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
ISG15	9636	broad.mit.edu	37	1	949562	949562	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:949562G>A	uc001acj.3	+	2	309	c.202G>A	c.(202-204)GGC>AGC	p.G68S		NM_005101	NP_005092	P05161	ISG15_HUMAN	ISG15 ubiquitin-like modifier precursor	68	Ubiquitin-like 1.				cell-cell signaling|interspecies interaction between organisms|ISG15-protein conjugation|negative regulation of type I interferon production|response to virus|type I interferon-mediated signaling pathway	cytosol|extracellular space	protein binding				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;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;4.05e-38)|OV - Ovarian serous cystadenocarcinoma(86;4.54e-23)|Colorectal(212;5.37e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00238)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)		CCTGGGCCCCGGCAGCACGGT	0.662													37	47	---	---	---	---	PASS
KIAA1751	85452	broad.mit.edu	37	1	1897928	1897928	+	Nonsense_Mutation	SNP	A	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1897928A>T	uc001aim.1	-	12	1439	c.1283T>A	c.(1282-1284)TTG>TAG	p.L428*	KIAA1751_uc009vkz.1_Nonsense_Mutation_p.L428*	NM_001080484	NP_001073953	Q9C0B2	K1751_HUMAN	hypothetical protein LOC85452	428										pancreas(1)	1	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;8.79e-39)|OV - Ovarian serous cystadenocarcinoma(86;9.61e-25)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;4.84e-05)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)		GACTTCCAGCAACCGAGAGGG	0.587													22	45	---	---	---	---	PASS
SPSB1	80176	broad.mit.edu	37	1	9416114	9416114	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9416114C>T	uc010oae.1	+	2	503	c.164C>T	c.(163-165)TCA>TTA	p.S55L	SPSB1_uc001apv.2_Missense_Mutation_p.S55L	NM_025106	NP_079382	Q96BD6	SPSB1_HUMAN	splA/ryanodine receptor domain and SOCS box	55	B30.2/SPRY.				intracellular signal transduction	cytoplasm					0	all_lung(157;0.194)	all_epithelial(116;4.38e-15)|all_lung(118;0.000156)|Lung NSC(185;0.000446)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;2.72e-07)|COAD - Colon adenocarcinoma(227;9.12e-05)|Kidney(185;0.000296)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00193)|BRCA - Breast invasive adenocarcinoma(304;0.00202)|READ - Rectum adenocarcinoma(331;0.0419)		CTGCTGCATTCATGGAACAAC	0.567													29	111	---	---	---	---	PASS
KIF1B	23095	broad.mit.edu	37	1	10386247	10386247	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10386247C>T	uc001aqx.3	+	27	2956	c.2754C>T	c.(2752-2754)TCC>TCT	p.S918S	KIF1B_uc001aqw.3_Silent_p.S872S|KIF1B_uc001aqy.2_Silent_p.S892S|KIF1B_uc001aqz.2_Silent_p.S918S|KIF1B_uc001ara.2_Silent_p.S878S|KIF1B_uc001arb.2_Silent_p.S904S	NM_015074	NP_055889	O60333	KIF1B_HUMAN	kinesin family member 1B isoform b	918					anterograde axon cargo transport|apoptosis|neuromuscular synaptic transmission|neuron-neuron synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		CGGCCGATTCCGACATCACTG	0.592													31	141	---	---	---	---	PASS
PLOD1	5351	broad.mit.edu	37	1	12016994	12016994	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12016994G>C	uc001atm.2	+	7	755	c.664G>C	c.(664-666)GAA>CAA	p.E222Q	PLOD1_uc010obb.1_Missense_Mutation_p.E269Q	NM_000302	NP_000293	Q02809	PLOD1_HUMAN	lysyl hydroxylase 1 precursor	222					epidermis development|hydroxylysine biosynthetic process|protein modification process|response to hypoxia	rough endoplasmic reticulum membrane	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-lysine 5-dioxygenase activity|protein homodimerization activity			ovary(2)|breast(1)	3	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000809)|KIRC - Kidney renal clear cell carcinoma(229;0.00267)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)	Minoxidil(DB00350)|Succinic acid(DB00139)|Vitamin C(DB00126)	GCTCAAGTTTGAAATGGGCCA	0.493													3	120	---	---	---	---	PASS
C1orf158	93190	broad.mit.edu	37	1	12820845	12820845	+	Silent	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12820845G>T	uc001auh.2	+	4	762	c.546G>T	c.(544-546)CCG>CCT	p.P182P		NM_152290	NP_689503	Q8N1D5	CA158_HUMAN	hypothetical protein LOC93190	182										ovary(1)|central_nervous_system(1)|skin(1)	3	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00575)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		ATGCGGTCCCGGTCCCTCCCC	0.587													6	84	---	---	---	---	PASS
PTAFR	5724	broad.mit.edu	37	1	28476843	28476843	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28476843C>T	uc001bpl.2	-	2	817	c.690G>A	c.(688-690)GCG>GCA	p.A230A	PTAFR_uc001bpm.3_Silent_p.A230A|PTAFR_uc009vte.2_Silent_p.A230A	NM_000952	NP_000943	P25105	PTAFR_HUMAN	platelet-activating factor receptor	230	Cytoplasmic (Potential).				chemotaxis|inflammatory response|interferon-gamma-mediated signaling pathway|phosphatidylinositol-mediated signaling	integral to plasma membrane|nucleus	phospholipid binding|platelet activating factor receptor activity				0		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00715)|all_lung(284;0.00732)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.215)|OV - Ovarian serous cystadenocarcinoma(117;6e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|STAD - Stomach adenocarcinoma(196;0.00678)|READ - Rectum adenocarcinoma(331;0.0649)		CCATCCACAGCGCCCGGCGCT	0.612													6	36	---	---	---	---	PASS
GMEB1	10691	broad.mit.edu	37	1	29010259	29010259	+	Intron	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29010259G>A	uc001bra.2	+						GMEB1_uc001bqz.2_Intron|GMEB1_uc001brb.2_Intron	NM_006582	NP_006573	Q9Y692	GMEB1_HUMAN	glucocorticoid modulatory element binding						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|metal ion binding|transcription coactivator activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Breast(348;0.00502)|Renal(390;0.00555)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)		AAGGGTAAGTGGCTAGAGATT	0.408													12	59	---	---	---	---	PASS
CDCA8	55143	broad.mit.edu	37	1	38158662	38158662	+	Silent	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38158662G>T	uc001cbr.2	+	3	287	c.180G>T	c.(178-180)CGG>CGT	p.R60R	C1orf109_uc010oig.1_5'Flank|C1orf109_uc001cbo.2_5'Flank|C1orf109_uc001cbp.2_5'Flank|C1orf109_uc001cbq.1_5'Flank|CDCA8_uc001cbs.2_Silent_p.R60R|CDCA8_uc010oih.1_5'UTR	NM_018101	NP_060571	Q53HL2	BOREA_HUMAN	cell division cycle associated 8	60	Required for centromere localization.|Required for interaction with SENP3.|Required to form a minimal CPC core complex that localizes to the central spindle and midbody and properly executes the role of the CPC during cytokinesis.|Required for interaction with INCENP and BIRC5.				cell division|chromosome organization|mitotic metaphase|mitotic prometaphase	chromosome passenger complex|chromosome, centromeric region|cytosol|nucleolus|spindle	protein binding			central_nervous_system(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				AGATCCTGCGGCTCCCCAAGG	0.567													23	42	---	---	---	---	PASS
MACF1	23499	broad.mit.edu	37	1	39798692	39798692	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39798692G>A	uc010oiu.1	+	1	1883	c.1752G>A	c.(1750-1752)TTG>TTA	p.L584L	MACF1_uc010ois.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc001cdb.1_Intron	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	2149					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)			GTGTGCCGTTGGTGGTTGACA	0.468													9	68	---	---	---	---	PASS
MACF1	23499	broad.mit.edu	37	1	39888172	39888172	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39888172G>C	uc010oiu.1	+	23	11394	c.11263G>C	c.(11263-11265)GAG>CAG	p.E3755Q	MACF1_uc010ois.1_Missense_Mutation_p.E3253Q|MACF1_uc001cda.1_Missense_Mutation_p.E3140Q|MACF1_uc001cdc.1_Missense_Mutation_p.E2319Q	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	5320	Spectrin 6.				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)			TGACATGGAAGAGATCAATGC	0.418													13	55	---	---	---	---	PASS
NT5C1A	84618	broad.mit.edu	37	1	40126838	40126838	+	Silent	SNP	C	A	A	rs144981890	by1000genomes	TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40126838C>A	uc001cdq.1	-	5	654	c.654G>T	c.(652-654)TCG>TCT	p.S218S		NM_032526	NP_115915	Q9BXI3	5NT1A_HUMAN	5'-nucleotidase, cytosolic IA	218					purine base metabolic process|purine nucleotide catabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	cytosol	5'-nucleotidase activity|magnesium ion binding|nucleotide binding			ovary(1)	1	Lung NSC(20;3.81e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;4.3e-17)|all cancers(16;8.48e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			CCGACTCGTCCGAGAAGAGCA	0.622													3	84	---	---	---	---	PASS
PTCH2	8643	broad.mit.edu	37	1	45292729	45292729	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45292729C>G	uc010olf.1	-	17	2552	c.2540G>C	c.(2539-2541)AGA>ACA	p.R847T	PTCH2_uc010olg.1_Missense_Mutation_p.R545T	NM_003738	NP_003729	Q9Y6C5	PTC2_HUMAN	patched 2	847	Extracellular (Potential).				protein complex assembly|spermatogenesis	integral to plasma membrane	hedgehog receptor activity			lung(6)|breast(6)|central_nervous_system(3)|skin(2)|ovary(1)	18	Acute lymphoblastic leukemia(166;0.155)					CAGTCCCTCTCTGTCCACCAG	0.642									Basal_Cell_Nevus_syndrome				35	96	---	---	---	---	PASS
PTCH2	8643	broad.mit.edu	37	1	45293550	45293550	+	Nonsense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45293550G>A	uc010olf.1	-	14	2035	c.2023C>T	c.(2023-2025)CAG>TAG	p.Q675*	PTCH2_uc010olg.1_Nonsense_Mutation_p.Q373*	NM_003738	NP_003729	Q9Y6C5	PTC2_HUMAN	patched 2	675	Cytoplasmic (Potential).				protein complex assembly|spermatogenesis	integral to plasma membrane	hedgehog receptor activity			lung(6)|breast(6)|central_nervous_system(3)|skin(2)|ovary(1)	18	Acute lymphoblastic leukemia(166;0.155)					GGGGCAAACTGATAGCGGGCG	0.597									Basal_Cell_Nevus_syndrome				12	76	---	---	---	---	PASS
FAAH	2166	broad.mit.edu	37	1	46874151	46874151	+	Silent	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46874151C>G	uc001cpu.2	+	8	1054	c.972C>G	c.(970-972)CCC>CCG	p.P324P	FAAH_uc001cpv.2_RNA	NM_001441	NP_001432	O00519	FAAH1_HUMAN	fatty acid amide hydrolase	324	Cytoplasmic (By similarity).				fatty acid catabolic process	cytoplasm|cytoskeleton|endomembrane system|integral to membrane|organelle membrane	carbon-nitrogen ligase activity, with glutamine as amido-N-donor|fatty acid amide hydrolase activity			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(166;0.155)				Propofol(DB00818)|Thiopental(DB00599)	GCTCTCAGCCCCTGCGTGTGG	0.602													14	347	---	---	---	---	PASS
JUN	3725	broad.mit.edu	37	1	59248409	59248409	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59248409C>T	uc001cze.2	-	1	1377	c.334G>A	c.(334-336)GAG>AAG	p.E112K	uc001czf.2_5'Flank|uc010oop.1_5'Flank	NM_002228	NP_002219	P05412	JUN_HUMAN	jun oncogene	112					innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation by host of viral transcription|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|positive regulation by host of viral transcription|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|SMAD protein import into nucleus|SMAD 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|transforming growth factor beta receptor signaling pathway		R-SMAD binding|Rho GTPase activator activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription coactivator activity|transcription factor binding|transcription regulatory region DNA binding				0	all_cancers(7;8.55e-07)				Arsenic trioxide(DB01169)|Irbesartan(DB01029)|Vinblastine(DB00570)	ACGAAGCCCTCGGCGAAGCCC	0.672			A		sarcoma								4	107	---	---	---	---	PASS
LHX8	431707	broad.mit.edu	37	1	75608891	75608891	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75608891G>C	uc001dgo.2	+	6	1142	c.478G>C	c.(478-480)GCA>CCA	p.A160P	LHX8_uc001dgq.2_Missense_Mutation_p.A99P	NM_001001933	NP_001001933	Q68G74	LHX8_HUMAN	LIM homeobox 8	160	LIM zinc-binding 2.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3						CTATCACTTGGCATGCTTTGC	0.473													35	80	---	---	---	---	PASS
IFI44	10561	broad.mit.edu	37	1	79119954	79119954	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79119954G>A	uc001dip.3	+	3	608	c.484G>A	c.(484-486)GGG>AGG	p.G162R	IFI44_uc010orr.1_Missense_Mutation_p.G162R|IFI44_uc010ors.1_5'UTR	NM_006417	NP_006408	Q8TCB0	IFI44_HUMAN	interferon-induced, hepatitis C-associated	162					response to virus	cytoplasm				ovary(1)|central_nervous_system(1)	2						AAAGATAAAAGGGGTCATTGA	0.303													18	51	---	---	---	---	PASS
LRRC8C	84230	broad.mit.edu	37	1	90179549	90179549	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90179549C>T	uc001dnl.3	+	3	1662	c.1420C>T	c.(1420-1422)CTG>TTG	p.L474L		NM_032270	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member	474	LRR 4.					endoplasmic reticulum membrane|integral to membrane				ovary(3)|skin(3)|pancreas(1)|central_nervous_system(1)	8		all_lung(203;0.126)		all cancers(265;0.00756)|Epithelial(280;0.0313)		AGAGCTCTCTCTGCACCAGTG	0.438													8	92	---	---	---	---	PASS
ABCA4	24	broad.mit.edu	37	1	94528861	94528861	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94528861C>A	uc001dqh.2	-	12	1671	c.1567G>T	c.(1567-1569)GAT>TAT	p.D523Y	ABCA4_uc010otn.1_Missense_Mutation_p.D523Y	NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	523	Extracellular.		D -> E (in STGD1).		phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		TCAAACTTATCCAGGACCAAG	0.483													15	115	---	---	---	---	PASS
ABCA4	24	broad.mit.edu	37	1	94528862	94528862	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94528862C>T	uc001dqh.2	-	12	1670	c.1566G>A	c.(1564-1566)CTG>CTA	p.L522L	ABCA4_uc010otn.1_Silent_p.L522L	NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	522	Extracellular.				phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		CAAACTTATCCAGGACCAAGC	0.488													15	113	---	---	---	---	PASS
OLFM3	118427	broad.mit.edu	37	1	102270254	102270254	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102270254C>T	uc001duf.2	-	6	1048	c.977G>A	c.(976-978)CGA>CAA	p.R326Q	OLFM3_uc001dug.2_Missense_Mutation_p.R306Q|OLFM3_uc001duh.2_RNA|OLFM3_uc001dui.2_RNA|OLFM3_uc001duj.2_Missense_Mutation_p.R231Q|OLFM3_uc001due.2_RNA	NM_058170	NP_477518	Q96PB7	NOE3_HUMAN	olfactomedin 3	326	Olfactomedin-like.					extracellular region				ovary(2)|skin(1)	3		all_epithelial(167;1.87e-06)|all_lung(203;8.12e-05)|Lung NSC(277;0.000189)		all cancers(265;0.0843)|Epithelial(280;0.0921)|COAD - Colon adenocarcinoma(174;0.145)		CTCCAGGCTTCGTTGGGCAAG	0.438													8	77	---	---	---	---	PASS
AKNAD1	254268	broad.mit.edu	37	1	109394332	109394332	+	Nonsense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109394332G>A	uc001dwa.2	-	2	1224	c.955C>T	c.(955-957)CAG>TAG	p.Q319*	AKNAD1_uc010ovb.1_Intron|AKNAD1_uc001dwb.2_RNA	NM_152763	NP_689976	Q5T1N1	AKND1_HUMAN	hypothetical protein LOC254268	319										ovary(3)	3						TTCCCTTTCTGCTCTTGATGT	0.413													29	174	---	---	---	---	PASS
CAPZA1	829	broad.mit.edu	37	1	113189874	113189874	+	Nonsense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113189874G>T	uc001ecj.1	+	2	474	c.82G>T	c.(82-84)GAA>TAA	p.E28*		NM_006135	NP_006126	P52907	CAZA1_HUMAN	F-actin capping protein alpha-1 subunit	28					actin cytoskeleton organization|actin filament capping|blood coagulation|cellular component movement|innate immune response|protein complex assembly	cytosol|extracellular region|F-actin capping protein complex|WASH complex	actin binding				0	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACCCCCAGGGGAATTTAATGA	0.328													50	129	---	---	---	---	PASS
WDR3	10885	broad.mit.edu	37	1	118494594	118494594	+	Intron	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118494594C>G	uc010oxe.1	+						WDR3_uc001ehi.2_Intron	NM_006784	NP_006775	Q9UNX4	WDR3_HUMAN	WD repeat-containing protein 3							nuclear membrane|nucleolus				upper_aerodigestive_tract(1)	1	Esophageal squamous(2;0.162)	all_cancers(81;2.72e-05)|Acute lymphoblastic leukemia(138;1e-08)|all_epithelial(167;4.4e-07)|all_lung(203;1.7e-06)|Lung NSC(69;1.98e-05)|Prostate(1639;0.00955)|Breast(1374;0.244)		OV - Ovarian serous cystadenocarcinoma(397;1.39e-08)|Epithelial(280;1.82e-07)|all cancers(265;2.04e-05)|Lung(183;0.0525)|BRCA - Breast invasive adenocarcinoma(282;0.0695)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.185)		TTTTATTTCTCATAGGATGGA	0.368													8	147	---	---	---	---	PASS
NOTCH2	4853	broad.mit.edu	37	1	120510147	120510147	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120510147C>G	uc001eik.2	-	8	1618	c.1362G>C	c.(1360-1362)GAG>GAC	p.E454D	NOTCH2_uc001eil.2_Missense_Mutation_p.E454D|NOTCH2_uc001eim.3_Missense_Mutation_p.E371D	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein	454	Extracellular (Potential).|EGF-like 11; calcium-binding (Potential).				anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGATGTCCATCTCACAACGAG	0.502			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				30	118	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144886112	144886112	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144886112G>A	uc001elw.3	-	23	3413	c.3122C>T	c.(3121-3123)TCA>TTA	p.S1041L	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.S1107L|PDE4DIP_uc001elv.3_Missense_Mutation_p.S48L	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	1041	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)		GTGGGACACTGAGGAGAATCC	0.537			T	PDGFRB	MPD								7	187	---	---	---	---	PASS
TARS2	80222	broad.mit.edu	37	1	150478153	150478153	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150478153C>T	uc001euq.2	+	17	1987	c.1980C>T	c.(1978-1980)GCC>GCT	p.A660A	TARS2_uc001eur.2_Silent_p.A578A|TARS2_uc009wlt.2_Silent_p.A286A|TARS2_uc009wls.2_Silent_p.A530A|ECM1_uc010pce.1_5'Flank|ECM1_uc010pcf.1_5'Flank|ECM1_uc001eus.2_5'Flank|ECM1_uc001eut.2_5'Flank|ECM1_uc001euu.2_5'Flank|ECM1_uc001euv.2_5'Flank|ECM1_uc009wlu.2_5'Flank	NM_025150	NP_079426	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial	660					threonyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|threonine-tRNA ligase activity			ovary(1)	1	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)	TCCGCCGGGCCCAGCTTGCCC	0.557													31	119	---	---	---	---	PASS
DCST1	149095	broad.mit.edu	37	1	155019728	155019728	+	Nonsense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155019728C>T	uc001fgn.1	+	14	1648	c.1552C>T	c.(1552-1554)CGA>TGA	p.R518*	DCST1_uc010pes.1_Nonsense_Mutation_p.R493*|uc001fgo.2_Intron	NM_152494	NP_689707	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1 isoform 1	518	Extracellular (Potential).					integral to membrane	zinc ion binding			ovary(1)|skin(1)	2	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			CCGGCTTCTTCGAAAAACCAT	0.547													4	109	---	---	---	---	PASS
MTX1	4580	broad.mit.edu	37	1	155180394	155180394	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155180394G>C	uc001fjb.2	+	3	760	c.654G>C	c.(652-654)AAG>AAC	p.K218N	RAG1AP1_uc010pey.1_Intron|THBS3_uc001fix.2_5'Flank|THBS3_uc009wqi.2_5'Flank|THBS3_uc001fiz.2_5'Flank|THBS3_uc001fiy.2_5'Flank|THBS3_uc010pfu.1_5'Flank|THBS3_uc010pfv.1_5'Flank|THBS3_uc001fja.2_5'Flank|THBS3_uc009wqj.1_5'Flank|MTX1_uc001fjc.2_Missense_Mutation_p.K218N	NM_002455	NP_002446	Q13505	MTX1_HUMAN	metaxin 1 isoform 1	218					protein targeting to mitochondrion	integral to membrane|mitochondrial outer membrane	protein binding			skin(1)	1	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			TTCCACACAAGATCATCACCC	0.438													9	215	---	---	---	---	PASS
ASH1L	55870	broad.mit.edu	37	1	155348296	155348296	+	Nonsense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155348296G>C	uc009wqq.2	-	9	6716	c.6236C>G	c.(6235-6237)TCA>TGA	p.S2079*	RAG1AP1_uc010pey.1_Intron|ASH1L_uc001fkt.2_Nonsense_Mutation_p.S2074*	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like	2079					cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TTACTCACTTGAACGAATTTT	0.338													5	109	---	---	---	---	PASS
KIAA0907	22889	broad.mit.edu	37	1	155891183	155891183	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155891183G>C	uc001fmi.1	-	10	1273	c.1249C>G	c.(1249-1251)CCA>GCA	p.P417A	KIAA0907_uc001fmj.1_Missense_Mutation_p.P417A|KIAA0907_uc009wrk.1_Missense_Mutation_p.P274A|KIAA0907_uc009wrl.1_RNA|SNORA42_uc001fmk.1_5'Flank|KIAA0907_uc001fml.1_Missense_Mutation_p.S383C	NM_014949	NP_055764	Q7Z7F0	K0907_HUMAN	hypothetical protein LOC22889	417	Pro-rich.										0	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)			GTGCTAGCTGGAGGCTGCACT	0.478													3	115	---	---	---	---	PASS
FCRL2	79368	broad.mit.edu	37	1	157738268	157738268	+	Nonsense_Mutation	SNP	A	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157738268A>T	uc001fre.2	-	5	878	c.819T>A	c.(817-819)TAT>TAA	p.Y273*	FCRL2_uc001frd.2_5'Flank|FCRL2_uc010phz.1_Nonsense_Mutation_p.Y273*|FCRL2_uc009wsp.2_Intron	NM_030764	NP_110391	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2 precursor	273	Ig-like C2-type 3.|Extracellular (Potential).				cell-cell signaling	integral to membrane|plasma membrane|soluble fraction	receptor activity|SH3/SH2 adaptor activity			ovary(1)|pancreas(1)	2	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			CTCTACAGTAATATTTGCCGG	0.493													40	190	---	---	---	---	PASS
VANGL2	57216	broad.mit.edu	37	1	160385679	160385679	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160385679C>T	uc001fwb.1	+	3	351	c.52C>T	c.(52-54)CGC>TGC	p.R18C	VANGL2_uc001fwc.1_Missense_Mutation_p.R18C	NM_020335	NP_065068	Q9ULK5	VANG2_HUMAN	vang-like 2	18	Cytoplasmic (Potential).				apical protein localization|heart looping|nonmotile primary cilium assembly	apical plasma membrane|integral to membrane				ovary(1)	1	all_cancers(52;1.08e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GGGCCACTCCCGCAGCTCCCG	0.672													7	66	---	---	---	---	PASS
CD84	8832	broad.mit.edu	37	1	160523878	160523878	+	Silent	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160523878A>G	uc001fwh.3	-	3	471	c.447T>C	c.(445-447)TGT>TGC	p.C149C	CD84_uc001fwf.3_Silent_p.C149C|CD84_uc001fwg.3_Silent_p.C149C|CD84_uc009wtn.2_Silent_p.C149C|CD84_uc001fwi.3_Silent_p.C35C|CD84_uc001fwj.2_Silent_p.C149C|CD84_uc001fwk.2_Silent_p.C149C	NM_003874	NP_003865	Q9UIB8	SLAF5_HUMAN	CD84 molecule	149	Extracellular (Potential).|Ig-like C2-type.				blood coagulation|defense response|homophilic cell adhesion|leukocyte migration	integral to plasma membrane	receptor activity			ovary(2)|central_nervous_system(1)|skin(1)	4	all_cancers(52;3.62e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			GTGTGACATTACAGGTGCTGT	0.403													49	72	---	---	---	---	PASS
ADCY10	55811	broad.mit.edu	37	1	167847723	167847723	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167847723G>C	uc001ger.2	-	12	1665	c.1367C>G	c.(1366-1368)TCT>TGT	p.S456C	ADCY10_uc009wvk.2_Missense_Mutation_p.S364C|ADCY10_uc010plj.1_Missense_Mutation_p.S303C|ADCY10_uc009wvl.2_Missense_Mutation_p.S455C	NM_018417	NP_060887	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10	456					intracellular signal transduction|spermatogenesis	cytoskeleton|cytosol|perinuclear region of cytoplasm|plasma membrane|soluble fraction	adenylate cyclase activity|ATP binding|magnesium ion binding			central_nervous_system(2)|ovary(1)	3						CAATGGTCCAGAATCTGCAAC	0.408													14	124	---	---	---	---	PASS
F5	2153	broad.mit.edu	37	1	169497285	169497285	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169497285G>C	uc001ggg.1	-	17	5612	c.5467C>G	c.(5467-5469)CAA>GAA	p.Q1823E		NM_000130	NP_000121	P12259	FA5_HUMAN	coagulation factor V precursor	1823	F5/8 type A 3.|Plastocyanin-like 6.				cell adhesion|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)	ACCCACTCTTGCTCATACATT	0.458													4	94	---	---	---	---	PASS
PAPPA2	60676	broad.mit.edu	37	1	176640118	176640118	+	Silent	SNP	T	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176640118T>C	uc001gkz.2	+	4	3168	c.2004T>C	c.(2002-2004)AGT>AGC	p.S668S	PAPPA2_uc001gky.1_Silent_p.S668S|PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	668	Metalloprotease.				cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16						CATACATGAGTGTGAAGGAGC	0.483													115	220	---	---	---	---	PASS
CDC73	79577	broad.mit.edu	37	1	193111196	193111196	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193111196G>T	uc001gtb.2	+	7	972	c.729G>T	c.(727-729)AAG>AAT	p.K243N		NM_024529	NP_078805	Q6P1J9	CDC73_HUMAN	parafibromin	243					cell cycle|histone H2B ubiquitination|histone monoubiquitination|transcription, DNA-dependent	Cdc73/Paf1 complex	protein binding			parathyroid(46)|ovary(1)|breast(1)|pancreas(1)	49						GCACAGGAAAGGTAATTAAAA	0.398									Hyperparathyroidism_Familial_Isolated|Hyperparathyroidism-Jaw_Tumor_Syndrome				6	31	---	---	---	---	PASS
KIF21B	23046	broad.mit.edu	37	1	200955982	200955982	+	Nonsense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200955982G>A	uc001gvs.1	-	26	3996	c.3679C>T	c.(3679-3681)CAG>TAG	p.Q1227*	KIF21B_uc001gvr.1_Nonsense_Mutation_p.Q1227*|KIF21B_uc009wzl.1_Nonsense_Mutation_p.Q1227*|KIF21B_uc010ppn.1_Nonsense_Mutation_p.Q1227*	NM_017596	NP_060066	O75037	KI21B_HUMAN	kinesin family member 21B	1227					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(3)	6						CTAATGGGCTGCCCTCGGTCG	0.527													13	67	---	---	---	---	PASS
PPP1R12B	4660	broad.mit.edu	37	1	202409923	202409923	+	Intron	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202409923C>T	uc001gya.1	+						PPP1R12B_uc001gxz.1_Intron	NM_002481	NP_002472	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory (inhibitor)						regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)			ACAGGTAATCCTAAAACCAGC	0.423													16	109	---	---	---	---	PASS
CYB5R1	51706	broad.mit.edu	37	1	202934595	202934595	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202934595C>G	uc001gyt.2	-	5	450	c.379G>C	c.(379-381)GAG>CAG	p.E127Q	CYB5R1_uc010pqe.1_RNA	NM_016243	NP_057327	Q9UHQ9	NB5R1_HUMAN	cytochrome b5 reductase 1	127	FAD-binding FR-type.				sterol biosynthetic process	integral to membrane	cytochrome-b5 reductase activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(75;0.141)			TTCCCTCCCTCAGGAAATTTG	0.488													6	194	---	---	---	---	PASS
PPFIA4	8497	broad.mit.edu	37	1	203025937	203025937	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203025937C>A	uc001gyz.2	+	6	1341	c.748C>A	c.(748-750)CCC>ACC	p.P250T	PPFIA4_uc009xaj.2_Missense_Mutation_p.P881T|PPFIA4_uc010pqf.1_Missense_Mutation_p.P463T|PPFIA4_uc001gza.2_Missense_Mutation_p.P250T|PPFIA4_uc001gzb.1_5'UTR	NM_015053	NP_055868	O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f	250					cell communication	cell surface|cytoplasm	protein binding			ovary(4)|skin(1)	5						GGGCAGCAACCCCAGCAGCAG	0.443													13	21	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	216074151	216074151	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216074151G>A	uc001hku.1	-	39	7784	c.7397C>T	c.(7396-7398)TCT>TTT	p.S2466F		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	2466	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)		GTATCTGGGAGAGCCAGGAGC	0.507										HNSCC(13;0.011)			20	204	---	---	---	---	PASS
TGFB2	7042	broad.mit.edu	37	1	218578578	218578578	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218578578G>A	uc001hlm.2	+	2	1067	c.414G>A	c.(412-414)GAG>GAA	p.E138E	TGFB2_uc001hll.2_Silent_p.E166E|TGFB2_uc001hln.2_Silent_p.E166E|TGFB2_uc010pue.1_RNA|TGFB2_uc001hlo.2_RNA	NM_003238	NP_003229	P61812	TGFB2_HUMAN	transforming growth factor, beta 2 isoform 2	138					activation of protein kinase activity|angiogenesis|cardiac epithelial to mesenchymal transition|cardiac muscle cell proliferation|cardioblast differentiation|catagen|cell cycle arrest|cell death|cell growth|cell-cell junction organization|cell-cell signaling|collagen fibril organization|dopamine biosynthetic process|embryonic digestive tract development|eye development|glial cell migration|hair follicle morphogenesis|hemopoiesis|menstrual cycle phase|negative regulation of alkaline phosphatase activity|negative regulation of cell growth|negative regulation of epithelial cell proliferation|negative regulation of immune response|negative regulation of macrophage cytokine production|neuron development|neutrophil chemotaxis|odontogenesis|pathway-restricted SMAD protein phosphorylation|platelet activation|platelet degranulation|positive regulation of cardioblast differentiation|positive regulation of catagen|positive regulation of cell adhesion mediated by integrin|positive regulation of cell cycle|positive regulation of cell division|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of epithelial cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of heart contraction|positive regulation of immune response|positive regulation of integrin biosynthetic process|positive regulation of neuron apoptosis|positive regulation of ossification|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein secretion|positive regulation of stress-activated MAPK cascade|regulation of transforming growth factor-beta2 production|response to hypoxia|response to progesterone stimulus|salivary gland morphogenesis|SMAD protein import into nucleus|somatic stem cell division|transforming growth factor beta receptor signaling pathway	axon|extracellular matrix|extracellular space|neuronal cell body|platelet alpha granule lumen	beta-amyloid binding|cytokine activity|growth factor activity|protein heterodimerization activity|protein homodimerization activity|receptor signaling protein serine/threonine kinase activity|type II transforming growth factor beta receptor binding				0				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)		CAGCAATGGAGAAGAATGCTT	0.423													20	413	---	---	---	---	PASS
MARK1	4139	broad.mit.edu	37	1	220791715	220791715	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220791715G>A	uc001hmn.3	+	8	1213	c.616G>A	c.(616-618)GAA>AAA	p.E206K	MARK1_uc009xdw.2_Missense_Mutation_p.E206K|MARK1_uc010pun.1_Missense_Mutation_p.E206K|MARK1_uc001hmm.3_Missense_Mutation_p.E184K	NM_018650	NP_061120	Q9P0L2	MARK1_HUMAN	MAP/microtubule affinity-regulating kinase 1	206	Protein kinase.				intracellular protein kinase cascade	cytoplasm|microtubule cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(4)|central_nervous_system(2)|skin(2)|stomach(1)|lung(1)	10				GBM - Glioblastoma multiforme(131;0.0407)		TTTTAGTAATGAATTTACAGT	0.383													6	158	---	---	---	---	PASS
DISP1	84976	broad.mit.edu	37	1	223176858	223176858	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223176858G>A	uc001hnu.1	+	8	2266	c.2119G>A	c.(2119-2121)GAA>AAA	p.E707K		NM_032890	NP_116279	Q96F81	DISP1_HUMAN	dispatched A	707					diaphragm development|protein homotrimerization|regulation of protein secretion|smoothened signaling pathway	basolateral plasma membrane|integral to membrane	hedgehog receptor activity|peptide transporter activity				0				GBM - Glioblastoma multiforme(131;0.102)		AATTTTTTTCGAAAAAGTATT	0.413													29	222	---	---	---	---	PASS
ENAH	55740	broad.mit.edu	37	1	225686076	225686076	+	Missense_Mutation	SNP	T	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225686076T>A	uc001hpc.1	-	14	2164	c.1711A>T	c.(1711-1713)ACA>TCA	p.T571S	ENAH_uc001hpd.1_Missense_Mutation_p.T550S|ENAH_uc001hpb.1_Missense_Mutation_p.T190S	NM_001008493	NP_001008493	Q8N8S7	ENAH_HUMAN	enabled homolog isoform a	571	Potential.|EVH2.|EVH2 block C.				axon guidance|intracellular transport|T cell receptor signaling pathway	cytosol|filopodium|focal adhesion|lamellipodium|synapse	actin binding|SH3 domain binding|WW domain binding			ovary(1)|skin(1)	2	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.19)		TTTAGCTTTGTTAATTCTTTT	0.264													4	66	---	---	---	---	PASS
ITPKB	3707	broad.mit.edu	37	1	226827342	226827342	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226827342C>T	uc010pvo.1	-	6	2809	c.2469G>A	c.(2467-2469)GTG>GTA	p.V823V		NM_002221	NP_002212	P27987	IP3KB_HUMAN	1D-myo-inositol-trisphosphate 3-kinase B	823							ATP binding|calmodulin binding|inositol trisphosphate 3-kinase activity			ovary(4)|central_nervous_system(1)	5		Prostate(94;0.0773)				AGTCCCGGTTCACGGTGCCGT	0.557													7	121	---	---	---	---	PASS
ITPKB	3707	broad.mit.edu	37	1	226923331	226923331	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226923331G>A	uc010pvo.1	-	2	2169	c.1829C>T	c.(1828-1830)TCA>TTA	p.S610L	ITPKB_uc001hqh.2_Missense_Mutation_p.S610L	NM_002221	NP_002212	P27987	IP3KB_HUMAN	1D-myo-inositol-trisphosphate 3-kinase B	610							ATP binding|calmodulin binding|inositol trisphosphate 3-kinase activity	p.S137del(1)		ovary(4)|central_nervous_system(1)	5		Prostate(94;0.0773)				TTCGTAGGATGAGGAGAAGCC	0.617													5	207	---	---	---	---	PASS
CDC42BPA	8476	broad.mit.edu	37	1	227300016	227300016	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227300016C>T	uc001hqr.2	-	14	2941	c.1998G>A	c.(1996-1998)CTG>CTA	p.L666L	CDC42BPA_uc001hqs.2_Silent_p.L585L|CDC42BPA_uc009xes.2_Silent_p.L666L|CDC42BPA_uc010pvs.1_Silent_p.L666L	NM_003607	NP_003598	Q5VT25	MRCKA_HUMAN	CDC42-binding protein kinase alpha isoform B	666	Potential.				actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)				AAGATACCTTCAGTCCCTCCA	0.393													7	247	---	---	---	---	PASS
TRIM11	81559	broad.mit.edu	37	1	228594100	228594100	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228594100C>T	uc001hss.2	-	1	418	c.163G>A	c.(163-165)GAG>AAG	p.E55K	TRIM11_uc010pvx.1_Missense_Mutation_p.E55K|TRIM11_uc001hst.1_Missense_Mutation_p.E55K	NM_145214	NP_660215	Q96F44	TRI11_HUMAN	tripartite motif-containing 11	55	RING-type.				response to virus	cytoplasm|nucleus	protein binding|zinc ion binding			lung(3)|ovary(1)	4		Prostate(94;0.0724)				TCGCGGCACTCGGGGCACGCG	0.721													7	9	---	---	---	---	PASS
ACTA1	58	broad.mit.edu	37	1	229568576	229568576	+	Nonsense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229568576G>A	uc001htm.2	-	3	286	c.181C>T	c.(181-183)CAG>TAG	p.Q61*		NM_001100	NP_001091	P68133	ACTS_HUMAN	actin, alpha 1, skeletal muscle	61					muscle filament sliding|skeletal muscle fiber development|skeletal muscle thin filament assembly	actin filament|cytosol|stress fiber|striated muscle thin filament	ADP binding|ATP binding|myosin binding|structural constituent of cytoskeleton				0	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.167)			Dornase Alfa(DB00003)	CTCTTGCTCTGAGCCTCGTCG	0.577													15	138	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237890482	237890482	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237890482C>T	uc001hyl.1	+	76	10941	c.10821C>T	c.(10819-10821)CCC>CCT	p.P3607P	RYR2_uc010pya.1_Silent_p.P3P	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	3607					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)			GGATGGCCCCCTTATATAATC	0.403													63	65	---	---	---	---	PASS
FMN2	56776	broad.mit.edu	37	1	240257029	240257029	+	Intron	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240257029G>T	uc010pyd.1	+						FMN2_uc010pye.1_Intron	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2						actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TCACAGGTGAGCGCGCCCTGC	0.706													7	11	---	---	---	---	PASS
ZNF496	84838	broad.mit.edu	37	1	247492815	247492815	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247492815C>G	uc001ico.2	-	3	531	c.66G>C	c.(64-66)AGG>AGC	p.R22S	ZNF496_uc009xgv.2_Missense_Mutation_p.R22S|ZNF496_uc001icp.2_Missense_Mutation_p.R22S|ZNF496_uc010pyv.1_Missense_Mutation_p.R22S	NM_032752	NP_116141	Q96IT1	ZN496_HUMAN	zinc finger protein 496	22					positive regulation of transcription, DNA-dependent|viral reproduction		DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_cancers(71;0.000136)|all_epithelial(71;2.62e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)		OV - Ovarian serous cystadenocarcinoma(106;0.00703)			CAGGTGGGCTCCTCATTTTCC	0.647													11	185	---	---	---	---	PASS
OR2M3	127062	broad.mit.edu	37	1	248366573	248366573	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248366573C>T	uc010pzg.1	+	1	204	c.204C>T	c.(202-204)CTC>CTT	p.L68L		NM_001004689	NP_001004689	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M,	68	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			AACTGTCCCTCATGGACCTCA	0.527													148	461	---	---	---	---	PASS
OR2T33	391195	broad.mit.edu	37	1	248436832	248436832	+	Silent	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248436832A>G	uc010pzi.1	-	1	285	c.285T>C	c.(283-285)TGT>TGC	p.C95C		NM_001004695	NP_001004695	Q8NG76	O2T33_HUMAN	olfactory receptor, family 2, subfamily T,	95	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|ovary(1)	2	all_cancers(71;0.000124)|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;0.0245)			TCTGCACACCACAGCCAGCGC	0.582													20	287	---	---	---	---	PASS
OR2T6	254879	broad.mit.edu	37	1	248550988	248550988	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248550988T>C	uc001iei.1	+	1	79	c.79T>C	c.(79-81)TTT>CTT	p.F27L		NM_001005471	NP_001005471	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T,	27	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3	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)			CTCAGGATTCTTTTTCGGTGT	0.443													79	85	---	---	---	---	PASS
ITSN2	50618	broad.mit.edu	37	2	24480961	24480961	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24480961C>T	uc002rfe.2	-	23	2942	c.2684G>A	c.(2683-2685)GGA>GAA	p.G895E	ITSN2_uc002rff.2_Missense_Mutation_p.G868E|ITSN2_uc002rfg.2_Missense_Mutation_p.G895E|ITSN2_uc002rfh.1_RNA	NM_006277	NP_006268	Q9NZM3	ITSN2_HUMAN	intersectin 2 isoform 1	895					endocytosis|regulation of Rho protein signal transduction	cytoplasm	calcium ion binding|Rho guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			kidney(2)|ovary(1)|central_nervous_system(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TACCACTTGTCCCTATGAATA	0.353													44	40	---	---	---	---	PASS
ADCY3	109	broad.mit.edu	37	2	25141765	25141765	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25141765C>G	uc002rfs.3	-	1	291	c.92G>C	c.(91-93)GGG>GCG	p.G31A	ADCY3_uc010ykm.1_Missense_Mutation_p.G31A	NM_004036	NP_004027	O60266	ADCY3_HUMAN	adenylate cyclase 3	31	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|sensory perception of smell|synaptic transmission|transmembrane transport|water transport	cytoplasm|integral to plasma membrane	ATP binding|calmodulin binding|metal ion binding			breast(3)|ovary(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					CCGGCCCACCCCGCGGTCAGG	0.552													27	19	---	---	---	---	PASS
CENPA	1058	broad.mit.edu	37	2	27015048	27015048	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27015048G>C	uc002rhr.2	+	2	333	c.150G>C	c.(148-150)GAG>GAC	p.E50D	CENPA_uc002rht.2_RNA|CENPA_uc002rhs.2_Missense_Mutation_p.E50D	NM_001809	NP_001800	P49450	CENPA_HUMAN	centromere protein A isoform a	50	H3-like.				CenH3-containing nucleosome assembly at centromere|establishment of mitotic spindle orientation|interspecies interaction between organisms|kinetochore assembly|mitotic prometaphase|protein localization to chromosome, centromeric region	condensed nuclear chromosome kinetochore|cytosol|nucleoplasm|nucleosome	chromatin binding|DNA binding|protein binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGCTAAAGGAGATCCGAAAGC	0.547													4	74	---	---	---	---	PASS
SLC30A3	7781	broad.mit.edu	37	2	27481676	27481676	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27481676C>A	uc002rjk.2	-	2	408	c.222G>T	c.(220-222)AGG>AGT	p.R74S	SLC30A3_uc002rjj.2_5'Flank|SLC30A3_uc010ylh.1_Missense_Mutation_p.R69S	NM_003459	NP_003450	Q99726	ZNT3_HUMAN	solute carrier family 30 (zinc transporter),	74	Cytoplasmic (Potential).				regulation of sequestering of zinc ion	cell junction|integral to plasma membrane|late endosome|membrane fraction|synaptic vesicle membrane	zinc transporting ATPase activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CATATAGCTGCCTCCGTGCAT	0.602													29	82	---	---	---	---	PASS
NRBP1	29959	broad.mit.edu	37	2	27657418	27657418	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27657418G>C	uc002rko.2	+	6	1348	c.516G>C	c.(514-516)ATG>ATC	p.M172I	NRBP1_uc002rkq.2_Missense_Mutation_p.M172I|NRBP1_uc002rkp.2_Missense_Mutation_p.M172I|NRBP1_uc002rkr.2_5'Flank	NM_013392	NP_037524	Q9UHY1	NRBP_HUMAN	nuclear receptor binding protein	172	Protein kinase.				ER to Golgi vesicle-mediated transport|gene expression|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cell cortex|endomembrane system|lamellipodium|membrane|nucleoplasm	ATP binding|protein homodimerization activity|protein kinase activity			ovary(2)|lung(1)	3	Acute lymphoblastic leukemia(172;0.155)					ACAAGACGATGAATGAAAAGG	0.408													15	157	---	---	---	---	PASS
NLRC4	58484	broad.mit.edu	37	2	32449811	32449811	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32449811G>A	uc002roi.2	-	9	3052	c.2806C>T	c.(2806-2808)CTG>TTG	p.L936L	NLRC4_uc002roj.1_Silent_p.L936L|NLRC4_uc010ezt.1_Silent_p.L271L	NM_021209	NP_067032	Q9NPP4	NLRC4_HUMAN	caspase recruitment domain protein 12	936	LRR 12.				activation of caspase activity|defense response to bacterium|detection of bacterium|interleukin-1 beta secretion|positive regulation of apoptosis	cytoplasm	ATP binding|magnesium ion binding|protein homodimerization activity			ovary(3)|large_intestine(1)|lung(1)|skin(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					AAGTTTTTCAGAGGGTTCTTT	0.338													14	57	---	---	---	---	PASS
BIRC6	57448	broad.mit.edu	37	2	32734914	32734914	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32734914G>T	uc010ezu.2	+	52	10224	c.10090G>T	c.(10090-10092)GCC>TCC	p.A3364S		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	3364					anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					GACTTGTGCGGCCTTATTGAT	0.448													71	225	---	---	---	---	PASS
VIT	5212	broad.mit.edu	37	2	37002179	37002179	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37002179C>G	uc002rpl.2	+	9	992	c.771C>G	c.(769-771)TTC>TTG	p.F257L	VIT_uc002rpm.2_Missense_Mutation_p.F250L|VIT_uc010ezv.2_Intron|VIT_uc010ezw.2_Missense_Mutation_p.F250L	NM_053276	NP_444506	Q6UXI7	VITRN_HUMAN	vitrin	257						proteinaceous extracellular matrix				ovary(1)|pancreas(1)	2		all_hematologic(82;0.248)				GAGCTGCCTTCCAGAAACCTG	0.507													13	109	---	---	---	---	PASS
PPM1B	5495	broad.mit.edu	37	2	44428720	44428720	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44428720G>C	uc002rtt.2	+	2	810	c.382G>C	c.(382-384)GAC>CAC	p.D128H	PPM1B_uc002rts.2_Missense_Mutation_p.D128H|PPM1B_uc002rtu.2_Missense_Mutation_p.D128H|PPM1B_uc002rtv.2_Intron|PPM1B_uc002rtw.2_Missense_Mutation_p.D128H|PPM1B_uc002rtx.2_Missense_Mutation_p.D128H	NM_002706	NP_002697	O75688	PPM1B_HUMAN	protein phosphatase 1B isoform 1	128					protein dephosphorylation	protein serine/threonine phosphatase complex	magnesium ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity			kidney(1)|skin(1)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				AAACGGGATGGACAGGAGTGG	0.393													9	120	---	---	---	---	PASS
NRXN1	9378	broad.mit.edu	37	2	50573818	50573818	+	Intron	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50573818C>T	uc010fbp.2	-						NRXN1_uc002rxb.3_Intron|NRXN1_uc010fbq.2_Intron|NRXN1_uc002rxe.3_Intron|NRXN1_uc002rxc.1_Intron	NM_138735	NP_620072	P58400	NRX1B_HUMAN	neurexin 1 isoform beta precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			AACTTGGCATCGCAGACCCAC	0.572													13	49	---	---	---	---	PASS
PSME4	23198	broad.mit.edu	37	2	54133835	54133835	+	Intron	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54133835G>C	uc002rxp.2	-						PSME4_uc010yop.1_Intron|PSME4_uc010yoq.1_Intron|PSME4_uc010fbu.1_Intron|PSME4_uc010fbv.1_Intron	NM_014614	NP_055429	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			ovary(2)|breast(2)|pancreas(1)	5			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			CCGTAGCTAAGAAAACAATCG	0.303													4	100	---	---	---	---	PASS
MTIF2	4528	broad.mit.edu	37	2	55490959	55490959	+	Silent	SNP	T	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55490959T>A	uc002ryn.2	-	5	773	c.36A>T	c.(34-36)CTA>CTT	p.L12L	MTIF2_uc010yox.1_5'UTR|MTIF2_uc002ryo.2_Silent_p.L12L|MTIF2_uc002ryp.1_RNA	NM_001005369	NP_001005369	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	12					regulation of translational initiation	mitochondrion	GTP binding|GTPase activity|ribosomal small subunit binding|translation initiation factor activity			ovary(1)	1						TGTGAAATCGTAGCAAGTTCT	0.363													47	216	---	---	---	---	PASS
VRK2	7444	broad.mit.edu	37	2	58275961	58275961	+	Splice_Site	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58275961G>C	uc002rzo.2	+	5	741	c.-4_splice	c.e5-1		VRK2_uc010fcb.2_Splice_Site|VRK2_uc002rzs.2_Splice_Site|VRK2_uc002rzr.2_Splice_Site|VRK2_uc010fcc.2_Splice_Site|VRK2_uc002rzv.2_Splice_Site|VRK2_uc010fcd.2_Intron|VRK2_uc002rzp.2_Splice_Site|VRK2_uc010ypg.1_Splice_Site|VRK2_uc002rzq.2_Splice_Site|VRK2_uc002rzu.2_Splice_Site|VRK2_uc002rzt.2_Splice_Site	NM_001130482	NP_001123954	Q86Y07	VRK2_HUMAN	vaccinia related kinase 2 isoform 2							integral to membrane	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1						TCTGCCAACAGAAGTGATGCC	0.383													4	67	---	---	---	---	PASS
KIAA1841	84542	broad.mit.edu	37	2	61297594	61297594	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61297594G>A	uc002saw.3	+	3	412	c.109G>A	c.(109-111)GAA>AAA	p.E37K	KIAA1841_uc002sax.3_5'UTR|KIAA1841_uc002say.2_Missense_Mutation_p.E37K|KIAA1841_uc002sav.3_Missense_Mutation_p.E37K	NM_001129993	NP_001123465	Q6NSI8	K1841_HUMAN	KIAA1841 protein isoform a	37											0			Epithelial(17;0.193)			TATCAACTGGGAAACTATAGC	0.368													31	117	---	---	---	---	PASS
UGP2	7360	broad.mit.edu	37	2	64113547	64113547	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64113547G>C	uc002scm.2	+	7	1252	c.946G>C	c.(946-948)GAC>CAC	p.D316H	UGP2_uc002scl.2_Missense_Mutation_p.D305H|UGP2_uc010ypx.1_Missense_Mutation_p.D325H	NM_006759	NP_006750	Q16851	UGPA_HUMAN	UDP-glucose pyrophosphorylase 2 isoform a	316					glycogen biosynthetic process|phosphorylation|UDP-glucose metabolic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	cytosol	metal ion binding|protein binding|UTP:glucose-1-phosphate uridylyltransferase activity				0						AGCACATGTAGACGAGTTCAA	0.408													7	219	---	---	---	---	PASS
SERTAD2	9792	broad.mit.edu	37	2	64863520	64863520	+	Silent	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64863520G>C	uc002sde.1	-	2	783	c.486C>G	c.(484-486)CTC>CTG	p.L162L		NM_014755	NP_055570	Q14140	SRTD2_HUMAN	SERTA domain containing 2	162					negative regulation of cell growth|transcription, DNA-dependent	cytoplasm|nucleus					0						TTTCTGGCAAGAGGGCTGGAG	0.617													9	108	---	---	---	---	PASS
NAGK	55577	broad.mit.edu	37	2	71305464	71305464	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71305464G>A	uc002shp.3	+	10	1267	c.861G>A	c.(859-861)CTG>CTA	p.L287L	NAGK_uc010fea.2_RNA|NAGK_uc002shq.3_Silent_p.L138L|NAGK_uc002shr.2_Silent_p.L236L	NM_017567	NP_060037	Q9UJ70	NAGK_HUMAN	N-Acetylglucosamine kinase	287					N-acetylglucosamine metabolic process|N-acetylmannosamine metabolic process		ATP binding|N-acetylglucosamine kinase activity|protein binding				0					N-Acetyl-D-glucosamine(DB00141)	TTCTGGCGCTGACCCAGGGCA	0.582													11	63	---	---	---	---	PASS
SPR	6697	broad.mit.edu	37	2	73115537	73115537	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73115537C>T	uc002sik.2	+	2	449	c.399C>T	c.(397-399)TGC>TGT	p.C133C		NM_003124	NP_003115	P35270	SPRE_HUMAN	sepiapterin reductase	133					nitric oxide biosynthetic process|tetrahydrobiopterin biosynthetic process	cytoplasm	aldo-keto reductase (NADP) activity|NADP binding|sepiapterin reductase activity			ovary(2)	2						CCATGCTCTGCCTGACTTCCA	0.547											OREG0014704	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	47	82	---	---	---	---	PASS
ALMS1	7840	broad.mit.edu	37	2	73829327	73829327	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73829327C>G	uc002sje.1	+	22	12244	c.12133C>G	c.(12133-12135)CAC>GAC	p.H4045D	ALMS1_uc002sjf.1_Missense_Mutation_p.H4001D|ALMS1_uc002sjh.1_Missense_Mutation_p.H3431D	NM_015120	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	4043					G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole				skin(3)|ovary(2)|breast(2)|pancreas(1)|lung(1)	9						GCTTCAGTTTCACAGACCTGA	0.483													10	39	---	---	---	---	PASS
SEMA4F	10505	broad.mit.edu	37	2	74901714	74901714	+	Silent	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74901714G>T	uc002sna.1	+	8	1023	c.912G>T	c.(910-912)CGG>CGT	p.R304R	SEMA4F_uc010ffq.1_Silent_p.R271R|SEMA4F_uc010ffr.1_5'UTR|SEMA4F_uc002snb.1_5'UTR|SEMA4F_uc002snc.1_Silent_p.R149R	NM_004263	NP_004254	O95754	SEM4F_HUMAN	semaphorin W precursor	304	Sema.|Extracellular (Potential).				cell-cell signaling	endoplasmic reticulum|integral to plasma membrane	receptor activity			ovary(2)|pancreas(1)|skin(1)	4						AGCATGGCCGGGCCTCCAGTG	0.602													78	79	---	---	---	---	PASS
LRRTM4	80059	broad.mit.edu	37	2	77746836	77746836	+	Silent	SNP	T	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77746836T>G	uc002snr.2	-	3	574	c.159A>C	c.(157-159)GCA>GCC	p.A53A	LRRTM4_uc002snq.2_Silent_p.A53A|LRRTM4_uc002sns.2_Silent_p.A53A|LRRTM4_uc002snt.2_Silent_p.A54A	NM_001134745	NP_001128217	Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	53	Extracellular (Potential).|LRRNT.					integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)		CAGGGATATCTGCGAAAGCAT	0.468													58	51	---	---	---	---	PASS
REG1B	5968	broad.mit.edu	37	2	79312344	79312344	+	Nonstop_Mutation	SNP	A	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79312344A>T	uc002sny.2	-	6	611	c.499T>A	c.(499-501)TAG>AAG	p.*167K		NM_006507	NP_006498	P48304	REG1B_HUMAN	regenerating islet-derived 1 beta precursor	167					cell proliferation	extracellular region	sugar binding	p.*167*(1)		central_nervous_system(1)|skin(1)	2						AGCTTCCTCTAGTTTTTGAAC	0.378													15	63	---	---	---	---	PASS
REG3A	5068	broad.mit.edu	37	2	79385464	79385464	+	Silent	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79385464A>G	uc002sod.1	-	3	576	c.321T>C	c.(319-321)CAT>CAC	p.H107H	REG3A_uc002soe.1_Silent_p.H107H|REG3A_uc002sof.1_Silent_p.H107H	NM_138938	NP_620355	Q06141	REG3A_HUMAN	pancreatitis-associated protein precursor	107	C-type lectin.				acute-phase response|cell proliferation|heterophilic cell-cell adhesion|multicellular organismal development	cytoplasm|extracellular space|soluble fraction	sugar binding			skin(1)	1						GTGTGGGGTCATGGAGCCCAA	0.572													29	36	---	---	---	---	PASS
CTNNA2	1496	broad.mit.edu	37	2	80816495	80816495	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80816495C>G	uc010ysh.1	+	14	2079	c.2074C>G	c.(2074-2076)CAA>GAA	p.Q692E	CTNNA2_uc010yse.1_Missense_Mutation_p.Q692E|CTNNA2_uc010ysf.1_Missense_Mutation_p.Q692E|CTNNA2_uc010ysg.1_Missense_Mutation_p.Q692E|CTNNA2_uc010ysi.1_Missense_Mutation_p.Q324E|CTNNA2_uc010ysj.1_Missense_Mutation_p.Q21E	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1	692					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						GATATTCCATCAAGAGAAAAG	0.488													12	61	---	---	---	---	PASS
TGOLN2	10618	broad.mit.edu	37	2	85554352	85554352	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85554352G>A	uc010fgd.1	-	2	792	c.503C>T	c.(502-504)TCA>TTA	p.S168L	TGOLN2_uc002soz.2_Missense_Mutation_p.S168L|TGOLN2_uc002spa.2_RNA|TGOLN2_uc002spb.2_Missense_Mutation_p.S168L|TGOLN2_uc002spc.1_Missense_Mutation_p.S168L	NM_006464	NP_006455	O43493	TGON2_HUMAN	trans-golgi network protein 2	168	Extracellular (Potential).|14 X 14 AA tandem repeats.|9.					integral to membrane|nucleus|plasma membrane|trans-Golgi network|transport vesicle	protein binding				0						CTCCGAACCTGACTTGCTAGG	0.607													90	397	---	---	---	---	PASS
ST3GAL5	8869	broad.mit.edu	37	2	86090519	86090519	+	Nonsense_Mutation	SNP	T	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86090519T>A	uc002sqq.1	-	2	301	c.172A>T	c.(172-174)AGA>TGA	p.R58*	ST3GAL5_uc010ysy.1_Nonsense_Mutation_p.R58*|ST3GAL5_uc010ysz.1_Nonsense_Mutation_p.R58*|ST3GAL5_uc010fgq.1_5'Flank|ST3GAL5_uc002sqp.1_Nonsense_Mutation_p.R35*	NM_003896	NP_003887	Q9UNP4	SIAT9_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase	58	Cytoplasmic (Potential).				ganglioside biosynthetic process|protein glycosylation	integral to Golgi membrane|integral to plasma membrane	lactosylceramide alpha-2,3-sialyltransferase activity|neolactotetraosylceramide alpha-2,3-sialyltransferase activity				0						CTGGGCCTTCTCATCTTGCTT	0.483													34	63	---	---	---	---	PASS
POU3F3	5455	broad.mit.edu	37	2	105473021	105473021	+	Nonsense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105473021C>A	uc010ywg.1	+	1	1053	c.1053C>A	c.(1051-1053)TAC>TAA	p.Y351*		NM_006236	NP_006227	P20264	PO3F3_HUMAN	POU class 3 homeobox 3	351	POU-specific.				metanephric ascending thin limb development|metanephric DCT cell differentiation|metanephric macula densa development|metanephric thick ascending limb development|negative regulation of apoptosis|positive regulation of cell proliferation	nucleus	sequence-specific DNA binding			ovary(1)	1						GCACACTCTACGGCAACGTGT	0.622													39	57	---	---	---	---	PASS
TGFBRAP1	9392	broad.mit.edu	37	2	105915078	105915078	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105915078G>A	uc002tcq.2	-	3	857	c.773C>T	c.(772-774)CCA>CTA	p.P258L	TGFBRAP1_uc010fjc.2_Missense_Mutation_p.P28L|TGFBRAP1_uc002tcr.3_Missense_Mutation_p.P258L	NM_004257	NP_004248	Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor	258	CNH.				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						TATGACGTATGGAAAGGACAC	0.537													8	88	---	---	---	---	PASS
SULT1C2	6819	broad.mit.edu	37	2	108921111	108921111	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108921111C>A	uc002tdy.2	+	5	910	c.457C>A	c.(457-459)CCT>ACT	p.P153T	SULT1C2_uc010ywp.1_Missense_Mutation_p.P68T|SULT1C2_uc002tdx.2_Missense_Mutation_p.P164T|SULT1C2_uc010ywq.1_Missense_Mutation_p.P167T	NM_001056	NP_001047	O00338	ST1C2_HUMAN	sulfotransferase family, cytosolic, 1C, member 1	153					3'-phosphoadenosine 5'-phosphosulfate metabolic process|amine metabolic process|sulfation|xenobiotic metabolic process	cytosol|microtubule cytoskeleton	sulfotransferase activity			ovary(1)	1						GCTTCCTGACCCTGGTACCTG	0.453													31	126	---	---	---	---	PASS
RANBP2	5903	broad.mit.edu	37	2	109380371	109380371	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109380371C>T	uc002tem.3	+	20	3502	c.3376C>T	c.(3376-3378)CGG>TGG	p.R1126W		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	1126					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18						TTCTGGTTTTCGGCGAAGTGA	0.403													17	100	---	---	---	---	PASS
RANBP2	5903	broad.mit.edu	37	2	109383184	109383184	+	Silent	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109383184C>G	uc002tem.3	+	20	6315	c.6189C>G	c.(6187-6189)CTC>CTG	p.L2063L		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	2063	RanBD1 2.				carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18						TAAAAATTCTCAAAAACGAGG	0.388													139	316	---	---	---	---	PASS
CXCR4	7852	broad.mit.edu	37	2	136873426	136873426	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136873426C>T	uc002tuz.2	-	2	167	c.72G>A	c.(70-72)ATG>ATA	p.M24I	CXCR4_uc002tuy.2_Missense_Mutation_p.M28I|CXCR4_uc010fnk.2_Missense_Mutation_p.M9I	NM_003467	NP_003458	P61073	CXCR4_HUMAN	chemokine (C-X-C motif) receptor 4 isoform b	24	Extracellular.				activation of MAPK activity|apoptosis|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|entry into host cell|inflammatory response|initiation of viral infection|regulation of chemotaxis|response to hypoxia|response to virus	cell leading edge|cell surface|cytoplasmic membrane-bounded vesicle|integral to membrane|plasma membrane	actin binding|C-X-C chemokine receptor activity|coreceptor activity|myosin light chain binding|ubiquitin binding|ubiquitin protein ligase binding			upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.155)	Framycetin(DB00452)	AGGGTTCCTTCATGGAGTCAT	0.428													37	97	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141032120	141032120	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141032120C>A	uc002tvj.1	-	85	13987	c.13015G>T	c.(13015-13017)GAT>TAT	p.D4339Y		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	4339	Extracellular (Potential).|EGF-like 13.				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)		CTTCCATCATCCCCAATGGTA	0.408										TSP Lung(27;0.18)			13	67	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141272243	141272243	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141272243C>G	uc002tvj.1	-	51	9220	c.8248G>C	c.(8248-8250)GAT>CAT	p.D2750H		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	2750	Extracellular (Potential).|LDL-receptor class A 16.				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)		TCACTTTCATCTAACCCATCC	0.353										TSP Lung(27;0.18)			21	54	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152544034	152544034	+	Nonsense_Mutation	SNP	T	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152544034T>A	uc010fnx.2	-	27	2727	c.2536A>T	c.(2536-2538)AAA>TAA	p.K846*		NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	846	Nebulin 19.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		TCATAGTCTTTCTTGTACATC	0.502													9	149	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152544035	152544035	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152544035C>T	uc010fnx.2	-	27	2726	c.2535G>A	c.(2533-2535)AAG>AAA	p.K845K		NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	845	Nebulin 19.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		CATAGTCTTTCTTGTACATCA	0.507													10	146	---	---	---	---	PASS
ABCB11	8647	broad.mit.edu	37	2	169874467	169874467	+	Intron	SNP	T	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169874467T>C	uc002ueo.1	-							NM_003742	NP_003733	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP),						bile acid biosynthetic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|bile acid-exporting ATPase activity|canalicular bile acid transmembrane transporter activity|sodium-exporting ATPase activity, phosphorylative mechanism			ovary(2)|large_intestine(2)|breast(1)	5					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Glibenclamide(DB01016)	CTGTTGCTGATTTTTTTCTGC	0.403													9	84	---	---	---	---	PASS
CYBRD1	79901	broad.mit.edu	37	2	172398276	172398276	+	Silent	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172398276G>C	uc002ugy.3	+	2	565	c.375G>C	c.(373-375)CTG>CTC	p.L125L	CYBRD1_uc002ugz.3_Intron	NM_024843	NP_079119	Q53TN4	CYBR1_HUMAN	cytochrome b reductase 1 isoform 1	125	Helical; Name=4; (Potential).|Cytochrome b561.				cellular iron ion homeostasis|electron transport chain|transmembrane transport	integral to membrane	ferric-chelate reductase activity|metal ion binding				0						GGGTTGGACTGATAGCTGTCA	0.353													14	83	---	---	---	---	PASS
AGPS	8540	broad.mit.edu	37	2	178388471	178388471	+	Intron	SNP	T	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178388471T>C	uc002ull.2	+						AGPS_uc010zfb.1_Intron	NM_003659	NP_003650	O00116	ADAS_HUMAN	alkyldihydroxyacetone phosphate synthase						ether lipid biosynthetic process	peroxisomal matrix|peroxisomal membrane|plasma membrane	alkylglycerone-phosphate synthase activity|flavin adenine dinucleotide binding|oxidoreductase activity			ovary(2)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)			TGTTTCCAAATACAGGCAGCT	0.388													18	54	---	---	---	---	PASS
PDE11A	50940	broad.mit.edu	37	2	178936577	178936577	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178936577C>T	uc002ulq.2	-	1	906	c.588G>A	c.(586-588)CTG>CTA	p.L196L	PDE11A_uc002ulr.2_Intron|PDE11A_uc002ult.1_Intron	NM_016953	NP_058649	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A isoform 4	196					platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding			ovary(3)|large_intestine(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)			TATGCTTTTTCAGATGGCACT	0.498									Primary_Pigmented_Nodular_Adrenocortical_Disease_Familial				31	92	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179425922	179425922	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179425922C>G	uc010zfg.1	-	275	77457	c.77233G>C	c.(77233-77235)GAA>CAA	p.E25745Q	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.E19440Q|TTN_uc010zfi.1_Missense_Mutation_p.E19373Q|TTN_uc010zfj.1_Missense_Mutation_p.E19248Q	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	26672							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)			TCAGTTACTTCAAAGTATGTT	0.428													9	73	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179477509	179477509	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179477509C>G	uc010zfg.1	-	214	42459	c.42235G>C	c.(42235-42237)GAG>CAG	p.E14079Q	uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.E7774Q|TTN_uc010zfi.1_Missense_Mutation_p.E7707Q|TTN_uc010zfj.1_Missense_Mutation_p.E7582Q	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	15006							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)			CATAGCTTCTCCCGGCAAAGC	0.423													7	35	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179591986	179591986	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179591986G>T	uc010zfg.1	-	66	16598	c.16374C>A	c.(16372-16374)TTC>TTA	p.F5458L	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.F2119L	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	6385							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)			GTTCATTTCGGAACCACACAA	0.423													21	46	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179604792	179604792	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179604792C>G	uc010zfh.1	-	46	12879	c.12655G>C	c.(12655-12657)GAG>CAG	p.E4219Q	TTN_uc010zfg.1_Intron|TTN_uc010zfi.1_Missense_Mutation_p.E4152Q|TTN_uc010zfj.1_Missense_Mutation_p.E4027Q|TTN_uc002umz.1_Intron	NM_133437	NP_597681	Q8WZ42	TITIN_HUMAN	titin isoform novex-2	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							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)			AATCTCTGCTCTTCTGGAATA	0.468													26	61	---	---	---	---	PASS
COL5A2	1290	broad.mit.edu	37	2	189922123	189922123	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189922123C>T	uc002uqk.2	-	34	2535	c.2260G>A	c.(2260-2262)GAT>AAT	p.D754N	COL5A2_uc010frx.2_Missense_Mutation_p.D330N	NM_000393	NP_000384	P05997	CO5A2_HUMAN	alpha 2 type V collagen preproprotein	754					axon guidance|collagen fibril organization|eye morphogenesis|skin development	collagen type V	extracellular matrix structural constituent			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			GGGCCTGTATCTCCAGGGGTC	0.393													6	93	---	---	---	---	PASS
ANKAR	150709	broad.mit.edu	37	2	190569858	190569858	+	Silent	SNP	G	A	A	rs145408486	byFrequency	TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190569858G>A	uc002uqw.1	+	7	1605	c.1605G>A	c.(1603-1605)CCG>CCA	p.P535P	ANKAR_uc002uqu.2_RNA	NM_144708	NP_653309	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	606	ANK 3.					integral to membrane	binding			ovary(2)|pancreas(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)			GCTGGATGCCGATTCACTTTG	0.443													40	79	---	---	---	---	PASS
FAM126B	285172	broad.mit.edu	37	2	201846388	201846388	+	Nonsense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201846388G>A	uc002uws.3	-	12	1386	c.1198C>T	c.(1198-1200)CGA>TGA	p.R400*	FAM126B_uc002uwu.2_Nonsense_Mutation_p.R374*|FAM126B_uc002uwv.2_Nonsense_Mutation_p.R400*	NM_173822	NP_776183	Q8IXS8	F126B_HUMAN	hypothetical protein LOC285172	400						intracellular				ovary(1)	1						ACTGAATCTCGAGGGCTCTCA	0.483													9	64	---	---	---	---	PASS
ALS2	57679	broad.mit.edu	37	2	202611303	202611303	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202611303G>C	uc002uyo.2	-	9	2340	c.1984C>G	c.(1984-1986)CTC>GTC	p.L662V	ALS2_uc002uyp.3_Missense_Mutation_p.L662V|ALS2_uc002uyq.2_Missense_Mutation_p.L662V|ALS2_uc010ftl.2_5'Flank	NM_020919	NP_065970	Q96Q42	ALS2_HUMAN	alsin isoform 1	662					cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size	centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle	protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity			skin(5)|lung(1)|breast(1)	7						CTACAGGAGAGAAGTACTGGA	0.418													40	225	---	---	---	---	PASS
ADAM23	8745	broad.mit.edu	37	2	207412171	207412171	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207412171C>A	uc002vbq.2	+	7	962	c.739C>A	c.(739-741)CAT>AAT	p.H247N	ADAM23_uc010ziv.1_RNA	NM_003812	NP_003803	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23 preproprotein	247					cell adhesion|central nervous system development|proteolysis	extracellular region|integral to plasma membrane	integrin binding|metalloendopeptidase activity|zinc ion binding			skin(2)|ovary(1)	3				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)		AGGTCGACCACATATAATCCA	0.343													4	52	---	---	---	---	PASS
CRYGD	1421	broad.mit.edu	37	2	208986547	208986547	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208986547G>T	uc002vcn.3	-	3	491	c.375C>A	c.(373-375)AAC>AAA	p.N125K		NM_006891	NP_008822	P07320	CRGD_HUMAN	crystallin, gamma D	125	Beta/gamma crystallin 'Greek key' 3.				cellular response to reactive oxygen species|visual perception	soluble fraction	protein binding|structural constituent of eye lens				0				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.0858)|Lung(261;0.133)		CCTCCAGCACGTTGAGGGAGT	0.572													28	84	---	---	---	---	PASS
MAP2	4133	broad.mit.edu	37	2	210545504	210545504	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210545504C>G	uc002vde.1	+	6	655	c.407C>G	c.(406-408)TCT>TGT	p.S136C	MAP2_uc002vdc.1_Missense_Mutation_p.S136C|MAP2_uc002vdd.1_Missense_Mutation_p.S136C|MAP2_uc002vdf.1_Missense_Mutation_p.S136C|MAP2_uc002vdg.1_Missense_Mutation_p.S136C|MAP2_uc002vdh.1_Missense_Mutation_p.S136C|MAP2_uc002vdi.1_Missense_Mutation_p.S136C	NM_002374	NP_002365	P11137	MAP2_HUMAN	microtubule-associated protein 2 isoform 1	136					central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)	CTGCCTCCTTCTCCACCCCCA	0.418													47	227	---	---	---	---	PASS
PTPRN	5798	broad.mit.edu	37	2	220162692	220162692	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220162692C>T	uc002vkz.2	-	13	1891	c.1802G>A	c.(1801-1803)CGG>CAG	p.R601Q	PTPRN_uc010zlc.1_Missense_Mutation_p.R511Q|PTPRN_uc002vla.2_Missense_Mutation_p.R572Q	NM_002846	NP_002837	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	601	Cytoplasmic (Potential).				response to reactive oxygen species	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(2)|lung(1)|skin(1)	4		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		CGCATGCTGCCGCACACACAG	0.667													10	29	---	---	---	---	PASS
ACCN4	55515	broad.mit.edu	37	2	220396713	220396713	+	Intron	SNP	T	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220396713T>C	uc002vma.2	+						ACCN4_uc010fwi.1_Intron|ACCN4_uc010fwj.1_Intron|ACCN4_uc002vly.1_Intron|ACCN4_uc002vlz.2_Intron|ACCN4_uc002vmb.2_Intron	NM_182847	NP_878267	Q96FT7	ACCN4_HUMAN	amiloride-sensitive cation channel 4 isoform 2							integral to plasma membrane	sodium channel activity|sodium ion transmembrane transporter activity			ovary(2)	2		Renal(207;0.0183)		Epithelial(149;5.47e-10)|all cancers(144;9e-08)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.0086)|READ - Rectum adenocarcinoma(5;0.156)		TCCCCATCTCTGCTGTGCAGA	0.637													70	153	---	---	---	---	PASS
SERPINE2	5270	broad.mit.edu	37	2	224862912	224862912	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224862912C>T	uc002vnu.2	-	3	650	c.407G>A	c.(406-408)TGT>TAT	p.C136Y	SERPINE2_uc002vnt.2_Missense_Mutation_p.C136Y|SERPINE2_uc010zlr.1_Missense_Mutation_p.C148Y|SERPINE2_uc002vnv.2_Missense_Mutation_p.C136Y	NM_006216	NP_006207	P07093	GDN_HUMAN	plasminogen activator inhibitor type 1, member 2	136					negative regulation of blood coagulation|negative regulation of plasminogen activation|negative regulation of platelet aggregation|positive regulation of astrocyte differentiation|regulation of cell migration	cytosol|extracellular matrix|extracellular space|extrinsic to external side of plasma membrane|neuromuscular junction|platelet alpha granule	heparin binding|receptor binding|serine-type endopeptidase inhibitor activity			breast(2)|ovary(1)|central_nervous_system(1)	4		Renal(207;0.025)|all_lung(227;0.0586)|Lung NSC(271;0.0682)|all_hematologic(139;0.0797)		Epithelial(121;5.68e-10)|all cancers(144;1.9e-07)|Lung(261;0.0088)|LUSC - Lung squamous cell carcinoma(224;0.00902)		CCGGACCTCACACTGGAACAC	0.448													10	69	---	---	---	---	PASS
CUL3	8452	broad.mit.edu	37	2	225422481	225422481	+	Missense_Mutation	SNP	A	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225422481A>C	uc002vny.2	-	2	543	c.159T>G	c.(157-159)AGT>AGG	p.S53R	CUL3_uc010zls.1_Intron|CUL3_uc010fwy.1_Missense_Mutation_p.S59R	NM_003590	NP_003581	Q13618	CUL3_HUMAN	cullin 3	53					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)		GCTCCTCAAAACTAAGACCAC	0.353													7	48	---	---	---	---	PASS
SPHKAP	80309	broad.mit.edu	37	2	228886480	228886480	+	Missense_Mutation	SNP	A	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228886480A>T	uc002vpq.2	-	6	691	c.644T>A	c.(643-645)CTC>CAC	p.L215H	SPHKAP_uc002vpp.2_Missense_Mutation_p.L215H|SPHKAP_uc010zlx.1_Missense_Mutation_p.L215H	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	215						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)		AGAAGCGGTGAGAAAGTCTTC	0.478													21	75	---	---	---	---	PASS
RAB17	64284	broad.mit.edu	37	2	238486673	238486673	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238486673G>A	uc002vwz.1	-	3	927	c.283C>T	c.(283-285)CTT>TTT	p.L95F	RAB17_uc002vxa.1_RNA|RAB17_uc002vxb.1_Intron	NM_022449	NP_071894	Q9H0T7	RAB17_HUMAN	RAB17, member RAS oncogene family	95					protein transport|small GTPase mediated signal transduction	intracellular|plasma membrane	GTP binding|protein binding				0		Renal(207;0.00272)|Breast(86;0.00297)|all_hematologic(139;0.182)|Ovarian(221;0.221)		Epithelial(121;9.36e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.26e-10)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000354)|Lung(119;0.011)|LUSC - Lung squamous cell carcinoma(224;0.026)		TACACCAGAAGCGCAGCGTTG	0.592													10	93	---	---	---	---	PASS
TRAF3IP1	26146	broad.mit.edu	37	2	239237975	239237975	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239237975G>A	uc002vye.2	+	5	1026	c.907G>A	c.(907-909)GAG>AAG	p.E303K	TRAF3IP1_uc002vyf.2_Missense_Mutation_p.E303K	NM_015650	NP_056465	Q8TDR0	MIPT3_HUMAN	TNF receptor-associated factor 3 interacting	303	Abolishes microtubules-binding when missing.|DISC1-interaction domain.					cytoplasm|cytoskeleton	protein binding			ovary(1)	1		all_epithelial(40;3.22e-10)|Breast(86;0.000523)|Renal(207;0.00571)|Ovarian(221;0.156)|all_hematologic(139;0.182)		Epithelial(121;9.92e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.85e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.01e-07)|BRCA - Breast invasive adenocarcinoma(100;7.72e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0184)		TGACAAACCTGAGAAAAAGGT	0.323													4	71	---	---	---	---	PASS
OR6B2	389090	broad.mit.edu	37	2	240968926	240968926	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240968926C>A	uc002vyr.2	-	2	967	c.921G>T	c.(919-921)TTG>TTT	p.L307F	OR6B2_uc010zoc.1_Missense_Mutation_p.L307F	NM_001005853	NP_001005853	Q6IFH4	OR6B2_HUMAN	olfactory receptor, family 6, subfamily B,	307	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		all_epithelial(40;1.64e-11)|Breast(86;0.000327)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.4e-29)|all cancers(36;2.08e-27)|OV - Ovarian serous cystadenocarcinoma(60;4.63e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.56e-05)|Lung(119;0.00344)|LUSC - Lung squamous cell carcinoma(224;0.0148)		AAGTTTGACCCAAGCCCAAGG	0.388													37	106	---	---	---	---	PASS
CIDEC	63924	broad.mit.edu	37	3	9908844	9908844	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9908844G>C	uc003btq.2	-	6	831	c.691C>G	c.(691-693)CCG>GCG	p.P231A	CIDEC_uc003bto.2_RNA|CIDEC_uc010hcp.2_Missense_Mutation_p.P115R|CIDEC_uc003btp.2_Missense_Mutation_p.P241A|CIDEC_uc003btr.2_Missense_Mutation_p.P157A|CIDEC_uc003bts.2_Missense_Mutation_p.P157A	NM_022094	NP_071377	Q96AQ7	CIDEC_HUMAN	cell death-inducing DFFA-like effector c	231					apoptosis|induction of apoptosis	cytosol|focal adhesion|nucleus				central_nervous_system(1)	1	Medulloblastoma(99;0.227)					AGACAGGTCGGGATAAGGGAT	0.587													41	93	---	---	---	---	PASS
IRAK2	3656	broad.mit.edu	37	3	10255156	10255156	+	Intron	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10255156C>G	uc003bve.1	+							NM_001570	NP_001561	O43187	IRAK2_HUMAN	interleukin-1 receptor-associated kinase 2						activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|interleukin-1-mediated signaling pathway|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of NF-kappaB transcription factor activity|positive regulation of NF-kappaB transcription factor activity|regulation of cytokine-mediated signaling pathway|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	cell surface|cytosol|endosome membrane|plasma membrane	ATP binding|NF-kappaB-inducing kinase activity|protein heterodimerization activity|protein homodimerization activity			lung(5)|breast(3)	8						GTTCTGATGTCTTTCTCTACA	0.488													24	38	---	---	---	---	PASS
TATDN2	9797	broad.mit.edu	37	3	10320103	10320103	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10320103G>C	uc003bvg.2	+	6	2683	c.2102G>C	c.(2101-2103)AGA>ACA	p.R701T	TATDN2_uc003bvf.2_Missense_Mutation_p.R701T|TATDN2_uc011atr.1_Missense_Mutation_p.R701T|TATDN2_uc011ats.1_RNA|TATDN2_uc011att.1_RNA|TATDN2_uc011atu.1_5'Flank|TATDN2_uc011atv.1_5'Flank|GHRLOS_uc011atw.1_5'Flank|GHRLOS_uc011atx.1_5'Flank|GHRLOS_uc011aty.1_5'Flank|GHRLOS_uc011atz.1_5'Flank|GHRLOS_uc011aua.1_5'Flank|GHRLOS_uc010hdl.2_5'Flank|GHRLOS_uc011aub.1_5'Flank|GHRLOS_uc010hdm.2_5'Flank|GHRLOS_uc011auc.1_5'Flank|GHRLOS_uc011aud.1_5'Flank|GHRLOS_uc011aue.1_5'Flank|GHRLOS_uc011auf.1_5'Flank|GHRLOS_uc011aug.1_5'Flank	NM_014760	NP_055575	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	701						nucleus	endodeoxyribonuclease activity, producing 5'-phosphomonoesters|metal ion binding			pancreas(2)	2						CCACTGGAGAGAATCATCGTG	0.597													7	211	---	---	---	---	PASS
SYN2	6854	broad.mit.edu	37	3	12192811	12192811	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12192811C>T	uc003bwm.2	+	9	923	c.759C>T	c.(757-759)CCC>CCT	p.P253P	SYN2_uc003bwl.1_Silent_p.P253P|SYN2_uc003bwn.2_5'UTR	NM_133625	NP_598328	Q92777	SYN2_HUMAN	synapsin II isoform IIa	253					neurotransmitter secretion	synaptic vesicle	ATP binding|ligase activity			ovary(1)|central_nervous_system(1)	2						CATACTACCCCAACCACAAAG	0.453													11	17	---	---	---	---	PASS
C3orf19	51244	broad.mit.edu	37	3	14711491	14711491	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14711491C>G	uc003byw.2	+	10	1094	c.1003C>G	c.(1003-1005)CCA>GCA	p.P335A	C3orf19_uc010hej.2_Missense_Mutation_p.P164A	NM_016474	NP_057558	Q6PII3	CC019_HUMAN	hypothetical protein LOC51244	335											0						TGTGCCAACCCCACGTCCTGC	0.498													18	30	---	---	---	---	PASS
DAZL	1618	broad.mit.edu	37	3	16636039	16636039	+	Splice_Site	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16636039C>T	uc003cbb.2	-	8	915	c.621_splice	c.e8+1	p.P207_splice	DAZL_uc003cba.2_Splice_Site_p.P227_splice	NM_001351	NP_001342	Q92904	DAZL_HUMAN	deleted in azoospermia-like						germ cell development|multicellular organismal development|positive regulation of translational initiation|spermatogenesis	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding|translation activator activity				0						ATTCACTTTACCGGAGGTACA	0.303													14	18	---	---	---	---	PASS
EFHB	151651	broad.mit.edu	37	3	19921152	19921152	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19921152C>A	uc003cbl.3	-	13	2669	c.2473G>T	c.(2473-2475)GAC>TAC	p.D825Y	EFHB_uc003cbm.2_Missense_Mutation_p.D695Y	NM_144715	NP_653316	Q8N7U6	EFHB_HUMAN	EF hand domain family, member B	825					signal transduction	proteinaceous extracellular matrix	calcium ion binding				0						TTGATCCGGTCTGCATGCCGT	0.338													60	113	---	---	---	---	PASS
ITGA9	3680	broad.mit.edu	37	3	37584079	37584079	+	Intron	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37584079C>G	uc003chd.2	+						ITGA9_uc003chc.2_Intron	NM_002207	NP_002198	Q13797	ITA9_HUMAN	integrin, alpha 9 precursor						axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			breast(3)|pancreas(1)|lung(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		ATGTGAAGGTCAGTCCTCTCC	0.463													18	28	---	---	---	---	PASS
TTC21A	199223	broad.mit.edu	37	3	39178864	39178864	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39178864A>G	uc003cjc.2	+	25	3634	c.3457A>G	c.(3457-3459)ATA>GTA	p.I1153V	TTC21A_uc003cje.2_Missense_Mutation_p.I1154V|TTC21A_uc003cjd.2_Intron|TTC21A_uc011ayx.1_Missense_Mutation_p.I1105V|TTC21A_uc003cjf.2_Missense_Mutation_p.I274V	NM_145755	NP_665698	Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A isoform 2	1153							binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		CTTCATCCAGATAGCGCAGGC	0.667													12	19	---	---	---	---	PASS
CCR9	10803	broad.mit.edu	37	3	45943155	45943155	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45943155C>T	uc003coz.1	+	3	1032	c.875C>T	c.(874-876)TCC>TTC	p.S292F	LZTFL1_uc003coy.1_Intron|LZTFL1_uc011bak.1_Intron|CCR9_uc010hiv.1_Missense_Mutation_p.S280F|CCR9_uc003cpa.1_Missense_Mutation_p.S280F	NM_031200	NP_112477	P51686	CCR9_HUMAN	chemokine (C-C motif) receptor 9 isoform A	292	Extracellular (Potential).				cellular defense response|chemotaxis|elevation of cytosolic calcium ion concentration|immune response	integral to plasma membrane				ovary(2)|breast(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.00118)|KIRC - Kidney renal clear cell carcinoma(197;0.0182)|Kidney(197;0.0214)		TGTGCCGTTTCCACCAACATT	0.498													7	89	---	---	---	---	PASS
PLXNB1	5364	broad.mit.edu	37	3	48459365	48459365	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48459365C>G	uc003csw.2	-	16	3599	c.3329G>C	c.(3328-3330)GGA>GCA	p.G1110A	PLXNB1_uc003csu.2_Missense_Mutation_p.G927A|PLXNB1_uc003csx.2_Missense_Mutation_p.G1110A|PLXNB1_uc010hjx.1_RNA|PLXNB1_uc003csy.1_5'Flank	NM_002673	NP_002664	O43157	PLXB1_HUMAN	plexin B1 precursor	1110	IPT/TIG 1.|Extracellular (Potential).				axon guidance|cell migration|intracellular signal transduction|regulation of cell shape|regulation of cytoskeleton organization|regulation of small GTPase mediated signal transduction|semaphorin-plexin signaling pathway	extracellular region|integral to plasma membrane|intracellular|semaphorin receptor complex	GTPase activator activity|semaphorin receptor activity|semaphorin receptor binding			ovary(2)|pancreas(1)|breast(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		ACAGGGCACTCCAGCCACCGT	0.667													8	46	---	---	---	---	PASS
COL7A1	1294	broad.mit.edu	37	3	48620816	48620816	+	Intron	SNP	T	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48620816T>C	uc003ctz.2	-							NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor						cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		ATCCCCCAACTGGTACTCACT	0.567													19	31	---	---	---	---	PASS
CELSR3	1951	broad.mit.edu	37	3	48665951	48665951	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48665951G>A	uc003cuf.1	-	52	11931	c.11931C>T	c.(11929-11931)CTC>CTT	p.L3977L	SLC26A6_uc003cug.2_Silent_p.L551L|SLC26A6_uc003cuh.2_Silent_p.L572L|SLC26A6_uc010hke.2_Silent_p.L423L|SLC26A6_uc003cuk.2_Silent_p.L465L|SLC26A6_uc003cui.2_Silent_p.L572L|SLC26A6_uc003cuj.2_Silent_p.L572L|SLC26A6_uc011bbp.1_Silent_p.L536L	NM_001407	NP_001398	Q9NYQ7	CELR3_HUMAN	cadherin EGF LAG seven-pass G-type receptor 3	Error:Variant_position_missing_in_Q9NYQ7_after_alignment					homophilic cell adhesion|multicellular organismal development|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(5)|upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		TCTGGGAGATGAGGAAGTCGA	0.552													11	117	---	---	---	---	PASS
TRAIP	10293	broad.mit.edu	37	3	49885009	49885009	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49885009G>C	uc003cxs.1	-	3	295	c.189C>G	c.(187-189)TTC>TTG	p.F63L	TRAIP_uc010hla.1_Missense_Mutation_p.F63L|TRAIP_uc011bcx.1_Missense_Mutation_p.F63L	NM_005879	NP_005870	Q9BWF2	TRAIP_HUMAN	TRAF interacting protein	63					cell proliferation|induction of apoptosis	perinuclear region of cytoplasm	protein binding|zinc ion binding			lung(4)|upper_aerodigestive_tract(1)|ovary(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CAAGATCAAAGAAGAGCTTAT	0.438													7	164	---	---	---	---	PASS
RBM6	10180	broad.mit.edu	37	3	50004983	50004983	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50004983G>C	uc003cyc.2	+	3	258	c.125G>C	c.(124-126)AGA>ACA	p.R42T	RBM6_uc011bdh.1_RNA|RBM6_uc010hlc.1_Intron|RBM6_uc003cyd.2_Intron|RBM6_uc003cye.2_Intron|RBM6_uc011bdi.1_Intron|RBM6_uc010hld.1_Intron|RBM6_uc010hle.1_Intron|RBM6_uc010hlf.1_Intron	NM_005777	NP_005768	P78332	RBM6_HUMAN	RNA binding motif protein 6	42					RNA processing	nucleus	DNA binding|nucleotide binding|RNA binding|zinc ion binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		GCTCAAGAGAGACACTCTGGC	0.493													16	87	---	---	---	---	PASS
FEZF2	55079	broad.mit.edu	37	3	62356029	62356029	+	Intron	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62356029C>G	uc003dlh.2	-						FEZF2_uc003dli.2_Intron	NM_018008	NP_060478	Q8TBJ5	FEZF2_HUMAN	FEZ family zinc finger 2						transcription, DNA-dependent	nucleus	zinc ion binding			lung(1)	1		Lung SC(41;0.0262)		BRCA - Breast invasive adenocarcinoma(55;0.000221)|KIRC - Kidney renal clear cell carcinoma(15;0.00834)|Kidney(15;0.00957)		TACAACAGATCAAGAACAAAA	0.547													17	82	---	---	---	---	PASS
ADAMTS9	56999	broad.mit.edu	37	3	64633726	64633726	+	Intron	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64633726C>G	uc003dmg.2	-						ADAMTS9_uc011bfo.1_Intron|ADAMTS9_uc003dmh.1_Intron|ADAMTS9_uc003dmk.1_Intron	NM_182920	NP_891550	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1						glycoprotein catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)|skin(1)	4		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		TGCATCTGCTCAATTCAATGA	0.468													34	41	---	---	---	---	PASS
UBA3	9039	broad.mit.edu	37	3	69117163	69117163	+	Intron	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69117163C>A	uc003dno.2	-						UBA3_uc003dnq.2_Intron|UBA3_uc011bfy.1_Intron|UBA3_uc011bfz.1_Intron	NM_003968	NP_003959	Q8TBC4	UBA3_HUMAN	ubiquitin-activating enzyme 3 isoform 1						protein neddylation|proteolysis	nucleus	acid-amino acid ligase activity|ATP binding|protein heterodimerization activity			ovary(1)	1		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.98e-05)|Epithelial(33;0.000363)|LUSC - Lung squamous cell carcinoma(21;0.012)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.206)|Kidney(39;0.241)		TTTAGGCCTACAGGaaaaata	0.279													26	25	---	---	---	---	PASS
CCDC80	151887	broad.mit.edu	37	3	112349095	112349095	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112349095C>G	uc003dzf.2	-	3	2118	c.1900G>C	c.(1900-1902)GAG>CAG	p.E634Q	CCDC80_uc011bhv.1_Missense_Mutation_p.E634Q|CCDC80_uc003dzg.2_Missense_Mutation_p.E634Q|CCDC80_uc003dzh.1_Missense_Mutation_p.E634Q	NM_199512	NP_955806	Q76M96	CCD80_HUMAN	steroid-sensitive protein 1 precursor	634										ovary(2)	2						ATATTGTTCTCAGCCTTGGGA	0.423													10	118	---	---	---	---	PASS
DRD3	1814	broad.mit.edu	37	3	113847578	113847578	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113847578C>G	uc003ebd.2	-	8	1611	c.1188G>C	c.(1186-1188)AAG>AAC	p.K396N	DRD3_uc010hqn.1_Missense_Mutation_p.K396N|DRD3_uc003ebb.1_Missense_Mutation_p.K363N|DRD3_uc003ebc.1_Missense_Mutation_p.K396N	NM_000796	NP_000787	P35462	DRD3_HUMAN	dopamine receptor D3 isoform a	396	Cytoplasmic.			K -> L (in Ref. 7; AAH95510).	activation of adenylate cyclase activity by dopamine receptor signaling pathway|arachidonic acid secretion|behavioral response to cocaine|cellular calcium ion homeostasis|circadian regulation of gene expression|G-protein coupled receptor internalization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|locomotory behavior|musculoskeletal movement, spinal reflex action|negative regulation of blood pressure|negative regulation of oligodendrocyte differentiation|negative regulation of protein kinase B signaling cascade|negative regulation of protein secretion|positive regulation of dopamine receptor signaling pathway|positive regulation of mitosis|prepulse inhibition|regulation of dopamine secretion|response to drug|response to histamine|response to morphine|social behavior|visual learning	integral to plasma membrane	dopamine D3 receptor activity|drug binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4					Apomorphine(DB00714)|Chlorprothixene(DB01239)|Cocaine(DB00907)|Methotrimeprazine(DB01403)|Olanzapine(DB00334)|Pramipexole(DB00413)|Ropinirole(DB00268)|Ziprasidone(DB00246)	AAGACAGGATCTTGAGGAAGG	0.527													163	378	---	---	---	---	PASS
C3orf1	51300	broad.mit.edu	37	3	119222385	119222385	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119222385G>C	uc003ecn.2	+	3	580	c.367G>C	c.(367-369)GCA>CCA	p.A123P	C3orf1_uc003eco.2_RNA|C3orf1_uc003ecp.2_RNA	NM_016589	NP_057673	Q9NPL8	TIDC1_HUMAN	hypothetical protein LOC51300	123						integral to membrane|mitochondrial inner membrane	protein transporter activity				0				GBM - Glioblastoma multiforme(114;0.186)		TTAGCAATCTGCACATCGTGC	0.408													7	18	---	---	---	---	PASS
HGD	3081	broad.mit.edu	37	3	120365209	120365209	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120365209C>A	uc003edw.2	-	9	924	c.554G>T	c.(553-555)GGA>GTA	p.G185V	HGD_uc003edv.2_Missense_Mutation_p.G44V	NM_000187	NP_000178	Q93099	HGD_HUMAN	homogentisate 1,2-dioxygenase	185					L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	homogentisate 1,2-dioxygenase activity|metal ion binding				0				GBM - Glioblastoma multiforme(114;0.158)		GAACCGCATTCCTCTCTGGAA	0.483													6	110	---	---	---	---	PASS
KALRN	8997	broad.mit.edu	37	3	124385400	124385400	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124385400C>T	uc003ehg.2	+	46	6574	c.6447C>T	c.(6445-6447)CTC>CTT	p.L2149L	KALRN_uc003ehi.2_Silent_p.L490L|KALRN_uc003ehk.2_Silent_p.L452L|KALRN_uc011bjz.1_Silent_p.L241L	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	2148	PH 2.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6						GCGTGTTCCTCTTCGAGCAGA	0.542													14	80	---	---	---	---	PASS
RHO	6010	broad.mit.edu	37	3	129249756	129249756	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129249756C>T	uc003emt.2	+	2	494	c.399C>T	c.(397-399)ATC>ATT	p.I133I		NM_000539	NP_000530	P08100	OPSD_HUMAN	rhodopsin	133	Helical; Name=3; (Potential).				protein-chromophore linkage|rhodopsin mediated signaling pathway	Golgi apparatus|integral to plasma membrane|photoreceptor inner segment membrane|photoreceptor outer segment membrane	G-protein coupled receptor activity|metal ion binding|photoreceptor activity|protein binding				0		all_neural(597;0.0227)|Myeloproliferative disorder(1037;0.0255)|Prostate(884;0.183)		GBM - Glioblastoma multiforme(114;2.58e-05)|Lung(219;0.0234)	Halothane(DB01159)	TCCTGGCCATCGAGCGGTACG	0.622													5	236	---	---	---	---	PASS
ATP2C1	27032	broad.mit.edu	37	3	130682866	130682866	+	Silent	SNP	G	A	A	rs147959633		TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130682866G>A	uc003enl.2	+	13	1173	c.951G>A	c.(949-951)ACG>ACA	p.T317T	ATP2C1_uc011blg.1_Silent_p.T351T|ATP2C1_uc011blh.1_Silent_p.T312T|ATP2C1_uc011bli.1_Silent_p.T351T|ATP2C1_uc003enk.2_Silent_p.T301T|ATP2C1_uc003enm.2_Silent_p.T317T|ATP2C1_uc003enn.2_Silent_p.T301T|ATP2C1_uc003eno.2_Silent_p.T317T|ATP2C1_uc003enp.2_Silent_p.T317T|ATP2C1_uc003enq.2_Silent_p.T317T|ATP2C1_uc003enr.2_Silent_p.T317T|ATP2C1_uc003ens.2_Silent_p.T317T|ATP2C1_uc003ent.2_Silent_p.T317T|ATP2C1_uc003enu.2_5'UTR	NM_014382	NP_055197	P98194	AT2C1_HUMAN	calcium-transporting ATPase 2C1 isoform 1a	317	Cytoplasmic (By similarity).				actin cytoskeleton reorganization|ATP biosynthetic process|calcium-dependent cell-cell adhesion|cellular calcium ion homeostasis|cellular manganese ion homeostasis|epidermis development|Golgi calcium ion homeostasis|Golgi calcium ion transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi apparatus|Golgi membrane|integral to membrane|trans-Golgi network	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|manganese ion binding|manganese-transporting ATPase activity|metal ion binding|signal transducer activity			skin(1)	1					Arsenic trioxide(DB01169)|Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Miconazole(DB01110)|Sevoflurane(DB01236)	TCACAGTGACGCTAGCTCTTG	0.403									Hailey-Hailey_disease				17	197	---	---	---	---	PASS
PLS1	5357	broad.mit.edu	37	3	142408474	142408474	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142408474G>A	uc010huv.2	+	10	1155	c.996G>A	c.(994-996)CTG>CTA	p.L332L	PLS1_uc003euz.2_Silent_p.L332L|PLS1_uc003eva.2_Silent_p.L332L	NM_001145319	NP_001138791	Q14651	PLSI_HUMAN	plastin 1	332	Actin-binding 1.|CH 2.					cytoplasm	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(1)	1						CAAATGACCTGAAGCGTGCTG	0.338													20	73	---	---	---	---	PASS
SERP1	27230	broad.mit.edu	37	3	150263869	150263869	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150263869G>A	uc003exy.2	-	1	560	c.54C>T	c.(52-54)ATC>ATT	p.I18I	SERP1_uc003exz.2_RNA|EIF2A_uc003eya.2_5'Flank|EIF2A_uc003eyb.2_5'Flank|EIF2A_uc003eyc.2_5'Flank|EIF2A_uc011bnv.1_5'Flank|EIF2A_uc011bnw.1_5'Flank	NM_014445	NP_055260	Q9Y6X1	SERP1_HUMAN	stress-associated endoplasmic reticulum protein	18	Cytoplasmic (Potential).				plasma membrane organization|protein glycosylation|protein transport|transmembrane transport	endoplasmic reticulum membrane|integral to membrane|ribosome					0			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			CGCGCTGGGTGATGTTCTTGC	0.677													11	131	---	---	---	---	PASS
RSRC1	51319	broad.mit.edu	37	3	157839955	157839955	+	Missense_Mutation	SNP	G	A	A	rs143641214	byFrequency	TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157839955G>A	uc003fbt.2	+	2	173	c.62G>A	c.(61-63)CGT>CAT	p.R21H	RSRC1_uc011bou.1_Missense_Mutation_p.R21H|RSRC1_uc003fbu.1_Missense_Mutation_p.R21H|RSRC1_uc003fbv.2_Missense_Mutation_p.R21H	NM_016625	NP_057709	Q96IZ7	RSRC1_HUMAN	arginine/serine-rich coiled-coil 1	21	Arg/Ser-rich.				nucleocytoplasmic transport	cytoplasm|nuclear speck	protein binding				0			Lung(72;0.00416)|LUSC - Lung squamous cell carcinoma(72;0.00575)			AAGAAACACCGTAGACGGTCC	0.388													10	36	---	---	---	---	PASS
SI	6476	broad.mit.edu	37	3	164786883	164786883	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164786883A>G	uc003fei.2	-	4	418	c.356T>C	c.(355-357)ATG>ACG	p.M119T		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	119	Lumenal.|Isomaltase.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)	TGTTGTTGTCATGTCTTGAAC	0.378										HNSCC(35;0.089)			25	48	---	---	---	---	PASS
SERPINI2	5276	broad.mit.edu	37	3	167183100	167183100	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167183100C>G	uc003fer.1	-	4	818	c.760G>C	c.(760-762)GCA>CCA	p.A254P	SERPINI2_uc003fes.1_Missense_Mutation_p.A264P|SERPINI2_uc003fet.1_Missense_Mutation_p.A254P	NM_006217	NP_006208	O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin),	254					cellular component movement|regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			skin(2)|urinary_tract(1)	3						ATACCTTCTGCAGGAAGTATG	0.343													40	229	---	---	---	---	PASS
NAALADL2	254827	broad.mit.edu	37	3	175473112	175473112	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175473112G>C	uc003fit.2	+	13	2182	c.2095G>C	c.(2095-2097)GAG>CAG	p.E699Q		NM_207015	NP_996898	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	699	Extracellular (Potential).				proteolysis	integral to membrane	peptidase activity			pancreas(1)	1	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		TGATCCCAAGGAGAGAGCACC	0.493													11	44	---	---	---	---	PASS
MCF2L2	23101	broad.mit.edu	37	3	182923970	182923970	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182923970C>A	uc003fli.1	-	24	2835	c.2745G>T	c.(2743-2745)AGG>AGT	p.R915S		NM_015078	NP_055893	Q86YR7	MF2L2_HUMAN	Rho family guanine-nucleotide exchange factor	915	PH.				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|large_intestine(2)|breast(1)	5	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			TATGGCTCCCCCTTCCAAGCT	0.423													44	161	---	---	---	---	PASS
MCF2L2	23101	broad.mit.edu	37	3	183035889	183035889	+	Silent	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183035889G>C	uc003fli.1	-	7	810	c.720C>G	c.(718-720)CTC>CTG	p.L240L	MCF2L2_uc003flj.1_Silent_p.L240L|MCF2L2_uc003flp.1_Silent_p.L275L	NM_015078	NP_055893	Q86YR7	MF2L2_HUMAN	Rho family guanine-nucleotide exchange factor	240					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|large_intestine(2)|breast(1)	5	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			TGTGGGACATGAGAAGGTCTT	0.597													9	59	---	---	---	---	PASS
ABCC5	10057	broad.mit.edu	37	3	183655773	183655773	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183655773C>G	uc003fmg.2	-	26	3935	c.3770G>C	c.(3769-3771)AGA>ACA	p.R1257T	ABCC5_uc011bqt.1_Missense_Mutation_p.R785T|ABCC5_uc010hxl.2_Missense_Mutation_p.R1214T	NM_005688	NP_005679	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C, member 5	1257	ABC transporter 2.					integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)	4	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			ATCACTGATTCTCACTCCATC	0.532													14	180	---	---	---	---	PASS
VPS8	23355	broad.mit.edu	37	3	184631309	184631309	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184631309G>A	uc003fpb.1	+	25	2314	c.2143G>A	c.(2143-2145)GAA>AAA	p.E715K	VPS8_uc010hyd.1_Missense_Mutation_p.E625K|VPS8_uc010hye.1_Missense_Mutation_p.E144K	NM_015303	NP_056118	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog isoform b	717							zinc ion binding			ovary(1)	1	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			TATTTTAGATGAACAAGTTGT	0.254													11	193	---	---	---	---	PASS
DNAJB11	51726	broad.mit.edu	37	3	186302269	186302269	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186302269G>C	uc003fqi.2	+	9	1123	c.903G>C	c.(901-903)AAG>AAC	p.K301N		NM_016306	NP_057390	Q9UBS4	DJB11_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 11	301					protein folding	endoplasmic reticulum lumen	heat shock protein binding			ovary(1)|lung(1)	2	all_cancers(143;2.84e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.44e-20)	GBM - Glioblastoma multiforme(93;0.0476)		AGCTATGGAAGAAAGGGGAAG	0.443													4	87	---	---	---	---	PASS
ATP13A5	344905	broad.mit.edu	37	3	193052756	193052756	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193052756G>C	uc011bsq.1	-	10	1076	c.1076C>G	c.(1075-1077)TCT>TGT	p.S359C		NM_198505	NP_940907	Q4VNC0	AT135_HUMAN	ATPase type 13A5	359					ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(5)|skin(4)|large_intestine(2)	11	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		CCCCTGCCCAGAGGGCTTGAC	0.463													14	167	---	---	---	---	PASS
OPA1	4976	broad.mit.edu	37	3	193332589	193332589	+	Missense_Mutation	SNP	C	T	T	rs149756039		TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193332589C>T	uc003ftm.2	+	2	344	c.110C>T	c.(109-111)TCA>TTA	p.S37L	OPA1_uc003ftg.2_Missense_Mutation_p.S37L|OPA1_uc003fth.2_Missense_Mutation_p.S37L|OPA1_uc003fti.2_Missense_Mutation_p.S37L|OPA1_uc003ftj.2_Missense_Mutation_p.S37L|OPA1_uc003ftk.2_Missense_Mutation_p.S37L|OPA1_uc003ftl.2_Missense_Mutation_p.S37L|OPA1_uc003ftn.2_Missense_Mutation_p.S37L	NM_015560	NP_056375	O60313	OPA1_HUMAN	optic atrophy 1 isoform 1	37					apoptosis|axon transport of mitochondrion|inner mitochondrial membrane organization|mitochondrial fission|mitochondrial fusion|positive regulation of anti-apoptosis|response to stimulus|visual perception	dendrite|integral to membrane|mitochondrial crista|mitochondrial intermembrane space|mitochondrial outer membrane	GTP binding|GTPase activity|magnesium ion binding|protein binding				0	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)		CATCTGGTTTCACGAAGCATT	0.303													21	85	---	---	---	---	PASS
OSTalpha	200931	broad.mit.edu	37	3	195954611	195954611	+	Intron	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195954611G>C	uc003fwd.2	+						OSTalpha_uc010iac.1_Intron|OSTalpha_uc003fwe.2_5'Flank	NM_152672	NP_689885	Q86UW1	OSTA_HUMAN	organic solute transporter alpha							integral to membrane|plasma membrane	transporter activity			ovary(1)	1	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;8.83e-25)|all cancers(36;8.38e-23)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;7.51e-07)|Lung(62;1.06e-06)	GBM - Glioblastoma multiforme(46;0.00202)		ATCACCTCGTGAGTGCCCTGC	0.622													22	60	---	---	---	---	PASS
ATP8A1	10396	broad.mit.edu	37	4	42558042	42558042	+	Silent	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42558042A>G	uc003gwr.2	-	16	1588	c.1356T>C	c.(1354-1356)TTT>TTC	p.F452F	ATP8A1_uc003gws.2_Silent_p.F437F|ATP8A1_uc011byz.1_Silent_p.F437F	NM_006095	NP_006086	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT),	452	Cytoplasmic (Potential).				ATP biosynthetic process	chromaffin granule membrane|integral to membrane|plasma membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			skin(2)|central_nervous_system(1)	3					Phosphatidylserine(DB00144)	TTTCATCTCCAAACTGTGAGT	0.318													6	28	---	---	---	---	PASS
GABRG1	2565	broad.mit.edu	37	4	46099262	46099262	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46099262G>A	uc003gxb.2	-	2	361	c.209C>T	c.(208-210)TCA>TTA	p.S70L		NM_173536	NP_775807	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid A receptor, gamma 1	70	Extracellular (Probable).				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)		TTGAAGCAATGAATTCAGAAT	0.383													49	123	---	---	---	---	PASS
CWH43	80157	broad.mit.edu	37	4	49009279	49009279	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49009279G>A	uc003gyv.2	+	8	1304	c.1122G>A	c.(1120-1122)TTG>TTA	p.L374L	CWH43_uc011bzl.1_Silent_p.L347L	NM_025087	NP_079363	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog	374					GPI anchor biosynthetic process	integral to membrane				skin(2)|ovary(1)	3						ACCTTGACTTGCTTCTTCAAA	0.284													19	33	---	---	---	---	PASS
KDR	3791	broad.mit.edu	37	4	55964928	55964928	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55964928C>A	uc003has.2	-	16	2611	c.2309G>T	c.(2308-2310)GGC>GTC	p.G770V	KDR_uc003hat.1_Missense_Mutation_p.G770V	NM_002253	NP_002244	P35968	VGFR2_HUMAN	kinase insert domain receptor precursor	770	Helical; (Potential).				angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(16)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|stomach(2)|skin(2)|ovary(2)|kidney(1)	33	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Sorafenib(DB00398)|Sunitinib(DB01268)	CACCGCCGTGCCTACTAGAAT	0.413			Mis		NSCLC|angiosarcoma				Familial_Infantile_Hemangioma	TSP Lung(20;0.16)			33	101	---	---	---	---	PASS
KDR	3791	broad.mit.edu	37	4	55964929	55964929	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55964929C>A	uc003has.2	-	16	2610	c.2308G>T	c.(2308-2310)GGC>TGC	p.G770C	KDR_uc003hat.1_Missense_Mutation_p.G770C	NM_002253	NP_002244	P35968	VGFR2_HUMAN	kinase insert domain receptor precursor	770	Helical; (Potential).				angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(16)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|stomach(2)|skin(2)|ovary(2)|kidney(1)	33	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Sorafenib(DB00398)|Sunitinib(DB01268)	ACCGCCGTGCCTACTAGAATA	0.408			Mis		NSCLC|angiosarcoma				Familial_Infantile_Hemangioma	TSP Lung(20;0.16)			32	101	---	---	---	---	PASS
LPHN3	23284	broad.mit.edu	37	4	62598726	62598726	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62598726G>T	uc010ihh.2	+	5	822	c.649G>T	c.(649-651)GCT>TCT	p.A217S	LPHN3_uc003hcq.3_Missense_Mutation_p.A217S|LPHN3_uc010ihg.1_Missense_Mutation_p.A285S|LPHN3_uc003hcs.1_Missense_Mutation_p.A46S	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor	217	Extracellular (Potential).|Olfactomedin-like.				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18						GTATGATGGAGCTTTGTTCTT	0.438													20	45	---	---	---	---	PASS
FRAS1	80144	broad.mit.edu	37	4	79391175	79391175	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79391175C>T	uc003hlb.2	+	51	7741	c.7301C>T	c.(7300-7302)CCG>CTG	p.P2434L		NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	2433	CSPG 12.|Extracellular (Potential).				cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						GACATCCTCCCGGTAGATGAT	0.507													9	34	---	---	---	---	PASS
FRAS1	80144	broad.mit.edu	37	4	79391176	79391176	+	Silent	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79391176G>T	uc003hlb.2	+	51	7742	c.7302G>T	c.(7300-7302)CCG>CCT	p.P2434P		NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	2433	CSPG 12.|Extracellular (Potential).				cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						ACATCCTCCCGGTAGATGATG	0.507													9	35	---	---	---	---	PASS
DMP1	1758	broad.mit.edu	37	4	88578214	88578214	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88578214G>T	uc003hqv.2	+	3	189	c.85G>T	c.(85-87)GAT>TAT	p.D29Y	DMP1_uc003hqw.2_Missense_Mutation_p.D29Y	NM_004407	NP_004398	Q13316	DMP1_HUMAN	dentin matrix acidic phosphoprotein 1 isoform 1	29					biomineral tissue development|ossification	cytoplasm|nucleus|proteinaceous extracellular matrix	calcium ion binding|integrin binding			pancreas(1)|skin(1)	2		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.227)		OV - Ovarian serous cystadenocarcinoma(123;0.000516)		TGAATCTGAGGATTCTGAAGA	0.254													22	35	---	---	---	---	PASS
TSPAN5	10098	broad.mit.edu	37	4	99403249	99403249	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99403249G>C	uc003hub.2	-	4	707	c.357C>G	c.(355-357)ATC>ATG	p.I119M	TSPAN5_uc011cdz.1_Missense_Mutation_p.I48M	NM_005723	NP_005714	P62079	TSN5_HUMAN	transmembrane 4 superfamily member 9	119	Extracellular (Potential).					integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(123;1.89e-07)		GCTGGTCTTTGATCCAGTCTT	0.378													3	119	---	---	---	---	PASS
PCDH10	57575	broad.mit.edu	37	4	134075499	134075499	+	Missense_Mutation	SNP	A	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134075499A>T	uc003iha.2	+	2	3495	c.2669A>T	c.(2668-2670)GAC>GTC	p.D890V		NM_032961	NP_116586	Q9P2E7	PCD10_HUMAN	protocadherin 10 isoform 1 precursor	890	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2				LUSC - Lung squamous cell carcinoma(193;0.227)		TATCTAGTTGACAGACCTCGC	0.373													12	26	---	---	---	---	PASS
LRBA	987	broad.mit.edu	37	4	151392889	151392889	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151392889C>T	uc010ipj.2	-	44	7061	c.6587G>A	c.(6586-6588)CGT>CAT	p.R2196H	LRBA_uc003ils.3_Missense_Mutation_p.R86H|LRBA_uc003ilt.3_Missense_Mutation_p.R844H|LRBA_uc003ilu.3_Missense_Mutation_p.R2185H	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and	2196						endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)					TAATGAAATACGTCTGCAAGA	0.308													18	62	---	---	---	---	PASS
TLR2	7097	broad.mit.edu	37	4	154624805	154624805	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154624805C>T	uc003inq.2	+	3	965	c.746C>T	c.(745-747)TCA>TTA	p.S249L	TLR2_uc003inr.2_Missense_Mutation_p.S249L|TLR2_uc003ins.2_Missense_Mutation_p.S249L	NM_003264	NP_003255	O60603	TLR2_HUMAN	toll-like receptor 2 precursor	249	Extracellular (Potential).				cellular response to diacyl bacterial lipopeptide|cellular response to lipoteichoic acid|cellular response to triacyl bacterial lipopeptide|detection of diacyl bacterial lipopeptide|detection of triacyl bacterial lipopeptide|I-kappaB phosphorylation|induction of apoptosis|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of chemokine production|positive regulation of interferon-beta production|positive regulation of interleukin-12 production|positive regulation of interleukin-18 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of toll-like receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of Wnt receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytoplasm|integral to plasma membrane|Toll-like receptor 1-Toll-like receptor 2 protein complex	Gram-positive bacterial cell surface binding|lipopolysaccharide receptor activity|peptidoglycan binding|protein heterodimerization activity|transmembrane receptor activity|triacyl lipopeptide binding			ovary(1)|lung(1)|breast(1)	3	all_hematologic(180;0.093)	Renal(120;0.117)				GAAACAAATTCATTGATTAAA	0.313													17	25	---	---	---	---	PASS
DCHS2	54798	broad.mit.edu	37	4	155219363	155219363	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155219363C>T	uc003inw.2	-	18	4738	c.4738G>A	c.(4738-4740)GAT>AAT	p.D1580N		NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1	1580	Cadherin 13.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		AAAACTGGATCATTGTCATTA	0.443													26	32	---	---	---	---	PASS
TKTL2	84076	broad.mit.edu	37	4	164393542	164393542	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164393542C>A	uc003iqp.3	-	1	1506	c.1345G>T	c.(1345-1347)GTT>TTT	p.V449F		NM_032136	NP_115512	Q9H0I9	TKTL2_HUMAN	transketolase-like 2	449						cytoplasm	metal ion binding|transketolase activity			ovary(2)|skin(2)|pancreas(1)	5	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				GGATAGAAAACAGTACAATTG	0.493													33	75	---	---	---	---	PASS
TKTL2	84076	broad.mit.edu	37	4	164393543	164393543	+	Silent	SNP	A	G	G	rs114733407	byFrequency	TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164393543A>G	uc003iqp.3	-	1	1505	c.1344T>C	c.(1342-1344)ACT>ACC	p.T448T		NM_032136	NP_115512	Q9H0I9	TKTL2_HUMAN	transketolase-like 2	448						cytoplasm	metal ion binding|transketolase activity			ovary(2)|skin(2)|pancreas(1)	5	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				GATAGAAAACAGTACAATTGG	0.488													34	73	---	---	---	---	PASS
STOX2	56977	broad.mit.edu	37	4	184931549	184931549	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184931549G>C	uc003ivz.1	+	3	2993	c.1558G>C	c.(1558-1560)GAC>CAC	p.D520H	STOX2_uc003iwa.1_Missense_Mutation_p.D209H	NM_020225	NP_064610	Q9P2F5	STOX2_HUMAN	storkhead box 2	520					embryo development|maternal placenta development						0		all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283)		all cancers(43;2.85e-26)|Epithelial(43;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-10)|Colorectal(24;8.23e-06)|GBM - Glioblastoma multiforme(59;1.64e-05)|STAD - Stomach adenocarcinoma(60;3.6e-05)|COAD - Colon adenocarcinoma(29;4.37e-05)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.227)		CAGCCAAGACGACCAGACCCC	0.532													9	25	---	---	---	---	PASS
FAT1	2195	broad.mit.edu	37	4	187541760	187541760	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187541760C>T	uc003izf.2	-	10	6168	c.5980G>A	c.(5980-5982)GAG>AAG	p.E1994K		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	1994	Extracellular (Potential).|Cadherin 18.				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12						GTTTCGGCCTCGGTGGAATTC	0.418										HNSCC(5;0.00058)			56	396	---	---	---	---	PASS
SDHA	6389	broad.mit.edu	37	5	256445	256445	+	Intron	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:256445C>G	uc003jao.3	+						SDHA_uc011clw.1_Intron|SDHA_uc003jap.3_Intron|SDHA_uc003jaq.3_Intron|SDHA_uc003jar.3_Intron	NM_004168	NP_004159	P31040	DHSA_HUMAN	succinate dehydrogenase complex, subunit A,						nervous system development|respiratory electron transport chain|succinate metabolic process|transport|tricarboxylic acid cycle	mitochondrial respiratory chain complex II	electron carrier activity|flavin adenine dinucleotide binding|protein binding|succinate dehydrogenase (ubiquinone) activity				0			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	CTCTTCTTTTCAAGGTCACTC	0.408									Familial_Paragangliomas				31	136	---	---	---	---	PASS
SLC6A3	6531	broad.mit.edu	37	5	1394869	1394869	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1394869C>G	uc003jck.2	-	15	1965	c.1844G>C	c.(1843-1845)CGC>CCC	p.R615P		NM_001044	NP_001035	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter	615	Cytoplasmic (Potential).				cell death|neurotransmitter biosynthetic process	axon|cytoplasm|integral to plasma membrane|neuronal cell body				ovary(3)|breast(2)|pancreas(1)	6			OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262)		Amphetamine(DB00182)|Benztropine(DB00245)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Duloxetine(DB00476)|Fencamfamine(DB01463)|Mazindol(DB00579)|Methylphenidate(DB00422)|Modafinil(DB00745)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721)	GAGCCAGTGGCGGAGCTGGAA	0.522													43	186	---	---	---	---	PASS
ADAMTS16	170690	broad.mit.edu	37	5	5303677	5303677	+	Intron	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5303677C>T	uc003jdl.2	+						ADAMTS16_uc003jdk.1_Intron	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8						CCTGACTGTTCTGTGCAGTGC	0.632													22	104	---	---	---	---	PASS
SEMA5A	9037	broad.mit.edu	37	5	9202090	9202090	+	Silent	SNP	G	A	A	rs144446567	byFrequency	TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9202090G>A	uc003jek.2	-	9	1621	c.909C>T	c.(907-909)ATC>ATT	p.I303I		NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor	303	Sema.|Extracellular (Potential).				cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2						AGATGCCATAGATCAAATCCA	0.438													6	91	---	---	---	---	PASS
CDH12	1010	broad.mit.edu	37	5	21854886	21854886	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21854886G>A	uc010iuc.2	-	4	998	c.540C>T	c.(538-540)CTC>CTT	p.L180L	CDH12_uc011cno.1_Intron|CDH12_uc003jgk.2_Silent_p.L180L	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein	180	Extracellular (Potential).|Cadherin 2.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						CCTTGACCTGGAGTACATATG	0.418										HNSCC(59;0.17)			10	99	---	---	---	---	PASS
AMACR	23600	broad.mit.edu	37	5	33989607	33989607	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33989607C>A	uc003jig.2	-	5	822	c.740G>T	c.(739-741)GGA>GTA	p.G247V	AMACR_uc003jih.2_Missense_Mutation_p.R193S|AMACR_uc003jii.2_Missense_Mutation_p.G232V|AMACR_uc003jij.2_Missense_Mutation_p.G247V	NM_014324	NP_055139	Q9UHK6	AMACR_HUMAN	alpha-methylacyl-CoA racemase isoform 1	247					bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	mitochondrion|peroxisomal matrix	alpha-methylacyl-CoA racemase activity				0						TAGTCCAAGTCCTGAGGAAAA	0.353													10	56	---	---	---	---	PASS
RAI14	26064	broad.mit.edu	37	5	34796083	34796083	+	Silent	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34796083C>G	uc003jir.2	+	4	403	c.207C>G	c.(205-207)CTC>CTG	p.L69L	RAI14_uc010iur.2_Silent_p.L69L|RAI14_uc011coj.1_Silent_p.L69L|RAI14_uc010ius.1_5'UTR|RAI14_uc003jis.2_Silent_p.L72L|RAI14_uc003jit.2_Silent_p.L69L|RAI14_uc011cok.1_Silent_p.L61L	NM_015577	NP_056392	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14 isoform a	69	ANK 2.					cell cortex|cytoskeleton	protein binding			ovary(1)	1	all_lung(31;0.000191)					TGGAATGCCTCAGGGTCATGA	0.438													7	320	---	---	---	---	PASS
SPEF2	79925	broad.mit.edu	37	5	35712973	35712973	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35712973G>T	uc003jjo.2	+	20	3010	c.2899G>T	c.(2899-2901)GCA>TCA	p.A967S	SPEF2_uc003jjp.1_Missense_Mutation_p.A453S	NM_024867	NP_079143	Q9C093	SPEF2_HUMAN	KPL2 protein isoform 1	967					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity			skin(2)|ovary(1)|central_nervous_system(1)	4	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			AGGTGAGACCGCACTCAAAAG	0.333													37	61	---	---	---	---	PASS
PRKAA1	5562	broad.mit.edu	37	5	40768986	40768986	+	Intron	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40768986C>T	uc003jmc.2	-						PRKAA1_uc003jmb.2_Intron	NM_006251	NP_006242	Q13131	AAPK1_HUMAN	protein kinase, AMP-activated, alpha 1 catalytic						activation of MAPK activity|cell cycle arrest|cholesterol biosynthetic process|fatty acid biosynthetic process|insulin receptor signaling pathway|negative regulation of glucosylceramide biosynthetic process|positive regulation of anti-apoptosis|positive regulation of cholesterol biosynthetic process|regulation of fatty acid oxidation|response to hypoxia	cytosol	ATP binding|cAMP-dependent protein kinase activity|metal ion binding|protein binding			breast(1)	1					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Phenformin(DB00914)	TTCATGTTCTCAATGCTGGTA	0.284													20	105	---	---	---	---	PASS
HEATR7B2	133558	broad.mit.edu	37	5	41004915	41004915	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41004915G>C	uc003jmj.3	-	36	4462	c.3972C>G	c.(3970-3972)ATC>ATG	p.I1324M	HEATR7B2_uc003jmi.3_Missense_Mutation_p.I879M	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	1324							binding			ovary(6)|central_nervous_system(2)	8						CGAGCCCTCGGATGGCCATCT	0.473													7	133	---	---	---	---	PASS
OXCT1	5019	broad.mit.edu	37	5	41853624	41853624	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41853624C>T	uc003jmn.2	-	4	642	c.311G>A	c.(310-312)CGG>CAG	p.R104Q		NM_000436	NP_000427	P55809	SCOT1_HUMAN	3-oxoacid CoA transferase 1 precursor	104					cellular lipid metabolic process|ketone body catabolic process	mitochondrial matrix	3-oxoacid CoA-transferase activity|protein homodimerization activity			ovary(2)|large_intestine(1)	3					Succinic acid(DB00139)	CTGCTTGGACCGAAGCAAAAG	0.408													27	53	---	---	---	---	PASS
HMGCS1	3157	broad.mit.edu	37	5	43299047	43299047	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43299047C>G	uc003jnr.3	-	3	228	c.21G>C	c.(19-21)TTG>TTC	p.L7F	HMGCS1_uc003jnq.3_Missense_Mutation_p.L7F	NM_001098272	NP_001091742	Q01581	HMCS1_HUMAN	hydroxymethylglutaryl-CoA synthase 1	7					cholesterol biosynthetic process|isoprenoid biosynthetic process	cytosol|soluble fraction	hydroxymethylglutaryl-CoA synthase activity				0						CTTCTGCATTCAAAGGAAGTG	0.363													11	109	---	---	---	---	PASS
C5orf28	64417	broad.mit.edu	37	5	43453863	43453863	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43453863C>G	uc003jny.2	-	2	352	c.209G>C	c.(208-210)GGA>GCA	p.G70A	C5orf28_uc003jnv.3_Missense_Mutation_p.G70A|C5orf28_uc003jnx.2_Missense_Mutation_p.G70A	NM_022483	NP_071928	Q0VDI3	CE028_HUMAN	hypothetical protein LOC64417	70						integral to membrane					0	Lung NSC(6;2.07e-05)					CTTCTTGATTCCAGTGACTAC	0.403													21	172	---	---	---	---	PASS
HCN1	348980	broad.mit.edu	37	5	45396766	45396766	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45396766A>G	uc003jok.2	-	4	1083	c.1058T>C	c.(1057-1059)ATG>ACG	p.M353T		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	353						integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1						CATGTGACTCATAGCTTTGAA	0.463													59	101	---	---	---	---	PASS
HCN1	348980	broad.mit.edu	37	5	45645431	45645431	+	Silent	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45645431G>T	uc003jok.2	-	2	730	c.705C>A	c.(703-705)ATC>ATA	p.I235I		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	235	Helical; Name=Segment S3; (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1						CAATAAGAAAGATATAATCCA	0.378													6	74	---	---	---	---	PASS
OTP	23440	broad.mit.edu	37	5	76932978	76932978	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76932978C>A	uc003kfg.2	-	2	263	c.115G>T	c.(115-117)GGG>TGG	p.G39W		NM_032109	NP_115485	Q5XKR4	OTP_HUMAN	orthopedia homeobox	39						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			pancreas(1)	1		all_lung(232;0.00051)|Lung NSC(167;0.000601)|Ovarian(174;0.0105)|Prostate(461;0.214)		OV - Ovarian serous cystadenocarcinoma(54;9.04e-51)|Epithelial(54;1.62e-45)|all cancers(79;4.4e-41)		GGATGGCCCCCGGGGTCGGAG	0.697													7	11	---	---	---	---	PASS
SCAMP1	9522	broad.mit.edu	37	5	77717666	77717666	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77717666G>T	uc003kfl.2	+	6	671	c.514G>T	c.(514-516)GCT>TCT	p.A172S	SCAMP1_uc010jaa.2_Intron|SCAMP1_uc011ctc.1_RNA|SCAMP1_uc011ctd.1_RNA|SCAMP1_uc003kfm.2_RNA	NM_004866	NP_004857	O15126	SCAM1_HUMAN	secretory carrier membrane protein 1	172	Helical; (Potential).				post-Golgi vesicle-mediated transport|protein transport	integral to membrane|recycling endosome membrane|trans-Golgi network	protein binding				0		all_lung(232;0.000397)|Lung NSC(167;0.00105)|Ovarian(174;0.0105)|Prostate(461;0.214)		OV - Ovarian serous cystadenocarcinoma(54;1.9e-46)|Epithelial(54;9.4e-43)|all cancers(79;1.12e-37)		CGGATGCTTGGCTTGGTTTTG	0.358													104	132	---	---	---	---	PASS
SLCO4C1	353189	broad.mit.edu	37	5	101572570	101572570	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101572570C>G	uc003knm.2	-	13	2454	c.2167G>C	c.(2167-2169)GAA>CAA	p.E723Q		NM_180991	NP_851322	Q6ZQN7	SO4C1_HUMAN	solute carrier organic anion transporter family,	723	Cytoplasmic (Potential).				cell differentiation|multicellular organismal development|sodium-independent organic anion transport|spermatogenesis	basolateral plasma membrane|integral to membrane	sodium-independent organic anion transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|pancreas(1)	4		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		TTTCACCCTTCTTTTACTATT	0.368													9	102	---	---	---	---	PASS
PPIP5K2	23262	broad.mit.edu	37	5	102472516	102472516	+	Missense_Mutation	SNP	A	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102472516A>T	uc003kod.3	+	4	910	c.391A>T	c.(391-393)ATA>TTA	p.I131L	PPIP5K2_uc011cva.1_RNA|PPIP5K2_uc003koe.2_Missense_Mutation_p.I131L|PPIP5K2_uc010jbo.1_Missense_Mutation_p.I53L	NM_015216	NP_056031	O43314	VIP2_HUMAN	Histidine acid phosphatase domain containing 1	131					inositol metabolic process	cytosol	acid phosphatase activity|ATP binding|diphosphoinositol-pentakisphosphate kinase activity|inositol 1,3,4,5,6-pentakisphosphate kinase activity|inositol hexakisphosphate 5-kinase activity			ovary(1)|skin(1)	2						GCAGTATCTCATACAAGATAG	0.274													121	140	---	---	---	---	PASS
PCDHA3	56145	broad.mit.edu	37	5	140182467	140182467	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140182467C>T	uc003lhf.2	+	1	1685	c.1685C>T	c.(1684-1686)GCG>GTG	p.A562V	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA2_uc011czy.1_Intron|PCDHA3_uc011czz.1_Missense_Mutation_p.A562V	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3 isoform 1 precursor	562	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(6)|skin(2)	8			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AACGACAACGCGCCGGCACTG	0.692													53	59	---	---	---	---	PASS
PCDHA5	56143	broad.mit.edu	37	5	140202001	140202001	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140202001C>G	uc003lhl.2	+	1	641	c.641C>G	c.(640-642)ACT>AGT	p.T214S	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Missense_Mutation_p.T214S|PCDHA5_uc003lhj.1_Missense_Mutation_p.T214S	NM_018908	NP_061731	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5 isoform 1 precursor	214	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(1)|breast(1)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGATTGCAACTGATGGAGGA	0.348													54	73	---	---	---	---	PASS
PCDHA7	56141	broad.mit.edu	37	5	140215871	140215871	+	Missense_Mutation	SNP	C	G	G	rs146878440		TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140215871C>G	uc003lhq.2	+	1	1903	c.1903C>G	c.(1903-1905)CGA>GGA	p.R635G	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc011dac.1_Missense_Mutation_p.R635G	NM_018910	NP_061733	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7 isoform 1 precursor	635	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(2)|skin(2)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGCACGACACGAGCCCTAGA	0.647													53	58	---	---	---	---	PASS
PCDHA10	56139	broad.mit.edu	37	5	140235693	140235693	+	Silent	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140235693C>A	uc003lhx.2	+	1	60	c.60C>A	c.(58-60)CTC>CTA	p.L20L	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Silent_p.L20L|PCDHA10_uc011dad.1_Silent_p.L20L	NM_018901	NP_061724	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10 isoform 1 precursor	20					homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			ovary(2)|skin(2)|breast(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCTTCTCCTCGCAGCCTGGG	0.602													8	94	---	---	---	---	PASS
PCDHB9	56127	broad.mit.edu	37	5	140569145	140569145	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140569145G>C	uc003liw.1	+	3	2254	c.2254G>C	c.(2254-2256)GAG>CAG	p.E752Q	PCDHB10_uc003lix.2_5'Flank	NM_019119	NP_061992	Q9Y5E1	PCDB9_HUMAN	protocadherin beta 9 precursor	752	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTACCAGTACGAGGTGTGTCT	0.622													12	197	---	---	---	---	PASS
PCDHGA7	56108	broad.mit.edu	37	5	140762918	140762918	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140762918G>A	uc003lka.1	+	1	452	c.452G>A	c.(451-453)CGG>CAG	p.R151Q	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003ljz.1_Missense_Mutation_p.R151Q	NM_018920	NP_061743	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7 isoform 1	151	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTGGGGTTCGGTTTCCGTTA	0.468													10	59	---	---	---	---	PASS
PCDHGC5	56097	broad.mit.edu	37	5	140869078	140869078	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140869078G>A	uc003lla.1	+	1	271	c.271G>A	c.(271-273)GAC>AAC	p.D91N	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc003lkt.1_Intron|PCDHGC3_uc003lkv.1_Intron|PCDHGC3_uc003lkw.1_Intron|PCDHGC4_uc003lky.1_Intron|PCDHGC5_uc011dbc.1_Missense_Mutation_p.D91N	NM_018929	NP_061752	Q9Y5F6	PCDGM_HUMAN	protocadherin gamma subfamily C, 5 isoform 1	91	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCAAAAGATTGACCGAGAAAG	0.552													45	40	---	---	---	---	PASS
NR3C1	2908	broad.mit.edu	37	5	142779948	142779948	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142779948C>T	uc003lmz.2	-	2	949	c.457G>A	c.(457-459)GAG>AAG	p.E153K	NR3C1_uc003lmy.2_Missense_Mutation_p.E153K|NR3C1_uc003lna.2_Missense_Mutation_p.E153K|NR3C1_uc003lnb.2_Missense_Mutation_p.E153K|NR3C1_uc011dbk.1_Intron|NR3C1_uc003lnc.2_Missense_Mutation_p.E153K|NR3C1_uc003lnd.2_Missense_Mutation_p.E153K|NR3C1_uc003lne.2_Missense_Mutation_p.E153K|NR3C1_uc003lnf.2_Missense_Mutation_p.E153K|NR3C1_uc003lng.2_Missense_Mutation_p.E153K|NR3C1_uc003lnh.2_Missense_Mutation_p.E153K|NR3C1_uc003lni.2_Missense_Mutation_p.E153K	NM_000176	NP_000167	P04150	GCR_HUMAN	glucocorticoid receptor isoform alpha	153	Modulating.				chromatin modification|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to protein stimulus|transcription from RNA polymerase II promoter	mitochondrial matrix|nucleoplasm	glucocorticoid receptor activity|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			ovary(2)	2		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Amcinonide(DB00288)|Betamethasone(DB00443)|Budesonide(DB01222)|Dexamethasone(DB01234)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluticasone Propionate(DB00588)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol Etabonate(DB00873)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Prednisone(DB00635)	AACTCCTTCTCTGTGGGGGCA	0.473													53	60	---	---	---	---	PASS
PDGFRB	5159	broad.mit.edu	37	5	149502770	149502770	+	Intron	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149502770G>A	uc003lro.2	-						PDGFRB_uc010jhd.2_Intron	NM_002609	NP_002600	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor beta						aorta morphogenesis|cardiac myofibril assembly|hemopoiesis|metanephric glomerular capillary formation|metanephric glomerular mesangial cell proliferation involved in metanephros development|peptidyl-tyrosine phosphorylation|positive regulation of calcium ion import|positive regulation of chemotaxis|positive regulation of DNA biosynthetic process|positive regulation of ERK1 and ERK2 cascade|positive regulation of MAP kinase activity|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway|positive regulation of mitosis|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of reactive oxygen species metabolic process|positive regulation of smooth muscle cell migration|positive regulation of smooth muscle cell proliferation|protein autophosphorylation|regulation of actin cytoskeleton organization|retina vasculature development in camera-type eye|smooth muscle cell chemotaxis	apical plasma membrane|cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet activating factor receptor activity|platelet-derived growth factor beta-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|vascular endothelial growth factor receptor activity			central_nervous_system(4)|lung(4)|breast(3)|stomach(2)|prostate(2)|large_intestine(1)|ovary(1)	17		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Sorafenib(DB00398)|Sunitinib(DB01268)	GGGTCCTGCAGAGGGACAGGC	0.547			T	ETV6|TRIP11|HIP1|RAB5EP|H4|NIN|HCMOGT-1|PDE4DIP	MPD|AML|CMML|CML								4	53	---	---	---	---	PASS
TCOF1	6949	broad.mit.edu	37	5	149751721	149751721	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149751721G>T	uc003lry.2	+	7	900	c.792G>T	c.(790-792)AAG>AAT	p.K264N	TCOF1_uc003lrw.2_Missense_Mutation_p.K264N|TCOF1_uc011dch.1_Missense_Mutation_p.K264N|TCOF1_uc003lrz.2_Missense_Mutation_p.K264N|TCOF1_uc003lrx.2_Intron|TCOF1_uc003lsa.2_Intron	NM_001135243	NP_001128715	Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	264					skeletal system development	nucleolus	protein binding|transporter activity			ovary(2)|large_intestine(1)	3		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGAGGGCCAAGAAGCCAGAAG	0.642													8	35	---	---	---	---	PASS
TCOF1	6949	broad.mit.edu	37	5	149751728	149751728	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149751728G>A	uc003lry.2	+	7	907	c.799G>A	c.(799-801)GAA>AAA	p.E267K	TCOF1_uc003lrw.2_Missense_Mutation_p.E267K|TCOF1_uc011dch.1_Missense_Mutation_p.E267K|TCOF1_uc003lrz.2_Missense_Mutation_p.E267K|TCOF1_uc003lrx.2_Intron|TCOF1_uc003lsa.2_Intron	NM_001135243	NP_001128715	Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	267					skeletal system development	nucleolus	protein binding|transporter activity			ovary(2)|large_intestine(1)	3		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CAAGAAGCCAGAAGAGGAGTC	0.647													5	32	---	---	---	---	PASS
FAT2	2196	broad.mit.edu	37	5	150945454	150945454	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150945454G>A	uc003lue.3	-	1	3052	c.3039C>T	c.(3037-3039)CTC>CTT	p.L1013L	GM2A_uc011dcs.1_Intron|FAT2_uc010jhx.1_Silent_p.L1013L	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	1013	Extracellular (Potential).|Cadherin 8.				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCACATGGCAGAGAGTCCTGC	0.602													5	35	---	---	---	---	PASS
GEMIN5	25929	broad.mit.edu	37	5	154317677	154317677	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154317677C>T	uc003lvx.3	-	1	100	c.17G>A	c.(16-18)CGG>CAG	p.R6Q	GEMIN5_uc011ddk.1_Missense_Mutation_p.R6Q|MRPL22_uc003lvy.3_5'Flank|MRPL22_uc003lvz.3_5'Flank	NM_015465	NP_056280	Q8TEQ6	GEMI5_HUMAN	gemin 5	6					ncRNA metabolic process|protein complex assembly|spliceosomal snRNP assembly	Cajal body|cytosol|spliceosomal complex	protein binding|snRNA binding			skin(2)|ovary(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CGGCAGCGTCCGCGGCTCCTG	0.687													5	8	---	---	---	---	PASS
SOX30	11063	broad.mit.edu	37	5	157075874	157075874	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157075874C>G	uc003lxb.1	-	2	1340	c.998G>C	c.(997-999)AGA>ACA	p.R333T	SOX30_uc003lxc.1_Missense_Mutation_p.R333T|SOX30_uc011dds.1_Missense_Mutation_p.R28T	NM_178424	NP_848511	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30 isoform a	333					regulation of transcription from RNA polymerase II promoter|regulation of transcription, DNA-dependent|response to corticosteroid stimulus|transcription, DNA-dependent	nucleus|nucleus	sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity			ovary(1)|central_nervous_system(1)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ATGACCATTTCTGTCCTTACT	0.433													8	108	---	---	---	---	PASS
GABRA1	2554	broad.mit.edu	37	5	161300148	161300148	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161300148G>T	uc010jiw.2	+	6	749	c.281G>T	c.(280-282)CGT>CTT	p.R94L	GABRA1_uc010jix.2_Missense_Mutation_p.R94L|GABRA1_uc010jiy.2_Missense_Mutation_p.R94L|GABRA1_uc003lyx.3_Missense_Mutation_p.R94L|GABRA1_uc010jiz.2_Missense_Mutation_p.R94L|GABRA1_uc010jja.2_Missense_Mutation_p.R94L|GABRA1_uc010jjb.2_Missense_Mutation_p.R94L	NM_000806	NP_000797	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha	94	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity	p.R94H(1)		ovary(2)|pancreas(1)	3	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.228)	Alprazolam(DB00404)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Halazepam(DB00801)|Halothane(DB01159)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Metharbital(DB00463)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Picrotoxin(DB00466)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Zaleplon(DB00962)|Zolpidem(DB00425)	GTATTTTTCCGTCAAAGCTGG	0.373													62	75	---	---	---	---	PASS
KIAA0319	9856	broad.mit.edu	37	6	24596840	24596840	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24596840G>A	uc011djo.1	-	3	299	c.62C>T	c.(61-63)GCC>GTC	p.A21V	KIAA0319_uc011djp.1_5'UTR|KIAA0319_uc003neh.1_Missense_Mutation_p.A21V|KIAA0319_uc011djq.1_Missense_Mutation_p.A12V|KIAA0319_uc011djr.1_Missense_Mutation_p.A21V	NM_014809	NP_055624	Q5VV43	K0319_HUMAN	KIAA0319 precursor	21	MANSC.|Extracellular (Potential).				negative regulation of dendrite development|neuron migration	early endosome membrane|integral to membrane|plasma membrane	protein binding			ovary(1)|skin(1)	2						CTGCTTACGGGCACAACCTTT	0.483													4	111	---	---	---	---	PASS
FLOT1	10211	broad.mit.edu	37	6	30697820	30697820	+	Silent	SNP	G	C	C	rs1802471		TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30697820G>C	uc003nrm.2	-	12	1397	c.1233C>G	c.(1231-1233)CTC>CTG	p.L411L	FLOT1_uc011dmr.1_Silent_p.L363L	NM_005803	NP_005794	O75955	FLOT1_HUMAN	flotillin 1	411						centriolar satellite|endosome|integral to membrane|melanosome|membrane fraction					0						TCACGCCTGTGAGTCTTTCCA	0.547													6	96	---	---	---	---	PASS
BAT1	7919	broad.mit.edu	37	6	31498931	31498931	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31498931G>T	uc003ntt.2	-	9	1652	c.1021C>A	c.(1021-1023)CTT>ATT	p.L341I	BAT1_uc003ntq.2_Missense_Mutation_p.L74I|BAT1_uc003ntr.2_Missense_Mutation_p.L148I|BAT1_uc003nts.2_Missense_Mutation_p.L341I|BAT1_uc011dnn.1_Missense_Mutation_p.L263I|BAT1_uc003ntu.2_Missense_Mutation_p.L341I|BAT1_uc003ntv.2_Missense_Mutation_p.L341I	NM_004640	NP_004631	Q13838	DX39B_HUMAN	HLA-B associated transcript 1	341	Helicase C-terminal.				intronless viral mRNA export from host nucleus|RNA secondary structure unwinding|spliceosome assembly	nuclear speck|spliceosomal complex|transcription export complex	ATP binding|ATP-dependent protein binding|ATP-dependent RNA helicase activity|identical protein binding|U4 snRNA binding|U6 snRNA binding				0						GTAGCCACAAGAATTCGTCGT	0.423													5	105	---	---	---	---	PASS
VARS	7407	broad.mit.edu	37	6	31752382	31752382	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31752382G>C	uc003nxe.2	-	11	1880	c.1457C>G	c.(1456-1458)TCT>TGT	p.S486C	VARS_uc011doi.1_RNA	NM_006295	NP_006286	P26640	SYVC_HUMAN	valyl-tRNA synthetase	486					translational elongation|valyl-tRNA aminoacylation	cytosol	ATP binding|protein binding|valine-tRNA ligase activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3					L-Valine(DB00161)	CTCAATGTCAGAGATGGCGGA	0.592													10	91	---	---	---	---	PASS
SCUBE3	222663	broad.mit.edu	37	6	35211449	35211449	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35211449G>C	uc003okf.1	+	16	1994	c.1988G>C	c.(1987-1989)AGA>ACA	p.R663T	SCUBE3_uc003okg.1_Missense_Mutation_p.R662T|SCUBE3_uc003okh.1_Missense_Mutation_p.R550T	NM_152753	NP_689966	Q8IX30	SCUB3_HUMAN	signal peptide, CUB domain, EGF-like 3	663					protein heterooligomerization|protein homooligomerization	cell surface|extracellular region	calcium ion binding|protein binding			skin(1)	1						TTCCAGGAGAGAGAAGGGCAG	0.647													5	76	---	---	---	---	PASS
CPNE5	57699	broad.mit.edu	37	6	36714258	36714258	+	Missense_Mutation	SNP	T	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36714258T>A	uc003omr.1	-	16	1182	c.1115A>T	c.(1114-1116)CAC>CTC	p.H372L	CPNE5_uc003omp.1_Missense_Mutation_p.H80L|CPNE5_uc010jwn.1_Missense_Mutation_p.H22L|CPNE5_uc003omq.1_Missense_Mutation_p.H22L	NM_020939	NP_065990	Q9HCH3	CPNE5_HUMAN	copine V	372	VWFA.									skin(1)	1						ACTGTCGTAGTGCTGGATGAT	0.627													67	39	---	---	---	---	PASS
BTBD9	114781	broad.mit.edu	37	6	38560460	38560460	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38560460G>C	uc003ooa.3	-	5	1282	c.706C>G	c.(706-708)CTG>GTG	p.L236V	BTBD9_uc003ony.3_Missense_Mutation_p.L168V|BTBD9_uc010jwv.2_Missense_Mutation_p.L168V|BTBD9_uc010jww.2_RNA|BTBD9_uc010jwx.2_Missense_Mutation_p.L236V	NM_052893	NP_443125	Q96Q07	BTBD9_HUMAN	BTB (POZ) domain containing 9 isoform a	236	BACK.				cell adhesion						0						ACAACATTCAGAAGCTCTGTG	0.468													45	64	---	---	---	---	PASS
DNAH8	1769	broad.mit.edu	37	6	38899745	38899745	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38899745G>C	uc003ooe.1	+	74	11382	c.10782G>C	c.(10780-10782)AGG>AGC	p.R3594S	DNAH8_uc003oog.1_Missense_Mutation_p.R43S|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						AGTTACTAAGGAGAGTCATTC	0.348													24	88	---	---	---	---	PASS
KCNK17	89822	broad.mit.edu	37	6	39271838	39271838	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39271838G>A	uc003ooo.2	-	4	723	c.583C>T	c.(583-585)CTG>TTG	p.L195L	KCNK17_uc003oop.2_Silent_p.L195L	NM_031460	NP_113648	Q96T54	KCNKH_HUMAN	potassium channel, subfamily K, member 17	195	Helical; (Potential).					integral to membrane	potassium channel activity|voltage-gated ion channel activity			skin(2)	2						AGCGGTGGCAGCAGCAGGAAG	0.647													33	64	---	---	---	---	PASS
TTBK1	84630	broad.mit.edu	37	6	43222319	43222319	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43222319A>G	uc003ouq.1	+	6	785	c.506A>G	c.(505-507)TAC>TGC	p.Y169C		NM_032538	NP_115927	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	169	Protein kinase.					cell junction|cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	9			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			CCCTCCACCTACAGGAAGTGC	0.662													30	69	---	---	---	---	PASS
GPR116	221395	broad.mit.edu	37	6	46827066	46827066	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46827066G>C	uc003oyo.3	-	17	2863	c.2574C>G	c.(2572-2574)ATC>ATG	p.I858M	GPR116_uc011dwj.1_Missense_Mutation_p.I413M|GPR116_uc011dwk.1_Missense_Mutation_p.I287M|GPR116_uc003oyp.3_Missense_Mutation_p.I716M|GPR116_uc003oyq.3_Missense_Mutation_p.I858M|GPR116_uc010jzi.1_Missense_Mutation_p.I530M	NM_001098518	NP_001091988	Q8IZF2	GP116_HUMAN	G-protein coupled receptor 116 precursor	858	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)|skin(1)	2			Lung(136;0.192)			GGCTGGACTTGATTACCATGC	0.448													3	83	---	---	---	---	PASS
GPR110	266977	broad.mit.edu	37	6	46979767	46979767	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46979767G>T	uc003oyt.2	-	10	1291	c.1092C>A	c.(1090-1092)TTC>TTA	p.F364L	GPR110_uc011dwl.1_Missense_Mutation_p.F52L	NM_153840	NP_722582	Q5T601	GP110_HUMAN	G-protein coupled receptor 110 isoform 1	364	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(2)|pancreas(1)	3						TGGACACCCTGAAATGGCTGG	0.468													11	54	---	---	---	---	PASS
CRISP3	10321	broad.mit.edu	37	6	49698956	49698956	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49698956C>A	uc003ozs.2	-	7	545	c.530G>T	c.(529-531)TGG>TTG	p.W177L		NM_006061	NP_006052	P54108	CRIS3_HUMAN	cysteine-rich secretory protein 3 precursor	177					innate immune response	proteinaceous extracellular matrix|specific granule				skin(2)	2	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)			TCTATTAGCCCAATTACCACT	0.343													40	71	---	---	---	---	PASS
TFAP2B	7021	broad.mit.edu	37	6	50791151	50791151	+	Nonsense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50791151C>A	uc003pag.2	+	2	279	c.113C>A	c.(112-114)TCG>TAG	p.S38*		NM_003221	NP_003212	Q92481	AP2B_HUMAN	transcription factor AP-2 beta	38					nervous system development|positive regulation of transcription from RNA polymerase II promoter		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity				0	Lung NSC(77;0.156)					AGCCACAGCTCGCGGCTCTCC	0.498													5	14	---	---	---	---	PASS
CD109	135228	broad.mit.edu	37	6	74533185	74533185	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74533185G>A	uc003php.2	+	33	4591	c.4166G>A	c.(4165-4167)AGA>AAA	p.R1389K	CD109_uc010kaz.2_Intron|CD109_uc003phq.2_Missense_Mutation_p.R1372K|CD109_uc010kba.2_Missense_Mutation_p.R1312K	NM_133493	NP_598000	Q6YHK3	CD109_HUMAN	CD109 antigen isoform 1 precursor	1389						anchored to membrane|extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			large_intestine(2)|ovary(2)	4						TGAACAGGGAGACAGGCTGTG	0.468													22	30	---	---	---	---	PASS
SPACA1	81833	broad.mit.edu	37	6	88769180	88769180	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88769180A>G	uc003pmn.2	+	5	601	c.484A>G	c.(484-486)ATA>GTA	p.I162V		NM_030960	NP_112222	Q9HBV2	SACA1_HUMAN	sperm acrosome associated 1 precursor	162	Extracellular (Potential).					integral to membrane					0		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.11)		GCAATCCATTATACTTGTAAA	0.333													11	22	---	---	---	---	PASS
TRDN	10345	broad.mit.edu	37	6	123687319	123687319	+	Nonsense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123687319G>A	uc003pzj.1	-	20	1304	c.1282C>T	c.(1282-1284)CGA>TGA	p.R428*	TRDN_uc003pzk.1_Nonsense_Mutation_p.R429*|TRDN_uc003pzl.1_Nonsense_Mutation_p.R429*|TRDN_uc010kem.1_Translation_Start_Site	NM_006073	NP_006064	Q13061	TRDN_HUMAN	triadin	428	Lumenal.				muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)		TCTTTGGCTCGTTCAGTTTCT	0.303													16	25	---	---	---	---	PASS
NKAIN2	154215	broad.mit.edu	37	6	125139577	125139577	+	Nonsense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125139577C>T	uc003pzo.2	+	6	857	c.580C>T	c.(580-582)CAG>TAG	p.Q194*	NKAIN2_uc003pzp.2_Nonsense_Mutation_p.Q193*|NKAIN2_uc010keq.2_Nonsense_Mutation_p.Q127*|NKAIN2_uc010ker.2_Nonsense_Mutation_p.Q104*	NM_001040214	NP_001035304	Q5VXU1	NKAI2_HUMAN	T-cell lymphoma breakpoint-associated target 1	194						integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)		TCAAGGGCCTCAGAAGACATC	0.363													7	69	---	---	---	---	PASS
L3MBTL3	84456	broad.mit.edu	37	6	130370465	130370465	+	Silent	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130370465A>G	uc003qbt.2	+	4	311	c.141A>G	c.(139-141)ACA>ACG	p.T47T	L3MBTL3_uc003qbu.2_Silent_p.T47T	NM_032438	NP_115814	Q96JM7	LMBL3_HUMAN	l(3)mbt-like 3 isoform a	47					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)		AAGTTATTACAGATGAGAATG	0.378													21	40	---	---	---	---	PASS
ARG1	383	broad.mit.edu	37	6	131902484	131902484	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131902484C>T	uc003qcp.1	+	4	489	c.431C>T	c.(430-432)CCT>CTT	p.P144L	ARG1_uc003qco.1_Missense_Mutation_p.P144L|ARG1_uc010kfm.1_Missense_Mutation_p.P152L|MED23_uc003qcq.2_Intron	NM_000045	NP_000036	P05089	ARGI1_HUMAN	arginase 1	144					arginine catabolic process|urea cycle	cytosol	arginase activity			ovary(1)	1	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0106)|OV - Ovarian serous cystadenocarcinoma(155;0.0713)	L-Ornithine(DB00129)	CATGGACAACCTGTATCTTTC	0.453													15	27	---	---	---	---	PASS
TAAR6	319100	broad.mit.edu	37	6	132892144	132892144	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132892144G>A	uc011eck.1	+	1	684	c.684G>A	c.(682-684)GCG>GCA	p.A228A		NM_175067	NP_778237	Q96RI8	TAAR6_HUMAN	trace amine associated receptor 6	228	Cytoplasmic (Potential).					plasma membrane	G-protein coupled receptor activity			ovary(2)|skin(1)	3	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.006)|GBM - Glioblastoma multiforme(226;0.00792)		GACGACAGGCGAAAAAGATAG	0.403													18	29	---	---	---	---	PASS
PLEKHG1	57480	broad.mit.edu	37	6	151121912	151121912	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151121912G>A	uc003qny.1	+	7	999	c.687G>A	c.(685-687)AGG>AGA	p.R229R	PLEKHG1_uc011eel.1_Silent_p.R269R|PLEKHG1_uc011eem.1_Silent_p.R288R|PLEKHG1_uc003qnz.2_Silent_p.R229R	NM_001029884	NP_001025055	Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G	229	DH.				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		AATTCTTCAGGGAGCGTCAGG	0.448													32	44	---	---	---	---	PASS
UNC93A	54346	broad.mit.edu	37	6	167711429	167711429	+	Intron	SNP	A	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167711429A>T	uc003qvq.2	+						UNC93A_uc003qvr.2_Intron	NM_018974	NP_061847	Q86WB7	UN93A_HUMAN	unc-93 homolog A isoform 1							integral to membrane|plasma membrane					0		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		CTCTGACTTCATAGAGACCCT	0.537													25	51	---	---	---	---	PASS
INTS1	26173	broad.mit.edu	37	7	1512808	1512808	+	Silent	SNP	G	A	A	rs138397380	by1000genomes	TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1512808G>A	uc003skn.2	-	43	6071	c.5970C>T	c.(5968-5970)TTC>TTT	p.F1990F	INTS1_uc003skm.1_Silent_p.F127F	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1	1990					snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		CACTGTTGTCGAAGGACAGGT	0.627													8	49	---	---	---	---	PASS
EIF2AK1	27102	broad.mit.edu	37	7	6077058	6077058	+	Silent	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6077058C>G	uc003spp.2	-	11	1475	c.1329G>C	c.(1327-1329)CTG>CTC	p.L443L	EIF2AK1_uc003spq.2_Silent_p.L442L|EIF2AK1_uc011jwm.1_Silent_p.L319L	NM_014413	NP_055228	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha	443	Protein kinase.				negative regulation of hemoglobin biosynthetic process|negative regulation of translational initiation by iron|protein autophosphorylation|response to external stimulus|response to stress	cytoplasm	ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|heme binding|protein homodimerization activity			upper_aerodigestive_tract(1)|stomach(1)|lung(1)|central_nervous_system(1)	4		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		CACTTACCTTCAGATCTCGGT	0.383													10	122	---	---	---	---	PASS
TMEM195	392636	broad.mit.edu	37	7	15405803	15405803	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15405803G>A	uc003stb.1	-	11	1289	c.1119C>T	c.(1117-1119)ATC>ATT	p.I373I		NM_001004320	NP_001004320	Q6ZNB7	ALKMO_HUMAN	transmembrane protein 195	373	Helical; (Potential).				ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0						TCAAGGTCAGGATAATGAAGC	0.388													3	21	---	---	---	---	PASS
DNAH11	8701	broad.mit.edu	37	7	21760441	21760441	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21760441C>G	uc003svc.2	+	45	7285	c.7254C>G	c.(7252-7254)ATC>ATG	p.I2418M		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2418					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						TTGCTTGTATCTGGGCTTTTG	0.423									Kartagener_syndrome				4	65	---	---	---	---	PASS
POU6F2	11281	broad.mit.edu	37	7	39500320	39500320	+	Intron	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39500320G>T	uc003thb.1	+							NM_007252	NP_009183	P78424	PO6F2_HUMAN	POU class 6 homeobox 2 isoform 1						central nervous system development|ganglion mother cell fate determination|transcription from RNA polymerase II promoter|visual perception		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1						TGCAGGTAACGCGCGCCTGCA	0.637													6	14	---	---	---	---	PASS
NPC1L1	29881	broad.mit.edu	37	7	44555412	44555412	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44555412G>A	uc003tlb.2	-	19	3923	c.3867C>T	c.(3865-3867)CTC>CTT	p.L1289L	NPC1L1_uc003tlc.2_Silent_p.L1262L|NPC1L1_uc011kbw.1_Silent_p.L1216L|NPC1L1_uc003tla.2_Intron	NM_013389	NP_037521	Q9UHC9	NPCL1_HUMAN	Niemann-Pick C1-like protein 1 isoform 1	1289	Cytoplasmic (Potential).				cholesterol biosynthetic process|intestinal cholesterol absorption|lipoprotein metabolic process	apical plasma membrane|cytoplasmic vesicle membrane|integral to membrane	hedgehog receptor activity|protein binding			ovary(3)|central_nervous_system(1)|skin(1)	5					Ezetimibe(DB00973)	CCACGTAGCTGAGGATGACGG	0.547													6	81	---	---	---	---	PASS
ADCY1	107	broad.mit.edu	37	7	45725805	45725805	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45725805C>T	uc003tne.3	+	13	2336	c.2318C>T	c.(2317-2319)ACC>ATC	p.T773I		NM_021116	NP_066939	Q08828	ADCY1_HUMAN	adenylate cyclase 1	773	Helical; (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|calmodulin binding|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6					Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	AGCGGATACACCAGGACTGGG	0.522													34	97	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48319431	48319431	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48319431C>G	uc003toq.2	+	18	8665	c.8640C>G	c.(8638-8640)TTC>TTG	p.F2880L	ABCA13_uc010kys.1_5'Flank	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	2880					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						CTTATAGTTTCAAACCATTTT	0.338													52	74	---	---	---	---	PASS
PHTF2	57157	broad.mit.edu	37	7	77578985	77578985	+	Intron	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77578985A>G	uc003ugs.3	+						PHTF2_uc003ugq.3_Intron|PHTF2_uc010ldv.2_Intron|PHTF2_uc003ugt.3_Intron|PHTF2_uc003ugu.3_Intron	NM_001127357	NP_001120829	Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum|nucleus	DNA binding			ovary(1)	1						TACCTTTTTCATACTTTTAGC	0.299													6	15	---	---	---	---	PASS
KIAA1324L	222223	broad.mit.edu	37	7	86509809	86509809	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86509809G>A	uc011kha.1	-	22	3253	c.3068C>T	c.(3067-3069)ACC>ATC	p.T1023I	KIAA1324L_uc003uif.1_Missense_Mutation_p.T783I|KIAA1324L_uc011kgz.1_Missense_Mutation_p.T909I|KIAA1324L_uc003uie.2_Missense_Mutation_p.T856I	NM_001142749	NP_001136221	A8MWY0	K132L_HUMAN	hypothetical protein LOC222223 isoform 1	1023	Cytoplasmic (Potential).					integral to membrane				ovary(6)|skin(1)	7	Esophageal squamous(14;0.0058)					GGATCTTGAGGTTTTCAGTTG	0.338													27	66	---	---	---	---	PASS
AKAP9	10142	broad.mit.edu	37	7	91699518	91699518	+	Nonsense_Mutation	SNP	A	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91699518A>T	uc003ulg.2	+	27	6730	c.6505A>T	c.(6505-6507)AAG>TAG	p.K2169*	AKAP9_uc003ulf.2_Intron|AKAP9_uc003uli.2_Nonsense_Mutation_p.K1792*|AKAP9_uc003ulj.2_Intron	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2	2181	Potential.|Glu-rich.				G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TACTTTTCAAAAGGTGTGGCA	0.328			T	BRAF	papillary thyroid								27	109	---	---	---	---	PASS
ASB4	51666	broad.mit.edu	37	7	95115428	95115428	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95115428G>C	uc011kij.1	+	1	145	c.145G>C	c.(145-147)GAA>CAA	p.E49Q	ASB4_uc003unx.2_Missense_Mutation_p.E49Q	NM_016116	NP_057200	Q9Y574	ASB4_HUMAN	ankyrin repeat and SOCS box-containing protein 4	49					intracellular signal transduction					central_nervous_system(1)	1	all_cancers(62;2.27e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.218)|all_lung(186;0.246)		STAD - Stomach adenocarcinoma(171;0.0151)			CACTGTTTTTGAAGTCGAAGA	0.328													5	134	---	---	---	---	PASS
SLC25A13	10165	broad.mit.edu	37	7	95751219	95751219	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95751219C>G	uc003uof.3	-	16	1873	c.1682G>C	c.(1681-1683)GGA>GCA	p.G561A	SLC25A13_uc003uog.3_Missense_Mutation_p.G562A|SLC25A13_uc011kik.1_Missense_Mutation_p.G453A	NM_014251	NP_055066	Q9UJS0	CMC2_HUMAN	solute carrier family 25, member 13 isoform 2	561	Solcar 3.				ATP biosynthetic process|gluconeogenesis|malate-aspartate shuttle|response to calcium ion	integral to plasma membrane|mitochondrial inner membrane	calcium ion binding|L-aspartate transmembrane transporter activity|L-glutamate transmembrane transporter activity			central_nervous_system(3)|skin(1)	4	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)	GTCTATCACTCCGCTGTAAGT	0.483													31	104	---	---	---	---	PASS
ZKSCAN1	7586	broad.mit.edu	37	7	99631580	99631580	+	Silent	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99631580G>T	uc003usk.1	+	6	1671	c.1452G>T	c.(1450-1452)ACG>ACT	p.T484T	ZKSCAN1_uc003usl.1_Silent_p.T448T|ZKSCAN1_uc003usm.1_Silent_p.T271T	NM_003439	NP_003430	P17029	ZKSC1_HUMAN	zinc finger protein 36	484					viral reproduction	mitochondrion|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			GAATTCACACGGGGGAGAAAC	0.473													32	99	---	---	---	---	PASS
ZCWPW1	55063	broad.mit.edu	37	7	99998905	99998905	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99998905G>A	uc003uut.2	-	18	1927	c.1679C>T	c.(1678-1680)TCA>TTA	p.S560L	ZCWPW1_uc011kjq.1_Missense_Mutation_p.S440L|ZCWPW1_uc003uur.2_Nonsense_Mutation_p.Q369*|ZCWPW1_uc003uus.2_Missense_Mutation_p.S389L|ZCWPW1_uc011kjr.1_Nonsense_Mutation_p.Q489*|ZCWPW1_uc011kjp.1_RNA	NM_017984	NP_060454	Q9H0M4	ZCPW1_HUMAN	zinc finger, CW type with PWWP domain 1	560							zinc ion binding				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TTTTCCCTCTGAAAAGCTGGC	0.512													14	100	---	---	---	---	PASS
CADPS2	93664	broad.mit.edu	37	7	122027211	122027211	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122027211C>G	uc010lkp.2	-	23	3344	c.3181G>C	c.(3181-3183)GAA>CAA	p.E1061Q	CADPS2_uc011knx.1_Missense_Mutation_p.E436Q|CADPS2_uc003vkg.3_Missense_Mutation_p.E715Q|CADPS2_uc010lkq.2_Missense_Mutation_p.E1015Q	NM_017954	NP_060424	Q86UW7	CAPS2_HUMAN	Ca2+-dependent activator protein for secretion 2	1061	Interaction with DRD2.				exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2						AGCTTGAGTTCAAATGCAGTT	0.363													3	17	---	---	---	---	PASS
CADPS2	93664	broad.mit.edu	37	7	122056162	122056162	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122056162C>G	uc010lkp.2	-	17	2696	c.2533G>C	c.(2533-2535)GAG>CAG	p.E845Q	CADPS2_uc011knx.1_Missense_Mutation_p.E223Q|CADPS2_uc003vkg.3_Missense_Mutation_p.E542Q|CADPS2_uc010lkq.2_Missense_Mutation_p.E842Q	NM_017954	NP_060424	Q86UW7	CAPS2_HUMAN	Ca2+-dependent activator protein for secretion 2	845	Interaction with DRD2.				exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2						ATGCAGAGCTCTGCCAGATGA	0.388													4	6	---	---	---	---	PASS
FAM180A	389558	broad.mit.edu	37	7	135418826	135418826	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135418826G>T	uc003vtd.2	-	3	685	c.419C>A	c.(418-420)TCC>TAC	p.S140Y	FAM180A_uc010lmt.2_RNA|FAM180A_uc010lmu.2_Missense_Mutation_p.S140Y	NM_205855	NP_995327	Q6UWF9	F180A_HUMAN	hypothetical protein LOC389558 precursor	140						extracellular region				ovary(2)	2						ATGGCCGTGGGACAGGGCTGT	0.617													34	65	---	---	---	---	PASS
OR9A2	135924	broad.mit.edu	37	7	142723506	142723506	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142723506G>A	uc003wcc.1	-	1	714	c.714C>T	c.(712-714)GCC>GCT	p.A238A		NM_001001658	NP_001001658	Q8NGT5	OR9A2_HUMAN	olfactory receptor, family 9, subfamily A,	238	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	Melanoma(164;0.059)					TGAAGTGGGAGGCAAAAGTGG	0.488													24	89	---	---	---	---	PASS
ZYX	7791	broad.mit.edu	37	7	143085896	143085896	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143085896A>G	uc003wcw.2	+	8	1506	c.1351A>G	c.(1351-1353)ATC>GTC	p.I451V	ZYX_uc011ktd.1_Missense_Mutation_p.I294V|ZYX_uc003wcx.2_Missense_Mutation_p.I451V|ZYX_uc011kte.1_Missense_Mutation_p.I420V|ZYX_uc011ktf.1_Missense_Mutation_p.I294V	NM_001010972	NP_001010972	Q15942	ZYX_HUMAN	zyxin	451	LIM zinc-binding 2.				cell adhesion|cell-cell signaling|interspecies interaction between organisms|signal transduction	cell-cell adherens junction|cytoplasm|focal adhesion|integral to plasma membrane|nucleus|stress fiber	protein binding|zinc ion binding				0	Melanoma(164;0.205)					CGGGGAGCCCATCACTGACCG	0.662													14	67	---	---	---	---	PASS
TAS2R60	338398	broad.mit.edu	37	7	143141402	143141402	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143141402A>G	uc011ktg.1	+	1	857	c.857A>G	c.(856-858)TAT>TGT	p.Y286C	uc003wda.2_Intron	NM_177437	NP_803186	P59551	T2R60_HUMAN	taste receptor, type 2, member 60	286	Cytoplasmic (Potential).				sensory perception of bitter taste	integral to membrane	G-protein coupled receptor activity			skin(6)	6	Melanoma(164;0.172)					TCAGTGATTTATCTGTGTGCA	0.493													117	180	---	---	---	---	PASS
KRBA1	84626	broad.mit.edu	37	7	149425626	149425626	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149425626G>A	uc003wfz.2	+	12	1886	c.1487G>A	c.(1486-1488)GGA>GAA	p.G496E	KRBA1_uc010lpj.2_RNA|KRBA1_uc003wga.2_RNA|KRBA1_uc003wgb.2_Missense_Mutation_p.G164E	NM_032534	NP_115923	A5PL33	KRBA1_HUMAN	KRAB A domain containing 1	496										ovary(1)|central_nervous_system(1)	2	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			AGCCCACCAGGAAGCTCCCCA	0.582													71	176	---	---	---	---	PASS
ZNF775	285971	broad.mit.edu	37	7	150094078	150094078	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150094078G>A	uc003whf.1	+	3	634	c.509G>A	c.(508-510)CGG>CAG	p.R170Q		NM_173680	NP_775951	Q96BV0	ZN775_HUMAN	zinc finger protein 775	170	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.0173)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GAGTGCGCGCGGCGCTTCAGC	0.697													10	22	---	---	---	---	PASS
ZNF775	285971	broad.mit.edu	37	7	150094922	150094922	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150094922C>T	uc003whf.1	+	3	1478	c.1353C>T	c.(1351-1353)TGC>TGT	p.C451C	LOC728743_uc003whg.2_5'Flank	NM_173680	NP_775951	Q96BV0	ZN775_HUMAN	zinc finger protein 775	451	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.0173)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCAACGAGTGCGGCAAGAGCT	0.731													5	14	---	---	---	---	PASS
MLL3	58508	broad.mit.edu	37	7	152055756	152055756	+	Nonsense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152055756G>A	uc003wla.2	-	2	385	c.166C>T	c.(166-168)CGA>TGA	p.R56*		NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	56					intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		CCCCTACTTCGAGGTCTACAG	0.358			N		medulloblastoma								80	218	---	---	---	---	PASS
PCM1	5108	broad.mit.edu	37	8	17819547	17819547	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17819547C>T	uc003wyi.3	+	16	2749	c.2327C>T	c.(2326-2328)TCA>TTA	p.S776L	PCM1_uc011kyh.1_Missense_Mutation_p.S776L|PCM1_uc003wyj.3_Missense_Mutation_p.S777L	NM_006197	NP_006188	Q15154	PCM1_HUMAN	pericentriolar material 1	776					centrosome organization|cilium assembly|G2/M transition of mitotic cell cycle|interkinetic nuclear migration|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome	centriolar satellite|cytosol|nuclear membrane|pericentriolar material	identical protein binding		PCM1/JAK2(30)	haematopoietic_and_lymphoid_tissue(30)|breast(4)|ovary(2)	36				Colorectal(111;0.0789)		TTTTAGCTGTCAGCTGCTAGT	0.358			T	RET|JAK2	papillary thyroid|CML|MPD								9	17	---	---	---	---	PASS
ADAM18	8749	broad.mit.edu	37	8	39495998	39495998	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39495998C>A	uc003xni.2	+	10	842	c.842C>A	c.(841-843)CCT>CAT	p.P281H	ADAM18_uc010lww.2_RNA|ADAM18_uc010lwx.2_Missense_Mutation_p.P257H	NM_014237	NP_055052	Q9Y3Q7	ADA18_HUMAN	a disintegrin and metalloprotease domain 18	281	Peptidase M12B.|Extracellular (Potential).				cell differentiation|multicellular organismal development|proteolysis|spermatogenesis	integral to membrane|membrane fraction	metalloendopeptidase activity|zinc ion binding			central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)|kidney(1)|skin(1)	6		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			AGGAAACATCCTAAATATGTG	0.279													18	127	---	---	---	---	PASS
PRKDC	5591	broad.mit.edu	37	8	48815131	48815131	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48815131G>C	uc003xqi.2	-	27	3324	c.3267C>G	c.(3265-3267)TTC>TTG	p.F1089L	PRKDC_uc003xqj.2_Missense_Mutation_p.F1089L|PRKDC_uc011ldh.1_Missense_Mutation_p.F1089L	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic	1089					cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)				TTACAAACCTGAATTCCCTGT	0.413								NHEJ					13	53	---	---	---	---	PASS
ASPH	444	broad.mit.edu	37	8	62580840	62580840	+	Intron	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62580840G>C	uc003xuj.2	-						ASPH_uc011leg.1_Intron|ASPH_uc003xuo.2_Intron|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Intron|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Intron|ASPH_uc003xun.2_Intron|ASPH_uc011lek.1_Intron|ASPH_uc003xum.2_Intron|ASPH_uc011lel.1_Intron|ASPH_uc011lem.1_Intron	NM_004318	NP_004309	Q12797	ASPH_HUMAN	aspartate beta-hydroxylase isoform a						muscle contraction	integral to endoplasmic reticulum membrane	calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle			ovary(3)	3	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)	TCCTTCTGTTGACATTTACAA	0.294													9	137	---	---	---	---	PASS
TTPA	7274	broad.mit.edu	37	8	63973878	63973878	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63973878T>C	uc003xux.1	-	5	802	c.770A>G	c.(769-771)CAG>CGG	p.Q257R		NM_000370	NP_000361	P49638	TTPA_HUMAN	tocopherol (alpha) transfer protein	257					lipid metabolic process		transporter activity|vitamin E binding				0	Breast(64;0.0716)	all_cancers(86;0.145)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.123)			Vitamin E(DB00163)	TGTCCATTCCTGACAAATGTC	0.388													18	88	---	---	---	---	PASS
PREX2	80243	broad.mit.edu	37	8	69104751	69104751	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69104751G>A	uc003xxv.1	+	37	4622	c.4595G>A	c.(4594-4596)GGT>GAT	p.G1532D		NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a	1532					G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17						TGCAGCAGCGGTGTGCATCGG	0.493													8	52	---	---	---	---	PASS
C8orf34	116328	broad.mit.edu	37	8	69445374	69445374	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69445374G>A	uc010lyz.2	+	7	886	c.837G>A	c.(835-837)ATG>ATA	p.M279I	C8orf34_uc010lyy.1_Missense_Mutation_p.M279I|C8orf34_uc003xyb.2_Missense_Mutation_p.M254I	NM_052958	NP_443190	Q49A92	CH034_HUMAN	hypothetical protein LOC116328	279					signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			ATGATGCAATGGAATTGCTGG	0.333													31	123	---	---	---	---	PASS
LACTB2	51110	broad.mit.edu	37	8	71574130	71574130	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71574130C>G	uc011lfd.1	-	2	217	c.125G>C	c.(124-126)AGA>ACA	p.R42T	LACTB2_uc003xyp.2_Missense_Mutation_p.R42T	NM_016027	NP_057111	Q53H82	LACB2_HUMAN	lactamase, beta 2	42							hydrolase activity|metal ion binding			ovary(1)	1	Breast(64;0.0716)		Epithelial(68;0.00319)|all cancers(69;0.0175)|OV - Ovarian serous cystadenocarcinoma(28;0.0628)|BRCA - Breast invasive adenocarcinoma(89;0.166)			AATGAGGATTCTCCTGAAAAT	0.353													28	107	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77617479	77617479	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77617479G>A	uc003yav.2	+	2	1543	c.1156G>A	c.(1156-1158)GCG>ACG	p.A386T	ZFHX4_uc003yat.1_Missense_Mutation_p.A386T|ZFHX4_uc003yau.1_Missense_Mutation_p.A386T|ZFHX4_uc003yaw.1_Missense_Mutation_p.A386T	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	386						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AAAAGGAAGCGCGAGCACCTC	0.537										HNSCC(33;0.089)			18	96	---	---	---	---	PASS
OSR2	116039	broad.mit.edu	37	8	99961747	99961747	+	Silent	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99961747C>A	uc003yir.2	+	2	1102	c.567C>A	c.(565-567)ATC>ATA	p.I189I	OSR2_uc010mbn.2_Silent_p.I189I|OSR2_uc003yiq.2_Silent_p.I189I|OSR2_uc011lgx.1_Silent_p.I310I	NM_001142462	NP_001135934	Q8N2R0	OSR2_HUMAN	odd-skipped related 2 isoform a	189	C2H2-type 1.				bone morphogenesis|chondrocyte differentiation|embryonic digit morphogenesis|embryonic forelimb morphogenesis|embryonic hindlimb morphogenesis|embryonic leg joint morphogenesis|embryonic skeletal joint morphogenesis|eyelid development in camera-type eye|head development|mesonephros development|metanephros development|middle ear morphogenesis|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|osteoblast proliferation|palate development|positive regulation of bone mineralization|positive regulation of epithelial cell proliferation|positive regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|zinc ion binding			central_nervous_system(1)	1	Breast(36;4.14e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.0136)			ATTTGCTCATCCATGAGAGGA	0.532													165	174	---	---	---	---	PASS
GRHL2	79977	broad.mit.edu	37	8	102570785	102570785	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102570785C>T	uc010mbu.2	+	4	753	c.423C>T	c.(421-423)ATC>ATT	p.I141I	GRHL2_uc011lhi.1_Silent_p.I141I	NM_024915	NP_079191	Q6ISB3	GRHL2_HUMAN	transcription factor CP2-like 3	141						cytoplasm|nucleus	DNA binding			ovary(2)|skin(1)	3	all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05)		Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213)			AGTACAGCATCAGCTTCCCCG	0.512													38	163	---	---	---	---	PASS
RIMS2	9699	broad.mit.edu	37	8	105025769	105025769	+	Intron	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105025769A>G	uc003yls.2	+						RIMS2_uc003ylp.2_Silent_p.E1048E|RIMS2_uc003ylw.2_Silent_p.E862E|RIMS2_uc003ylq.2_Silent_p.E862E|RIMS2_uc003ylr.2_Silent_p.E887E	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2						intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			GATCCACTGAACGTCCTGATA	0.498										HNSCC(12;0.0054)			5	143	---	---	---	---	PASS
ABRA	137735	broad.mit.edu	37	8	107773726	107773726	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107773726C>G	uc003ymm.3	-	2	739	c.685G>C	c.(685-687)GAG>CAG	p.E229Q		NM_139166	NP_631905	Q8N0Z2	ABRA_HUMAN	actin-binding Rho activating protein	229					positive regulation of Rho protein signal transduction|positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent|transmembrane transport	actin cytoskeleton|plasma membrane|sarcomere	actin binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(57;3.83e-09)			TTGAGTTTCTCTGTAAATCTG	0.433													5	113	---	---	---	---	PASS
ANGPT1	284	broad.mit.edu	37	8	108334175	108334175	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108334175C>T	uc003ymn.2	-	4	1225	c.757G>A	c.(757-759)GAG>AAG	p.E253K	ANGPT1_uc011lhv.1_Missense_Mutation_p.E53K|ANGPT1_uc003ymo.2_Missense_Mutation_p.E253K|ANGPT1_uc003ymp.3_Missense_Mutation_p.E53K	NM_001146	NP_001137	Q15389	ANGP1_HUMAN	angiopoietin 1 precursor	253	Potential.				activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|blood coagulation|cell differentiation|heparin biosynthetic process|leukocyte migration|negative regulation of cell adhesion|negative regulation of endothelial cell apoptosis|negative regulation of vascular permeability|positive chemotaxis|positive regulation of blood vessel endothelial cell migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of protein ubiquitination|positive regulation of receptor internalization|protein localization at cell surface|regulation of satellite cell proliferation|sprouting angiogenesis|Tie receptor signaling pathway	extracellular space|membrane raft|microvillus|plasma membrane	receptor tyrosine kinase binding			ovary(3)|skin(3)|upper_aerodigestive_tract(1)	7	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)			TCCATCAGCTCCAGTTGCTGC	0.403													43	141	---	---	---	---	PASS
COLEC10	10584	broad.mit.edu	37	8	120118073	120118073	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120118073C>T	uc003yoo.2	+	6	574	c.477C>T	c.(475-477)TTC>TTT	p.F159F		NM_006438	NP_006429	Q9Y6Z7	COL10_HUMAN	collectin sub-family member 10 precursor	159	C-type lectin.					collagen|cytoplasm	mannose binding			ovary(2)|skin(1)	3	all_cancers(13;4.13e-26)|Lung NSC(37;1.36e-07)|Ovarian(258;0.018)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00113)			AAGAGAAATTCTACTACATCG	0.438													4	68	---	---	---	---	PASS
MAL2	114569	broad.mit.edu	37	8	120252475	120252475	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120252475C>G	uc003yop.2	+	4	476	c.374C>G	c.(373-375)TCC>TGC	p.S125C		NM_052886	NP_443118	Q969L2	MAL2_HUMAN	MAL2 proteolipid protein	125	Lumenal (Potential).|MARVEL.					apical plasma membrane|endomembrane system|integral to membrane|perinuclear region of cytoplasm	protein binding				0	all_cancers(13;1.91e-26)|Lung NSC(37;8.61e-08)|Ovarian(258;0.018)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000967)			GCAGCCACATCCCTGCATGAT	0.398													11	126	---	---	---	---	PASS
MTBP	27085	broad.mit.edu	37	8	121514775	121514775	+	Silent	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121514775C>A	uc003ypc.1	+	15	1698	c.1653C>A	c.(1651-1653)ACC>ACA	p.T551T		NM_022045	NP_071328	Q96DY7	MTBP_HUMAN	Mdm2, transformed 3T3 cell double minute 2, p53	551	Interaction with MDM2 (By similarity).				cell cycle arrest					skin(2)|ovary(1)	3	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			TAATGGAAACCAATCCTCTGG	0.313													16	53	---	---	---	---	PASS
WDR67	93594	broad.mit.edu	37	8	124146371	124146371	+	Silent	SNP	A	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124146371A>T	uc003ypp.1	+	17	2514	c.2424A>T	c.(2422-2424)CGA>CGT	p.R808R	WDR67_uc011lig.1_Intron|WDR67_uc011lih.1_Silent_p.R698R|WDR67_uc003ypq.1_RNA|WDR67_uc003yps.1_Silent_p.R442R|WDR67_uc003ypt.1_Silent_p.R265R|WDR67_uc003ypu.1_Silent_p.R265R	NM_145647	NP_663622	Q96DN5	WDR67_HUMAN	WD repeat domain 67 isoform 1	808	Potential.					centrosome	Rab GTPase activator activity			skin(1)	1	Lung NSC(37;7e-10)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			TGAGAGATCGAGAAATTGCTG	0.323													30	148	---	---	---	---	PASS
RNF139	11236	broad.mit.edu	37	8	125499022	125499022	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125499022C>T	uc003yrc.2	+	2	1475	c.1132C>T	c.(1132-1134)CTC>TTC	p.L378F		NM_007218	NP_009149	Q8WU17	RN139_HUMAN	ring finger protein 139	378					negative regulation of cell proliferation|regulation of protein ubiquitination	endoplasmic reticulum membrane|integral to membrane	protein binding|receptor activity|ubiquitin-protein ligase activity|zinc ion binding			kidney(1)	1	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			ATTAATGTCTCTCAGTGCCTC	0.398									Renal_Cell_Cancer_associated_with_constitutional_translocation_of_chromosome_3				8	571	---	---	---	---	PASS
SLA	6503	broad.mit.edu	37	8	134063088	134063088	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134063088C>G	uc003ytz.2	-	4	966	c.134G>C	c.(133-135)CGA>CCA	p.R45P	TG_uc003ytw.2_Intron|TG_uc010mdw.2_Intron|TG_uc011ljb.1_Intron|TG_uc011ljc.1_Intron|SLA_uc011lje.1_Missense_Mutation_p.R62P|SLA_uc011ljf.1_5'UTR|SLA_uc011ljg.1_Missense_Mutation_p.R62P|SLA_uc010mdy.1_Missense_Mutation_p.R45P|SLA_uc010mdz.1_Missense_Mutation_p.R45P|SLA_uc010mea.2_RNA|SLA_uc011ljd.1_Missense_Mutation_p.R85P	NM_001045556	NP_001039021	Q13239	SLAP1_HUMAN	Src-like-adaptor isoform a	45	SH3.					endosome	SH3/SH2 adaptor activity			lung(1)|liver(1)	2	all_epithelial(106;3.51e-21)|Lung NSC(106;4.24e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0279)|Breast(495;0.037)	BRCA - Breast invasive adenocarcinoma(115;0.000701)			TTTCTCCCCTCGGCGGAATAT	0.502													9	130	---	---	---	---	PASS
CYP11B1	1584	broad.mit.edu	37	8	143959226	143959226	+	Intron	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143959226G>T	uc003yxi.2	-						CYP11B1_uc010mex.2_5'Flank|CYP11B1_uc003yxh.2_5'Flank|CYP11B1_uc003yxj.2_Intron|CYP11B1_uc010mey.2_Silent_p.S185S	NM_000497	NP_000488	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B,						aldosterone biosynthetic process|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|glucose homeostasis|immune response|regulation of blood pressure|response to stress|xenobiotic metabolic process	mitochondrial inner membrane	electron carrier activity|steroid 11-beta-monooxygenase activity			ovary(3)	3	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Mitotane(DB00648)	ATGGTGGGGAGGAATTTCCCC	0.522									Familial_Hyperaldosteronism_type_I				11	116	---	---	---	---	PASS
CYP11B1	1584	broad.mit.edu	37	8	143959227	143959227	+	Intron	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143959227G>T	uc003yxi.2	-						CYP11B1_uc010mex.2_5'Flank|CYP11B1_uc003yxh.2_5'Flank|CYP11B1_uc003yxj.2_Intron|CYP11B1_uc010mey.2_Missense_Mutation_p.S185Y	NM_000497	NP_000488	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B,						aldosterone biosynthetic process|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|glucose homeostasis|immune response|regulation of blood pressure|response to stress|xenobiotic metabolic process	mitochondrial inner membrane	electron carrier activity|steroid 11-beta-monooxygenase activity			ovary(3)	3	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Mitotane(DB00648)	TGGTGGGGAGGAATTTCCCCT	0.527									Familial_Hyperaldosteronism_type_I				11	115	---	---	---	---	PASS
EPPK1	83481	broad.mit.edu	37	8	144942409	144942409	+	Silent	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144942409G>C	uc003zaa.1	-	1	5026	c.5013C>G	c.(5011-5013)CTC>CTG	p.L1671L		NM_031308	NP_112598	P58107	EPIPL_HUMAN	epiplakin 1	1671	Plectin 28.					cytoplasm|cytoskeleton	protein binding|structural molecule activity			pancreas(1)|skin(1)	2	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CCCGGACGATGAGGTCCTTCT	0.687													9	166	---	---	---	---	PASS
EPPK1	83481	broad.mit.edu	37	8	144943418	144943418	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144943418G>A	uc003zaa.1	-	1	4017	c.4004C>T	c.(4003-4005)TCC>TTC	p.S1335F		NM_031308	NP_112598	P58107	EPIPL_HUMAN	epiplakin 1	1335	Plectin 23.					cytoplasm|cytoskeleton	protein binding|structural molecule activity			pancreas(1)|skin(1)	2	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CAGAGAGAGGGAGGCCCTAGA	0.687													20	111	---	---	---	---	PASS
SLC39A4	55630	broad.mit.edu	37	8	145641346	145641346	+	Missense_Mutation	SNP	C	T	T	rs144726882		TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145641346C>T	uc003zcq.2	-	2	422	c.322G>A	c.(322-324)GAG>AAG	p.E108K	SLC39A4_uc003zcm.1_5'Flank|SLC39A4_uc003zcn.2_5'Flank|SLC39A4_uc003zco.2_5'Flank|SLC39A4_uc003zcp.2_Missense_Mutation_p.E83K	NM_130849	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter),	108	Extracellular (Potential).					cytoplasmic membrane-bounded vesicle|integral to membrane|recycling endosome membrane	zinc ion transmembrane transporter activity				0	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;1.12e-40)|all cancers(56;8.17e-36)|BRCA - Breast invasive adenocarcinoma(115;0.0407)|Colorectal(110;0.055)			CAGGTGCCCTCGGGGTTGCTG	0.736													8	33	---	---	---	---	PASS
KDM4C	23081	broad.mit.edu	37	9	6984310	6984310	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6984310G>A	uc003zkh.2	+	10	1840	c.1260G>A	c.(1258-1260)GTG>GTA	p.V420V	KDM4C_uc010mhu.2_Silent_p.V442V|KDM4C_uc011lmi.1_Silent_p.V420V|KDM4C_uc011lmj.1_RNA|KDM4C_uc003zkg.2_Silent_p.V420V|KDM4C_uc011lmk.1_Silent_p.V239V|KDM4C_uc011lml.1_Silent_p.V107V	NM_015061	NP_055876	Q9H3R0	KDM4C_HUMAN	jumonji domain containing 2C isoform 1	420					positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1						AAGCAGCAGTGAAGCTGAGGA	0.483													4	54	---	---	---	---	PASS
DENND4C	55667	broad.mit.edu	37	9	19372047	19372047	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19372047A>G	uc003znq.2	+	28	4931	c.4898A>G	c.(4897-4899)AAT>AGT	p.N1633S	DENND4C_uc011lnc.1_Missense_Mutation_p.N963S|DENND4C_uc011lnd.1_Missense_Mutation_p.N921S|DENND4C_uc003znr.2_3'UTR|DENND4C_uc003zns.2_3'UTR	NM_017925	NP_060395	Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1633						integral to membrane				ovary(1)|skin(1)	2						GCATTTGACAATGAATATGGA	0.358													16	117	---	---	---	---	PASS
IFNA8	3445	broad.mit.edu	37	9	21409532	21409532	+	Silent	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21409532G>T	uc003zpc.1	+	1	387	c.357G>T	c.(355-357)CTG>CTT	p.L119L		NM_002170	NP_002161	P32881	IFNA8_HUMAN	interferon, alpha 8 precursor	119					blood coagulation|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	extracellular space	cytokine activity|cytokine receptor binding				0				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0174)		TGAATGACCTGGAGTCCTGTG	0.483													15	140	---	---	---	---	PASS
IFNA8	3445	broad.mit.edu	37	9	21409534	21409534	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21409534A>G	uc003zpc.1	+	1	389	c.359A>G	c.(358-360)GAG>GGG	p.E120G		NM_002170	NP_002161	P32881	IFNA8_HUMAN	interferon, alpha 8 precursor	120					blood coagulation|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	extracellular space	cytokine activity|cytokine receptor binding				0				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0174)		AATGACCTGGAGTCCTGTGTG	0.478													15	138	---	---	---	---	PASS
C9orf11	54586	broad.mit.edu	37	9	27284754	27284754	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27284754C>T	uc003zql.2	-	8	936	c.852G>A	c.(850-852)GAG>GAA	p.E284E	NCRNA00032_uc010mjd.1_5'Flank|C9orf11_uc011lnq.1_Silent_p.E255E	NM_020641	NP_065692	Q9NQ60	AFAF_HUMAN	Acr formation associated factor isoform 1	284	Cytoplasmic (Potential).					acrosomal membrane|integral to membrane				ovary(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(39;7.39e-08)|Lung(218;1.26e-05)|LUSC - Lung squamous cell carcinoma(38;0.000106)		TTTCATGCATCTCATTATCTG	0.358													11	89	---	---	---	---	PASS
TOPORS	10210	broad.mit.edu	37	9	32543189	32543189	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32543189G>A	uc003zrb.2	-	3	1501	c.1334C>T	c.(1333-1335)TCA>TTA	p.S445L	TOPORS_uc003zrc.2_Missense_Mutation_p.S378L	NM_005802	NP_005793	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich	445	Required for sumoylation and localization to discrete nuclear foci.|Interaction with SUMO1.				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)		TTCTTCATCTGAACTGTCAGA	0.418													6	100	---	---	---	---	PASS
UNC13B	10497	broad.mit.edu	37	9	35236593	35236593	+	Intron	SNP	T	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35236593T>C	uc003zwq.2	+						UNC13B_uc010mkl.1_Intron|UNC13B_uc003zwr.2_Intron	NM_006377	NP_006368	O14795	UN13B_HUMAN	UNC13 (C. elegans)-like						excretion|induction of apoptosis|intracellular signal transduction	cell junction|Golgi apparatus|synapse	metal ion binding|receptor activity			ovary(3)|large_intestine(1)|skin(1)	5	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			GGTCAGTCATTGCATTTTCTG	0.478													44	184	---	---	---	---	PASS
C9orf128	392307	broad.mit.edu	37	9	35819993	35819993	+	Silent	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35819993G>C	uc010mlc.2	-	4	1032	c.747C>G	c.(745-747)CTC>CTG	p.L249L	C9orf128_uc003zyj.2_RNA|C9orf128_uc011lpg.1_Silent_p.L249L	NM_001012446	NP_001012448	A6H8Z2	CI128_HUMAN	hypothetical protein LOC392307	249											0	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)			AGCCAATGTAGAGACCTAGGT	0.502													3	63	---	---	---	---	PASS
C9orf102	375748	broad.mit.edu	37	9	98740391	98740391	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98740391G>C	uc004avu.2	+	12	2504	c.1259G>C	c.(1258-1260)GGA>GCA	p.G420A	uc010msa.1_Missense_Mutation_p.G110A|uc011lun.1_Missense_Mutation_p.G110A			Q5T890	RAD26_HUMAN	Homo sapiens cDNA, FLJ97452.	Error:Variant_position_missing_in_Q5T890_after_alignment					DNA repair	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding				0		Acute lymphoblastic leukemia(62;0.0559)				AATGTAATTGGATCGAGCAAA	0.403													3	67	---	---	---	---	PASS
OR13C4	138804	broad.mit.edu	37	9	107289477	107289477	+	Missense_Mutation	SNP	T	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107289477T>A	uc011lvn.1	-	1	14	c.14A>T	c.(13-15)AAC>ATC	p.N5I		NM_001001919	NP_001001919	Q8NGS5	O13C4_HUMAN	olfactory receptor, family 13, subfamily C,	5	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1						AAATGTCTGGTTTATCTTGTC	0.368													12	51	---	---	---	---	PASS
ABCA1	19	broad.mit.edu	37	9	107574967	107574967	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107574967C>A	uc004bcl.2	-	28	4251	c.3938G>T	c.(3937-3939)GGC>GTC	p.G1313V		NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1	1313					Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	GGACCCTTTGCCATCCATCCC	0.493													41	85	---	---	---	---	PASS
ABCA1	19	broad.mit.edu	37	9	107574968	107574968	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107574968C>A	uc004bcl.2	-	28	4250	c.3937G>T	c.(3937-3939)GGC>TGC	p.G1313C		NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1	1313					Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	GACCCTTTGCCATCCATCCCA	0.493													41	85	---	---	---	---	PASS
HSPA5	3309	broad.mit.edu	37	9	128000963	128000963	+	Missense_Mutation	SNP	A	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128000963A>T	uc004bpn.2	-	6	1396	c.1140T>A	c.(1138-1140)AAT>AAA	p.N380K		NM_005347	NP_005338	P11021	GRP78_HUMAN	heat shock 70kDa protein 5	380					anti-apoptosis|cellular response to glucose starvation|ER-associated protein catabolic process|platelet activation|platelet degranulation|regulation of protein folding in endoplasmic reticulum	cell surface|endoplasmic reticulum chaperone complex|endoplasmic reticulum lumen|ER-Golgi intermediate compartment|integral to endoplasmic reticulum membrane|melanosome|midbody|nucleus|perinuclear region of cytoplasm	ATP binding|ATPase activity|calcium ion binding|caspase inhibitor activity|chaperone binding|misfolded protein binding|protein binding, bridging|protein domain specific binding|ubiquitin protein ligase binding|unfolded protein binding			ovary(3)|skin(1)	4					Antihemophilic Factor(DB00025)	GTTCCTTGCCATTGAAGAACT	0.448										Prostate(1;0.17)			5	79	---	---	---	---	PASS
MAPKAP1	79109	broad.mit.edu	37	9	128434763	128434763	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128434763G>C	uc004bpv.2	-	2	424	c.91C>G	c.(91-93)CTC>GTC	p.L31V	MAPKAP1_uc004bpw.2_Intron|MAPKAP1_uc004bpx.2_Intron|MAPKAP1_uc004bpy.2_Missense_Mutation_p.L31V|MAPKAP1_uc004bpz.2_Missense_Mutation_p.L31V|MAPKAP1_uc010mxa.2_RNA|MAPKAP1_uc004bqa.2_Missense_Mutation_p.L31V	NM_001006617	NP_001006618	Q9BPZ7	SIN1_HUMAN	mitogen-activated protein kinase associated	31	Interaction with MAP3K2.				nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|response to stress|T cell costimulation	cytoplasmic membrane-bounded vesicle|cytosol|nucleus|plasma membrane	Ras GTPase binding			ovary(2)|lung(2)	4						TGATCAATGAGAACCATCTCA	0.458													4	51	---	---	---	---	PASS
GARNL3	84253	broad.mit.edu	37	9	130116584	130116584	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130116584C>G	uc011mae.1	+	19	2055	c.1654C>G	c.(1654-1656)CGC>GGC	p.R552G	GARNL3_uc011mad.1_Missense_Mutation_p.R530G|GARNL3_uc010mxi.2_5'Flank	NM_032293	NP_115669	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3	552	CNH.				regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity|small GTPase regulator activity			ovary(1)|central_nervous_system(1)|skin(1)	3						AAAAGATGCTCGCCTCTTTGT	0.483													16	82	---	---	---	---	PASS
ST6GALNAC6	30815	broad.mit.edu	37	9	130653125	130653125	+	Silent	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130653125C>G	uc004bso.1	-	5	614	c.495G>C	c.(493-495)CTG>CTC	p.L165L	ST6GALNAC6_uc004bsn.1_Silent_p.L131L|ST6GALNAC6_uc011man.1_Intron|ST6GALNAC6_uc004bsp.1_Silent_p.L165L|ST6GALNAC6_uc004bsq.1_Silent_p.L131L|ST6GALNAC6_uc004bsr.2_Silent_p.L131L|ST6GALNAC6_uc010mxp.1_RNA	NM_013443	NP_038471	Q969X2	SIA7F_HUMAN	sialytransferase 7F	165	Lumenal (Potential).				protein glycosylation	integral to Golgi membrane|plasma membrane					0						GGGGCCTCCTCAGCACGCGGA	0.612													3	44	---	---	---	---	PASS
PFKP	5214	broad.mit.edu	37	10	3162113	3162113	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3162113C>T	uc001igp.2	+	16	1596	c.1560C>T	c.(1558-1560)GCC>GCT	p.A520A	PFKP_uc001igq.2_Silent_p.A512A|PFKP_uc009xhr.2_Silent_p.A482A|PFKP_uc009xhs.1_Silent_p.A304A|PFKP_uc009xht.2_Silent_p.A258A|PFKP_uc009xhu.2_Silent_p.A26A	NM_002627	NP_002618	Q01813	K6PP_HUMAN	phosphofructokinase, platelet	520					glycolysis	6-phosphofructokinase complex	6-phosphofructokinase activity|ATP binding|metal ion binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)|lung(1)	3				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		AGCTGTCAGCCGCCCGGGAGA	0.622											OREG0019976	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	21	74	---	---	---	---	PASS
PFKP	5214	broad.mit.edu	37	10	3176761	3176761	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3176761G>C	uc001igp.2	+	20	2145	c.2109G>C	c.(2107-2109)GAG>GAC	p.E703D	PFKP_uc001igq.2_Missense_Mutation_p.E695D|PFKP_uc009xhr.2_Missense_Mutation_p.E665D|PFKP_uc009xht.2_Missense_Mutation_p.E441D|PFKP_uc009xhu.2_Missense_Mutation_p.E209D	NM_002627	NP_002618	Q01813	K6PP_HUMAN	phosphofructokinase, platelet	703					glycolysis	6-phosphofructokinase complex	6-phosphofructokinase activity|ATP binding|metal ion binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)|lung(1)	3				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		AACTCAAGGAGGCCCGGGGCA	0.562													11	284	---	---	---	---	PASS
ATP5C1	509	broad.mit.edu	37	10	7830204	7830204	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7830204G>C	uc001iju.2	+	1	112	c.34G>C	c.(34-36)GCC>CCC	p.A12P	KIN_uc010qaz.1_5'Flank|KIN_uc001ijt.2_5'Flank|KIN_uc009xip.2_5'Flank|KIN_uc010qba.1_5'Flank|ATP5C1_uc010qbb.1_Missense_Mutation_p.A12P|ATP5C1_uc009xiq.1_Missense_Mutation_p.A12P|ATP5C1_uc010qbc.1_5'UTR|ATP5C1_uc001ijv.2_Missense_Mutation_p.A12P	NM_001001973	NP_001001973	P36542	ATPG_HUMAN	ATP synthase, H+ transporting, mitochondrial F1	12					oxidative phosphorylation|respiratory electron transport chain	mitochondrial matrix|mitochondrial proton-transporting ATP synthase complex, catalytic core F(1)	hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism				0						TGGGCTGTCGGCCTGGACCTT	0.667													28	54	---	---	---	---	PASS
ITGA8	8516	broad.mit.edu	37	10	15688934	15688934	+	Missense_Mutation	SNP	T	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15688934T>A	uc001ioc.1	-	12	1118	c.1118A>T	c.(1117-1119)GAC>GTC	p.D373V	ITGA8_uc010qcb.1_Missense_Mutation_p.D358V	NM_003638	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8 precursor	373	Extracellular (Potential).|FG-GAP 6.				cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity			ovary(3)|lung(3)	6						GATCTGGGGGTCTCTGAAGAG	0.483													42	122	---	---	---	---	PASS
SLC39A12	221074	broad.mit.edu	37	10	18250593	18250593	+	Silent	SNP	T	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18250593T>A	uc001ipo.2	+	3	618	c.345T>A	c.(343-345)TCT>TCA	p.S115S	SLC39A12_uc001ipn.2_Silent_p.S115S|SLC39A12_uc001ipp.2_Silent_p.S115S|SLC39A12_uc010qck.1_5'UTR	NM_001145195	NP_001138667	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter),	115	Extracellular (Potential).				zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)|breast(1)	2						AGAGAGTTTCTCTTCTCCTTC	0.363													50	105	---	---	---	---	PASS
MPP7	143098	broad.mit.edu	37	10	28345547	28345547	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28345547C>T	uc001iua.1	-	18	1817	c.1413G>A	c.(1411-1413)GTG>GTA	p.V471V	MPP7_uc009xkz.1_RNA|MPP7_uc001iub.1_Silent_p.V471V|MPP7_uc009xla.2_Silent_p.V471V|MPP7_uc010qdv.1_RNA	NM_173496	NP_775767	Q5T2T1	MPP7_HUMAN	palmitoylated membrane protein 7	471	Guanylate kinase-like.				establishment of cell polarity|positive regulation of protein complex assembly|protein localization to adherens junction|tight junction assembly	MPP7-DLG1-LIN7 complex|tight junction	protein complex scaffold|protein domain specific binding|protein heterodimerization activity|signaling adaptor activity			ovary(1)	1						TTAAATGCTTCACTGTCTACA	0.308													5	125	---	---	---	---	PASS
ANKRD30A	91074	broad.mit.edu	37	10	37442554	37442554	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37442554C>A	uc001iza.1	+	13	1693	c.1594C>A	c.(1594-1596)CAA>AAA	p.Q532K		NM_052997	NP_443723	Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	588						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(7)|breast(1)|skin(1)	9						GGCTACACATCAAAAAGAAAT	0.313													68	409	---	---	---	---	PASS
PCDH15	65217	broad.mit.edu	37	10	55582959	55582959	+	Silent	SNP	A	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55582959A>T	uc001jju.1	-	33	4922	c.4527T>A	c.(4525-4527)TCT>TCA	p.S1509S	PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Silent_p.S1506S|PCDH15_uc010qhw.1_Silent_p.S1469S|PCDH15_uc010qhx.1_Silent_p.S1440S|PCDH15_uc010qhy.1_Silent_p.S1516S|PCDH15_uc010qhz.1_Silent_p.S1511S|PCDH15_uc010qia.1_Silent_p.S1489S|PCDH15_uc010qib.1_Silent_p.S1486S	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	1509	Cytoplasmic (Potential).				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				ATTTTCTTGCAGACTTCAGTT	0.373										HNSCC(58;0.16)			53	48	---	---	---	---	PASS
EGR2	1959	broad.mit.edu	37	10	64573229	64573229	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64573229C>G	uc010qim.1	-	3	1323	c.1169G>C	c.(1168-1170)CGC>CCC	p.R390P	EGR2_uc010qin.1_Missense_Mutation_p.R340P|EGR2_uc001jmi.2_Missense_Mutation_p.R390P|EGR2_uc010qio.1_Missense_Mutation_p.R403P|EGR2_uc009xph.2_Missense_Mutation_p.R390P	NM_001136177	NP_001129649	P11161	EGR2_HUMAN	early growth response 2 protein isoform a	390	C2H2-type 2.				fat cell differentiation|protein export from nucleus|transcription from RNA polymerase II promoter	cytoplasm|nucleus	chromatin binding|RNA polymerase II activating transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|ubiquitin protein ligase binding|zinc ion binding			ovary(2)	2	Prostate(12;0.0297)|all_hematologic(501;0.228)					GGTGTGGGTGCGGATATGGGT	0.587													28	197	---	---	---	---	PASS
PLAU	5328	broad.mit.edu	37	10	75675040	75675040	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75675040G>C	uc001jwa.2	+	10	1148	c.1002G>C	c.(1000-1002)ATG>ATC	p.M334I	C10orf55_uc001jvz.1_Intron|PLAU_uc010qkw.1_Missense_Mutation_p.M317I|PLAU_uc010qkx.1_Missense_Mutation_p.M248I|PLAU_uc001jwb.2_RNA|PLAU_uc001jwc.2_Missense_Mutation_p.M334I|PLAU_uc009xrq.1_Missense_Mutation_p.M298I	NM_002658	NP_002649	P00749	UROK_HUMAN	plasminogen activator, urokinase isoform 1	334	Peptidase S1.				blood coagulation|chemotaxis|fibrinolysis|proteolysis|regulation of cell adhesion mediated by integrin|regulation of receptor activity|regulation of smooth muscle cell migration|regulation of smooth muscle cell-matrix adhesion|signal transduction	cell surface|extracellular space|plasma membrane	serine-type endopeptidase activity			ovary(2)|kidney(1)	3	Prostate(51;0.0112)				Amiloride(DB00594)|Urokinase(DB00013)	AGCTGAAAATGACTGTTGTGA	0.532													73	63	---	---	---	---	PASS
NOC3L	64318	broad.mit.edu	37	10	96098477	96098477	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96098477T>C	uc001kjq.1	-	18	2067	c.1979A>G	c.(1978-1980)GAT>GGT	p.D660G		NM_022451	NP_071896	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog	660						nuclear speck|nucleolus	binding			ovary(1)	1		Colorectal(252;0.0897)				AAGCAGTAGATCTGTTTTGGG	0.393													47	47	---	---	---	---	PASS
CYP17A1	1586	broad.mit.edu	37	10	104590510	104590510	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104590510C>G	uc001kwg.2	-	8	1648	c.1476G>C	c.(1474-1476)AAG>AAC	p.K492N	C10orf26_uc009xxg.1_RNA	NM_000102	NP_000093	P05093	CP17A_HUMAN	cytochrome P450, family 17	492					androgen biosynthetic process|glucocorticoid biosynthetic process|sex differentiation|xenobiotic metabolic process	endoplasmic reticulum membrane	electron carrier activity|heme binding|oxygen binding|steroid 17-alpha-monooxygenase activity				0		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)	NADH(DB00157)|Progesterone(DB00396)	GCACCTTGATCTTCACTTTGA	0.587													15	17	---	---	---	---	PASS
DUSP5	1847	broad.mit.edu	37	10	112270047	112270047	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112270047G>T	uc001kzd.2	+	4	1273	c.1018G>T	c.(1018-1020)GGC>TGC	p.G340C		NM_004419	NP_004410	Q16690	DUS5_HUMAN	dual specificity phosphatase 5	340	Tyrosine-protein phosphatase.				endoderm formation|inactivation of MAPK activity	nucleoplasm	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)	1		Breast(234;0.0848)		Epithelial(162;0.000276)|all cancers(201;0.00465)|BRCA - Breast invasive adenocarcinoma(275;0.12)		TTCACTGATAGGCCATTTGCA	0.617													25	31	---	---	---	---	PASS
PNLIPRP3	119548	broad.mit.edu	37	10	118203982	118203982	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118203982G>A	uc001lcl.3	+	4	514	c.413G>A	c.(412-414)CGT>CAT	p.R138H		NM_001011709	NP_001011709	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3 precursor	138					lipid catabolic process	extracellular region	triglyceride lipase activity			ovary(1)	1				all cancers(201;0.0131)		AACAATCTCCGTGTTGTTGGT	0.353													114	78	---	---	---	---	PASS
PNLIPRP1	5407	broad.mit.edu	37	10	118364922	118364922	+	Silent	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118364922C>G	uc001lco.1	+	12	1215	c.1197C>G	c.(1195-1197)ACC>ACG	p.T399T	PNLIPRP1_uc001lcp.2_Silent_p.T399T	NM_006229	NP_006220	P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1 precursor	399	PLAT.				lipid metabolic process		calcium ion binding|triglyceride lipase activity			ovary(1)|breast(1)	2				all cancers(201;0.0161)		CAGGCTCAACCCATTCCTATG	0.408													80	77	---	---	---	---	PASS
ADAM12	8038	broad.mit.edu	37	10	127789652	127789652	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127789652C>T	uc001ljk.2	-	9	1322	c.909G>A	c.(907-909)GCG>GCA	p.A303A	ADAM12_uc010qul.1_Silent_p.A254A|ADAM12_uc001ljm.2_Silent_p.A303A|ADAM12_uc001ljn.2_Silent_p.A300A|ADAM12_uc001ljl.3_Silent_p.A300A	NM_003474	NP_003465	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12 isoform 1	303	Extracellular (Potential).|Peptidase M12B.				cell adhesion|epidermal growth factor receptor signaling pathway|myoblast fusion|proteolysis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|protein binding|SH3 domain binding|zinc ion binding			breast(4)|ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	9		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		TGACAAGCTGCGCATTGTCAT	0.507													36	32	---	---	---	---	PASS
KNDC1	85442	broad.mit.edu	37	10	135015346	135015346	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135015346G>T	uc001llz.1	+	17	3332	c.3331G>T	c.(3331-3333)GTG>TTG	p.V1111L	KNDC1_uc001lma.1_Missense_Mutation_p.V1046L|KNDC1_uc001lmb.1_Missense_Mutation_p.V523L	NM_152643	NP_689856	Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND)	1111					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction					upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		CCACAACTACGTGAAGGACCT	0.726													5	3	---	---	---	---	PASS
NLRP6	171389	broad.mit.edu	37	11	281085	281085	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:281085G>A	uc010qvs.1	+	4	1351	c.1351G>A	c.(1351-1353)GAG>AAG	p.E451K	NLRP6_uc010qvt.1_Missense_Mutation_p.E451K	NM_138329	NP_612202	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	451	NACHT.					cytoplasm	ATP binding			upper_aerodigestive_tract(1)|skin(1)	2		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		CCTGGCCCGCGAGGGCGTCCT	0.627													4	93	---	---	---	---	PASS
MUC2	4583	broad.mit.edu	37	11	1088759	1088759	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1088759G>C	uc001lsx.1	+	26	3571	c.3544G>C	c.(3544-3546)GTC>CTC	p.V1182L		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	1182						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GAAGAAGTGTGTCACTGCAGA	0.602													9	9	---	---	---	---	PASS
SMPD1	6609	broad.mit.edu	37	11	6413084	6413084	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6413084G>C	uc001mcw.2	+	2	963	c.789G>C	c.(787-789)TTG>TTC	p.L263F	SMPD1_uc001mcv.1_Intron|SMPD1_uc009yex.2_RNA|SMPD1_uc001mcx.2_Missense_Mutation_p.L263F|SMPD1_uc009yew.2_Missense_Mutation_p.L262F	NM_000543	NP_000534	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid	261					cell death|ceramide biosynthetic process|negative regulation of MAP kinase activity|nervous system development|positive regulation of protein dephosphorylation|signal transduction|sphingomyelin catabolic process|termination of signal transduction	lysosome	hydrolase activity, acting on glycosyl bonds|sphingomyelin phosphodiesterase activity				0		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Desipramine(DB01151)	AGAGCCTGTTGAGTGGGCTGG	0.647													11	113	---	---	---	---	PASS
ABCC8	6833	broad.mit.edu	37	11	17464794	17464794	+	Silent	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17464794G>T	uc001mnc.2	-	9	1524	c.1398C>A	c.(1396-1398)GTC>GTA	p.V466V	ABCC8_uc010rcy.1_Silent_p.V465V	NM_000352	NP_000343	Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C, member 8	466	Helical; Name=9; (By similarity).|ABC transmembrane type-1 1.				carbohydrate metabolic process|energy reserve metabolic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium ion transmembrane transporter activity|sulfonylurea receptor activity			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)	GTAGAATGATGACAGCTGCTC	0.537													32	55	---	---	---	---	PASS
ANO5	203859	broad.mit.edu	37	11	22291958	22291958	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22291958C>G	uc001mqi.2	+	18	2316	c.1999C>G	c.(1999-2001)CTT>GTT	p.L667V	ANO5_uc001mqj.2_Missense_Mutation_p.L666V	NM_213599	NP_998764	Q75V66	ANO5_HUMAN	anoctamin 5 isoform a	667	Extracellular (Potential).					chloride channel complex|endoplasmic reticulum membrane	chloride channel activity			central_nervous_system(3)|ovary(1)	4						TTTTGGACCCCTTGGGCTTTT	0.428													29	66	---	---	---	---	PASS
LGR4	55366	broad.mit.edu	37	11	27402514	27402514	+	Splice_Site	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27402514C>G	uc001mrj.3	-	8	1244	c.759_splice	c.e8-1	p.L253_splice	LGR4_uc001mrk.3_Splice_Site_p.L229_splice	NM_018490	NP_060960	Q9BXB1	LGR4_HUMAN	leucine-rich repeat-containing G protein-coupled							integral to membrane|plasma membrane	protein-hormone receptor activity			ovary(1)	1						ATGAAATCCTCTAGAAAGATA	0.299													8	65	---	---	---	---	PASS
FBXO3	26273	broad.mit.edu	37	11	33763558	33763558	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33763558C>G	uc001muz.2	-	11	1340	c.1312G>C	c.(1312-1314)GAT>CAT	p.D438H	FBXO3_uc010rej.1_Missense_Mutation_p.D125H|FBXO3_uc001muy.2_Missense_Mutation_p.D325H|FBXO3_uc009ykb.2_RNA	NM_012175	NP_036307	Q9UK99	FBX3_HUMAN	F-box only protein 3 isoform 1	438	Asp/Glu-rich (highly acidic).				proteolysis	nucleus	ubiquitin-protein ligase activity			pancreas(1)	1		Lung NSC(402;0.0804)		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)		TCTGCTGAATCATCAtcctcg	0.338													17	24	---	---	---	---	PASS
ABTB2	25841	broad.mit.edu	37	11	34378571	34378571	+	Missense_Mutation	SNP	A	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34378571A>T	uc001mvl.1	-	1	232	c.2T>A	c.(1-3)ATG>AAG	p.M1K		NM_145804	NP_665803	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing	1							DNA binding			central_nervous_system(1)|skin(1)	2		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)				GCCGGCGCTCATGCTGTACAG	0.697													6	10	---	---	---	---	PASS
MADD	8567	broad.mit.edu	37	11	47297746	47297746	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47297746A>G	uc001ner.1	+	4	1147	c.956A>G	c.(955-957)GAG>GGG	p.E319G	MADD_uc001neq.2_Missense_Mutation_p.E319G|MADD_uc001nev.1_Missense_Mutation_p.E319G|MADD_uc001nes.1_Missense_Mutation_p.E319G|MADD_uc001net.1_Missense_Mutation_p.E319G|MADD_uc009yln.1_Missense_Mutation_p.E319G|MADD_uc001neu.1_Missense_Mutation_p.E319G|MADD_uc001nex.2_Missense_Mutation_p.E319G|MADD_uc001nez.2_Missense_Mutation_p.E319G|MADD_uc001new.2_Missense_Mutation_p.E319G	NM_003682	NP_003673	Q8WXG6	MADD_HUMAN	MAP-kinase activating death domain-containing	319	DENN.				activation of MAPK activity|apoptosis|cell surface receptor linked signaling pathway|regulation of apoptosis|regulation of cell cycle	cytoplasm|integral to membrane|plasma membrane	death receptor binding|protein kinase activator activity|Rab guanyl-nucleotide exchange factor activity			ovary(5)|skin(4)|central_nervous_system(2)	11				Lung(87;0.182)		ATTCTGTTAGAGCACAAGGTG	0.418													25	55	---	---	---	---	PASS
OR4X2	119764	broad.mit.edu	37	11	48267494	48267494	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48267494C>T	uc001ngs.1	+	1	839	c.839C>T	c.(838-840)TCT>TTT	p.S280F		NM_001004727	NP_001004727	Q8NGF9	OR4X2_HUMAN	olfactory receptor, family 4, subfamily X,	280	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						GTCATCTACTCTCTGAGAAAT	0.458													14	62	---	---	---	---	PASS
OR5I1	10798	broad.mit.edu	37	11	55703185	55703185	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55703185C>T	uc010ris.1	-	1	692	c.692G>A	c.(691-693)CGC>CAC	p.R231H		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						ACTGAAAGAGCGGATCTTTAA	0.458													3	18	---	---	---	---	PASS
OR5J2	282775	broad.mit.edu	37	11	55945005	55945005	+	Silent	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55945005C>A	uc010rjb.1	+	1	912	c.912C>A	c.(910-912)GCC>GCA	p.A304A		NM_001005492	NP_001005492	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J,	304	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	p.A304D(1)		ovary(1)|large_intestine(1)|breast(1)|pancreas(1)	4	Esophageal squamous(21;0.00693)					TGAAAAGGGCCATAGAAATGA	0.383													7	22	---	---	---	---	PASS
TMX2	51075	broad.mit.edu	37	11	57506183	57506183	+	Silent	SNP	T	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57506183T>C	uc001nlc.1	+	5	538	c.489T>C	c.(487-489)TTT>TTC	p.F163F	CTNND1_uc001nlf.1_Intron|TMX2_uc001nld.1_Silent_p.F69F|TMX2_uc001nle.1_Silent_p.F125F|C11orf31_uc010rjx.1_5'Flank	NM_015959	NP_057043	Q9Y320	TMX2_HUMAN	thioredoxin domain containing 14 isoform 1	163	Cytoplasmic (Potential).|Thioredoxin.				cell redox homeostasis	integral to membrane					0						TGGAGTTCTTTGCCAATTGGT	0.488													64	114	---	---	---	---	PASS
OR1S1	219959	broad.mit.edu	37	11	57982687	57982687	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57982687C>T	uc010rkc.1	+	1	471	c.471C>T	c.(469-471)CTC>CTT	p.L157L		NM_001004458	NP_001004458	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S,	157	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(1)	1		Breast(21;0.0589)				GCATTTTGCTCACAGTCATCT	0.468													7	232	---	---	---	---	PASS
FAM111A	63901	broad.mit.edu	37	11	58920951	58920951	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58920951G>C	uc010rkp.1	+	5	2037	c.1810G>C	c.(1810-1812)GAA>CAA	p.E604Q	FAM111A_uc010rkq.1_Missense_Mutation_p.E604Q|FAM111A_uc010rkr.1_Missense_Mutation_p.E604Q|FAM111A_uc001nno.2_Missense_Mutation_p.E604Q|FAM111A_uc001nnp.2_Missense_Mutation_p.E604Q|FAM111A_uc001nnq.2_Missense_Mutation_p.E604Q	NM_001142521	NP_001135993	Q96PZ2	F111A_HUMAN	hypothetical protein LOC63901	604					proteolysis		serine-type endopeptidase activity			ovary(3)	3		all_epithelial(135;0.139)				GCAGGATGTAGAAATGATGAG	0.358													7	72	---	---	---	---	PASS
OR4D11	219986	broad.mit.edu	37	11	59271208	59271208	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59271208C>T	uc001noa.1	+	1	160	c.160C>T	c.(160-162)CGC>TGC	p.R54C		NM_001004706	NP_001004706	Q8NGI4	OR4DB_HUMAN	olfactory receptor, family 4, subfamily D,	54	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						CTGTGAGTCTCGCCTTCACAC	0.498													8	233	---	---	---	---	PASS
OR4D11	219986	broad.mit.edu	37	11	59271475	59271475	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59271475G>C	uc001noa.1	+	1	427	c.427G>C	c.(427-429)GCC>CCC	p.A143P		NM_001004706	NP_001004706	Q8NGI4	OR4DB_HUMAN	olfactory receptor, family 4, subfamily D,	143	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						GCAATGCACTGCCCTCATCTC	0.532													59	92	---	---	---	---	PASS
MS4A6A	64231	broad.mit.edu	37	11	59945733	59945733	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59945733C>A	uc001nor.2	-	4	577	c.339G>T	c.(337-339)TTG>TTT	p.L113F	MS4A6A_uc001noq.2_Missense_Mutation_p.L113F|MS4A6A_uc001nos.3_Missense_Mutation_p.L141F|MS4A6A_uc009ymv.2_Missense_Mutation_p.L113F|MS4A6A_uc001not.2_Missense_Mutation_p.L113F|MS4A6A_uc010rla.1_Missense_Mutation_p.L141F|MS4A6A_uc010rlb.1_Missense_Mutation_p.L68F	NM_152852	NP_690591	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member	113	Cytoplasmic (Potential).					integral to membrane	receptor activity				0						TCTTACTCACCAAAAGCTTGG	0.368													10	78	---	---	---	---	PASS
DAK	26007	broad.mit.edu	37	11	61110288	61110288	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61110288C>G	uc001nre.2	+	10	1094	c.837C>G	c.(835-837)ATC>ATG	p.I279M	DDB1_uc010rlf.1_5'Flank|DAK_uc009ynm.1_Missense_Mutation_p.I209M	NM_015533	NP_056348	Q3LXA3	DHAK_HUMAN	dihydroxyacetone kinase 2	279	DhaK.				glycerol metabolic process	cytosol	ATP binding|FAD-AMP lyase (cyclizing) activity|glycerone kinase activity|metal ion binding				0						AACTGGGCATCATAGCCGACG	0.527													4	66	---	---	---	---	PASS
FKBP2	2286	broad.mit.edu	37	11	64011431	64011431	+	Intron	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64011431C>G	uc001nyy.2	+						FKBP2_uc010rnh.1_Intron|FKBP2_uc001nyz.2_Intron	NM_004470	NP_004461	P26885	FKBP2_HUMAN	FK506 binding protein 2, 13kDa precursor						protein folding	endoplasmic reticulum membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity|protein binding				0						CTCCCCTTCTCCCCTACAGGT	0.582													7	133	---	---	---	---	PASS
RASGRP2	10235	broad.mit.edu	37	11	64510342	64510342	+	5'UTR	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64510342C>A	uc009ypu.2	-	2					RASGRP2_uc001oat.2_5'Flank|RASGRP2_uc001oau.2_5'Flank|RASGRP2_uc009ypv.2_5'UTR|RASGRP2_uc009ypw.2_5'UTR|RASGRP2_uc001oaw.1_Missense_Mutation_p.R302L	NM_001098671	NP_001092141	Q7LDG7	GRP2_HUMAN	RAS guanyl releasing protein 2						platelet activation|Ras protein signal transduction|regulation of cell growth|regulation of small GTPase mediated signal transduction	cell junction|cytosol|ruffle membrane|synapse|synaptosome	calcium ion binding|diacylglycerol binding|guanyl-nucleotide exchange factor activity				0						CTGCCATGGCCGCCGGCGCGG	0.741													6	6	---	---	---	---	PASS
ATG2A	23130	broad.mit.edu	37	11	64670836	64670836	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64670836T>C	uc001obx.2	-	26	3651	c.3536A>G	c.(3535-3537)GAT>GGT	p.D1179G	ATG2A_uc001obw.2_5'UTR	NM_015104	NP_055919	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	1179							protein binding			ovary(1)|central_nervous_system(1)	2						ACAGACATAATCTGCAGCAGA	0.577											OREG0004027	type=REGULATORY REGION|Gene=BC053596|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	7	53	---	---	---	---	PASS
SNX32	254122	broad.mit.edu	37	11	65618269	65618269	+	Silent	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65618269G>C	uc001ofr.2	+	6	673	c.546G>C	c.(544-546)CTG>CTC	p.L182L		NM_152760	NP_689973	Q86XE0	SNX32_HUMAN	sorting nexin 6B	182					cell communication|protein transport		phosphatidylinositol binding				0				READ - Rectum adenocarcinoma(159;0.171)		GAGGGTTTCTGAGGAATATTG	0.592													3	29	---	---	---	---	PASS
LRFN4	78999	broad.mit.edu	37	11	66626556	66626556	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66626556C>T	uc001ojr.2	+	1	1681	c.1341C>T	c.(1339-1341)CTC>CTT	p.L447L	PC_uc001ojo.1_Intron|PC_uc001ojp.1_Intron|PC_uc001ojn.1_Intron|LRFN4_uc001ojs.2_Intron	NM_024036	NP_076941	Q6PJG9	LRFN4_HUMAN	leucine rich repeat and fibronectin type III	447	Extracellular (Potential).|Fibronectin type-III.					integral to membrane					0						ATGAGACCCTCATCTACCGGT	0.652													9	103	---	---	---	---	PASS
MYEOV	26579	broad.mit.edu	37	11	69063147	69063147	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69063147G>T	uc001oov.2	+	3	680	c.230G>T	c.(229-231)CGG>CTG	p.R77L	MYEOV_uc001oox.2_Intron|MYEOV_uc009ysl.2_Missense_Mutation_p.R77L|MYEOV_uc001oow.2_Missense_Mutation_p.R19L	NM_138768	NP_620123	Q96EZ4	MYEOV_HUMAN	myeloma overexpressed	77											0	all_lung(4;2.21e-19)|Lung NSC(4;6.13e-19)|Melanoma(5;0.00128)		LUSC - Lung squamous cell carcinoma(11;3.33e-11)|STAD - Stomach adenocarcinoma(18;0.00654)|LUAD - Lung adenocarcinoma(13;0.0713)	Kidney(183;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.00361)|LUSC - Lung squamous cell carcinoma(976;0.0153)		GGCAGATCCCGGGGCCGCCTC	0.612													22	85	---	---	---	---	PASS
ARAP1	116985	broad.mit.edu	37	11	72409030	72409030	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72409030C>G	uc001osu.2	-	19	2852	c.2663G>C	c.(2662-2664)GGC>GCC	p.G888A	ARAP1_uc001osv.2_Missense_Mutation_p.G888A|ARAP1_uc001osr.2_Missense_Mutation_p.G648A|ARAP1_uc001oss.2_Missense_Mutation_p.G643A|ARAP1_uc009yth.2_Missense_Mutation_p.G582A|ARAP1_uc010rre.1_Missense_Mutation_p.G643A|ARAP1_uc001osw.1_Missense_Mutation_p.G176A	NM_001040118	NP_001035207	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH	888					actin filament reorganization involved in cell cycle|negative regulation of stress fiber assembly|positive regulation of Cdc42 GTPase activity|positive regulation of filopodium assembly|regulation of ARF GTPase activity|regulation of cell shape|regulation of cellular component movement|small GTPase mediated signal transduction	cytosol|Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|Rho GTPase activator activity|zinc ion binding			skin(1)	1						GAGCTCCGAGCCACTGAGAGA	0.652													11	20	---	---	---	---	PASS
C2CD3	26005	broad.mit.edu	37	11	73765647	73765647	+	Intron	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73765647C>T	uc001ouu.2	-						C2CD3_uc001out.2_Intron	NM_015531	NP_056346	Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3							centrosome				ovary(4)|pancreas(2)|skin(1)	7	Breast(11;4.16e-06)					TAACAGAGTTCATACCTCCTT	0.328													9	137	---	---	---	---	PASS
PCF11	51585	broad.mit.edu	37	11	82880471	82880471	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82880471G>C	uc001ozx.3	+	8	3439	c.3094G>C	c.(3094-3096)GAA>CAA	p.E1032Q	PCF11_uc010rsu.1_Missense_Mutation_p.E1163Q	NM_015885	NP_056969	O94913	PCF11_HUMAN	pre-mRNA cleavage complex II protein Pcf11	1032	Gly-rich.				mRNA 3'-end processing|mRNA cleavage|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage factor complex				ovary(1)	1						TCCAAGATTTGAAGGTTGTCA	0.493													17	31	---	---	---	---	PASS
BIRC3	330	broad.mit.edu	37	11	102207664	102207664	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102207664G>A	uc001pgx.2	+	10	1868	c.1646G>A	c.(1645-1647)CGG>CAG	p.R549Q		NM_182962	NP_892007	Q13489	BIRC3_HUMAN	baculoviral IAP repeat-containing protein 3	549					anti-apoptosis|apoptosis|cell surface receptor linked signaling pathway	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|skin(1)	4	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)		GAACAATTGCGGAGACTACAA	0.343			T	MALT1	MALT								20	38	---	---	---	---	PASS
C11orf65	160140	broad.mit.edu	37	11	108253848	108253848	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108253848G>A	uc001pkh.2	-	9	912	c.842C>T	c.(841-843)TCA>TTA	p.S281L	C11orf65_uc010rvx.1_Intron|C11orf65_uc009yxu.1_RNA	NM_152587	NP_689800	Q8NCR3	CK065_HUMAN	hypothetical protein LOC160140	281										ovary(1)	1		all_cancers(61;1.38e-11)|all_epithelial(67;3.16e-07)|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;8.21e-06)|BRCA - Breast invasive adenocarcinoma(274;1.01e-05)|all cancers(92;0.000189)|Colorectal(284;0.114)|OV - Ovarian serous cystadenocarcinoma(223;0.144)		TTGCATCTTTGATATGTCTCC	0.308													4	113	---	---	---	---	PASS
DDX10	1662	broad.mit.edu	37	11	108564235	108564235	+	Intron	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108564235C>T	uc001pkm.2	+						DDX10_uc001pkl.1_Intron	NM_004398	NP_004389	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10								ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity			breast(2)|lung(1)|prostate(1)	4		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		CACATCCCTTCTCTGTAGATT	0.428			T	NUP98	AML*								25	343	---	---	---	---	PASS
CADM1	23705	broad.mit.edu	37	11	115099956	115099956	+	Missense_Mutation	SNP	T	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115099956T>A	uc001ppi.3	-	5	727	c.598A>T	c.(598-600)ACT>TCT	p.T200S	CADM1_uc001ppf.3_Missense_Mutation_p.T200S|CADM1_uc001ppk.3_Missense_Mutation_p.T200S|CADM1_uc001ppj.3_Missense_Mutation_p.T200S|CADM1_uc001ppl.2_Missense_Mutation_p.T200S	NM_014333	NP_055148	Q9BY67	CADM1_HUMAN	immunoglobulin superfamily, member 4D isoform 1	200	Ig-like C2-type 1.|Extracellular (Potential).				adherens junction organization|apoptosis|cell differentiation|cell junction assembly|cell recognition|detection of stimulus|heterophilic cell-cell adhesion|homophilic cell adhesion|multicellular organismal development|positive regulation of cytokine secretion|spermatogenesis|susceptibility to natural killer cell mediated cytotoxicity	basolateral plasma membrane|cell-cell junction|integral to membrane	PDZ domain binding|protein C-terminus binding|protein homodimerization activity|receptor binding			ovary(2)	2	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)		CTGGTCACAGTGTACATGTCT	0.517													19	36	---	---	---	---	PASS
GRIK4	2900	broad.mit.edu	37	11	120811158	120811158	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120811158C>A	uc001pxn.2	+	14	1866	c.1579C>A	c.(1579-1581)CGC>AGC	p.R527S	GRIK4_uc009zav.1_Missense_Mutation_p.R527S|GRIK4_uc009zaw.1_Missense_Mutation_p.R527S|GRIK4_uc009zax.1_Missense_Mutation_p.R527S	NM_014619	NP_055434	Q16099	GRIK4_HUMAN	glutamate receptor KA1 precursor	527	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)	CATTCTTTACCGCGTTCATAT	0.398													3	82	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	124135522	124135522	+	IGR	SNP	A	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124135522A>C								OR8G2 (39212 upstream) : OR8D1 (44215 downstream)																							CGCTACACTGAGGGCAGGTCC	0.488													40	86	---	---	---	---	PASS
OR8B3	390271	broad.mit.edu	37	11	124267208	124267208	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124267208G>A	uc010saj.1	-	1	40	c.40C>T	c.(40-42)CTT>TTT	p.L14F	OR8B2_uc001qab.3_RNA	NM_001005467	NP_001005467	Q8NGG8	OR8B3_HUMAN	olfactory receptor, family 8, subfamily B,	14	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		AATCCAGCAAGAATAAATTCA	0.383													10	20	---	---	---	---	PASS
CACNA1C	775	broad.mit.edu	37	12	2676922	2676922	+	Silent	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2676922C>G	uc009zdu.1	+	13	2170	c.1857C>G	c.(1855-1857)CTC>CTG	p.L619L	CACNA1C_uc009zdv.1_Silent_p.L616L|CACNA1C_uc001qkb.2_Silent_p.L619L|CACNA1C_uc001qkc.2_Silent_p.L619L|CACNA1C_uc001qke.2_Silent_p.L619L|CACNA1C_uc001qkf.2_Silent_p.L619L|CACNA1C_uc001qjz.2_Silent_p.L619L|CACNA1C_uc001qkd.2_Silent_p.L619L|CACNA1C_uc001qkg.2_Silent_p.L619L|CACNA1C_uc009zdw.1_Silent_p.L619L|CACNA1C_uc001qkh.2_Silent_p.L619L|CACNA1C_uc001qkl.2_Silent_p.L619L|CACNA1C_uc001qkn.2_Silent_p.L619L|CACNA1C_uc001qko.2_Silent_p.L619L|CACNA1C_uc001qkp.2_Silent_p.L619L|CACNA1C_uc001qkr.2_Silent_p.L619L|CACNA1C_uc001qku.2_Silent_p.L619L|CACNA1C_uc001qkq.2_Silent_p.L619L|CACNA1C_uc001qks.2_Silent_p.L619L|CACNA1C_uc001qkt.2_Silent_p.L619L|CACNA1C_uc001qka.1_Silent_p.L154L|CACNA1C_uc001qki.1_Silent_p.L355L|CACNA1C_uc001qkj.1_Silent_p.L355L|CACNA1C_uc001qkk.1_Silent_p.L355L|CACNA1C_uc001qkm.1_Silent_p.L355L	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	619	II.|Helical; Name=S4 of repeat II; (Potential).				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	TCTCCGTGCTCAGATGCGTCC	0.567													3	26	---	---	---	---	PASS
DYRK4	8798	broad.mit.edu	37	12	4722667	4722667	+	Intron	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4722667C>G	uc001qmx.2	+						DYRK4_uc001qmy.1_Intron|DYRK4_uc001qmz.1_Intron|DYRK4_uc001qna.1_Intron|DYRK4_uc010ser.1_Intron	NM_003845	NP_003836	Q9NR20	DYRK4_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation							Golgi apparatus	ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)|skin(1)	3			Colorectal(7;0.103)			TCTGTCTTCTCTCTCCTTTAG	0.403													11	38	---	---	---	---	PASS
KCNA6	3742	broad.mit.edu	37	12	4920788	4920788	+	Silent	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4920788G>T	uc001qng.2	+	1	2447	c.1581G>T	c.(1579-1581)ACG>ACT	p.T527T		NM_002235	NP_002226	P17658	KCNA6_HUMAN	potassium voltage-gated channel, shaker-related	527	PDZ-binding (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			skin(2)|ovary(1)	3						GAATGCTCACGGAGGTCTGAC	0.557										HNSCC(72;0.22)			3	92	---	---	---	---	PASS
CHD4	1108	broad.mit.edu	37	12	6696654	6696654	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6696654C>G	uc001qpo.2	-	25	3939	c.3775G>C	c.(3775-3777)GAC>CAC	p.D1259H	CHD4_uc001qpn.2_Missense_Mutation_p.D1252H|CHD4_uc001qpp.2_Missense_Mutation_p.D1256H	NM_001273	NP_001264	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	1259					chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding			central_nervous_system(2)	2						TGGTTACGGTCTAGCAGCCGT	0.453													12	182	---	---	---	---	PASS
FOXJ2	55810	broad.mit.edu	37	12	8203146	8203146	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8203146C>T	uc001qtu.2	+	10	2651	c.1566C>T	c.(1564-1566)CCC>CCT	p.P522P		NM_018416	NP_060886	Q9P0K8	FOXJ2_HUMAN	forkhead box J2	522					embryo development|organ development|pattern specification process|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|tissue development	nucleolus|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding			upper_aerodigestive_tract(2)|ovary(2)|skin(1)	5				Kidney(36;0.0944)		CACAAGCTCCCCACCTCTACC	0.527													54	75	---	---	---	---	PASS
KLRC2	3822	broad.mit.edu	37	12	10583707	10583707	+	3'UTR	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10583707G>A	uc001qyk.2	-	6					KLRC3_uc001qyh.2_Intron|KLRC2_uc010she.1_Intron	NM_002260	NP_002251	P26717	NKG2C_HUMAN	killer cell lectin-like receptor subfamily C,						cellular defense response	integral to plasma membrane	sugar binding|transmembrane receptor activity				0						AAACGCAAATGCTTTACTTCT	0.308													12	96	---	---	---	---	PASS
PRB2	653247	broad.mit.edu	37	12	11546403	11546403	+	Silent	SNP	T	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11546403T>G	uc010shk.1	-	3	644	c.609A>C	c.(607-609)GGA>GGC	p.G203G		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)			GTGGGGGTGGTCCTTGTGGCT	0.602													88	207	---	---	---	---	PASS
GRIN2B	2904	broad.mit.edu	37	12	13768424	13768424	+	Intron	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13768424C>G	uc001rbt.2	-							NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	TGTGGACACTCACCTCTCCAA	0.358													21	201	---	---	---	---	PASS
PIK3C2G	5288	broad.mit.edu	37	12	18435469	18435469	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18435469G>T	uc001rdt.2	+	2	570	c.454G>T	c.(454-456)GAT>TAT	p.D152Y	PIK3C2G_uc010sia.1_RNA|PIK3C2G_uc010sib.1_Missense_Mutation_p.D152Y|PIK3C2G_uc010sic.1_5'UTR	NM_004570	NP_004561	O75747	P3C2G_HUMAN	phosphoinositide-3-kinase, class 2 gamma	152					cell communication|phosphatidylinositol-mediated signaling	membrane|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2)	21		Hepatocellular(102;0.194)				CACAAGTTTGGATAAAATTAA	0.343													4	50	---	---	---	---	PASS
PLEKHA5	54477	broad.mit.edu	37	12	19489488	19489488	+	Missense_Mutation	SNP	T	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19489488T>A	uc001reb.2	+	16	2265	c.2179T>A	c.(2179-2181)TAC>AAC	p.Y727N	PLEKHA5_uc010sie.1_Missense_Mutation_p.Y830N|PLEKHA5_uc001rea.2_Missense_Mutation_p.Y785N|PLEKHA5_uc009zin.2_Missense_Mutation_p.Y485N|PLEKHA5_uc010sif.1_Missense_Mutation_p.Y658N|PLEKHA5_uc010sig.1_Missense_Mutation_p.Y646N|PLEKHA5_uc010sih.1_Missense_Mutation_p.Y619N|PLEKHA5_uc001rec.1_Missense_Mutation_p.Y473N|PLEKHA5_uc009zio.2_Missense_Mutation_p.Y49N	NM_019012	NP_061885	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A	727							1-phosphatidylinositol binding|protein binding			ovary(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					TAAGTTAGAATACGATGTAAC	0.343													23	54	---	---	---	---	PASS
PFKM	5213	broad.mit.edu	37	12	48528749	48528749	+	Silent	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48528749C>G	uc001rrc.2	+	9	941	c.771C>G	c.(769-771)CTC>CTG	p.L257L	PFKM_uc001rra.1_5'UTR|PFKM_uc001rrb.1_Silent_p.L328L|PFKM_uc001rrd.2_5'UTR|PFKM_uc001rre.1_Silent_p.L257L|PFKM_uc001rrg.1_Silent_p.L257L	NM_000289	NP_000280	P08237	K6PF_HUMAN	phosphofructokinase, muscle	257					fructose 6-phosphate metabolic process|glycolysis|muscle cell homeostasis	6-phosphofructokinase complex|apical plasma membrane	6-phosphofructokinase activity|ATP binding|identical protein binding|kinase binding|metal ion binding|protein C-terminus binding			ovary(2)|upper_aerodigestive_tract(1)|kidney(1)	4						GTTCTCGTCTCAACATCATCA	0.463													44	67	---	---	---	---	PASS
H1FNT	341567	broad.mit.edu	37	12	48723390	48723390	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48723390G>C	uc001rrm.2	+	1	628	c.316G>C	c.(316-318)GCC>CCC	p.A106P		NM_181788	NP_861453	Q75WM6	H1FNT_HUMAN	H1 histone family, member N, testis-specific	106					chromosome condensation|multicellular organismal development|sperm chromatin condensation|spermatid nucleus elongation	nuclear chromatin	ATP binding|DNA binding			pancreas(1)	1						GCAGGCCAAGGCCACGCTCCT	0.682													3	32	---	---	---	---	PASS
MLL2	8085	broad.mit.edu	37	12	49427912	49427912	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49427912C>T	uc001rta.3	-	38	10678	c.10678G>A	c.(10678-10680)GAT>AAT	p.D3560N		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	3560	Gln-rich.				chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41						TTCTCAGCATCAGCTTCTGGG	0.552			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			11	76	---	---	---	---	PASS
KRT81	3887	broad.mit.edu	37	12	52680957	52680957	+	Silent	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52680957C>G	uc001sab.2	-	7	1226	c.1176G>C	c.(1174-1176)GTG>GTC	p.V392V	KRT86_uc010snq.1_Intron|KRT86_uc009zmg.2_Intron|KRT81_uc001sac.2_Silent_p.V11V	NM_002281	NP_002272	Q14533	KRT81_HUMAN	keratin, hair, basic, 1	392	Rod.|Coil 2.					keratin filament	protein binding|structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(357;0.189)		TGGAGTTCATCACCTCCTGGT	0.657													6	133	---	---	---	---	PASS
KRT81	3887	broad.mit.edu	37	12	52681494	52681494	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52681494C>A	uc001sab.2	-	6	962	c.912G>T	c.(910-912)ATG>ATT	p.M304I	KRT86_uc010snq.1_Intron|KRT86_uc009zmg.2_Intron|KRT81_uc001sac.2_Intron	NM_002281	NP_002272	Q14533	KRT81_HUMAN	keratin, hair, basic, 1	304	Rod.|Coil 2.					keratin filament	protein binding|structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(357;0.189)		CCGTGGCCTTCATCTCCTCAC	0.542													4	55	---	---	---	---	PASS
HOXC10	3226	broad.mit.edu	37	12	54379211	54379211	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54379211G>T	uc001sen.2	+	1	266	c.168G>T	c.(166-168)AGG>AGT	p.R56S		NM_017409	NP_059105	Q9NYD6	HXC10_HUMAN	homeobox C10	56					positive regulation of cell proliferation	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			pancreas(1)	1						TCTCCAAGAGGGACGAGGGCA	0.647													25	31	---	---	---	---	PASS
NCKAP1L	3071	broad.mit.edu	37	12	54903687	54903687	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54903687G>T	uc001sgc.3	+	7	732	c.653G>T	c.(652-654)GGG>GTG	p.G218V	NCKAP1L_uc010sox.1_5'UTR|NCKAP1L_uc010soy.1_Missense_Mutation_p.G168V	NM_005337	NP_005328	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	218					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						AGAAACCAGGGGGCTGAGCAG	0.517													93	123	---	---	---	---	PASS
NCKAP1L	3071	broad.mit.edu	37	12	54903688	54903688	+	Silent	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54903688G>T	uc001sgc.3	+	7	733	c.654G>T	c.(652-654)GGG>GGT	p.G218G	NCKAP1L_uc010sox.1_5'UTR|NCKAP1L_uc010soy.1_Silent_p.G168G	NM_005337	NP_005328	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	218					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						GAAACCAGGGGGCTGAGCAGT	0.517													91	123	---	---	---	---	PASS
PDE1B	5153	broad.mit.edu	37	12	54964134	54964134	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54964134G>T	uc001sgd.1	+	6	753	c.587G>T	c.(586-588)CGC>CTC	p.R196L	PDE1B_uc010soz.1_Missense_Mutation_p.R59L|PDE1B_uc010spa.1_Missense_Mutation_p.R155L|PDE1B_uc001sgf.2_Missense_Mutation_p.R59L|PDE1B_uc001sge.2_Missense_Mutation_p.R176L|PDE1B_uc009znq.2_5'UTR	NM_000924	NP_000915	Q01064	PDE1B_HUMAN	phosphodiesterase 1B isoform 1	196					activation of phospholipase C activity|apoptosis|nerve growth factor receptor signaling pathway|platelet activation	cytosol|nucleus	3',5'-cyclic-AMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			upper_aerodigestive_tract(1)|ovary(1)	2						CTCATCAGCCGCTTCAAGGTT	0.502													50	78	---	---	---	---	PASS
KIAA0748	9840	broad.mit.edu	37	12	55356572	55356572	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55356572C>T	uc001sgn.3	-	9	1220	c.1110G>A	c.(1108-1110)CAG>CAA	p.Q370Q	KIAA0748_uc001sgl.3_Silent_p.Q232Q|KIAA0748_uc001sgm.3_Silent_p.Q117Q|KIAA0748_uc010spb.1_Silent_p.Q117Q|KIAA0748_uc010spc.1_Silent_p.Q232Q|KIAA0748_uc010spd.1_Silent_p.Q370Q|KIAA0748_uc001sgo.3_RNA	NM_001098815	NP_001092285	A2RU30	K0748_HUMAN	hypothetical protein LOC9840	370										ovary(1)|central_nervous_system(1)	2						TGGACATCCTCTGCTGTGTTT	0.522													5	64	---	---	---	---	PASS
LRIG3	121227	broad.mit.edu	37	12	59282752	59282752	+	Intron	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:59282752G>C	uc001sqr.2	-						LRIG3_uc009zqh.2_Intron|LRIG3_uc010ssh.1_Intron	NM_153377	NP_700356	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like							integral to membrane				skin(3)|ovary(1)	4			GBM - Glioblastoma multiforme(1;1.17e-18)			TCGCTGCATTGAGTATTACAA	0.348													12	123	---	---	---	---	PASS
GLIPR1L2	144321	broad.mit.edu	37	12	75785038	75785038	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75785038G>A	uc001sxr.1	+	1	150	c.142G>A	c.(142-144)GAG>AAG	p.E48K	CAPS2_uc001sxm.3_5'Flank|CAPS2_uc009zsa.2_5'Flank|GLIPR1L2_uc001sxp.1_Missense_Mutation_p.E48K|GLIPR1L2_uc001sxq.1_5'UTR	NM_152436	NP_689649	Q4G1C9	GRPL2_HUMAN	GLI pathogenesis-related 1 like 2	48						integral to membrane				ovary(1)	1						TTTGCCAGACGAGGAGGACGT	0.562											OREG0021999	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	103	---	---	---	---	PASS
NAV3	89795	broad.mit.edu	37	12	78225318	78225318	+	Missense_Mutation	SNP	T	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78225318T>A	uc001syp.2	+	1	250	c.77T>A	c.(76-78)ATA>AAA	p.I26K	NAV3_uc001syo.2_Missense_Mutation_p.I26K	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	26						nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						GCTCTTCCGATACCAAATCTT	0.458										HNSCC(70;0.22)			98	127	---	---	---	---	PASS
NAV3	89795	broad.mit.edu	37	12	78594313	78594313	+	Missense_Mutation	SNP	A	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78594313A>C	uc001syp.2	+	38	6949	c.6776A>C	c.(6775-6777)GAT>GCT	p.D2259A	NAV3_uc001syo.2_Missense_Mutation_p.D2237A|NAV3_uc010sub.1_Missense_Mutation_p.D1716A|NAV3_uc009zsf.2_Missense_Mutation_p.D1068A	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	2259						nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						TGGTTCATGGATCTCTGGAAC	0.338										HNSCC(70;0.22)			49	77	---	---	---	---	PASS
DCN	1634	broad.mit.edu	37	12	91552164	91552164	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91552164G>A	uc001tbs.2	-	3	541	c.447C>T	c.(445-447)CCC>CCT	p.P149P	DCN_uc001tbo.2_Intron|DCN_uc001tbp.2_Intron|DCN_uc001tbq.2_Intron|DCN_uc001tbr.2_Intron|DCN_uc001tbt.2_Silent_p.P149P|DCN_uc001tbu.2_Silent_p.P149P	NM_133503	NP_598010	P07585	PGS2_HUMAN	decorin isoform a preproprotein	149	LRR 4.				organ morphogenesis	extracellular space				central_nervous_system(2)|ovary(1)|lung(1)	4						GAAGAGTTTTGGGCATTTTTT	0.418													76	97	---	---	---	---	PASS
PLXNC1	10154	broad.mit.edu	37	12	94620959	94620959	+	Missense_Mutation	SNP	G	C	C	rs143304608		TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94620959G>C	uc001tdc.2	+	9	2177	c.1928G>C	c.(1927-1929)GGA>GCA	p.G643A		NM_005761	NP_005752	O60486	PLXC1_HUMAN	plexin C1 precursor	643	Extracellular (Potential).				axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3						AAGACATCAGGAGGAGGAAGA	0.468													4	90	---	---	---	---	PASS
PLXNC1	10154	broad.mit.edu	37	12	94691141	94691141	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94691141G>A	uc001tdc.2	+	26	4265	c.4016G>A	c.(4015-4017)CGA>CAA	p.R1339Q	PLXNC1_uc010sut.1_Missense_Mutation_p.R386Q|PLXNC1_uc009zsv.2_Missense_Mutation_p.R78Q	NM_005761	NP_005752	O60486	PLXC1_HUMAN	plexin C1 precursor	1339	Cytoplasmic (Potential).				axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3						AAGAGACATCGAGGGAAGCAC	0.463													15	23	---	---	---	---	PASS
ALDH2	217	broad.mit.edu	37	12	112247365	112247365	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112247365C>G	uc001tst.2	+	13	1981	c.1540C>G	c.(1540-1542)CAG>GAG	p.Q514E	ALDH2_uc010syi.1_Missense_Mutation_p.Q467E|ALDH2_uc009zvy.2_Missense_Mutation_p.Q438E	NM_000690	NP_000681	P05091	ALDH2_HUMAN	mitochondrial aldehyde dehydrogenase 2	514					carbohydrate metabolic process|ethanol oxidation|neurotransmitter biosynthetic process|xenobiotic metabolic process	mitochondrial matrix	aldehyde dehydrogenase (NAD) activity|aldehyde dehydrogenase|electron carrier activity			skin(2)|ovary(1)|central_nervous_system(1)	4					Disulfiram(DB00822)|Guanidine(DB00536)|NADH(DB00157)|Nitroglycerin(DB00727)	CAAAGTGCCTCAGAAGAACTC	0.478			T	HMGA2	leiomyoma								36	49	---	---	---	---	PASS
OAS1	4938	broad.mit.edu	37	12	113346551	113346551	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113346551G>C	uc001tud.2	+	2	497	c.391G>C	c.(391-393)GCG>CCG	p.A131P	OAS1_uc010syn.1_Missense_Mutation_p.A130P|OAS1_uc010syo.1_Missense_Mutation_p.A130P|OAS1_uc001tub.2_Missense_Mutation_p.A131P|OAS1_uc001tuc.2_Missense_Mutation_p.A131P|OAS1_uc009zwf.2_Missense_Mutation_p.A130P	NM_016816	NP_058132	P00973	OAS1_HUMAN	2',5'-oligoadenylate synthetase 1 isoform 1	131	Necessary for binding to dsRNA.				interferon-gamma-mediated signaling pathway|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|type I interferon-mediated signaling pathway	endoplasmic reticulum|microsome|mitochondrion|nucleus	ATP binding|nucleotidyltransferase activity|RNA binding			ovary(2)	2						CAACCCCCGTGCGCTCAGCTT	0.572													45	60	---	---	---	---	PASS
RASAL1	8437	broad.mit.edu	37	12	113544952	113544952	+	Nonsense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113544952G>C	uc001tum.1	-	16	1900	c.1607C>G	c.(1606-1608)TCA>TGA	p.S536*	RASAL1_uc010syp.1_Nonsense_Mutation_p.S536*|RASAL1_uc001tul.2_Nonsense_Mutation_p.S536*|RASAL1_uc001tun.1_Nonsense_Mutation_p.S537*|RASAL1_uc010syq.1_Nonsense_Mutation_p.S536*|RASAL1_uc001tuo.3_Nonsense_Mutation_p.S536*|RASAL1_uc010syr.1_3'UTR	NM_004658	NP_004649	O95294	RASL1_HUMAN	RAS protein activator like 1	536					intracellular signal transduction|negative regulation of Ras protein signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	metal ion binding|phospholipid binding|Ras GTPase activator activity			ovary(2)|skin(2)	4						TCTCACACGTGAGACACACTG	0.607													4	63	---	---	---	---	PASS
SBNO1	55206	broad.mit.edu	37	12	123805416	123805416	+	Intron	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123805416G>C	uc010tap.1	-						SBNO1_uc010tao.1_Intron|SBNO1_uc010taq.1_Intron|SBNO1_uc001uet.2_Intron|SBNO1_uc001ueu.2_Intron|SBNO1_uc001uev.2_Intron|SBNO1_uc009zxy.1_Intron	NM_018183	NP_060653	A3KN83	SBNO1_HUMAN	sno, strawberry notch homolog 1								ATP binding|DNA binding|hydrolase activity			breast(5)|skin(2)|ovary(1)|kidney(1)	9	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		CCAGGGATCTGAGTGTTAAGG	0.269													5	73	---	---	---	---	PASS
ATP8A2	51761	broad.mit.edu	37	13	26129135	26129135	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26129135G>A	uc001uqk.2	+	13	1334	c.1192G>A	c.(1192-1194)GAT>AAT	p.D398N	ATP8A2_uc010tdi.1_Missense_Mutation_p.D358N|ATP8A2_uc010tdj.1_RNA|ATP8A2_uc001uql.1_Missense_Mutation_p.D358N	NM_016529	NP_057613	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter-like,	358	Cytoplasmic (Potential).				ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)|skin(1)	4		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		TCAGGACACAGATATGTATTA	0.388													4	96	---	---	---	---	PASS
KLHL1	57626	broad.mit.edu	37	13	70514251	70514251	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:70514251G>A	uc001vip.2	-	4	1729	c.935C>T	c.(934-936)TCT>TTT	p.S312F	KLHL1_uc010thm.1_Missense_Mutation_p.S251F	NM_020866	NP_065917	Q9NR64	KLHL1_HUMAN	kelch-like 1 protein	312					actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding				0		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)		TAAACAGTTAGATGGATGCAA	0.468													9	27	---	---	---	---	PASS
GAS6	2621	broad.mit.edu	37	13	114541067	114541067	+	Silent	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114541067G>C	uc001vud.2	-	6	717	c.564C>G	c.(562-564)CTC>CTG	p.L188L	GAS6_uc001vuf.2_5'Flank	NM_000820	NP_000811	Q14393	GAS6_HUMAN	growth arrest-specific 6 isoform 1 precursor	188	EGF-like 2; calcium-binding (Potential).				cell proliferation|leukocyte migration|peptidyl-glutamic acid carboxylation|platelet activation|platelet degranulation|positive regulation of ERK1 and ERK2 cascade|positive regulation of fibroblast proliferation|post-translational protein modification|proteolysis|regulation of growth	endoplasmic reticulum lumen|extracellular space|Golgi lumen|platelet alpha granule lumen	calcium ion binding|receptor agonist activity			central_nervous_system(4)	4	Lung NSC(43;0.00976)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0176)|all_epithelial(44;0.0104)|all_lung(25;0.0249)|Lung NSC(25;0.0908)|Breast(118;0.188)				CATCAGAGGAGAGCTCGAAGC	0.592													14	111	---	---	---	---	PASS
OR4Q3	441669	broad.mit.edu	37	14	20216323	20216323	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20216323C>G	uc010tkt.1	+	1	737	c.737C>G	c.(736-738)ACA>AGA	p.T246R		NM_172194	NP_751944	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q,	246	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(3)	3	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TCTCACCTGACAGTGGTCAGC	0.453													44	76	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	22446940	22446940	+	Intron	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22446940G>T	uc001wbw.2	+						uc010tmh.1_Intron|uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_5'Flank|uc010tml.1_RNA|uc010tmm.1_Missense_Mutation_p.A8S|uc010tmn.1_5'Flank					SubName: Full=Alpha-chain C region; Flags: Fragment;																		GCTCGTCCCAGCGTTCCAGGT	0.507											OREG0022573	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	53	91	---	---	---	---	PASS
ADCY4	196883	broad.mit.edu	37	14	24792232	24792232	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24792232G>C	uc001wov.2	-	18	2226	c.2220C>G	c.(2218-2220)TTC>TTG	p.F740L	ADCY4_uc001wow.2_Missense_Mutation_p.F740L|ADCY4_uc010toh.1_Missense_Mutation_p.F426L|ADCY4_uc001wox.2_Missense_Mutation_p.F740L|ADCY4_uc001woy.2_Missense_Mutation_p.F740L	NM_139247	NP_640340	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	740					activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding|protein binding			ovary(1)|lung(1)|pancreas(1)	3				GBM - Glioblastoma multiforme(265;0.0192)		GCTTCAGCTCGAAGCTCATGT	0.632													4	34	---	---	---	---	PASS
EGLN3	112399	broad.mit.edu	37	14	34419786	34419786	+	Missense_Mutation	SNP	T	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34419786T>A	uc001wsa.3	-	1	499	c.173A>T	c.(172-174)GAC>GTC	p.D58V	EGLN3_uc001wry.2_Intron|EGLN3_uc001wrz.2_Missense_Mutation_p.D58V|EGLN3_uc001wsb.1_Missense_Mutation_p.D58V	NM_022073	NP_071356	Q9H6Z9	EGLN3_HUMAN	egl nine homolog 3	58					apoptosis	cytoplasm|nucleus	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding				0	Breast(36;0.0303)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.000246)|Lung(238;0.000959)|Epithelial(34;0.155)	GBM - Glioblastoma multiforme(112;0.0118)	Vitamin C(DB00126)	CAGCTGGCCGTCCCGCAGGGC	0.716													8	16	---	---	---	---	PASS
PPIL5	122769	broad.mit.edu	37	14	50074710	50074710	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50074710G>A	uc001wwn.2	+	3	1199	c.875G>A	c.(874-876)AGA>AAA	p.R292K	SDCCAG1_uc010anj.1_Intron|PPIL5_uc001wwo.2_Intron|PPIL5_uc010ank.2_Missense_Mutation_p.R233K|PPIL5_uc001wwp.2_RNA	NM_152329	NP_689542	Q96L50	LLR1_HUMAN	peptidylprolyl isomerase (cyclophilin)-like 5	292	LRR 6.										0	all_epithelial(31;0.0021)|Breast(41;0.0124)					AGTGAATTTAGAAATTTATCC	0.333													3	54	---	---	---	---	PASS
WDHD1	11169	broad.mit.edu	37	14	55408302	55408302	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55408302T>C	uc001xbm.1	-	26	3374	c.3296A>G	c.(3295-3297)AAA>AGA	p.K1099R	WDHD1_uc010aom.1_Missense_Mutation_p.K616R|WDHD1_uc001xbn.1_Missense_Mutation_p.K976R	NM_007086	NP_009017	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	1099						cytoplasm|nucleoplasm	DNA binding			skin(1)	1						CTCTTTTGCTTTTTCTTCCTG	0.373													31	55	---	---	---	---	PASS
FUT8	2530	broad.mit.edu	37	14	66209111	66209111	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66209111C>G	uc001xin.2	+	11	2908	c.1711C>G	c.(1711-1713)CCT>GCT	p.P571A	FUT8_uc001xio.2_Missense_Mutation_p.P571A|FUT8_uc010tsp.1_Missense_Mutation_p.P408A|FUT8_uc001xir.3_RNA|FUT8_uc001xip.2_Missense_Mutation_p.P571A|FUT8_uc001xiq.2_Missense_Mutation_p.P442A|FUT8_uc001xis.2_Missense_Mutation_p.P165A	NM_178155	NP_835368	Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 isoform a	571	Lumenal (Potential).				in utero embryonic development|L-fucose catabolic process|N-glycan processing|oligosaccharide biosynthetic process|post-translational protein modification|protein glycosylation in Golgi|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	glycoprotein 6-alpha-L-fucosyltransferase activity|SH3 domain binding			ovary(1)	1				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)		CCCCACATATCCTGAGGCTGA	0.438													4	57	---	---	---	---	PASS
DYNC1H1	1778	broad.mit.edu	37	14	102498739	102498739	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102498739C>T	uc001yks.2	+	52	10178	c.10014C>T	c.(10012-10014)ATC>ATT	p.I3338I		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	3338	Stalk (By similarity).				cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10						GGAAGCAGATCCGCTCCATCA	0.562													38	59	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	22483126	22483126	+	IGR	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22483126C>A								OR4N3P (68741 upstream) : MIR1268 (30103 downstream)																							ACCAACTGGTCCTGAGAGTGC	0.517													21	147	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	22483127	22483127	+	IGR	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22483127C>A								OR4N3P (68742 upstream) : MIR1268 (30102 downstream)																							CCAACTGGTCCTGAGAGTGCG	0.517													20	147	---	---	---	---	PASS
APBA2	321	broad.mit.edu	37	15	29400588	29400588	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29400588G>C	uc001zck.2	+	12	2240	c.2033G>C	c.(2032-2034)GGA>GCA	p.G678A	APBA2_uc010azj.2_Missense_Mutation_p.G666A|APBA2_uc010uat.1_Missense_Mutation_p.G666A|APBA2_uc001zcl.2_Missense_Mutation_p.G666A	NM_005503	NP_005494	Q99767	APBA2_HUMAN	amyloid beta A4 precursor protein-binding,	678	PDZ 2.				nervous system development|protein transport		protein binding				0		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		GTGCAGAATGGAATTGTGAGT	0.617													25	60	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	34135745	34135745	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34135745C>A	uc001zhi.2	+	92	13336	c.13266C>A	c.(13264-13266)TTC>TTA	p.F4422L	RYR3_uc010bar.2_Missense_Mutation_p.F4417L	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	4422	Helical; Name=M5; (Potential).				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TTGTAGCCTTCGCTATCAACT	0.393													14	11	---	---	---	---	PASS
BUB1B	701	broad.mit.edu	37	15	40498506	40498506	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40498506C>G	uc001zkx.3	+	15	2068	c.1856C>G	c.(1855-1857)TCC>TGC	p.S619C	BUB1B_uc010ucl.1_Missense_Mutation_p.S487C	NM_001211	NP_001202	O60566	BUB1B_HUMAN	budding uninhibited by benzimidazoles 1 beta	619					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell division|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|phosphatidylinositol-mediated signaling|protein localization to kinetochore|spindle organization	anaphase-promoting complex|condensed chromosome outer kinetochore|cytosol|microtubule organizing center|perinuclear region of cytoplasm|spindle midzone	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)|kidney(1)	4		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)		CGTTTTGTATCCACTCCTTTT	0.453			Mis|N|F|S			rhabdomyosarcoma			Mosaic_Variegated_Aneuploidy_Syndrome				9	68	---	---	---	---	PASS
BUB1B	701	broad.mit.edu	37	15	40498627	40498627	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40498627C>T	uc001zkx.3	+	15	2189	c.1977C>T	c.(1975-1977)ATC>ATT	p.I659I	BUB1B_uc010ucl.1_Silent_p.I527I	NM_001211	NP_001202	O60566	BUB1B_HUMAN	budding uninhibited by benzimidazoles 1 beta	659					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell division|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|phosphatidylinositol-mediated signaling|protein localization to kinetochore|spindle organization	anaphase-promoting complex|condensed chromosome outer kinetochore|cytosol|microtubule organizing center|perinuclear region of cytoplasm|spindle midzone	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)|kidney(1)	4		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)		GTGGCACTATCTACAGTCAGA	0.448			Mis|N|F|S			rhabdomyosarcoma			Mosaic_Variegated_Aneuploidy_Syndrome				13	119	---	---	---	---	PASS
PLCB2	5330	broad.mit.edu	37	15	40594805	40594805	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40594805C>G	uc001zld.2	-	4	538	c.237G>C	c.(235-237)CAG>CAC	p.Q79H	PLCB2_uc010bbo.2_Missense_Mutation_p.Q79H|PLCB2_uc010ucm.1_Missense_Mutation_p.Q79H|PLCB2_uc001zle.3_Missense_Mutation_p.Q79H	NM_004573	NP_004564	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	79					activation of phospholipase C activity|intracellular signal transduction|lipid catabolic process|phospholipid metabolic process|synaptic transmission	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(3)|breast(3)|kidney(1)|pancreas(1)	8		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		CCCGGAGCTTCTGGCTCTGCA	0.597													4	51	---	---	---	---	PASS
MGA	23269	broad.mit.edu	37	15	42005472	42005472	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42005472C>A	uc001zog.1	+	9	3299	c.3208C>A	c.(3208-3210)CAC>AAC	p.H1070N	MGA_uc010ucy.1_Missense_Mutation_p.H1070N|MGA_uc010ucz.1_Missense_Mutation_p.H1070N	NM_001080541	NP_001074010	Q8IWI9	MGAP_HUMAN	MAX-interacting protein isoform 2	1070						MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	12		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)		CCAACCTGCTCACTGCCGCCG	0.468													14	101	---	---	---	---	PASS
EHD4	30844	broad.mit.edu	37	15	42201981	42201981	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42201981G>C	uc001zot.2	-	5	1068	c.1005C>G	c.(1003-1005)ATC>ATG	p.I335M		NM_139265	NP_644670	Q9H223	EHD4_HUMAN	EH-domain containing 4	335					endocytic recycling|protein homooligomerization	early endosome membrane|endoplasmic reticulum|nucleus|recycling endosome membrane	ATP binding|calcium ion binding|GTP binding|GTPase activity|nucleic acid binding|protein binding			ovary(2)	2		all_cancers(109;2.54e-12)|all_epithelial(112;6.59e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		OV - Ovarian serous cystadenocarcinoma(18;1.6e-19)|GBM - Glioblastoma multiforme(94;3.77e-06)|COAD - Colon adenocarcinoma(120;0.0474)|Colorectal(105;0.0538)		GTAGCCTGCTGATAAGCTCTC	0.493													9	119	---	---	---	---	PASS
ONECUT1	3175	broad.mit.edu	37	15	53081346	53081346	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53081346C>A	uc002aci.1	-	1	864	c.736G>T	c.(736-738)GGC>TGC	p.G246C		NM_004498	NP_004489	Q9UBC0	HNF6_HUMAN	one cut homeobox 1	246					endocrine pancreas development	nucleus	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific DNA binding				0				all cancers(107;0.0708)		GGAGGAAGGCCGTTGATGGGC	0.726													56	69	---	---	---	---	PASS
TLN2	83660	broad.mit.edu	37	15	63111816	63111816	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63111816G>C	uc002alb.3	+	50	6873	c.6873G>C	c.(6871-6873)ATG>ATC	p.M2291I	TLN2_uc002alc.3_Missense_Mutation_p.M684I|TLN2_uc010uic.1_5'Flank	NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	2291					cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11						CGGAAGCCATGAAAGGTAGGC	0.572													3	69	---	---	---	---	PASS
ZWILCH	55055	broad.mit.edu	37	15	66828295	66828295	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66828295G>A	uc002aqb.2	+	15	1612	c.1366G>A	c.(1366-1368)GAT>AAT	p.D456N	ZWILCH_uc010bhu.1_Missense_Mutation_p.D342N|ZWILCH_uc002aqa.2_Missense_Mutation_p.D342N|ZWILCH_uc010bhv.2_Missense_Mutation_p.D342N	NM_017975	NP_060445	Q9H900	ZWILC_HUMAN	Zwilch	456					cell division|mitotic cell cycle checkpoint|mitotic prometaphase	condensed chromosome kinetochore|cytosol	protein binding			ovary(1)	1						TCCATCAGTAGATATACAAGA	0.333													7	75	---	---	---	---	PASS
PAQR5	54852	broad.mit.edu	37	15	69677078	69677078	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69677078C>A	uc002arz.2	+	5	620	c.242C>A	c.(241-243)TCC>TAC	p.S81Y	PAQR5_uc002asa.2_Missense_Mutation_p.S81Y	NM_017705	NP_060175	Q9NXK6	MPRG_HUMAN	progestin and adipoQ receptor family member V	81	Helical; Name=2; (Potential).				cell differentiation|multicellular organismal development|oogenesis	integral to membrane	receptor activity|steroid binding			ovary(2)	2						GACAGCTACTCCTGGCCCATG	0.522													12	189	---	---	---	---	PASS
LARP6	55323	broad.mit.edu	37	15	71124721	71124721	+	Nonsense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71124721C>T	uc002ass.2	-	3	1217	c.1146G>A	c.(1144-1146)TGG>TGA	p.W382*		NM_018357	NP_060827	Q9BRS8	LARP6_HUMAN	La ribonucleoprotein domain family, member 6	382					RNA processing	Golgi apparatus|nucleus|ribonucleoprotein complex	nucleotide binding|RNA binding				0						AGGGGCTGCTCCAAGGACTTG	0.607													6	57	---	---	---	---	PASS
SLC28A1	9154	broad.mit.edu	37	15	85488008	85488008	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85488008G>T	uc002blg.2	+	18	1986	c.1784G>T	c.(1783-1785)GGG>GTG	p.G595V	SLC28A1_uc010bnb.2_Missense_Mutation_p.G595V|SLC28A1_uc010upe.1_Missense_Mutation_p.G429V|SLC28A1_uc010upf.1_Missense_Mutation_p.G595V|SLC28A1_uc010upg.1_Intron	NM_004213	NP_004204	O00337	S28A1_HUMAN	solute carrier family 28, member 1 isoform 1	595					nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(143;0.0587)			ATGCCCAGGGGGGCTGAAGTT	0.602													4	116	---	---	---	---	PASS
IQGAP1	8826	broad.mit.edu	37	15	90999476	90999476	+	Nonsense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90999476G>T	uc002bpl.1	+	15	1806	c.1705G>T	c.(1705-1707)GAG>TAG	p.E569*		NM_003870	NP_003861	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	569					energy reserve metabolic process|regulation of insulin secretion|small GTPase mediated signal transduction	actin filament|cytoplasm|midbody|nucleus|plasma membrane	calmodulin binding|GTPase inhibitor activity|protein phosphatase binding|Ras GTPase activator activity			ovary(2)|lung(2)|central_nervous_system(2)|pancreas(1)|skin(1)	8	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			AGCTAAACTTGAGGGAGTCCT	0.463													12	67	---	---	---	---	PASS
FES	2242	broad.mit.edu	37	15	91428389	91428389	+	Silent	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91428389C>G	uc002bpv.2	+	2	210	c.114C>G	c.(112-114)GTC>GTG	p.V38V	FES_uc010uqj.1_Silent_p.V38V|FES_uc010uqk.1_Silent_p.V38V|FES_uc002bpw.2_RNA|FES_uc010bny.2_Silent_p.V38V|FES_uc002bpx.2_Silent_p.V38V|FES_uc002bpy.2_Silent_p.V38V	NM_002005	NP_001996	P07332	FES_HUMAN	feline sarcoma oncogene isoform 1	38	FCH.|Important for interaction with membranes containing phosphoinositides.				axon guidance|cell proliferation|peptidyl-tyrosine phosphorylation	cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(2)	2	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			CCCAGCGGGTCAAGAGTGACA	0.642													14	145	---	---	---	---	PASS
PDPK1	5170	broad.mit.edu	37	16	2647199	2647199	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2647199G>C	uc002cqs.2	+	13	1621	c.1477G>C	c.(1477-1479)GTT>CTT	p.V493L	PDPK1_uc002cqt.2_Missense_Mutation_p.V366L|PDPK1_uc010bsn.2_Intron|PDPK1_uc002cqu.2_Missense_Mutation_p.V466L	NM_002613	NP_002604	O15530	PDPK1_HUMAN	3-phosphoinositide dependent protein kinase-1	493	PH.				actin cytoskeleton organization|activation of protein kinase B activity|insulin receptor signaling pathway|negative regulation of protein kinase activity|nerve growth factor receptor signaling pathway|peptidyl-threonine phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|synaptic transmission|T cell costimulation|T cell receptor signaling pathway	cytosol|nucleoplasm|plasma membrane	3-phosphoinositide-dependent protein kinase activity|ATP binding			central_nervous_system(2)|ovary(1)	3		Ovarian(90;0.17)			Celecoxib(DB00482)	TGTCAACAAAGTTCTGAAAGG	0.428													5	96	---	---	---	---	PASS
CORO7	79585	broad.mit.edu	37	16	4457696	4457696	+	Intron	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4457696G>C	uc002cwh.3	-						CORO7_uc002cwe.2_5'Flank|CORO7_uc002cwf.2_Intron|CORO7_uc002cwg.3_Intron|CORO7_uc010uxh.1_Intron|CORO7_uc010uxi.1_Intron|CORO7_uc002cwi.1_5'Flank|CORO7_uc010uxj.1_Intron|CORO7_uc010btp.1_Intron|CORO7_uc010btr.1_Intron	NM_024535	NP_078811	P57737	CORO7_HUMAN	coronin 7							cytoplasmic membrane-bounded vesicle|cytosol|Golgi membrane|integral to membrane of membrane fraction|soluble fraction					0						CTGCAAGAAAGACCAAGTCCG	0.652													4	16	---	---	---	---	PASS
ACSM2A	123876	broad.mit.edu	37	16	20492206	20492206	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20492206C>T	uc010bwe.2	+	13	1711	c.1472C>T	c.(1471-1473)ACG>ATG	p.T491M	ACSM2A_uc010vax.1_Missense_Mutation_p.T412M|ACSM2A_uc002dhf.3_Missense_Mutation_p.T491M|ACSM2A_uc002dhg.3_Missense_Mutation_p.T491M|ACSM2A_uc010vay.1_Missense_Mutation_p.T412M|ACSM2A_uc002dhh.3_Missense_Mutation_p.T121M	NM_001010845	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member	491					fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding			skin(2)|breast(1)	3						GTGGTTGAGACGGCTGTGATC	0.522													26	36	---	---	---	---	PASS
GSG1L	146395	broad.mit.edu	37	16	27856301	27856301	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27856301G>C	uc002doz.2	-	4	717	c.632C>G	c.(631-633)CCC>CGC	p.P211R	GSG1L_uc010bya.1_Missense_Mutation_p.P160R|GSG1L_uc010bxz.1_Missense_Mutation_p.P56R|GSG1L_uc002doy.2_Missense_Mutation_p.P56R	NM_001109763	NP_001103233	Q6UXU4	GSG1L_HUMAN	GSG1-like isoform 1	211						integral to membrane				ovary(1)	1						CCAGGAATGGGGTCTCCAGTC	0.612													7	8	---	---	---	---	PASS
SEZ6L2	26470	broad.mit.edu	37	16	29888751	29888751	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29888751C>T	uc002duq.3	-	11	1990	c.1750G>A	c.(1750-1752)GAC>AAC	p.D584N	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|SEZ6L2_uc002dup.3_Missense_Mutation_p.D514N|SEZ6L2_uc002dur.3_Missense_Mutation_p.D514N|SEZ6L2_uc002dus.3_Missense_Mutation_p.D470N|SEZ6L2_uc010vec.1_Missense_Mutation_p.D584N|SEZ6L2_uc010ved.1_Missense_Mutation_p.D540N	NM_201575	NP_963869	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2 isoform	584	CUB 3.|Extracellular (Potential).					endoplasmic reticulum membrane|integral to membrane|plasma membrane				ovary(1)|skin(1)	2						CCGTCCCCGTCGAACAGCGTC	0.682													9	30	---	---	---	---	PASS
SALL1	6299	broad.mit.edu	37	16	51171035	51171035	+	Silent	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51171035G>T	uc010vgs.1	-	3	3994	c.3963C>A	c.(3961-3963)ATC>ATA	p.I1321I	SALL1_uc010vgr.1_Silent_p.I1224I|SALL1_uc010cbv.2_Silent_p.I173I	NM_002968	NP_002959	Q9NSC2	SALL1_HUMAN	sal-like 1 isoform a	1321					adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development	chromocenter|cytoplasm|heterochromatin|nucleus	beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(5)|ovary(3)	8		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			AACTCGTGACGATCTCCTTGC	0.592													16	25	---	---	---	---	PASS
CDH8	1006	broad.mit.edu	37	16	61854866	61854866	+	Silent	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61854866A>G	uc002eog.1	-	6	1239	c.987T>C	c.(985-987)GAT>GAC	p.D329D	CDH8_uc002eoh.2_Silent_p.D98D	NM_001796	NP_001787	P55286	CADH8_HUMAN	cadherin 8, type 2 preproprotein	329	Extracellular (Potential).|Cadherin 3.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		GGGCCTGGGCATCAGAAGTGA	0.383													29	28	---	---	---	---	PASS
ACD	65057	broad.mit.edu	37	16	67694088	67694088	+	Nonsense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67694088C>T	uc002etq.3	-	1	631	c.294G>A	c.(292-294)TGG>TGA	p.W98*	ACD_uc002etp.3_Nonsense_Mutation_p.W98*|ACD_uc002etr.3_Nonsense_Mutation_p.W98*|ACD_uc010vjt.1_Nonsense_Mutation_p.W88*|PARD6A_uc002ets.2_5'Flank|PARD6A_uc002ett.2_5'Flank|PARD6A_uc002etu.2_5'Flank	NM_001082486	NP_001075955	Q96AP0	ACD_HUMAN	adrenocortical dysplasia homolog isoform 1	98	PWI.				intracellular protein transport|negative regulation of telomere maintenance via telomerase|positive regulation of single-stranded telomeric DNA binding|positive regulation of telomerase activity|protection from non-homologous end joining at telomere|protein localization to chromosome, telomeric region|telomere assembly	nuclear telomere cap complex|nucleoplasm	DNA binding|DNA polymerase binding			pancreas(1)	1		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.047)|all cancers(182;0.228)		GCTCCCGAATCCAGGGCCGTA	0.701													19	81	---	---	---	---	PASS
NFATC3	4775	broad.mit.edu	37	16	68225270	68225270	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68225270G>A	uc002evo.1	+	9	2908	c.2698G>A	c.(2698-2700)GAC>AAC	p.D900N	NFATC3_uc010vkl.1_Missense_Mutation_p.D421N|NFATC3_uc010vkm.1_Missense_Mutation_p.D421N|NFATC3_uc010vkn.1_Missense_Mutation_p.D421N|NFATC3_uc010vko.1_Missense_Mutation_p.D421N|NFATC3_uc010vkp.1_Missense_Mutation_p.D421N|NFATC3_uc010vkq.1_Missense_Mutation_p.D421N|NFATC3_uc002evl.2_Missense_Mutation_p.D421N|NFATC3_uc002evk.2_Missense_Mutation_p.D900N|NFATC3_uc002evm.1_Missense_Mutation_p.D900N|NFATC3_uc002evn.1_Missense_Mutation_p.D900N|NFATC3_uc010vkr.1_Missense_Mutation_p.D421N|NFATC3_uc010vks.1_Missense_Mutation_p.D421N|NFATC3_uc010vkt.1_Missense_Mutation_p.D421N|NFATC3_uc010vku.1_Missense_Mutation_p.D421N|NFATC3_uc010vkv.1_Missense_Mutation_p.D421N|NFATC3_uc010vkw.1_Missense_Mutation_p.D421N|NFATC3_uc010vkx.1_Missense_Mutation_p.D421N|NFATC3_uc010vky.1_Missense_Mutation_p.D421N|NFATC3_uc010vkz.1_Missense_Mutation_p.D421N|NFATC3_uc010vla.1_Missense_Mutation_p.D421N|NFATC3_uc010vlb.1_Missense_Mutation_p.D421N|NFATC3_uc010vlc.1_Missense_Mutation_p.D421N	NM_173165	NP_775188	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells,	900					inflammatory response|transcription from RNA polymerase II promoter	nucleolus|plasma membrane	DNA binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	3		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		TCCAGTGGCTGACCAGATTAC	0.463													6	140	---	---	---	---	PASS
CIRH1A	84916	broad.mit.edu	37	16	69170611	69170611	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69170611C>G	uc002ews.3	+	3	268	c.172C>G	c.(172-174)CAT>GAT	p.H58D	CIRH1A_uc002ewr.2_Missense_Mutation_p.H58D|CIRH1A_uc002ewt.3_5'UTR|CIRH1A_uc010cfi.2_5'UTR	NM_032830	NP_116219	Q969X6	CIR1A_HUMAN	cirhin	58	WD 2.					nucleolus	protein binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.125)		TTTCCCAGGTCATGAGTCTCG	0.463													14	289	---	---	---	---	PASS
LDHD	197257	broad.mit.edu	37	16	75148111	75148111	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75148111G>C	uc002fdm.2	-	6	698	c.651C>G	c.(649-651)ATC>ATG	p.I217M	LDHD_uc002fdn.2_Intron	NM_153486	NP_705690	Q86WU2	LDHD_HUMAN	D-lactate dehydrogenase isoform 1 precursor	217	FAD-binding PCMH-type.						D-lactate dehydrogenase (cytochrome) activity|flavin adenine dinucleotide binding|protein binding				0						TGTGATGAGGGATTTCTGGCC	0.632													5	194	---	---	---	---	PASS
CNTNAP4	85445	broad.mit.edu	37	16	76574669	76574669	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76574669G>C	uc002feu.1	+	23	3809	c.3424G>C	c.(3424-3426)GTA>CTA	p.V1142L	CNTNAP4_uc002fev.1_Missense_Mutation_p.V1006L|CNTNAP4_uc010chb.1_Missense_Mutation_p.V1069L|CNTNAP4_uc002fex.1_Missense_Mutation_p.V1145L	NM_033401	NP_207837	Q9C0A0	CNTP4_HUMAN	cell recognition protein CASPR4 isoform 1	1142	Extracellular (Potential).|Laminin G-like 4.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2						CAAATCTCTGGTATTGGGCAG	0.368													6	9	---	---	---	---	PASS
PKD1L2	114780	broad.mit.edu	37	16	81134720	81134720	+	3'UTR	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81134720C>A	uc002fgh.1	-	45					PKD1L2_uc002fgf.1_3'UTR|PKD1L2_uc002fgg.1_RNA	NM_052892	NP_443124	Q7Z442	PK1L2_HUMAN	polycystin 1-like 2 isoform a						neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3						GGCGTGTGGACGAACAGCTTA	0.582													17	61	---	---	---	---	PASS
MPHOSPH6	10200	broad.mit.edu	37	16	82197736	82197736	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82197736T>C	uc002fgw.2	-	2	164	c.115A>G	c.(115-117)ATT>GTT	p.I39V		NM_005792	NP_005783	Q99547	MPH6_HUMAN	M-phase phosphoprotein 6	39					M phase of mitotic cell cycle|maturation of 5.8S rRNA	cytoplasm|nucleolus	protein binding|RNA binding				0						TCTTCACTAATGATTTTCTTT	0.353													38	74	---	---	---	---	PASS
ZCCHC14	23174	broad.mit.edu	37	16	87451175	87451175	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87451175G>A	uc002fjz.1	-	8	890	c.863C>T	c.(862-864)TCC>TTC	p.S288F	ZCCHC14_uc002fka.1_RNA|ZCCHC14_uc002fkb.2_Missense_Mutation_p.S64F	NM_015144	NP_055959	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	288					cell communication		nucleic acid binding|phosphatidylinositol binding|zinc ion binding			upper_aerodigestive_tract(1)|breast(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0285)		CTGCAGACTGGAAGGCATGAG	0.602													91	212	---	---	---	---	PASS
ZCCHC14	23174	broad.mit.edu	37	16	87454329	87454329	+	Intron	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87454329G>A	uc002fjz.1	-						ZCCHC14_uc002fka.1_Intron|ZCCHC14_uc002fkb.2_Intron	NM_015144	NP_055959	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14						cell communication		nucleic acid binding|phosphatidylinositol binding|zinc ion binding			upper_aerodigestive_tract(1)|breast(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0285)		ATAGCTGGAAGAGAGGACAAG	0.532													4	14	---	---	---	---	PASS
ANKRD11	29123	broad.mit.edu	37	16	89345518	89345518	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89345518G>T	uc002fmx.1	-	9	7893	c.7432C>A	c.(7432-7434)CTG>ATG	p.L2478M	ANKRD11_uc002fmy.1_Missense_Mutation_p.L2478M|ANKRD11_uc002fnc.1_Missense_Mutation_p.L2478M|ANKRD11_uc002fna.1_Missense_Mutation_p.L143M|ANKRD11_uc002fnb.1_Missense_Mutation_p.L2435M	NM_013275	NP_037407	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	2478						nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		TTGCCGTCCAGGAGGTAGGAG	0.647													11	27	---	---	---	---	PASS
DPH1	1801	broad.mit.edu	37	17	1946404	1946404	+	3'UTR	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1946404C>G	uc002fts.2	+	13					DPH1_uc002ftr.1_RNA|DPH1_uc002ftt.2_3'UTR|DPH1_uc010cjx.2_3'UTR|DPH1_uc010vqs.1_3'UTR|DPH1_uc002ftu.2_3'UTR|DPH1_uc002ftv.2_3'UTR|DPH1_uc002ftw.2_3'UTR|OVCA2_uc002ftx.2_3'UTR	NM_001383	NP_001374	Q9BZG8	DPH1_HUMAN	diptheria toxin resistance protein required for						peptidyl-diphthamide biosynthetic process from peptidyl-histidine|translation	cytoplasm|nucleus				pancreas(1)	1						AGTGAAAGATCAAGAAATGTC	0.582													5	93	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7577153	7577153	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7577153C>A	uc002gim.2	-	8	979	c.785G>T	c.(784-786)GGT>GTT	p.G262V	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Missense_Mutation_p.G262V|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.G130V|TP53_uc010cng.1_Missense_Mutation_p.G130V|TP53_uc002gii.1_Missense_Mutation_p.G130V|TP53_uc010cnh.1_Missense_Mutation_p.G262V|TP53_uc010cni.1_Missense_Mutation_p.G262V|TP53_uc002gij.2_Missense_Mutation_p.G262V	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	262	|Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		GN -> PD (in a sporadic cancer; somatic mutation).|G -> D (in sporadic cancers; somatic mutation).|G -> V (in sporadic cancers; somatic mutation).|G -> C (in a sporadic cancer; somatic mutation).|G -> H (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|G -> S (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.G262V(11)|p.0?(7)|p.G262D(4)|p.G262fs*83(4)|p.?(3)|p.G262_F270delGNLLGRNSF(2)|p.G262_S269delGNLLGRNS(2)|p.G262del(2)|p.G262S(2)|p.G262H(1)|p.G262G(1)|p.E258fs*71(1)|p.S261_L264>R(1)|p.S261_G262insX(1)|p.G262fs*2(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)		CAGTAGATTACCACTACTCAG	0.517		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)			14	10	---	---	---	---	PASS
PIK3R6	146850	broad.mit.edu	37	17	8741176	8741176	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8741176C>T	uc002glq.1	-	5	442	c.202G>A	c.(202-204)GAC>AAC	p.D68N	PIK3R6_uc002glr.1_RNA|PIK3R6_uc002gls.1_RNA	NM_001010855	NP_001010855	Q5UE93	PI3R6_HUMAN	phosphoinositide-3-kinase, regulatory subunit 6	68					platelet activation	cytosol					0						TGCCGGAGGTCCTGGCTTTCC	0.582													11	64	---	---	---	---	PASS
FOXN1	8456	broad.mit.edu	37	17	26861480	26861480	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26861480C>G	uc010crm.2	+	7	1257	c.1059C>G	c.(1057-1059)ATC>ATG	p.I353M	FOXN1_uc002hbj.2_Missense_Mutation_p.I353M	NM_003593	NP_003584	O15353	FOXN1_HUMAN	forkhead box N1	353	Fork-head.				defense response|embryo development|epithelial cell proliferation|keratinocyte differentiation|organ morphogenesis|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter|thymus 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	Lung NSC(42;0.00431)					CGGCCAAGATCGACAAGATGC	0.567													32	49	---	---	---	---	PASS
KIAA0100	9703	broad.mit.edu	37	17	26967585	26967585	+	Nonsense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26967585G>A	uc002hbu.2	-	8	982	c.883C>T	c.(883-885)CAA>TAA	p.Q295*	KIAA0100_uc002hbv.2_Nonsense_Mutation_p.Q295*|KIAA0100_uc010crr.1_Nonsense_Mutation_p.Q152*	NM_014680	NP_055495	Q14667	K0100_HUMAN	hypothetical protein LOC9703 precursor	295						extracellular region				ovary(2)|breast(1)|skin(1)	4	Lung NSC(42;0.00431)					CACCTCTTTTGACTATTCATG	0.488													52	61	---	---	---	---	PASS
CPD	1362	broad.mit.edu	37	17	28783264	28783264	+	Intron	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28783264C>G	uc002hfb.1	+						CPD_uc010wbo.1_Intron|CPD_uc010wbp.1_Intron	NM_001304	NP_001295	O75976	CBPD_HUMAN	carboxypeptidase D precursor						proteolysis	integral to membrane	metallocarboxypeptidase activity|serine-type carboxypeptidase activity|zinc ion binding			liver(1)|skin(1)	2						CTAAATTTTTCTTTCTATAGT	0.358													3	69	---	---	---	---	PASS
NF1	4763	broad.mit.edu	37	17	29548922	29548922	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29548922C>G	uc002hgg.2	+	15	2029	c.1696C>G	c.(1696-1698)CCT>GCT	p.P566A	NF1_uc002hgf.1_Missense_Mutation_p.P566A|NF1_uc002hgh.2_Missense_Mutation_p.P566A|NF1_uc010csn.1_Missense_Mutation_p.P426A	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	566					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(2)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TCCTGATGCTCCTGTAGAAAC	0.274			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			6	73	---	---	---	---	PASS
MPP3	4356	broad.mit.edu	37	17	41879119	41879119	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41879119C>G	uc002iei.3	-	20	1874	c.1708G>C	c.(1708-1710)GAG>CAG	p.E570Q	MPP3_uc002ieh.2_Missense_Mutation_p.E595Q|MPP3_uc002iej.2_RNA	NM_001932	NP_001923	Q13368	MPP3_HUMAN	palmitoylated membrane protein 3	570	Guanylate kinase-like.				signal transduction	cell surface|integral to plasma membrane	guanylate kinase activity			large_intestine(1)|skin(1)	2		Breast(137;0.00394)		BRCA - Breast invasive adenocarcinoma(366;0.119)		CTCAGCTTCTCTAAGACCACT	0.423													21	165	---	---	---	---	PASS
ATXN7L3	56970	broad.mit.edu	37	17	42271946	42271946	+	Silent	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42271946A>G	uc002iga.2	-	11	925	c.834T>C	c.(832-834)TCT>TCC	p.S278S	ATXN7L3_uc010wiv.1_Silent_p.S60S|ATXN7L3_uc002ifz.2_Silent_p.S285S	NM_001098833	NP_001092303	Q14CW9	AT7L3_HUMAN	ataxin 7-like 3 isoform b	278					histone deubiquitination|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	SAGA complex	ligand-dependent nuclear receptor transcription coactivator activity|metal ion binding|protein binding				0		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.113)		GTGAGAGGTCAGAGGAGCCGT	0.577													22	39	---	---	---	---	PASS
HEXIM2	124790	broad.mit.edu	37	17	43246634	43246634	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43246634G>C	uc002iih.1	+	4	558	c.319G>C	c.(319-321)GAG>CAG	p.E107Q	HEXIM2_uc010daf.1_Missense_Mutation_p.E129Q|HEXIM2_uc002iii.1_Missense_Mutation_p.E107Q|HEXIM2_uc002iij.1_Missense_Mutation_p.E107Q|uc002iik.1_RNA	NM_144608	NP_653209	Q96MH2	HEXI2_HUMAN	hexamthylene bis-acetamide inducible 2	107					negative regulation of cyclin-dependent protein kinase activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	cyclin-dependent protein kinase inhibitor activity|protein binding|snRNA binding				0						ACCCTACCTGGAGCTGAGCTG	0.672													4	62	---	---	---	---	PASS
SKAP1	8631	broad.mit.edu	37	17	46474081	46474081	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46474081C>T	uc002ini.1	-	2	225	c.113G>A	c.(112-114)AGA>AAA	p.R38K	SKAP1_uc002inj.1_Missense_Mutation_p.R38K|SKAP1_uc010dbd.1_5'UTR|SKAP1_uc010dbe.1_Missense_Mutation_p.R38K	NM_003726	NP_003717	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1 isoform	38					positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway	cytoplasm|nucleus|plasma membrane	antigen binding|protein kinase binding|SH2 domain binding				0						AATATGGTCTCTGTGATCCCT	0.378													112	309	---	---	---	---	PASS
MKS1	54903	broad.mit.edu	37	17	56291733	56291733	+	Silent	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56291733G>C	uc002ivr.1	-	6	606	c.531C>G	c.(529-531)CTC>CTG	p.L177L	MKS1_uc010wnq.1_5'UTR|MKS1_uc002ivs.1_Silent_p.L177L	NM_017777	NP_060247	Q9NXB0	MKS1_HUMAN	Meckel syndrome type 1 protein isoform 1	177					cilium assembly	centrosome|cilium|microtubule basal body	protein binding			ovary(1)	1						TGCGTGACTTGAGGATGCCGC	0.557													8	65	---	---	---	---	PASS
ACE	1636	broad.mit.edu	37	17	61561865	61561865	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61561865G>C	uc002jau.1	+	12	1906	c.1884G>C	c.(1882-1884)TGG>TGC	p.W628C	ACE_uc010ddu.1_Missense_Mutation_p.W445C|ACE_uc002jav.1_5'Flank|ACE_uc010ddv.1_5'Flank|ACE_uc010wpj.1_5'Flank|ACE_uc002jaw.1_5'Flank|ACE_uc010wpk.1_5'Flank	NM_000789	NP_000780	P12821	ACE_HUMAN	angiotensin I converting enzyme 1 isoform 1	628	Extracellular (Potential).|Peptidase M2 1.				arachidonic acid secretion|hormone catabolic process|kidney development|peptide catabolic process|regulation of smooth muscle cell migration	endosome|external side of plasma membrane|extracellular space|integral to membrane|membrane fraction|plasma membrane	actin binding|bradykinin receptor binding|carboxypeptidase activity|chloride ion binding|drug binding|metallopeptidase activity|peptidyl-dipeptidase activity|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4					Benazepril(DB00542)|Captopril(DB01197)|Deserpidine(DB01089)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	AGTACCAGTGGCACCCGCCGT	0.632													3	19	---	---	---	---	PASS
SMURF2	64750	broad.mit.edu	37	17	62551115	62551115	+	Intron	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62551115G>T	uc002jep.1	-						SMURF2_uc002jeq.1_Intron|SMURF2_uc002jer.1_Intron	NM_022739	NP_073576	Q9HAU4	SMUF2_HUMAN	SMAD specific E3 ubiquitin protein ligase 2						BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|membrane raft|nucleus|plasma membrane|ubiquitin ligase complex	identical protein binding|SMAD binding|ubiquitin-protein ligase activity			skin(3)|lung(1)	4	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)			ATTCTCACTGGATAGGAAAGA	0.318													14	56	---	---	---	---	PASS
CCDC46	201134	broad.mit.edu	37	17	64092382	64092382	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64092382A>G	uc002jfl.2	-	8	974	c.755T>C	c.(754-756)ATA>ACA	p.I252T	CCDC46_uc002jfm.2_Missense_Mutation_p.I252T|CCDC46_uc010dep.2_Intron	NM_145036	NP_659473	Q8N8E3	CE112_HUMAN	coiled-coil domain containing 46 isoform a	252						centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)			TTTCTCACGTATTCGAGAGAG	0.323													54	91	---	---	---	---	PASS
PRKAR1A	5573	broad.mit.edu	37	17	66511538	66511538	+	5'UTR	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66511538A>G	uc002jhg.2	+	2					PRKAR1A_uc002jhh.2_5'UTR|PRKAR1A_uc002jhi.2_5'UTR|PRKAR1A_uc002jhj.2_5'UTR|PRKAR1A_uc002jhk.2_5'UTR|PRKAR1A_uc002jhl.2_5'UTR|PRKAR1A_uc002jhm.2_5'UTR	NM_212471	NP_997636	P10644	KAP0_HUMAN	cAMP-dependent protein kinase, regulatory						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|intracellular signal transduction|nerve growth factor receptor signaling pathway|regulation of insulin secretion|regulation of transcription from RNA polymerase II promoter|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity|protein binding			adrenal_gland(4)|lung(3)|thyroid(2)|soft_tissue(2)|breast(1)	12	Breast(10;1.64e-13)					CTCGCAGAGAACCATGGAGTC	0.443			T|Mis|N|F|S	RET	papillary thyroid	myxoma|endocrine|papillary thyroid			Carney_Complex|Primary_Pigmented_Nodular_Adrenocortical_Disease_Familial|Cardiac_Myxomas_Familial_Clustering_of				16	48	---	---	---	---	PASS
FAM104A	84923	broad.mit.edu	37	17	71228242	71228242	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71228242G>A	uc002jji.3	-	1	292	c.204C>T	c.(202-204)AGC>AGT	p.S68S	FAM104A_uc002jjj.3_Silent_p.S68S|C17orf80_uc010wqu.1_5'Flank|C17orf80_uc010dfj.2_5'Flank|C17orf80_uc002jjk.1_5'Flank|C17orf80_uc002jjm.3_5'Flank|C17orf80_uc002jjl.3_5'Flank	NM_032837	NP_116226	Q969W3	F104A_HUMAN	hypothetical protein LOC84923 isoform 2	68											0			LUSC - Lung squamous cell carcinoma(166;0.197)			GGAGGCGCTCGCTCATGGCAG	0.692													11	10	---	---	---	---	PASS
HRH4	59340	broad.mit.edu	37	18	22057058	22057058	+	Missense_Mutation	SNP	G	T	T	rs116314403	by1000genomes	TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22057058G>T	uc002kvi.2	+	3	805	c.705G>T	c.(703-705)AGG>AGT	p.R235S	HRH4_uc010xbd.1_3'UTR|HRH4_uc010dlx.2_Missense_Mutation_p.R147S	NM_021624	NP_067637	Q9H3N8	HRH4_HUMAN	histamine H4 receptor isoform 1	235	Cytoplasmic (Potential).					integral to membrane|plasma membrane	histamine receptor activity			ovary(2)	2	all_cancers(21;0.000545)|all_epithelial(16;6.56e-06)|Lung NSC(20;0.0027)|all_lung(20;0.0085)|Colorectal(14;0.0361)|Ovarian(20;0.0991)				Clozapine(DB00363)	TATCTTCAAGGAGATCTCTTT	0.453													26	92	---	---	---	---	PASS
DYM	54808	broad.mit.edu	37	18	46645102	46645102	+	Intron	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46645102A>G	uc002ldi.1	-						DYM_uc010xdf.1_Intron|DYM_uc002ldj.3_Silent_p.N408N	NM_017653	NP_060123	Q7RTS9	DYM_HUMAN	dymeclin							Golgi apparatus					0						AAATGTCTTCATTTACACTCA	0.308													12	36	---	---	---	---	PASS
WDR7	23335	broad.mit.edu	37	18	54424078	54424078	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54424078G>C	uc002lgk.1	+	15	2465	c.2254G>C	c.(2254-2256)GAG>CAG	p.E752Q	WDR7_uc010dpk.1_RNA|WDR7_uc002lgl.1_Missense_Mutation_p.E752Q	NM_015285	NP_056100	Q9Y4E6	WDR7_HUMAN	rabconnectin-3 beta isoform 1	752										ovary(2)|skin(1)	3				Lung(128;0.0238)|Colorectal(16;0.0296)		AACGATCAAAGAGAACATCAA	0.433													7	33	---	---	---	---	PASS
ATP8B1	5205	broad.mit.edu	37	18	55368444	55368444	+	Intron	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55368444C>T	uc002lgw.2	-						uc002lgv.1_Intron	NM_005603	NP_005594	O43520	AT8B1_HUMAN	ATPase, class I, type 8B, member 1						ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent	apical plasma membrane|integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			breast(5)|ovary(2)|central_nervous_system(2)|lung(1)	10		Colorectal(73;0.229)				GAGAAATCCTCACCACATCGT	0.468									Byler_disease				29	53	---	---	---	---	PASS
SERPINB5	5268	broad.mit.edu	37	18	61160277	61160277	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61160277G>A	uc002liz.3	+	5	658	c.516G>A	c.(514-516)ATG>ATA	p.M172I	SERPINB5_uc002liy.2_Missense_Mutation_p.M172I	NM_002639	NP_002630	P36952	SPB5_HUMAN	serine (or cysteine) proteinase inhibitor, clade	172					cellular component movement|regulation of proteolysis	cytoplasm|extracellular space	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)	1						GCAAGTGGATGAAGAAATTTT	0.413													27	93	---	---	---	---	PASS
SERPINB10	5273	broad.mit.edu	37	18	61600392	61600392	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61600392C>T	uc010xev.1	+	7	834	c.744C>T	c.(742-744)CTC>CTT	p.L248L	SERPINB10_uc010xew.1_Silent_p.L248L	NM_005024	NP_005015	P48595	SPB10_HUMAN	serine (or cysteine) proteinase inhibitor, clade	248						cytoplasm|nucleus	serine-type endopeptidase inhibitor activity			lung(1)|kidney(1)|skin(1)	3		Esophageal squamous(42;0.131)				GCCGTGACCTCAGCCTGCTTA	0.403													14	199	---	---	---	---	PASS
DSEL	92126	broad.mit.edu	37	18	65180604	65180604	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65180604G>A	uc002lke.1	-	2	2496	c.1272C>T	c.(1270-1272)AAC>AAT	p.N424N		NM_032160	NP_115536	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	414						integral to membrane	isomerase activity|sulfotransferase activity			ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	6		Esophageal squamous(42;0.129)				CCACACCCCAGTTAGGGAATG	0.488													25	44	---	---	---	---	PASS
ADNP2	22850	broad.mit.edu	37	18	77895799	77895799	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77895799G>T	uc002lnw.2	+	4	2958	c.2503G>T	c.(2503-2505)GGG>TGG	p.G835W		NM_014913	NP_055728	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2	835					cellular response to oxidative stress|cellular response to retinoic acid|negative regulation of cell death|neuron differentiation|positive regulation of cell growth	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|breast(3)|central_nervous_system(1)	8		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)		GGAGAAGCTTGGGGAGCGGGA	0.522													34	70	---	---	---	---	PASS
PIP5K1C	23396	broad.mit.edu	37	19	3633507	3633507	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3633507C>G	uc002lyj.1	-	17	1989	c.1932G>C	c.(1930-1932)GAG>GAC	p.E644D	PIP5K1C_uc010xhq.1_Intron	NM_012398	NP_036530	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type	644	Mediates interaction with TLN2.				axon guidance	cytosol|plasma membrane	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding			stomach(2)|skin(2)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		CCCAGCTCCTCTCATCGGTGG	0.692													3	20	---	---	---	---	PASS
TYK2	7297	broad.mit.edu	37	19	10465286	10465286	+	Splice_Site	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10465286C>G	uc002moc.3	-	19	2996	c.2618_splice	c.e19-1	p.N873_splice	TYK2_uc010dxe.2_Splice_Site_p.N688_splice	NM_003331	NP_003322	P29597	TYK2_HUMAN	tyrosine kinase 2						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)			TCAGCAAGATCTGGAAGAGTT	0.572													7	54	---	---	---	---	PASS
ZNF136	7695	broad.mit.edu	37	19	12298398	12298398	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12298398A>G	uc002mti.2	+	4	1305	c.1205A>G	c.(1204-1206)CAT>CGT	p.H402R	ZNF136_uc010xmh.1_Missense_Mutation_p.H336R	NM_003437	NP_003428	P52737	ZN136_HUMAN	zinc finger protein 136	402	C2H2-type 10.				negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|transcription corepressor activity|zinc ion binding			ovary(1)|pancreas(1)	2						AAACCCTTTCATTCTCTGAGT	0.378													18	33	---	---	---	---	PASS
ZNF254	9534	broad.mit.edu	37	19	24310330	24310330	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24310330A>G	uc002nru.2	+	4	1662	c.1528A>G	c.(1528-1530)ATA>GTA	p.I510V	ZNF254_uc010xrk.1_Missense_Mutation_p.I425V	NM_203282	NP_975011	O75437	ZN254_HUMAN	zinc finger protein 254	510	C2H2-type 11.				negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)				TACACATAAGATAATTCATAC	0.378													23	35	---	---	---	---	PASS
ZNF507	22847	broad.mit.edu	37	19	32844195	32844195	+	Silent	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32844195G>C	uc002nte.2	+	3	731	c.459G>C	c.(457-459)GTG>GTC	p.V153V	ZNF507_uc002ntc.2_Silent_p.V153V|ZNF507_uc010xrn.1_Silent_p.V153V|ZNF507_uc002ntd.2_Silent_p.V153V	NM_001136156	NP_001129628	Q8TCN5	ZN507_HUMAN	zinc finger protein 507	153					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)|kidney(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(110;0.162)					AAAATGAAGTGATACTGATGT	0.418													9	121	---	---	---	---	PASS
GPATCH1	55094	broad.mit.edu	37	19	33586724	33586724	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33586724G>C	uc002nug.1	+	6	924	c.610G>C	c.(610-612)GAG>CAG	p.E204Q		NM_018025	NP_060495	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	204						catalytic step 2 spliceosome	nucleic acid binding			skin(1)	1	Esophageal squamous(110;0.137)					GGAAGGATCTGAGGTATTGCA	0.413													10	179	---	---	---	---	PASS
CHST8	64377	broad.mit.edu	37	19	34263690	34263690	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34263690C>T	uc002nus.3	+	5	1502	c.997C>T	c.(997-999)CGG>TGG	p.R333W	CHST8_uc002nut.3_Missense_Mutation_p.R333W|CHST8_uc002nuu.2_Missense_Mutation_p.R333W	NM_001127895	NP_001121367	Q9H2A9	CHST8_HUMAN	carbohydrate (N-acetylgalactosamine 4-0)	333	Lumenal (Potential).				carbohydrate biosynthetic process|central nervous system development|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			skin(2)|large_intestine(1)|ovary(1)	4	Esophageal squamous(110;0.162)					CCATGTCAGCCGGCTCTGCAG	0.632													43	36	---	---	---	---	PASS
HAUS5	23354	broad.mit.edu	37	19	36113809	36113809	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36113809G>C	uc002oam.1	+	19	1867	c.1816G>C	c.(1816-1818)GAG>CAG	p.E606Q		NM_015302	NP_056117	O94927	HAUS5_HUMAN	HAUS augmin-like complex, subunit 5	606					cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle					0						CGCCCTCTCTGAGGAGCTCTG	0.657													10	101	---	---	---	---	PASS
TMEM149	79713	broad.mit.edu	37	19	36230525	36230525	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36230525G>T	uc002obc.2	-	5	825	c.724C>A	c.(724-726)CTG>ATG	p.L242M	TMEM149_uc002obb.2_Missense_Mutation_p.L54M|TMEM149_uc002obd.3_Missense_Mutation_p.L242M|TMEM149_uc010xsy.1_RNA|TMEM149_uc010eej.2_Missense_Mutation_p.L322M	NM_024660	NP_078936	Q9H665	IGFR1_HUMAN	transmembrane protein 149 precursor	242	Cytoplasmic (Potential).					integral to membrane|plasma membrane	protein binding|receptor activity				0	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			AGACTGGACAGTTCTGGAAGA	0.627													3	92	---	---	---	---	PASS
SPTBN4	57731	broad.mit.edu	37	19	41063031	41063031	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41063031G>A	uc002ony.2	+	26	5478	c.5392G>A	c.(5392-5394)GGC>AGC	p.G1798S	SPTBN4_uc002onx.2_Missense_Mutation_p.G1798S|SPTBN4_uc002onz.2_Missense_Mutation_p.G1798S|SPTBN4_uc010egx.2_Missense_Mutation_p.G541S|SPTBN4_uc002ooa.2_Missense_Mutation_p.G474S	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform	1798	Spectrin 15.				actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GATCGAGTGTGGCCATACAGC	0.627													41	22	---	---	---	---	PASS
CYP2A13	1553	broad.mit.edu	37	19	41594860	41594860	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41594860C>T	uc002opt.2	+	2	216	c.207C>T	c.(205-207)TTC>TTT	p.F69F		NM_000766	NP_000757	Q16696	CP2AD_HUMAN	cytochrome P450, family 2, subfamily A,	69					xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|coumarin 7-hydroxylase activity|electron carrier activity|heme binding			ovary(2)|skin(1)	3					Clomipramine(DB01242)|Nicotine(DB00184)	GCCCTGTGTTCACCATTCACT	0.622													7	127	---	---	---	---	PASS
HIF3A	64344	broad.mit.edu	37	19	46807269	46807269	+	Silent	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46807269C>G	uc002peh.2	+	2	170	c.141C>G	c.(139-141)GTC>GTG	p.V47V	HIF3A_uc002pef.1_Silent_p.V47V|HIF3A_uc002peg.3_Silent_p.V47V|HIF3A_uc010xxx.1_RNA|HIF3A_uc002pei.3_5'UTR|HIF3A_uc002pej.1_Nonsense_Mutation_p.S27*|HIF3A_uc002pek.2_5'UTR|HIF3A_uc010xxy.1_Nonsense_Mutation_p.S27*|HIF3A_uc002pel.2_Silent_p.V45V|HIF3A_uc010xxz.1_Nonsense_Mutation_p.S45*	NM_152795	NP_690008	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	47	Helix-loop-helix motif.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)		CCCGCGGCGTCAGCGCCCACC	0.697													2	16	---	---	---	---	PASS
GRLF1	2909	broad.mit.edu	37	19	47422627	47422627	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47422627C>A	uc010ekv.2	+	1	695	c.695C>A	c.(694-696)TCC>TAC	p.S232Y		NM_004491	NP_004482	Q9NRY4	RHG35_HUMAN	glucocorticoid receptor DNA binding factor 1	232					axon guidance|negative regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol	DNA binding|Rho GTPase activator activity|transcription corepressor activity			central_nervous_system(1)	1		all_cancers(25;1.51e-09)|all_epithelial(76;1.87e-07)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|Ovarian(192;0.0129)|all_neural(266;0.026)|Breast(70;0.077)		all cancers(93;2.03e-05)|OV - Ovarian serous cystadenocarcinoma(262;2.57e-05)|Epithelial(262;0.00135)|GBM - Glioblastoma multiforme(486;0.0289)		TCAGCGAGATCCAATGTAAAC	0.433													14	126	---	---	---	---	PASS
GRLF1	2909	broad.mit.edu	37	19	47425500	47425500	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47425500G>C	uc010ekv.2	+	1	3568	c.3568G>C	c.(3568-3570)GAG>CAG	p.E1190Q		NM_004491	NP_004482	Q9NRY4	RHG35_HUMAN	glucocorticoid receptor DNA binding factor 1	1190					axon guidance|negative regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol	DNA binding|Rho GTPase activator activity|transcription corepressor activity			central_nervous_system(1)	1		all_cancers(25;1.51e-09)|all_epithelial(76;1.87e-07)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|Ovarian(192;0.0129)|all_neural(266;0.026)|Breast(70;0.077)		all cancers(93;2.03e-05)|OV - Ovarian serous cystadenocarcinoma(262;2.57e-05)|Epithelial(262;0.00135)|GBM - Glioblastoma multiforme(486;0.0289)		CCGGAAGAAAGAGGAGGATCA	0.562													4	67	---	---	---	---	PASS
NAPA	8775	broad.mit.edu	37	19	48018127	48018127	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48018127G>C	uc002pha.1	-	1	371	c.71C>G	c.(70-72)TCG>TGG	p.S24W	NAPA_uc002phb.1_Missense_Mutation_p.S24W|NAPA_uc002phc.1_5'UTR|NAPA_uc002phd.1_Missense_Mutation_p.S24W|NAPA_uc010elf.1_5'UTR|NAPA_uc010elg.1_RNA|NAPA_uc002phe.2_Missense_Mutation_p.S24W	NM_003827	NP_003818	P54920	SNAA_HUMAN	N-ethylmaleimide-sensitive factor attachment	24					cellular membrane fusion|intra-Golgi vesicle-mediated transport|post-Golgi vesicle-mediated transport	cytosol					0		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000466)|all cancers(93;0.000739)|Epithelial(262;0.0168)|GBM - Glioblastoma multiforme(486;0.049)		GAAGGACTGCGAGTTCTTCAC	0.642													25	25	---	---	---	---	PASS
GLTSCR1	29998	broad.mit.edu	37	19	48204587	48204587	+	Nonsense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48204587G>T	uc002phh.3	+	15	3792	c.3598G>T	c.(3598-3600)GAG>TAG	p.E1200*	GLTSCR1_uc002phi.3_Nonsense_Mutation_p.E958*	NM_015711	NP_056526	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	1200							protein binding			pancreas(3)	3		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		TTCTGCAGACGAGTACGTGTC	0.657													13	21	---	---	---	---	PASS
PPFIA3	8541	broad.mit.edu	37	19	49632235	49632235	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49632235C>G	uc002pmr.2	+	4	805	c.473C>G	c.(472-474)TCT>TGT	p.S158C	PPFIA3_uc010yai.1_RNA|PPFIA3_uc010emt.2_Missense_Mutation_p.S82C|PPFIA3_uc010yaj.1_RNA|PPFIA3_uc002pms.2_Missense_Mutation_p.S26C	NM_003660	NP_003651	O75145	LIPA3_HUMAN	PTPRF interacting protein alpha 3	158						cell surface|cytoplasm	protein binding			lung(1)	1		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)		GCTCTAAAGTCTCTCTTCGAG	0.562													3	78	---	---	---	---	PASS
PRMT1	3276	broad.mit.edu	37	19	50185235	50185235	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50185235C>T	uc010enf.1	+	4	303	c.261C>T	c.(259-261)TTC>TTT	p.F87F	PRMT1_uc002ppc.1_RNA|PRMT1_uc002ppd.2_Silent_p.F63F|PRMT1_uc002ppe.2_Silent_p.F69F|PRMT1_uc002ppf.2_RNA|PRMT1_uc002ppg.2_Silent_p.F34F|PRMT1_uc010yba.1_RNA	NM_001536	NP_001527	Q8WUW5	Q8WUW5_HUMAN	HMT1 hnRNP methyltransferase-like 2 isoform 1	68						cytoplasm	protein methyltransferase activity			ovary(1)	1		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00103)|GBM - Glioblastoma multiforme(134;0.012)		GGCACCTCTTCAAGGACAAGG	0.612													4	59	---	---	---	---	PASS
ZNF581	51545	broad.mit.edu	37	19	56156399	56156399	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56156399C>G	uc002qln.2	+	2	1178	c.462C>G	c.(460-462)TTC>TTG	p.F154L	ZNF581_uc002qlq.2_Missense_Mutation_p.F154L|CCDC106_uc002qlr.2_5'Flank	NM_016535	NP_057619	Q9P0T4	ZN581_HUMAN	zinc finger protein 581	154	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.105)		CTCGCCGCTTCCGGGATGCGG	0.677													6	151	---	---	---	---	PASS
NLRP8	126205	broad.mit.edu	37	19	56467201	56467201	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56467201C>T	uc002qmh.2	+	3	1848	c.1777C>T	c.(1777-1779)CTG>TTG	p.L593L	NLRP8_uc010etg.2_Silent_p.L593L	NM_176811	NP_789781	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	593						cytoplasm	ATP binding			ovary(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|kidney(1)	13		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		AGTCATACCTCTGTTGCATAA	0.507													3	69	---	---	---	---	PASS
ZNF418	147686	broad.mit.edu	37	19	58437712	58437712	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58437712G>T	uc002qqs.1	-	4	2129	c.1837C>A	c.(1837-1839)CAT>AAT	p.H613N	ZNF418_uc010yhn.1_RNA|ZNF418_uc010yho.1_Missense_Mutation_p.H528N	NM_133460	NP_597717	Q8TF45	ZN418_HUMAN	zinc finger protein 418	613	C2H2-type 14.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0158)		CCTCGAGTATGAAGTCTCTGA	0.453													24	97	---	---	---	---	PASS
DEFB125	245938	broad.mit.edu	37	20	76774	76774	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:76774G>A	uc002wcw.2	+	2	187	c.187G>A	c.(187-189)GAA>AAA	p.E63K		NM_153325	NP_697020	Q8N687	DB125_HUMAN	defensin, beta 125 preproprotein	63					defense response to bacterium	extracellular region				ovary(1)|central_nervous_system(1)|skin(1)	3		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.156)			AATATCACATGAATATACTCG	0.368													16	172	---	---	---	---	PASS
PDYN	5173	broad.mit.edu	37	20	1961213	1961213	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1961213C>T	uc010gaj.2	-	3	763	c.521G>A	c.(520-522)CGC>CAC	p.R174H	uc002wfu.1_Intron|PDYN_uc002wfv.2_Missense_Mutation_p.R174H|PDYN_uc010zpt.1_Missense_Mutation_p.R19H	NM_024411	NP_077722	P01213	PDYN_HUMAN	beta-neoendorphin-dynorphin preproprotein	174					cell death|neuropeptide signaling pathway|synaptic transmission	extracellular region|plasma membrane	opioid peptide activity			upper_aerodigestive_tract(1)|ovary(1)	2						GCCCCCATAGCGTTTGACCTG	0.582													26	84	---	---	---	---	PASS
BPIL1	80341	broad.mit.edu	37	20	31598853	31598853	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31598853C>T	uc002wyj.2	+	3	327	c.133C>T	c.(133-135)CTC>TTC	p.L45F		NM_025227	NP_079503	Q8N4F0	BPIL1_HUMAN	bactericidal/permeability-increasing	45						extracellular region	lipid binding			skin(2)|large_intestine(1)|ovary(1)	4						GAAAGCCCCTCTCCAGCGGGC	0.607													20	122	---	---	---	---	PASS
CTNNBL1	56259	broad.mit.edu	37	20	36488755	36488755	+	Intron	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36488755G>C	uc010zvw.1	+						CTNNBL1_uc002xhh.2_Intron|CTNNBL1_uc002xhi.2_Intron|CTNNBL1_uc002xhj.2_Intron	NM_030877	NP_110517	Q8WYA6	CTBL1_HUMAN	beta catenin-like 1						apoptosis|positive regulation of apoptosis|somatic diversification of immunoglobulins	nucleus	enzyme binding			ovary(2)	2		Myeloproliferative disorder(115;0.00878)				GGGTGAGTTGGATGCTACTCA	0.458													31	86	---	---	---	---	PASS
CHD6	84181	broad.mit.edu	37	20	40080608	40080608	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40080608C>T	uc002xka.1	-	22	3559	c.3381G>A	c.(3379-3381)GAG>GAA	p.E1127E		NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1127					chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)				CCATGTCCTTCTCGTTCAGAT	0.517													6	111	---	---	---	---	PASS
PTPRT	11122	broad.mit.edu	37	20	40713386	40713386	+	Nonsense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40713386G>A	uc002xkg.2	-	29	4256	c.4072C>T	c.(4072-4074)CGA>TGA	p.R1358*	PTPRT_uc010ggj.2_Nonsense_Mutation_p.R1377*|PTPRT_uc010ggi.2_Nonsense_Mutation_p.R561*	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1358	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 2.				homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				TCCAGTCGTCGGACCACTTTG	0.597													11	42	---	---	---	---	PASS
HNF4A	3172	broad.mit.edu	37	20	43034759	43034759	+	Silent	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43034759G>C	uc002xma.2	+	2	266	c.177G>C	c.(175-177)CTG>CTC	p.L59L	HNF4A_uc010zwo.1_Missense_Mutation_p.C50S|HNF4A_uc002xlt.2_Silent_p.L37L|HNF4A_uc002xlu.2_Silent_p.L37L|HNF4A_uc002xlv.2_Silent_p.L37L|HNF4A_uc002xly.2_Silent_p.L59L|HNF4A_uc002xlz.2_Silent_p.L59L|HNF4A_uc010ggq.2_Silent_p.L52L	NM_000457	NP_000448	P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4 alpha isoform b	59	Nuclear receptor.				blood coagulation|endocrine pancreas development|glucose homeostasis|negative regulation of cell growth|negative regulation of cell proliferation|ornithine metabolic process|phospholipid homeostasis|positive regulation of cholesterol homeostasis|regulation of growth hormone receptor signaling pathway|regulation of insulin secretion|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to glucose stimulus|triglyceride homeostasis|xenobiotic metabolic process	cytoplasm	activating transcription factor binding|protein homodimerization activity|receptor binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			TCAGCGCCCTGTGTGCCATCT	0.637													32	125	---	---	---	---	PASS
ZSWIM3	140831	broad.mit.edu	37	20	44505750	44505750	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44505750G>A	uc002xqd.2	+	2	756	c.553G>A	c.(553-555)GAT>AAT	p.D185N	ZSWIM3_uc010zxg.1_Missense_Mutation_p.D179N	NM_080752	NP_542790	Q96MP5	ZSWM3_HUMAN	zinc finger, SWIM domain containing 3	185							zinc ion binding			ovary(2)	2		Myeloproliferative disorder(115;0.0122)				TCTTAAGGTAGATGAGGGTTC	0.517													5	141	---	---	---	---	PASS
ZMYND8	23613	broad.mit.edu	37	20	45905101	45905101	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45905101G>T	uc002xta.1	-	11	1631	c.1377C>A	c.(1375-1377)TTC>TTA	p.F459L	ZMYND8_uc010ghq.1_Missense_Mutation_p.F136L|ZMYND8_uc010ghr.1_Missense_Mutation_p.F434L|ZMYND8_uc002xst.1_Missense_Mutation_p.F434L|ZMYND8_uc002xsu.1_Missense_Mutation_p.F459L|ZMYND8_uc002xsv.1_Missense_Mutation_p.F434L|ZMYND8_uc002xsw.1_Missense_Mutation_p.F211L|ZMYND8_uc002xsx.1_Missense_Mutation_p.F211L|ZMYND8_uc002xsy.1_Missense_Mutation_p.F434L|ZMYND8_uc002xsz.1_Missense_Mutation_p.F396L|ZMYND8_uc010zxy.1_Missense_Mutation_p.F486L|ZMYND8_uc002xtb.1_Missense_Mutation_p.F479L|ZMYND8_uc002xss.2_Missense_Mutation_p.F459L|ZMYND8_uc010zxz.1_Missense_Mutation_p.F454L|ZMYND8_uc002xtc.1_Missense_Mutation_p.F479L|ZMYND8_uc002xtd.1_Missense_Mutation_p.F454L|ZMYND8_uc002xte.1_Missense_Mutation_p.F459L|ZMYND8_uc010zya.1_Missense_Mutation_p.F459L|ZMYND8_uc002xtf.1_Missense_Mutation_p.F479L|ZMYND8_uc002xtg.2_Missense_Mutation_p.F453L|ZMYND8_uc010ghs.1_Missense_Mutation_p.F453L	NM_012408	NP_036540	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8 isoform b	459							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)			CGCTCGCACTGAAGTGGCTCG	0.627													3	29	---	---	---	---	PASS
ZMYND8	23613	broad.mit.edu	37	20	45905323	45905323	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45905323G>A	uc002xta.1	-	11	1409	c.1155C>T	c.(1153-1155)AGC>AGT	p.S385S	ZMYND8_uc010ghq.1_Silent_p.S62S|ZMYND8_uc010ghr.1_Silent_p.S360S|ZMYND8_uc002xst.1_Silent_p.S360S|ZMYND8_uc002xsu.1_Silent_p.S385S|ZMYND8_uc002xsv.1_Silent_p.S360S|ZMYND8_uc002xsw.1_Silent_p.S137S|ZMYND8_uc002xsx.1_Silent_p.S137S|ZMYND8_uc002xsy.1_Silent_p.S360S|ZMYND8_uc002xsz.1_Silent_p.S322S|ZMYND8_uc010zxy.1_Silent_p.S412S|ZMYND8_uc002xtb.1_Silent_p.S405S|ZMYND8_uc002xss.2_Silent_p.S385S|ZMYND8_uc010zxz.1_Silent_p.S380S|ZMYND8_uc002xtc.1_Silent_p.S405S|ZMYND8_uc002xtd.1_Silent_p.S380S|ZMYND8_uc002xte.1_Silent_p.S385S|ZMYND8_uc010zya.1_Silent_p.S385S|ZMYND8_uc002xtf.1_Silent_p.S405S|ZMYND8_uc002xtg.2_Silent_p.S379S|ZMYND8_uc010ghs.1_Silent_p.S379S	NM_012408	NP_036540	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8 isoform b	385							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)			CAGTGCCGGCGCTGGGGTTGG	0.527													6	224	---	---	---	---	PASS
SULF2	55959	broad.mit.edu	37	20	46307536	46307536	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46307536G>A	uc002xto.2	-	8	1407	c.1077C>T	c.(1075-1077)ATC>ATT	p.I359I	SULF2_uc002xtr.2_Silent_p.I359I|SULF2_uc002xtq.2_Silent_p.I359I	NM_018837	NP_061325	Q8IWU5	SULF2_HUMAN	sulfatase 2 isoform a precursor	359					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						TGTTGAGGACGATGTGGGGAT	0.632													10	128	---	---	---	---	PASS
SPATA2	9825	broad.mit.edu	37	20	48524804	48524804	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48524804C>A	uc010gie.2	-	2	574	c.224G>T	c.(223-225)CGC>CTC	p.R75L	SPATA2_uc002xuw.2_Missense_Mutation_p.R75L|SPATA2_uc010zyn.1_Intron	NM_001135773	NP_001129245	Q9UM82	SPAT2_HUMAN	spermatogenesis associated 2	75					cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm|nucleus				central_nervous_system(1)|skin(1)	2	Hepatocellular(150;0.133)		BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			GCTGAGCGAGCGCAAGGAGCT	0.597													30	82	---	---	---	---	PASS
NFATC2	4773	broad.mit.edu	37	20	50071200	50071200	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50071200G>A	uc002xwd.2	-	6	1954	c.1734C>T	c.(1732-1734)CCC>CCT	p.P578P	NFATC2_uc002xwc.2_Silent_p.P578P|NFATC2_uc010zyv.1_Silent_p.P359P|NFATC2_uc010zyw.1_Silent_p.P359P|NFATC2_uc010zyx.1_Silent_p.P558P|NFATC2_uc010zyy.1_Silent_p.P359P|NFATC2_uc010zyz.1_Silent_p.P359P|NFATC2_uc002xwe.2_Silent_p.P558P|hsa-mir-3194|MI0014239_5'Flank	NM_173091	NP_775114	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells,	578					B cell receptor signaling pathway|positive regulation of B cell proliferation|response to DNA damage stimulus|response to drug	actin cytoskeleton|nucleus|plasma membrane	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	Hepatocellular(150;0.248)					TTTCAACCATGGGCAGCTCGT	0.502													67	190	---	---	---	---	PASS
RBM38	55544	broad.mit.edu	37	20	55967819	55967819	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55967819G>A	uc010zzj.1	+	2	522	c.347G>A	c.(346-348)CGG>CAG	p.R116Q	RBM38_uc010zzk.1_Missense_Mutation_p.R116Q	NM_017495	NP_059965	Q9H0Z9	RBM38_HUMAN	RNA-binding region containing protein 1 isoform	116				RS -> WC (in Ref. 4; CAA53063/CAA53064).	3'-UTR-mediated mRNA stabilization|cell cycle|cell cycle arrest|cell differentiation|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 transcription of p21 class mediator|mRNA processing|negative regulation of cell proliferation|regulation of RNA splicing|RNA splicing	cytosol|cytosol|nucleus|nucleus	mRNA 3'-UTR binding|mRNA binding|nucleotide binding|RNA binding				0	Lung NSC(12;0.00242)|all_lung(29;0.00767)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;1.55e-12)|Epithelial(14;9.49e-09)|all cancers(14;5.01e-08)			GCCAAGCCGCGGAGCCTCCAG	0.627													15	96	---	---	---	---	PASS
ZBP1	81030	broad.mit.edu	37	20	56186895	56186895	+	Silent	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56186895G>A	uc002xyo.2	-	6	1043	c.762C>T	c.(760-762)ATC>ATT	p.I254I	ZBP1_uc010gjm.2_Silent_p.I253I|ZBP1_uc002xyp.2_Silent_p.I179I	NM_030776	NP_110403	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1 isoform a	254	RIP homotypic interaction motif (RHIM) 2.					cytoplasm|nucleus	double-stranded RNA adenosine deaminase activity|left-handed Z-DNA binding|RNA binding			ovary(2)	2	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)			GCTCCATGTGGATGTCCTGGG	0.647													6	17	---	---	---	---	PASS
UCKL1	54963	broad.mit.edu	37	20	62571824	62571824	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62571824C>T	uc010gkn.2	-	13	1360	c.1317G>A	c.(1315-1317)AGG>AGA	p.R439R	UCKL1_uc002yhj.2_Silent_p.R82R|UCKL1_uc011abm.1_Silent_p.R424R|UCKL1_uc011abn.1_RNA	NM_017859	NP_060329	Q9NWZ5	UCKL1_HUMAN	uridine-cytidine kinase 1-like 1	439					interspecies interaction between organisms	endoplasmic reticulum|nucleus	ATP binding|phosphotransferase activity, alcohol group as acceptor|protein binding|uridine kinase activity				0	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CCTTGGGCAGCCTCAGGTAGT	0.677													9	25	---	---	---	---	PASS
TPTE	7179	broad.mit.edu	37	21	10941899	10941899	+	Intron	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10941899G>C	uc002yip.1	-						TPTE_uc002yis.1_Intron|TPTE_uc002yiq.1_Intron|TPTE_uc002yir.1_Intron|TPTE_uc010gkv.1_Intron	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GTCAGATAAAGACCCTTACCT	0.323													14	150	---	---	---	---	PASS
USP25	29761	broad.mit.edu	37	21	17183533	17183533	+	Intron	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17183533G>C	uc002yjy.1	+						USP25_uc011aby.1_Intron|USP25_uc002yjz.1_Intron|USP25_uc010gla.1_Intron	NM_013396	NP_037528	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25						protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		CTTGAAGGTAGAGTTATACAT	0.323													10	114	---	---	---	---	PASS
RNF160	26046	broad.mit.edu	37	21	30359114	30359114	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30359114C>G	uc002ymr.2	-	2	335	c.322G>C	c.(322-324)GAT>CAT	p.D108H	RNF160_uc010gll.1_RNA	NM_015565	NP_056380	O94822	LTN1_HUMAN	zinc finger protein 294	62							ligase activity|zinc ion binding				0						AAATCAGAATCTACAAGACTG	0.368													4	117	---	---	---	---	PASS
KRTAP27-1	643812	broad.mit.edu	37	21	31709364	31709364	+	Silent	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31709364C>T	uc002ynx.1	-	1	649	c.623G>A	c.(622-624)TGA>TAA	p.*208*		NM_001077711	NP_001071179	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	208						intermediate filament				ovary(2)	2						TACAGATCTTCACTTACTAGG	0.378													7	56	---	---	---	---	PASS
SYNJ1	8867	broad.mit.edu	37	21	34029363	34029363	+	Silent	SNP	T	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34029363T>C	uc002yqh.2	-	20	2646	c.2646A>G	c.(2644-2646)CCA>CCG	p.P882P	SYNJ1_uc011ads.1_Silent_p.P838P|SYNJ1_uc002yqf.2_Silent_p.P843P|SYNJ1_uc002yqg.2_Silent_p.P838P|SYNJ1_uc002yqi.2_Silent_p.P882P	NM_003895	NP_003886	O43426	SYNJ1_HUMAN	synaptojanin 1 isoform a	843	Catalytic (Potential).						inositol-polyphosphate 5-phosphatase activity|nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			ovary(4)|skin(1)	5						GCAAAGTGCCTGGAGTCCACG	0.383													14	43	---	---	---	---	PASS
GART	2618	broad.mit.edu	37	21	34892833	34892833	+	Nonsense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34892833G>A	uc002yrx.2	-	14	1675	c.1540C>T	c.(1540-1542)CAA>TAA	p.Q514*	GART_uc002yrz.2_Nonsense_Mutation_p.Q514*|GART_uc010gmd.2_Nonsense_Mutation_p.Q176*|GART_uc002yry.2_Nonsense_Mutation_p.Q514*	NM_000819	NP_000810	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase,	514	AIRS.				'de novo' IMP biosynthetic process|purine base biosynthetic process	cytosol	ATP binding|metal ion binding|methyltransferase activity|phosphoribosylamine-glycine ligase activity|phosphoribosylformylglycinamidine cyclo-ligase activity|phosphoribosylglycinamide formyltransferase activity|protein binding			ovary(1)	1					Pemetrexed(DB00642)	ACCAAATCTTGACCAATGGTA	0.368													8	38	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22569377	22569377	+	Intron	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22569377G>A	uc011aim.1	+						uc011aio.1_RNA					Parts of antibodies, mostly variable regions.												0						AGGCAGGGCTGACTCAGCCAC	0.587													17	12	---	---	---	---	PASS
SMTN	6525	broad.mit.edu	37	22	31484020	31484020	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31484020G>A	uc003ajl.1	+	3	339	c.121G>A	c.(121-123)GAG>AAG	p.E41K	SMTN_uc003ajk.1_Missense_Mutation_p.E41K|SMTN_uc003ajm.1_Missense_Mutation_p.E41K|SMTN_uc011ale.1_Missense_Mutation_p.E95K|SMTN_uc011alf.1_Missense_Mutation_p.E97K|SMTN_uc003ajn.1_Missense_Mutation_p.E33K|SMTN_uc011alg.1_5'Flank	NM_006932	NP_008863	P53814	SMTN_HUMAN	smoothelin isoform c	41	Potential.				muscle organ development|smooth muscle contraction	actin cytoskeleton|cytoplasm	actin binding|structural constituent of muscle			large_intestine(2)|pancreas(1)	3						GCAGCGGCAGGAGCTGGAGCG	0.652													8	45	---	---	---	---	PASS
INPP5J	27124	broad.mit.edu	37	22	31524234	31524234	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31524234A>G	uc003aju.3	+	8	2026	c.1934A>G	c.(1933-1935)AAG>AGG	p.K645R	INPP5J_uc003ajv.3_Missense_Mutation_p.K278R|INPP5J_uc003ajs.3_Missense_Mutation_p.K278R|INPP5J_uc011alk.1_Missense_Mutation_p.K578R|INPP5J_uc010gwg.2_Missense_Mutation_p.K210R|INPP5J_uc003ajw.2_Missense_Mutation_p.K81R|INPP5J_uc003ajt.3_Missense_Mutation_p.K277R|INPP5J_uc003ajx.2_Missense_Mutation_p.K10R|INPP5J_uc003ajy.2_Missense_Mutation_p.K10R|INPP5J_uc003ajz.2_Missense_Mutation_p.K85R	NM_001002837	NP_001002837	Q15735	PI5PA_HUMAN	phosphatidylinositol (4,5) bisphosphate	645	Catalytic (Potential).					cytoplasm|ruffle	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|SH3 domain binding			skin(1)	1						CCCATTCTGAAGGGCTTTCAG	0.582													3	22	---	---	---	---	PASS
EIF4ENIF1	56478	broad.mit.edu	37	22	31867895	31867895	+	Silent	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31867895G>C	uc003akz.1	-	3	269	c.105C>G	c.(103-105)CTC>CTG	p.L35L	EIF4ENIF1_uc003ala.1_Silent_p.L35L|EIF4ENIF1_uc003alb.1_Silent_p.L35L|EIF4ENIF1_uc003alc.1_Silent_p.L35L	NM_019843	NP_062817	Q9NRA8	4ET_HUMAN	eukaryotic translation initiation factor 4E	35	EIF4E-binding.					nucleus	protein binding|protein transporter activity			ovary(1)	1						TTATATCCAAGAGTTCTTCCT	0.353													80	140	---	---	---	---	PASS
TNRC6B	23112	broad.mit.edu	37	22	40662452	40662452	+	Nonsense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40662452C>T	uc011aor.1	+	5	2429	c.2218C>T	c.(2218-2220)CAA>TAA	p.Q740*	TNRC6B_uc003aym.2_Intron|TNRC6B_uc003ayn.3_Nonsense_Mutation_p.Q740*|TNRC6B_uc003ayo.2_Nonsense_Mutation_p.Q544*	NM_001162501	NP_001155973	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B isoform 1	740					gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0						CCAGCCCAATCAAGGATGGTC	0.522													4	58	---	---	---	---	PASS
MOV10L1	54456	broad.mit.edu	37	22	50581585	50581585	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50581585C>T	uc003bjj.2	+	17	2376	c.2293C>T	c.(2293-2295)CCG>TCG	p.P765S	MOV10L1_uc003bjk.3_Missense_Mutation_p.P765S|MOV10L1_uc011arp.1_Missense_Mutation_p.P745S|MOV10L1_uc011arq.1_Missense_Mutation_p.P526S	NM_018995	NP_061868	Q9BXT6	M10L1_HUMAN	MOV10-like 1 isoform 1	765					germ cell development|multicellular organismal development|spermatogenesis		ATP binding|ATP-dependent RNA helicase activity|magnesium ion binding|RNA binding			ovary(2)|skin(1)	3		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		CCGTCCCCTCCCGTATATTCT	0.483													47	86	---	---	---	---	PASS
MXRA5	25878	broad.mit.edu	37	X	3242837	3242837	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3242837C>G	uc004crg.3	-	5	1046	c.889G>C	c.(889-891)GAA>CAA	p.E297Q		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	297						extracellular region				ovary(5)|lung(1)|central_nervous_system(1)|skin(1)	8		all_lung(23;0.00031)|Lung NSC(23;0.000946)				TCTTCCTGTTCTTGCTCCTCC	0.502													19	90	---	---	---	---	PASS
RAI2	10742	broad.mit.edu	37	X	17818858	17818858	+	Nonsense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17818858C>A	uc004cyf.2	-	3	1843	c.1273G>T	c.(1273-1275)GAA>TAA	p.E425*	RAI2_uc004cyg.2_Nonsense_Mutation_p.E425*|RAI2_uc010nfa.2_Nonsense_Mutation_p.E425*|RAI2_uc004cyh.3_Nonsense_Mutation_p.E425*|RAI2_uc011miy.1_Nonsense_Mutation_p.E375*	NM_021785	NP_068557	Q9Y5P3	RAI2_HUMAN	retinoic acid induced 2	425					embryo development					ovary(1)|breast(1)	2	Hepatocellular(33;0.183)					ATGTTATTTTCAGCCTTGACT	0.552													9	163	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	X	26179268	26179268	+	IGR	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:26179268C>G								MAGEB18 (20416 upstream) : MAGEB6 (31289 downstream)																							TCCAAGAGAGCTGCGTTCTTT	0.468													17	55	---	---	---	---	PASS
IL1RAPL1	11141	broad.mit.edu	37	X	29973281	29973281	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:29973281C>T	uc004dby.2	+	11	1943	c.1435C>T	c.(1435-1437)CCA>TCA	p.P479S		NM_014271	NP_055086	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	479	Cytoplasmic (Potential).|TIR.				innate immune response|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of exocytosis|regulation of neuron projection development	cytoplasm|integral to membrane|plasma membrane	protein binding|transmembrane receptor activity			ovary(3)|lung(1)|pancreas(1)	5						TGTCATGACCCCAAATTACGT	0.388													45	59	---	---	---	---	PASS
CXorf22	170063	broad.mit.edu	37	X	35974215	35974215	+	Missense_Mutation	SNP	A	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35974215A>C	uc004ddj.2	+	8	1371	c.1312A>C	c.(1312-1314)AAT>CAT	p.N438H	CXorf22_uc010ngv.2_RNA	NM_152632	NP_689845	Q6ZTR5	CX022_HUMAN	hypothetical protein LOC170063	438										large_intestine(1)|lung(1)|ovary(1)	3						CATCATAAAAAATCAATGCGA	0.378													31	39	---	---	---	---	PASS
NYX	60506	broad.mit.edu	37	X	41307168	41307168	+	Missense_Mutation	SNP	T	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41307168T>A	uc004dfh.2	+	1	456	c.26T>A	c.(25-27)CTG>CAG	p.L9Q	NYX_uc011mku.1_Missense_Mutation_p.L4Q	NM_022567	NP_072089	Q9GZU5	NYX_HUMAN	nyctalopin precursor	9					response to stimulus|visual perception	intracellular|proteinaceous extracellular matrix				lung(2)	2						ATGTTGGTCCTGCTTCTGCAT	0.592													9	17	---	---	---	---	PASS
GLRA4	441509	broad.mit.edu	37	X	102974156	102974156	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102974156C>A	uc011mse.1	-	7	1183	c.762G>T	c.(760-762)CAG>CAT	p.Q254H	GLRA4_uc010nou.2_Missense_Mutation_p.Q254H	NM_001024452	NP_001019623	Q5JXX5	GLRA4_HUMAN	glycine receptor, alpha 4 precursor	254	Extracellular (Potential).					cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|glycine binding|receptor activity|transmitter-gated ion channel activity				0						AGTAGCCCATCTGCCGTTCCA	0.557													74	103	---	---	---	---	PASS
TBC1D8B	54885	broad.mit.edu	37	X	106082562	106082562	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106082562G>C	uc004emo.2	+	8	1393	c.1228G>C	c.(1228-1230)GAG>CAG	p.E410Q	MORC4_uc004emp.3_Intron|TBC1D8B_uc004emn.2_Missense_Mutation_p.E410Q	NM_017752	NP_060222	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)	410						intracellular	calcium ion binding|Rab GTPase activator activity			ovary(2)|central_nervous_system(1)|skin(1)	4						TGAGTCTACAGAGCCATCTGA	0.373													42	65	---	---	---	---	PASS
DCX	1641	broad.mit.edu	37	X	110644424	110644424	+	Missense_Mutation	SNP	T	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110644424T>A	uc004epd.2	-	3	914	c.742A>T	c.(742-744)AGT>TGT	p.S248C	DCX_uc011msv.1_Missense_Mutation_p.S248C|DCX_uc004epe.2_Missense_Mutation_p.S167C|DCX_uc004epf.2_Missense_Mutation_p.S167C|DCX_uc004epg.2_Missense_Mutation_p.S167C	NM_000555	NP_000546	O43602	DCX_HUMAN	doublecortin isoform a	248					axon guidance|central nervous system development|intracellular signal transduction	cytosol|microtubule associated complex	microtubule binding			central_nervous_system(2)|lung(1)|skin(1)	4						GCCTGTGCACTGTTGCTGCTA	0.522													32	52	---	---	---	---	PASS
LONRF3	79836	broad.mit.edu	37	X	118123389	118123389	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118123389C>T	uc004eqw.2	+	4	1109	c.1078C>T	c.(1078-1080)CAT>TAT	p.H360Y	LONRF3_uc004eqx.2_Missense_Mutation_p.H319Y|LONRF3_uc004eqy.2_RNA|LONRF3_uc004eqz.2_Missense_Mutation_p.H104Y	NM_001031855	NP_001027026	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger	360					proteolysis		ATP-dependent peptidase activity|protein binding|zinc ion binding			breast(1)|central_nervous_system(1)	2						GGAGCTCCCACATTGTTCTAG	0.498													25	59	---	---	---	---	PASS
GLUD2	2747	broad.mit.edu	37	X	120181736	120181736	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:120181736C>G	uc004eto.2	+	1	275	c.198C>G	c.(196-198)TTC>TTG	p.F66L		NM_012084	NP_036216	P49448	DHE4_HUMAN	glutamate dehydrogenase 2 precursor	66					glutamate biosynthetic process|glutamate catabolic process	mitochondrial matrix	ADP binding|glutamate dehydrogenase|glutamate dehydrogenase activity|GTP binding|leucine binding			pancreas(1)	1					L-Glutamic Acid(DB00142)|NADH(DB00157)	ACCCCAACTTCTTCAAGATGG	0.677													13	78	---	---	---	---	PASS
GRIA3	2892	broad.mit.edu	37	X	122319713	122319713	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122319713G>C	uc004etq.3	+	3	432	c.139G>C	c.(139-141)GAG>CAG	p.E47Q	GRIA3_uc004etr.3_Missense_Mutation_p.E47Q|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_Missense_Mutation_p.E31Q|GRIA3_uc010nqs.1_Missense_Mutation_p.E47Q	NM_007325	NP_015564	P42263	GRIA3_HUMAN	glutamate receptor, ionotrophic, AMPA 3 isoform	47	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5					L-Glutamic Acid(DB00142)	CACAGTGCAGGAGCACAGCGC	0.488													10	68	---	---	---	---	PASS
BCORL1	63035	broad.mit.edu	37	X	129155069	129155069	+	Missense_Mutation	SNP	A	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129155069A>T	uc004evb.1	+	5	3665	c.3551A>T	c.(3550-3552)AAG>ATG	p.K1184M	BCORL1_uc010nrd.1_Missense_Mutation_p.K1086M	NM_021946	NP_068765	Q5H9F3	BCORL_HUMAN	BCL6 co-repressor-like 1	1184					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(4)|breast(2)|lung(1)	7						AAGCACCGGAAGCCGACAAAG	0.627													10	38	---	---	---	---	PASS
FLNA	2316	broad.mit.edu	37	X	153589882	153589882	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153589882G>C	uc004fkk.2	-	21	3250	c.3001C>G	c.(3001-3003)CAA>GAA	p.Q1001E	FLNA_uc010nuu.1_Missense_Mutation_p.Q1001E	NM_001110556	NP_001104026	P21333	FLNA_HUMAN	filamin A, alpha isoform 2	1001	Filamin 8.				actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering	cell cortex|cytosol|extracellular region|nucleus|plasma membrane	actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					ACTTTGCCTTGACCACCAGCA	0.577													55	102	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	146582209	146582209	+	IGR	DEL	T	-	-	rs149481029		TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146582209delT								LOC728989 (67610 upstream) : PRKAB2 (44478 downstream)																							AATATTAATATTGACTAATAA	0.269													3	4	---	---	---	---	
STON1-GTF2A1L	286749	broad.mit.edu	37	2	48807594	48807594	+	5'Flank	DEL	T	-	-			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48807594delT	uc010yol.1	+						STON1_uc002rwo.3_Intron|STON1_uc010fbm.2_Intron|STON1-GTF2A1L_uc002rwp.1_Intron|STON1_uc002rwr.2_5'Flank|STON1_uc002rwq.2_5'Flank	NM_006873	NP_006864	B7ZL16	B7ZL16_HUMAN	stonin 1						endocytosis|intracellular protein transport|transcription initiation from RNA polymerase II promoter	clathrin adaptor complex|transcription factor TFIIA complex				ovary(3)|pancreas(1)|skin(1)	5		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ttggatcatgtttttttttta	0.100													3	5	---	---	---	---	
C2orf3	6936	broad.mit.edu	37	2	75900439	75900439	+	Intron	DEL	A	-	-			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75900439delA	uc002sno.2	-						C2orf3_uc010ffs.2_Intron|C2orf3_uc002snn.2_Intron|C2orf3_uc010fft.2_Intron	NM_003203	NP_003194	P16383	GCF_HUMAN	hypothetical protein LOC6936						negative regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2						gtctcaaaagaaaaaaaaaaa	0.085													4	2	---	---	---	---	
ADCY5	111	broad.mit.edu	37	3	123066917	123066918	+	Intron	DEL	CA	-	-	rs10551109		TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123066917_123066918delCA	uc003egh.1	-						ADCY5_uc003egg.1_Intron|ADCY5_uc003egi.1_Intron	NM_183357	NP_899200	O95622	ADCY5_HUMAN	adenylate cyclase 5						activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)	4				GBM - Glioblastoma multiforme(114;0.0342)		tgtgtctgtgcatgtgtgtgta	0.460													4	2	---	---	---	---	
GNB4	59345	broad.mit.edu	37	3	179119234	179119236	+	Intron	DEL	AAT	-	-	rs74384746		TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179119234_179119236delAAT	uc003fjv.3	-						GNB4_uc003fju.3_Intron	NM_021629	NP_067642	Q9HAV0	GBB4_HUMAN	guanine nucleotide-binding protein, beta-4						cellular response to glucagon stimulus|energy reserve metabolic process	plasma membrane	signal transducer activity			skin(2)	2	all_cancers(143;2.01e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.237)			TCAGttaaaaaataataataatt	0.271													3	4	---	---	---	---	
FAM153B	202134	broad.mit.edu	37	5	175524559	175524560	+	Intron	INS	-	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175524559_175524560insA	uc003mdk.2	+						FAM153B_uc010jjy.1_Intron	NM_001079529	NP_001072997	P0C7A2	F153B_HUMAN	hypothetical protein LOC202134											ovary(1)	1	all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164)	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)	Kidney(146;0.0965)		gatttcatctcaaaaaaaaaaa	0.178													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	29770021	29770021	+	IGR	DEL	A	-	-			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29770021delA								HCG4 (9171 upstream) : HLA-G (24735 downstream)																							TAGGGGTGGGAAGAGTGATCC	0.532													4	3	---	---	---	---	
FAM135A	57579	broad.mit.edu	37	6	71236468	71236469	+	Intron	DEL	AT	-	-	rs111717563		TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71236468_71236469delAT	uc003pfj.2	+						FAM135A_uc003pfi.2_Intron|FAM135A_uc003pfh.2_Intron|FAM135A_uc003pfl.2_Intron|FAM135A_uc003pfn.2_Intron|FAM135A_uc003pfo.1_Intron|FAM135A_uc010kan.1_5'Flank	NM_001162529	NP_001156001	Q9P2D6	F135A_HUMAN	hypothetical protein LOC57579 isoform c											central_nervous_system(1)	1						acacacacacatacacacacac	0.218													2	5	---	---	---	---	
AHI1	54806	broad.mit.edu	37	6	135759594	135759594	+	Frame_Shift_Del	DEL	C	-	-			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135759594delC	uc003qgi.2	-	15	2339	c.1955delG	c.(1954-1956)GGCfs	p.G652fs	AHI1_uc003qgf.2_RNA|AHI1_uc003qgg.2_Frame_Shift_Del_p.G102fs|AHI1_uc003qgh.2_Frame_Shift_Del_p.G652fs|AHI1_uc003qgj.2_Frame_Shift_Del_p.G652fs|AHI1_uc003qgk.3_RNA|AHI1_uc003qgl.3_Frame_Shift_Del_p.G652fs	NM_001134831	NP_001128303	Q8N157	AHI1_HUMAN	Abelson helper integration site 1 isoform a	652	WD 2.					adherens junction|cilium|microtubule basal body				ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		ATTGAGGTGGCCACACAATTC	0.353													4	2	---	---	---	---	
PLEKHA8	84725	broad.mit.edu	37	7	30101796	30101797	+	Intron	INS	-	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30101796_30101797insT	uc003tam.1	+						PLEKHA8_uc003tao.2_Intron|PLEKHA8_uc003tap.1_Intron|PLEKHA8_uc003tan.2_Intron	NM_032639	NP_116028	Q96JA3	PKHA8_HUMAN	pleckstrin homology domain containing, family A						protein transport	cytoplasm	glycolipid binding|glycolipid transporter activity			breast(3)|ovary(1)	4						ATACCACCTTATTTTTTTTTTG	0.312											OREG0017934	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
FAM188B	84182	broad.mit.edu	37	7	30831331	30831331	+	Intron	DEL	A	-	-	rs60449260		TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30831331delA	uc003tbt.2	+						FAM188B_uc010kwe.2_Intron	NM_032222	NP_115598	Q4G0A6	F188B_HUMAN	hypothetical protein LOC84182												0						CCGGCAAGGTAGAGTTTGTTA	0.428													3	5	---	---	---	---	
CAMK2B	816	broad.mit.edu	37	7	44268438	44268439	+	Frame_Shift_Ins	INS	-	G	G			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44268438_44268439insG	uc003tkq.2	-	19	1634_1635	c.1424_1425insC	c.(1423-1425)CCGfs	p.P475fs	CAMK2B_uc003tkp.2_Intron|CAMK2B_uc003tkx.2_Intron|CAMK2B_uc010kyd.2_Intron|CAMK2B_uc003tkr.2_Intron|CAMK2B_uc003tks.2_Intron|CAMK2B_uc003tku.2_Intron|CAMK2B_uc003tkv.2_Intron|CAMK2B_uc003tkt.2_Intron|CAMK2B_uc003tkw.2_Intron|CAMK2B_uc010kyc.2_Intron|CAMK2B_uc003tkn.2_Frame_Shift_Ins_p.P108fs	NM_001220	NP_001211	Q13554	KCC2B_HUMAN	calcium/calmodulin-dependent protein kinase II	475					interferon-gamma-mediated signaling pathway|synaptic transmission	cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			large_intestine(1)|ovary(1)	2						ACAGGCAGGGCGGGGGCCCCGC	0.673													8	4	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	3855370	3855370	+	Intron	DEL	A	-	-	rs11303985		TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3855370delA	uc011kwk.1	-							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)		TCGTTGGGGGAAAAAACGGGG	0.468													5	4	---	---	---	---	
EFR3A	23167	broad.mit.edu	37	8	132966046	132966046	+	Intron	DEL	T	-	-	rs112472883		TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132966046delT	uc003yte.2	+							NM_015137	NP_055952	Q14156	EFR3A_HUMAN	EFR3 homolog A							plasma membrane	binding			ovary(3)|breast(1)|central_nervous_system(1)	5	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			ATTTTCTTCCTTTTTTTTTTT	0.323													9	5	---	---	---	---	
LMX1B	4010	broad.mit.edu	37	9	129453241	129453242	+	Frame_Shift_Ins	INS	-	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129453241_129453242insA	uc004bqj.2	+	3	434_435	c.384_385insA	c.(382-387)CGCAAGfs	p.R128fs	LMX1B_uc004bqi.2_Frame_Shift_Ins_p.R128fs|LMX1B_uc011maa.1_Frame_Shift_Ins_p.R128fs	NM_002316	NP_002307	O60663	LMX1B_HUMAN	LIM homeobox transcription factor 1, beta	128_129	LIM zinc-binding 2.				dorsal/ventral pattern formation|in utero embryonic development	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						GGCAGCTACGCAAGGGCGACGA	0.629									Nail-Patella_Syndrome				28	15	---	---	---	---	
STAM	8027	broad.mit.edu	37	10	17756346	17756347	+	Intron	DEL	AC	-	-			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17756346_17756347delAC	uc001ipj.1	+						STAM_uc009xjw.1_Intron	NM_003473	NP_003464	Q92783	STAM1_HUMAN	signal transducing adaptor molecule 1						cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway	cytosol|early endosome membrane	SH3/SH2 adaptor activity			large_intestine(1)|ovary(1)	2						TGGTTAAATAACACACATATTT	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	64011615	64011616	+	IGR	DEL	TG	-	-	rs150253900		TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64011615_64011616delTG								FKBP2 (9 upstream) : PPP1R14B (337 downstream)																							GGAGTAAGCCTGTGTGTGTTTG	0.480													5	7	---	---	---	---	
SF3B2	10992	broad.mit.edu	37	11	65825443	65825444	+	Intron	INS	-	A	A			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65825443_65825444insA	uc001ogy.1	+							NM_006842	NP_006833	Q13435	SF3B2_HUMAN	splicing factor 3B subunit 2						interspecies interaction between organisms	catalytic step 2 spliceosome|nucleoplasm|U12-type spliceosomal complex	nucleic acid binding|protein binding			ovary(2)|breast(1)	3						aactccgtctcaaaaaaaaaaa	0.183													4	2	---	---	---	---	
FAT3	120114	broad.mit.edu	37	11	92498315	92498316	+	Intron	INS	-	A	A	rs112861336		TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92498315_92498316insA	uc001pdj.3	+							NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3						homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				AAGCAACTaggaaaaaaaaaaa	0.332										TCGA Ovarian(4;0.039)			5	3	---	---	---	---	
RPS25	6230	broad.mit.edu	37	11	118887969	118887969	+	Intron	DEL	T	-	-			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118887969delT	uc001pun.2	-						TRAPPC4_uc010ryn.1_5'Flank|TRAPPC4_uc010ryo.1_5'Flank|TRAPPC4_uc010ryp.1_5'Flank|TRAPPC4_uc001pup.2_5'Flank|TRAPPC4_uc010ryq.1_5'Flank	NM_001028	NP_001019	P62851	RS25_HUMAN	ribosomal protein S25						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleolus	protein binding|RNA binding				0	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)		CAAGCCACGCTTTTTTTTTTT	0.328													5	3	---	---	---	---	
PPFIBP1	8496	broad.mit.edu	37	12	27800899	27800899	+	Intron	DEL	A	-	-	rs112008008		TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27800899delA	uc001ric.1	+						PPFIBP1_uc010sjr.1_Intron|PPFIBP1_uc001rib.1_Intron|PPFIBP1_uc001ria.2_Intron|PPFIBP1_uc001rid.1_Intron	NM_003622	NP_003613	Q86W92	LIPB1_HUMAN	PTPRF interacting protein binding protein 1						cell adhesion	plasma membrane	protein binding		PPFIBP1/ALK(3)	soft_tissue(3)|kidney(1)|skin(1)	5	Lung SC(9;0.0873)					CCAGCACATTAAAAAAAAAAA	0.348													6	4	---	---	---	---	
POLE	5426	broad.mit.edu	37	12	133258000	133258004	+	Intron	DEL	GCTCA	-	-	rs5744732		TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133258000_133258004delGCTCA	uc001uks.1	-						POLE_uc010tbq.1_Intron|POLE_uc009zyu.1_Intron	NM_006231	NP_006222	Q07864	DPOE1_HUMAN	DNA-directed DNA polymerase epsilon						base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)		tgtgatctcggctcactgcaagctc	0.054								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					3	4	---	---	---	---	
POU4F1	5457	broad.mit.edu	37	13	79176484	79176486	+	In_Frame_Del	DEL	TGG	-	-			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79176484_79176486delTGG	uc001vkv.2	-	2	558_560	c.324_326delCCA	c.(322-327)CACCAG>CAG	p.H108del	uc001vku.1_Intron	NM_006237	NP_006228	Q01851	PO4F1_HUMAN	POU domain, class 4, transcription factor 1	108	Poly-His.				axonogenesis|regulation of transcription from RNA polymerase II promoter|synapse assembly	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.129)		TTCGAGCGCCtggtggtggtggt	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	22409899	22409899	+	Intron	DEL	G	-	-			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22409899delG	uc001wbw.2	+						uc010tmg.1_Intron|uc010tmh.1_Intron|uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron					SubName: Full=Alpha-chain C region; Flags: Fragment;																		TGAGCAGCACGGGGGGCCCGG	0.547													15	16	---	---	---	---	
DKFZP434L187	26082	broad.mit.edu	37	15	30517243	30517245	+	Intron	DEL	CCG	-	-			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30517243_30517245delCCG	uc001zds.2	+											Homo sapiens cDNA FLJ43588 fis, clone SKNSH2009991.												0						GGGCCTCTTCCCGCCGCCGCCGC	0.690													4	2	---	---	---	---	
SEMA6D	80031	broad.mit.edu	37	15	48058484	48058484	+	Intron	DEL	G	-	-	rs528882	by1000genomes	TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48058484delG	uc010bek.2	+						SEMA6D_uc001zvw.2_Intron|SEMA6D_uc001zvy.2_Intron|SEMA6D_uc001zvz.2_Intron|SEMA6D_uc001zwa.2_Intron|SEMA6D_uc001zwb.2_Intron|SEMA6D_uc001zwc.2_Intron	NM_153618	NP_705871	Q8NFY4	SEM6D_HUMAN	semaphorin 6D isoform 4 precursor						axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		CTTTTTTTTTGTTGTTATGGG	0.358													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	75541370	75541371	+	IGR	INS	-	T	T			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75541370_75541371insT								C15orf39 (36862 upstream) : GOLGA6C (9528 downstream)																							TATATAACGAGTTTTTTTTTTT	0.287													4	5	---	---	---	---	
SMG1	23049	broad.mit.edu	37	16	18893710	18893710	+	Intron	DEL	A	-	-			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18893710delA	uc002dfm.2	-						SMG1_uc010bwb.2_Intron	NM_015092	NP_055907	Q96Q15	SMG1_HUMAN	PI-3-kinase-related kinase SMG-1						DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16						TGttttaaataaaaaaaaaaa	0.338													6	4	---	---	---	---	
MED13	9969	broad.mit.edu	37	17	60129744	60129744	+	Intron	DEL	A	-	-			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60129744delA	uc002izo.2	-							NM_005121	NP_005112	Q9UHV7	MED13_HUMAN	mediator complex subunit 13						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			large_intestine(1)|ovary(1)	2						AAAGTGGTTTAAAAAAAAAAA	0.323													4	2	---	---	---	---	
FCER2	2208	broad.mit.edu	37	19	7762654	7762655	+	Intron	DEL	TA	-	-	rs151220343		TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7762654_7762655delTA	uc002mhn.2	-						FCER2_uc010xjs.1_Intron|FCER2_uc010xjt.1_Intron|FCER2_uc002mhm.2_Intron|FCER2_uc010dvo.2_Intron	NM_002002	NP_001993	P06734	FCER2_HUMAN	Fc fragment of IgE, low affinity II, receptor						positive regulation of killing of cells of other organism|positive regulation of nitric-oxide synthase 2 biosynthetic process|positive regulation of nitric-oxide synthase activity	extracellular region|integral to plasma membrane	IgE binding|integrin binding|receptor activity|sugar binding				0						TATAATGAACTACTGTGTACCT	0.426													2	4	---	---	---	---	
ICAM5	7087	broad.mit.edu	37	19	10403104	10403105	+	Intron	INS	-	G	G	rs145394131	by1000genomes	TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10403104_10403105insG	uc002mnu.3	+						ICAM5_uc002mnv.3_Intron	NM_003259	NP_003250	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5 precursor						cell-cell adhesion	integral to plasma membrane				breast(3)	3			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			GCGTGGCCCGAGGGGCGGGGCA	0.703													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	53703995	53703995	+	IGR	DEL	T	-	-	rs113703393		TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53703995delT								ZNF665 (7376 upstream) : ZNF677 (34643 downstream)																							TGTTTCCCCCttttttttttt	0.229													4	2	---	---	---	---	
KIR3DX1	90011	broad.mit.edu	37	19	55049049	55049050	+	Intron	INS	-	AAA	AAA			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55049049_55049050insAAA	uc010erm.2	+						KIR3DX1_uc010yfa.1_Intron|KIR3DX1_uc010yfb.1_Intron|KIR3DX1_uc010yfc.1_Intron|KIR3DX1_uc010yfd.1_Intron					Homo sapiens killer cell immunoglobulin-like receptor, three domains, X1, mRNA (cDNA clone IMAGE:4849085).											ovary(1)	1				GBM - Glioblastoma multiforme(193;0.099)		gactccatctcaaaaaaaaaaa	0.074													7	5	---	---	---	---	
SGK2	10110	broad.mit.edu	37	20	42195812	42195812	+	Intron	DEL	C	-	-			TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42195812delC	uc002xkv.2	+						SGK2_uc002xkt.2_Intron|SGK2_uc002xkr.2_Intron|SGK2_uc010ggm.2_Intron|SGK2_uc002xks.2_Intron|SGK2_uc002xku.2_Intron|SGK2_uc002xkq.1_Intron	NM_016276	NP_057360	Q9HBY8	SGK2_HUMAN	serum/glucocorticoid regulated kinase 2 isoform						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)			ATACCTGGCTCCCCTTGCCTT	0.532													21	11	---	---	---	---	
GCFC1	94104	broad.mit.edu	37	21	34133212	34133213	+	Intron	DEL	GC	-	-	rs8133271		TCGA-34-5928-01	TCGA-34-5928-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34133212_34133213delGC	uc002yqn.2	-						GCFC1_uc002yqo.2_Intron|GCFC1_uc002yqp.2_Intron|GCFC1_uc002yqr.2_Intron	NM_016631	NP_057715	Q9Y5B6	GCFC1_HUMAN	GC-rich sequence DNA-binding factor candidate							cytosol|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2						gtgcgtgcgtgcgtgtgtgtgt	0.277													3	5	---	---	---	---	
