Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
DVL1	1855	broad.mit.edu	37	1	1274966	1274966	+	Silent	SNP	T	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1274966T>C	uc001aer.3	-	10	1097	c.1050A>G	c.(1048-1050)CCA>CCG	p.P350P	DVL1_uc002quu.2_Silent_p.P67P|DVL1_uc009vka.2_Silent_p.P33P|DVL1_uc001aeu.1_Missense_Mutation_p.H37R	NM_004421	NP_004412	O14640	DVL1_HUMAN	dishevelled 1	350					canonical Wnt receptor signaling pathway|dendrite morphogenesis|intracellular signal transduction|negative regulation of protein binding|negative regulation of protein kinase activity|neural tube development|neuromuscular junction development|neurotransmitter secretion|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway|protein localization to nucleus|receptor clustering|transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, planar cell polarity pathway	cytoplasmic membrane-bounded vesicle|cytosol|plasma membrane|synapse|synaptosome	frizzled binding|identical protein binding|protein kinase binding|signal transducer activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		ACTCACCCCGTGGGACGGTGA	0.687													7	14	---	---	---	---	PASS
AJAP1	55966	broad.mit.edu	37	1	4772101	4772101	+	Silent	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4772101G>A	uc001alm.1	+	2	552	c.171G>A	c.(169-171)CCG>CCA	p.P57P	AJAP1_uc001aln.2_Silent_p.P57P	NM_001042478	NP_001035943	Q9UKB5	AJAP1_HUMAN	adherens junction associated protein 1	57	Extracellular (Potential).				cell adhesion	adherens junction|apical plasma membrane|basolateral plasma membrane|integral to membrane				lung(1)	1	all_cancers(77;0.071)|Ovarian(185;0.0721)	all_cancers(23;1.77e-36)|all_epithelial(116;1.26e-21)|all_lung(118;3.51e-08)|Lung NSC(185;3.47e-06)|all_neural(13;8.84e-06)|all_hematologic(16;7.61e-05)|Breast(487;0.000507)|Renal(390;0.0007)|Colorectal(325;0.00117)|Hepatocellular(190;0.0071)|Glioma(11;0.0155)|Myeloproliferative disorder(586;0.0258)|Ovarian(437;0.0409)|Lung SC(97;0.133)|Medulloblastoma(700;0.215)		Epithelial(90;3.89e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.97e-19)|GBM - Glioblastoma multiforme(42;3.71e-19)|Colorectal(212;4.57e-06)|COAD - Colon adenocarcinoma(227;0.00019)|Kidney(185;0.000969)|BRCA - Breast invasive adenocarcinoma(365;0.00122)|STAD - Stomach adenocarcinoma(132;0.00578)|KIRC - Kidney renal clear cell carcinoma(229;0.0126)|READ - Rectum adenocarcinoma(331;0.0689)		cgcggtcgccgccccggccgc	0.592													20	30	---	---	---	---	PASS
GPR153	387509	broad.mit.edu	37	1	6311556	6311556	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6311556G>A	uc001amp.1	-	4	1081	c.821C>T	c.(820-822)TCA>TTA	p.S274L	GPR153_uc001amo.1_5'Flank	NM_207370	NP_997253	Q6NV75	GP153_HUMAN	G protein-coupled receptor 153	274	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0	Ovarian(185;0.0634)	all_cancers(23;8.07e-33)|all_epithelial(116;4.45e-18)|all_lung(118;1.09e-06)|all_neural(13;3.68e-06)|Lung NSC(185;1.52e-05)|all_hematologic(16;2.39e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00475)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;1.91e-37)|GBM - Glioblastoma multiforme(13;4.87e-29)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;1.33e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.246)		CCAGGGCGCTGAGGCGTCGGC	0.697													22	34	---	---	---	---	PASS
CROCC	9696	broad.mit.edu	37	1	17271961	17271961	+	Missense_Mutation	SNP	A	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17271961A>G	uc001azt.2	+	15	2065	c.1996A>G	c.(1996-1998)AGA>GGA	p.R666G	CROCC_uc009voz.1_Missense_Mutation_p.R429G|CROCC_uc001azu.2_Translation_Start_Site	NM_014675	NP_055490	Q5TZA2	CROCC_HUMAN	ciliary rootlet coiled-coil	666	Potential.				cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		CCACAGCCATAGACAACTAGA	0.642													7	43	---	---	---	---	PASS
KLHDC7A	127707	broad.mit.edu	37	1	18808885	18808885	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18808885C>G	uc001bax.2	+	1	1462	c.1410C>G	c.(1408-1410)GAC>GAG	p.D470E	KLHDC7A_uc009vpg.2_Missense_Mutation_p.D252E	NM_152375	NP_689588	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	470						integral to membrane				ovary(2)|upper_aerodigestive_tract(1)	3		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GCAGCCCGGACATCTACGGGT	0.657													60	98	---	---	---	---	PASS
EPHA8	2046	broad.mit.edu	37	1	22913059	22913059	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22913059G>A	uc001bfx.1	+	4	1035	c.910G>A	c.(910-912)GCC>ACC	p.A304T	EPHA8_uc001bfw.2_Missense_Mutation_p.A304T	NM_020526	NP_065387	P29322	EPHA8_HUMAN	ephrin receptor EphA8 isoform 1 precursor	304	Extracellular (Potential).|Cys-rich.					integral to plasma membrane	ATP binding|ephrin receptor activity			central_nervous_system(5)|breast(3)|lung(2)|large_intestine(1)|stomach(1)|skin(1)	13		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		AGCTCCAGCCGCCCAAGCCTG	0.657													5	69	---	---	---	---	PASS
MYOM3	127294	broad.mit.edu	37	1	24390025	24390025	+	Intron	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24390025C>T	uc001bin.3	-						MYOM3_uc001bil.3_Intron|MYOM3_uc001bim.3_Intron	NM_152372	NP_689585	Q5VTT5	MYOM3_HUMAN	myomesin family, member 3											skin(2)|ovary(1)	3		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		CCAGGGCTGGCGGGAAACAGA	0.607													4	154	---	---	---	---	PASS
RHCE	6006	broad.mit.edu	37	1	25717382	25717382	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25717382C>A	uc001bkf.2	-	5	745	c.659G>T	c.(658-660)TGG>TTG	p.W220L	RHCE_uc001bkg.2_Missense_Mutation_p.W220L|RHCE_uc001bkh.2_Intron|RHCE_uc001bki.2_Intron|RHCE_uc001bkj.2_Missense_Mutation_p.W204L	NM_020485	NP_065231	P18577	RHCE_HUMAN	Rhesus blood group, CcEe antigens isoform 1	220	Helical; (Potential).					integral to plasma membrane					0		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0426)|OV - Ovarian serous cystadenocarcinoma(117;2.12e-27)|Colorectal(126;3.16e-08)|COAD - Colon adenocarcinoma(152;1.72e-06)|STAD - Stomach adenocarcinoma(196;0.00035)|KIRC - Kidney renal clear cell carcinoma(1967;0.000769)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|GBM - Glioblastoma multiforme(114;0.00458)|READ - Rectum adenocarcinoma(331;0.0649)		GACACTTGGCCAGAACATCCA	0.537													123	254	---	---	---	---	PASS
C1orf91	56063	broad.mit.edu	37	1	32686721	32686721	+	Intron	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32686721C>A	uc009vub.1	-						C1orf91_uc001buo.3_Intron|C1orf91_uc001bup.3_Intron|C1orf91_uc010oha.1_Intron|C1orf91_uc001buq.3_Intron|EIF3I_uc001bur.3_5'Flank|EIF3I_uc009vuc.2_5'Flank|EIF3I_uc001bus.2_5'Flank			Q8WY98	TM234_HUMAN	RecName: Full=UPF0546 membrane protein C1orf91;							integral to membrane					0		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CAGTTCCAAGCCAGGACCCAC	0.547													14	38	---	---	---	---	PASS
MACF1	23499	broad.mit.edu	37	1	39818716	39818716	+	Missense_Mutation	SNP	A	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39818716A>G	uc010oiu.1	+	8	6688	c.6557A>G	c.(6556-6558)AAG>AGG	p.K2186R	MACF1_uc010ois.1_Missense_Mutation_p.K1684R|MACF1_uc001cda.1_Missense_Mutation_p.K1592R|MACF1_uc001cdc.1_Missense_Mutation_p.K771R|MACF1_uc001cdb.1_Missense_Mutation_p.K771R	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	3751					cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			AACAAGAAGAAGATCGATGCT	0.488													56	91	---	---	---	---	PASS
HIVEP3	59269	broad.mit.edu	37	1	42041309	42041309	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42041309C>A	uc001cgz.3	-	5	6326	c.5113G>T	c.(5113-5115)GTG>TTG	p.V1705L	HIVEP3_uc001cha.3_Missense_Mutation_p.V1705L|HIVEP3_uc001cgy.2_RNA	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer	1705					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				TCCTTCTCCACTCTAGCTAGA	0.552													104	212	---	---	---	---	PASS
MYSM1	114803	broad.mit.edu	37	1	59147875	59147875	+	Missense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59147875G>C	uc009wab.1	-	8	864	c.841C>G	c.(841-843)CAA>GAA	p.Q281E	MYSM1_uc001czc.2_RNA	NM_001085487	NP_001078956	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1	281					histone deubiquitination|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin remodeling complex	DNA binding|histone binding|metal ion binding|metallopeptidase activity|transcription coactivator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(1)	1	all_cancers(7;9.36e-06)					TTTTCATTTTGAAGACAGCCC	0.368													26	552	---	---	---	---	PASS
ANGPTL3	27329	broad.mit.edu	37	1	63066783	63066783	+	Nonsense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63066783G>T	uc001das.1	+	3	688	c.637G>T	c.(637-639)GAA>TAA	p.E213*	DOCK7_uc001dan.2_Intron|DOCK7_uc001dao.2_Intron|DOCK7_uc001dap.2_Intron|DOCK7_uc001daq.2_Intron|DOCK7_uc009wah.1_Intron	NM_014495	NP_055310	Q9Y5C1	ANGL3_HUMAN	angiopoietin-like 3 precursor	213					acylglycerol homeostasis|artery morphogenesis|cell-matrix adhesion|cholesterol homeostasis|cholesterol metabolic process|fatty acid metabolic process|glycerol metabolic process|integrin-mediated signaling pathway|lipid storage|negative regulation of lipoprotein lipase activity|negative regulation of phospholipase activity|phospholipid catabolic process|phospholipid homeostasis|positive regulation of angiogenesis|positive regulation of cell migration|positive regulation of lipid catabolic process|triglyceride homeostasis	extracellular space	cell surface binding|growth factor activity|integrin binding|phospholipase inhibitor activity				0						AGAACCCACAGAAATTTCTCT	0.338													54	98	---	---	---	---	PASS
SGIP1	84251	broad.mit.edu	37	1	67142743	67142743	+	Nonsense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67142743G>T	uc001dcr.2	+	13	920	c.703G>T	c.(703-705)GAG>TAG	p.E235*	SGIP1_uc010opd.1_Nonsense_Mutation_p.E2*|SGIP1_uc001dcs.2_Nonsense_Mutation_p.E2*|SGIP1_uc001dct.2_Nonsense_Mutation_p.E2*|uc010ope.1_5'Flank|SGIP1_uc009wat.2_Nonsense_Mutation_p.E2*	NM_032291	NP_115667	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting	235	Pro-rich.				positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3						TCCAAGCATGGAGTCGCCAAA	0.398													107	185	---	---	---	---	PASS
MIER1	57708	broad.mit.edu	37	1	67411870	67411870	+	Silent	SNP	A	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67411870A>T	uc001dde.2	+	4	365	c.231A>T	c.(229-231)CCA>CCT	p.P77P	MIER1_uc001dda.3_Missense_Mutation_p.H102L|MIER1_uc010opf.1_Silent_p.P41P|MIER1_uc009way.2_Silent_p.P41P|MIER1_uc001ddc.2_Silent_p.P77P|MIER1_uc001ddh.2_Intron|MIER1_uc001ddf.2_Silent_p.P41P|MIER1_uc001ddg.2_5'UTR|MIER1_uc010opg.1_Silent_p.P41P|MIER1_uc001ddj.1_Silent_p.P24P|MIER1_uc001ddi.2_Silent_p.P24P	NM_001077700	NP_001071168	Q8N108	MIER1_HUMAN	mesoderm induction early response 1 isoform b	48					positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity	p.P24P(1)		ovary(1)	1						AATTTGATCCATCAGCTGACA	0.343													116	201	---	---	---	---	PASS
SLC44A5	204962	broad.mit.edu	37	1	75672357	75672357	+	Missense_Mutation	SNP	C	G	G	rs78856933	byFrequency	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75672357C>G	uc001dgu.2	-	24	2239	c.2095G>C	c.(2095-2097)GTA>CTA	p.V699L	SLC44A5_uc001dgt.2_Intron|SLC44A5_uc001dgs.2_Intron|SLC44A5_uc001dgr.2_Intron|SLC44A5_uc010oqz.1_Intron|SLC44A5_uc010ora.1_Missense_Mutation_p.V693L|SLC44A5_uc010orb.1_Missense_Mutation_p.V569L	NM_152697	NP_689910	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5 isoform A	699	Cytoplasmic (Potential).					integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4						TTAGGGGTTACGAAGTAGGGT	0.413													164	376	---	---	---	---	PASS
ST6GALNAC5	81849	broad.mit.edu	37	1	77510188	77510188	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77510188C>A	uc001dhi.2	+	3	736	c.561C>A	c.(559-561)AAC>AAA	p.N187K	ST6GALNAC5_uc010ori.1_Intron|ST6GALNAC5_uc009wbw.2_RNA	NM_030965	NP_112227	Q9BVH7	SIA7E_HUMAN	sialyltransferase 7E	187	Lumenal (Potential).				protein glycosylation	integral to Golgi membrane	sialyltransferase activity			pancreas(1)|skin(1)	2						AGGTCTACAACAACCTGCATC	0.597													84	157	---	---	---	---	PASS
AK5	26289	broad.mit.edu	37	1	77763405	77763405	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77763405G>T	uc001dhn.2	+	4	834	c.577G>T	c.(577-579)GCC>TCC	p.A193S	AK5_uc001dho.2_Missense_Mutation_p.A167S|AK5_uc001dhm.1_Missense_Mutation_p.A169S	NM_174858	NP_777283	Q9Y6K8	KAD5_HUMAN	adenylate kinase 5 isoform 1	193					ADP biosynthetic process|ATP metabolic process|dADP biosynthetic process|nucleobase, nucleoside and nucleotide interconversion|pyrimidine ribonucleotide biosynthetic process|signal transduction	centrosome|cytosol	adenylate kinase activity|ATP binding|cAMP-dependent protein kinase regulator activity|nucleoside kinase activity			skin(1)	1						TGGAGAATTGGCCCCACAGGT	0.353													82	158	---	---	---	---	PASS
NEXN	91624	broad.mit.edu	37	1	78392291	78392291	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78392291G>T	uc001dic.3	+	7	979	c.682G>T	c.(682-684)GTT>TTT	p.V228F	NEXN_uc001dia.3_Missense_Mutation_p.V214F|NEXN_uc009wcb.1_Missense_Mutation_p.V150F|NEXN_uc001dib.3_Missense_Mutation_p.V164F|NEXN_uc001did.1_Missense_Mutation_p.V138F|NEXN_uc001dif.1_Missense_Mutation_p.V120F	NM_144573	NP_653174	Q0ZGT2	NEXN_HUMAN	nexilin (F actin binding protein)	228	Glu-rich.				regulation of cell migration|regulation of cytoskeleton organization	cytoskeleton|Z disc	actin filament binding|structural constituent of muscle			ovary(2)	2				Colorectal(170;0.114)		TCTTTCATTAGTTATGGTAAA	0.333													11	221	---	---	---	---	PASS
CTBS	1486	broad.mit.edu	37	1	85028993	85028993	+	Missense_Mutation	SNP	T	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85028993T>G	uc001dka.2	-	6	969	c.904A>C	c.(904-906)ATT>CTT	p.I302L	SPATA1_uc001djz.1_Intron|CTBS_uc001dkc.2_Missense_Mutation_p.I211L|CTBS_uc001dkd.2_Missense_Mutation_p.I96L|CTBS_uc001dkb.2_Missense_Mutation_p.I96L	NM_004388	NP_004379	Q01459	DIAC_HUMAN	chitobiase, di-N-acetyl- precursor	302						lysosome	cation binding				0				all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)		TTTCCAGAAATAGAACTATTT	0.393													37	59	---	---	---	---	PASS
SLC30A7	148867	broad.mit.edu	37	1	101377756	101377756	+	Missense_Mutation	SNP	T	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101377756T>G	uc001dtn.2	+	5	660	c.473T>G	c.(472-474)GTT>GGT	p.V158G	SLC30A7_uc001dto.2_Missense_Mutation_p.V158G	NM_001144884	NP_001138356	Q8NEW0	ZNT7_HUMAN	zinc transporter like 2	158	Helical; (Potential).				zinc ion transport	Golgi apparatus|integral to membrane	cation transmembrane transporter activity|protein binding				0		all_epithelial(167;0.000445)|all_lung(203;0.00645)|Lung NSC(277;0.0119)		Epithelial(280;0.0437)|all cancers(265;0.0498)|COAD - Colon adenocarcinoma(174;0.162)|Colorectal(144;0.19)|Lung(183;0.201)		GGAATATTTGTTTTCAAACAT	0.388													288	538	---	---	---	---	PASS
COL11A1	1301	broad.mit.edu	37	1	103345240	103345240	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103345240G>T	uc001dul.2	-	66	5591	c.5273C>A	c.(5272-5274)GCG>GAG	p.A1758E	COL11A1_uc001duk.2_Missense_Mutation_p.A954E|COL11A1_uc001dum.2_Missense_Mutation_p.A1770E|COL11A1_uc001dun.2_Missense_Mutation_p.A1719E|COL11A1_uc009weh.2_Missense_Mutation_p.A1642E	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A	1758	Fibrillar collagen NC1.			A -> T (in Ref. 1; AAA51891).	collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging	p.A1770V(1)		ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		TATACTCACCGCACAACCATC	0.428													66	128	---	---	---	---	PASS
COL11A1	1301	broad.mit.edu	37	1	103481252	103481252	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103481252C>A	uc001dul.2	-	12	1778	c.1460G>T	c.(1459-1461)GGT>GTT	p.G487V	COL11A1_uc001duk.2_5'UTR|COL11A1_uc001dum.2_Missense_Mutation_p.G499V|COL11A1_uc001dun.2_Missense_Mutation_p.G448V|COL11A1_uc009weh.2_Missense_Mutation_p.G371V	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A	487	Triple-helical region (interrupted).				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		ACCAGGAGGACCAGGTAGACC	0.353													7	17	---	---	---	---	PASS
TMEM167B	56900	broad.mit.edu	37	1	109637043	109637043	+	Silent	SNP	T	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109637043T>C	uc001dwn.2	+	3	239	c.147T>C	c.(145-147)GCT>GCC	p.A49A	TMEM167B_uc009weu.2_RNA	NM_020141	NP_064526	Q9NRX6	KISHB_HUMAN	transmembrane protein 167B precursor	49	Extracellular (Potential).					Golgi membrane|integral to membrane					0						TGCTAGCCGCTGTGATTGGAA	0.453													10	270	---	---	---	---	PASS
CD101	9398	broad.mit.edu	37	1	117561007	117561007	+	Silent	SNP	G	T	T	rs79996128	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117561007G>T	uc010oxb.1	+	6	1900	c.1842G>T	c.(1840-1842)ACG>ACT	p.T614T	CD101_uc009whd.2_Silent_p.T614T|CD101_uc010oxc.1_Silent_p.T614T|CD101_uc010oxd.1_Silent_p.T552T	NM_004258	NP_004249	Q93033	IGSF2_HUMAN	immunoglobulin superfamily, member 2 precursor	614	Extracellular (Potential).|Ig-like C2-type 5.				cell surface receptor linked signaling pathway	integral to membrane|plasma membrane	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4						AAAAGAAGACGAAAGTGTCGC	0.453													4	401	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144917580	144917580	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144917580C>G	uc001elw.3	-	12	1815	c.1524G>C	c.(1522-1524)CAG>CAC	p.Q508H	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Missense_Mutation_p.Q574H|PDE4DIP_uc001emc.1_Missense_Mutation_p.Q508H|PDE4DIP_uc001emd.1_Missense_Mutation_p.Q508H|PDE4DIP_uc001emb.1_Missense_Mutation_p.Q671H|PDE4DIP_uc001eme.1_Missense_Mutation_p.Q37H|PDE4DIP_uc001emf.1_Missense_Mutation_p.Q295H	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	508	Potential.				cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CAAGACGAAGCTGGCGCAGTT	0.438			T	PDGFRB	MPD								185	723	---	---	---	---	PASS
ITGA10	8515	broad.mit.edu	37	1	145534931	145534931	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145534931G>A	uc001eoa.2	+	15	1910	c.1834G>A	c.(1834-1836)GGC>AGC	p.G612S	NBPF10_uc001emp.3_Intron|ITGA10_uc010oyv.1_Missense_Mutation_p.G481S|ITGA10_uc009wiw.2_Missense_Mutation_p.G469S|ITGA10_uc010oyw.1_Missense_Mutation_p.G557S	NM_003637	NP_003628	O75578	ITA10_HUMAN	integrin, alpha 10 precursor	612	Extracellular (Potential).|FG-GAP 7.				cell-matrix adhesion|integrin-mediated signaling pathway	integrin complex	collagen binding|receptor activity			lung(2)|ovary(2)|kidney(2)|large_intestine(1)|skin(1)	8	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CAGCTACTTTGGCCGAAGTGT	0.582													93	195	---	---	---	---	PASS
HRNR	388697	broad.mit.edu	37	1	152191689	152191689	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152191689G>A	uc001ezt.1	-	3	2492	c.2416C>T	c.(2416-2418)CAT>TAT	p.H806Y		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	806	8.				keratinization		calcium ion binding|protein binding			skin(2)|ovary(1)	3	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GACTCATAATGGCCACAGCTG	0.582													29	75	---	---	---	---	PASS
CD1B	910	broad.mit.edu	37	1	158300604	158300604	+	Missense_Mutation	SNP	C	G	G	rs62642468	byFrequency	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158300604C>G	uc001frx.2	-	2	418	c.310G>C	c.(310-312)GGT>CGT	p.G104R	CD1B_uc001frw.2_5'UTR|CD1B_uc010pic.1_Missense_Mutation_p.G104R	NM_001764	NP_001755	P29016	CD1B_HUMAN	CD1B antigen precursor	104	Extracellular (Potential).				antigen processing and presentation|immune response	endosome membrane|integral to membrane|lysosomal membrane|plasma membrane	protein binding			ovary(2)	2	all_hematologic(112;0.0378)					TGGAAATCACCGGCAAAGTCT	0.433													9	777	---	---	---	---	PASS
RGS5	8490	broad.mit.edu	37	1	163117134	163117134	+	Nonstop_Mutation	SNP	A	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163117134A>G	uc001gcn.2	-	5	791	c.544T>C	c.(544-546)TAG>CAG	p.*182Q	RGS5_uc009wvb.2_RNA	NM_003617	NP_003608	O15539	RGS5_HUMAN	regulator of G-protein signalling 5	182					negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity				0			LUSC - Lung squamous cell carcinoma(543;0.187)			CTAAATTACTACTTGATTAAC	0.428													68	100	---	---	---	---	PASS
RXRG	6258	broad.mit.edu	37	1	165386447	165386447	+	Nonsense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165386447G>T	uc001gda.2	-	4	753	c.453C>A	c.(451-453)TAC>TAA	p.Y151*		NM_006917	NP_008848	P48443	RXRG_HUMAN	retinoid X receptor, gamma isoform a	151	NR C4-type.|Nuclear receptor.				regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding				0	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tretinoin(DB00755)	TGTATACCCCGTAGTGCTTTC	0.428													151	214	---	---	---	---	PASS
GPA33	10223	broad.mit.edu	37	1	167038337	167038337	+	Silent	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167038337G>A	uc001gea.1	-	3	581	c.237C>T	c.(235-237)TAC>TAT	p.Y79Y		NM_005814	NP_005805	Q99795	GPA33_HUMAN	transmembrane glycoprotein A33 precursor	79	Ig-like V-type.|Extracellular (Potential).					integral to plasma membrane	receptor activity				0						CACCATGGATGTAGTTTTTGT	0.507													41	96	---	---	---	---	PASS
TNR	7143	broad.mit.edu	37	1	175324640	175324640	+	Missense_Mutation	SNP	T	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175324640T>G	uc001gkp.1	-	15	3329	c.3248A>C	c.(3247-3249)AAG>ACG	p.K1083T	TNR_uc009wwu.1_Missense_Mutation_p.K1083T	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor	1083	Fibronectin type-III 9.				axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					AAATCTCACCTTGCGGCTTCC	0.502													74	131	---	---	---	---	PASS
DHX9	1660	broad.mit.edu	37	1	182846038	182846038	+	Missense_Mutation	SNP	A	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182846038A>G	uc001gpr.2	+	19	2361	c.2198A>G	c.(2197-2199)AAG>AGG	p.K733R	DHX9_uc001gps.2_Missense_Mutation_p.K519R|DHX9_uc001gpt.2_5'Flank	NM_001357	NP_001348	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 9	733	Helicase C-terminal.				CRD-mediated mRNA stabilization|nuclear mRNA splicing, via spliceosome	centrosome|CRD-mediated mRNA stability complex|nucleolus|nucleoplasm|ribonucleoprotein complex	ATP binding|ATP-dependent DNA helicase activity|ATP-dependent RNA helicase activity|DNA binding|double-stranded RNA binding|protein binding			ovary(2)	2						GACTCCTGCAAGTAAGTTACT	0.348													44	83	---	---	---	---	PASS
CDC73	79577	broad.mit.edu	37	1	193172942	193172942	+	Silent	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193172942G>T	uc001gtb.2	+	11	1233	c.990G>T	c.(988-990)CGG>CGT	p.R330R		NM_024529	NP_078805	Q6P1J9	CDC73_HUMAN	parafibromin	330					cell cycle|histone H2B ubiquitination|histone monoubiquitination|transcription, DNA-dependent	Cdc73/Paf1 complex	protein binding			parathyroid(46)|ovary(1)|breast(1)|pancreas(1)	49						CATCTGCCCGGAAGACTCAGA	0.343									Hyperparathyroidism_Familial_Isolated|Hyperparathyroidism-Jaw_Tumor_Syndrome				23	111	---	---	---	---	PASS
CFHR3	10878	broad.mit.edu	37	1	196748446	196748446	+	Silent	SNP	T	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196748446T>C	uc001gtl.2	+	2	300	c.213T>C	c.(211-213)CAT>CAC	p.H71H	CFHR3_uc001gtk.2_Silent_p.H71H|CFHR3_uc010poy.1_Silent_p.H71H|CFHR1_uc001gtm.2_Silent_p.H34H	NM_021023	NP_066303	Q02985	FHR3_HUMAN	complement factor H-related 3 precursor	71	Sushi 1.					extracellular space					0						ATTACATTCATTGCACACAAA	0.383													116	164	---	---	---	---	PASS
LAMB3	3914	broad.mit.edu	37	1	209791299	209791299	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209791299G>T	uc001hhg.2	-	19	3394	c.3004C>A	c.(3004-3006)CAA>AAA	p.Q1002K	LAMB3_uc009xco.2_Missense_Mutation_p.Q1002K|LAMB3_uc001hhh.2_Missense_Mutation_p.Q1002K	NM_001017402	NP_001017402	Q13751	LAMB3_HUMAN	laminin, beta 3 precursor	1002	Domain I.|Potential.				cell adhesion|epidermis development|hemidesmosome assembly		structural molecule activity			central_nervous_system(2)|skin(2)|large_intestine(1)|ovary(1)	6				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		CTGGTGCCTTGCATGGTGTCC	0.587													39	68	---	---	---	---	PASS
PROX1	5629	broad.mit.edu	37	1	214171384	214171384	+	Silent	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214171384C>T	uc001hkh.2	+	2	1778	c.1506C>T	c.(1504-1506)GGC>GGT	p.G502G	PROX1_uc001hkg.1_Silent_p.G502G	NM_002763	NP_002754	Q92786	PROX1_HUMAN	prospero homeobox 1	502					aorta smooth muscle tissue morphogenesis|atrial cardiac muscle tissue morphogenesis|brain development|dorsal spinal cord development|embryonic retina morphogenesis in camera-type eye|endocardium formation|hepatocyte differentiation|kidney development|lens fiber cell morphogenesis|lung development|lymphangiogenesis|negative regulation of bile acid biosynthetic process|negative regulation of cell proliferation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of viral genome replication|neural tube development|olfactory placode formation|optic placode formation involved in camera-type eye formation|otic placode formation|pancreas development|positive regulation of cyclin-dependent protein kinase activity|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of heart growth|positive regulation of S phase of mitotic cell cycle|positive regulation of sarcomere organization|positive regulation of transcription, DNA-dependent|regulation of transcription involved in lymphatic endothelial cell fate commitment|skeletal muscle thin filament assembly|venous blood vessel morphogenesis|ventricular cardiac muscle tissue morphogenesis|ventricular cardiac myofibril development|ventricular septum morphogenesis	cytoplasm|nucleus	DBD domain binding|LBD domain binding|ligand-dependent nuclear receptor binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription corepressor activity|transcription regulatory region DNA binding			ovary(3)|lung(1)|central_nervous_system(1)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219)		CTCCCTCCGGCTCCTTCTCTG	0.562													16	325	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	216074145	216074145	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216074145C>A	uc001hku.1	-	39	7790	c.7403G>T	c.(7402-7404)AGA>ATA	p.R2468I		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	2468	Extracellular (Potential).|Fibronectin type-III 11.				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GAGTTGGTATCTGGGAGAGCC	0.502										HNSCC(13;0.011)			96	170	---	---	---	---	PASS
C1orf69	200205	broad.mit.edu	37	1	228362383	228362383	+	Intron	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228362383C>G	uc001hsl.3	+						C1orf69_uc010pvw.1_Intron	NM_001010867	NP_001010867	Q5T440	CAF17_HUMAN	hypothetical protein LOC200205 precursor						glycine catabolic process|heme biosynthetic process	mitochondrion	aminomethyltransferase activity				0		Prostate(94;0.0405)				CCCTGCCTCTCTCCCTGCAGG	0.647													5	11	---	---	---	---	PASS
SLC35F3	148641	broad.mit.edu	37	1	234445022	234445022	+	Silent	SNP	T	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234445022T>C	uc001hwa.1	+	3	805	c.577T>C	c.(577-579)TTG>CTG	p.L193L	SLC35F3_uc001hvy.1_Silent_p.L262L	NM_173508	NP_775779	Q8IY50	S35F3_HUMAN	solute carrier family 35, member F3	193	Helical; (Potential).				transport	integral to membrane				ovary(2)	2	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)			TTTTGTGTTCTTGCTCTCATG	0.428													75	139	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237961380	237961380	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237961380G>T	uc001hyl.1	+	97	14120	c.14000G>T	c.(13999-14001)AGT>ATT	p.S4667I	RYR2_uc010pyb.1_Missense_Mutation_p.S100I	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	4667					cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GACAGAATCAGTGAATTACTT	0.413													15	34	---	---	---	---	PASS
OR6F1	343169	broad.mit.edu	37	1	247875538	247875538	+	Missense_Mutation	SNP	T	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247875538T>C	uc001idj.1	-	1	520	c.520A>G	c.(520-522)ATC>GTC	p.I174V		NM_001005286	NP_001005286	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F,	174	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0168)			AAGTGGTTGATGGCACGGGGG	0.587													100	198	---	---	---	---	PASS
OR2AK2	391191	broad.mit.edu	37	1	248129609	248129609	+	Missense_Mutation	SNP	T	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248129609T>A	uc010pzd.1	+	1	976	c.976T>A	c.(976-978)TGT>AGT	p.C326S	OR2L13_uc001ids.2_Intron	NM_001004491	NP_001004491	Q8NG84	O2AK2_HUMAN	olfactory receptor, family 2, subfamily AK,	326	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			TTGGATATGCTGTAGAAAATA	0.378													83	194	---	---	---	---	PASS
OR2T4	127074	broad.mit.edu	37	1	248525364	248525364	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248525364C>A	uc001ieh.1	+	1	482	c.482C>A	c.(481-483)CCT>CAT	p.P161H		NM_001004696	NP_001004696	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T,	161	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ATCTGCCATCCTCTCCGTTAC	0.527													7	561	---	---	---	---	PASS
PXDN	7837	broad.mit.edu	37	2	1680797	1680797	+	Silent	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1680797G>A	uc002qxa.2	-	8	814	c.750C>T	c.(748-750)TCC>TCT	p.S250S	PXDN_uc002qxb.1_Silent_p.S250S|PXDN_uc002qxc.1_Silent_p.S67S	NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor	250	Ig-like C2-type 1.				extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity	p.S250S(1)		pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		CCTGGGGCTCGGAGGTGATCC	0.517													23	33	---	---	---	---	PASS
MYT1L	23040	broad.mit.edu	37	2	1812863	1812863	+	Missense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1812863G>C	uc002qxe.2	-	22	3984	c.3157C>G	c.(3157-3159)CAG>GAG	p.Q1053E	MYT1L_uc002qxd.2_Missense_Mutation_p.Q1051E|MYT1L_uc010ewk.2_Missense_Mutation_p.Q49E	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	1053					cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		CTGGCCCGCTGTTTGATGGTC	0.612													86	141	---	---	---	---	PASS
MYT1L	23040	broad.mit.edu	37	2	1915841	1915841	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1915841C>A	uc002qxe.2	-	12	2487	c.1660G>T	c.(1660-1662)GGC>TGC	p.G554C	MYT1L_uc002qxd.2_Missense_Mutation_p.G552C|MYT1L_uc010ewl.1_RNA	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	554	C2HC-type 3.				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		CCCGTGCAGCCCGGAGTGGGG	0.602													16	22	---	---	---	---	PASS
CMPK2	129607	broad.mit.edu	37	2	6991813	6991813	+	Missense_Mutation	SNP	A	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6991813A>T	uc002qyo.2	-	4	1103	c.994T>A	c.(994-996)TAC>AAC	p.Y332N	CMPK2_uc002qyn.1_RNA|CMPK2_uc010yis.1_Intron|CMPK2_uc010ewv.2_Missense_Mutation_p.Y332N	NM_207315	NP_997198	Q5EBM0	CMPK2_HUMAN	UMP-CMP kinase 2 precursor	332					dTDP biosynthetic process	mitochondrion	ATP binding|cytidylate kinase activity|thymidylate kinase activity|UMP kinase activity				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CTGTGCCAGTACCTGAGAAGG	0.552													32	76	---	---	---	---	PASS
KIDINS220	57498	broad.mit.edu	37	2	8871992	8871992	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8871992C>A	uc002qzc.2	-	30	4356	c.4174G>T	c.(4174-4176)GCT>TCT	p.A1392S	KIDINS220_uc010yiv.1_Intron|KIDINS220_uc002qzd.2_Missense_Mutation_p.A1293S|KIDINS220_uc002qzb.2_Missense_Mutation_p.A246S	NM_020738	NP_065789	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate of 220 kDa	1392	Cytoplasmic (Potential).				activation of MAPKK activity|nerve growth factor receptor signaling pathway	cytosol|integral to membrane				ovary(3)|central_nervous_system(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GACATCTGAGCAATGTATTCT	0.458													145	321	---	---	---	---	PASS
GREB1	9687	broad.mit.edu	37	2	11733133	11733133	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11733133C>G	uc002rbk.1	+	11	1877	c.1577C>G	c.(1576-1578)GCC>GGC	p.A526G	GREB1_uc002rbo.1_Missense_Mutation_p.A160G	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	526						integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		TACTCCCTGGCCGAGGGCCTC	0.672													5	16	---	---	---	---	PASS
OTOF	9381	broad.mit.edu	37	2	26699110	26699110	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26699110G>T	uc002rhk.2	-	23	2879	c.2752C>A	c.(2752-2754)CTC>ATC	p.L918I	OTOF_uc010yla.1_5'Flank|OTOF_uc002rhh.2_Missense_Mutation_p.L171I|OTOF_uc002rhi.2_Missense_Mutation_p.L228I|OTOF_uc002rhj.2_Missense_Mutation_p.L171I	NM_194248	NP_919224	Q9HC10	OTOF_HUMAN	otoferlin isoform a	918	Cytoplasmic (Potential).				cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis	basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane	calcium ion binding			ovary(3)|breast(2)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGTTTGCTGAGGCCCAGCCAC	0.682													28	55	---	---	---	---	PASS
PLB1	151056	broad.mit.edu	37	2	28828788	28828788	+	Missense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28828788G>C	uc002rmb.1	+	42	3030	c.3030G>C	c.(3028-3030)CAG>CAC	p.Q1010H	PLB1_uc010ezj.1_Missense_Mutation_p.Q999H|PLB1_uc002rme.1_Intron|PLB1_uc002rmf.1_RNA	NM_153021	NP_694566	Q6P1J6	PLB1_HUMAN	phospholipase B1 precursor	1010	4 X 308-326 AA approximate repeats.|Extracellular (Potential).|3.				lipid catabolic process|retinoid metabolic process|steroid metabolic process	apical plasma membrane|integral to membrane	lysophospholipase activity|phospholipase A2 activity|retinyl-palmitate esterase activity			ovary(4)|large_intestine(2)|skin(2)|breast(1)	9	Acute lymphoblastic leukemia(172;0.155)					TCCACTCCCAGCTGGCCAGAG	0.517													217	383	---	---	---	---	PASS
C2orf71	388939	broad.mit.edu	37	2	29294247	29294247	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29294247G>T	uc002rmt.1	-	1	2881	c.2881C>A	c.(2881-2883)CAC>AAC	p.H961N		NM_001029883	NP_001025054	A6NGG8	CB071_HUMAN	hypothetical protein LOC388939	961					response to stimulus|visual perception	photoreceptor outer segment				skin(1)	1						CCGGAGTGGTGCCAGGCGATG	0.647													4	83	---	---	---	---	PASS
FBXO11	80204	broad.mit.edu	37	2	48063100	48063100	+	Missense_Mutation	SNP	T	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48063100T>C	uc010fbl.2	-	5	490	c.376A>G	c.(376-378)ATG>GTG	p.M126V	FBXO11_uc002rwe.2_Missense_Mutation_p.M126V|FBXO11_uc002rwf.2_Missense_Mutation_p.M126V|FBXO11_uc002rwg.1_Missense_Mutation_p.M126V	NM_025133	NP_079409	Q86XK2	FBX11_HUMAN	F-box only protein 11 isoform 1	210					ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|ubiquitin ligase complex	protein binding|protein-arginine N-methyltransferase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)	2		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GGATGCATCATAGGGCGAGTA	0.333													43	69	---	---	---	---	PASS
USP34	9736	broad.mit.edu	37	2	61607309	61607309	+	Missense_Mutation	SNP	T	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61607309T>A	uc002sbe.2	-	7	1031	c.1009A>T	c.(1009-1011)ATA>TTA	p.I337L		NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	337					positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			CTTACTGTTATCTGACTCAAT	0.264													37	61	---	---	---	---	PASS
EHBP1	23301	broad.mit.edu	37	2	63264694	63264694	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63264694C>A	uc002sby.2	+	22	3823	c.3341C>A	c.(3340-3342)GCT>GAT	p.A1114D	EHBP1_uc010fcp.2_Missense_Mutation_p.A1043D|EHBP1_uc002sbz.2_Missense_Mutation_p.A1043D|EHBP1_uc002scb.2_Missense_Mutation_p.A1079D	NM_015252	NP_056067	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1 isoform 1	1114						cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			GAAGAAGAAGCTATGATGCAG	0.323									Hereditary_Prostate_Cancer				5	103	---	---	---	---	PASS
ARHGAP25	9938	broad.mit.edu	37	2	69049996	69049996	+	Missense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69049996G>C	uc002seu.2	+	10	2086	c.1722G>C	c.(1720-1722)CAG>CAC	p.Q574H	ARHGAP25_uc010fdg.2_Missense_Mutation_p.Q575H|ARHGAP25_uc010yql.1_Missense_Mutation_p.Q535H|ARHGAP25_uc002sew.2_Missense_Mutation_p.Q567H|ARHGAP25_uc002sex.2_Missense_Mutation_p.Q568H|ARHGAP25_uc002sey.2_Missense_Mutation_p.Q301H	NM_001007231	NP_001007232	P42331	RHG25_HUMAN	Rho GTPase activating protein 25 isoform a	574	Potential.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(2)|breast(2)	4						ATGAGGAACAGATTAAAAAGT	0.428													4	196	---	---	---	---	PASS
CLEC4F	165530	broad.mit.edu	37	2	71043874	71043874	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71043874G>T	uc002shf.2	-	4	716	c.639C>A	c.(637-639)CAC>CAA	p.H213Q	CLEC4F_uc010yqv.1_Missense_Mutation_p.H213Q	NM_173535	NP_775806	Q8N1N0	CLC4F_HUMAN	C-type lectin, superfamily member 13	213	Extracellular (Potential).				endocytosis	integral to membrane	receptor activity|sugar binding			ovary(5)	5						TGCTTAGCACGTGGAGCTCAA	0.428													69	107	---	---	---	---	PASS
LOXL3	84695	broad.mit.edu	37	2	74763510	74763510	+	Missense_Mutation	SNP	C	T	T	rs138480120		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74763510C>T	uc002smp.1	-	6	1073	c.1001G>A	c.(1000-1002)CGC>CAC	p.R334H	LOXL3_uc002smo.1_5'UTR|LOXL3_uc010ffm.1_Missense_Mutation_p.R334H|LOXL3_uc002smq.1_Missense_Mutation_p.R189H|LOXL3_uc010ffn.1_Missense_Mutation_p.R189H	NM_032603	NP_115992	P58215	LOXL3_HUMAN	lysyl oxidase-like 3 precursor	334	SRCR 3.					extracellular space|membrane	copper ion binding|protein-lysine 6-oxidase activity|scavenger receptor activity				0						GTCCCACTTGCGGTCACAGAC	0.647													5	277	---	---	---	---	PASS
SEMA4F	10505	broad.mit.edu	37	2	74884684	74884684	+	Intron	SNP	T	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74884684T>A	uc002sna.1	+						SEMA4F_uc010ysb.1_Intron|SEMA4F_uc010ffq.1_Intron|SEMA4F_uc010ffr.1_Intron|SEMA4F_uc002snb.1_Intron|SEMA4F_uc002snc.1_Intron	NM_004263	NP_004254	O95754	SEM4F_HUMAN	semaphorin W precursor						cell-cell signaling	endoplasmic reticulum|integral to plasma membrane	receptor activity			ovary(2)|pancreas(1)|skin(1)	4						TCACTTCTCCTTTCTCAGATT	0.438													65	112	---	---	---	---	PASS
HK2	3099	broad.mit.edu	37	2	75118043	75118043	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75118043G>A	uc002snd.2	+	18	4655	c.2729G>A	c.(2728-2730)CGC>CAC	p.R910H		NM_000189	NP_000180	P52789	HXK2_HUMAN	hexokinase 2	910	Catalytic.				apoptotic mitochondrial changes|glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane	ATP binding|glucokinase activity			ovary(1)|lung(1)	2						GTGGCCTGCCGCATCCGTGAG	0.542													26	38	---	---	---	---	PASS
REG3G	130120	broad.mit.edu	37	2	79253881	79253881	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79253881G>A	uc002snw.2	+	3	204	c.119G>A	c.(118-120)TGT>TAT	p.C40Y	REG3G_uc002snx.2_Missense_Mutation_p.C40Y|REG3G_uc010ffu.2_Missense_Mutation_p.C40Y	NM_198448	NP_940850	Q6UW15	REG3G_HUMAN	regenerating islet-derived 3 gamma precursor	40					acute-phase response	extracellular region	sugar binding				0						CGGATCAGCTGTCCCAAAGGC	0.527													66	97	---	---	---	---	PASS
CTNNA2	1496	broad.mit.edu	37	2	80085205	80085205	+	Missense_Mutation	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80085205C>T	uc010ysh.1	+	3	370	c.365C>T	c.(364-366)ACC>ATC	p.T122I	CTNNA2_uc010yse.1_Missense_Mutation_p.T122I|CTNNA2_uc010ysf.1_Missense_Mutation_p.T122I|CTNNA2_uc010ysg.1_Missense_Mutation_p.T122I	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1	122				T -> A (in Ref. 3; BAH12003).	axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9						AAGCGCGGCACCATGGTACGG	0.567													88	151	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	89345942	89345942	+	Intron	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89345942G>T	uc010ytr.1	-						uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																		CCCAGGAGCTGAGCGGGGACC	0.562													62	264	---	---	---	---	PASS
TRIM43	129868	broad.mit.edu	37	2	96260880	96260880	+	Missense_Mutation	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96260880C>T	uc002suv.2	+	3	630	c.494C>T	c.(493-495)GCC>GTC	p.A165V		NM_138800	NP_620155	Q96BQ3	TRI43_HUMAN	tripartite motif-containing 43	165						intracellular	zinc ion binding			ovary(1)	1						GGAAGAACAGCCTTCCTCTGG	0.388													21	55	---	---	---	---	PASS
ADRA2B	151	broad.mit.edu	37	2	96780641	96780641	+	Missense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96780641G>C	uc002svi.2	-	3	1257	c.1257C>G	c.(1255-1257)AGC>AGG	p.S419R		NM_000682	NP_000673	P18089	ADA2B_HUMAN	alpha-2B-adrenergic receptor	419	Helical; Name=7; (By similarity).				activation of MAPK activity by adrenergic receptor signaling pathway|activation of protein kinase B activity|blood coagulation|cell-cell signaling|epidermal growth factor receptor transactivation by G-protein coupled receptor signaling pathway|negative regulation of epinephrine secretion|negative regulation of norepinephrine secretion|positive regulation of neuron differentiation	integral to plasma membrane	alpha2-adrenergic receptor activity|epinephrine binding|protein binding			ovary(2)|lung(1)	3					Bethanidine(DB00217)|Brimonidine(DB00484)|Debrisoquin(DB04840)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Lofexidine(DB04948)|Norepinephrine(DB00368)|Yohimbine(DB01392)	GGTTCAGTGAGCTGTTGCAGT	0.597													3	17	---	---	---	---	PASS
VWA3B	200403	broad.mit.edu	37	2	98928769	98928769	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98928769C>A	uc002syo.2	+	28	4106	c.3842C>A	c.(3841-3843)ACC>AAC	p.T1281N	VWA3B_uc002syr.1_3'UTR|VWA3B_uc002sys.2_RNA	NM_144992	NP_659429	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	1281										ovary(3)|large_intestine(2)|skin(1)	6						CTCCAAGCCACCCACAGCAGC	0.617													30	67	---	---	---	---	PASS
LONRF2	164832	broad.mit.edu	37	2	100906843	100906843	+	Silent	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100906843C>G	uc002tal.3	-	10	2437	c.1797G>C	c.(1795-1797)GTG>GTC	p.V599V	LONRF2_uc010yvs.1_RNA	NM_198461	NP_940863	Q1L5Z9	LONF2_HUMAN	LON peptidase N-terminal domain and ring finger	599	Lon.				proteolysis		ATP-dependent peptidase activity|zinc ion binding			large_intestine(1)|skin(1)	2						GAAACGTTCTCACGTCCTTAA	0.473													106	219	---	---	---	---	PASS
TGFBRAP1	9392	broad.mit.edu	37	2	105900831	105900831	+	Missense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105900831G>C	uc002tcq.2	-	5	1147	c.1063C>G	c.(1063-1065)CAG>GAG	p.Q355E	TGFBRAP1_uc010fjc.2_Missense_Mutation_p.Q125E|TGFBRAP1_uc002tcr.3_Missense_Mutation_p.Q355E	NM_004257	NP_004248	Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor	355					regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	cytoplasm|membrane	SMAD binding|small GTPase regulator activity|transforming growth factor beta receptor binding			central_nervous_system(1)|skin(1)	2						AATCCCGCCTGCTGCAGAATC	0.453													58	105	---	---	---	---	PASS
SULT1C4	27233	broad.mit.edu	37	2	108998942	108998942	+	Intron	SNP	A	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108998942A>G	uc002tea.1	+						SULT1C4_uc002tdz.2_3'UTR|SULT1C4_uc010ywr.1_Intron|SULT1C4_uc002teb.1_Intron	NM_006588	NP_006579	O75897	ST1C4_HUMAN	sulfotransferase family, cytosolic, 1C, member						3'-phosphoadenosine 5'-phosphosulfate metabolic process|sulfation|xenobiotic metabolic process	cytosol	sulfotransferase activity				0						CTGTAAGGTAAAAAAGCAAAA	0.373													205	292	---	---	---	---	PASS
ANKRD57	65124	broad.mit.edu	37	2	110373346	110373346	+	Missense_Mutation	SNP	A	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110373346A>G	uc002tfb.2	+	1	1436	c.1280A>G	c.(1279-1281)AAA>AGA	p.K427R	SEPT10_uc010ywu.1_5'Flank|SEPT10_uc002tew.2_5'Flank|SEPT10_uc002tex.2_5'Flank|SEPT10_uc002tey.2_5'Flank|SEPT10_uc010ywv.1_5'Flank	NM_023016	NP_075392	Q53LP3	ANR57_HUMAN	ankyrin repeat domain 57	427											0						ATCACCTACAAACTCTCACAC	0.642													9	140	---	---	---	---	PASS
ANAPC1	64682	broad.mit.edu	37	2	112608443	112608443	+	Silent	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112608443C>A	uc002thi.2	-	14	1807	c.1560G>T	c.(1558-1560)ACG>ACT	p.T520T		NM_022662	NP_073153	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	520					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|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|cytosol|nucleoplasm				skin(2)	2						TGTTGGACATCGTCAGAGAGG	0.428													4	200	---	---	---	---	PASS
DPP10	57628	broad.mit.edu	37	2	116534783	116534783	+	Splice_Site	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116534783G>T	uc002tla.1	+	14	1679	c.1222_splice	c.e14-1	p.S408_splice	DPP10_uc002tlb.1_Splice_Site_p.S358_splice|DPP10_uc002tlc.1_Splice_Site_p.S404_splice|DPP10_uc002tle.2_Splice_Site_p.S412_splice|DPP10_uc002tlf.1_Splice_Site_p.S401_splice	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10						TTTCTTTGCAGAGTAAAAGTG	0.368													58	73	---	---	---	---	PASS
MARCO	8685	broad.mit.edu	37	2	119735500	119735500	+	Missense_Mutation	SNP	T	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119735500T>G	uc002tln.1	+	8	887	c.755T>G	c.(754-756)CTG>CGG	p.L252R	MARCO_uc010yyf.1_Missense_Mutation_p.L174R	NM_006770	NP_006761	Q9UEW3	MARCO_HUMAN	macrophage receptor with collagenous structure	252	Collagen-like.|Extracellular (Potential).				cell surface receptor linked signaling pathway|innate immune response	collagen|integral to plasma membrane	pattern recognition receptor activity|scavenger receptor activity			ovary(3)|skin(2)|central_nervous_system(1)	6						AAAGGAGACCTGGGTCTCCCA	0.607													5	23	---	---	---	---	PASS
CNTNAP5	129684	broad.mit.edu	37	2	125175154	125175154	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125175154C>A	uc002tno.2	+	4	880	c.516C>A	c.(514-516)TAC>TAA	p.Y172*	CNTNAP5_uc010flu.2_Nonsense_Mutation_p.Y172*	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	172	F5/8 type C.|Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		TCGAGGTCTACGGATGTTCCT	0.473													22	24	---	---	---	---	PASS
CNTNAP5	129684	broad.mit.edu	37	2	125175156	125175156	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125175156G>A	uc002tno.2	+	4	882	c.518G>A	c.(517-519)GGA>GAA	p.G173E	CNTNAP5_uc010flu.2_Missense_Mutation_p.G173E	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	173	F5/8 type C.|Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		GAGGTCTACGGATGTTCCTAT	0.473													23	23	---	---	---	---	PASS
POTEE	445582	broad.mit.edu	37	2	131976356	131976356	+	Silent	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131976356C>A	uc002tsn.2	+	1	433	c.381C>A	c.(379-381)GCC>GCA	p.A127A	PLEKHB2_uc002tsh.2_Intron|POTEE_uc002tsk.2_5'UTR|POTEE_uc002tsl.2_5'UTR	NM_001083538	NP_001077007	Q6S8J3	POTEE_HUMAN	protein expressed in prostate, ovary, testis,	127							ATP binding				0						ATGACAGCGCCTTCATGGAGC	0.597													124	102	---	---	---	---	PASS
LCT	3938	broad.mit.edu	37	2	136575347	136575347	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136575347G>T	uc002tuu.1	-	6	1282	c.1271C>A	c.(1270-1272)GCG>GAG	p.A424E		NM_002299	NP_002290	P09848	LPH_HUMAN	lactase-phlorizin hydrolase preproprotein	424	Extracellular (Potential).|4 X approximate repeats.|2.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|integral to plasma membrane|membrane fraction	cation binding|glycosylceramidase activity|lactase activity			ovary(7)|central_nervous_system(2)|skin(2)|pancreas(1)|lung(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.169)		CTCCAGCGTCGCTTGGCCCTC	0.632													57	83	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141215062	141215062	+	Missense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141215062G>C	uc002tvj.1	-	61	10756	c.9784C>G	c.(9784-9786)CAG>GAG	p.Q3262E		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	3262	Extracellular (Potential).|LDL-receptor class B 32.				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)		TGATACACCTGGATATCTGTG	0.383										TSP Lung(27;0.18)			59	229	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141771249	141771249	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141771249G>T	uc002tvj.1	-	14	3228	c.2256C>A	c.(2254-2256)TTC>TTA	p.F752L	LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	752	Extracellular (Potential).				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)		AATCAGTCCAGAACACATAAT	0.388										TSP Lung(27;0.18)			28	184	---	---	---	---	PASS
SCN2A	6326	broad.mit.edu	37	2	166231454	166231454	+	Missense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166231454G>C	uc002udc.2	+	22	4522	c.4232G>C	c.(4231-4233)GGA>GCA	p.G1411A	SCN2A_uc002udd.2_Missense_Mutation_p.G1411A|SCN2A_uc002ude.2_Missense_Mutation_p.G1411A	NM_001040142	NP_001035232	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha	1411	III.				myelination	node of Ranvier|voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|breast(1)|pancreas(1)	8					Lamotrigine(DB00555)	GTAGGACTTGGATATCTGTCT	0.328													15	60	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179397670	179397670	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179397670G>A	uc010zfg.1	-	307	96192	c.95968C>T	c.(95968-95970)CGC>TGC	p.R31990C	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.R25685C|TTN_uc010zfi.1_Missense_Mutation_p.R25618C|TTN_uc010zfj.1_Missense_Mutation_p.R25493C	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	32917							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGCTTGATGCGTTGGTCTTCT	0.433													182	189	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179578804	179578804	+	Missense_Mutation	SNP	T	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179578804T>C	uc010zfg.1	-	89	23073	c.22849A>G	c.(22849-22851)ACT>GCT	p.T7617A	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.T4278A	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	8544							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AACCACTTAGTACTGAGTTCA	0.423													18	53	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179612908	179612908	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179612908G>A	uc002unb.2	-	46	14443	c.14219C>T	c.(14218-14220)TCT>TTT	p.S4740F	TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron	NM_133379	NP_596870	Q8WZ42	TITIN_HUMAN	titin isoform novex-3	851							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TATATCTGCAGATGAGGTTGG	0.358													56	81	---	---	---	---	PASS
ZNF385B	151126	broad.mit.edu	37	2	180634308	180634308	+	Missense_Mutation	SNP	G	A	A	rs138550246		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180634308G>A	uc002unn.3	-	3	779	c.175C>T	c.(175-177)CGC>TGC	p.R59C		NM_152520	NP_689733	Q569K4	Z385B_HUMAN	zinc finger protein 385B isoform 1	59	Matrin-type 1.					nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			ACTCGTTTGCGGTGGGATTTG	0.577													4	85	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	186672547	186672547	+	Intron	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186672547G>T	uc002upm.2	+						uc010zfu.1_Missense_Mutation_p.D670Y					Homo sapiens cDNA FLJ44048 fis, clone TESTI4030669.																		TTCACATGCTGATAAGCTGTC	0.323													57	67	---	---	---	---	PASS
ASNSD1	54529	broad.mit.edu	37	2	190532263	190532263	+	Missense_Mutation	SNP	A	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190532263A>G	uc002uqt.2	+	4	1839	c.1405A>G	c.(1405-1407)AGA>GGA	p.R469G		NM_019048	NP_061921	Q9NWL6	ASND1_HUMAN	asparagine synthetase domain containing 1	469	Asparagine synthetase.				asparagine biosynthetic process|glutamine metabolic process		asparagine synthase (glutamine-hydrolyzing) activity			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0449)|all cancers(119;0.118)			GTTTGCTTCTAGAGGAATTGG	0.428													169	171	---	---	---	---	PASS
HECW2	57520	broad.mit.edu	37	2	197184220	197184220	+	Nonsense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197184220G>C	uc002utm.1	-	9	1577	c.1394C>G	c.(1393-1395)TCA>TGA	p.S465*	HECW2_uc002utl.1_Nonsense_Mutation_p.S109*	NM_020760	NP_065811	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin	465					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18						TTCTTCATCTGAATCAATATG	0.517													33	31	---	---	---	---	PASS
FN1	2335	broad.mit.edu	37	2	216300472	216300472	+	Silent	SNP	C	G	G	rs149268490	byFrequency	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216300472C>G	uc002vfa.2	-	1	320	c.54G>C	c.(52-54)GGG>GGC	p.G18G	FN1_uc002vfb.2_Silent_p.G18G|FN1_uc002vfc.2_Silent_p.G18G|FN1_uc002vfd.2_Silent_p.G18G|FN1_uc002vfe.2_Silent_p.G18G|FN1_uc002vff.2_Silent_p.G18G|FN1_uc002vfg.2_Silent_p.G18G|FN1_uc002vfh.2_Silent_p.G18G|FN1_uc002vfi.2_Silent_p.G18G|FN1_uc002vfj.2_Silent_p.G18G|FN1_uc002vfl.2_Silent_p.G18G	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	18					acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	GCACCGCTGTCCCCAGGCACT	0.667													4	4	---	---	---	---	PASS
CTDSP1	58190	broad.mit.edu	37	2	219267090	219267090	+	Missense_Mutation	SNP	T	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219267090T>G	uc002vhy.2	+	4	676	c.340T>G	c.(340-342)TTC>GTC	p.F114V	CTDSP1_uc002vhx.2_Missense_Mutation_p.F113V|CTDSP1_uc002vhz.2_5'UTR|uc010zkd.1_5'Flank|MIR26B_hsa-mir-26b|MI0000084_5'Flank	NM_021198	NP_067021	Q9GZU7	CTDS1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II,	114	FCP1 homology.				protein dephosphorylation|regulation of transcription from RNA polymerase II promoter	nucleus	CTD phosphatase activity|metal ion binding|protein binding			ovary(1)	1		Renal(207;0.0915)		Epithelial(149;9.96e-07)|all cancers(144;0.00017)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CAACGCGGACTTCATCATCCC	0.632													74	99	---	---	---	---	PASS
DES	1674	broad.mit.edu	37	2	220283366	220283366	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220283366G>T	uc002vll.2	+	1	268	c.182G>T	c.(181-183)GGC>GTC	p.G61V		NM_001927	NP_001918	P17661	DESM_HUMAN	desmin	61	Head.				cytoskeleton organization|muscle filament sliding|regulation of heart contraction	cytosol|Z disc	protein binding|structural constituent of cytoskeleton			central_nervous_system(2)	2		Renal(207;0.0183)		Epithelial(149;5.25e-07)|all cancers(144;0.000103)|Lung(261;0.00533)|LUSC - Lung squamous cell carcinoma(224;0.008)		CGCACGTCGGGCGGGGCCGGG	0.741													3	7	---	---	---	---	PASS
CUL3	8452	broad.mit.edu	37	2	225339077	225339077	+	Missense_Mutation	SNP	T	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225339077T>A	uc002vny.2	-	16	2576	c.2192A>T	c.(2191-2193)AAG>ATG	p.K731M	CUL3_uc010zls.1_Missense_Mutation_p.K665M|CUL3_uc010fwy.1_Missense_Mutation_p.K737M	NM_003590	NP_003581	Q13618	CUL3_HUMAN	cullin 3	731					cell cycle arrest|cell migration|cyclin catabolic process|cytokinesis|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|mitotic anaphase|negative regulation of Rho protein signal transduction|positive regulation of cell proliferation|protein ubiquitination|stress fiber assembly	Cul3-RING ubiquitin ligase complex|Golgi apparatus|nucleus|polar microtubule	ubiquitin protein ligase binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|kidney(1)	4		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		GAATCGCGCCTTCAACTGCTG	0.333													58	48	---	---	---	---	PASS
IRS1	3667	broad.mit.edu	37	2	227660841	227660841	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227660841G>T	uc002voh.3	-	1	2666	c.2614C>A	c.(2614-2616)CCT>ACT	p.P872T		NM_005544	NP_005535	P35568	IRS1_HUMAN	insulin receptor substrate 1	872					fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity	caveola|cytosol|insulin receptor complex|microsome|nucleus	insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity			lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1)	12		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		CGGGCCCGAGGTAAGGTGCTG	0.557													17	37	---	---	---	---	PASS
SPHKAP	80309	broad.mit.edu	37	2	228884548	228884548	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228884548G>T	uc002vpq.2	-	7	1069	c.1022C>A	c.(1021-1023)CCA>CAA	p.P341Q	SPHKAP_uc002vpp.2_Missense_Mutation_p.P341Q|SPHKAP_uc010zlx.1_Missense_Mutation_p.P341Q	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	341						cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		AGCATCTTTTGGAATATACAG	0.418													71	374	---	---	---	---	PASS
SPHKAP	80309	broad.mit.edu	37	2	228884549	228884549	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228884549G>T	uc002vpq.2	-	7	1068	c.1021C>A	c.(1021-1023)CCA>ACA	p.P341T	SPHKAP_uc002vpp.2_Missense_Mutation_p.P341T|SPHKAP_uc010zlx.1_Missense_Mutation_p.P341T	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	341						cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		GCATCTTTTGGAATATACAGT	0.423													72	379	---	---	---	---	PASS
ANKMY1	51281	broad.mit.edu	37	2	241463551	241463551	+	Missense_Mutation	SNP	T	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241463551T>C	uc002vyz.1	-	7	1545	c.1316A>G	c.(1315-1317)AAG>AGG	p.K439R	ANKMY1_uc002vza.1_Missense_Mutation_p.K298R|ANKMY1_uc010fzd.1_Missense_Mutation_p.K528R|ANKMY1_uc002vzb.1_Intron|ANKMY1_uc002vzc.1_Missense_Mutation_p.K298R|ANKMY1_uc002vzd.1_Missense_Mutation_p.K298R|ANKMY1_uc010fze.1_Missense_Mutation_p.K108R|ANKMY1_uc002vze.2_Missense_Mutation_p.K200R	NM_016552	NP_057636	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	439							zinc ion binding			central_nervous_system(1)	1		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		AAGGCTGCCCTTCACCAACGG	0.617													51	53	---	---	---	---	PASS
SLC4A7	9497	broad.mit.edu	37	3	27459966	27459966	+	Intron	SNP	T	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27459966T>C	uc003cdv.2	-						SLC4A7_uc011awu.1_Intron|SLC4A7_uc011awv.1_Intron|SLC4A7_uc003cdu.3_Intron|SLC4A7_uc011aww.1_Intron|SLC4A7_uc011awx.1_Intron|SLC4A7_uc011awy.1_Intron|SLC4A7_uc011awz.1_Intron|SLC4A7_uc011axa.1_Intron|SLC4A7_uc011axb.1_Intron|SLC4A7_uc010hfl.2_Intron|SLC4A7_uc003cdw.2_Intron	NM_003615	NP_003606	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate							apical plasma membrane|basolateral plasma membrane|integral to membrane|stereocilium	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|central_nervous_system(1)|skin(1)	5						AGAATAGCTCTGGATTCTTAC	0.299													64	45	---	---	---	---	PASS
TRIM71	131405	broad.mit.edu	37	3	32933223	32933223	+	Missense_Mutation	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32933223C>T	uc003cff.2	+	4	2590	c.2527C>T	c.(2527-2529)CGC>TGC	p.R843C		NM_001039111	NP_001034200	Q2Q1W2	LIN41_HUMAN	tripartite motif-containing 71	843	NHL 6.				multicellular organismal development	cytoplasm	zinc ion binding			ovary(2)|large_intestine(1)	3						GCAGATGGACCGCCCTTCCGG	0.537													12	245	---	---	---	---	PASS
UBP1	7342	broad.mit.edu	37	3	33437660	33437660	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33437660G>A	uc003cfq.3	-	13	1914	c.1384C>T	c.(1384-1386)CCC>TCC	p.P462S	FBXL2_uc011axq.1_Intron|FBXL2_uc011axr.1_Intron|UBP1_uc003cfr.3_Missense_Mutation_p.P426S|UBP1_uc010hga.2_Missense_Mutation_p.P462S	NM_014517	NP_055332	Q9NZI7	UBIP1_HUMAN	upstream binding protein 1 (LBP-1a) isoform a	462					negative regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|viral genome replication	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			kidney(2)	2						CTACCATAGGGTGCCCCACTG	0.532													121	90	---	---	---	---	PASS
PTPN23	25930	broad.mit.edu	37	3	47448608	47448608	+	Intron	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47448608C>T	uc003crf.1	+						PTPN23_uc011baw.1_Intron|PTPN23_uc011bax.1_Intron|PTPN23_uc011bay.1_Intron	NM_015466	NP_056281	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type						cilium morphogenesis	cilium|cytoplasmic membrane-bounded vesicle|microtubule basal body	protein tyrosine phosphatase activity			breast(1)|central_nervous_system(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GCTTTCCTGCCACCCTCCACA	0.597													20	18	---	---	---	---	PASS
SMARCC1	6599	broad.mit.edu	37	3	47742825	47742825	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47742825C>A	uc003crq.2	-	11	1226	c.1108G>T	c.(1108-1110)GAT>TAT	p.D370Y	SMARCC1_uc011bbd.1_Missense_Mutation_p.D261Y	NM_003074	NP_003065	Q92922	SMRC1_HUMAN	SWI/SNF-related matrix-associated	370					chromatin remodeling|nervous system development|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex|WINAC complex	DNA binding|protein N-terminus binding|transcription coactivator activity			skin(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)		TCTTCCATATCCTTGGTTAGA	0.368													103	54	---	---	---	---	PASS
CAMP	820	broad.mit.edu	37	3	48266082	48266082	+	Intron	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48266082C>T	uc003csj.1	+							NM_004345	NP_004336	P49913	CAMP_HUMAN	cathelicidin antimicrobial peptide						killing by host of symbiont cells|negative regulation of growth of symbiont on or near host surface	extracellular region				upper_aerodigestive_tract(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000614)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		CCTTGAGCTTCTCCTTTCCAG	0.552													91	59	---	---	---	---	PASS
CADPS	8618	broad.mit.edu	37	3	62464080	62464080	+	Missense_Mutation	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62464080C>T	uc003dll.2	-	23	3545	c.3185G>A	c.(3184-3186)GGC>GAC	p.G1062D	CADPS_uc003dlj.1_Missense_Mutation_p.G12D|CADPS_uc003dlk.1_Missense_Mutation_p.G510D|CADPS_uc003dlm.2_Missense_Mutation_p.G1023D|CADPS_uc003dln.2_Missense_Mutation_p.G983D	NM_003716	NP_003707	Q9ULU8	CAPS1_HUMAN	Ca2+-dependent secretion activator isoform 1	1062	MHD1.|Interaction with DRD2.				exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|cytosol|synapse	lipid binding|metal ion binding			central_nervous_system(2)|ovary(1)	3		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		TTCTGAGGTGCCTGACCCATT	0.498													28	26	---	---	---	---	PASS
COL8A1	1295	broad.mit.edu	37	3	99514202	99514202	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99514202G>A	uc003dtg.1	+	5	1702	c.1457G>A	c.(1456-1458)GGA>GAA	p.G486E	COL8A1_uc003dth.1_Missense_Mutation_p.G486E|COL8A1_uc003dti.1_Missense_Mutation_p.G487E	NM_001850	NP_001841	P27658	CO8A1_HUMAN	alpha 1 type VIII collagen precursor	486	Triple-helical region (COL1).				angiogenesis|cell adhesion	basement membrane|collagen type VIII					0						GGAGAGCCAGGAATCCCAGGG	0.627													8	28	---	---	---	---	PASS
CBLB	868	broad.mit.edu	37	3	105438956	105438956	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105438956C>A	uc003dwc.2	-	10	1664	c.1342G>T	c.(1342-1344)GAC>TAC	p.D448Y	CBLB_uc011bhi.1_Missense_Mutation_p.D470Y|CBLB_uc003dwd.1_Missense_Mutation_p.D448Y|CBLB_uc003dwe.1_Missense_Mutation_p.D448Y|CBLB_uc011bhj.1_RNA	NM_170662	NP_733762	Q13191	CBLB_HUMAN	Cas-Br-M (murine) ecotropic retroviral	448					cell surface receptor linked signaling pathway|NLS-bearing substrate import into nucleus	cytoplasm|nucleus	calcium ion binding|ligase activity|signal transducer activity|zinc ion binding			lung(4)|ovary(3)|breast(1)|skin(1)	9						TCGTCCAAGTCTAGCATCGGC	0.468			Mis S		AML								40	103	---	---	---	---	PASS
WDR52	55779	broad.mit.edu	37	3	113098141	113098141	+	Intron	SNP	A	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113098141A>G	uc003eae.1	-							NM_018338	NP_060808	Q96MT7	WDR52_HUMAN	WD repeat domain 52 isoform 2											central_nervous_system(1)	1						AAATTATTACATTGTTACTTA	0.308													55	61	---	---	---	---	PASS
SNX4	8723	broad.mit.edu	37	3	125216958	125216958	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125216958C>A	uc003eib.2	-	3	386	c.344G>T	c.(343-345)AGC>ATC	p.S115I	SNX4_uc011bkf.1_5'UTR	NM_003794	NP_003785	O95219	SNX4_HUMAN	sorting nexin 4	115	PX.				cell communication|endocytic recycling|endocytosis|protein transport	cytoplasmic dynein complex|early endosome membrane	phosphatidylinositol binding|protein binding			breast(2)|ovary(1)|central_nervous_system(1)	4						TAAAAGGTAGCTTCTCAACAA	0.413													57	191	---	---	---	---	PASS
COPG	22820	broad.mit.edu	37	3	128976393	128976393	+	Silent	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128976393G>A	uc003els.2	+	9	760	c.660G>A	c.(658-660)CGG>CGA	p.R220R	COPG_uc010htb.2_Silent_p.R126R	NM_016128	NP_057212	Q9Y678	COPG_HUMAN	coatomer protein complex, subunit gamma 1	220					COPI coating of Golgi vesicle|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol	protein binding|structural molecule activity			ovary(3)|breast(1)	4						AGGTCACACGGCATGGCCTTA	0.542													6	769	---	---	---	---	PASS
SLCO2A1	6578	broad.mit.edu	37	3	133670154	133670154	+	Nonsense_Mutation	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133670154C>T	uc003eqa.3	-	6	1033	c.759G>A	c.(757-759)TGG>TGA	p.W253*	SLCO2A1_uc003eqb.3_Nonsense_Mutation_p.W177*|SLCO2A1_uc011blv.1_Intron|SLCO2A1_uc010htw.1_Nonsense_Mutation_p.W85*	NM_005630	NP_005621	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family,	253	Extracellular (Potential).				sodium-independent organic anion transport	integral to plasma membrane|membrane fraction	prostaglandin transmembrane transporter activity|protein binding			central_nervous_system(1)	1						AGGCTCCAATCCATCGGGGGT	0.478													106	136	---	---	---	---	PASS
EPHB1	2047	broad.mit.edu	37	3	134911504	134911504	+	Missense_Mutation	SNP	T	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134911504T>G	uc003eqt.2	+	11	2189	c.1969T>G	c.(1969-1971)TAC>GAC	p.Y657D	EPHB1_uc003equ.2_Missense_Mutation_p.Y218D	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor	657	Cytoplasmic (Potential).|Protein kinase.					integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30						GAAGGCAGGGTACTCGGAGAA	0.547													30	119	---	---	---	---	PASS
A4GNT	51146	broad.mit.edu	37	3	137849900	137849900	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137849900C>A	uc003ers.2	-	2	401	c.199G>T	c.(199-201)GTC>TTC	p.V67F		NM_016161	NP_057245	Q9UNA3	A4GCT_HUMAN	alpha-1,4-N-acetylglucosaminyltransferase	67	Lumenal (Potential).				protein O-linked glycosylation	Golgi membrane|Golgi stack|integral to membrane|membrane fraction	acetylglucosaminyltransferase activity|galactosyltransferase activity			central_nervous_system(1)	1						GAACAGGAGACCAAATGGGGT	0.527													58	205	---	---	---	---	PASS
SLC9A9	285195	broad.mit.edu	37	3	142985611	142985611	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142985611C>A	uc003evn.2	-	16	2053	c.1871G>T	c.(1870-1872)GGA>GTA	p.G624V		NM_173653	NP_775924	Q8IVB4	SL9A9_HUMAN	solute carrier family 9 (sodium/hydrogen	624					regulation of pH	integral to membrane|late endosome membrane|recycling endosome	sodium:hydrogen antiporter activity			ovary(2)|skin(1)	3						GCCGAGGTCTCCCTCATAAAT	0.502													115	371	---	---	---	---	PASS
SLC9A9	285195	broad.mit.edu	37	3	143371213	143371213	+	Intron	SNP	A	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143371213A>G	uc003evn.2	-						SLC9A9_uc011bnk.1_Intron	NM_173653	NP_775924	Q8IVB4	SL9A9_HUMAN	solute carrier family 9 (sodium/hydrogen						regulation of pH	integral to membrane|late endosome membrane|recycling endosome	sodium:hydrogen antiporter activity			ovary(2)|skin(1)	3						CTAGGAAGACACACACAAACA	0.458													17	25	---	---	---	---	PASS
ZIC1	7545	broad.mit.edu	37	3	147128643	147128643	+	Silent	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147128643C>A	uc003ewe.2	+	1	1463	c.744C>A	c.(742-744)ACC>ACA	p.T248T		NM_003412	NP_003403	Q15915	ZIC1_HUMAN	zinc finger protein of the cerebellum 1	248	C2H2-type 1; atypical.				behavior|brain development|cell differentiation|inner ear morphogenesis|pattern specification process|positive regulation of protein import into nucleus|positive regulation of transcription, DNA-dependent|regulation of smoothened signaling pathway	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2						CTTTCAGCACCATGCACGAGC	0.577													57	141	---	---	---	---	PASS
CLRN1	7401	broad.mit.edu	37	3	150644630	150644630	+	3'UTR	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150644630G>T	uc003eyk.1	-	3					CLRN1OS_uc011bny.1_Intron|CLRN1_uc003eyj.2_3'UTR	NM_174878	NP_777367	P58418	CLRN1_HUMAN	clarin 1 isoform a						equilibrioception|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	integral to membrane					0			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			GGAAGGGTCAGTTCCAGGCTC	0.498													85	241	---	---	---	---	PASS
AADACL2	344752	broad.mit.edu	37	3	151463307	151463307	+	Missense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151463307G>C	uc003ezc.2	+	4	562	c.442G>C	c.(442-444)GCT>CCT	p.A148P	AADACL2_uc010hvn.2_5'UTR	NM_207365	NP_997248	Q6P093	ADCL2_HUMAN	arylacetamide deacetylase-like 2 precursor	148						extracellular region|integral to membrane	carboxylesterase activity				0			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			CTATAGGCTGGCTCCTCAACA	0.353													176	500	---	---	---	---	PASS
VEPH1	79674	broad.mit.edu	37	3	157034971	157034971	+	Silent	SNP	T	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157034971T>G	uc003fbj.1	-	10	2072	c.1755A>C	c.(1753-1755)GTA>GTC	p.V585V	VEPH1_uc003fbk.1_Silent_p.V585V|VEPH1_uc010hvu.1_Silent_p.V585V	NM_024621	NP_078897	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain homolog 1	585						plasma membrane				breast(3)|ovary(1)|lung(1)	5			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			ACAACTTTGCTACACAACTTC	0.398													11	346	---	---	---	---	PASS
ZBBX	79740	broad.mit.edu	37	3	167023679	167023679	+	Missense_Mutation	SNP	T	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167023679T>A	uc003fep.2	-	17	1800	c.1477A>T	c.(1477-1479)ATT>TTT	p.I493F	ZBBX_uc011bpc.1_Missense_Mutation_p.I493F|ZBBX_uc003feq.2_Missense_Mutation_p.I464F	NM_024687	NP_078963	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	493						intracellular	zinc ion binding			ovary(2)	2						ATTTTTTCAATGTCAGAAGAA	0.313													30	94	---	---	---	---	PASS
SERPINI1	5274	broad.mit.edu	37	3	167510553	167510553	+	Silent	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167510553G>A	uc003ffa.3	+	4	855	c.657G>A	c.(655-657)CAG>CAA	p.Q219Q	SERPINI1_uc003ffb.3_Silent_p.Q219Q	NM_001122752	NP_001116224	Q99574	NEUS_HUMAN	neuroserpin precursor	219					central nervous system development|peripheral nervous system development|regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			skin(1)	1						TGATGTATCAGCAAGGAGAAT	0.333													80	280	---	---	---	---	PASS
MYNN	55892	broad.mit.edu	37	3	169492342	169492342	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169492342C>A	uc003fft.2	+	2	688	c.259C>A	c.(259-261)CTT>ATT	p.L87I	MYNN_uc011bpm.1_Intron|MYNN_uc003ffu.2_Missense_Mutation_p.L87I|MYNN_uc003ffv.2_5'UTR|MYNN_uc010hwo.2_Missense_Mutation_p.L87I	NM_018657	NP_061127	Q9NPC7	MYNN_HUMAN	myoneurin	87	BTB.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1	all_cancers(22;9.55e-22)|all_epithelial(15;2.04e-26)|all_lung(20;5.05e-16)|Lung NSC(18;2.19e-15)|Ovarian(172;0.000223)|Breast(254;0.197)		Epithelial(2;4.03e-64)|all cancers(2;2.19e-58)|Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)			AACTTTAAATCTTGACAGGTA	0.343													70	551	---	---	---	---	PASS
LRRC15	131578	broad.mit.edu	37	3	194080379	194080379	+	Missense_Mutation	SNP	A	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194080379A>T	uc003ftu.2	-	2	1480	c.1394T>A	c.(1393-1395)ATT>AAT	p.I465N	LRRC15_uc003ftt.2_Missense_Mutation_p.I471N	NM_130830	NP_570843	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15 isoform b	465	LRRCT.|Extracellular (Potential).					integral to membrane				ovary(3)	3	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		ATTGATGATAATGAGGGACTG	0.557													25	35	---	---	---	---	PASS
FYTTD1	84248	broad.mit.edu	37	3	197503814	197503814	+	Missense_Mutation	SNP	A	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197503814A>T	uc003fyi.2	+	7	892	c.673A>T	c.(673-675)ACA>TCA	p.T225S	FYTTD1_uc011bui.1_Missense_Mutation_p.T199S|FYTTD1_uc011buj.1_RNA|FYTTD1_uc011buk.1_Missense_Mutation_p.T158S	NM_032288	NP_115664	Q96QD9	UIF_HUMAN	forty-two-three domain containing 1 isoform 1	225					mRNA export from nucleus	nuclear speck	mRNA binding|protein binding				0	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.175)		GACTTCCACCACAAATGGAGG	0.303													77	198	---	---	---	---	PASS
HTRA3	94031	broad.mit.edu	37	4	8271847	8271847	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8271847G>T	uc003gla.2	+	1	356	c.152G>T	c.(151-153)TGC>TTC	p.C51F	HTRA3_uc003gkz.2_Missense_Mutation_p.C51F	NM_053044	NP_444272	P83110	HTRA3_HUMAN	HtrA serine peptidase 3 precursor	51	IGFBP N-terminal.				proteolysis|regulation of cell growth	extracellular region	insulin-like growth factor binding|serine-type endopeptidase activity			ovary(1)	1						TGCAACTGCTGCCTGGTGTGC	0.771													10	6	---	---	---	---	PASS
GPR125	166647	broad.mit.edu	37	4	22390767	22390767	+	Silent	SNP	G	A	A	rs138178541	byFrequency	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22390767G>A	uc003gqm.1	-	18	2932	c.2667C>T	c.(2665-2667)TGC>TGT	p.C889C	GPR125_uc010ieo.1_Silent_p.C745C|GPR125_uc003gql.1_Silent_p.C16C	NM_145290	NP_660333	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125 precursor	889	Helical; Name=4; (Potential).				neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity			skin(1)	1		Breast(46;0.198)				CAGTTATGCCGCAAACAATGA	0.423													5	432	---	---	---	---	PASS
GRXCR1	389207	broad.mit.edu	37	4	42895576	42895576	+	Missense_Mutation	SNP	A	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42895576A>G	uc003gwt.2	+	1	293	c.293A>G	c.(292-294)AAC>AGC	p.N98S		NM_001080476	NP_001073945	A8MXD5	GRCR1_HUMAN	glutaredoxin, cysteine rich 1	98					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						AGAAGAGTCAACATTTTAAGC	0.428													147	119	---	---	---	---	PASS
LRRC66	339977	broad.mit.edu	37	4	52861681	52861681	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:52861681C>A	uc003gzi.2	-	4	1520	c.1507G>T	c.(1507-1509)GGT>TGT	p.G503C		NM_001024611	NP_001019782	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	503						integral to membrane				ovary(1)|central_nervous_system(1)|skin(1)	3						TAGACTGCACCATCATTTCCA	0.522													104	93	---	---	---	---	PASS
C4orf14	84273	broad.mit.edu	37	4	57842861	57842861	+	Silent	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57842861C>A	uc003hck.2	-	1	966	c.891G>T	c.(889-891)GGG>GGT	p.G297G	POLR2B_uc003hcl.1_5'Flank|POLR2B_uc011cae.1_5'Flank|POLR2B_uc011caf.1_5'Flank	NM_032313	NP_115689	Q8NC60	CD014_HUMAN	hypothetical protein LOC84273	297							GTP binding			ovary(1)|breast(1)	2	Glioma(25;0.08)|all_neural(26;0.181)					TCGGATTCTCCCCGTCCTGTG	0.677													28	18	---	---	---	---	PASS
TECRL	253017	broad.mit.edu	37	4	65188413	65188413	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65188413C>G	uc003hcv.2	-	4	538	c.429G>C	c.(427-429)TGG>TGC	p.W143C	TECRL_uc003hcw.2_Missense_Mutation_p.W143C	NM_001010874	NP_001010874	Q5HYJ1	TECRL_HUMAN	steroid 5 alpha-reductase 2-like 2	143	Helical; (Potential).				lipid metabolic process	cytoplasm|integral to membrane	oxidoreductase activity, acting on the CH-CH group of donors				0						TTACTGTGGTCCAACTGACTT	0.343													30	20	---	---	---	---	PASS
GRIA2	2891	broad.mit.edu	37	4	158242640	158242640	+	Silent	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158242640C>G	uc003ipm.3	+	6	1230	c.771C>G	c.(769-771)GTC>GTG	p.V257V	GRIA2_uc011cit.1_Silent_p.V210V|GRIA2_uc003ipl.3_Silent_p.V257V|GRIA2_uc003ipk.3_Silent_p.V210V|GRIA2_uc010iqh.1_RNA	NM_001083619	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2 isoform 2	257	Extracellular (Potential).				synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|endoplasmic reticulum membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			central_nervous_system(3)|ovary(1)	4	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	L-Glutamic Acid(DB00142)	GTGCAAATGTCTCTGGATTTC	0.363													166	120	---	---	---	---	PASS
ODZ3	55714	broad.mit.edu	37	4	183601509	183601509	+	Intron	SNP	A	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183601509A>C	uc003ivd.1	+						ODZ3_uc003ive.1_Intron	NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3						signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		AGAGGTATGCAAGTTAGATTC	0.443													31	18	---	---	---	---	PASS
IRX4	50805	broad.mit.edu	37	5	1879718	1879718	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1879718G>T	uc003jcz.2	-	4	755	c.636C>A	c.(634-636)AAC>AAA	p.N212K	IRX4_uc011cmf.1_Missense_Mutation_p.N73K	NM_016358	NP_057442	P78413	IRX4_HUMAN	iroquois homeobox 4	212					heart development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0				GBM - Glioblastoma multiforme(108;0.242)		CTGCGCACTTGTTCCGCGGCG	0.483													24	67	---	---	---	---	PASS
NSUN2	54888	broad.mit.edu	37	5	6616870	6616870	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6616870C>G	uc003jdu.2	-	9	1056	c.991G>C	c.(991-993)GTC>CTC	p.V331L	NSUN2_uc003jdt.2_Missense_Mutation_p.V95L|NSUN2_uc011cmk.1_Missense_Mutation_p.V296L|NSUN2_uc003jdv.2_Missense_Mutation_p.V95L	NM_017755	NP_060225	Q08J23	NSUN2_HUMAN	NOL1/NOP2/Sun domain family, member 2	331						cytoplasm|nucleolus	tRNA (cytosine-5-)-methyltransferase activity|tRNA binding			ovary(1)	1						GATGCTATGACTGCTTCATCC	0.423													79	212	---	---	---	---	PASS
TAS2R1	50834	broad.mit.edu	37	5	9629613	9629613	+	Missense_Mutation	SNP	A	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9629613A>T	uc003jem.1	-	1	851	c.532T>A	c.(532-534)TCT>ACT	p.S178T		NM_019599	NP_062545	Q9NYW7	TA2R1_HUMAN	taste receptor T2R1	178	Extracellular (Potential).				chemosensory behavior|sensory perception of taste	integral to membrane	taste receptor activity			ovary(3)	3						GCAACAAAAGAGAAAATCTGT	0.403													115	332	---	---	---	---	PASS
CCT5	22948	broad.mit.edu	37	5	10254914	10254914	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10254914G>T	uc003jeq.2	+	3	466	c.295G>T	c.(295-297)GAT>TAT	p.D99Y	CCT5_uc011cmq.1_Intron|CCT5_uc003jer.2_Missense_Mutation_p.D99Y|CCT5_uc010its.2_Missense_Mutation_p.D99Y|CCT5_uc011cmr.1_Intron|CCT5_uc011cms.1_Missense_Mutation_p.D61Y|CCT5_uc011cmt.1_Intron	NM_012073	NP_036205	P48643	TCPE_HUMAN	chaperonin containing TCP1, subunit 5 (epsilon)	99					'de novo' posttranslational protein folding|response to virus	microtubule organizing center|nucleolus	ATP binding|unfolded protein binding			ovary(2)	2						CAAGTCTCAGGATGATGAAAT	0.428													92	300	---	---	---	---	PASS
CDH18	1016	broad.mit.edu	37	5	19747071	19747071	+	Missense_Mutation	SNP	A	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19747071A>T	uc003jgc.2	-	3	880	c.503T>A	c.(502-504)GTG>GAG	p.V168E	CDH18_uc003jgd.2_Missense_Mutation_p.V168E|CDH18_uc011cnm.1_Missense_Mutation_p.V168E	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	168	Extracellular (Potential).|Cadherin 2.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)					CATTTCAGGCACAGTAACAAT	0.333													178	187	---	---	---	---	PASS
CDH18	1016	broad.mit.edu	37	5	19747228	19747228	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19747228G>T	uc003jgc.2	-	3	723	c.346C>A	c.(346-348)CTA>ATA	p.L116I	CDH18_uc003jgd.2_Missense_Mutation_p.L116I|CDH18_uc011cnm.1_Missense_Mutation_p.L116I	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	116	Extracellular (Potential).|Cadherin 1.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)					TCTCTGTCTAGGCTTTTTGTT	0.438													123	418	---	---	---	---	PASS
CDH12	1010	broad.mit.edu	37	5	21975332	21975332	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21975332C>G	uc010iuc.2	-	3	852	c.394G>C	c.(394-396)GTG>CTG	p.V132L	CDH12_uc011cno.1_Missense_Mutation_p.V132L|CDH12_uc003jgk.2_Missense_Mutation_p.V132L	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein	132	Cadherin 1.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						TCTATGTCCACAGCCTGAGCA	0.428										HNSCC(59;0.17)			92	243	---	---	---	---	PASS
CDH10	1008	broad.mit.edu	37	5	24488134	24488134	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24488134C>A	uc003jgr.1	-	12	2337	c.2005G>T	c.(2005-2007)GCC>TCC	p.A669S	CDH10_uc011cnu.1_RNA	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein	669	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)		ATATCAAAGGCCTGGGTGTCC	0.463										HNSCC(23;0.051)			55	186	---	---	---	---	PASS
CDH9	1007	broad.mit.edu	37	5	26915908	26915908	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26915908C>A	uc003jgs.1	-	3	522	c.353G>T	c.(352-354)AGA>ATA	p.R118I	CDH9_uc010iug.2_Missense_Mutation_p.R118I	NM_016279	NP_057363	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 preproprotein	118	Extracellular (Potential).|Cadherin 1.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|skin(2)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)	9						TTTTTCTTCTCTGTCTAGTTT	0.383													6	639	---	---	---	---	PASS
C5orf22	55322	broad.mit.edu	37	5	31551433	31551433	+	Missense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31551433G>C	uc003jhj.3	+	8	1220	c.1093G>C	c.(1093-1095)GAA>CAA	p.E365Q	C5orf22_uc011cnw.1_RNA|C5orf22_uc003jhk.3_Missense_Mutation_p.E100Q|C5orf22_uc010iuj.2_Missense_Mutation_p.E100Q	NM_018356	NP_060826	Q49AR2	CE022_HUMAN	hypothetical protein LOC55322	365										ovary(2)	2						CGATTATTCAGAACTTCCTCA	0.323													83	225	---	---	---	---	PASS
NNT	23530	broad.mit.edu	37	5	43628327	43628327	+	Missense_Mutation	SNP	T	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43628327T>A	uc003joe.2	+	7	1057	c.802T>A	c.(802-804)TCT>ACT	p.S268T	NNT_uc003jof.2_Missense_Mutation_p.S268T	NM_012343	NP_036475	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	268	Mitochondrial matrix.				tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain	NAD binding|NAD(P)+ transhydrogenase (AB-specific) activity|NAD(P)+ transhydrogenase (B-specific) activity|NADP binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(6;2.58e-06)				NADH(DB00157)	ACAGTTCAAGTCTCTTGGTGC	0.418													168	409	---	---	---	---	PASS
SV2C	22987	broad.mit.edu	37	5	75469543	75469543	+	Intron	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75469543C>A	uc003kei.1	+						uc003kej.2_RNA	NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C						neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		TAAAAGATCTCATTAACATTT	0.368													224	187	---	---	---	---	PASS
SV2C	22987	broad.mit.edu	37	5	75469544	75469544	+	Intron	SNP	A	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75469544A>T	uc003kei.1	+						uc003kej.2_RNA	NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C						neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		AAAAGATCTCATTAACATTTA	0.363													223	187	---	---	---	---	PASS
FAM170A	340069	broad.mit.edu	37	5	118970272	118970272	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118970272C>G	uc003ksm.2	+	3	1039	c.829C>G	c.(829-831)CAA>GAA	p.Q277E	FAM170A_uc003ksl.2_Intron|FAM170A_uc003ksn.2_Missense_Mutation_p.Q277E|FAM170A_uc003kso.2_Missense_Mutation_p.Q230E	NM_182761	NP_877438	A1A519	F170A_HUMAN	family with sequence similarity 170, member A	277	Glu-rich.					intracellular	zinc ion binding			skin(1)	1						AGAGAGCACCCaagatgagca	0.343													163	159	---	---	---	---	PASS
IL9	3578	broad.mit.edu	37	5	135229765	135229765	+	Silent	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135229765G>A	uc003lbb.1	-	4	270	c.259C>T	c.(259-261)CTG>TTG	p.L87L		NM_000590	NP_000581	P15248	IL9_HUMAN	interleukin 9 precursor	87					immune response|inflammatory response|positive regulation of cell proliferation|positive regulation of interleukin-5 biosynthetic process	extracellular space	cytokine activity|cytokine receptor binding|growth factor activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTGAAAATCAGTGGGTATCTT	0.388													71	46	---	---	---	---	PASS
TMEM173	340061	broad.mit.edu	37	5	138857016	138857016	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138857016C>A	uc003lep.2	-	7	1095	c.844G>T	c.(844-846)GAG>TAG	p.E282*		NM_198282	NP_938023	Q86WV6	TM173_HUMAN	transmembrane protein 173	282	Cytoplasmic (Potential).				activation of innate immune response|apoptosis|cellular response to exogenous dsRNA|defense response to virus|innate immune response|interferon-beta production|positive regulation of defense response to virus by host|positive regulation of protein binding|positive regulation of protein import into nucleus, translocation|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter	endoplasmic reticulum membrane|integral to membrane|mitochondrial outer membrane|perinuclear region of cytoplasm|plasma membrane	protein homodimerization activity|protein kinase binding|transcription factor binding			upper_aerodigestive_tract(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AGCCTATCCTCCCGGCTAAAG	0.562													113	52	---	---	---	---	PASS
PCDHB4	56131	broad.mit.edu	37	5	140502219	140502219	+	Silent	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140502219G>C	uc003lip.1	+	1	639	c.639G>C	c.(637-639)GCG>GCC	p.A213A		NM_018938	NP_061761	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4 precursor	213	Cadherin 2.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	cytoplasm|integral to plasma membrane|intermediate filament cytoskeleton	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCCTCGTGGCGCTGGATGGTG	0.512													153	67	---	---	---	---	PASS
PCDHB7	56129	broad.mit.edu	37	5	140554282	140554282	+	Silent	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140554282C>T	uc003lit.2	+	1	2040	c.1866C>T	c.(1864-1866)GGC>GGT	p.G622G		NM_018940	NP_061763	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7 precursor	622	Cadherin 6.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|central_nervous_system(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGCACAATGGCGAGGTGCGTA	0.697													6	112	---	---	---	---	PASS
CSNK1A1	1452	broad.mit.edu	37	5	148930407	148930407	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148930407C>A	uc003lqx.1	-	1	601	c.121G>T	c.(121-123)GAG>TAG	p.E41*	CSNK1A1_uc011dcc.1_5'Flank|CSNK1A1_uc003lqv.1_5'Flank|CSNK1A1_uc003lqw.1_Nonsense_Mutation_p.E41*|CSNK1A1_uc003lqy.1_Nonsense_Mutation_p.E41*|CSNK1A1_uc010jha.1_Nonsense_Mutation_p.E41*	NM_001892	NP_001883	P48729	KC1A_HUMAN	casein kinase 1, alpha 1 isoform 2	41	Protein kinase.				cell division|mitosis|Wnt receptor signaling pathway	centrosome|condensed chromosome kinetochore|cytosol|nuclear speck	ATP binding|protein binding|protein binding|protein serine/threonine kinase activity			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)		ATGATTACCTCGCCGTTGGTG	0.547													86	39	---	---	---	---	PASS
ZNF192	7745	broad.mit.edu	37	6	28120957	28120957	+	Missense_Mutation	SNP	A	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28120957A>G	uc003nkn.1	+	6	1083	c.899A>G	c.(898-900)GAA>GGA	p.E300G	ZNF192_uc010jqx.1_Missense_Mutation_p.E300G|ZNF192_uc010jqy.1_Missense_Mutation_p.E113G|ZNF192_uc011dkz.1_Missense_Mutation_p.E113G	NM_006298	NP_006289	Q15776	ZN192_HUMAN	zinc finger protein 192	300	KRAB.				viral reproduction	cytoplasm|nucleolus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						CTTGAGCATGAAGAAGCCCGA	0.483													73	129	---	---	---	---	PASS
COL11A2	1302	broad.mit.edu	37	6	33147525	33147525	+	Nonsense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33147525G>A	uc003ocx.1	-	13	1645	c.1417C>T	c.(1417-1419)CAG>TAG	p.Q473*	COL11A2_uc010jul.1_5'Flank|COL11A2_uc003ocy.1_Nonsense_Mutation_p.Q387*|COL11A2_uc003ocz.1_Nonsense_Mutation_p.Q366*	NM_080680	NP_542411	P13942	COBA2_HUMAN	collagen, type XI, alpha 2 isoform 1	473	Nonhelical region.				cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging			ovary(3)|skin(2)	5						GCCTGGGCCTGAGCCTCCTGG	0.637													41	90	---	---	---	---	PASS
MLN	4295	broad.mit.edu	37	6	33768842	33768842	+	Silent	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33768842G>A	uc003off.1	-	2	170	c.99C>T	c.(97-99)GGC>GGT	p.G33G	MLN_uc003ofg.1_Silent_p.G33G|MLN_uc011drn.1_Silent_p.G33G	NM_002418	NP_002409	P12872	MOTI_HUMAN	motilin isoform 1 preproprotein	33					cell-cell signaling|G-protein coupled receptor protein signaling pathway	extracellular region|soluble fraction	hormone activity				0						TCTGGAGTTCGCCATAGGTGA	0.567													219	312	---	---	---	---	PASS
DNAH8	1769	broad.mit.edu	37	6	38835933	38835933	+	Silent	SNP	T	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38835933T>A	uc003ooe.1	+	46	6738	c.6138T>A	c.(6136-6138)ATT>ATA	p.I2046I		NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						AATTAAGCATTGTCATGAGAG	0.353													120	154	---	---	---	---	PASS
DNAH8	1769	broad.mit.edu	37	6	38835954	38835954	+	Silent	SNP	T	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38835954T>C	uc003ooe.1	+	46	6759	c.6159T>C	c.(6157-6159)GAT>GAC	p.D2053D		NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						GACTAAGAGATATGAACCTTT	0.363													62	168	---	---	---	---	PASS
DNAH8	1769	broad.mit.edu	37	6	38891790	38891790	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38891790G>T	uc003ooe.1	+	71	10763	c.10163G>T	c.(10162-10164)TGC>TTC	p.C3388F	uc003oof.1_Intron	NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						ATTCTGCTGTGCACGGGATTC	0.428													158	310	---	---	---	---	PASS
DNAH8	1769	broad.mit.edu	37	6	38980082	38980082	+	Missense_Mutation	SNP	T	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38980082T>C	uc003ooe.1	+	88	13412	c.12812T>C	c.(12811-12813)ATA>ACA	p.I4271T		NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						GTCATTTCAATACTCCGCAGT	0.358													106	220	---	---	---	---	PASS
LRFN2	57497	broad.mit.edu	37	6	40400370	40400370	+	Silent	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40400370G>C	uc003oph.1	-	2	948	c.483C>G	c.(481-483)CTC>CTG	p.L161L		NM_020737	NP_065788	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III	161	LRR 5.|Extracellular (Potential).					cell junction|integral to membrane|postsynaptic membrane				ovary(2)|skin(1)	3	Ovarian(28;0.0418)|Colorectal(47;0.196)					GCAGGCCATGGAGGTTGTTGT	0.582													65	98	---	---	---	---	PASS
APOBEC2	10930	broad.mit.edu	37	6	41029329	41029329	+	Missense_Mutation	SNP	G	A	A	rs142866037	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41029329G>A	uc003opl.2	+	2	541	c.394G>A	c.(394-396)GCT>ACT	p.A132T	UNC5CL_uc010jxe.1_Intron|APOBEC2_uc010jxf.2_RNA	NM_006789	NP_006780	Q9Y235	ABEC2_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic	132					DNA demethylation|mRNA processing		cytidine deaminase activity|RNA binding|zinc ion binding				0	Ovarian(28;0.0418)|Colorectal(47;0.196)					TGCAGCGTGTGCTGACCGCAT	0.567													222	333	---	---	---	---	PASS
CRISP1	167	broad.mit.edu	37	6	49825094	49825094	+	Missense_Mutation	SNP	A	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49825094A>C	uc003ozw.2	-	2	99	c.20T>G	c.(19-21)TTG>TGG	p.L7W	CRISP1_uc003ozx.2_Missense_Mutation_p.L7W	NM_001131	NP_001122	P54107	CRIS1_HUMAN	acidic epididymal glycoprotein-like 1 isoform 1	7					fusion of sperm to egg plasma membrane	extracellular space					0	Lung NSC(77;0.0358)					AACCAAAAACAAGAGGTGTTT	0.303													35	105	---	---	---	---	PASS
TFAP2D	83741	broad.mit.edu	37	6	50718997	50718997	+	Missense_Mutation	SNP	A	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50718997A>G	uc003paf.2	+	7	1611	c.1099A>G	c.(1099-1101)ATT>GTT	p.I367V	TFAP2D_uc011dwt.1_RNA	NM_172238	NP_758438	Q7Z6R9	AP2D_HUMAN	transcription factor AP-2 beta-like 1	367	H-S-H (helix-span-helix), dimerization.						DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|breast(1)	7	Lung NSC(77;0.0334)					ACCCACTCCAATTCTAGACCT	0.368													60	135	---	---	---	---	PASS
EYS	346007	broad.mit.edu	37	6	66053931	66053931	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66053931C>A	uc011dxu.1	-	10	2137	c.1599G>T	c.(1597-1599)GAG>GAT	p.E533D	EYS_uc003peq.2_Missense_Mutation_p.E533D|EYS_uc003per.1_Missense_Mutation_p.E533D	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1	533					response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						ATTACCTTACCTCTTTTGTGC	0.328													54	110	---	---	---	---	PASS
SYNCRIP	10492	broad.mit.edu	37	6	86324793	86324793	+	Missense_Mutation	SNP	C	A	A	rs146447694		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86324793C>A	uc003pla.2	-	11	2094	c.1553G>T	c.(1552-1554)CGC>CTC	p.R518L	SYNCRIP_uc003pku.2_Missense_Mutation_p.R518L|SYNCRIP_uc003pkw.2_Missense_Mutation_p.R483L|SYNCRIP_uc003pky.2_Missense_Mutation_p.R420L|SYNCRIP_uc003pkv.2_Missense_Mutation_p.R518L|SYNCRIP_uc003pkx.2_Missense_Mutation_p.R366L|SYNCRIP_uc003pkz.2_Missense_Mutation_p.R483L	NM_006372	NP_006363	O60506	HNRPQ_HUMAN	synaptotagmin binding, cytoplasmic RNA	518	Interaction with SMN.|Interaction with APOBEC1.|8 X 3 AA repeats of R-G-G.				CRD-mediated mRNA stabilization|interspecies interaction between organisms	catalytic step 2 spliceosome|CRD-mediated mRNA stability complex|endoplasmic reticulum|histone pre-mRNA 3'end processing complex|microsome|nucleoplasm	nucleotide binding|protein binding			ovary(2)	2		all_cancers(76;0.000137)|Acute lymphoblastic leukemia(125;3.66e-08)|Prostate(29;8.2e-07)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0297)		BRCA - Breast invasive adenocarcinoma(108;0.0389)		GGCTCTACCGCGGGGAGGAGC	0.577													128	214	---	---	---	---	PASS
GJA10	84694	broad.mit.edu	37	6	90604959	90604959	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90604959C>A	uc011eaa.1	+	1	772	c.772C>A	c.(772-774)CCA>ACA	p.P258T		NM_032602	NP_115991	Q969M2	CXA10_HUMAN	gap junction protein, alpha 10	258	Cytoplasmic (Potential).				synaptic transmission	connexon complex|integral to membrane	gap junction channel activity				0		all_cancers(76;5.71e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.0915)		AACAGGCCCTCCATTCCATTT	0.393													101	161	---	---	---	---	PASS
LAMA4	3910	broad.mit.edu	37	6	112451081	112451081	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112451081G>A	uc003pvu.2	-	30	4439	c.4130C>T	c.(4129-4131)ACC>ATC	p.T1377I	LAMA4_uc003pvv.2_Missense_Mutation_p.T1370I|LAMA4_uc003pvt.2_Missense_Mutation_p.T1370I	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor	1377	Laminin G-like 3.				cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		attataCCTGGTAAAGTAGGC	0.323													23	34	---	---	---	---	PASS
GPRC6A	222545	broad.mit.edu	37	6	117121962	117121962	+	Intron	SNP	A	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117121962A>G	uc003pxj.1	-						GPRC6A_uc003pxk.1_Intron|GPRC6A_uc003pxl.1_Intron	NM_148963	NP_683766	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, family C, group 6,						response to amino acid stimulus		G-protein coupled receptor activity			ovary(4)|skin(2)	6		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		CCAAGTAACTATAAAAAATAA	0.299													30	80	---	---	---	---	PASS
LAMA2	3908	broad.mit.edu	37	6	129609151	129609151	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129609151G>T	uc003qbn.2	+	19	2802	c.2697G>T	c.(2695-2697)GAG>GAT	p.E899D	LAMA2_uc003qbo.2_Missense_Mutation_p.E899D	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	899	Laminin EGF-like 8.				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GGTACTGTGAGCTCTGTGCTG	0.473													214	446	---	---	---	---	PASS
L3MBTL3	84456	broad.mit.edu	37	6	130374031	130374031	+	Missense_Mutation	SNP	A	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130374031A>C	uc003qbt.2	+	7	647	c.477A>C	c.(475-477)GAA>GAC	p.E159D	L3MBTL3_uc003qbu.2_Missense_Mutation_p.E134D	NM_032438	NP_115814	Q96JM7	LMBL3_HUMAN	l(3)mbt-like 3 isoform a	159					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)		GGGACGTAGAAGAAGACAATG	0.378													28	80	---	---	---	---	PASS
TAAR5	9038	broad.mit.edu	37	6	132910451	132910451	+	Silent	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132910451G>T	uc003qdk.2	-	1	427	c.375C>A	c.(373-375)CTC>CTA	p.L125L		NM_003967	NP_003958	O14804	TAAR5_HUMAN	trace amine associated receptor 5	125	Helical; Name=3; (Potential).				synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity			skin(1)	1	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.00604)|GBM - Glioblastoma multiforme(226;0.015)		AAATGAAACAGAGATGGAAGA	0.567													73	117	---	---	---	---	PASS
ECT2L	345930	broad.mit.edu	37	6	139164314	139164314	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139164314C>G	uc003qif.1	+	4	644	c.541C>G	c.(541-543)CAA>GAA	p.Q181E	ECT2L_uc011edq.1_Missense_Mutation_p.Q112E	NM_001077706	NP_001071174	Q008S8	ECT2L_HUMAN	epithelial cell transforming sequence 2	181					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity				0						ACTGGAGAGACAAAGAGAAAA	0.413													11	237	---	---	---	---	PASS
STX11	8676	broad.mit.edu	37	6	144508138	144508138	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144508138C>G	uc003qks.3	+	2	566	c.374C>G	c.(373-375)GCG>GGG	p.A125G		NM_003764	NP_003755	O75558	STX11_HUMAN	syntaxin 11	125				HSAVAR -> ALGSGG (in Ref. 1; AAD02107).	cellular membrane fusion|intracellular protein transport|vesicle-mediated transport	Golgi apparatus|membrane	SNAP receptor activity			ovary(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(155;2.17e-06)|GBM - Glioblastoma multiforme(68;0.0492)		TCGGCAGTGGCGCGCATTTCG	0.672									Familial_Hemophagocytic_Lymphohistiocytosis				11	23	---	---	---	---	PASS
SHPRH	257218	broad.mit.edu	37	6	146262959	146262959	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146262959C>A	uc003qlf.2	-	10	2689	c.2290G>T	c.(2290-2292)GAA>TAA	p.E764*	SHPRH_uc003qld.2_Nonsense_Mutation_p.E764*|SHPRH_uc003qle.2_Nonsense_Mutation_p.E764*|SHPRH_uc003qlg.1_Nonsense_Mutation_p.E320*|SHPRH_uc003qlj.1_Nonsense_Mutation_p.E653*	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a	764	Helicase ATP-binding; second part.				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)		ATATCCTGTTCTGCCAAAAAA	0.383													58	79	---	---	---	---	PASS
AKAP12	9590	broad.mit.edu	37	6	151672421	151672421	+	Silent	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151672421C>T	uc011eep.1	+	4	3135	c.2895C>T	c.(2893-2895)GTC>GTT	p.V965V	AKAP12_uc003qoe.2_Silent_p.V965V|AKAP12_uc003qof.2_Silent_p.V867V|AKAP12_uc010kim.2_Intron|AKAP12_uc003qog.2_Silent_p.V860V	NM_005100	NP_005091	Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12 isoform 1	965					G-protein coupled receptor protein signaling pathway|positive regulation of cAMP biosynthetic process|positive regulation of protein kinase A signaling cascade|protein targeting	cell cortex|cytoskeleton|plasma membrane	adenylate cyclase binding|protein kinase A binding			large_intestine(2)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1)	8		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		GCGACACGGTCGTTAGTGAGG	0.547													61	156	---	---	---	---	PASS
SNX9	51429	broad.mit.edu	37	6	158349731	158349731	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158349731G>T	uc003qqv.1	+	12	1458	c.1285G>T	c.(1285-1287)GGC>TGC	p.G429C		NM_016224	NP_057308	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	429	BAR.				cell communication|intracellular protein transport|lipid tube assembly|positive regulation of GTPase activity|positive regulation of protein oligomerization|receptor-mediated endocytosis	clathrin-coated vesicle|cytoplasmic vesicle membrane|extrinsic to internal side of plasma membrane|ruffle|trans-Golgi network	1-phosphatidylinositol binding|protein homodimerization activity|ubiquitin protein ligase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)		GCGCTGCACGGGCCGTAAGTC	0.597													11	14	---	---	---	---	PASS
SUN1	23353	broad.mit.edu	37	7	895996	895996	+	Missense_Mutation	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:895996C>T	uc011jvp.1	+	13	1431	c.1352C>T	c.(1351-1353)GCC>GTC	p.A451V	GET4_uc003sjj.1_RNA|SUN1_uc003sjf.2_Missense_Mutation_p.A368V|SUN1_uc011jvq.1_Missense_Mutation_p.A348V|SUN1_uc003sjg.2_Missense_Mutation_p.A356V|SUN1_uc011jvr.1_Missense_Mutation_p.A249V|SUN1_uc003sji.2_Missense_Mutation_p.A289V|SUN1_uc003sjk.2_Missense_Mutation_p.A90V	NM_001130965	NP_001124437	O94901	SUN1_HUMAN	unc-84 homolog A isoform a	478	Perinuclear space.|Potential.				cytoskeletal anchoring at nuclear membrane|nuclear matrix anchoring at nuclear membrane	integral to membrane|nuclear inner membrane|SUN-KASH complex	protein binding				0						ACTTTTTAGGCCATCCAGAAG	0.348													4	235	---	---	---	---	PASS
C7orf50	84310	broad.mit.edu	37	7	1166901	1166901	+	Missense_Mutation	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1166901C>T	uc003sju.2	-	2	191	c.121G>A	c.(121-123)GGC>AGC	p.G41S	C7orf50_uc011jvt.1_Missense_Mutation_p.G41S|C7orf50_uc011jvu.1_Missense_Mutation_p.G41S	NM_032350	NP_115726	Q9BRJ6	CG050_HUMAN	hypothetical protein LOC84310	41							protein binding				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0216)|OV - Ovarian serous cystadenocarcinoma(56;1.3e-15)		ACCTTGGAGCCGGCTCCTTCG	0.597													12	21	---	---	---	---	PASS
TTYH3	80727	broad.mit.edu	37	7	2691859	2691859	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2691859G>T	uc003smp.2	+	8	1097	c.910G>T	c.(910-912)GCC>TCC	p.A304S	TTYH3_uc010ksn.2_Missense_Mutation_p.A24S|TTYH3_uc003smq.2_Missense_Mutation_p.A133S	NM_025250	NP_079526	Q9C0H2	TTYH3_HUMAN	tweety 3	304	Extracellular (Potential).					chloride channel complex|plasma membrane	chloride channel activity				0		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.04e-14)		GCCCCGCGCCGCCAACCCCTT	0.652													15	38	---	---	---	---	PASS
THSD7A	221981	broad.mit.edu	37	7	11464387	11464387	+	Missense_Mutation	SNP	A	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11464387A>T	uc003ssf.3	-	15	3571	c.3319T>A	c.(3319-3321)TGC>AGC	p.C1107S		NM_015204	NP_056019	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	1107	TSP type-1 11.|Extracellular (Potential).					integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		GTCACCTTGCAGATGCTCCAG	0.488										HNSCC(18;0.044)			177	323	---	---	---	---	PASS
DNAH11	8701	broad.mit.edu	37	7	21744074	21744074	+	Missense_Mutation	SNP	A	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21744074A>T	uc003svc.2	+	39	6348	c.6317A>T	c.(6316-6318)GAT>GTT	p.D2106V		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2106					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						GCATTAAGGGATTTCAATATG	0.413									Kartagener_syndrome				20	49	---	---	---	---	PASS
DNAH11	8701	broad.mit.edu	37	7	21824066	21824066	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21824066G>T	uc003svc.2	+	59	9557	c.9526G>T	c.(9526-9528)GTG>TTG	p.V3176L		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	3176	Stalk (By similarity).				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						TCAGACTGAAGTGTTCCAGAA	0.418									Kartagener_syndrome				21	45	---	---	---	---	PASS
NFE2L3	9603	broad.mit.edu	37	7	26225342	26225342	+	Missense_Mutation	SNP	T	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26225342T>C	uc003sxq.2	+	4	2296	c.2024T>C	c.(2023-2025)GTA>GCA	p.V675A		NM_004289	NP_004280	Q9Y4A8	NF2L3_HUMAN	nuclear factor erythroid 2-like 3	675					transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			skin(3)|ovary(1)	4						ATCTTGATAGTACCCAAAGAA	0.408													13	247	---	---	---	---	PASS
HOXA10	3206	broad.mit.edu	37	7	27211732	27211732	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27211732C>A	uc011jzm.1	-	2	1049	c.1019G>T	c.(1018-1020)CGC>CTC	p.R340L	MIR196B_hsa-mir-196b|MI0001150_5'Flank|HOXA10_uc003syw.3_Missense_Mutation_p.R24L	NM_018951	NP_061824	P31260	HXA10_HUMAN	homeobox A10 isoform a	340	Homeobox.				spermatogenesis		protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						GTAGGGGCAGCGCTTCTTCCG	0.522													64	135	---	---	---	---	PASS
FAM188B	84182	broad.mit.edu	37	7	30890066	30890066	+	Intron	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30890066G>A	uc003tbt.2	+						FAM188B_uc010kwe.2_Intron|AQP1_uc011kac.1_5'Flank	NM_032222	NP_115598	Q4G0A6	F188B_HUMAN	hypothetical protein LOC84182												0						TTTCTTGTCCGCAGGGGACTG	0.607													14	18	---	---	---	---	PASS
NEUROD6	63974	broad.mit.edu	37	7	31378572	31378572	+	Missense_Mutation	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31378572C>T	uc003tch.2	-	2	664	c.311G>A	c.(310-312)AGG>AAG	p.R104K		NM_022728	NP_073565	Q96NK8	NDF6_HUMAN	neurogenic differentiation 6	104	Basic motif.				cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)	2						CATCCTGTTCCTCTCGCGCGC	0.478													228	328	---	---	---	---	PASS
PDE1C	5137	broad.mit.edu	37	7	31887681	31887681	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31887681C>A	uc003tcm.1	-	9	1350	c.881G>T	c.(880-882)AGA>ATA	p.R294I	PDE1C_uc003tcn.1_Missense_Mutation_p.R294I|PDE1C_uc003tco.1_Missense_Mutation_p.R354I|PDE1C_uc003tcr.2_Missense_Mutation_p.R294I|PDE1C_uc003tcs.2_Missense_Mutation_p.R294I	NM_005020	NP_005011	Q14123	PDE1C_HUMAN	phosphodiesterase 1C	294	Catalytic (By similarity).				activation of phospholipase C activity|nerve growth factor receptor signaling pathway	cytosol	calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(3)|central_nervous_system(1)	4			GBM - Glioblastoma multiforme(11;0.216)			CAGTACAGATCTGTCATTATA	0.388													84	180	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48311842	48311842	+	Missense_Mutation	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48311842C>T	uc003toq.2	+	17	2604	c.2579C>T	c.(2578-2580)TCT>TTT	p.S860F	ABCA13_uc010kyr.2_Missense_Mutation_p.S363F	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	860					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						TTAAATTTTTCTGTTCCAGAA	0.318													70	97	---	---	---	---	PASS
DLX5	1749	broad.mit.edu	37	7	96650125	96650125	+	Missense_Mutation	SNP	T	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96650125T>C	uc003uon.2	-	3	1001	c.793A>G	c.(793-795)AGC>GGC	p.S265G		NM_005221	NP_005212	P56178	DLX5_HUMAN	distal-less homeobox 5	265					cell proliferation|endochondral ossification|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(1)	1	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					TTGATTGAGCTGGCTGCACTT	0.622													30	79	---	---	---	---	PASS
ZAN	7455	broad.mit.edu	37	7	100389695	100389695	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100389695C>A	uc003uwj.2	+	42	7802	c.7637C>A	c.(7636-7638)GCC>GAC	p.A2546D	ZAN_uc003uwk.2_Missense_Mutation_p.A2546D|ZAN_uc003uwl.2_RNA|ZAN_uc010lhh.2_RNA|ZAN_uc010lhi.2_RNA|ZAN_uc011kke.1_Missense_Mutation_p.P539T	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	2546	Extracellular (Potential).				binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			AGCACCCAGGCCTGTAGGGTG	0.677													12	24	---	---	---	---	PASS
SLC12A9	56996	broad.mit.edu	37	7	100459152	100459152	+	Silent	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100459152G>T	uc003uwp.2	+	11	1624	c.1482G>T	c.(1480-1482)GCG>GCT	p.A494A	SLC12A9_uc003uwq.2_Silent_p.A405A|SLC12A9_uc011kki.1_Silent_p.A25A|SLC12A9_uc003uwr.2_Silent_p.A230A|SLC12A9_uc003uws.2_Silent_p.A25A|SLC12A9_uc003uwt.2_Silent_p.A230A|SLC12A9_uc003uwv.2_Silent_p.A25A	NM_020246	NP_064631	Q9BXP2	S12A9_HUMAN	solute carrier family 12 (potassium/chloride	494	Extracellular (Potential).					integral to membrane|plasma membrane	cation:chloride symporter activity				0	Lung NSC(181;0.041)|all_lung(186;0.0581)					TGCTCACCGCGCGAGGAGGCC	0.652													64	99	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100675524	100675524	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100675524C>G	uc003uxp.1	+	3	880	c.827C>G	c.(826-828)CCA>CGA	p.P276R	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	276	Extracellular (Potential).|59 X approximate tandem repeats.|2.|Ser-rich.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					GGAAGCACTCCATTAACAAGA	0.507													150	380	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100679577	100679577	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100679577G>T	uc003uxp.1	+	3	4933	c.4880G>T	c.(4879-4881)AGT>ATT	p.S1627I	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	1627	Extracellular (Potential).|Ser-rich.|59 X approximate tandem repeats.|25.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					TCAACTCCTAGTGAAGGAAGT	0.493													295	479	---	---	---	---	PASS
RELN	5649	broad.mit.edu	37	7	103183247	103183247	+	Missense_Mutation	SNP	T	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103183247T>C	uc003vca.2	-	43	6762	c.6602A>G	c.(6601-6603)AAC>AGC	p.N2201S	RELN_uc010liz.2_Missense_Mutation_p.N2201S	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	2201					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		AAAGAGGTTGTTTCCACTAGA	0.373													93	179	---	---	---	---	PASS
FOXP2	93986	broad.mit.edu	37	7	114302136	114302136	+	Missense_Mutation	SNP	A	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114302136A>G	uc003vhb.2	+	14	2038	c.1664A>G	c.(1663-1665)AAT>AGT	p.N555S	FOXP2_uc003vgu.2_RNA|FOXP2_uc003vgz.2_Missense_Mutation_p.N580S|FOXP2_uc003vha.2_Missense_Mutation_p.N463S|FOXP2_uc011kmu.1_Missense_Mutation_p.N572S|FOXP2_uc011kmv.1_Missense_Mutation_p.N554S|FOXP2_uc010ljz.1_Missense_Mutation_p.N370S|FOXP2_uc003vhe.1_Missense_Mutation_p.N125S	NM_014491	NP_055306	O15409	FOXP2_HUMAN	forkhead box P2 isoform I	555	Fork-head.				camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|breast(1)|skin(1)	8						GTACGTCATAATCTTAGCCTG	0.363													49	74	---	---	---	---	PASS
ARF5	381	broad.mit.edu	37	7	127231089	127231089	+	Missense_Mutation	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127231089C>T	uc003vmb.1	+	5	439	c.403C>T	c.(403-405)CCC>TCC	p.P135S	FSCN3_uc003vmc.1_5'Flank|FSCN3_uc011kog.1_5'Flank|FSCN3_uc011koh.1_5'Flank|FSCN3_uc003vmd.1_5'Flank|FSCN3_uc010llc.1_5'Flank	NM_001662	NP_001653	P84085	ARF5_HUMAN	ADP-ribosylation factor 5	135					protein transport|small GTPase mediated signal transduction|vesicle-mediated transport	Golgi apparatus|perinuclear region of cytoplasm	GTP binding|GTPase activity|protein binding			ovary(1)	1						CAACGCCATGCCCGTGAGCGA	0.612													6	333	---	---	---	---	PASS
FAM180A	389558	broad.mit.edu	37	7	135418840	135418840	+	Nonsense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135418840G>C	uc003vtd.2	-	3	671	c.405C>G	c.(403-405)TAC>TAG	p.Y135*	FAM180A_uc010lmt.2_RNA|FAM180A_uc010lmu.2_Nonsense_Mutation_p.Y135*	NM_205855	NP_995327	Q6UWF9	F180A_HUMAN	hypothetical protein LOC389558 precursor	135						extracellular region				ovary(2)	2						GGGCTGTGCGGTAGGCTGTGT	0.617													49	88	---	---	---	---	PASS
BRAF	673	broad.mit.edu	37	7	140453108	140453108	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140453108C>A	uc003vwc.3	-	15	1888	c.1827G>T	c.(1825-1827)CAG>CAT	p.Q609H		NM_004333	NP_004324	P15056	BRAF_HUMAN	B-Raf	609	Protein kinase.				activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	p.Q609R(1)|p.Q609Q(1)|p.Q609*(1)	KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)	ACTGTTCAAACTGATGGGACC	0.393		61	Mis|T|O	AKAP9|KIAA1549	melanoma|colorectal|papillary thyroid|borderline ov|Non small-cell lung cancer (NSCLC)|cholangiocarcinoma|pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous_syndrome				83	176	---	---	---	---	PASS
WEE2	494551	broad.mit.edu	37	7	141427144	141427144	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141427144C>A	uc003vwn.2	+	10	1839	c.1433C>A	c.(1432-1434)GCA>GAA	p.A478E	FLJ40852_uc011krh.1_RNA|FLJ40852_uc010lnm.2_RNA|FLJ40852_uc010lnn.2_Intron|FLJ40852_uc003vwm.3_Intron|FLJ40852_uc010lno.2_Intron	NM_001105558	NP_001099028	P0C1S8	WEE2_HUMAN	WEE1 homolog 2	478	Protein kinase.				egg activation|female meiosis|female pronucleus assembly|meiotic metaphase II|meiotic prophase I|mitosis|negative regulation of oocyte development|regulation of meiosis I	centrosome|nucleus	ATP binding|magnesium ion binding|non-membrane spanning protein tyrosine kinase activity|protein serine/threonine kinase activity			ovary(1)|stomach(1)	2	Melanoma(164;0.0171)					CCTTCTGCAGCAGCTCTGGCC	0.468													6	414	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	142423454	142423454	+	Intron	SNP	A	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142423454A>T	uc011krr.1	+						uc003vzp.2_Intron|uc011ksh.1_Intron|uc011ksi.1_Intron|uc003vzw.1_Intron|uc010loj.1_Intron|uc003wad.2_5'Flank|uc011ksg.1_Intron|uc010lol.1_Missense_Mutation_p.K37M|uc011ksj.1_RNA					SubName: Full=V_segment translation product; Flags: Fragment;																		ACTGGAAAGAAGTTAACAGTG	0.483													60	95	---	---	---	---	PASS
OR2A2	442361	broad.mit.edu	37	7	143806781	143806781	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143806781C>A	uc011ktz.1	+	1	106	c.106C>A	c.(106-108)CTC>ATC	p.L36I		NM_001005480	NP_001005480	Q6IF42	OR2A2_HUMAN	olfactory receptor, family 2, subfamily A,	36	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2	Melanoma(164;0.0783)					CTTCTATACACTCACCCTGCT	0.517													161	291	---	---	---	---	PASS
CNTNAP2	26047	broad.mit.edu	37	7	148112556	148112556	+	Silent	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148112556C>T	uc003weu.1	+	24	4360	c.3844C>T	c.(3844-3846)CTG>TTG	p.L1282L	CNTNAP2_uc003wev.1_Silent_p.L59L	NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor	1282	Helical; (Potential).				behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			CCTGGTCTTCCTGATCCGGTA	0.582										HNSCC(39;0.1)			52	85	---	---	---	---	PASS
KRBA1	84626	broad.mit.edu	37	7	149426415	149426415	+	Missense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149426415G>C	uc003wfz.2	+	14	2164	c.1765G>C	c.(1765-1767)GAC>CAC	p.D589H	KRBA1_uc010lpj.2_RNA|KRBA1_uc003wga.2_Intron|KRBA1_uc003wgb.2_Intron	NM_032534	NP_115923	A5PL33	KRBA1_HUMAN	KRAB A domain containing 1	589										ovary(1)|central_nervous_system(1)	2	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GGGGTTCAAAGACCCTGGGGC	0.652													11	26	---	---	---	---	PASS
REPIN1	29803	broad.mit.edu	37	7	150069554	150069554	+	Silent	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150069554C>T	uc010lpq.1	+	4	1713	c.1224C>T	c.(1222-1224)TGC>TGT	p.C408C	REPIN1_uc003whd.2_Silent_p.C397C|REPIN1_uc010lpr.1_Silent_p.C465C|REPIN1_uc003whc.2_Silent_p.C408C|REPIN1_uc003whe.2_Silent_p.C408C	NM_013400	NP_037532	Q9BWE0	REPI1_HUMAN	replication initiator 1 isoform 1	408	C2H2-type 10.				DNA replication	nuclear origin of replication recognition complex	DNA binding|zinc ion binding			pancreas(1)	1	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.011)			GCGCCGAGTGCGGGAAGAACT	0.721													5	6	---	---	---	---	PASS
ACCN3	9311	broad.mit.edu	37	7	150747277	150747277	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150747277G>A	uc003win.2	+	2	987	c.619G>A	c.(619-621)GGC>AGC	p.G207S	ACCN3_uc003wio.2_Missense_Mutation_p.G207S|ACCN3_uc003wip.2_Missense_Mutation_p.G207S|ACCN3_uc003wiq.2_RNA	NM_004769	NP_004760	Q9UHC3	ACCN3_HUMAN	amiloride-sensitive cation channel 3 isoform a	207	Extracellular (Potential).				sensory perception|signal transduction	cytoplasm|integral to plasma membrane	ligand-gated sodium channel activity			ovary(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GGGTGGCATGGGCAATGGGCT	0.577													34	107	---	---	---	---	PASS
SPAG11B	10407	broad.mit.edu	37	8	7320355	7320355	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:7320355G>T	uc003wrk.2	-	2	255	c.88C>A	c.(88-90)CAC>AAC	p.H30N	SPAG11B_uc003wrg.1_Missense_Mutation_p.H30N|SPAG11B_uc003wrh.1_Missense_Mutation_p.H30N|SPAG11B_uc003wrl.2_Missense_Mutation_p.H30N|SPAG11B_uc003wrm.2_Missense_Mutation_p.H30N	NM_016512	NP_057596	Q08648	SG11B_HUMAN	sperm associated antigen 11B isoform A	30					spermatogenesis	extracellular region					0				COAD - Colon adenocarcinoma(149;0.0162)|READ - Rectum adenocarcinoma(644;0.236)		GTGGCTGAGTGGTTCACATGT	0.587													30	136	---	---	---	---	PASS
DOK2	9046	broad.mit.edu	37	8	21769830	21769830	+	Silent	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21769830G>A	uc003wzy.1	-	2	348	c.255C>T	c.(253-255)TTC>TTT	p.F85F	DOK2_uc003wzx.1_Silent_p.F85F|DOK2_uc003wzz.1_5'UTR|DOK2_uc010lth.1_Intron	NM_003974	NP_003965	O60496	DOK2_HUMAN	docking protein 2	85	PH.				blood coagulation|leukocyte migration	cytosol	identical protein binding|insulin receptor binding				0				Colorectal(74;0.0145)|COAD - Colon adenocarcinoma(73;0.0608)		TGGTCTCCAGGAAGAAGGCAC	0.716													3	2	---	---	---	---	PASS
DOK2	9046	broad.mit.edu	37	8	21769833	21769833	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21769833G>T	uc003wzy.1	-	2	345	c.252C>A	c.(250-252)TTC>TTA	p.F84L	DOK2_uc003wzx.1_Missense_Mutation_p.F84L|DOK2_uc003wzz.1_5'UTR|DOK2_uc010lth.1_Intron	NM_003974	NP_003965	O60496	DOK2_HUMAN	docking protein 2	84	PH.				blood coagulation|leukocyte migration	cytosol	identical protein binding|insulin receptor binding				0				Colorectal(74;0.0145)|COAD - Colon adenocarcinoma(73;0.0608)		TCTCCAGGAAGAAGGCACTGG	0.711													3	1	---	---	---	---	PASS
PPP3CC	5533	broad.mit.edu	37	8	22332669	22332669	+	Intron	SNP	A	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22332669A>G	uc003xbs.2	+						PPP3CC_uc003xbr.1_Intron|PPP3CC_uc011kzi.1_Intron|PPP3CC_uc003xbt.2_Intron	NM_005605	NP_005596	P48454	PP2BC_HUMAN	protein phosphatase 3, catalytic subunit, gamma						activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals	cytosol	calmodulin binding|metal ion binding|phosphoprotein phosphatase activity			ovary(1)	1		Prostate(55;0.104)		BRCA - Breast invasive adenocarcinoma(99;0.00756)|Colorectal(74;0.0238)|COAD - Colon adenocarcinoma(73;0.0835)		TCACAGGTATAAAAAGTCTTT	0.363													46	32	---	---	---	---	PASS
EIF4EBP1	1978	broad.mit.edu	37	8	37914609	37914609	+	Silent	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37914609C>T	uc003xks.2	+	2	228	c.156C>T	c.(154-156)ATC>ATT	p.I52I		NM_004095	NP_004086	Q13541	4EBP1_HUMAN	eukaryotic translation initiation factor 4E	52					G1/S transition of mitotic cell cycle|insulin receptor signaling pathway|positive regulation of mitotic cell cycle|TOR signaling cascade|translation	cytosol					0	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)				GTACCAGGATCATCTATGACC	0.552													44	42	---	---	---	---	PASS
XKR4	114786	broad.mit.edu	37	8	56436018	56436018	+	Silent	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56436018G>A	uc003xsf.2	+	3	1217	c.1185G>A	c.(1183-1185)TCG>TCA	p.S395S		NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related	395						integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)			TCTTTGCCTCGGTTTTCCAGC	0.512													105	385	---	---	---	---	PASS
TRPA1	8989	broad.mit.edu	37	8	72942187	72942187	+	Silent	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72942187G>A	uc003xza.2	-	24	3061	c.2886C>T	c.(2884-2886)GGC>GGT	p.G962G	uc011lff.1_Intron|uc003xyy.2_Intron	NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1	962	Cytoplasmic (Potential).					integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)	CAGCAATGTCGCCAACTGCCA	0.299													16	65	---	---	---	---	PASS
GDF6	392255	broad.mit.edu	37	8	97172832	97172832	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97172832G>A	uc003yhp.2	-	1	189	c.89C>T	c.(88-90)TCC>TTC	p.S30F		NM_001001557	NP_001001557	Q6KF10	GDF6_HUMAN	growth differentiation factor 6 precursor	30	Poly-Ser.				activin receptor signaling pathway|BMP signaling pathway|growth|pathway-restricted SMAD protein phosphorylation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of transcription, DNA-dependent	extracellular space	cytokine activity|growth factor activity			ovary(1)|breast(1)|pancreas(1)	3	Breast(36;2.67e-05)					CGACGAGGAGGATGAGATGGA	0.642													65	73	---	---	---	---	PASS
GDF6	392255	broad.mit.edu	37	8	97172833	97172833	+	Missense_Mutation	SNP	A	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97172833A>T	uc003yhp.2	-	1	188	c.88T>A	c.(88-90)TCC>ACC	p.S30T		NM_001001557	NP_001001557	Q6KF10	GDF6_HUMAN	growth differentiation factor 6 precursor	30	Poly-Ser.				activin receptor signaling pathway|BMP signaling pathway|growth|pathway-restricted SMAD protein phosphorylation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of transcription, DNA-dependent	extracellular space	cytokine activity|growth factor activity			ovary(1)|breast(1)|pancreas(1)	3	Breast(36;2.67e-05)					GACGAGGAGGATGAGATGGAA	0.642													65	73	---	---	---	---	PASS
LYNX1	66004	broad.mit.edu	37	8	143846491	143846491	+	Missense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143846491G>C	uc003yxb.2	-	4	849	c.222C>G	c.(220-222)TGC>TGG	p.C74W	LYNX1_uc003yxa.2_Missense_Mutation_p.C40W	NM_023946	NP_076435	Q9BZG9	LYNX1_HUMAN	Ly-6 neurotoxin-like protein 1 isoform a	Error:Variant_position_missing_in_Q9BZG9_after_alignment						anchored to membrane|plasma membrane					0	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					AGTCCCTCAGGCATCTGGATC	0.617													3	29	---	---	---	---	PASS
CYC1	1537	broad.mit.edu	37	8	145151504	145151504	+	Missense_Mutation	SNP	A	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145151504A>T	uc003zaz.3	+	5	672	c.629A>T	c.(628-630)TAC>TTC	p.Y210F	CYC1_uc003zay.2_Missense_Mutation_p.Y151F	NM_001916	NP_001907	P08574	CY1_HUMAN	cytochrome c-1	210					respiratory electron transport chain|transport	cell junction|integral to membrane|mitochondrial inner membrane|respiratory chain	electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity|heme binding				0	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;8.71e-40)|all cancers(56;3e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GGTGAGGACTACGTCTTCTCC	0.612											OREG0019052	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	32	105	---	---	---	---	PASS
RLN2	6019	broad.mit.edu	37	9	5300201	5300201	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5300201C>A	uc003zja.1	-	2	455	c.455G>T	c.(454-456)GGC>GTC	p.G152V	RLN2_uc003ziz.1_3'UTR	NM_134441	NP_604390	P04090	REL2_HUMAN	relaxin 2 isoform 1 preproprotein	152					female pregnancy	extracellular region	hormone activity				0	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0201)|Lung(218;0.0987)		AGTATCCAAGCCTAAGTATTT	0.363													120	75	---	---	---	---	PASS
TOPORS	10210	broad.mit.edu	37	9	32541488	32541488	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32541488G>A	uc003zrb.2	-	3	3202	c.3035C>T	c.(3034-3036)CCC>CTC	p.P1012L	TOPORS_uc003zrc.2_Missense_Mutation_p.P945L	NM_005802	NP_005793	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich	1012					DNA damage response, signal transduction resulting in induction of apoptosis|maintenance of protein location in nucleus|proteasomal ubiquitin-dependent protein catabolic process|protein sumoylation|transcription, DNA-dependent	nuclear speck|PML body	antigen binding|DNA binding|DNA topoisomerase I binding|SUMO ligase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		AATGTTACTGGGCTGGTTCTC	0.423													64	155	---	---	---	---	PASS
PRUNE2	158471	broad.mit.edu	37	9	79321366	79321366	+	Missense_Mutation	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79321366C>T	uc010mpk.2	-	8	5948	c.5824G>A	c.(5824-5826)GTG>ATG	p.V1942M	PRUNE2_uc004akj.3_5'Flank|PRUNE2_uc010mpl.1_5'Flank	NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	1942					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0						GCAGCAGACACAAAGGTTTGC	0.483													78	49	---	---	---	---	PASS
NTRK2	4915	broad.mit.edu	37	9	87570193	87570193	+	Intron	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87570193C>A	uc004aoa.1	+						NTRK2_uc004any.1_Intron|NTRK2_uc004anz.1_Intron	NM_001018064	NP_001018074	Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2						activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development	integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein tyrosine kinase activity			lung(11)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|liver(1)	16						CATGTCCTTCCCCAGGGCACA	0.642										TSP Lung(25;0.17)			8	7	---	---	---	---	PASS
KIAA0368	23392	broad.mit.edu	37	9	114246757	114246757	+	Silent	SNP	A	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114246757A>C	uc004bfe.1	-	2	156	c.156T>G	c.(154-156)CGT>CGG	p.R52R	KIAA0368_uc010muc.1_5'Flank	NM_001080398	NP_001073867			KIAA0368 protein												0						TCAGTCCCGGACGAGCCCCTG	0.711													6	9	---	---	---	---	PASS
TRAF1	7185	broad.mit.edu	37	9	123675781	123675781	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123675781G>A	uc004bku.1	-	5	1102	c.530C>T	c.(529-531)GCC>GTC	p.A177V	TRAF1_uc011lyg.1_Missense_Mutation_p.A55V|TRAF1_uc010mvl.1_Missense_Mutation_p.A177V	NM_005658	NP_005649	Q13077	TRAF1_HUMAN	TNF receptor-associated factor 1	177					apoptosis|positive regulation of NF-kappaB transcription factor activity|protein complex assembly|regulation of apoptosis|signal transduction	cytoplasm	protein binding|zinc ion binding			skin(2)|ovary(1)	3						GTGCTGCAGGGCCAGCTCCTC	0.612													55	29	---	---	---	---	PASS
DENND1A	57706	broad.mit.edu	37	9	126439038	126439038	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126439038C>A	uc004bnz.1	-	6	566	c.333G>T	c.(331-333)AAG>AAT	p.K111N	DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Missense_Mutation_p.K79N|DENND1A_uc004boa.1_Missense_Mutation_p.K111N|DENND1A_uc004bob.1_Missense_Mutation_p.K81N|DENND1A_uc004boc.2_Missense_Mutation_p.K79N	NM_020946	NP_065997	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A isoform 1	111	DENN.					cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2						TGTTAAGCAGCTTATAAAATA	0.318													52	56	---	---	---	---	PASS
SEC16A	9919	broad.mit.edu	37	9	139369734	139369734	+	Silent	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139369734C>G	uc004chx.2	-	3	2643	c.2334G>C	c.(2332-2334)CCG>CCC	p.P778P	SEC16A_uc004chv.3_Silent_p.P405P|SEC16A_uc004chw.2_Silent_p.P778P|SEC16A_uc010nbn.2_Silent_p.P778P|SEC16A_uc010nbo.1_Silent_p.P778P	NM_014866	NP_055681	O15027	SC16A_HUMAN	SEC16 homolog A	600					protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane					0		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		GGCTCTGCACCGGGGCCGCCG	0.592													9	16	---	---	---	---	PASS
KIAA1984	84960	broad.mit.edu	37	9	139693672	139693672	+	Silent	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139693672G>A	uc004cjf.2	+	2	237	c.189G>A	c.(187-189)AAG>AAA	p.K63K		NM_001039374	NP_001034463	Q5T5S1	K1984_HUMAN	hypothetical protein LOC84960	63										ovary(1)	1	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.33e-06)|Epithelial(140;0.000124)		CTTTGGCCAAGAAGGTACACA	0.652													17	18	---	---	---	---	PASS
FBXW5	54461	broad.mit.edu	37	9	139835710	139835710	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139835710C>A	uc004cjx.2	-	8	1601	c.1450G>T	c.(1450-1452)GTG>TTG	p.V484L	FBXW5_uc010nbx.2_RNA|FBXW5_uc004cjy.2_Missense_Mutation_p.V232L|FBXW5_uc004cjz.2_Missense_Mutation_p.V214L	NM_018998	NP_061871	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	484	WD 2.						catalytic activity|protein binding				0	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)		CACCTGGCCACGAAGTCCCTG	0.716													18	9	---	---	---	---	PASS
TAF3	83860	broad.mit.edu	37	10	7860717	7860717	+	Silent	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7860717G>T	uc010qbd.1	+	1	45	c.45G>T	c.(43-45)GCG>GCT	p.A15A		NM_031923	NP_114129	Q5VWG9	TAF3_HUMAN	RNA polymerase II transcription factor TAFII140	15					maintenance of protein location in nucleus|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding			ovary(1)	1						TCTCGGTGGCGCAGATCTGCC	0.692													21	13	---	---	---	---	PASS
CUBN	8029	broad.mit.edu	37	10	17152948	17152948	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17152948C>G	uc001ioo.2	-	9	1037	c.985G>C	c.(985-987)GGG>CGG	p.G329R		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	329	EGF-like 4; calcium-binding (Potential).				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TGGGAAGACCCAGGTGTATTC	0.512													59	157	---	---	---	---	PASS
DNAJC1	64215	broad.mit.edu	37	10	22209861	22209861	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22209861C>G	uc001irc.2	-	4	690	c.403G>C	c.(403-405)GAT>CAT	p.D135H	DNAJC1_uc001ird.2_Missense_Mutation_p.D21H	NM_022365	NP_071760	Q96KC8	DNJC1_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 1	135	Lumenal (By similarity).				negative regulation of proteolysis|regulation of protein secretion|regulation of transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane|microsome|nuclear membrane	ATPase activator activity|DNA binding|heat shock protein binding|unfolded protein binding			lung(1)	1		Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262)				TGTCGCCAATCTGGAAGTCCA	0.378													46	100	---	---	---	---	PASS
YME1L1	10730	broad.mit.edu	37	10	27425295	27425295	+	Silent	SNP	A	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27425295A>C	uc001iti.2	-	6	803	c.621T>G	c.(619-621)GGT>GGG	p.G207G	YME1L1_uc001itj.2_Silent_p.G150G|YME1L1_uc010qdl.1_Silent_p.G117G|YME1L1_uc009xkv.2_RNA	NM_139312	NP_647473	Q96TA2	YMEL1_HUMAN	YME1-like 1 isoform 1	207					protein catabolic process|proteolysis	membrane|mitochondrion	ATP binding|metal ion binding|metalloendopeptidase activity|nucleoside-triphosphatase activity			ovary(1)	1						AAGTTTTAAAACCCCGAGACT	0.373													14	116	---	---	---	---	PASS
CDH23	64072	broad.mit.edu	37	10	73563143	73563143	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73563143G>A	uc001jrx.3	+	53	8215	c.7838G>A	c.(7837-7839)CGC>CAC	p.R2613H	CDH23_uc001jsg.3_Missense_Mutation_p.R373H|CDH23_uc001jsh.3_Missense_Mutation_p.R373H|CDH23_uc001jsi.3_Missense_Mutation_p.R373H	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	2613	Extracellular (Potential).				calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11						GTCTTTGTGCGCCCACCCAAC	0.612													3	7	---	---	---	---	PASS
GRID1	2894	broad.mit.edu	37	10	87362465	87362465	+	Intron	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87362465G>A	uc001kdl.1	-						GRID1_uc009xsu.1_Intron|GRID1_uc010qmf.1_Intron|uc001kdk.1_Intron	NM_017551	NP_060021	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1							cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)	TGTCCTGGAGGGAAGGCATAG	0.552										Multiple Myeloma(13;0.14)			13	30	---	---	---	---	PASS
CYP2C19	1557	broad.mit.edu	37	10	96534956	96534956	+	Missense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96534956G>C	uc010qnz.1	+	2	310	c.310G>C	c.(310-312)GAA>CAA	p.E104Q	CYP2C19_uc009xus.1_Intron|CYP2C19_uc010qny.1_Missense_Mutation_p.E82Q	NM_000769	NP_000760	P33261	CP2CJ_HUMAN	cytochrome P450, family 2, subfamily C,	104					exogenous drug catabolic process|heterocycle metabolic process|monoterpenoid metabolic process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	(S)-limonene 6-monooxygenase activity|(S)-limonene 7-monooxygenase activity|4-hydroxyacetophenone monooxygenase activity|electron carrier activity|enzyme binding|heme binding|oxygen binding|steroid hydroxylase activity			ovary(4)|central_nervous_system(1)|skin(1)	6		Colorectal(252;0.09)		all cancers(201;6.02e-07)|KIRC - Kidney renal clear cell carcinoma(50;0.0672)|Kidney(138;0.0838)	Adinazolam(DB00546)|Aminophenazone(DB01424)|Amitriptyline(DB00321)|Amoxicillin(DB01060)|Arformoterol(DB01274)|Bortezomib(DB00188)|Carisoprodol(DB00395)|Chlorzoxazone(DB00356)|Cilostazol(DB01166)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Desipramine(DB01151)|Desloratadine(DB00967)|Diclofenac(DB00586)|Diltiazem(DB00343)|Efavirenz(DB00625)|Esomeprazole(DB00736)|Famotidine(DB00927)|Felbamate(DB00949)|Finasteride(DB01216)|Flunitrazepam(DB01544)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Guanfacine(DB01018)|Imipramine(DB00458)|Indomethacin(DB00328)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Loratadine(DB00455)|Melatonin(DB01065)|Mephenytoin(DB00532)|Methadone(DB00333)|Methylphenobarbital(DB00849)|Moclobemide(DB01171)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Nilutamide(DB00665)|Norgestrel(DB00506)|Omeprazole(DB00338)|Oxcarbazepine(DB00776)|Pantoprazole(DB00213)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Primidone(DB00794)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Quinidine(DB00908)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ritonavir(DB00503)|Selegiline(DB01037)|Sertraline(DB01104)|Temazepam(DB00231)|Teniposide(DB00444)|Terfenadine(DB00342)|Thalidomide(DB01041)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tolbutamide(DB01124)|Topiramate(DB00273)|Tranylcypromine(DB00752)|Troglitazone(DB00197)|Troleandomycin(DB01361)|Voriconazole(DB00582)	CCCACTGGCTGAAAGAGCTAA	0.517													138	266	---	---	---	---	PASS
TCTN3	26123	broad.mit.edu	37	10	97440360	97440360	+	Missense_Mutation	SNP	T	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97440360T>G	uc001klb.3	-	13	1703	c.1459A>C	c.(1459-1461)AAC>CAC	p.N487H	TCTN3_uc001kla.3_Missense_Mutation_p.N331H|TCTN3_uc010qoi.1_Missense_Mutation_p.N339H	NM_015631	NP_056446	Q6NUS6	TECT3_HUMAN	tectonic 3 isoform a precursor	487	Extracellular (Potential).				apoptosis	integral to membrane					0		Colorectal(252;0.0815)		Epithelial(162;1.69e-07)|all cancers(201;5.63e-06)		GAAGTACAGTTTATAGCCTGC	0.448													157	213	---	---	---	---	PASS
CRTAC1	55118	broad.mit.edu	37	10	99695956	99695956	+	Missense_Mutation	SNP	T	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99695956T>C	uc001kou.1	-	3	748	c.392A>G	c.(391-393)TAC>TGC	p.Y131C	CRTAC1_uc001kov.2_Missense_Mutation_p.Y120C|CRTAC1_uc001kot.1_5'UTR	NM_018058	NP_060528	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1 precursor	131	FG-GAP 2; atypical.					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)		GTTGAGGAAGTAGATCTCCTC	0.632													30	78	---	---	---	---	PASS
ABCC2	1244	broad.mit.edu	37	10	101591359	101591359	+	Intron	SNP	A	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101591359A>G	uc001kqf.2	+							NM_000392	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP),							apical plasma membrane|integral to plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Norgestimate(DB00957)|Pravastatin(DB00175)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)	TGAGGTGGGGACTTTGCAGGT	0.448													154	301	---	---	---	---	PASS
PDZD7	79955	broad.mit.edu	37	10	102781698	102781698	+	Missense_Mutation	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102781698C>T	uc001kso.1	-	6	939	c.724G>A	c.(724-726)GAC>AAC	p.D242N	PDZD7_uc001ksn.2_Missense_Mutation_p.D242N	NM_024895	NP_079171	Q9H5P4	PDZD7_HUMAN	PDZ domain containing 7	242	PDZ 2.					cilium|nucleus	protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3				Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)		CCACCATGGTCCACTCTGAGG	0.627													42	77	---	---	---	---	PASS
LBX1	10660	broad.mit.edu	37	10	102987051	102987051	+	Silent	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102987051G>A	uc001ksx.2	-	2	967	c.822C>T	c.(820-822)GAC>GAT	p.D274D	uc010qpy.1_5'Flank	NM_006562	NP_006553	P52954	LBX1_HUMAN	ladybird homeobox 1	274	Asp/Glu-rich (highly acidic).				muscle organ development		sequence-specific DNA binding				0		Colorectal(252;0.234)		Epithelial(162;3.22e-09)|all cancers(201;1.79e-07)		CGATCTCTTCGTCTTCCTCGT	0.726													67	73	---	---	---	---	PASS
PNLIPRP3	119548	broad.mit.edu	37	10	118203937	118203937	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118203937G>T	uc001lcl.3	+	4	469	c.368G>T	c.(367-369)TGG>TTG	p.W123L		NM_001011709	NP_001011709	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3 precursor	123					lipid catabolic process	extracellular region	triglyceride lipase activity			ovary(1)	1				all cancers(201;0.0131)		AATTTAGATTGGATCAACGGT	0.363													98	186	---	---	---	---	PASS
PTPRE	5791	broad.mit.edu	37	10	129877825	129877825	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129877825G>A	uc001lkb.2	+	20	2173	c.1894G>A	c.(1894-1896)GCC>ACC	p.A632T	PTPRE_uc009yat.2_Missense_Mutation_p.A643T|PTPRE_uc009yau.2_Missense_Mutation_p.A632T|PTPRE_uc001lkd.2_Missense_Mutation_p.A574T|PTPRE_uc010quq.1_Intron	NM_006504	NP_006495	P23469	PTPRE_HUMAN	protein tyrosine phosphatase, receptor type, E	632	Tyrosine-protein phosphatase 2.|Cytoplasmic (Potential).				negative regulation of insulin receptor signaling pathway|protein phosphorylation	cytoplasm|integral to membrane|intermediate filament cytoskeleton|nucleus|plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(1)	1		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)				TCTCTGCAGTGCCGGAGCTGG	0.483													71	169	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	2356687	2356687	+	Intron	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2356687C>T	uc001lwe.2	-											Homo sapiens, clone IMAGE:4940779, mRNA.																		TGGGTGAATGCCCACGTGGAC	0.478													5	332	---	---	---	---	PASS
DCHS1	8642	broad.mit.edu	37	11	6648382	6648382	+	Missense_Mutation	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6648382C>T	uc001mem.1	-	14	6298	c.5888G>A	c.(5887-5889)AGT>AAT	p.S1963N		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	1963	Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCGCAGAGGACTGGTGGGGAA	0.617													48	33	---	---	---	---	PASS
DCHS1	8642	broad.mit.edu	37	11	6652605	6652605	+	Missense_Mutation	SNP	T	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6652605T>A	uc001mem.1	-	8	4119	c.3709A>T	c.(3709-3711)ACG>TCG	p.T1237S		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	1237	Cadherin 12.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGCAGAGTCGTCACCAGTGTT	0.537													143	98	---	---	---	---	PASS
GALNTL4	374378	broad.mit.edu	37	11	11292798	11292798	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11292798C>A	uc001mjo.2	-	11	2138	c.1717G>T	c.(1717-1719)GAG>TAG	p.E573*		NM_198516	NP_940918	Q6P9A2	GLTL4_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	573	Lumenal (Potential).|Ricin B-type lectin.					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0				all cancers(16;3.67e-05)|Epithelial(150;0.000184)		TCCTGCAGCTCCAGACAGCGC	0.602													96	70	---	---	---	---	PASS
OR4A16	81327	broad.mit.edu	37	11	55111377	55111377	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55111377C>A	uc010rie.1	+	1	701	c.701C>A	c.(700-702)GCC>GAC	p.A234D		NM_001005274	NP_001005274	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A,	234	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(2)|pancreas(1)	3						AGGCATAAAGCCCTGCCTACC	0.413													80	180	---	---	---	---	PASS
OR5I1	10798	broad.mit.edu	37	11	55703186	55703186	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55703186G>A	uc010ris.1	-	1	691	c.691C>T	c.(691-693)CGC>TGC	p.R231C		NM_006637	NP_006628	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I,	231	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						CTGAAAGAGCGGATCTTTAAG	0.453													21	26	---	---	---	---	PASS
OR8J3	81168	broad.mit.edu	37	11	55904850	55904850	+	Silent	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55904850C>T	uc010riz.1	-	1	345	c.345G>A	c.(343-345)CTG>CTA	p.L115L		NM_001004064	NP_001004064	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J,	115	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2	Esophageal squamous(21;0.00693)					CCATCACAGCCAGCATCATTA	0.483													112	205	---	---	---	---	PASS
OR5B17	219965	broad.mit.edu	37	11	58125912	58125912	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58125912C>G	uc010rke.1	-	1	631	c.631G>C	c.(631-633)GTT>CTT	p.V211L		NM_001005489	NP_001005489	Q8NGF7	OR5BH_HUMAN	olfactory receptor, family 5, subfamily B,	211	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				ATCAAGGTAACAAGAAGTGCA	0.383													65	92	---	---	---	---	PASS
OR5A2	219981	broad.mit.edu	37	11	59189633	59189633	+	Missense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59189633G>C	uc010rkt.1	-	1	794	c.794C>G	c.(793-795)TCC>TGC	p.S265C		NM_001001954	NP_001001954	Q8NGI9	OR5A2_HUMAN	olfactory receptor, family 5, subfamily A,	265	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						GGAGTAGCTGGAACTGGGTCG	0.488													51	101	---	---	---	---	PASS
MS4A8B	83661	broad.mit.edu	37	11	60470880	60470880	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60470880C>A	uc001npv.2	+	3	452	c.249C>A	c.(247-249)CAC>CAA	p.H83Q	MS4A8B_uc009yne.1_Missense_Mutation_p.H83Q	NM_031457	NP_113645	Q9BY19	M4A8B_HUMAN	membrane-spanning 4-domains, subfamily A, member	83	Helical; (Potential).			H -> R (in Ref. 3; AAH22895).		integral to membrane	receptor activity				0						GCCTGGCTCACATCGGCCTCG	0.552													76	119	---	---	---	---	PASS
RAB3IL1	5866	broad.mit.edu	37	11	61672267	61672267	+	Missense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61672267G>C	uc001nso.2	-	6	903	c.745C>G	c.(745-747)CGA>GGA	p.R249G	RAB3IL1_uc001nsp.2_Missense_Mutation_p.R223G	NM_013401	NP_037533	Q8TBN0	R3GEF_HUMAN	RAB3A interacting protein (rabin3)-like 1	249							protein binding			skin(2)|central_nervous_system(1)	3						ACGTCCTCTCGGTACACCCTT	0.667													4	18	---	---	---	---	PASS
MUS81	80198	broad.mit.edu	37	11	65630596	65630596	+	Silent	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65630596G>T	uc001ofv.3	+	7	1019	c.666G>T	c.(664-666)CTG>CTT	p.L222L	MUS81_uc001ofw.3_RNA|MUS81_uc001ofx.3_5'UTR	NM_025128	NP_079404	Q96NY9	MUS81_HUMAN	MUS81 endonuclease homolog	222	Interaction with BLM.				DNA recombination|DNA repair	nucleolus	3'-flap endonuclease activity|DNA binding|metal ion binding|protein binding				0				READ - Rectum adenocarcinoma(159;0.166)		CAGAAGGCCTGAGCTTGCTGA	0.622								Homologous_recombination					52	96	---	---	---	---	PASS
LRP5	4041	broad.mit.edu	37	11	68174200	68174200	+	Silent	SNP	G	T	T	rs143304197		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68174200G>T	uc001ont.2	+	9	2085	c.2010G>T	c.(2008-2010)CCG>CCT	p.P670P	LRP5_uc009ysg.2_Silent_p.P80P	NM_002335	NP_002326	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein	670	Beta-propeller 3.|Extracellular (Potential).				adipose tissue development|bone marrow development|bone morphogenesis|canonical Wnt receptor signaling pathway|cholesterol homeostasis|endocytosis|glucose catabolic process|negative regulation of osteoblast differentiation|negative regulation of protein serine/threonine kinase activity|positive regulation of fat cell differentiation|positive regulation of mesenchymal cell proliferation|positive regulation of mitosis|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of canonical Wnt receptor signaling pathway|retina morphogenesis in camera-type eye|retinal blood vessel morphogenesis|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	endoplasmic reticulum|integral to membrane|plasma membrane|receptor complex	protein binding|receptor activity			lung(2)|skin(2)|ovary(1)|pancreas(1)|breast(1)	7						TGGCCATCCCGCTCACGGGCG	0.582													41	59	---	---	---	---	PASS
OR2AT4	341152	broad.mit.edu	37	11	74800303	74800303	+	Missense_Mutation	SNP	A	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74800303A>T	uc010rro.1	-	1	456	c.456T>A	c.(454-456)AGT>AGA	p.S152R		NM_001005285	NP_001005285	A6NND4	O2AT4_HUMAN	olfactory receptor, family 2, subfamily AT,	152	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						TTAGCCAGGCACTGGCTGCCA	0.552													89	105	---	---	---	---	PASS
CAPN5	726	broad.mit.edu	37	11	76826625	76826625	+	Nonsense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76826625G>A	uc001oxx.2	+	6	1069	c.884G>A	c.(883-885)TGG>TAG	p.W295*	CAPN5_uc009yup.2_Nonsense_Mutation_p.W335*|CAPN5_uc009yuq.2_Nonsense_Mutation_p.W331*|CAPN5_uc001oxy.2_Nonsense_Mutation_p.W335*	NM_004055	NP_004046	O15484	CAN5_HUMAN	calpain 5	295	Calpain catalytic.				proteolysis|signal transduction	intracellular	calcium-dependent cysteine-type endopeptidase activity				0						AACGGGCCCTGGAGTGACACG	0.662													29	31	---	---	---	---	PASS
KCTD14	65987	broad.mit.edu	37	11	77727702	77727702	+	Silent	SNP	C	T	T	rs151197596	byFrequency	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77727702C>T	uc001oyw.3	-	2	730	c.705G>A	c.(703-705)ACG>ACA	p.T235T		NM_023930	NP_076419	Q9BQ13	KCD14_HUMAN	potassium channel tetramerisation domain	235						voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)	2	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1e-24)			TGGTGGGGTACGTCAGGTAGA	0.498													98	117	---	---	---	---	PASS
PCF11	51585	broad.mit.edu	37	11	82880718	82880718	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82880718C>A	uc001ozx.3	+	8	3686	c.3341C>A	c.(3340-3342)ACA>AAA	p.T1114K	PCF11_uc010rsu.1_Missense_Mutation_p.T1245K	NM_015885	NP_056969	O94913	PCF11_HUMAN	pre-mRNA cleavage complex II protein Pcf11	1114					mRNA 3'-end processing|mRNA cleavage|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage factor complex				ovary(1)	1						CTTCAAGGCACAAGATTTGAC	0.428													4	245	---	---	---	---	PASS
CCDC83	220047	broad.mit.edu	37	11	85627088	85627088	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85627088C>G	uc001pbh.1	+	10	1404	c.892C>G	c.(892-894)CAA>GAA	p.Q298E	CCDC83_uc001pbg.1_Missense_Mutation_p.Q329E|CCDC83_uc001pbi.1_RNA|CCDC83_uc001pbj.1_Missense_Mutation_p.Q198E	NM_173556	NP_775827	Q8IWF9	CCD83_HUMAN	coiled-coil domain containing 83	298										skin(1)	1		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				GTCAGAATTGCAACCCACAGA	0.318													73	157	---	---	---	---	PASS
FOLH1B	219595	broad.mit.edu	37	11	89424614	89424614	+	Splice_Site	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89424614G>T	uc001pda.2	+	12	1491	c.965_splice	c.e12-1	p.D322_splice		NM_153696	NP_710163	Q9HBA9	FOH1B_HUMAN	folate hydrolase 1B						proteolysis	cytoplasm	dipeptidase activity|metal ion binding|metallopeptidase activity			ovary(3)|skin(2)|central_nervous_system(1)	6						TTCTATTTCAGATTCACTTTT	0.313													37	67	---	---	---	---	PASS
ATM	472	broad.mit.edu	37	11	108181051	108181051	+	Intron	SNP	A	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108181051A>C	uc001pkb.1	+						ATM_uc009yxr.1_Intron|C11orf65_uc010rvx.1_Intron|ATM_uc001pke.1_Intron|ATM_uc001pkg.1_Intron|ATM_uc009yxt.1_Intron	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1						cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		AGGTAATGGAATTTAGAATTT	0.318			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			72	104	---	---	---	---	PASS
EXPH5	23086	broad.mit.edu	37	11	108384166	108384166	+	Missense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108384166G>C	uc001pkk.2	-	6	2179	c.2068C>G	c.(2068-2070)CCC>GCC	p.P690A	EXPH5_uc010rvy.1_Missense_Mutation_p.P502A|EXPH5_uc010rvz.1_Missense_Mutation_p.P534A|EXPH5_uc010rwa.1_Missense_Mutation_p.P614A	NM_015065	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5 isoform a	690					intracellular protein transport		Rab GTPase binding			skin(3)|ovary(2)	5		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		AAGATATTGGGCTGGCTTTTG	0.418													146	207	---	---	---	---	PASS
NCAM1	4684	broad.mit.edu	37	11	113102370	113102370	+	Silent	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113102370C>T	uc009yyq.1	+	11	1511	c.817C>T	c.(817-819)CTG>TTG	p.L273L		NM_001076682	NP_001070150	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1 isoform 3	365	Ig-like C2-type 4.|Extracellular (Potential).				axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane				ovary(1)	1		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		CCGGCAGACTCTGGATGGGCA	0.627													16	55	---	---	---	---	PASS
TTC12	54970	broad.mit.edu	37	11	113196235	113196235	+	Intron	SNP	T	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113196235T>A	uc001pnu.2	+						TTC12_uc001pnv.2_Intron|TTC12_uc001pnw.2_Intron|TTC12_uc001pnx.2_Intron	NM_017868	NP_060338	Q9H892	TTC12_HUMAN	tetratricopeptide repeat domain 12								binding			pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4		all_cancers(61;2.73e-16)|all_epithelial(67;8.64e-10)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.183)|Renal(330;0.187)		BRCA - Breast invasive adenocarcinoma(274;5.3e-06)|Epithelial(105;8.37e-05)|all cancers(92;0.000694)		GTGTAACTTATATTCCCATAG	0.418													83	143	---	---	---	---	PASS
ZBTB16	7704	broad.mit.edu	37	11	114113012	114113012	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114113012C>A	uc001pop.2	+	5	1841	c.1577C>A	c.(1576-1578)ACC>AAC	p.T526N	ZBTB16_uc001poq.2_Missense_Mutation_p.T526N	NM_006006	NP_005997	Q05516	ZBT16_HUMAN	promyelocytic leukemia zinc finger protein	526	C2H2-type 5.				apoptosis|central nervous system development|mesonephros development|myeloid cell differentiation|negative regulation of myeloid cell differentiation|negative regulation of transcription, DNA-dependent	nuclear speck|PML body|transcriptional repressor complex	protein homodimerization activity|zinc ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)		TGCAACCGCACCTTCCCCAGC	0.627													12	23	---	---	---	---	PASS
ADAMTS15	170689	broad.mit.edu	37	11	130341141	130341141	+	Silent	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130341141C>T	uc010scd.1	+	7	1941	c.1941C>T	c.(1939-1941)TCC>TCT	p.S647S		NM_139055	NP_620686	Q8TE58	ATS15_HUMAN	a disintegrin-like and metalloprotease	647	Cys-rich.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(2)|pancreas(1)|lung(1)|skin(1)	5	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0631)|Lung(977;0.215)		ACTCCACCTCCGTCTGTGTCC	0.587													51	79	---	---	---	---	PASS
OPCML	4978	broad.mit.edu	37	11	132398959	132398959	+	Silent	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132398959G>T	uc001qgs.2	-	3	572	c.522C>A	c.(520-522)GTC>GTA	p.V174V	OPCML_uc001qgu.2_Silent_p.V167V|OPCML_uc010sck.1_Silent_p.V174V|OPCML_uc001qgt.2_Silent_p.V174V|OPCML_uc010scl.1_Silent_p.V133V	NM_002545	NP_002536	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion	174	Ig-like C2-type 2.				cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		CCTTACCCTTGACTGACAGGT	0.473													64	116	---	---	---	---	PASS
ZNF384	171017	broad.mit.edu	37	12	6778300	6778300	+	Missense_Mutation	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6778300C>T	uc010sfh.1	-	10	1437	c.1229G>A	c.(1228-1230)CGG>CAG	p.R410Q	ZNF384_uc001qpz.2_Missense_Mutation_p.R349Q|ZNF384_uc001qqa.2_Missense_Mutation_p.R349Q|ZNF384_uc001qqb.2_Missense_Mutation_p.R333Q|ZNF384_uc001qqc.2_Missense_Mutation_p.R349Q|ZNF384_uc001qqd.2_Missense_Mutation_p.R294Q|ZNF384_uc001qqe.2_Missense_Mutation_p.R333Q	NM_001135734	NP_001129206	Q8TF68	ZN384_HUMAN	nuclear matrix transcription factor 4 isoform d	410	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding		EWSR1/ZNF384(4)	haematopoietic_and_lymphoid_tissue(4)|central_nervous_system(3)|kidney(1)	8						CGTGTACGCCCGATGACAGTT	0.493			T	EWSR1|TAF15 	ALL								67	49	---	---	---	---	PASS
ZNF705A	440077	broad.mit.edu	37	12	8330040	8330040	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8330040G>A	uc001qud.1	+	5	836	c.764G>A	c.(763-765)TGT>TAT	p.C255Y	FAM66C_uc001que.3_5'Flank|FAM66C_uc001quf.3_5'Flank|FAM66C_uc009zgc.2_5'Flank|FAM66C_uc001qug.3_5'Flank	NM_001004328	NP_001004328	Q6ZN79	Z705A_HUMAN	zinc finger protein 705A	255					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				Kidney(36;0.0877)		GGAAAAAAGTGTTATGAATGT	0.393													148	116	---	---	---	---	PASS
SLCO1B3	28234	broad.mit.edu	37	12	21229394	21229394	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21229394C>G	uc010sil.1	+	15	2004	c.1939C>G	c.(1939-1941)CTA>GTA	p.L647V	LST-3TM12_uc010sim.1_Missense_Mutation_p.L586V|LST-3TM12_uc010sin.1_Missense_Mutation_p.L539V			Q9NPD5	SO1B3_HUMAN	SubName: Full=Liver-specific organic anion transporter 3TM13; SubName: Full=Organic anion transporter LST-3c;	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity	p.M647L(1)		large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)					AGGAGGTATTCTAGTTCCAAT	0.368													165	98	---	---	---	---	PASS
C12orf40	283461	broad.mit.edu	37	12	40037721	40037721	+	Splice_Site	SNP	T	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40037721T>A	uc001rmc.2	+	3	369	c.202_splice	c.e3+2	p.E68_splice	C12orf40_uc009zjv.1_Intron	NM_001031748	NP_001026918	Q86WS4	CL040_HUMAN	hypothetical protein LOC283461											ovary(6)	6						AAATTCCTGGTAAGTCATTCC	0.323													30	39	---	---	---	---	PASS
LARP4	113251	broad.mit.edu	37	12	50860745	50860745	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50860745C>G	uc001rwp.1	+	13	1531	c.1387C>G	c.(1387-1389)CCT>GCT	p.P463A	LARP4_uc001rwo.1_Missense_Mutation_p.P469A|LARP4_uc001rwq.1_Missense_Mutation_p.P392A|LARP4_uc001rwr.1_Missense_Mutation_p.P392A|LARP4_uc001rws.1_Missense_Mutation_p.P462A|LARP4_uc009zlr.1_Missense_Mutation_p.P282A|LARP4_uc001rwt.1_Missense_Mutation_p.P54A	NM_052879	NP_443111	Q71RC2	LARP4_HUMAN	c-Mpl binding protein isoform a	463							nucleotide binding|RNA binding			ovary(1)	1						ATTTTAGAGACCTCATCCTTC	0.393													95	85	---	---	---	---	PASS
NCKAP1L	3071	broad.mit.edu	37	12	54912486	54912486	+	Missense_Mutation	SNP	A	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54912486A>T	uc001sgc.3	+	14	1469	c.1390A>T	c.(1390-1392)AGT>TGT	p.S464C	NCKAP1L_uc010sox.1_Missense_Mutation_p.S6C|NCKAP1L_uc010soy.1_Missense_Mutation_p.S414C	NM_005337	NP_005328	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	464					actin polymerization-dependent cell motility|B cell homeostasis|B cell receptor signaling pathway|cortical actin cytoskeleton organization|erythrocyte development|maintenance of cell polarity|myeloid cell homeostasis|negative regulation of apoptosis|negative regulation of interleukin-17 production|negative regulation of interleukin-6 production|negative regulation of myosin-light-chain-phosphatase activity|neutrophil chemotaxis|positive regulation of actin filament polymerization|positive regulation of B cell differentiation|positive regulation of B cell proliferation|positive regulation of CD4-positive, alpha-beta T cell differentiation|positive regulation of CD8-positive, alpha-beta T cell differentiation|positive regulation of cell adhesion mediated by integrin|positive regulation of erythrocyte differentiation|positive regulation of gamma-delta T cell differentiation|positive regulation of neutrophil chemotaxis|positive regulation of phagocytosis, engulfment|positive regulation of T cell proliferation|protein complex assembly|response to drug|T cell homeostasis	cytosol|integral to plasma membrane|membrane fraction|SCAR complex	protein complex binding|protein kinase activator activity|Rac GTPase activator activity			ovary(3)|central_nervous_system(1)	4						CTCATTCGTCAGTATCCTCTC	0.473													95	76	---	---	---	---	PASS
OR6C75	390323	broad.mit.edu	37	12	55759647	55759647	+	Missense_Mutation	SNP	T	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55759647T>A	uc010spk.1	+	1	753	c.753T>A	c.(751-753)AGT>AGA	p.S251R		NM_001005497	NP_001005497	A6NL08	O6C75_HUMAN	olfactory receptor, family 6, subfamily C,	251	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|large_intestine(1)	3						TCTCTTACAGTAGCTGTATCT	0.418													89	70	---	---	---	---	PASS
PIP4K2C	79837	broad.mit.edu	37	12	57989764	57989764	+	Missense_Mutation	SNP	T	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57989764T>C	uc001sou.2	+	4	594	c.463T>C	c.(463-465)TCC>CCC	p.S155P	PIP4K2C_uc001sot.2_Missense_Mutation_p.S155P|PIP4K2C_uc010srs.1_Missense_Mutation_p.S137P|PIP4K2C_uc010srt.1_Intron	NM_001146258	NP_001139730	Q8TBX8	PI42C_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type	155	PIPK.					cytoplasm|membrane	1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding|identical protein binding			central_nervous_system(2)|lung(1)	3	Melanoma(17;0.122)					CAAAGAAGTATCCAGTGAGGA	0.527													125	65	---	---	---	---	PASS
TRHDE	29953	broad.mit.edu	37	12	73046262	73046262	+	Missense_Mutation	SNP	T	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:73046262T>A	uc001sxa.2	+	16	2731	c.2701T>A	c.(2701-2703)TTA>ATA	p.L901I		NM_013381	NP_037513	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	901	Extracellular (Potential).				cell-cell signaling|proteolysis|signal transduction	integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(2)|skin(1)	3						CAGGAATTTATTAAACAGGTA	0.333													11	96	---	---	---	---	PASS
SLC17A8	246213	broad.mit.edu	37	12	100795605	100795605	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100795605C>A	uc010svi.1	+	6	1040	c.727C>A	c.(727-729)CAG>AAG	p.Q243K	SLC17A8_uc009ztx.2_Missense_Mutation_p.Q243K	NM_139319	NP_647480	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (sodium-dependent	243	Vesicular (Potential).				neurotransmitter transport|sensory perception of sound|sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)	3						GGTGTTGGTGCAGTACATTGG	0.453													176	186	---	---	---	---	PASS
ANO4	121601	broad.mit.edu	37	12	101295627	101295627	+	Intron	SNP	T	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101295627T>C	uc010svm.1	+						ANO4_uc010svl.1_Intron|ANO4_uc001thw.2_Intron|ANO4_uc001thx.2_Intron	NM_178826	NP_849148	Q32M45	ANO4_HUMAN	anoctamin 4							chloride channel complex	chloride channel activity			ovary(4)|skin(2)	6						AGGTGATGCATGGGGAAGTTC	0.438										HNSCC(74;0.22)			97	71	---	---	---	---	PASS
STAB2	55576	broad.mit.edu	37	12	104149394	104149394	+	Silent	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104149394G>A	uc001tjw.2	+	63	7071	c.6885G>A	c.(6883-6885)GTG>GTA	p.V2295V	STAB2_uc009zug.2_Intron	NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	2295	Extracellular (Potential).				angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14						CTCCAGATGTGAACTGCACCT	0.587													119	73	---	---	---	---	PASS
ASCL4	121549	broad.mit.edu	37	12	108169159	108169159	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108169159C>G	uc001tmr.2	+	1	998	c.167C>G	c.(166-168)GCA>GGA	p.A56G		NM_203436	NP_982260	Q6XD76	ASCL4_HUMAN	achaete-scute complex-like 4	55					regulation of transcription from RNA polymerase II promoter|skin development|transcription, DNA-dependent	nucleus	DNA binding			central_nervous_system(1)	1						AGCGGCTGCGCACGGGGATGG	0.756													9	6	---	---	---	---	PASS
GCN1L1	10985	broad.mit.edu	37	12	120587531	120587531	+	Intron	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120587531G>C	uc001txo.2	-							NM_006836	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis						regulation of translation	ribosome	protein binding|translation factor activity, nucleic acid binding			ovary(4)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CAGCCTCAAGGGGGGAGAAAA	0.517													42	25	---	---	---	---	PASS
RIMBP2	23504	broad.mit.edu	37	12	130919366	130919366	+	Silent	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130919366G>A	uc001uil.2	-	11	2279	c.2115C>T	c.(2113-2115)GAC>GAT	p.D705D	RIMBP2_uc001uim.2_Silent_p.D613D|RIMBP2_uc001uin.1_Silent_p.D364D	NM_015347	NP_056162	O15034	RIMB2_HUMAN	RIM-binding protein 2	705						cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		CGTCCTCCTCGTCTGAGGCGG	0.597													107	54	---	---	---	---	PASS
MTUS2	23281	broad.mit.edu	37	13	29599829	29599829	+	Missense_Mutation	SNP	C	A	A	rs182740	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29599829C>A	uc001usl.3	+	1	1082	c.1024C>A	c.(1024-1026)CTG>ATG	p.L342M		NM_001033602	NP_001028774	Q5JR59	MTUS2_HUMAN	hypothetical protein LOC23281 isoform a	332						cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0						GGAAGGGTATCTGGGATGCCA	0.547													53	79	---	---	---	---	PASS
FREM2	341640	broad.mit.edu	37	13	39264593	39264593	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39264593G>T	uc001uwv.2	+	1	3421	c.3112G>T	c.(3112-3114)GAT>TAT	p.D1038Y		NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	1038	CSPG 6.|Extracellular (Potential).				cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		GAGTCTGTCAGATATGTCTCA	0.453													165	285	---	---	---	---	PASS
FREM2	341640	broad.mit.edu	37	13	39454818	39454818	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39454818G>T	uc001uwv.2	+	24	9713	c.9404G>T	c.(9403-9405)TGC>TTC	p.C3135F		NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	3135	Cytoplasmic (Potential).				cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		GTGCTGATGTGCAGGGGCAAG	0.587													29	71	---	---	---	---	PASS
COG3	83548	broad.mit.edu	37	13	46067577	46067577	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46067577G>A	uc001vak.2	+	12	1384	c.1283G>A	c.(1282-1284)GGG>GAG	p.G428E	COG3_uc001vai.2_Missense_Mutation_p.G428E|COG3_uc001vaj.1_Missense_Mutation_p.G428E|COG3_uc010tfv.1_Missense_Mutation_p.G265E|COG3_uc010aci.2_Missense_Mutation_p.G204E	NM_031431	NP_113619	Q96JB2	COG3_HUMAN	component of golgi transport complex 3	428					ER to Golgi vesicle-mediated transport|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein glycosylation|protein localization to organelle|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	cis-Golgi network|Golgi cisterna membrane|Golgi transport complex	protein binding|protein transporter activity			breast(1)|skin(1)	2		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		GAACTTTGTGGGATTCTTAAA	0.353													82	210	---	---	---	---	PASS
EBPL	84650	broad.mit.edu	37	13	50265552	50265552	+	Silent	SNP	A	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50265552A>G	uc001vdg.2	-	1	72	c.9T>C	c.(7-9)GCT>GCC	p.A3A	EBPL_uc001vdh.2_RNA|EBPL_uc001vdi.2_Silent_p.A3A	NM_032565	NP_115954	Q9BY08	EBPL_HUMAN	emopamil binding related protein, delta8-delta7	3					sterol metabolic process	endoplasmic reticulum membrane|integral to membrane	cholestenol delta-isomerase activity				0		Lung NSC(96;0.000468)|Breast(56;0.0011)|Prostate(109;0.00243)|Hepatocellular(98;0.0556)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.06e-09)		GCTCCCACTCAGCGCCCATGC	0.433													6	16	---	---	---	---	PASS
C13orf1	57213	broad.mit.edu	37	13	50495673	50495673	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50495673C>A	uc001vdl.2	-	4	696	c.434G>T	c.(433-435)GGA>GTA	p.G145V	C13orf1_uc001vdm.2_Missense_Mutation_p.G106V|C13orf1_uc010tgm.1_RNA|C13orf1_uc010adj.2_Missense_Mutation_p.G145V	NM_020456	NP_065189	Q5W111	SPRY7_HUMAN	chromosome 13 open reading frame 1 isoform 1	145	B30.2/SPRY.										0		Lung NSC(96;7.5e-06)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Acute lymphoblastic leukemia(7;0.117)		GBM - Glioblastoma multiforme(99;1.72e-10)|COAD - Colon adenocarcinoma(199;0.208)		CATGTTTTTTCCATTCAAGTA	0.343													63	134	---	---	---	---	PASS
SPRY2	10253	broad.mit.edu	37	13	80911698	80911698	+	Missense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80911698G>C	uc001vli.2	-	2	1121	c.143C>G	c.(142-144)GCC>GGC	p.A48G	SPRY2_uc001vlj.2_Missense_Mutation_p.A48G	NM_005842	NP_005833	O43597	SPY2_HUMAN	sprouty 2	48					epidermal growth factor receptor signaling pathway|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|positive regulation of ERK1 and ERK2 cascade|positive regulation of gene expression|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein kinase B signaling cascade	cytosol|microtubule|ruffle membrane	protein serine/threonine kinase activator activity			ovary(1)|lung(1)	2	Medulloblastoma(90;0.18)	Acute lymphoblastic leukemia(28;0.218)|Breast(118;0.244)		GBM - Glioblastoma multiforme(99;0.0318)		GTTTCGGATGGCTCTGATCTG	0.612													86	151	---	---	---	---	PASS
SLITRK5	26050	broad.mit.edu	37	13	88327697	88327697	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88327697G>A	uc001vln.2	+	2	273	c.54G>A	c.(52-54)ATG>ATA	p.M18I	SLITRK5_uc010tic.1_Intron	NM_015567	NP_056382	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5 precursor	18						integral to membrane				ovary(2)|pancreas(2)|central_nervous_system(1)	5	all_neural(89;0.101)|Medulloblastoma(90;0.163)					ACAGAAAAATGCATAGCTGGA	0.438													88	165	---	---	---	---	PASS
FARP1	10160	broad.mit.edu	37	13	99047633	99047633	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99047633G>T	uc001vnj.2	+	13	1653	c.1317G>T	c.(1315-1317)CAG>CAT	p.Q439H	FARP1_uc001vnh.2_Missense_Mutation_p.Q439H	NM_005766	NP_005757	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF, and pleckstrin domain protein 1	439					regulation of Rho protein signal transduction	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			GTAACAAGCAGGCGGACGGAG	0.687													34	28	---	---	---	---	PASS
NALCN	259232	broad.mit.edu	37	13	101890194	101890194	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101890194G>T	uc001vox.1	-	12	1535	c.1346C>A	c.(1345-1347)TCT>TAT	p.S449Y	NALCN_uc001voy.2_Missense_Mutation_p.S164Y|NALCN_uc001voz.2_Missense_Mutation_p.S449Y|NALCN_uc001vpa.2_Missense_Mutation_p.S449Y	NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	449	Helical; Name=S3 of repeat II; (Potential).					integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TTTGTGGAGAGATGAGCTAAT	0.338													70	118	---	---	---	---	PASS
ITGBL1	9358	broad.mit.edu	37	13	102367913	102367913	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102367913G>A	uc001vpb.2	+	11	1613	c.1394G>A	c.(1393-1395)GGG>GAG	p.G465E	ITGBL1_uc010agb.2_Missense_Mutation_p.G416E|ITGBL1_uc001vpc.3_Missense_Mutation_p.G324E	NM_004791	NP_004782	O95965	ITGBL_HUMAN	integrin, beta-like 1 (with EGF-like repeat	465	X.|Cysteine-rich tandem repeats.				cell-matrix adhesion|integrin-mediated signaling pathway	extracellular region|integrin complex	binding|receptor activity			ovary(1)|skin(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TTTATTGCAGGGAATGGAATA	0.338													140	330	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	22592108	22592108	+	Intron	SNP	A	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22592108A>C	uc001wbw.2	+						uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Missense_Mutation_p.I65L|uc010ajj.1_Missense_Mutation_p.I65L|uc001wde.1_Missense_Mutation_p.I39L|uc010aji.1_Missense_Mutation_p.I65L					SubName: Full=Alpha-chain C region; Flags: Fragment;																		ACAGTATATCATTCATGGTCT	0.458													54	95	---	---	---	---	PASS
AKAP6	9472	broad.mit.edu	37	14	33291723	33291723	+	Missense_Mutation	SNP	T	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33291723T>G	uc001wrq.2	+	13	4874	c.4704T>G	c.(4702-4704)ATT>ATG	p.I1568M		NM_004274	NP_004265	Q13023	AKAP6_HUMAN	A-kinase anchor protein 6	1568	Ser-rich.				protein targeting	calcium channel complex|nuclear membrane|sarcoplasmic reticulum	protein kinase A binding|receptor binding			breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1)	21	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		GTTCATCTATTGAGTCCCTTT	0.403													153	315	---	---	---	---	PASS
SLC25A21	89874	broad.mit.edu	37	14	37180664	37180664	+	Silent	SNP	T	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37180664T>A	uc001wtz.1	-	7	772	c.462A>T	c.(460-462)GCA>GCT	p.A154A		NM_030631	NP_085134	Q9BQT8	ODC_HUMAN	solute carrier family 25 (mitochondrial	154	Solcar 2.				lysine catabolic process	integral to membrane|mitochondrial inner membrane	alpha-ketoglutarate transmembrane transporter activity|binding			skin(1)	1	Esophageal squamous(585;0.164)|Breast(36;0.179)|Hepatocellular(127;0.213)		Lung(8;2.16e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.0112)|all cancers(34;0.0274)|LUSC - Lung squamous cell carcinoma(13;0.149)	GBM - Glioblastoma multiforme(112;0.00204)		TGATTTGTCTTGCATAACCCA	0.438													56	101	---	---	---	---	PASS
GCH1	2643	broad.mit.edu	37	14	55312518	55312518	+	Silent	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55312518C>A	uc001xbh.1	-	5	755	c.594G>T	c.(592-594)CGG>CGT	p.R198R	GCH1_uc001xbi.1_Silent_p.R198R|GCH1_uc001xbj.1_Silent_p.R198R|GCH1_uc001xbk.1_Silent_p.R198R|GCH1_uc010aol.1_Intron|GCH1_uc001xbl.1_Silent_p.R198R	NM_001024024	NP_001019195	P30793	GCH1_HUMAN	GTP cyclohydrolase 1 isoform 1	198					dopamine biosynthetic process|GTP catabolic process|neuromuscular process controlling posture|nitric oxide biosynthetic process|positive regulation of nitric-oxide synthase activity|protein homooligomerization|response to interferon-gamma|response to lipopolysaccharide|response to pain|response to tumor necrosis factor|tetrahydrobiopterin biosynthetic process|tetrahydrofolate biosynthetic process	cytoplasmic vesicle|cytosol|nuclear membrane|protein complex	GTP binding|GTP cyclohydrolase I activity|protein homodimerization activity|zinc ion binding			skin(1)	1						CTCCAGCAGGCCGCAAGGCTT	0.468													76	184	---	---	---	---	PASS
SIX1	6495	broad.mit.edu	37	14	61115580	61115580	+	Missense_Mutation	SNP	G	C	C	rs80356459		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61115580G>C	uc001xfb.3	-	1	576	c.328C>G	c.(328-330)CGG>GGG	p.R110G		NM_005982	NP_005973	Q15475	SIX1_HUMAN	SIX homeobox 1	110			R -> Q (in BOS3).|R -> W (in BOS3; crucial for EYA1-SIX1 interaction).		branching involved in ureteric bud morphogenesis|embryonic cranial skeleton morphogenesis|epithelial cell differentiation|inner ear morphogenesis|mesonephric tubule formation|metanephric mesenchyme development|myoblast migration|negative regulation of neuron apoptosis|organ induction|pattern specification process|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of ureteric bud formation|protein localization to nucleus|regulation of branch elongation involved in ureteric bud branching|regulation of neuron differentiation|skeletal muscle tissue development|thymus development|thyroid gland development	nucleolus|transcription factor complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.0201)		CGGCGCACCCGATATTTGCCC	0.632													64	83	---	---	---	---	PASS
NRXN3	9369	broad.mit.edu	37	14	79433705	79433705	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79433705C>G	uc001xun.2	+	10	2304	c.1813C>G	c.(1813-1815)CAG>GAG	p.Q605E	NRXN3_uc001xum.1_RNA|NRXN3_uc010asv.1_Missense_Mutation_p.Q730E	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor	978	Extracellular (Potential).|Laminin G-like 5.				axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		AGTGGTCACTCAGGTTATCAA	0.403													50	68	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106054595	106054595	+	RNA	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106054595C>G	uc010tyt.1	-	3650		c.62891G>C			uc001yrs.2_RNA|uc001yrt.2_Missense_Mutation_p.Q52H					Parts of antibodies, mostly variable regions.												0						CGGTCACGTTCTGTCCGCTTT	0.642													31	53	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106311969	106311969	+	RNA	SNP	A	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106311969A>G	uc010tyt.1	-	3608		c.56954T>C			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Intron|uc001ysf.2_Intron|uc001ysj.2_Missense_Mutation_p.C29R|uc001ysk.1_Missense_Mutation_p.C29R|uc001ysl.1_Missense_Mutation_p.C29R|uc001ysm.1_5'UTR|uc001ysn.1_5'UTR|uc001yso.1_5'UTR					Parts of antibodies, mostly variable regions.												0						GGGTGTCTGCACCCTGATATG	0.582													52	94	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	107199225	107199225	+	RNA	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107199225G>T	uc010tyt.1	-	21		c.1473C>A								Parts of antibodies, mostly variable regions.												0						TCCACCAGCTGCACCTCACAC	0.547													86	139	---	---	---	---	PASS
C15orf53	400359	broad.mit.edu	37	15	38990597	38990597	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38990597C>G	uc001zkf.1	+	2	401	c.391C>G	c.(391-393)CGC>GGC	p.R131G		NM_207444	NP_997327	Q8NAA6	CO053_HUMAN	hypothetical protein LOC400359	131											0		all_cancers(109;1.75e-13)|all_epithelial(112;1.02e-11)|Lung NSC(122;1.9e-09)|all_lung(180;4.04e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)		GBM - Glioblastoma multiforme(113;8.39e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0321)		AACTGTGCCCCGCCGTTCACC	0.547													24	15	---	---	---	---	PASS
DUOX2	50506	broad.mit.edu	37	15	45390241	45390241	+	Missense_Mutation	SNP	C	A	A	rs144254445		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45390241C>A	uc010bea.2	-	27	3734	c.3531G>T	c.(3529-3531)CAG>CAT	p.Q1177H	DUOX2_uc001zun.2_Missense_Mutation_p.Q1177H	NM_014080	NP_054799	Q9NRD8	DUOX2_HUMAN	dual oxidase 2 precursor	1177	Extracellular (Potential).|Interaction with TXNDC11 (By similarity).|Ferric oxidoreductase.				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|response to virus	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|peroxidase activity			ovary(2)|skin(2)|pancreas(1)	5		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		AATAGAACTTCTGGGGAAGCT	0.562													55	36	---	---	---	---	PASS
FBN1	2200	broad.mit.edu	37	15	48766523	48766523	+	Missense_Mutation	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48766523C>T	uc001zwx.1	-	34	4467	c.4139G>A	c.(4138-4140)TGC>TAC	p.C1380Y		NM_000138	NP_000129	P35555	FBN1_HUMAN	fibrillin 1 precursor	1380	EGF-like 23; calcium-binding.				heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		GGTATTCTTGCAGTCTGCATG	0.423													57	33	---	---	---	---	PASS
DMXL2	23312	broad.mit.edu	37	15	51750748	51750748	+	Missense_Mutation	SNP	T	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51750748T>A	uc002abf.2	-	35	8312	c.8087A>T	c.(8086-8088)CAG>CTG	p.Q2696L	DMXL2_uc002abd.2_Missense_Mutation_p.Q788L|DMXL2_uc010ufy.1_Missense_Mutation_p.Q2697L|DMXL2_uc010bfa.2_Missense_Mutation_p.Q2060L	NM_015263	NP_056078	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	2696						cell junction|synaptic vesicle membrane	Rab GTPase binding			ovary(6)|skin(3)	9				all cancers(107;0.00494)		TATGTATGACTGACAGGCCAG	0.358													63	36	---	---	---	---	PASS
UACA	55075	broad.mit.edu	37	15	70957052	70957052	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70957052C>G	uc002asr.2	-	17	4166	c.4062G>C	c.(4060-4062)CAG>CAC	p.Q1354H	UACA_uc010uke.1_Missense_Mutation_p.Q1245H|UACA_uc002asq.2_Missense_Mutation_p.Q1341H	NM_018003	NP_060473	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and	1354	Potential.					cytoskeleton|extracellular region				ovary(2)|pancreas(1)|skin(1)	4						TGTCAATCAGCTGGCTCTGCC	0.512													58	35	---	---	---	---	PASS
NR2E3	10002	broad.mit.edu	37	15	72106440	72106440	+	Missense_Mutation	SNP	A	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72106440A>C	uc002ati.2	+	8	1272	c.1082A>C	c.(1081-1083)CAC>CCC	p.H361P	NR2E3_uc002ath.1_Missense_Mutation_p.H361P	NM_014249	NP_055064	Q9Y5X4	NR2E3_HUMAN	photoreceptor-specific nuclear receptor isoform	361					phototransduction|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription from RNA polymerase II promoter|visual perception	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding				0						AAGGCCCACCACCCCAGCCAG	0.622													3	15	---	---	---	---	PASS
CYP11A1	1583	broad.mit.edu	37	15	74632057	74632057	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74632057G>A	uc002axt.2	-	6	1183	c.1028C>T	c.(1027-1029)GCA>GTA	p.A343V	CYP11A1_uc002axs.2_Missense_Mutation_p.A185V|CYP11A1_uc010bjm.1_Missense_Mutation_p.A185V|CYP11A1_uc010bjn.1_RNA|CYP11A1_uc010bjo.1_Intron|CYP11A1_uc010bjp.1_RNA|CYP11A1_uc010ulj.1_Missense_Mutation_p.A123V	NM_000781	NP_000772	P05108	CP11A_HUMAN	cytochrome P450, family 11, subfamily A,	343					C21-steroid hormone biosynthetic process|cholesterol metabolic process|vitamin D metabolic process|xenobiotic metabolic process	mitochondrial matrix	cholesterol monooxygenase (side-chain-cleaving) activity|electron carrier activity|heme binding			ovary(2)	2					Aminoglutethimide(DB00357)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Clotrimazole(DB00257)|Digitoxin(DB01396)|Digoxin(DB00390)|Medroxyprogesterone(DB00603)|Ouabain(DB01092)|Progesterone(DB00396)|Testosterone(DB00624)|Trilostane(DB01108)	CAGGTTGCGTGCCATCTCATA	0.627													42	28	---	---	---	---	PASS
ZSCAN2	54993	broad.mit.edu	37	15	85164140	85164140	+	Silent	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85164140C>A	uc002bkr.2	+	3	940	c.714C>A	c.(712-714)ATC>ATA	p.I238I	ZSCAN2_uc010bmz.1_Silent_p.I236I|ZSCAN2_uc010bna.2_Silent_p.I88I|ZSCAN2_uc010uox.1_Intron|ZSCAN2_uc010uoy.1_Intron|ZSCAN2_uc010uoz.1_Intron	NM_181877	NP_870992	Q7Z7L9	ZSCA2_HUMAN	zinc finger protein 29 isoform 1	238	C2H2-type 1.				cell differentiation|multicellular organismal development|spermatogenesis|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (272;0.168)|all cancers(203;5.43e-22)		CCCACCTCATCACACACGAGA	0.493													5	319	---	---	---	---	PASS
SNX29	92017	broad.mit.edu	37	16	12571616	12571616	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12571616G>T	uc002dby.3	+	12	979	c.923G>T	c.(922-924)CGC>CTC	p.R308L		NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	308	PX.				cell communication		phosphatidylinositol binding			ovary(1)	1						AATATTTATCGCCGGTATACA	0.403													25	83	---	---	---	---	PASS
NOMO2	283820	broad.mit.edu	37	16	18544504	18544504	+	Intron	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18544504G>A	uc002dfe.2	-						NOMO2_uc002dff.2_Intron|NOMO2_uc010bvx.2_Intron	NM_001004060	NP_001004060	Q5JPE7	NOMO2_HUMAN	nodal modulator 2 isoform 1							endoplasmic reticulum membrane|integral to membrane	carbohydrate binding|carboxypeptidase activity|protein binding			skin(1)	1						CACTGAACCTGCAAAGAGAAG	0.463													95	229	---	---	---	---	PASS
C16orf62	57020	broad.mit.edu	37	16	19659206	19659206	+	Splice_Site	SNP	T	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19659206T>G	uc002dgn.1	+	24	2040	c.2028_splice	c.e24+2	p.H676_splice	C16orf62_uc002dgo.1_Splice_Site_p.H609_splice|C16orf62_uc002dgp.1_Splice_Site_p.H425_splice	NM_020314	NP_064710	Q7Z3J2	CP062_HUMAN	hypothetical protein LOC57020							integral to membrane				ovary(1)	1						TTGATTCATGTAAGTATTTTC	0.299													159	255	---	---	---	---	PASS
PDILT	204474	broad.mit.edu	37	16	20387453	20387453	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20387453G>T	uc002dhc.1	-	4	703	c.480C>A	c.(478-480)AAC>AAA	p.N160K		NM_174924	NP_777584	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis	160					cell differentiation|cell redox homeostasis|multicellular organismal development|spermatogenesis	endoplasmic reticulum	isomerase activity			large_intestine(1)	1						GCTCGCTGCTGTTGAACAAAA	0.488													61	124	---	---	---	---	PASS
DNAH3	55567	broad.mit.edu	37	16	21065766	21065766	+	Silent	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21065766C>A	uc010vbe.1	-	28	4014	c.4014G>T	c.(4012-4014)GGG>GGT	p.G1338G		NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1338	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)		CCGTGAGGGCCCCGAGAGTGA	0.547													26	53	---	---	---	---	PASS
POLR3E	55718	broad.mit.edu	37	16	22314317	22314317	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22314317G>T	uc002dkk.2	+	2	184	c.28G>T	c.(28-30)GTA>TTA	p.V10L	POLR3E_uc002dkj.1_Missense_Mutation_p.V10L|POLR3E_uc002dkm.2_Intron|POLR3E_uc010vbr.1_Missense_Mutation_p.V10L|POLR3E_uc002dkl.2_Missense_Mutation_p.V10L|POLR3E_uc010vbs.1_Missense_Mutation_p.V10L|POLR3E_uc010vbt.1_5'UTR	NM_018119	NP_060589	Q9NVU0	RPC5_HUMAN	RNA polymerase III polypeptide E	10					innate immune response|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	nucleoplasm	DNA-directed RNA polymerase activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(48;0.012)		TGACCCAGTTGTACAGGAGGT	0.572													127	170	---	---	---	---	PASS
SRCAP	10847	broad.mit.edu	37	16	30734316	30734316	+	Missense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30734316G>C	uc002dze.1	+	24	4310	c.3925G>C	c.(3925-3927)GTG>CTG	p.V1309L	SRCAP_uc002dzf.2_RNA|SRCAP_uc002dzg.1_Missense_Mutation_p.V1104L|SRCAP_uc010bzz.1_Missense_Mutation_p.V879L	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	1309	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)			TACAGGCGTGGTGAAGATTGT	0.527													22	174	---	---	---	---	PASS
PRSS36	146547	broad.mit.edu	37	16	31160456	31160456	+	Missense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31160456G>C	uc002ebd.2	-	4	269	c.210C>G	c.(208-210)CAC>CAG	p.H70Q	PRSS36_uc010vff.1_5'UTR|PRSS36_uc010vfg.1_Missense_Mutation_p.H70Q|PRSS36_uc010vfh.1_Missense_Mutation_p.H70Q	NM_173502	NP_775773	Q5K4E3	POLS2_HUMAN	protease, serine, 36 precursor	70	Peptidase S1 1.				proteolysis	cytoplasm|proteinaceous extracellular matrix	serine-type endopeptidase activity			ovary(1)	1						CCCCGCAGATGTGGCCACCTC	0.682													4	3	---	---	---	---	PASS
CYLD	1540	broad.mit.edu	37	16	50828243	50828243	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50828243G>T	uc002egp.1	+	18	3005	c.2590G>T	c.(2590-2592)GTT>TTT	p.V864F	CYLD_uc010cbs.1_Missense_Mutation_p.V861F|CYLD_uc002egq.1_Missense_Mutation_p.V861F|CYLD_uc002egr.1_Missense_Mutation_p.V861F	NM_015247	NP_056062	Q9NQC7	CYLD_HUMAN	ubiquitin carboxyl-terminal hydrolase CYLD	864					cell cycle|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|protein K63-linked deubiquitination|regulation of microtubule cytoskeleton organization|regulation of mitotic cell cycle|translation|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	cytosol|extrinsic to internal side of plasma membrane|microtubule|perinuclear region of cytoplasm|ribosome	proline-rich region binding|protein kinase binding|structural constituent of ribosome|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			skin(19)|large_intestine(3)|haematopoietic_and_lymphoid_tissue(3)|central_nervous_system(3)	28		all_cancers(37;0.0156)				GTTATTTGCTGTTCTCTGCAT	0.478			Mis|N|F|S		cylindroma	cylindroma			Familial_Cylindromatosis|Multiple_Trichoepithelioma_Familial				146	256	---	---	---	---	PASS
RSPRY1	89970	broad.mit.edu	37	16	57243027	57243027	+	Silent	SNP	T	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57243027T>G	uc002elb.2	+	4	722	c.444T>G	c.(442-444)GTT>GTG	p.V148V	RSPRY1_uc002elc.2_Silent_p.V148V|RSPRY1_uc002eld.2_Silent_p.V148V	NM_133368	NP_588609	Q96DX4	RSPRY_HUMAN	ring finger and SPRY domain containing 1	148						extracellular region	zinc ion binding			ovary(1)	1						TAATTAGAGTTATTCCACTGG	0.333													6	515	---	---	---	---	PASS
BCAR1	9564	broad.mit.edu	37	16	75268934	75268934	+	Silent	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75268934C>G	uc002fdv.2	-	5	1986	c.1863G>C	c.(1861-1863)CTG>CTC	p.L621L	BCAR1_uc002fdt.2_Silent_p.L74L|BCAR1_uc002fdu.2_Silent_p.L411L|BCAR1_uc010cgu.2_Silent_p.L610L|BCAR1_uc010vna.1_Silent_p.L619L|BCAR1_uc010vnb.1_Silent_p.L667L|BCAR1_uc002fdw.2_Silent_p.L621L|BCAR1_uc010vnc.1_Silent_p.L473L|BCAR1_uc010vnd.1_Silent_p.L639L|BCAR1_uc002fdx.2_Silent_p.L639L	NM_014567	NP_055382	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	621					actin filament organization|B cell receptor signaling pathway|blood coagulation|cell adhesion|cell division|cell migration|cell proliferation|epidermal growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|integrin-mediated signaling pathway|nerve growth factor receptor signaling pathway|platelet-derived growth factor receptor signaling pathway|positive regulation of cell migration|regulation of apoptosis|regulation of cell growth|T cell receptor signaling pathway	cytosol|focal adhesion|membrane fraction|ruffle	protein kinase binding|protein phosphatase binding|SH3 domain binding|signal transducer activity			central_nervous_system(5)|breast(2)|prostate(1)	8				BRCA - Breast invasive adenocarcinoma(221;0.169)		GGTTGGGGTGCAGGGTGCCAC	0.652													39	73	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7577556	7577556	+	Missense_Mutation	SNP	C	A	A	rs121912655		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7577556C>A	uc002gim.2	-	7	919	c.725G>T	c.(724-726)TGC>TTC	p.C242F	TP53_uc002gig.1_Missense_Mutation_p.C242F|TP53_uc002gih.2_Missense_Mutation_p.C242F|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.C110F|TP53_uc010cng.1_Missense_Mutation_p.C110F|TP53_uc002gii.1_Missense_Mutation_p.C110F|TP53_uc010cnh.1_Missense_Mutation_p.C242F|TP53_uc010cni.1_Missense_Mutation_p.C242F|TP53_uc002gij.2_Missense_Mutation_p.C242F|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Missense_Mutation_p.C149F|TP53_uc002gio.2_Missense_Mutation_p.C110F	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	242	|Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain.|Interaction with AXIN1 (By similarity).	Zinc.	C -> F (in sporadic cancers; somatic mutation).|C -> G (in sporadic cancers; somatic mutation).|C -> S (in sporadic cancers; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.C242F(63)|p.C242Y(37)|p.C242S(25)|p.C242fs*5(16)|p.C242R(11)|p.C242W(7)|p.0?(7)|p.N239_C242delNSSC(3)|p.C242*(3)|p.C242C(2)|p.C242G(2)|p.C242fs*20(1)|p.C242fs*23(1)|p.Y236_M243delYMCNSSCM(1)|p.C242_M246>L(1)|p.N239fs*4(1)|p.C238_M246delCNSSCMGGM(1)|p.S241_C242insX(1)|p.C238fs*21(1)|p.C242fs*98(1)|p.H233_C242del10(1)|p.N239_C242>S(1)|p.S241_G245delSCMGG(1)|p.N239_C242del(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		GCCGCCCATGCAGGAACTGTT	0.577		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			53	55	---	---	---	---	PASS
RAI1	10743	broad.mit.edu	37	17	17700660	17700660	+	Silent	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17700660G>A	uc002grm.2	+	3	4867	c.4398G>A	c.(4396-4398)CGG>CGA	p.R1466R	RAI1_uc002grn.1_Silent_p.R1466R	NM_030665	NP_109590	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1466						cytoplasm|nucleus	zinc ion binding			central_nervous_system(1)|skin(1)	2				READ - Rectum adenocarcinoma(1115;0.0276)		TGGAGAAGCGGCCCTATCTTG	0.667													18	13	---	---	---	---	PASS
TBC1D29	26083	broad.mit.edu	37	17	28887175	28887175	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28887175G>T	uc002hfh.2	+	2	202	c.53G>T	c.(52-54)TGG>TTG	p.W18L	TBC1D29_uc002hfi.2_RNA|uc002hfj.1_5'Flank	NM_015594	NP_056409	Q9UFV1	TBC29_HUMAN	TBC1 domain family, member 29	18	Rab-GAP TBC; truncated.					intracellular	Rab GTPase activator activity				0		Myeloproliferative disorder(56;0.0255)				TCATTCAGCTGGCTTCTCCGG	0.612													8	18	---	---	---	---	PASS
ATAD5	79915	broad.mit.edu	37	17	29221655	29221655	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29221655C>A	uc002hfs.1	+	22	5717	c.5371C>A	c.(5371-5373)CAA>AAA	p.Q1791K		NM_024857	NP_079133	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1791					response to DNA damage stimulus	nucleus	ATP binding|nucleoside-triphosphatase activity			ovary(3)	3		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				GGGTAATAGACAAGCTAGTAT	0.338													4	94	---	---	---	---	PASS
UTP6	55813	broad.mit.edu	37	17	30226662	30226662	+	Intron	SNP	T	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30226662T>G	uc002hgr.2	-						UTP6_uc010cst.2_Intron|UTP6_uc010wbw.1_Intron	NM_018428	NP_060898	Q9NYH9	UTP6_HUMAN	hepatocellular carcinoma-associated antigen 66						rRNA processing	nucleolus	binding			ovary(1)	1		all_hematologic(16;0.0149)|Ovarian(249;0.021)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|Breast(31;0.231)				ATTACACACTTACTTGAACAT	0.209													25	59	---	---	---	---	PASS
KRT27	342574	broad.mit.edu	37	17	38938435	38938435	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38938435G>T	uc002hvg.2	-	1	352	c.311C>A	c.(310-312)GCC>GAC	p.A104D		NM_181537	NP_853515	Q7Z3Y8	K1C27_HUMAN	keratin 27	104	Rod.|Coil 1A.					cytoplasm|intermediate filament	structural molecule activity				0		Breast(137;0.000812)				CTCCTCTAGGGCTCGAACATT	0.542													8	242	---	---	---	---	PASS
STAT3	6774	broad.mit.edu	37	17	40474352	40474352	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40474352G>T	uc002hzl.1	-	21	2289	c.2049C>A	c.(2047-2049)TTC>TTA	p.F683L	STAT3_uc002hzk.1_Missense_Mutation_p.F683L|STAT3_uc002hzm.1_Missense_Mutation_p.F683L|STAT3_uc010wgh.1_Missense_Mutation_p.F585L|STAT3_uc002hzn.1_Missense_Mutation_p.F683L	NM_139276	NP_644805	P40763	STAT3_HUMAN	signal transducer and activator of transcription	683					cellular component movement|eating behavior|eye photoreceptor cell differentiation|glucose homeostasis|interleukin-6-mediated signaling pathway|interspecies interaction between organisms|JAK-STAT cascade involved in growth hormone signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|protein import into nucleus|response to estradiol stimulus|sexual reproduction|temperature homeostasis	cytosol|nucleus|plasma membrane	calcium ion binding|ligand-regulated transcription factor activity|protein dimerization activity|protein kinase binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)|lung(1)|breast(1)|central_nervous_system(1)	4		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)		AATACTTTCCGAATGCCTCCT	0.458									Hyperimmunoglobulin_E_Recurrent_Infection_Syndrome				4	222	---	---	---	---	PASS
NPEPPS	9520	broad.mit.edu	37	17	45668158	45668158	+	Missense_Mutation	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45668158C>T	uc002ilr.3	+	10	1394	c.1171C>T	c.(1171-1173)CCA>TCA	p.P391S	NPEPPS_uc010wkt.1_Missense_Mutation_p.P387S|NPEPPS_uc010wku.1_Missense_Mutation_p.P355S|NPEPPS_uc010wkv.1_5'UTR	NM_006310	NP_006301	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	391					proteolysis	cytosol|nucleus	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0						CCACTGCTTCCCAGAGTATGA	0.413													31	290	---	---	---	---	PASS
SP2	6668	broad.mit.edu	37	17	45994334	45994334	+	Missense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45994334G>C	uc002imk.2	+	3	1034	c.897G>C	c.(895-897)CAG>CAC	p.Q299H	SP2_uc002iml.2_Missense_Mutation_p.Q292H|uc002imm.2_Intron	NM_003110	NP_003101	Q02086	SP2_HUMAN	Sp2 transcription factor	299					immune response|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|histone deacetylase binding|zinc ion binding				0						CTGTGGTCCAGCAGGTCCAGG	0.647													9	119	---	---	---	---	PASS
ABCA5	23461	broad.mit.edu	37	17	67282383	67282383	+	Nonsense_Mutation	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67282383C>T	uc002jif.2	-	15	3329	c.2111G>A	c.(2110-2112)TGG>TAG	p.W704*	ABCA5_uc002jic.2_5'UTR|ABCA5_uc002jid.2_5'UTR|ABCA5_uc002jie.2_RNA|ABCA5_uc002jig.2_Nonsense_Mutation_p.W704*|ABCA5_uc002jih.2_Nonsense_Mutation_p.W704*|ABCA5_uc010dfe.2_Nonsense_Mutation_p.W704*	NM_018672	NP_061142	Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A , member 5	704	ABC transporter 1.				cholesterol efflux|high-density lipoprotein particle remodeling|negative regulation of macrophage derived foam cell differentiation	Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(10;3.72e-11)					GCCGATCCCCCATTTACTTTT	0.338													33	27	---	---	---	---	PASS
TMEM104	54868	broad.mit.edu	37	17	72832362	72832362	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72832362G>A	uc002jls.3	+	10	1189	c.1027G>A	c.(1027-1029)GCG>ACG	p.A343T	TMEM104_uc010wrf.1_Intron|TMEM104_uc010wrg.1_Intron|TMEM104_uc010dfx.2_Missense_Mutation_p.A343T	NM_017728	NP_060198	Q8NE00	TM104_HUMAN	transmembrane protein 104	343	Extracellular (Potential).					integral to membrane					0	all_lung(278;0.23)					CCTCAACTTCGCGCGCTGTGA	0.612													207	300	---	---	---	---	PASS
FDXR	2232	broad.mit.edu	37	17	72860614	72860614	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72860614C>A	uc002jly.2	-	8	877	c.790G>T	c.(790-792)GAC>TAC	p.D264Y	FDXR_uc010wri.1_Missense_Mutation_p.D212Y|FDXR_uc010wrj.1_Missense_Mutation_p.D262Y|FDXR_uc002jlw.2_Missense_Mutation_p.D21Y|FDXR_uc002jlx.2_Missense_Mutation_p.D270Y|FDXR_uc002jmc.2_Intron|FDXR_uc010wrk.1_Missense_Mutation_p.D295Y|FDXR_uc010wrl.1_Missense_Mutation_p.D307Y|FDXR_uc002jma.2_Missense_Mutation_p.D265Y|FDXR_uc010wrm.1_Missense_Mutation_p.D224Y|FDXR_uc002jlz.2_Missense_Mutation_p.D256Y|FDXR_uc002jmb.2_Intron	NM_024417	NP_077728	P22570	ADRO_HUMAN	ferredoxin reductase isoform 1 precursor	264					cholesterol metabolic process|electron transport chain|steroid biosynthetic process|transport	mitochondrial matrix	ferredoxin-NADP+ reductase activity|protein binding				0	all_lung(278;0.172)|Lung NSC(278;0.207)					TTGATCTTGTCCTGGAGACCC	0.607											OREG0024720	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	34	67	---	---	---	---	PASS
SIRT7	51547	broad.mit.edu	37	17	79870473	79870473	+	Missense_Mutation	SNP	A	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79870473A>C	uc002kcj.1	-	10	1055	c.1022T>G	c.(1021-1023)TTC>TGC	p.F341C	PCYT2_uc010wva.1_5'Flank|PCYT2_uc010wvb.1_5'Flank|PCYT2_uc002kce.1_5'Flank|PCYT2_uc002kcf.1_5'Flank|PCYT2_uc002kcg.1_5'Flank|PCYT2_uc002kch.1_5'Flank|PCYT2_uc002kci.1_5'Flank|PCYT2_uc010dii.1_5'Flank|PCYT2_uc010wvc.1_5'Flank|SIRT7_uc002kck.1_Missense_Mutation_p.F192C|SIRT7_uc002kcl.1_Missense_Mutation_p.F259C	NM_016538	NP_057622	Q9NRC8	SIRT7_HUMAN	sirtuin 7	341					chromatin silencing|positive regulation of transcription on exit from mitosis|protein deacetylation|rRNA transcription	cytoplasm|nucleolus organizer region	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides|NAD+ binding|protein binding|zinc ion binding				0	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0165)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			CGCCAGTGAGAAAATGGGATC	0.647													4	24	---	---	---	---	PASS
DLGAP1	9229	broad.mit.edu	37	18	3742328	3742328	+	Intron	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3742328C>T	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron|DLGAP1_uc002kmk.2_Intron	NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				GCCCTGACGGCCCTCACCTGG	0.577													18	54	---	---	---	---	PASS
CEP192	55125	broad.mit.edu	37	18	13067966	13067966	+	Intron	SNP	A	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13067966A>C	uc010xac.1	+						CEP192_uc010dlf.1_Intron|CEP192_uc010xad.1_Intron|CEP192_uc002kru.2_Intron|CEP192_uc002krv.2_Intron|CEP192_uc002krw.2_5'Flank	NM_032142	NP_115518	E9PF99	E9PF99_HUMAN	centrosomal protein 192kDa											ovary(4)|pancreas(1)	5						GTAAGTATGAACATACAGTAA	0.363													11	272	---	---	---	---	PASS
ZNF521	25925	broad.mit.edu	37	18	22807238	22807238	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22807238C>G	uc002kvk.2	-	4	891	c.644G>C	c.(643-645)AGT>ACT	p.S215T	ZNF521_uc010xbe.1_RNA|ZNF521_uc010dly.2_Missense_Mutation_p.S215T|ZNF521_uc002kvl.2_5'UTR	NM_015461	NP_056276	Q96K83	ZN521_HUMAN	zinc finger protein 521	215	C2H2-type 5.				cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					GTGTAAGGAACTAGAGGACAG	0.493			T	PAX5	ALL								60	73	---	---	---	---	PASS
TCEB3B	51224	broad.mit.edu	37	18	44561184	44561184	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44561184G>T	uc002lcr.1	-	1	805	c.452C>A	c.(451-453)CCC>CAC	p.P151H	KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lco.2_Intron|KATNAL2_uc002lcp.3_Intron	NM_016427	NP_057511	Q8IYF1	ELOA2_HUMAN	elongin A2	151					regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter	integral to membrane|nucleus	DNA binding			ovary(2)|large_intestine(1)|pancreas(1)	4						CTCAGCTCTGGGCTCGCGACT	0.662													79	174	---	---	---	---	PASS
CDH7	1005	broad.mit.edu	37	18	63548089	63548089	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63548089G>A	uc002ljz.2	+	12	2642	c.2317G>A	c.(2317-2319)GCG>ACG	p.A773T	CDH7_uc002lkb.2_Missense_Mutation_p.A773T	NM_033646	NP_387450	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2 preproprotein	773	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	p.A773T(1)		ovary(2)|pancreas(1)|skin(1)	4		Esophageal squamous(42;0.129)				TAAACGACTCGCGGACATGTA	0.408													80	139	---	---	---	---	PASS
C18orf62	284274	broad.mit.edu	37	18	73130763	73130763	+	Missense_Mutation	SNP	T	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73130763T>C	uc002lma.1	-	2	309	c.238A>G	c.(238-240)AGG>GGG	p.R80G	C18orf62_uc010dqw.1_Intron|C18orf62_uc002lmb.1_RNA	NM_001037331	NP_001032408	Q3B7S5	CR062_HUMAN	hypothetical protein LOC284274	80						integral to membrane					0		Esophageal squamous(42;0.131)|Prostate(75;0.155)		OV - Ovarian serous cystadenocarcinoma(15;6.21e-06)		ctgttggcccttttccagtct	0.109													4	445	---	---	---	---	PASS
MAP2K2	5605	broad.mit.edu	37	19	4099227	4099227	+	Silent	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4099227C>A	uc002lzk.2	-	7	1145	c.891G>T	c.(889-891)CGG>CGT	p.R297R	MAP2K2_uc002lzj.2_Silent_p.R107R	NM_030662	NP_109587	P36507	MP2K2_HUMAN	mitogen-activated protein kinase kinase 2	297	Protein kinase.|Pro-rich.				activation of MAPK activity|activation of MAPKK activity|axon guidance|epidermal growth factor receptor signaling pathway|ERK1 and ERK2 cascade|innate immune response|insulin receptor signaling pathway|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|Ras protein signal transduction|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|extracellular region	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGGCCTCGGCCGAGGCGAGA	0.711									Cardiofaciocutaneous_syndrome				8	7	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9087266	9087266	+	Missense_Mutation	SNP	A	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9087266A>T	uc002mkp.2	-	1	4753	c.4549T>A	c.(4549-4551)TTG>ATG	p.L1517M		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	1517	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						TGCTGATCCAACGTTGTTGAA	0.448													20	385	---	---	---	---	PASS
ZNF560	147741	broad.mit.edu	37	19	9581175	9581175	+	Missense_Mutation	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9581175C>T	uc002mlp.1	-	7	551	c.341G>A	c.(340-342)AGT>AAT	p.S114N	ZNF560_uc010dwr.1_Missense_Mutation_p.S8N	NM_152476	NP_689689	Q96MR9	ZN560_HUMAN	zinc finger protein 560	114	KRAB 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)|large_intestine(1)|pancreas(1)|liver(1)	6						CACAGCCACACTGTCAAAGGT	0.498													109	58	---	---	---	---	PASS
TYK2	7297	broad.mit.edu	37	19	10468502	10468502	+	Missense_Mutation	SNP	C	A	A	rs148148659		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10468502C>A	uc002moc.3	-	17	2782	c.2404G>T	c.(2404-2406)GCC>TCC	p.A802S	TYK2_uc010dxe.2_Missense_Mutation_p.A617S|TYK2_uc002mod.2_Missense_Mutation_p.A802S	NM_003331	NP_003322	P29597	TYK2_HUMAN	tyrosine kinase 2	802	Protein kinase 1.				intracellular protein kinase cascade|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|large_intestine(2)|ovary(1)|breast(1)	9			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			AGGAGGGTGGCGCCAAACCCC	0.667													19	25	---	---	---	---	PASS
SMARCA4	6597	broad.mit.edu	37	19	11114047	11114047	+	Nonsense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11114047G>T	uc002mqf.3	+	13	2259	c.1975G>T	c.(1975-1977)GAA>TAA	p.E659*	SMARCA4_uc010dxp.2_Nonsense_Mutation_p.E659*|SMARCA4_uc010dxo.2_Nonsense_Mutation_p.E659*|SMARCA4_uc002mqg.1_Nonsense_Mutation_p.E659*|SMARCA4_uc010dxq.2_Nonsense_Mutation_p.E659*|SMARCA4_uc010dxr.2_Nonsense_Mutation_p.E659*|SMARCA4_uc002mqj.3_Nonsense_Mutation_p.E659*|SMARCA4_uc010dxs.2_Nonsense_Mutation_p.E659*	NM_003072	NP_003063	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated	659					chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity	p.?(1)		lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)				TGATAGTGAAGAAAGTGGCTC	0.473			F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				147	153	---	---	---	---	PASS
B3GNT3	10331	broad.mit.edu	37	19	17918884	17918884	+	Missense_Mutation	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17918884C>T	uc002nhk.1	+	2	353	c.268C>T	c.(268-270)CGC>TGC	p.R90C	B3GNT3_uc002nhl.1_Missense_Mutation_p.R90C|B3GNT3_uc010ebd.1_Missense_Mutation_p.R90C|B3GNT3_uc010ebe.1_Missense_Mutation_p.R90C	NM_014256	NP_055071	Q9Y2A9	B3GN3_HUMAN	UDP-GlcNAc:betaGal	90	Lumenal (Potential).				protein glycosylation	Golgi membrane|integral to plasma membrane	galactosyltransferase activity			upper_aerodigestive_tract(1)	1						CAGACACTGCCGCCACTTTCC	0.642													14	9	---	---	---	---	PASS
ZNF93	81931	broad.mit.edu	37	19	20044388	20044388	+	Missense_Mutation	SNP	A	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20044388A>T	uc002non.2	+	4	735	c.624A>T	c.(622-624)AAA>AAT	p.K208N		NM_031218	NP_112495	P35789	ZNF93_HUMAN	zinc finger protein 93	208	C2H2-type 3.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)	1						AATGTGGCAAAGCCTTTAAGT	0.373													40	26	---	---	---	---	PASS
SHKBP1	92799	broad.mit.edu	37	19	41086391	41086391	+	Missense_Mutation	SNP	G	A	A	rs145900196		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41086391G>A	uc002oob.2	+	7	611	c.562G>A	c.(562-564)GGA>AGA	p.G188R	SHKBP1_uc002ooc.2_Missense_Mutation_p.G188R|SHKBP1_uc002ood.2_Missense_Mutation_p.G188R|SHKBP1_uc010xvl.1_Missense_Mutation_p.G111R|SHKBP1_uc002ooe.2_Missense_Mutation_p.G25R|SHKBP1_uc002oof.2_Missense_Mutation_p.G25R|SHKBP1_uc010xvm.1_Missense_Mutation_p.G25R|SHKBP1_uc010xvn.1_Missense_Mutation_p.G66R	NM_138392	NP_612401	Q8TBC3	SHKB1_HUMAN	SH3KBP1 binding protein 1	188						voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|pancreas(1)	2			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CTCACCCTCAGGTACGTTTCT	0.617													33	56	---	---	---	---	PASS
DMRTC2	63946	broad.mit.edu	37	19	42353006	42353006	+	Silent	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42353006G>C	uc002ors.2	+	5	674	c.591G>C	c.(589-591)CTG>CTC	p.L197L	DMRTC2_uc002orr.1_Silent_p.L74L|DMRTC2_uc010xwe.1_Silent_p.L197L	NM_001040283	NP_001035373	Q8IXT2	DMRTD_HUMAN	DMRT-like family C2	197	Pro-rich.				cell differentiation|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity				0						GCCGCCTGCTGTACCAAGAAC	0.468													78	60	---	---	---	---	PASS
PSG9	5678	broad.mit.edu	37	19	43762597	43762597	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43762597G>T	uc002owd.3	-	5	1099	c.1000C>A	c.(1000-1002)CTC>ATC	p.L334I	PSG9_uc002owe.3_Missense_Mutation_p.L241I|PSG9_uc010xwm.1_Missense_Mutation_p.L241I|PSG9_uc002owf.3_Missense_Mutation_p.L148I|PSG9_uc002owg.2_Missense_Mutation_p.L241I|PSG9_uc002owh.2_Missense_Mutation_p.L148I	NM_002784	NP_002775	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	334					female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00682)				ATTCTGGGGAGGTCTGGACCA	0.493													213	91	---	---	---	---	PASS
ZNF284	342909	broad.mit.edu	37	19	44590676	44590676	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44590676G>A	uc002oyg.1	+	5	1261	c.1045G>A	c.(1045-1047)GGA>AGA	p.G349R	ZNF284_uc010ejd.2_RNA	NM_001037813	NP_001032902	Q2VY69	ZN284_HUMAN	zinc finger protein 284	349	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0435)				TGAAGAATGTGGAAGGAGCTT	0.398													85	54	---	---	---	---	PASS
ZNF611	81856	broad.mit.edu	37	19	53210037	53210037	+	Missense_Mutation	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53210037G>C	uc002pzz.2	-	7	588	c.271C>G	c.(271-273)CAA>GAA	p.Q91E	ZNF611_uc010eqc.2_Missense_Mutation_p.Q21E|ZNF611_uc010ydo.1_Missense_Mutation_p.Q21E|ZNF611_uc010ydr.1_Missense_Mutation_p.Q22E|ZNF611_uc010ydp.1_Missense_Mutation_p.Q91E|ZNF611_uc010ydq.1_Missense_Mutation_p.Q91E|ZNF611_uc002qaa.3_Missense_Mutation_p.Q21E	NM_030972	NP_112234	Q8N823	ZN611_HUMAN	zinc finger protein 611 isoform a	91	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		TCATGTCTTTGCAATGTCCCT	0.378													310	203	---	---	---	---	PASS
MIR521-1	574494	broad.mit.edu	37	19	54251905	54251905	+	RNA	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54251905C>T	hsa-mir-521-1|MI0003176	+			c.16C>T			MIR522_hsa-mir-522|MI0003177_5'Flank																	0						GGCTGTGACCCTCCAAAGGGA	0.403													100	90	---	---	---	---	PASS
LILRA1	11024	broad.mit.edu	37	19	55107869	55107869	+	Missense_Mutation	SNP	T	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55107869T>A	uc002qgh.1	+	7	1356	c.1174T>A	c.(1174-1176)TCG>ACG	p.S392T	LILRA2_uc010yfg.1_Missense_Mutation_p.S390T|LILRA1_uc010yfh.1_Missense_Mutation_p.S392T	NM_006863	NP_006854	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor,	392	Ig-like C2-type 4.|Extracellular (Potential).				cell surface receptor linked signaling pathway|defense response|regulation of immune response	integral to membrane|plasma membrane	antigen binding|transmembrane receptor activity			skin(2)|ovary(1)	3				GBM - Glioblastoma multiforme(193;0.0348)		CTCAGCCCACTCGGGGACCTA	0.587													159	86	---	---	---	---	PASS
ZSCAN5A	79149	broad.mit.edu	37	19	56733262	56733262	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56733262C>A	uc002qmq.2	-	5	1339	c.1173G>T	c.(1171-1173)AAG>AAT	p.K391N	ZSCAN5A_uc010ygi.1_Missense_Mutation_p.K274N|ZSCAN5A_uc002qmr.2_Missense_Mutation_p.K391N|ZSCAN5A_uc002qms.1_Missense_Mutation_p.K390N	NM_024303	NP_077279	Q9BUG6	ZSA5A_HUMAN	zinc finger and SCAN domain containing 5A	391	C2H2-type 2.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3						GCATGAAGCGCTTCCCACAGA	0.507													35	23	---	---	---	---	PASS
ZSCAN1	284312	broad.mit.edu	37	19	58565155	58565155	+	Silent	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58565155G>A	uc002qrc.1	+	6	1210	c.963G>A	c.(961-963)CCG>CCA	p.P321P		NM_182572	NP_872378	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	321	C2H2-type 2.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		GGCCCTTTCCGTGCCCCGAGT	0.627													64	30	---	---	---	---	PASS
ZNF135	7694	broad.mit.edu	37	19	58579304	58579304	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58579304C>A	uc010yhq.1	+	5	1584	c.1488C>A	c.(1486-1488)CAC>CAA	p.H496Q	ZNF135_uc002qre.2_Missense_Mutation_p.H484Q|ZNF135_uc002qrd.1_Intron|ZNF135_uc002qrf.2_Missense_Mutation_p.H442Q|ZNF135_uc002qrg.2_Missense_Mutation_p.H454Q|ZNF135_uc010yhr.1_Missense_Mutation_p.H305Q	NM_003436	NP_003427	B4DHH9	B4DHH9_HUMAN	zinc finger protein 135 isoform 2	496					regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)		TCACCCAACACCAGCGAATCC	0.567													72	46	---	---	---	---	PASS
TGM6	343641	broad.mit.edu	37	20	2380260	2380260	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2380260C>A	uc002wfy.1	+	6	787	c.726C>A	c.(724-726)TAC>TAA	p.Y242*	TGM6_uc010gal.1_Nonsense_Mutation_p.Y242*	NM_198994	NP_945345	O95932	TGM3L_HUMAN	transglutaminase 6	242					cell death|peptide cross-linking		acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(3)|skin(1)	4					L-Glutamine(DB00130)	AGGGCAAGTACGGCGGCGGCA	0.652													38	82	---	---	---	---	PASS
C20orf94	128710	broad.mit.edu	37	20	10603960	10603960	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10603960C>G	uc010zre.1	+	8	1340	c.1160C>G	c.(1159-1161)ACT>AGT	p.T387S		NM_001009608	NP_001009608	Q5VYV7	CT094_HUMAN	hypothetical protein LOC128710	387							protein binding				0						GCCACAAACACTGAAAGATTA	0.433													61	118	---	---	---	---	PASS
SSTR4	6754	broad.mit.edu	37	20	23016993	23016993	+	Silent	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23016993C>T	uc002wsr.2	+	1	937	c.873C>T	c.(871-873)ACC>ACT	p.T291T		NM_001052	NP_001043	P31391	SSR4_HUMAN	somatostatin receptor 4	291	Extracellular (Potential).				G-protein signaling, coupled to cyclic nucleotide second messenger|negative regulation of cell proliferation	integral to plasma membrane	somatostatin receptor activity			ovary(1)	1	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					TTGATGCCACCGTCAACCACG	0.572													39	157	---	---	---	---	PASS
CST5	1473	broad.mit.edu	37	20	23858245	23858245	+	Missense_Mutation	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23858245C>T	uc002wtr.1	-	2	309	c.242G>A	c.(241-243)GGG>GAG	p.G81E		NM_001900	NP_001891	P28325	CYTD_HUMAN	cystatin D precursor	81						extracellular region	cysteine-type endopeptidase inhibitor activity|protein binding				0						GTAGTTCACCCCACCCACGAT	0.527													96	137	---	---	---	---	PASS
TMEM90B	79953	broad.mit.edu	37	20	24646078	24646078	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24646078G>A	uc002wtw.1	+	4	1348	c.715G>A	c.(715-717)GGC>AGC	p.G239S		NM_024893	NP_079169	Q9H7V2	SYNG1_HUMAN	transmembrane protein 90B	239					response to biotic stimulus	early endosome membrane|integral to membrane|plasma membrane					0						CATTGGGACTGGCGTCTATGT	0.647													91	194	---	---	---	---	PASS
DNMT3B	1789	broad.mit.edu	37	20	31394017	31394017	+	Silent	SNP	A	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31394017A>G	uc002wyc.2	+	22	2625	c.2304A>G	c.(2302-2304)TTA>TTG	p.L768L	DNMT3B_uc002wyd.2_Silent_p.L748L|DNMT3B_uc002wye.2_Intron|DNMT3B_uc010gee.2_RNA|DNMT3B_uc010gef.2_Intron|DNMT3B_uc010ztz.1_Intron|DNMT3B_uc010zua.1_Intron|DNMT3B_uc002wyf.2_Silent_p.L760L|DNMT3B_uc002wyg.2_Intron|DNMT3B_uc010geg.2_Intron|DNMT3B_uc010geh.2_RNA	NM_006892	NP_008823	Q9UBC3	DNM3B_HUMAN	DNA cytosine-5 methyltransferase 3 beta isoform	768					negative regulation of histone H3-K9 methylation|positive regulation of gene expression|positive regulation of histone H3-K4 methylation		metal ion binding|protein binding|transcription corepressor activity			lung(3)|ovary(2)	5						TTCTCCAGTTAAAGAAAGTAC	0.453													90	124	---	---	---	---	PASS
CTNNBL1	56259	broad.mit.edu	37	20	36500353	36500353	+	Missense_Mutation	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36500353C>T	uc010zvw.1	+	17	1721	c.1630C>T	c.(1630-1632)CGG>TGG	p.R544W	CTNNBL1_uc002xhh.2_Missense_Mutation_p.R357W|CTNNBL1_uc002xhi.2_RNA|CTNNBL1_uc002xhj.2_Missense_Mutation_p.R292W	NM_030877	NP_110517	Q8WYA6	CTBL1_HUMAN	beta catenin-like 1	544					apoptosis|positive regulation of apoptosis|somatic diversification of immunoglobulins	nucleus	enzyme binding			ovary(2)	2		Myeloproliferative disorder(115;0.00878)				CGGGGACGGCCGGAGCCCGGA	0.587													55	119	---	---	---	---	PASS
SGK2	10110	broad.mit.edu	37	20	42196603	42196603	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42196603G>T	uc002xkv.2	+	4	591	c.372G>T	c.(370-372)AAG>AAT	p.K124N	SGK2_uc002xkt.2_RNA|SGK2_uc002xkr.2_Missense_Mutation_p.K64N|SGK2_uc010ggm.2_Missense_Mutation_p.K64N|SGK2_uc002xks.2_Missense_Mutation_p.K64N|SGK2_uc002xku.2_Missense_Mutation_p.K64N|SGK2_uc002xkq.1_Missense_Mutation_p.K64N	NM_016276	NP_057360	Q9HBY8	SGK2_HUMAN	serum/glucocorticoid regulated kinase 2 isoform	124	Protein kinase.	ATP (By similarity).			intracellular protein kinase cascade|response to oxidative stress		ATP binding|potassium channel regulator activity|protein serine/threonine kinase activity|sodium channel regulator activity			lung(3)|upper_aerodigestive_tract(1)|breast(1)|central_nervous_system(1)	6		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			ATGCAGTGAAGGTACTACAGA	0.493													82	153	---	---	---	---	PASS
JPH2	57158	broad.mit.edu	37	20	42744475	42744475	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42744475G>T	uc002xli.1	-	4	2713	c.1840C>A	c.(1840-1842)CCT>ACT	p.P614T		NM_020433	NP_065166	Q9BR39	JPH2_HUMAN	junctophilin 2 isoform 1	614	Pro-rich.|Cytoplasmic (Potential).				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane					0		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			TCGCGTGCAGGCTCGGGGCCT	0.731													8	14	---	---	---	---	PASS
TNNC2	7125	broad.mit.edu	37	20	44452778	44452778	+	Intron	SNP	A	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44452778A>T	uc002xpr.2	-							NM_003279	NP_003270	P02585	TNNC2_HUMAN	fast skeletal muscle troponin C						muscle filament sliding|regulation of muscle contraction|skeletal muscle contraction	cytosol|troponin complex	calcium ion binding			upper_aerodigestive_tract(1)	1		Myeloproliferative disorder(115;0.0122)				TTCAGGTCCGAGGGACAGGGC	0.672													77	175	---	---	---	---	PASS
ZMYND8	23613	broad.mit.edu	37	20	45856033	45856033	+	Intron	SNP	G	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45856033G>C	uc002xta.1	-						ZMYND8_uc010ghq.1_Intron|ZMYND8_uc010ghr.1_Intron|ZMYND8_uc002xst.1_Intron|ZMYND8_uc002xsu.1_Intron|ZMYND8_uc002xsv.1_Intron|ZMYND8_uc002xsw.1_Intron|ZMYND8_uc002xsx.1_Intron|ZMYND8_uc002xsy.1_Intron|ZMYND8_uc002xsz.1_Intron|ZMYND8_uc010zxy.1_Intron|ZMYND8_uc002xtb.1_Intron|ZMYND8_uc002xss.2_Intron|ZMYND8_uc010zxz.1_Intron|ZMYND8_uc002xtc.1_Intron|ZMYND8_uc002xtd.1_Intron|ZMYND8_uc002xte.1_Intron|ZMYND8_uc010zya.1_Intron|ZMYND8_uc002xtf.1_Intron|ZMYND8_uc002xsr.1_Intron	NM_012408	NP_036540	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8 isoform b								protein binding|zinc ion binding			central_nervous_system(2)|urinary_tract(1)|ovary(1)|skin(1)	5			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)			ATCTGGAAGAGGGAGAGTGAG	0.527													64	154	---	---	---	---	PASS
SULF2	55959	broad.mit.edu	37	20	46313280	46313280	+	Silent	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46313280G>T	uc002xto.2	-	6	1113	c.783C>A	c.(781-783)ATC>ATA	p.I261I	SULF2_uc002xtr.2_Silent_p.I261I|SULF2_uc002xtq.2_Silent_p.I261I	NM_018837	NP_061325	Q8IWU5	SULF2_HUMAN	sulfatase 2 isoform a precursor	261					bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			ovary(2)|breast(2)|pancreas(1)|skin(1)	6						TGTAGCGCATGATCCAGTGTT	0.602													29	45	---	---	---	---	PASS
PREX1	57580	broad.mit.edu	37	20	47259002	47259002	+	Silent	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47259002C>T	uc002xtw.1	-	28	3650	c.3627G>A	c.(3625-3627)CGG>CGA	p.R1209R	PREX1_uc002xtv.1_Silent_p.R506R	NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,	1209					actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CAGATGGGATCCGCATGTCAC	0.572													25	71	---	---	---	---	PASS
PREX1	57580	broad.mit.edu	37	20	47269240	47269240	+	Missense_Mutation	SNP	A	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47269240A>T	uc002xtw.1	-	21	2374	c.2351T>A	c.(2350-2352)CTG>CAG	p.L784Q	PREX1_uc002xtv.1_Missense_Mutation_p.L81Q	NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,	784					actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CCACTGGTACAGGCCCTGCCA	0.647													20	45	---	---	---	---	PASS
SNAI1	6615	broad.mit.edu	37	20	48600469	48600469	+	Missense_Mutation	SNP	T	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48600469T>A	uc002xuz.2	+	2	261	c.191T>A	c.(190-192)GTC>GAC	p.V64D		NM_005985	NP_005976	O95863	SNAI1_HUMAN	snail 1 homolog	64					epithelial to mesenchymal transition|mesoderm formation|negative regulation of transcription from RNA polymerase II promoter|osteoblast differentiation|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	kinase binding|zinc ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			TGGGACTCTGTCCTGGCGCCC	0.657													43	77	---	---	---	---	PASS
PPP1R3D	5509	broad.mit.edu	37	20	58514404	58514404	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58514404C>A	uc002ybb.2	-	1	949	c.583G>T	c.(583-585)GTG>TTG	p.V195L	C20orf177_uc002yba.2_Intron|C20orf177_uc010zzx.1_5'Flank|C20orf177_uc002ybc.2_5'Flank	NM_006242	NP_006233	O95685	PPR3D_HUMAN	protein phosphatase 1, regulatory subunit 3D	195	CBM21.				glycogen metabolic process		protein binding|protein serine/threonine phosphatase activity				0	all_lung(29;0.00391)		BRCA - Breast invasive adenocarcinoma(7;5.12e-09)			ACGTTGCACACGCGCACCGTA	0.701													18	27	---	---	---	---	PASS
ADAMTS5	11096	broad.mit.edu	37	21	28315775	28315775	+	Silent	SNP	A	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28315775A>T	uc002ymg.2	-	3	2058	c.1329T>A	c.(1327-1329)CTT>CTA	p.L443L		NM_007038	NP_008969	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1	443	Peptidase M12B.				proteolysis	proteinaceous extracellular matrix	integrin binding|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4						CAATGCTGGTAAGGATGGAAG	0.453													34	75	---	---	---	---	PASS
KRTAP24-1	643803	broad.mit.edu	37	21	31654547	31654547	+	Missense_Mutation	SNP	G	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31654547G>T	uc002ynv.2	-	1	730	c.704C>A	c.(703-705)CCC>CAC	p.P235H		NM_001085455	NP_001078924	Q3LI83	KR241_HUMAN	keratin associated protein 24-1	235	6 X 10 AA repeats of Y-[ILR]-[SVPC]- [NRTS]-[SNTG]-X-[QHRP]-[PSY]-[QSL]-[SRK].|5.					keratin filament	structural molecule activity				0						AAAGGTACTGGGTATATAGCT	0.428													97	168	---	---	---	---	PASS
CHAF1B	8208	broad.mit.edu	37	21	37763859	37763859	+	Silent	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37763859C>A	uc002yvj.2	+	4	408	c.270C>A	c.(268-270)ATC>ATA	p.I90I		NM_005441	NP_005432	Q13112	CAF1B_HUMAN	chromatin assembly factor 1 subunit B	90	WD 2.				cell cycle|DNA repair|DNA replication|DNA replication-dependent nucleosome assembly|protein complex assembly|regulation of transcription, DNA-dependent|transcription, DNA-dependent	CAF-1 complex|cytoplasm	chromatin binding|histone binding|unfolded protein binding			ovary(1)|skin(1)	2						ATGCTGTCATCCTATTGTGGA	0.418													26	73	---	---	---	---	PASS
XKR3	150165	broad.mit.edu	37	22	17288960	17288960	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17288960C>A	uc002zlv.2	-	2	102	c.4G>T	c.(4-6)GAG>TAG	p.E2*	XKR3_uc011agf.1_Nonsense_Mutation_p.E2*	NM_175878	NP_787074	Q5GH77	XKR3_HUMAN	X Kell blood group precursor-related family,	2						integral to membrane|plasma membrane				large_intestine(1)|ovary(1)|skin(1)	3	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				AACACTGTCTCCATTCTCAGG	0.383													83	164	---	---	---	---	PASS
MICAL3	57553	broad.mit.edu	37	22	18300435	18300435	+	Silent	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18300435C>T	uc002zng.3	-	26	5345	c.4992G>A	c.(4990-4992)AAG>AAA	p.K1664K	MICAL3_uc011agl.1_Silent_p.K1580K|MICAL3_uc010gre.1_5'Flank	NM_015241	NP_056056	Q7RTP6	MICA3_HUMAN	microtubule associated monoxygenase, calponin	1664						cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding				0		all_epithelial(15;0.198)		Lung(27;0.0427)		TGGCTTCATGCTTCAGGGTGG	0.682													13	17	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	23063529	23063529	+	RNA	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23063529G>A	uc011aim.1	+	167		c.9728G>A								Parts of antibodies, mostly variable regions.												0						ATCCCAGACCGATTCTCTGGC	0.537													32	79	---	---	---	---	PASS
SEZ6L	23544	broad.mit.edu	37	22	26701973	26701973	+	Silent	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26701973C>T	uc003acb.2	+	6	1533	c.1377C>T	c.(1375-1377)GCC>GCT	p.A459A	SEZ6L_uc003acc.2_Silent_p.A459A|SEZ6L_uc011akc.1_Silent_p.A459A|SEZ6L_uc003acd.2_Silent_p.A459A|SEZ6L_uc011akd.1_Silent_p.A459A|SEZ6L_uc003ace.2_Silent_p.A459A|SEZ6L_uc003acf.1_Silent_p.A232A|SEZ6L_uc010gvc.1_Silent_p.A232A	NM_021115	NP_066938	Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	459	CUB 2.|Extracellular (Potential).					endoplasmic reticulum membrane|integral to membrane				ovary(4)|central_nervous_system(1)|pancreas(1)	6						TGCACAATGCCACCATCGGCC	0.458													32	70	---	---	---	---	PASS
EFCAB6	64800	broad.mit.edu	37	22	43950942	43950942	+	Missense_Mutation	SNP	C	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43950942C>T	uc003bdy.1	-	27	3670	c.3455G>A	c.(3454-3456)GGC>GAC	p.G1152D	EFCAB6_uc003bdz.1_Missense_Mutation_p.G1000D|EFCAB6_uc010gzi.1_Missense_Mutation_p.G1000D|EFCAB6_uc010gzj.1_Missense_Mutation_p.G378D	NM_022785	NP_073622	Q5THR3	EFCB6_HUMAN	CAP-binding protein complex interacting protein	1152					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	7		Ovarian(80;0.0247)|all_neural(38;0.025)				AGGCGGCGGGCCTTTGGGCAT	0.532													71	41	---	---	---	---	PASS
KLHL34	257240	broad.mit.edu	37	X	21675117	21675117	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21675117G>A	uc004czz.1	-	1	1332	c.790C>T	c.(790-792)CGC>TGC	p.R264C		NM_153270	NP_695002	Q8N239	KLH34_HUMAN	kelch-like 34	264										ovary(1)	1						AGCGGCTGGCGGGAGGGCGTC	0.692													12	7	---	---	---	---	PASS
MAGEB4	4115	broad.mit.edu	37	X	30260892	30260892	+	Missense_Mutation	SNP	T	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30260892T>A	uc004dcb.2	+	1	724	c.640T>A	c.(640-642)TGT>AGT	p.C214S	MAGEB1_uc004dcc.2_5'Flank|MAGEB1_uc004dcd.2_5'Flank	NM_002367	NP_002358	O15481	MAGB4_HUMAN	melanoma antigen family B, 4	214	MAGE.									ovary(1)	1						AAATGGCAACTGTGCCCGTGA	0.507													99	58	---	---	---	---	PASS
TMEM47	83604	broad.mit.edu	37	X	34657478	34657478	+	Missense_Mutation	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34657478G>A	uc004ddh.2	-	2	512	c.253C>T	c.(253-255)CTC>TTC	p.L85F	TMEM47_uc010ngs.2_RNA	NM_031442	NP_113630	Q9BQJ4	TMM47_HUMAN	transmembrane protein 47	85	Helical; (Potential).					integral to membrane				lung(1)	1						CCGCCCAGGAGTAAAGCCAGA	0.448													13	10	---	---	---	---	PASS
IQSEC2	23096	broad.mit.edu	37	X	53277929	53277929	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53277929C>A	uc004dsd.2	-	6	2634	c.2433G>T	c.(2431-2433)CAG>CAT	p.Q811H	IQSEC2_uc004dsc.2_Missense_Mutation_p.Q606H	NM_001111125	NP_001104595	Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2 isoform1	801	SEC7.				regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3						TGAACTGCTTCTGCCGGTTCC	0.607													5	127	---	---	---	---	PASS
GDPD2	54857	broad.mit.edu	37	X	69647202	69647202	+	Silent	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69647202C>A	uc004dyh.2	+	10	1076	c.825C>A	c.(823-825)CTC>CTA	p.L275L	GDPD2_uc010nkx.1_Intron|GDPD2_uc010nky.1_Silent_p.L61L|GDPD2_uc011mpk.1_Silent_p.L275L|GDPD2_uc011mpl.1_Silent_p.L196L|GDPD2_uc011mpm.1_Silent_p.L196L	NM_017711	NP_060181	Q9HCC8	GDPD2_HUMAN	osteoblast differentiation promoting factor	275	GDPD.|Extracellular (Potential).				glycerol metabolic process|lipid metabolic process	cytoplasm|cytoskeleton|integral to membrane|plasma membrane	glycerophosphodiester phosphodiesterase activity|glycerophosphoinositol inositolphosphodiesterase activity|metal ion binding			ovary(2)	2	Renal(35;0.156)					ATGAGCACCTCAGCAGGACCA	0.567													59	28	---	---	---	---	PASS
ATRX	546	broad.mit.edu	37	X	76937345	76937345	+	Missense_Mutation	SNP	T	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76937345T>A	uc004ecp.3	-	9	3635	c.3403A>T	c.(3403-3405)AGG>TGG	p.R1135W	ATRX_uc004ecq.3_Missense_Mutation_p.R1097W|ATRX_uc004eco.3_Missense_Mutation_p.R920W|ATRX_uc004ecr.2_Missense_Mutation_p.R1067W|ATRX_uc010nlx.1_Missense_Mutation_p.R1106W|ATRX_uc010nly.1_Missense_Mutation_p.R1080W	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	1135					DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	CTTCTTTCCCTCAATTCTATT	0.323			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						146	72	---	---	---	---	PASS
BRWD3	254065	broad.mit.edu	37	X	79999572	79999572	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79999572C>A	uc004edt.2	-	8	1035	c.772G>T	c.(772-774)GCA>TCA	p.A258S	BRWD3_uc004edo.2_5'UTR|BRWD3_uc004edp.2_Missense_Mutation_p.A87S|BRWD3_uc004edq.2_5'UTR|BRWD3_uc010nmj.1_5'UTR|BRWD3_uc004edr.2_5'UTR|BRWD3_uc004eds.2_5'UTR|BRWD3_uc004edu.2_5'UTR|BRWD3_uc004edv.2_5'UTR|BRWD3_uc004edw.2_5'UTR|BRWD3_uc004edx.2_5'UTR|BRWD3_uc004edy.2_5'UTR|BRWD3_uc004edz.2_5'UTR|BRWD3_uc004eea.2_5'UTR|BRWD3_uc004eeb.2_Intron	NM_153252	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	258	WD 3.									ovary(4)	4						TGAAGGACTGCAACGGGTGCA	0.388													98	92	---	---	---	---	PASS
PCDH11X	27328	broad.mit.edu	37	X	91134266	91134266	+	Silent	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:91134266C>G	uc004efk.1	+	2	3872	c.3027C>G	c.(3025-3027)ACC>ACG	p.T1009T	PCDH11X_uc004efl.1_Silent_p.T1009T|PCDH11X_uc004efo.1_Silent_p.T1009T|PCDH11X_uc010nmv.1_Silent_p.T1009T|PCDH11X_uc004efm.1_Silent_p.T1009T|PCDH11X_uc004efn.1_Silent_p.T1009T|PCDH11X_uc004efh.1_Silent_p.T1009T|PCDH11X_uc004efj.1_Silent_p.T1009T	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	1009	Cytoplasmic (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						CCGTACACACCAGACCGGTAG	0.398													128	130	---	---	---	---	PASS
TMEM164	84187	broad.mit.edu	37	X	109388078	109388078	+	Missense_Mutation	SNP	T	C	C			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109388078T>C	uc004eom.2	+	5	879	c.560T>C	c.(559-561)GTA>GCA	p.V187A	TMEM164_uc004eol.2_Missense_Mutation_p.V38A|TMEM164_uc010npq.2_Missense_Mutation_p.V148A	NM_032227	NP_115603	Q5U3C3	TM164_HUMAN	transmembrane protein 164 isoform b	187	Helical; (Potential).					integral to membrane				large_intestine(1)|lung(1)|skin(1)	3						CTCTACGTGGTACCCATCTAC	0.473													6	157	---	---	---	---	PASS
SAGE1	55511	broad.mit.edu	37	X	134989135	134989135	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134989135C>A	uc004ezh.2	+	8	954	c.787C>A	c.(787-789)CCC>ACC	p.P263T	SAGE1_uc010nry.1_Missense_Mutation_p.P232T|SAGE1_uc011mvv.1_Intron	NM_018666	NP_061136	Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	263										ovary(2)|skin(1)	3	Acute lymphoblastic leukemia(192;0.000127)					AAAGGGCCAACCCCAACCTGA	0.463													188	133	---	---	---	---	PASS
ATP11C	286410	broad.mit.edu	37	X	138882219	138882219	+	Missense_Mutation	SNP	C	G	G			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138882219C>G	uc004faz.2	-	8	818	c.719G>C	c.(718-720)AGG>ACG	p.R240T	ATP11C_uc004fay.2_5'Flank|ATP11C_uc004fba.2_Missense_Mutation_p.R240T	NM_173694	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C isoform a	240	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(5)|large_intestine(3)	8	Acute lymphoblastic leukemia(192;0.000127)					GCAAACTTACCTGGCAACAGC	0.353													66	40	---	---	---	---	PASS
SPANXN2	494119	broad.mit.edu	37	X	142795397	142795397	+	Missense_Mutation	SNP	C	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142795397C>A	uc004fbz.2	-	2	1035	c.281G>T	c.(280-282)GGA>GTA	p.G94V		NM_001009615	NP_001009615	Q5MJ10	SPXN2_HUMAN	SPANX-N2 protein	94										ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)					CTGTGAAGATCCTTCAGCTGA	0.502													389	319	---	---	---	---	PASS
GAB3	139716	broad.mit.edu	37	X	153940970	153940970	+	Silent	SNP	G	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153940970G>A	uc004fmj.1	-	4	648	c.600C>T	c.(598-600)CCC>CCT	p.P200P	GAB3_uc004fmk.1_Silent_p.P201P|GAB3_uc010nve.1_Silent_p.P201P|GAB3_uc004fml.1_Intron	NM_080612	NP_542179	Q8WWW8	GAB3_HUMAN	Gab3 protein isoform 2	200										ovary(1)	1	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CACATCTGGTGGGTAGACTGG	0.502													18	47	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	4204666	4204667	+	IGR	DEL	CA	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4204666_4204667delCA								LOC100133612 (370789 upstream) : LOC284661 (267444 downstream)																							ccaccaccatcacaccattatc	0.025													7	8	---	---	---	---	
DHRS3	9249	broad.mit.edu	37	1	12677526	12677526	+	5'UTR	DEL	A	-	-	rs144540991		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12677526delA	uc001auc.2	-	1					DHRS3_uc001aub.2_5'Flank|DHRS3_uc009vnm.2_5'UTR|DHRS3_uc001aud.3_5'UTR	NM_004753	NP_004744	O75911	DHRS3_HUMAN	dehydrogenase/reductase (SDR family) member 3						retinol metabolic process|visual perception	integral to membrane	electron carrier activity|NADP-retinol dehydrogenase activity|nucleotide binding			skin(1)	1	Ovarian(185;0.249)	Lung NSC(185;4.11e-05)|all_lung(284;4.58e-05)|Renal(390;0.000147)|Colorectal(325;0.000585)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|Colorectal(212;9.25e-07)|COAD - Colon adenocarcinoma(227;0.000326)|BRCA - Breast invasive adenocarcinoma(304;0.000344)|Kidney(185;0.00235)|KIRC - Kidney renal clear cell carcinoma(229;0.00656)|STAD - Stomach adenocarcinoma(313;0.00798)|READ - Rectum adenocarcinoma(331;0.0419)	Vitamin A(DB00162)	TGAGaaaaagaaaaaaaaaaa	0.448													4	2	---	---	---	---	
PAX7	5081	broad.mit.edu	37	1	18990961	18990962	+	Intron	DEL	GC	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18990961_18990962delGC	uc001bay.2	+						PAX7_uc001baz.2_Intron|PAX7_uc010oct.1_Intron	NM_002584	NP_002575	P23759	PAX7_HUMAN	paired box 7 isoform 1						anti-apoptosis	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		PAX7/FOXO1(197)	soft_tissue(197)|lung(3)|prostate(1)|ovary(1)|breast(1)	203		Colorectal(325;3.46e-05)|all_lung(284;0.000439)|Renal(390;0.000518)|Lung NSC(340;0.000543)|Breast(348;0.00093)|Ovarian(437;0.00768)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00609)|BRCA - Breast invasive adenocarcinoma(304;4.71e-05)|Kidney(64;0.000279)|KIRC - Kidney renal clear cell carcinoma(64;0.00371)|STAD - Stomach adenocarcinoma(196;0.00658)|READ - Rectum adenocarcinoma(331;0.0576)		AGGGAGGAGGGCGAGGCAGCCA	0.446			T	FOXO1A	alveolar rhabdomyosarcoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	30196204	30196205	+	IGR	INS	-	CAC	CAC	rs147183868	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30196204_30196205insCAC								PTPRU (542889 upstream) : MATN1 (987921 downstream)																							accaccatcatcaccaccacca	0.000													5	4	---	---	---	---	
GLIS1	148979	broad.mit.edu	37	1	53980753	53980760	+	Intron	DEL	TGTGTGTG	-	-	rs71706015		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53980753_53980760delTGTGTGTG	uc001cvr.1	-							NM_147193	NP_671726	Q8NBF1	GLIS1_HUMAN	GLIS family zinc finger 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			skin(1)	1						tgtgtgtatatgtgtgtgtgtgtgtgtg	0.058													3	4	---	---	---	---	
SLC35D1	23169	broad.mit.edu	37	1	67487406	67487407	+	Intron	DEL	AG	-	-	rs71711790		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67487406_67487407delAG	uc001ddk.2	-						SLC35D1_uc010oph.1_Intron	NM_015139	NP_055954	Q9NTN3	S35D1_HUMAN	solute carrier family 35 (UDP-glucuronic						chondroitin sulfate biosynthetic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	integral to endoplasmic reticulum membrane	UDP-glucuronic acid transmembrane transporter activity|UDP-N-acetylgalactosamine transmembrane transporter activity				0					Lorazepam(DB00186)	acacagacacagacacacacac	0.248													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	90776583	90776584	+	IGR	INS	-	C	C	rs150148268	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90776583_90776584insC								ZNF326 (282489 upstream) : BARHL2 (400996 downstream)																							Ttttcttccttcttctttcctt	0.134													7	4	---	---	---	---	
VAV3	10451	broad.mit.edu	37	1	108303599	108303600	+	Intron	INS	-	TTT	TTT	rs146717004	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108303599_108303600insTTT	uc001dvk.1	-						VAV3_uc010ouw.1_Intron|VAV3_uc001dvl.1_Intron|VAV3_uc010oux.1_Intron	NM_006113	NP_006104	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(5)|lung(2)|breast(2)	9		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		AAATGAGTGCGTTTGTTTCCTT	0.287													7	4	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145368208	145368213	+	Intron	DEL	TCTCTG	-	-	rs72354261		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145368208_145368213delTCTCTG	uc001end.3	+						NBPF9_uc010oye.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_Intron|NBPF10_uc010oyk.1_Intron|NBPF10_uc010oyl.1_Intron	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GGTCACTTTCtctctgtctctgtctc	0.320													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149047679	149047679	+	IGR	DEL	C	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149047679delC								LOC645166 (94625 upstream) : LOC388692 (231797 downstream)																							TGTACCCAGACCCCCATGCTT	0.488													23	14	---	---	---	---	
CELF3	11189	broad.mit.edu	37	1	151677295	151677298	+	Intron	DEL	GTGA	-	-	rs72441705	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151677295_151677298delGTGA	uc001eys.1	-						CELF3_uc010pdh.1_Intron|CELF3_uc001eyr.2_Intron|CELF3_uc009wmy.2_Intron|CELF3_uc009wmx.1_Intron	NM_007185	NP_009116	Q5SZQ8	CELF3_HUMAN	trinucleotide repeat containing 4						nuclear mRNA splicing, via spliceosome|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	mRNA binding|nucleotide binding			ovary(1)|central_nervous_system(1)	2						GTGTGTGTGTGTgagagagagaga	0.475													5	3	---	---	---	---	
DDR2	4921	broad.mit.edu	37	1	162600973	162600980	+	5'Flank	DEL	TGTGTGTG	-	-	rs145277924		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162600973_162600980delTGTGTGTG	uc001gcf.2	+						DDR2_uc001gcg.2_5'Flank	NM_001014796	NP_001014796	Q16832	DDR2_HUMAN	discoidin domain receptor family, member 2						cell adhesion	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(2)|central_nervous_system(2)|ovary(1)|kidney(1)	6	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)			CCACCCTCATtgtgtgtgtgtgtgtgtg	0.380													4	2	---	---	---	---	
GPA33	10223	broad.mit.edu	37	1	167032750	167032750	+	Intron	DEL	C	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167032750delC	uc001gea.1	-							NM_005814	NP_005805	Q99795	GPA33_HUMAN	transmembrane glycoprotein A33 precursor							integral to plasma membrane	receptor activity				0						CAAGTTGCAGCCCCTAGCCAA	0.587													100	62	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	172716755	172716769	+	IGR	DEL	TTCTTTCTTTCTTTC	-	-	rs141470296		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172716755_172716769delTTCTTTCTTTCTTTC								FASLG (80745 upstream) : TNFSF18 (293591 downstream)																							ctttctttctttctttctttctttctttctttctt	0.084													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	178682325	178682326	+	IGR	DEL	AA	-	-	rs138482742	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178682325_178682326delAA								C1orf220 (164301 upstream) : RALGPS2 (11974 downstream)																							agaaagaaagaaagagaaagag	0.000													4	2	---	---	---	---	
SLC30A10	55532	broad.mit.edu	37	1	220091756	220091756	+	Frame_Shift_Del	DEL	G	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220091756delG	uc001hlw.2	-	3	1010	c.799delC	c.(799-801)CTGfs	p.L267fs	SLC30A10_uc001hlu.1_RNA|SLC30A10_uc001hlv.2_Frame_Shift_Del_p.L22fs|SLC30A10_uc001hlx.2_Frame_Shift_Del_p.L42fs	NM_018713	NP_061183	Q6XR72	ZNT10_HUMAN	solute carrier family 30 (zinc transporter),	267	Extracellular (Potential).				zinc ion transport	integral to membrane|plasma membrane	cation transmembrane transporter activity				0				GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.209)		TCACTCTTCAGGGGAAGCACA	0.507													326	162	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	247348801	247348802	+	IGR	DEL	TC	-	-	rs138501449		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247348801_247348802delTC								ZNF124 (13483 upstream) : VN1R5 (70572 downstream)																							GCGGGTGTTTTCTCTTTTTACT	0.485													3	4	---	---	---	---	
TPO	7173	broad.mit.edu	37	2	1484485	1484510	+	Intron	DEL	CTCCTTCATCCGTCCAAACCATGTTT	-	-	rs56310302		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1484485_1484510delCTCCTTCATCCGTCCAAACCATGTTT	uc002qww.2	+						TPO_uc010ewj.2_Intron|TPO_uc002qwu.2_Intron|TPO_uc002qwr.2_Intron|TPO_uc002qwx.2_Intron|TPO_uc010yio.1_Intron|TPO_uc010yip.1_Intron	NM_000547	NP_000538	P07202	PERT_HUMAN	thyroid peroxidase isoform a						cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process	cell surface|cytoplasm|integral to plasma membrane	calcium ion binding|heme binding|iodide peroxidase activity			ovary(7)|pancreas(6)|skin(5)|lung(1)|kidney(1)	20	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550)	CACCTCCCTCCTCCTTCATCCGTCCAAACCATGTTTCTCCTGCTGC	0.593													5	4	---	---	---	---	
PXDN	7837	broad.mit.edu	37	2	1656703	1656706	+	Intron	DEL	TGTG	-	-	rs71985242		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1656703_1656706delTGTG	uc002qxa.2	-							NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor						extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		CTCCGTGCTCtgtgtgtgtgtgtg	0.314													3	4	---	---	---	---	
HEATR5B	54497	broad.mit.edu	37	2	37260027	37260028	+	Intron	INS	-	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37260027_37260028insT	uc002rpp.1	-							NM_019024	NP_061897	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B								binding			ovary(5)|skin(2)|breast(1)	8		all_hematologic(82;0.21)				Gttttgttttgttttttttttt	0.094													5	3	---	---	---	---	
PREPL	9581	broad.mit.edu	37	2	44586467	44586473	+	Intron	DEL	TACTCTT	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44586467_44586473delTACTCTT	uc002ruf.2	-						PREPL_uc002rug.2_Intron|PREPL_uc002ruh.2_Intron|PREPL_uc010fax.2_Intron|PREPL_uc002rui.3_Intron|PREPL_uc002ruj.1_Intron|PREPL_uc002ruk.1_Intron|C2orf34_uc002rum.2_5'Flank|C2orf34_uc002rul.2_5'Flank	NM_006036	NP_006027	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like isoform C						proteolysis	cytosol	serine-type endopeptidase activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				tcgATGTATATACTCTTTTATACTTAC	0.150													6	4	---	---	---	---	
KCNIP3	30818	broad.mit.edu	37	2	95963242	95963242	+	Intron	DEL	C	-	-	rs112957151		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95963242delC	uc002sup.2	+						KCNIP3_uc002sun.1_Intron|KCNIP3_uc002suo.1_Intron	NM_013434	NP_038462	Q9Y2W7	CSEN_HUMAN	Kv channel interacting protein 3 isoform 1						apoptosis|signal transduction|transcription, DNA-dependent	endoplasmic reticulum|Golgi apparatus|nucleus|plasma membrane	calcium ion binding|DNA binding|potassium channel activity|transcription corepressor activity|voltage-gated ion channel activity			breast(2)|ovary(1)	3				READ - Rectum adenocarcinoma(193;0.13)		GGAGGGGGGTCGGGGGGAGGA	0.587													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	98248129	98248130	+	IGR	INS	-	GAAG	GAAG	rs141641657	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98248129_98248130insGAAG								ANKRD36B (41701 upstream) : COX5B (14391 downstream)																							tcAgaaagaaagaaggaaggaa	0.000													11	5	---	---	---	---	
LOC541471	541471	broad.mit.edu	37	2	112173008	112173009	+	Intron	INS	-	GT	GT	rs72117666		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112173008_112173009insGT	uc002the.2	-						LOC541471_uc010yxl.1_Intron					Homo sapiens hypothetical LOC541471, mRNA (cDNA clone IMAGE:3459303).												0						TGTAGACAAGGgtgtgtgtgtg	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	206813725	206813725	+	IGR	DEL	A	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206813725delA								NRP2 (150869 upstream) : INO80D (44721 downstream)																							accctatctcaaaaaaaaaaG	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	220873075	220873076	+	IGR	DEL	CC	-	-	rs72294968	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220873075_220873076delCC								SLC4A3 (366374 upstream) : None (None downstream)																							cacacacacacCCCCCATACCA	0.371													4	2	---	---	---	---	
WDR69	164781	broad.mit.edu	37	2	228761345	228761348	+	Intron	DEL	TGTA	-	-	rs3057687		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228761345_228761348delTGTA	uc002vpn.1	+						WDR69_uc010zlw.1_Intron|WDR69_uc002vpo.1_Intron	NM_178821	NP_849143	Q8N136	WDR69_HUMAN	WD repeat domain 69											breast(1)	1		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;1.22e-10)|all cancers(144;8.11e-08)|Lung(261;0.011)|LUSC - Lung squamous cell carcinoma(224;0.0148)		tgtgtgtgtgtgtatgAGAGAGAG	0.304													4	2	---	---	---	---	
AGAP1	116987	broad.mit.edu	37	2	236630122	236630123	+	Intron	DEL	TG	-	-	rs35681991		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236630122_236630123delTG	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208	Q9UPQ3	AGAP1_HUMAN	centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3						CTTAATATTAtgtgtgtgtgtg	0.243													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	20255106	20255107	+	IGR	INS	-	CCTT	CCTT	rs140541938	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20255106_20255107insCCTT								SGOL1 (27423 upstream) : None (None downstream)																							cttccttccttcctccctccct	0.109													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	23768001	23768001	+	IGR	DEL	G	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23768001delG								UBE2E2 (135705 upstream) : UBE2E1 (79438 downstream)																							aagaaagaaagaaagaaagaa	0.000													3	4	---	---	---	---	
SCN11A	11280	broad.mit.edu	37	3	38946481	38946481	+	Intron	DEL	C	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38946481delC	uc011ays.1	-							NM_014139	NP_054858	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha						response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			skin(6)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)|pancreas(1)	9				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)	TTAGAGTGGGCCCACAGGGAA	0.517													13	16	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	106339608	106339609	+	IGR	INS	-	GAAGGAAGGAAG	GAAGGAAGGAAG			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106339608_106339609insGAAGGAAGGAAG								CBLB (751342 upstream) : LOC100302640 (216051 downstream)																							GAgaagaaagagaaggaaggaa	0.188													10	6	---	---	---	---	
RAB7A	7879	broad.mit.edu	37	3	128532447	128532448	+	3'UTR	DEL	CA	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128532447_128532448delCA	uc003eks.1	+	6					RAB7A_uc010hsv.1_3'UTR|RAB7A_uc003ekt.2_Frame_Shift_Del_p.H194fs	NM_004637	NP_004628	P51149	RAB7A_HUMAN	RAB7, member RAS oncogene family						endocytosis|endosome to lysosome transport|epidermal growth factor catabolic process|protein transport|small GTPase mediated signal transduction	Golgi apparatus|late endosome|lysosome|melanosome|phagocytic vesicle	GDP binding|GTP binding|GTPase activity|protein binding				0				GBM - Glioblastoma multiforme(114;0.231)		cacacacacgcacacacacaca	0.426													4	4	---	---	---	---	
UBXN7	26043	broad.mit.edu	37	3	196101855	196101856	+	Intron	INS	-	AGGG	AGGG			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196101855_196101856insAGGG	uc003fwm.3	-						UBXN7_uc003fwn.3_Intron|UBXN7_uc010iae.2_Intron	NM_015562	NP_056377	O94888	UBXN7_HUMAN	UBX domain containing 7								protein binding			ovary(2)|pancreas(1)	3						ggaaggaaggaagggagggagg	0.000													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	196395233	196395234	+	IGR	INS	-	AAATGA	AAATGA	rs143273785	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196395233_196395234insAAATGA								LRRC33 (6361 upstream) : C3orf34 (37915 downstream)																							gagagagagagagaaatgaagg	0.084													9	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	34373434	34373435	+	IGR	DEL	TG	-	-	rs34289687		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:34373434_34373435delTG								None (None upstream) : None (None downstream)																							GAtgtgtttttgtgtgtgtgtg	0.431													3	3	---	---	---	---	
GABRG1	2565	broad.mit.edu	37	4	46050736	46050736	+	Intron	DEL	G	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46050736delG	uc003gxb.2	-							NM_173536	NP_775807	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid A receptor, gamma 1						gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity			ovary(2)	2				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)		aggaaAAATagaaagcgagca	0.080													12	16	---	---	---	---	
UBA6	55236	broad.mit.edu	37	4	68531131	68531132	+	Intron	INS	-	T	T	rs72340884		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68531131_68531132insT	uc003hdg.3	-						UBA6_uc003hdi.2_Intron|UBA6_uc003hdj.2_Intron	NM_018227	NP_060697	A0AVT1	UBA6_HUMAN	ubiquitin-activating enzyme E1-like 2						protein ubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm	ATP binding|FAT10 activating enzyme activity|ligase activity|protein binding				0						CCAGCATAGTGtttttttttgt	0.243													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	117589584	117589586	+	IGR	DEL	CTC	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117589584_117589586delCTC								MIR1973 (368660 upstream) : TRAM1L1 (415130 downstream)																							cttcatccttctcctcctcctCc	0.005													4	2	---	---	---	---	
TRPC3	7222	broad.mit.edu	37	4	122833102	122833102	+	Frame_Shift_Del	DEL	G	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122833102delG	uc003ieg.2	-	5	1562	c.1488delC	c.(1486-1488)CCCfs	p.P496fs	TRPC3_uc010inr.2_Frame_Shift_Del_p.P368fs|TRPC3_uc003ief.2_Frame_Shift_Del_p.P423fs|TRPC3_uc011cgl.1_Frame_Shift_Del_p.P160fs	NM_001130698	NP_001124170	Q13507	TRPC3_HUMAN	transient receptor potential cation channel,	411	Cytoplasmic (Potential).				axon guidance|phototransduction|platelet activation	integral to plasma membrane	protein binding|store-operated calcium channel activity			ovary(2)	2						AGATCTGTTTGGGATAGTCAG	0.418													114	121	---	---	---	---	
TBC1D9	23158	broad.mit.edu	37	4	141583014	141583015	+	Intron	INS	-	T	T			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141583014_141583015insT	uc010ioj.2	-							NM_015130	NP_055945	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)							intracellular	calcium ion binding|Rab GTPase activator activity			ovary(1)	1	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				attttattttatttttttaGCA	0.317													10	20	---	---	---	---	
ZFP42	132625	broad.mit.edu	37	4	188924487	188924487	+	Frame_Shift_Del	DEL	C	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188924487delC	uc003izg.1	+	3	771	c.526delC	c.(526-528)CCCfs	p.P176fs	ZFP42_uc003izh.1_Frame_Shift_Del_p.P176fs|ZFP42_uc003izi.1_Frame_Shift_Del_p.P176fs	NM_174900	NP_777560	Q96MM3	ZFP42_HUMAN	zinc finger protein 42	176					female gonad development|male gonad development|meiosis	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)		TAGAAAGAAGCCCCCCATAAA	0.468													177	187	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	144974724	144974725	+	IGR	INS	-	AC	AC	rs34644736		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:144974724_144974725insAC								None (None upstream) : PRELID2 (163857 downstream)																							AGTCATAATAGacacacacaca	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	155110005	155110006	+	IGR	INS	-	TGTGTG	TGTGTG	rs144425663	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155110005_155110006insTGTGTG								KIF4B (712320 upstream) : SGCD (25057 downstream)																							ggtagagcagctgtgtgtgtgt	0.084													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	162833964	162833965	+	IGR	INS	-	ACAC	ACAC	rs138801634	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162833964_162833965insACAC								None (None upstream) : CCNG1 (30612 downstream)																							ctctgtctcaaacacacacaca	0.139													4	2	---	---	---	---	
CPLX2	10814	broad.mit.edu	37	5	175287502	175287523	+	Intron	DEL	AAAGAAAGAAAGAAAGAAAAAG	-	-	rs59334477		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175287502_175287523delAAAGAAAGAAAGAAAGAAAAAG	uc003mde.1	+							NM_006650	NP_006641	Q6PUV4	CPLX2_HUMAN	complexin 2						mast cell degranulation|positive regulation of synaptic plasticity|vesicle docking involved in exocytosis	cytosol				ovary(1)	1	all_cancers(89;0.004)|Renal(175;0.000269)|Lung NSC(126;0.00441)|all_lung(126;0.00747)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			gaaagaaagaaaagaaagaaagaaagaaaaagaaagaaagaa	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	176527040	176527043	+	IGR	DEL	CCTC	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176527040_176527043delCCTC								FGFR4 (1916 upstream) : NSD1 (33037 downstream)																							ttctctctctcctccctccctccc	0.000													2	4	---	---	---	---	
FARS2	10667	broad.mit.edu	37	6	5444325	5444326	+	Intron	INS	-	GTGT	GTGT	rs139887475	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5444325_5444326insGTGT	uc010jnv.1	+						FARS2_uc003mwr.2_Intron	NM_006567	NP_006558	O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2 precursor						phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)	GGAAGATCCTCgtgtgtgtgtg	0.337													5	3	---	---	---	---	
RNF144B	255488	broad.mit.edu	37	6	18459626	18459627	+	Intron	INS	-	TAAT	TAAT	rs141870285	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18459626_18459627insTAAT	uc003ncs.2	+							NM_182757	NP_877434	Q7Z419	R144B_HUMAN	IBR domain containing 2						apoptosis|positive regulation of anti-apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	integral to membrane|mitochondrial membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0	Ovarian(93;0.00365)|Breast(50;0.0145)	all_hematologic(90;0.0536)	OV - Ovarian serous cystadenocarcinoma(7;0.00165)|all cancers(50;0.0102)|Epithelial(50;0.0105)			GGTGGAAACTGTAATTATATAA	0.327													5	4	---	---	---	---	
GRM4	2914	broad.mit.edu	37	6	34003089	34003090	+	Intron	INS	-	G	G	rs113135129		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34003089_34003090insG	uc003oir.3	-						GRM4_uc011dsn.1_Intron|GRM4_uc010jvh.2_Intron|GRM4_uc010jvi.2_Intron|GRM4_uc003oio.2_Intron|GRM4_uc003oip.2_Intron|GRM4_uc011dsl.1_Intron|GRM4_uc003oiq.2_Intron|GRM4_uc011dsm.1_Intron	NM_000841	NP_000832	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4 precursor						activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6					L-Glutamic Acid(DB00142)	aaagaggaggagggggaaggag	0.079													4	2	---	---	---	---	
COL21A1	81578	broad.mit.edu	37	6	55925758	55925758	+	Frame_Shift_Del	DEL	C	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55925758delC	uc003pcs.2	-	26	2515	c.2283delG	c.(2281-2283)GGGfs	p.G761fs	COL21A1_uc010jzz.2_Frame_Shift_Del_p.G146fs|COL21A1_uc011dxg.1_Frame_Shift_Del_p.G134fs|COL21A1_uc011dxh.1_Frame_Shift_Del_p.G146fs|COL21A1_uc003pcr.2_Frame_Shift_Del_p.G118fs	NM_030820	NP_110447	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1 precursor	761	Collagen-like 5.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(2)	2	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			GACCTGCGGGCCCCATCAAGC	0.517													78	50	---	---	---	---	
KIAA0776	23376	broad.mit.edu	37	6	96972044	96972044	+	Intron	DEL	A	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96972044delA	uc003por.2	+						KIAA0776_uc010kck.2_Intron	NM_015323	NP_056138	O94874	UFL1_HUMAN	hypothetical protein LOC23376						negative regulation of NF-kappaB transcription factor activity|negative regulation of protein ubiquitination|protein ufmylation	endoplasmic reticulum|nucleus	protein binding|UFM1 conjugating enzyme activity			ovary(1)	1		all_cancers(76;5.83e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0604)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0934)		GATGttatttaaaaaaaaaaa	0.333													4	2	---	---	---	---	
TUBE1	51175	broad.mit.edu	37	6	112400625	112400625	+	Intron	DEL	A	-	-	rs111683493		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112400625delA	uc003pvq.2	-						TUBE1_uc003pvr.2_Intron	NM_016262	NP_057346	Q9UJT0	TBE_HUMAN	tubulin, epsilon 1						centrosome cycle|microtubule-based movement|protein polymerization	microtubule|pericentriolar material	GTP binding|GTPase activity|structural constituent of cytoskeleton			ovary(1)	1		all_cancers(87;0.0101)|all_hematologic(75;0.000258)|Colorectal(196;0.0466)|all_epithelial(87;0.1)		all cancers(137;0.0217)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0636)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)		GGCTTACATTAaaaaaaaaaa	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	139383236	139383251	+	IGR	DEL	AAGGGAGAAAGGAAGC	-	-	rs12665587		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139383236_139383251delAAGGGAGAAAGGAAGC								C6orf115 (18797 upstream) : HECA (72998 downstream)																							gggagggaggaagggagaaaggaagcaaggaaggaa	0.009													11	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	149915719	149915725	+	IGR	DEL	AAAAAAA	-	-	rs113339415		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149915719_149915725delAAAAAAA								C6orf72 (3652 upstream) : KATNA1 (447 downstream)																							TTTATATACCaaaaaaaaaaaaaaaaa	0.411													4	3	---	---	---	---	
SNX9	51429	broad.mit.edu	37	6	158261481	158261484	+	Intron	DEL	TTCC	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158261481_158261484delTTCC	uc003qqv.1	+							NM_016224	NP_057308	Q9Y5X1	SNX9_HUMAN	sorting nexin 9						cell communication|intracellular protein transport|lipid tube assembly|positive regulation of GTPase activity|positive regulation of protein oligomerization|receptor-mediated endocytosis	clathrin-coated vesicle|cytoplasmic vesicle membrane|extrinsic to internal side of plasma membrane|ruffle|trans-Golgi network	1-phosphatidylinositol binding|protein homodimerization activity|ubiquitin protein ligase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)		tttctttcctttccttccttcctt	0.157													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	1429841	1429845	+	IGR	DEL	GGAAG	-	-	rs140250546	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1429841_1429845delGGAAG								UNCX (153229 upstream) : MICALL2 (44151 downstream)																							aaggaaggaaggaagggagAGAGAA	0.039													7	4	---	---	---	---	
HDAC9	9734	broad.mit.edu	37	7	18826444	18826463	+	Intron	DEL	TTCCTTCCTTCCTTCATTCC	-	-	rs142730759	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18826444_18826463delTTCCTTCCTTCCTTCATTCC	uc003suh.2	+						HDAC9_uc003sue.2_Intron|HDAC9_uc011jyd.1_Intron|HDAC9_uc003sui.2_Intron|HDAC9_uc003suj.2_Intron|HDAC9_uc003sua.1_Intron	NM_058176	NP_478056	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9 isoform 1						B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)	ccttccttcattccttccttccttcattccttccttcctt	0.227													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	19657181	19657182	+	IGR	DEL	CT	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19657181_19657182delCT								FERD3L (472137 upstream) : TWISTNB (77903 downstream)																							cctccctccccttttctttcct	0.000													4	2	---	---	---	---	
CDK14	5218	broad.mit.edu	37	7	90408162	90408169	+	Intron	DEL	CCTTCCTT	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90408162_90408169delCCTTCCTT	uc003uky.2	+						CDK14_uc003ukt.1_Intron|CDK14_uc003ukv.1_Intron|CDK14_uc003uku.1_Intron|CDK14_uc003ukx.1_Intron|CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527	O94921	CDK14_HUMAN	PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4						AATTGACCGAccttccttccttccttcc	0.101													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	109701226	109701227	+	IGR	DEL	AC	-	-	rs113595688		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:109701226_109701227delAC								EIF3IP1 (100956 upstream) : IMMP2L (601883 downstream)																							acacacacatacacacacacac	0.248													4	2	---	---	---	---	
PTPRZ1	5803	broad.mit.edu	37	7	121616705	121616706	+	Intron	INS	-	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121616705_121616706insA	uc003vjy.2	+						PTPRZ1_uc003vjz.2_Intron	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,						central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9						CACCTAGCTATAAAAAAAGTGT	0.218													22	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	121790419	121790424	+	IGR	DEL	ACACAC	-	-	rs72368329	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121790419_121790424delACACAC								AASS (6075 upstream) : FEZF1 (151025 downstream)																							atgggggaaTacacacacacacacac	0.126													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	131513711	131513712	+	IGR	INS	-	CT	CT	rs10652168		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131513711_131513712insCT								PODXL (272335 upstream) : PLXNA4 (294380 downstream)																							ttctttctttctctttctttct	0.000													3	4	---	---	---	---	
LOC93432	93432	broad.mit.edu	37	7	141835524	141835525	+	Intron	DEL	AC	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141835524_141835525delAC	uc003vwz.2	+							NR_003715				RecName: Full=Putative maltase-glucoamylase-like protein LOC93432;												0						ACTTAGAGTTacacacacacac	0.297													4	2	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	2832213	2832213	+	Intron	DEL	C	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2832213delC	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc010lrg.2_Intron	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TGGAAAATCTCCCATACAGAC	0.363													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	42640964	42640967	+	IGR	DEL	AAAG	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42640964_42640967delAAAG								CHRNA6 (17345 upstream) : THAP1 (50851 downstream)																							gaaggaaggaaaagaaagaaagaa	0.000													2	6	---	---	---	---	
TRPS1	7227	broad.mit.edu	37	8	116616283	116616303	+	In_Frame_Del	DEL	TCAGGGGTGGTGAATGAACAC	-	-	rs13282485		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116616283_116616303delTCAGGGGTGGTGAATGAACAC	uc003ynz.2	-	3	2313_2333	c.1854_1874delGTGTTCATTCACCACCCCTGA	c.(1852-1875)CAGTGTTCATTCACCACCCCTGAC>CAC	p.618_625QCSFTTPD>H	TRPS1_uc011lhy.1_In_Frame_Del_p.622_629QCSFTTPD>H|TRPS1_uc003yny.2_In_Frame_Del_p.631_638QCSFTTPD>H|TRPS1_uc010mcy.2_In_Frame_Del_p.618_625QCSFTTPD>H	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	618_625	C2H2-type 3; atypical.				negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			TACATCTACGTCAGGGGTGGTGAATGAACACTGATGGCACT	0.493									Langer-Giedion_syndrome				68	31	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	6669801	6669801	+	IGR	DEL	T	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6669801delT								GLDC (24109 upstream) : KDM4C (46694 downstream)																							TAAAGACTCCTTTGTAGTCAT	0.388													130	142	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	29021676	29021683	+	IGR	DEL	AAGAAAGG	-	-	rs71837184		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:29021676_29021683delAAGAAAGG								MIR873 (132723 upstream) : None (None downstream)																							gaagaaagaaaagaaaggaaggaaggaa	0.043													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66960591	66960592	+	IGR	INS	-	TC	TC			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66960591_66960592insTC								LOC442421 (457564 upstream) : AQP7P1 (293675 downstream)																							GCATACAGGTTTCCACCCCCCC	0.406													10	5	---	---	---	---	
LOC100129066	100129066	broad.mit.edu	37	9	92286506	92286508	+	Intron	DEL	TGG	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92286506_92286508delTGG	uc004aqs.2	+							NR_024280				Homo sapiens cDNA FLJ42342 fis, clone UTERU2000794.												0						gtgatggagatggtggtgatgat	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	27620447	27620448	+	IGR	INS	-	TT	TT	rs142562667	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27620447_27620448insTT								LOC387646 (79212 upstream) : PTCHD3 (66669 downstream)																							ACTCAGGCTTCTTTCCGCCAAG	0.465													13	7	---	---	---	---	
CTNNA3	29119	broad.mit.edu	37	10	69420998	69420999	+	Intron	INS	-	A	A			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69420998_69420999insA	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_Intron|CTNNA3_uc009xpo.1_Intron|CTNNA3_uc001jna.2_Intron	NM_001127384	NP_001120856	Q9UI47	CTNA3_HUMAN	catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8						tttactaaaacaaaaaaAAAAG	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	91621122	91621124	+	IGR	DEL	TCC	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91621122_91621124delTCC								KIF20B (86422 upstream) : HTR7 (879454 downstream)																							cctctcctcttcctcttcttcct	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	102441054	102441055	+	IGR	INS	-	ACACAC	ACACAC	rs66514472		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102441054_102441055insACACAC								HIF1AN (127374 upstream) : PAX2 (64413 downstream)																							ACCCCTTCCCTacacacacaca	0.490													3	3	---	---	---	---	
SORCS1	114815	broad.mit.edu	37	10	108850678	108850679	+	Intron	DEL	AC	-	-	rs10569833		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108850678_108850679delAC	uc001kym.2	-						SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_Intron	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		ATTCTAAAGTacacacacacac	0.317													6	3	---	---	---	---	
MGMT	4255	broad.mit.edu	37	10	131362930	131362930	+	Intron	DEL	C	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131362930delC	uc001lkh.2	+							NM_002412	NP_002403	P16455	MGMT_HUMAN	O-6-methylguanine-DNA methyltransferase											ovary(1)|breast(1)	2		all_cancers(35;9.44e-09)|all_epithelial(44;6.98e-08)|Lung NSC(174;0.0157)|all_lung(145;0.0201)|all_neural(114;0.0732)|Colorectal(57;0.0792)|Breast(234;0.167)		OV - Ovarian serous cystadenocarcinoma(35;0.00291)		tctccttcctccccctcctct	0.119								Direct_reversal_of_damage					6	3	---	---	---	---	
RRAS2	22800	broad.mit.edu	37	11	14380349	14380349	+	Frame_Shift_Del	DEL	C	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14380349delC	uc001mlf.3	-	1	381	c.68delG	c.(67-69)GGCfs	p.G23fs	RRAS2_uc009ygq.2_5'Flank|RRAS2_uc010rco.1_Frame_Shift_Del_p.G23fs	NM_012250	NP_036382	P62070	RRAS2_HUMAN	related RAS viral (r-ras) oncogene homolog 2	23	GTP.					endoplasmic reticulum|plasma membrane	GTP binding|GTPase activity|protein binding			breast(1)	1				Epithelial(150;0.203)		GCCCACGCCGCCCCCGCCGAC	0.537													5	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	18993302	18993302	+	IGR	DEL	C	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18993302delC								MRGPRX1 (36753 upstream) : MRGPRX2 (82703 downstream)																							GAATCTGCTTCCCGACAGCTC	0.562													29	36	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	68412067	68412068	+	IGR	INS	-	G	G	rs74620594		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68412067_68412068insG								SAPS3 (29268 upstream) : GAL (39915 downstream)																							aaggaaggaaagaaggaaggaa	0.000													5	3	---	---	---	---	
ARHGEF17	9828	broad.mit.edu	37	11	73077186	73077187	+	Intron	DEL	GC	-	-	rs55848894		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73077186_73077187delGC	uc001otu.2	+							NM_014786	NP_055601	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity				0						gtgtgtgtgtgCGCACCTGCAT	0.366													4	4	---	---	---	---	
FOXR1	283150	broad.mit.edu	37	11	118840332	118840333	+	5'Flank	DEL	AA	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118840332_118840333delAA	uc001pui.2	+						FOXR1_uc001puj.2_5'Flank	NM_181721	NP_859072	Q6PIV2	FOXR1_HUMAN	forkhead box R1						embryo development|organ development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue 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 activator activity|transcription factor binding			skin(1)	1	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)		ggaaagaaagaaagaaaggaag	0.000													4	6	---	---	---	---	
ASAM	79827	broad.mit.edu	37	11	123021238	123021244	+	Intron	DEL	AAGAAAC	-	-	rs71057397		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123021238_123021244delAAGAAAC	uc001pyt.2	-							NM_024769	NP_079045	Q9H6B4	CLMP_HUMAN	adipocyte-specific adhesion molecule precursor							integral to membrane|tight junction					0		Breast(109;0.0025)|Lung NSC(97;0.0179)|all_lung(97;0.0182)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.73e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0446)		gaaggaaggaaagaaacaagcaaggaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	133746051	133746054	+	IGR	DEL	GTGT	-	-	rs35467165		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133746051_133746054delGTGT								SPATA19 (30659 upstream) : LOC283174 (20276 downstream)																							ctacttttaagtgtgtgtgtgtgt	0.000													3	3	---	---	---	---	
PRB2	653247	broad.mit.edu	37	12	11546395	11546395	+	Frame_Shift_Del	DEL	G	-	-	rs11054277		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11546395delG	uc010shk.1	-	3	652	c.617delC	c.(616-618)CCAfs	p.P206fs		NM_006248	NP_006239			proline-rich protein BstNI subfamily 2												0		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			GCCTCCTTGTGGGGGTGGTCC	0.602													305	240	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	115633997	115633998	+	IGR	INS	-	TTCCTTCC	TTCCTTCC	rs139227338	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115633997_115633998insTTCCTTCC								TBX3 (512028 upstream) : MED13L (762385 downstream)																							ttctcttttctttccttccttc	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	119145754	119145756	+	IGR	DEL	TGG	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119145754_119145756delTGG								SUDS3 (289915 upstream) : SRRM4 (273640 downstream)																							gtgatggtgatggtggtggtggt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	25705105	25705132	+	IGR	DEL	AGGAAGGAAGGAAGGAAGGAAGGAAGGA	-	-	rs68042865	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25705105_25705132delAGGAAGGAAGGAAGGAAGGAAGGAAGGA								PABPC3 (32403 upstream) : FAM123A (37541 downstream)																							ggagggagggaggaaggaaggaaggaaggaaggaaggaaggaaggaag	0.136													8	5	---	---	---	---	
EDNRB	1910	broad.mit.edu	37	13	78474726	78474726	+	Frame_Shift_Del	DEL	G	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78474726delG	uc001vko.2	-	5	1273	c.1015delC	c.(1015-1017)CTTfs	p.L339fs	EDNRB_uc001vkq.1_Frame_Shift_Del_p.L339fs|uc001vkn.1_Intron|EDNRB_uc010aez.1_Frame_Shift_Del_p.L339fs|EDNRB_uc001vkp.1_Frame_Shift_Del_p.L422fs	NM_001122659	NP_001116131	P24530	EDNRB_HUMAN	endothelin receptor type B isoform 1 precursor	339	Helical; Name=6; (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|enteric nervous system development|enteric smooth muscle cell differentiation|macrophage chemotaxis|negative regulation of adenylate cyclase activity|negative regulation of cellular protein metabolic process|negative regulation of neuron maturation|negative regulation of transcription from RNA polymerase II promoter|vein smooth muscle contraction	integral to plasma membrane	endothelin-B receptor activity|peptide hormone binding				0		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)	CTGAGGTGAAGGGGAAGCCAG	0.433													85	42	---	---	---	---	
ABCC4	10257	broad.mit.edu	37	13	95884362	95884364	+	Intron	DEL	TGC	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95884362_95884364delTGC	uc001vmd.3	-						ABCC4_uc010afk.2_Intron|ABCC4_uc001vme.2_Intron|ABCC4_uc010tih.1_Intron|ABCC4_uc001vmf.2_Intron|ABCC4_uc010afl.1_Intron|ABCC4_uc010afm.1_Intron	NM_005845	NP_005836	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)	atgatgatgatgctgctgctgct	0.227													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	100240683	100240698	+	IGR	DEL	TTCTTTCTTTCCTTCC	-	-	rs12560994	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100240683_100240698delTTCTTTCTTTCCTTCC								TM9SF2 (25407 upstream) : CLYBL (18238 downstream)																							cttcctttctttctttctttccttccttccttcctt	0.074													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	39304295	39304296	+	Intron	INS	-	AA	AA	rs137880780	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39304295_39304296insAA	uc001wun.2	-						uc001wuo.2_Intron|uc010amw.1_Intron					Homo sapiens cDNA FLJ43028 fis, clone BRTHA3000297.																		CCCTGCTCcacacacacacaca	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	51949392	51949393	+	IGR	INS	-	TGTGTGTGTG	TGTGTGTGTG	rs145338790	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51949392_51949393insTGTGTGTGTG								TMX1 (225022 upstream) : FRMD6 (6462 downstream)																							TTTGCAGGAACTGTGTGTGTGT	0.252													4	2	---	---	---	---	
SNW1	22938	broad.mit.edu	37	14	78185057	78185057	+	Intron	DEL	T	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78185057delT	uc001xuf.2	-						SNW1_uc010tvm.1_Intron|SNW1_uc010asu.2_Intron|SNW1_uc010tvn.1_Intron	NM_012245	NP_036377	Q13573	SNW1_HUMAN	SKI-interacting protein						negative regulation of transcription, DNA-dependent|nuclear mRNA splicing, via spliceosome|regulation of transcription from RNA polymerase II promoter	catalytic step 2 spliceosome|nucleoplasm	Notch binding			ovary(1)	1			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		CTTTGGAttcttttttttttt	0.154													4	2	---	---	---	---	
SERPINA13	388007	broad.mit.edu	37	14	95104846	95104847	+	5'Flank	INS	-	AC	AC	rs149521691	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95104846_95104847insAC	uc001ydt.2	+							NR_015340				RecName: Full=Serpin A13; Flags: Precursor;											lung(1)|skin(1)	2						cacacacacctacacacacaca	0.396													2	4	---	---	---	---	
HHIPL1	84439	broad.mit.edu	37	14	100126463	100126482	+	Intron	DEL	CACGCCAGCCCTGCTGTGGG	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100126463_100126482delCACGCCAGCCCTGCTGTGGG	uc010avs.2	+						HHIPL1_uc001ygl.1_Intron	NM_001127258	NP_001120730	Q96JK4	HIPL1_HUMAN	HHIP-like protein 1 isoform a						carbohydrate metabolic process	extracellular region|membrane	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding|scavenger receptor activity			skin(2)	2		Melanoma(154;0.128)				CGCTTTCCACCACGCCAGCCCTGCTGTGGGCACGCCAGCC	0.700													3	3	---	---	---	---	
GABRG3	2567	broad.mit.edu	37	15	27633498	27633509	+	Intron	DEL	GTAAGGAAGGAA	-	-	rs71397224	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27633498_27633509delGTAAGGAAGGAA	uc001zbg.1	+						GABRG3_uc001zbf.2_Intron	NM_033223	NP_150092	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)		gggagggagggtaaggaaggaaggaagaaagg	0.090													7	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	39738952	39738953	+	IGR	DEL	CG	-	-	rs6492890	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39738952_39738953delCG								C15orf54 (191904 upstream) : THBS1 (134327 downstream)																							cacacacacacgcacacacTCA	0.307													4	2	---	---	---	---	
PRTG	283659	broad.mit.edu	37	15	55976160	55976160	+	Intron	DEL	A	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55976160delA	uc002adg.2	-							NM_173814	NP_776175	Q2VWP7	PRTG_HUMAN	protogenin precursor						multicellular organismal development	integral to membrane				large_intestine(1)|ovary(1)|skin(1)	3				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		AATTCAGAATAAGTGCATGAA	0.368													23	33	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	84063040	84063041	+	IGR	INS	-	AGGG	AGGG			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84063040_84063041insAGGG								BNC1 (109572 upstream) : SH3GL3 (53050 downstream)																							gggagggagggaggaaggatgg	0.203													15	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33939019	33939019	+	IGR	DEL	C	-	-	rs113683091		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33939019delC								None (None upstream) : MIR1826 (26489 downstream)																							GTTGCACAGGCCGCCTGCGTG	0.667													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33942128	33942129	+	IGR	INS	-	T	T	rs76660512	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33942128_33942129insT								None (None upstream) : MIR1826 (23379 downstream)																							TGGAAAAAATACCACTTGTTAC	0.267													4	3	---	---	---	---	
RBL2	5934	broad.mit.edu	37	16	53524205	53524205	+	Frame_Shift_Del	DEL	C	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53524205delC	uc002ehi.3	+	22	3531	c.3413delC	c.(3412-3414)TCCfs	p.S1138fs	RBL2_uc002ehj.2_Frame_Shift_Del_p.S848fs|RBL2_uc010vgw.1_Frame_Shift_Del_p.S517fs	NM_005611	NP_005602	Q08999	RBL2_HUMAN	retinoblastoma-like 2 (p130)	1138					cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(2)|lung(2)|upper_aerodigestive_tract(1)	5						GACCGTGGTTCCCACTGAGGT	0.403													282	158	---	---	---	---	
CNTNAP4	85445	broad.mit.edu	37	16	76513513	76513513	+	Intron	DEL	G	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76513513delG	uc002feu.1	+						CNTNAP4_uc002fev.1_Intron|CNTNAP4_uc010chb.1_Intron|CNTNAP4_uc002fex.1_Intron|CNTNAP4_uc002few.2_Intron	NM_033401	NP_207837	Q9C0A0	CNTP4_HUMAN	cell recognition protein CASPR4 isoform 1						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2						GAAATAAGCAGAATGTTGACG	0.239													24	15	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	85512552	85512555	+	IGR	DEL	TTTT	-	-	rs34166351		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85512552_85512555delTTTT								FAM92B (366438 upstream) : KIAA0182 (132474 downstream)																							tctttctttctttttttttctttc	0.000													5	3	---	---	---	---	
ULK2	9706	broad.mit.edu	37	17	19752998	19752998	+	Intron	DEL	A	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19752998delA	uc002gwm.3	-						ULK2_uc002gwn.2_Intron	NM_001142610	NP_001136082	Q8IYT8	ULK2_HUMAN	unc-51-like kinase 2						signal transduction		ATP binding|protein binding|protein serine/threonine kinase activity			skin(2)|large_intestine(1)|stomach(1)	4	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)					GCTAGAATCtaaaaaaaaaaa	0.229													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	31275023	31275023	+	IGR	DEL	T	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31275023delT								TMEM98 (6358 upstream) : SPACA3 (43859 downstream)																							AGAGAGCCAGTTTTTTTTTtt	0.259													5	3	---	---	---	---	
SETBP1	26040	broad.mit.edu	37	18	42448632	42448633	+	Intron	INS	-	GA	GA	rs147824825	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42448632_42448633insGA	uc010dni.2	+						SETBP1_uc002lay.2_Intron	NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a							nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		tgtactccagcgagagagagag	0.000									Schinzel-Giedion_syndrome				6	3	---	---	---	---	
DCC	1630	broad.mit.edu	37	18	50866418	50866419	+	Intron	DEL	AC	-	-	rs3217360		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50866418_50866419delAC	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		CTGTCTATCTacacacacacac	0.233													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	54969573	54969574	+	IGR	DEL	GT	-	-	rs73961054		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54969573_54969574delGT								WDR7 (272537 upstream) : ST8SIA3 (50147 downstream)																							TGTGTAGGGGgtgtgtgtgtgt	0.297													4	4	---	---	---	---	
KHSRP	8570	broad.mit.edu	37	19	6414239	6414239	+	Intron	DEL	C	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6414239delC	uc002mer.3	-							NM_003685	NP_003676	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein						mRNA processing|mRNA transport|regulation of transcription, DNA-dependent|RNA splicing, via transesterification reactions|transcription, DNA-dependent	cytosol|nucleus	DNA binding|protein binding|RNA binding			skin(1)	1						GGCCAGGAAGCCCCCTCCCAA	0.632													7	5	---	---	---	---	
UNC13A	23025	broad.mit.edu	37	19	17757078	17757079	+	Intron	INS	-	TGTT	TGTT	rs142508123	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17757078_17757079insTGTT	uc002nhd.2	-							NM_001080421	NP_001073890	Q9UPW8	UN13A_HUMAN	unc-13 homolog A						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3						Ggttttttgtgtgtttgtttgt	0.272													3	3	---	---	---	---	
ZNF738	148203	broad.mit.edu	37	19	21567870	21567873	+	3'UTR	DEL	TGAC	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21567870_21567873delTGAC	uc002nps.3	+	5						NR_027130				SubName: Full=cDNA FLJ14673 fis, clone NT2RP2003714, moderately similar to Zinc finger protein 430;												0						TAAAAGAGTTTgactgggtgcggt	0.245													6	3	---	---	---	---	
SBSN	374897	broad.mit.edu	37	19	36017741	36017741	+	Frame_Shift_Del	DEL	G	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36017741delG	uc002oae.1	-	2	484	c.414delC	c.(412-414)CACfs	p.H138fs	SBSN_uc002oad.1_Frame_Shift_Del_p.H481fs	NM_198538	NP_940940	Q6UWP8	SBSN_HUMAN	suprabasin isoform 2 precursor	138	Ala/Gly/His-rich.					extracellular region				ovary(1)	1	all_lung(56;1.62e-08)|Lung NSC(56;2.47e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GGACCCCAGTGTGGAACCCTT	0.597													39	47	---	---	---	---	
PRKCG	5582	broad.mit.edu	37	19	54395680	54395680	+	Intron	DEL	C	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54395680delC	uc002qcq.1	+						PRKCG_uc010eqz.1_Intron|PRKCG_uc010yef.1_Intron|PRKCG_uc010yeg.1_Intron|PRKCG_uc010yeh.1_Intron	NM_002739	NP_002730	P05129	KPCG_HUMAN	protein kinase C, gamma						activation of phospholipase C activity|cell death|intracellular signal transduction|negative regulation of protein catabolic process|negative regulation of protein ubiquitination|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of mismatch repair|synaptic transmission	cytosol	ATP binding|protein kinase C activity|zinc ion binding			lung(4)|ovary(2)|pancreas(2)|large_intestine(1)	9	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)		GCTGGGTTTGCCCCCACCTCC	0.652													4	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	54810610	54810614	+	IGR	DEL	CTTCT	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54810610_54810614delCTTCT								LILRA6 (6372 upstream) : LILRA5 (7740 downstream)																							ccctccctcccttctctccctccct	0.044													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	36231838	36231845	+	IGR	DEL	TTTCTTTG	-	-	rs57438742		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36231838_36231845delTTTCTTTG								BLCAP (75535 upstream) : CTNNBL1 (90589 downstream)																							tcttccttcctttctttgtttcttcctt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	36740457	36740458	+	IGR	INS	-	CCTTCCTTCCCTC	CCTTCCTTCCCTC	rs149380856	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36740457_36740458insCCTTCCTTCCCTC								RPRD1B (19693 upstream) : TGM2 (16408 downstream)																							cttccttctttccttctttcct	0.099													4	4	---	---	---	---	
AURKA	6790	broad.mit.edu	37	20	54949073	54949074	+	Intron	DEL	AC	-	-	rs144437309		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54949073_54949074delAC	uc002xxd.1	-						AURKA_uc002xxe.1_Intron|AURKA_uc002xxf.1_Intron|AURKA_uc002xxg.1_Intron|AURKA_uc002xxh.1_Intron|AURKA_uc002xxi.1_Intron|AURKA_uc002xxj.1_Intron|AURKA_uc002xxk.1_Intron|AURKA_uc010zzd.1_Intron	NM_198433	NP_940835	O14965	AURKA_HUMAN	serine/threonine protein kinase 6						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|phosphatidylinositol-mediated signaling|regulation of protein stability|spindle organization	cytosol|nucleus|perinuclear region of cytoplasm|spindle microtubule|spindle pole centrosome	ATP binding|protein kinase binding|protein serine/threonine kinase activity			lung(3)|ovary(2)|breast(1)|large_intestine(1)|skin(1)	8			Colorectal(105;0.202)			ATAGGAGTCTacacacacacac	0.193													3	4	---	---	---	---	
GMEB2	26205	broad.mit.edu	37	20	62234126	62234127	+	Intron	INS	-	C	C	rs138079876	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62234126_62234127insC	uc002yfp.1	-						GMEB2_uc002yfo.1_Intron|GMEB2_uc002yfq.1_Intron	NM_012384	NP_036516	Q9UKD1	GMEB2_HUMAN	glucocorticoid modulatory element binding						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|metal ion binding				0	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;4.79e-09)|all cancers(9;2.76e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.0114)			CGGGAGGGCCTCCCAGCCTCCC	0.614													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	33659555	33659556	+	IGR	DEL	CA	-	-	rs73901378	by1000genomes	TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33659555_33659556delCA								C21orf45 (8179 upstream) : MRAP (4568 downstream)																							ctctctttctcacacacacaca	0.000													4	4	---	---	---	---	
TTC3	7267	broad.mit.edu	37	21	38536643	38536643	+	Intron	DEL	T	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38536643delT	uc002yvz.2	+						TTC3_uc011aee.1_Intron|TTC3_uc002ywa.2_Intron|TTC3_uc002ywb.2_Intron|TTC3_uc010gnf.2_Intron|TTC3_uc002ywc.2_Intron|TTC3_uc002ywd.1_Intron	NM_001001894	NP_001001894	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3						protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			skin(3)|ovary(2)|lung(2)|breast(2)	9		Myeloproliferative disorder(46;0.0412)				TAATTTAGGAttttttttttt	0.144													7	5	---	---	---	---	
ATXN10	25814	broad.mit.edu	37	22	46136560	46136567	+	Intron	DEL	ACACACAC	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46136560_46136567delACACACAC	uc003bgm.1	+						ATXN10_uc011aqt.1_Intron|ATXN10_uc003bgn.1_Intron	NM_013236	NP_037368	Q9UBB4	ATX10_HUMAN	ataxin 10						cell death|neuron projection development	dendrite|neuronal cell body|perinuclear region of cytoplasm				ovary(1)|kidney(1)	2		Ovarian(80;0.00973)|all_neural(38;0.0417)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0223)		ttatatgaatacacacacacacacacac	0.163													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	504699	504699	+	IGR	DEL	A	-	-			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:504699delA								PPP2R3B (157072 upstream) : SHOX (80380 downstream)																							aGCCTTCCAGAAAAAAAAAAA	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	5189386	5189387	+	IGR	INS	-	CCTT	CCTT			TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:5189386_5189387insCCTT								None (None upstream) : NLGN4X (618697 downstream)																							tttctttcttacctttccttcc	0.054													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	117359358	117359361	+	IGR	DEL	CACA	-	-	rs72469154		TCGA-37-4141-01A-02D-1352-08	TCGA-37-4141-10A-01D-1352-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117359358_117359361delCACA								KLHL13 (108570 upstream) : WDR44 (120681 downstream)																							ATCGGCCCAGcacacacacacaca	0.373													4	2	---	---	---	---	
