mutation	SNP	G	A	A	rs149916347		TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr20:3672817G>A	uc002wja.2	-	16	4063	c.4063C>T	c.(4063-4065)CGG>TGG	p.R1355W	SIGLEC1_uc002wjb.1_5'UTR|SIGLEC1_uc002wiz.3_Missense_Mutation_p.R1355W	NM_023068	NP_075556	Q9BZZ2	SN_HUMAN	sialoadhesin precursor	1355	Ig-like C2-type 14.|Extracellular (Potential).				cell-cell adhesion|cell-matrix adhesion|endocytosis|inflammatory response	extracellular region|integral to membrane|plasma membrane	sugar binding			pancreas(4)|ovary(2)|skin(2)|breast(1)|central_nervous_system(1)	10						CTGGAGTCCCGGAAGGAGGAC	0.612													13	30	---	---	---	---	PASS
CXADR	1525	broad.mit.edu	37	21	18924180	18924180	+	Silent	SNP	G	A	A			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr21:18924180G>A	uc002yki.2	+	3	442	c.324G>A	c.(322-324)ACG>ACA	p.T108T	CXADR_uc002ykh.1_Silent_p.T108T|CXADR_uc010gld.1_Silent_p.T108T|CXADR_uc010gle.1_Intron|CXADR_uc002ykj.1_Silent_p.T81T	NM_001338	NP_001329	P78310	CXAR_HUMAN	coxsackie virus and adenovirus receptor	108	Extracellular (Potential).|Ig-like C2-type 1.				blood coagulation|cell adhesion|interspecies interaction between organisms|leukocyte migration|regulation of immune response	adherens junction|basolateral plasma membrane|extracellular region|integral to plasma membrane|nucleus|tight junction	receptor activity			ovary(1)	1				Epithelial(23;0.000206)|all cancers(11;0.000302)|OV - Ovarian serous cystadenocarcinoma(11;0.0194)|Lung(58;0.0233)|COAD - Colon adenocarcinoma(22;0.0389)|Colorectal(24;0.0483)|LUSC - Lung squamous cell carcinoma(23;0.0782)		TAAATGTAACGAATTTACAAC	0.358													20	149	---	---	---	---	PASS
FTCD	10841	broad.mit.edu	37	21	47570139	47570139	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr21:47570139G>T	uc002zif.2	-	7	844	c.800C>A	c.(799-801)TCA>TAA	p.S267*	FTCD_uc002zig.2_Nonsense_Mutation_p.S267*|FTCD_uc002zih.2_Nonsense_Mutation_p.S267*|FTCD_uc010gqf.2_Nonsense_Mutation_p.S267*|FTCD_uc010gqg.1_Nonsense_Mutation_p.S136*	NM_006657	NP_006648	O95954	FTCD_HUMAN	formiminotransferase cyclodeaminase	267	Formiminotransferase C-subdomain (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)	CACCAGCTGTGAGCCCACCAC	0.672													3	18	---	---	---	---	PASS
SDF2L1	23753	broad.mit.edu	37	22	21997279	21997279	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr22:21997279C>T	uc002zvf.2	+	2	400	c.316C>T	c.(316-318)CTC>TTC	p.L106F		NM_022044	NP_071327	Q9HCN8	SDF2L_HUMAN	stromal cell-derived factor 2-like 1 precursor	106	MIR 2.					endoplasmic reticulum lumen|membrane					0	Colorectal(54;0.105)					GGCGGTGAGGCTCACGCATGT	0.706											OREG0026342	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	2	4	---	---	---	---	PASS
PPEF1	5475	broad.mit.edu	37	X	18842131	18842131	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chrX:18842131A>G	uc004cyq.2	+	17	2073	c.1592A>G	c.(1591-1593)AAC>AGC	p.N531S	PPEF1_uc004cyp.2_Missense_Mutation_p.N503S|PPEF1_uc004cyr.2_Missense_Mutation_p.N469S|PPEF1_uc004cys.2_Missense_Mutation_p.N531S|PPEF1_uc011mja.1_Missense_Mutation_p.N466S|PPEF1_uc011mjb.1_Missense_Mutation_p.N475S	NM_006240	NP_006231	O14829	PPE1_HUMAN	protein phosphatase with EF hand calcium-binding	531					detection of stimulus involved in sensory perception|protein dephosphorylation		calcium ion binding|iron ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity				0	Hepatocellular(33;0.183)					AATCTGGTAAACATAGACCAA	0.423													97	51	---	---	---	---	PASS
FRMD7	90167	broad.mit.edu	37	X	131212512	131212512	+	Silent	SNP	A	G	G	rs5977623	byFrequency	TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chrX:131212512A>G	uc004ewn.2	-	12	1711	c.1533T>C	c.(1531-1533)ATT>ATC	p.I511I	FRMD7_uc011muy.1_Silent_p.I496I	NM_194277	NP_919253	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	511					regulation of neuron projection development	cytoskeleton|growth cone|neuronal cell body	binding			skin(1)	1	Acute lymphoblastic leukemia(192;0.000127)					CCTCTGCTCTAATTGGGGACC	0.488													5	290	---	---	---	---	PASS
PCDHGB3	56102	broad.mit.edu	37	5	140751730	140751739	+	Frame_Shift_Del	DEL	AGGTGGTGGC	-	-			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr5:140751730_140751739delAGGTGGTGGC	uc003ljw.1	+	1	1769_1778	c.1769_1778delAGGTGGTGGC	c.(1768-1779)AAGGTGGTGGCGfs	p.K590fs	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGA6_uc003ljy.1_5'Flank|PCDHGB3_uc011dat.1_Frame_Shift_Del_p.K590fs|PCDHGA6_uc011dau.1_5'Flank	NM_018924	NP_061747	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3 isoform 1	590_593	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGTGACCAAGGTGGTGGCGGTGGACGCA	0.657													81	20	---	---	---	---	
RSPO2	340419	broad.mit.edu	37	8	109001381	109001383	+	In_Frame_Del	DEL	GAA	-	-			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr8:109001381_109001383delGAA	uc003yms.2	-	3	842_844	c.184_186delTTC	c.(184-186)TTCdel	p.F62del	RSPO2_uc003ymq.2_5'UTR|RSPO2_uc003ymr.2_Intron	NM_178565	NP_848660	Q6UXX9	RSPO2_HUMAN	R-spondin family, member 2 precursor	62					Wnt receptor signaling pathway	extracellular region	heparin binding			skin(3)|ovary(2)|pancreas(1)|lung(1)	7			OV - Ovarian serous cystadenocarcinoma(57;1.55e-09)			CTCTTCGAAGGAAGAAGAACAAC	0.468													108	47	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68413605	68413606	+	RNA	DEL	CT	-	-			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr9:68413605_68413606delCT	uc004aex.2	+	1		c.160_161delCT								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		TTTGCTGAAACTCTGGGGTTGA	0.609													6	4	---	---	---	---	
B3GNT4	79369	broad.mit.edu	37	12	122691205	122691209	+	Frame_Shift_Del	DEL	CTATC	-	-			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr12:122691205_122691209delCTATC	uc001ubx.2	+	3	625_629	c.407_411delCTATC	c.(406-411)GCTATCfs	p.A136fs	B3GNT4_uc001uby.2_Frame_Shift_Del_p.A111fs	NM_030765	NP_110392	Q9C0J1	B3GN4_HUMAN	UDP-GlcNAc:betaGal	136_137	Lumenal (Potential).				protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity			ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000297)|Epithelial(86;0.000497)|BRCA - Breast invasive adenocarcinoma(302;0.222)		CGACGTGCGGCTATCCGCAGCACGT	0.629													169	9	---	---	---	---	
B3GNT4	79369	broad.mit.edu	37	12	122691220	122691221	+	Frame_Shift_Ins	INS	-	CT	CT			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chr12:122691220_122691221insCT	uc001ubx.2	+	3	640_641	c.422_423insCT	c.(421-423)TGGfs	p.W141fs	B3GNT4_uc001uby.2_Frame_Shift_Ins_p.W116fs	NM_030765	NP_110392	Q9C0J1	B3GN4_HUMAN	UDP-GlcNAc:betaGal	141	Lumenal (Potential).				protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity			ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000297)|Epithelial(86;0.000497)|BRCA - Breast invasive adenocarcinoma(302;0.222)		CGCAGCACGTGGGGCAGGGTGG	0.644													133	22	---	---	---	---	
NUDT11	55190	broad.mit.edu	37	X	51239296	51239309	+	Translation_Start_Site	DEL	TCCTCGAGGCAGCC	-	-			TCGA-CH-5791-01A-11D-1576-08	TCGA-CH-5791-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	3f104f5f-f816-42cf-bdf5-65cbf9d7a5d4	8b462258-f66d-4893-a6f8-245278d1ce9d	g.chrX:51239296_51239309delTCCTCGAGGCAGCC	uc010njt.2	-	1						NM_018159	NP_060629	Q96G61	NUD11_HUMAN	nudix-type motif 11							cytoplasm	diphosphoinositol-polyphosphate diphosphatase activity|metal ion binding				0	Ovarian(276;0.236)					TTGCACTTCATCCTCGAGGCAGCCTCCTCGAGGC	0.584										HNSCC(48;0.14)			7	4	---	---	---	---	
