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
GABRD	2563	broad.mit.edu	37	1	1961080	1961080	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1961080A>T	uc001aip.2	+	8	1033	c.938A>T	c.(937-939)TAC>TTC	p.Y313F		NM_000815	NP_000806	O14764	GBRD_HUMAN	gamma-aminobutyric acid (GABA) A receptor, delta	313	Helical; (Probable).					cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3	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;2.7e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.17e-24)|GBM - Glioblastoma multiforme(42;9.56e-08)|Colorectal(212;4.12e-05)|COAD - Colon adenocarcinoma(227;0.000194)|Kidney(185;0.00231)|BRCA - Breast invasive adenocarcinoma(365;0.00441)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)		CTGGACGTCTACTTCTGGATC	0.587													6	39	---	---	---	---	PASS
MMEL1	79258	broad.mit.edu	37	1	2529710	2529710	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2529710A>T	uc001ajy.2	-	13	1422	c.1208T>A	c.(1207-1209)CTG>CAG	p.L403Q	MMEL1_uc009vlg.1_RNA	NM_033467	NP_258428	Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	403	Lumenal (Potential).				proteolysis	extracellular region|integral to membrane|intracellular membrane-bounded organelle	metal ion binding|metalloendopeptidase activity				0	all_cancers(77;0.000233)|all_epithelial(69;8.55e-05)|all_lung(157;0.0228)|Lung NSC(156;0.0402)|Ovarian(185;0.0634)	all_epithelial(116;1.03e-20)|all_lung(118;5.15e-09)|Lung NSC(185;9.02e-07)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;8.52e-23)|GBM - Glioblastoma multiforme(42;1.49e-08)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;0.000213)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00219)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.131)		GTCCAGCACCAGGCGCCAGAC	0.592													7	65	---	---	---	---	PASS
ACTRT2	140625	broad.mit.edu	37	1	2938634	2938634	+	Missense_Mutation	SNP	C	G	G	rs137995220		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2938634C>G	uc001ajz.2	+	1	589	c.384C>G	c.(382-384)TTC>TTG	p.F128L		NM_080431	NP_536356	Q8TDY3	ACTT2_HUMAN	actin-related protein M2	128						cytoplasm|cytoskeleton					0	all_cancers(77;0.00205)|all_epithelial(69;0.0011)|Ovarian(185;0.0634)|Lung NSC(156;0.0893)|all_lung(157;0.0909)	all_epithelial(116;2.66e-20)|all_lung(118;1.56e-08)|Lung NSC(185;2.54e-06)|Breast(487;0.00156)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;7.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.15e-22)|GBM - Glioblastoma multiforme(42;1.1e-12)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000329)|BRCA - Breast invasive adenocarcinoma(365;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.125)		AAGTCATGTTCGAGAACTTCG	0.632													18	31	---	---	---	---	PASS
CHD5	26038	broad.mit.edu	37	1	6170001	6170001	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6170001T>C	uc001amb.1	-	38	5532	c.5432A>G	c.(5431-5433)TAC>TGC	p.Y1811C	CHD5_uc001alz.1_Missense_Mutation_p.Y668C|CHD5_uc001ama.1_RNA	NM_015557	NP_056372	Q8TDI0	CHD5_HUMAN	chromodomain helicase DNA binding protein 5	1811					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding|zinc ion binding			central_nervous_system(3)|breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1)	12	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		CATGTTCAGGTACGCGGCCCT	0.701													5	28	---	---	---	---	PASS
KIF1B	23095	broad.mit.edu	37	1	10328302	10328302	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10328302C>A	uc001aqx.3	+	7	903	c.701C>A	c.(700-702)ACC>AAC	p.T234N	KIF1B_uc001aqv.3_Missense_Mutation_p.T234N|KIF1B_uc001aqw.3_Missense_Mutation_p.T234N|KIF1B_uc001aqy.2_Missense_Mutation_p.T234N|KIF1B_uc001aqz.2_Missense_Mutation_p.T234N|KIF1B_uc001ara.2_Missense_Mutation_p.T234N|KIF1B_uc001arb.2_Missense_Mutation_p.T234N|KIF1B_uc009vmt.2_RNA	NM_015074	NP_055889	O60333	KIF1B_HUMAN	kinesin family member 1B isoform b	234	Kinesin-motor.				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)		GATAATGAGACCAACCTTTCC	0.433													13	10	---	---	---	---	PASS
KIAA2013	90231	broad.mit.edu	37	1	11983449	11983449	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11983449C>T	uc001atk.2	-	2	1325	c.1131G>A	c.(1129-1131)CTG>CTA	p.L377L	KIAA2013_uc001atl.1_Silent_p.L377L	NM_138346	NP_612355	Q8IYS2	K2013_HUMAN	hypothetical protein LOC90231 precursor	377	Extracellular (Potential).					integral to membrane				ovary(1)	1	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00149)|all_lung(284;0.00189)|Breast(348;0.00586)|Colorectal(325;0.0062)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0556)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AGGGGCTGAGCAGTGGGGCTG	0.597													5	58	---	---	---	---	PASS
VPS13D	55187	broad.mit.edu	37	1	12567003	12567003	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12567003C>T	uc001atv.2	+	69	13032	c.12891C>T	c.(12889-12891)GCC>GCT	p.A4297A	VPS13D_uc001atw.2_Silent_p.A4272A|VPS13D_uc001atx.2_Silent_p.A3484A|VPS13D_uc009vnl.2_RNA|VPS13D_uc010obd.1_Silent_p.A295A|SNORA59B_uc001atz.1_5'Flank	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1	4296					protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		ATCGAGAAGCCATTTTCCTAG	0.493													15	82	---	---	---	---	PASS
PRAMEF8	391002	broad.mit.edu	37	1	12979852	12979852	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12979852C>A	uc001aup.2	+	4	1127	c.1044C>A	c.(1042-1044)GCC>GCA	p.A348A		NM_001012276	NP_001012276	Q5VWM4	PRAM8_HUMAN	PRAME family member 8	348	LRR 2.										0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AAGTTGTGGCCACCCTGCAGA	0.602													22	56	---	---	---	---	PASS
PADI1	29943	broad.mit.edu	37	1	17552641	17552641	+	Missense_Mutation	SNP	T	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17552641T>G	uc001bah.1	+	6	732	c.640T>G	c.(640-642)TTC>GTC	p.F214V		NM_013358	NP_037490	Q9ULC6	PADI1_HUMAN	peptidylarginine deiminase type I	214					peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm	calcium ion binding|protein-arginine deiminase activity				0		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)	AGTGAGGGTCTTCTGTGCCAG	0.512													16	35	---	---	---	---	PASS
TCEB3	6924	broad.mit.edu	37	1	24078941	24078941	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24078941G>A	uc001bho.2	+	5	1608	c.1548G>A	c.(1546-1548)GCG>GCA	p.A516A		NM_003198	NP_003189	Q14241	ELOA1_HUMAN	elongin A	516					positive regulation of viral transcription|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|viral reproduction	integral to membrane	DNA binding			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.42e-24)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;4.74e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|KIRC - Kidney renal clear cell carcinoma(1967;0.00334)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		CGTTACCCGCGATACAGGCCA	0.507													10	8	---	---	---	---	PASS
MYOM3	127294	broad.mit.edu	37	1	24421985	24421985	+	Intron	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24421985C>T	uc001bin.3	-						MYOM3_uc001bim.3_5'Flank|MYOM3_uc001bio.2_Intron|MYOM3_uc001bip.1_Intron	NM_152372	NP_689585	Q5VTT5	MYOM3_HUMAN	myomesin family, member 3											skin(2)|ovary(1)	3		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		AGCTGAAAAACCAAAGGCAAA	0.368													48	58	---	---	---	---	PASS
C1orf201	90529	broad.mit.edu	37	1	24706237	24706237	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24706237T>C	uc001bjc.2	-	5	503	c.368A>G	c.(367-369)AAG>AGG	p.K123R	C1orf201_uc001bja.2_Missense_Mutation_p.K76R|C1orf201_uc001bjb.2_Missense_Mutation_p.K31R|C1orf201_uc001bjd.2_Missense_Mutation_p.K123R|C1orf201_uc001bje.1_Missense_Mutation_p.K76R|C1orf201_uc001bjf.2_5'UTR			Q5TH74	CA201_HUMAN	RecName: Full=UPF0490 protein C1orf201;	123										ovary(1)|breast(1)	2		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.0191)|all_lung(284;0.0251)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.056)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.48e-25)|Colorectal(126;7.29e-08)|COAD - Colon adenocarcinoma(152;3.85e-06)|GBM - Glioblastoma multiforme(114;0.000399)|BRCA - Breast invasive adenocarcinoma(304;0.00107)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00393)|READ - Rectum adenocarcinoma(331;0.0672)|Lung(427;0.145)		AAAGTCTCTCTTGGAAATAAA	0.413													33	37	---	---	---	---	PASS
PTAFR	5724	broad.mit.edu	37	1	28477001	28477001	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28477001C>T	uc001bpl.2	-	2	659	c.532G>A	c.(532-534)GAG>AAG	p.E178K	PTAFR_uc001bpm.3_Missense_Mutation_p.E178K|PTAFR_uc009vte.2_Missense_Mutation_p.E178K	NM_000952	NP_000943	P25105	PTAFR_HUMAN	platelet-activating factor receptor	178	Extracellular (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)		CTGCCCTTCTCGTAATGCTCA	0.542													12	26	---	---	---	---	PASS
YTHDF2	51441	broad.mit.edu	37	1	29070237	29070237	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29070237G>T	uc001brc.2	+	4	1952	c.1455G>T	c.(1453-1455)GTG>GTT	p.V485V	YTHDF2_uc001brd.2_Silent_p.V482V|YTHDF2_uc010ofx.1_Silent_p.V435V|YTHDF2_uc001bre.2_Silent_p.V435V	NM_016258	NP_057342	Q9Y5A9	YTHD2_HUMAN	high glucose-regulated protein 8	485	YTH.				humoral immune response					ovary(1)|skin(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.000601)|all_lung(284;0.000771)|Breast(348;0.00502)|Renal(390;0.00758)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;5.46e-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)		GTGCAGGTGTGTGGTCCCAGG	0.493													23	39	---	---	---	---	PASS
CSMD2	114784	broad.mit.edu	37	1	34102088	34102088	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34102088A>T	uc001bxn.1	-	30	4750	c.4721T>A	c.(4720-4722)CTG>CAG	p.L1574Q	CSMD2_uc001bxm.1_Missense_Mutation_p.L1614Q|CSMD2_uc001bxo.1_Missense_Mutation_p.L487Q	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1574	Extracellular (Potential).|Sushi 9.					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GCCCAGCTTCAGGTCGGACCC	0.582													15	9	---	---	---	---	PASS
CSMD2	114784	broad.mit.edu	37	1	34191097	34191097	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34191097C>A	uc001bxn.1	-	17	2457	c.2428G>T	c.(2428-2430)GAT>TAT	p.D810Y	CSMD2_uc001bxm.1_Missense_Mutation_p.D850Y	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	810	CUB 5.|Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GTCCGCCCATCGCGTACTTCC	0.493													19	33	---	---	---	---	PASS
DLGAP3	58512	broad.mit.edu	37	1	35365738	35365738	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35365738G>C	uc001byc.2	-	2	1244	c.1244C>G	c.(1243-1245)ACA>AGA	p.T415R		NM_001080418	NP_001073887	O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated	415					cell-cell signaling	cell junction|postsynaptic density|postsynaptic membrane				ovary(3)	3		Myeloproliferative disorder(586;0.0393)				TTTGGGAGATGTCTTGGGGCT	0.662													10	48	---	---	---	---	PASS
KIAA0319L	79932	broad.mit.edu	37	1	35921739	35921739	+	Nonsense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35921739G>A	uc001byx.2	-	10	1789	c.1531C>T	c.(1531-1533)CAA>TAA	p.Q511*	KIAA0319L_uc001byw.2_5'Flank|KIAA0319L_uc010ohv.1_Nonsense_Mutation_p.Q153*	NM_024874	NP_079150	Q8IZA0	K319L_HUMAN	dyslexia susceptibility 2-like	511	PKD 3.|Extracellular (Potential).					cytoplasmic vesicle part|integral to membrane	protein binding			skin(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GTGATCACTTGGTTGGGGCCT	0.532													69	46	---	---	---	---	PASS
GRIK3	2899	broad.mit.edu	37	1	37325587	37325587	+	Missense_Mutation	SNP	C	A	A	rs114188187	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37325587C>A	uc001caz.2	-	6	953	c.818G>T	c.(817-819)CGC>CTC	p.R273L	GRIK3_uc001cba.1_Missense_Mutation_p.R273L	NM_000831	NP_000822	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	273	Extracellular (Potential).				negative regulation of synaptic transmission, glutamatergic|regulation of membrane potential|synaptic transmission	cell junction|dendrite cytoplasm|integral to plasma membrane|perikaryon|postsynaptic membrane|terminal button	adenylate cyclase inhibiting metabotropic glutamate receptor activity|extracellular-glutamate-gated ion channel activity|G-protein-coupled receptor binding|kainate selective glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)|breast(1)	7		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)			L-Glutamic Acid(DB00142)	GCCTGAGTAGCGGTAGGGCTC	0.567													35	34	---	---	---	---	PASS
MACF1	23499	broad.mit.edu	37	1	39715746	39715746	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39715746C>G	uc010ois.1	+	5	548	c.343C>G	c.(343-345)CTG>GTG	p.L115V	MACF1_uc001cda.1_Missense_Mutation_p.L23V|MACF1_uc010oit.1_Missense_Mutation_p.L78V	NM_012090	NP_036222	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	115	Actin-binding.|CH 1.				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)			CCTGATCTCTCTGTTGGAGGT	0.433													69	41	---	---	---	---	PASS
KIAA0754	643314	broad.mit.edu	37	1	39876940	39876940	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39876940G>C	uc009vvt.1	+	1	1765	c.1003G>C	c.(1003-1005)GAG>CAG	p.E335Q	MACF1_uc010ois.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc010oiu.1_Intron	NM_015038	NP_055853	O94854	K0754_HUMAN	hypothetical protein LOC643314	199											0	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	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)			GGCTGAGGGAGAGTGGGAGGA	0.448											OREG0013393	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	11	53	---	---	---	---	PASS
MACF1	23499	broad.mit.edu	37	1	39945559	39945559	+	Nonsense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39945559C>T	uc010oiu.1	+	62	17439	c.17308C>T	c.(17308-17310)CGA>TGA	p.R5770*	MACF1_uc010ois.1_Nonsense_Mutation_p.R5262*|MACF1_uc001cde.1_Nonsense_Mutation_p.R139*|MACF1_uc001cdf.1_Nonsense_Mutation_p.R145*|MACF1_uc001cdg.2_Nonsense_Mutation_p.R53*|MACF1_uc001cdh.2_Nonsense_Mutation_p.R53*	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	7220	C-terminal tail (By similarity).				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)			CTCACGGGGTCGAAGGTCCAA	0.522													11	37	---	---	---	---	PASS
CTPS	1503	broad.mit.edu	37	1	41474386	41474386	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41474386G>T	uc001cgk.3	+	15	1957	c.1449G>T	c.(1447-1449)GAG>GAT	p.E483D	CTPS_uc010ojo.1_Missense_Mutation_p.E252D|CTPS_uc001cgl.3_Missense_Mutation_p.E483D|CTPS_uc010ojq.1_Missense_Mutation_p.E327D|CTPS_uc009vwe.2_Intron	NM_001905	NP_001896	P17812	PYRG1_HUMAN	CTP synthase	483	Glutamine amidotransferase type-1.				CTP biosynthetic process|glutamine metabolic process|nucleobase, nucleoside and nucleotide interconversion|response to drug	cytosol	ATP binding|CTP synthase activity|protein binding				0	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Breast(333;0.1)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0255)			L-Glutamine(DB00130)	ACCGATTTGAGGTGAGGATTC	0.468													25	40	---	---	---	---	PASS
CLDN19	149461	broad.mit.edu	37	1	43204186	43204186	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43204186G>C	uc001cht.1	-	2	485	c.294C>G	c.(292-294)AGC>AGG	p.S98R	CLDN19_uc001chu.2_Missense_Mutation_p.S98R|CLDN19_uc010ojv.1_Missense_Mutation_p.S98R	NM_148960	NP_683763	Q8N6F1	CLD19_HUMAN	claudin 19 isoform a	98	Helical; (Potential).				calcium-independent cell-cell adhesion|response to stimulus|visual perception	basolateral plasma membrane|integral to membrane|tight junction	identical protein binding				0	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TGCCAACTACGCTGAGGACCA	0.642													4	27	---	---	---	---	PASS
TIE1	7075	broad.mit.edu	37	1	43777783	43777783	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43777783C>T	uc001ciu.2	+	11	1690	c.1611C>T	c.(1609-1611)CTC>CTT	p.L537L	TIE1_uc010okd.1_Silent_p.L537L|TIE1_uc010oke.1_Silent_p.L492L|TIE1_uc009vwq.2_Silent_p.L493L|TIE1_uc010okf.1_Silent_p.L182L|TIE1_uc010okg.1_Silent_p.L182L	NM_005424	NP_005415	P35590	TIE1_HUMAN	tyrosine kinase with immunoglobulin-like and	537	Extracellular (Potential).|Fibronectin type-III 1.				mesoderm development	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			lung(3)|stomach(1)|salivary_gland(1)|ovary(1)|skin(1)	7	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CTCCCACCCTCATGACCACAG	0.612													17	9	---	---	---	---	PASS
KIF2C	11004	broad.mit.edu	37	1	45223802	45223802	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45223802A>G	uc001cmg.3	+	13	1329	c.1214A>G	c.(1213-1215)TAC>TGC	p.Y405C	KIF2C_uc010olb.1_Missense_Mutation_p.Y364C|KIF2C_uc010olc.1_Missense_Mutation_p.Y292C|KIF2C_uc001cmh.3_Missense_Mutation_p.Y351C	NM_006845	NP_006836	Q99661	KIF2C_HUMAN	kinesin family member 2C	405	Kinesin-motor.				blood coagulation|cell division|cell proliferation|chromosome segregation|establishment or maintenance of microtubule cytoskeleton polarity|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|kinesin complex|microtubule|nucleus	ATP binding|centromeric DNA binding|microtubule motor activity|microtubule plus-end binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)					TTCGAGATCTACAATGGGAAG	0.507													20	62	---	---	---	---	PASS
HECTD3	79654	broad.mit.edu	37	1	45469374	45469374	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45469374C>T	uc009vxk.2	-	20	2566	c.2468G>A	c.(2467-2469)TGC>TAC	p.C823Y	HECTD3_uc001cmx.3_Missense_Mutation_p.C172Y|HECTD3_uc001cmy.3_Missense_Mutation_p.C433Y|HECTD3_uc010olh.1_Missense_Mutation_p.C539Y	NM_024602	NP_078878	Q5T447	HECD3_HUMAN	HECT domain containing 3	823	HECT.	Glycyl thioester intermediate.		C->A: Loss of ubiquitin-ligase activity.	proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm	ubiquitin-protein ligase activity				0	Acute lymphoblastic leukemia(166;0.155)					GGTGCTGGAGCAAGTGGAAGA	0.597													20	19	---	---	---	---	PASS
CYP4B1	1580	broad.mit.edu	37	1	47283849	47283849	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47283849A>G	uc001cqm.3	+	11	1400	c.1316A>G	c.(1315-1317)CAT>CGT	p.H439R	CYP4B1_uc001cqn.3_Missense_Mutation_p.H440R|CYP4B1_uc009vym.2_Missense_Mutation_p.H425R|CYP4B1_uc010omk.1_Missense_Mutation_p.H276R	NM_000779	NP_000770	P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B,	439					xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(166;0.155)					TCCAAACGCCATCCCTTTGCC	0.562													43	26	---	---	---	---	PASS
ELAVL4	1996	broad.mit.edu	37	1	50642799	50642799	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50642799C>G	uc001csb.2	+	3	557	c.289C>G	c.(289-291)CCA>GCA	p.P97A	ELAVL4_uc001cry.3_Missense_Mutation_p.P100A|ELAVL4_uc001crz.3_Missense_Mutation_p.P97A|ELAVL4_uc001csa.3_Missense_Mutation_p.P114A|ELAVL4_uc001csc.3_Missense_Mutation_p.P97A|ELAVL4_uc009vyu.2_Missense_Mutation_p.P102A|ELAVL4_uc010omz.1_Missense_Mutation_p.P102A	NM_021952	NP_068771	P26378	ELAV4_HUMAN	ELAV-like 4 isoform 1	97	RRM 1.				mRNA processing		AU-rich element binding|mRNA 3'-UTR binding|nucleotide binding			ovary(1)|pancreas(1)	2						CTATATTGATCCAAAGGATGC	0.313													10	49	---	---	---	---	PASS
C1orf168	199920	broad.mit.edu	37	1	57216842	57216842	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57216842T>A	uc001cym.3	-	9	1668	c.1262A>T	c.(1261-1263)CAG>CTG	p.Q421L	C1orf168_uc009vzu.1_RNA|C1orf168_uc001cyl.2_RNA	NM_001004303	NP_001004303	Q5VWT5	CA168_HUMAN	hypothetical protein LOC199920	421										ovary(3)|skin(2)	5						GTTGGTCATCTGAATTTTTTC	0.458													6	33	---	---	---	---	PASS
EFCAB7	84455	broad.mit.edu	37	1	64034182	64034182	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64034182G>A	uc001dbf.2	+	12	1993	c.1699G>A	c.(1699-1701)GAA>AAA	p.E567K		NM_032437	NP_115813	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	567							calcium ion binding				0						GTCAGTTATTGAAAACAAGGT	0.333													10	17	---	---	---	---	PASS
SGIP1	84251	broad.mit.edu	37	1	67205146	67205146	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67205146C>A	uc001dcr.2	+	22	2377	c.2160C>A	c.(2158-2160)CTC>CTA	p.L720L	SGIP1_uc010opd.1_Silent_p.L320L|SGIP1_uc001dcs.2_Silent_p.L320L|SGIP1_uc001dct.2_Silent_p.L322L|SGIP1_uc009wat.2_Silent_p.L514L|SGIP1_uc001dcu.2_Silent_p.L225L	NM_032291	NP_115667	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting	720					positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3						CTGTGGCCCTCAACAATGTGC	0.527													23	34	---	---	---	---	PASS
WDR78	79819	broad.mit.edu	37	1	67390477	67390477	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67390477G>C	uc001dcx.2	-	1	94	c.38C>G	c.(37-39)GCC>GGC	p.A13G	WDR78_uc001dcy.2_Missense_Mutation_p.A13G|WDR78_uc001dcz.2_Missense_Mutation_p.A13G|MIER1_uc001dda.3_5'Flank|MIER1_uc010opf.1_5'Flank|MIER1_uc009way.2_5'Flank|MIER1_uc001ddc.2_5'Flank|MIER1_uc001ddh.2_5'Flank|MIER1_uc001ddf.2_5'Flank|MIER1_uc001ddg.2_5'Flank|MIER1_uc010opg.1_5'Flank|MIER1_uc001dde.2_5'Flank	NM_024763	NP_079039	Q5VTH9	WDR78_HUMAN	WD repeat domain 78 isoform 1	13										ovary(2)	2						TCCGTTAGCGGCTCGGGCCGA	0.682													38	39	---	---	---	---	PASS
LRRC7	57554	broad.mit.edu	37	1	70477575	70477575	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70477575T>C	uc001dep.2	+	10	1016	c.986T>C	c.(985-987)GTT>GCT	p.V329A	LRRC7_uc009wbg.2_5'UTR	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	329	LRR 14.					centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14						ACATTAGCAGTTGATGAGAAT	0.318													16	15	---	---	---	---	PASS
NEGR1	257194	broad.mit.edu	37	1	72241934	72241934	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72241934T>A	uc001dfw.2	-	3	556	c.456A>T	c.(454-456)GAA>GAT	p.E152D	NEGR1_uc001dfv.2_Missense_Mutation_p.E24D|NEGR1_uc010oqs.1_Missense_Mutation_p.E152D	NM_173808	NP_776169	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1 precursor	152	Ig-like C2-type 2.				cell adhesion	anchored to membrane|plasma membrane				ovary(1)	1		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)		CGTTGGTTCCTTCATTGACGG	0.383													17	20	---	---	---	---	PASS
LRRIQ3	127255	broad.mit.edu	37	1	74507259	74507259	+	Silent	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74507259T>C	uc001dfy.3	-	7	1548	c.1356A>G	c.(1354-1356)AGA>AGG	p.R452R	LRRIQ3_uc001dfz.3_Intron	NM_001105659	NP_001099129	A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	452										ovary(2)	2						CTACTCTAACTCTTTCTCGAG	0.318													19	81	---	---	---	---	PASS
FPGT	8790	broad.mit.edu	37	1	74671168	74671168	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74671168G>C	uc001dgb.1	+	4	1474	c.1437G>C	c.(1435-1437)AAG>AAC	p.K479N	TNNI3K_uc001dgc.1_Intron|TNNI3K_uc001dgd.2_Intron|TNNI3K_uc001dge.1_Intron|FPGT_uc010oqt.1_Missense_Mutation_p.K104N|FPGT_uc010oqu.1_Missense_Mutation_p.K225N|FPGT_uc010oqv.1_Intron	NM_003838	NP_003829	O14772	FPGT_HUMAN	fucose-1-phosphate guanyltransferase	479					fucose metabolic process	cytoplasm	fucose-1-phosphate guanylyltransferase activity|GTP binding			skin(1)	1						ACTTGAAAAAGAGTGTGAAAA	0.363													4	46	---	---	---	---	PASS
MCOLN3	55283	broad.mit.edu	37	1	85486931	85486931	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85486931C>A	uc001dkp.2	-	12	1442	c.1349G>T	c.(1348-1350)TGC>TTC	p.C450F	MCOLN3_uc001dko.2_Missense_Mutation_p.C69F|MCOLN3_uc001dkq.2_Missense_Mutation_p.C394F	NM_018298	NP_060768	Q8TDD5	MCLN3_HUMAN	mucolipin 3	450						integral to membrane	ion channel activity			skin(1)	1				all cancers(265;0.00957)|Epithelial(280;0.0254)		AGAGAAAAGGCACTCAGAGAC	0.373													30	43	---	---	---	---	PASS
COL24A1	255631	broad.mit.edu	37	1	86590593	86590593	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86590593C>T	uc001dlj.2	-	3	1468	c.1426G>A	c.(1426-1428)GAG>AAG	p.E476K	COL24A1_uc010osd.1_5'UTR|COL24A1_uc001dlk.2_RNA|COL24A1_uc010ose.1_RNA|COL24A1_uc010osf.1_RNA|COL24A1_uc009wcq.2_Missense_Mutation_p.E476K	NM_152890	NP_690850	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1 precursor	476					cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)		TTTAGATCCTCATAATAATAA	0.338													23	19	---	---	---	---	PASS
GBP4	115361	broad.mit.edu	37	1	89654377	89654377	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89654377G>A	uc001dnb.2	-	8	1414	c.1298C>T	c.(1297-1299)ACA>ATA	p.T433I		NM_052941	NP_443173	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	433						cytoplasm	GTP binding|GTPase activity				0				all cancers(265;0.00723)|Epithelial(280;0.0291)		AATGCTTTCTGTCAGGTGCTC	0.448													88	191	---	---	---	---	PASS
ABCA4	24	broad.mit.edu	37	1	94502704	94502704	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94502704T>A	uc001dqh.2	-	25	3914	c.3810A>T	c.(3808-3810)GAA>GAT	p.E1270D		NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	1270	Cytoplasmic.				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)		ACTTTACCTCTTCCAGGGGAG	0.453													72	81	---	---	---	---	PASS
LPPR4	9890	broad.mit.edu	37	1	99771402	99771402	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99771402C>T	uc001dse.2	+	7	1234	c.1128C>T	c.(1126-1128)CTC>CTT	p.L376L	LPPR4_uc010oue.1_Silent_p.L318L	NM_014839	NP_055654	Q7Z2D5	LPPR4_HUMAN	plasticity related gene 1	376							phosphatidate phosphatase activity			ovary(3)	3		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)		AAGGCATCCTCAACCGAAACC	0.468													8	103	---	---	---	---	PASS
OLFM3	118427	broad.mit.edu	37	1	102270177	102270177	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102270177C>T	uc001duf.2	-	6	1125	c.1054G>A	c.(1054-1056)GAT>AAT	p.D352N	OLFM3_uc001dug.2_Missense_Mutation_p.D332N|OLFM3_uc001duh.2_RNA|OLFM3_uc001dui.2_RNA|OLFM3_uc001duj.2_Missense_Mutation_p.D257N|OLFM3_uc001due.2_RNA	NM_058170	NP_477518	Q96PB7	NOE3_HUMAN	olfactomedin 3	352	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)		CCGATTTCATCAGCCATTAGG	0.478													24	29	---	---	---	---	PASS
OLFM3	118427	broad.mit.edu	37	1	102302551	102302551	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102302551C>A	uc001duf.2	-	2	231	c.160G>T	c.(160-162)GTG>TTG	p.V54L	OLFM3_uc001dug.2_Missense_Mutation_p.V34L|OLFM3_uc001duh.2_RNA|OLFM3_uc001dui.2_RNA|OLFM3_uc001duj.2_5'UTR|OLFM3_uc001due.2_RNA	NM_058170	NP_477518	Q96PB7	NOE3_HUMAN	olfactomedin 3	54						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)		GAGCTGTACACCTGCCACCCT	0.473													4	46	---	---	---	---	PASS
COL11A1	1301	broad.mit.edu	37	1	103352543	103352543	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103352543C>A	uc001dul.2	-	63	4996	c.4678G>T	c.(4678-4680)GGC>TGC	p.G1560C	COL11A1_uc001duk.2_Missense_Mutation_p.G756C|COL11A1_uc001dum.2_Missense_Mutation_p.G1572C|COL11A1_uc001dun.2_Missense_Mutation_p.G1521C|COL11A1_uc009weh.2_Missense_Mutation_p.G1444C	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A	1560	Nonhelical region (C-terminal).				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		GCTTGCATGCCTTCAGTATGT	0.393													15	86	---	---	---	---	PASS
COL11A1	1301	broad.mit.edu	37	1	103428220	103428220	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103428220C>T	uc001dul.2	-	39	3331	c.3013G>A	c.(3013-3015)GAA>AAA	p.E1005K	COL11A1_uc001duk.2_Missense_Mutation_p.E201K|COL11A1_uc001dum.2_Missense_Mutation_p.E1017K|COL11A1_uc001dun.2_Missense_Mutation_p.E966K|COL11A1_uc009weh.2_Missense_Mutation_p.E889K	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A	1005	Triple-helical region.				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		TTTGCACCTTCTTTTCCTGCA	0.468													7	29	---	---	---	---	PASS
COL11A1	1301	broad.mit.edu	37	1	103453221	103453221	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103453221C>A	uc001dul.2	-	30	2788	c.2470G>T	c.(2470-2472)GAC>TAC	p.D824Y	COL11A1_uc001duk.2_Missense_Mutation_p.E14D|COL11A1_uc001dum.2_Missense_Mutation_p.D836Y|COL11A1_uc001dun.2_Missense_Mutation_p.D785Y|COL11A1_uc009weh.2_Missense_Mutation_p.D708Y	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A	824	Triple-helical region.				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		GGACCTGGGTCTCCAGTTGGG	0.453													14	52	---	---	---	---	PASS
CELSR2	1952	broad.mit.edu	37	1	109803812	109803812	+	Silent	SNP	G	T	T	rs148583272		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109803812G>T	uc001dxa.3	+	3	4168	c.4107G>T	c.(4105-4107)ACG>ACT	p.T1369T		NM_001408	NP_001399	Q9HCU4	CELR2_HUMAN	cadherin EGF LAG seven-pass G-type receptor 2	1369	Extracellular (Potential).|Laminin G-like 1.				dendrite morphogenesis|homophilic cell adhesion|neural plate anterior/posterior regionalization|neuropeptide signaling pathway|regulation of cell-cell adhesion|regulation of transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(4)|lung(3)|skin(1)	8		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		AGGTGACCACGCGCAGCTTCC	0.632													13	52	---	---	---	---	PASS
EPS8L3	79574	broad.mit.edu	37	1	110293279	110293279	+	Intron	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110293279C>T	uc001dyr.1	-						EPS8L3_uc001dys.1_Intron|EPS8L3_uc001dyq.1_Intron|EPS8L3_uc009wfm.1_Intron	NM_133181	NP_573444	Q8TE67	ES8L3_HUMAN	epidermal growth factor receptor pathway							cytoplasm	protein binding			ovary(2)|skin(1)	3		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Lung(183;0.0245)|Colorectal(144;0.0365)|all cancers(265;0.103)|Epithelial(280;0.109)|LUSC - Lung squamous cell carcinoma(189;0.137)|COAD - Colon adenocarcinoma(174;0.141)		AGGGTGTCCTCACCCCCAGCA	0.612													14	31	---	---	---	---	PASS
KCNA3	3738	broad.mit.edu	37	1	111216168	111216168	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111216168C>T	uc001dzv.1	-	1	1488	c.1264G>A	c.(1264-1266)GAC>AAC	p.D422N		NM_002232	NP_002223	P22001	KCNA3_HUMAN	potassium voltage-gated channel, shaker-related	422						voltage-gated potassium channel complex	delayed rectifier potassium channel activity			ovary(4)|pancreas(1)	5		all_cancers(81;3.92e-06)|all_epithelial(167;1.28e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0235)|Colorectal(144;0.0306)|all cancers(265;0.0752)|Epithelial(280;0.0821)|COAD - Colon adenocarcinoma(174;0.132)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTGGGGTCGTCTGCCTCGGCA	0.557													24	39	---	---	---	---	PASS
RSBN1	54665	broad.mit.edu	37	1	114308797	114308797	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114308797C>A	uc001edq.2	-	7	2250	c.2214G>T	c.(2212-2214)AGG>AGT	p.R738S	RSBN1_uc001edr.2_RNA	NM_018364	NP_060834	Q5VWQ0	RSBN1_HUMAN	round spermatid basic protein 1	738						nucleus				ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CAGTTTTTATCCTCACACATT	0.413													26	57	---	---	---	---	PASS
RSBN1	54665	broad.mit.edu	37	1	114310948	114310948	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114310948G>C	uc001edq.2	-	5	1758	c.1722C>G	c.(1720-1722)CTC>CTG	p.L574L	RSBN1_uc001edr.2_RNA	NM_018364	NP_060834	Q5VWQ0	RSBN1_HUMAN	round spermatid basic protein 1	574						nucleus				ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TATCTTCAAAGAGAACTTCGC	0.438													13	76	---	---	---	---	PASS
TRIM33	51592	broad.mit.edu	37	1	114944091	114944091	+	Intron	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114944091C>A	uc001eew.2	-						TRIM33_uc010owr.1_Intron|TRIM33_uc010ows.1_Intron|TRIM33_uc001eex.2_Intron	NM_015906	NP_056990	Q9UPN9	TRI33_HUMAN	tripartite motif-containing 33 protein isoform						negative regulation of BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination|regulation of transforming growth factor beta receptor signaling pathway|transcription, DNA-dependent	nucleus	co-SMAD binding|DNA binding|ligase activity|R-SMAD binding|zinc ion binding			lung(4)|central_nervous_system(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	11	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		CATTTCTGGCCCAAACAAGGA	0.373			T	RET	papillary thyroid								8	24	---	---	---	---	PASS
TRIM33	51592	broad.mit.edu	37	1	114970445	114970445	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114970445C>T	uc001eew.2	-	7	1311	c.1227G>A	c.(1225-1227)GTG>GTA	p.V409V	TRIM33_uc010owr.1_Silent_p.V17V|TRIM33_uc010ows.1_Silent_p.V17V|TRIM33_uc001eex.2_Silent_p.V409V	NM_015906	NP_056990	Q9UPN9	TRI33_HUMAN	tripartite motif-containing 33 protein isoform	409					negative regulation of BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination|regulation of transforming growth factor beta receptor signaling pathway|transcription, DNA-dependent	nucleus	co-SMAD binding|DNA binding|ligase activity|R-SMAD binding|zinc ion binding			lung(4)|central_nervous_system(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	11	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TAACATGCTTCACCTGCCGGG	0.433			T	RET	papillary thyroid								19	23	---	---	---	---	PASS
NOTCH2	4853	broad.mit.edu	37	1	120509091	120509091	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120509091T>C	uc001eik.2	-	9	1731	c.1475A>G	c.(1474-1476)GAA>GGA	p.E492G	NOTCH2_uc001eil.2_Missense_Mutation_p.E492G|NOTCH2_uc001eim.3_Missense_Mutation_p.E409G	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein	492	Extracellular (Potential).|EGF-like 12; 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)		TATTTCTAATTCACAATGCAC	0.418			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				28	59	---	---	---	---	PASS
HFE2	148738	broad.mit.edu	37	1	145415320	145415320	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145415320G>C	uc001eni.2	+	3	464	c.139G>C	c.(139-141)GTA>CTA	p.V47L	NBPF10_uc001emp.3_Intron|HFE2_uc001enj.2_Intron|HFE2_uc001enk.2_5'UTR|HFE2_uc001enl.2_Intron	NM_213653	NP_998818	Q6ZVN8	RGMC_HUMAN	hemojuvelin isoform a precursor	47					axon guidance	anchored to membrane				ovary(1)	1	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TGCTGAGTACGTATCGTCCAC	0.582													7	69	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145581401	145581401	+	Intron	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145581401C>G	uc001emp.3	+						PIAS3_uc001eoc.1_Intron|PIAS3_uc001eod.1_Intron	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		TGCTTCTCCTCAGCTAGGGAA	0.517													19	35	---	---	---	---	PASS
BCL9	607	broad.mit.edu	37	1	147084987	147084987	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147084987C>G	uc001epq.2	+	5	1099	c.359C>G	c.(358-360)TCT>TGT	p.S120C	BCL9_uc010ozr.1_Intron	NM_004326	NP_004317	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	120					Wnt receptor signaling pathway	nucleus	protein binding			ovary(2)|large_intestine(2)|breast(1)|skin(1)	6	all_hematologic(923;0.115)					AACGATGACTCTGACATTAAA	0.498			T	IGH@|IGL@	B-ALL								10	35	---	---	---	---	PASS
TCHHL1	126637	broad.mit.edu	37	1	152058373	152058373	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152058373C>T	uc001ezo.1	-	3	1850	c.1785G>A	c.(1783-1785)CAG>CAA	p.Q595Q		NM_001008536	NP_001008536	Q5QJ38	TCHL1_HUMAN	trichohyalin-like 1	595							calcium ion binding			ovary(1)|skin(1)	2	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)			TTCCCTGCCTCTGGGTATCTG	0.547													30	75	---	---	---	---	PASS
RPTN	126638	broad.mit.edu	37	1	152129161	152129161	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152129161C>T	uc001ezs.1	-	3	479	c.414G>A	c.(412-414)GAG>GAA	p.E138E		NM_001122965	NP_001116437	Q6XPR3	RPTN_HUMAN	repetin	138	Gln-rich.					proteinaceous extracellular matrix	calcium ion binding				0						CGTCTTGTCTCTCAGGCTGAC	0.522													64	170	---	---	---	---	PASS
SYT11	23208	broad.mit.edu	37	1	155838213	155838213	+	Silent	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155838213A>G	uc001fmg.2	+	2	755	c.492A>G	c.(490-492)TCA>TCG	p.S164S	SYT11_uc010pgq.1_Intron	NM_152280	NP_689493	Q9BT88	SYT11_HUMAN	synaptotagmin XI	164	Cytoplasmic (Potential).					cell junction|synaptic vesicle membrane	protein binding|transporter activity			ovary(1)|skin(1)	2	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;0.000162)			TCACCTTCTCAGTGGACTATA	0.542													14	79	---	---	---	---	PASS
FCRL3	115352	broad.mit.edu	37	1	157665335	157665335	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157665335G>A	uc001frb.2	-	8	1487	c.1195C>T	c.(1195-1197)CTG>TTG	p.L399L	FCRL3_uc001fqx.3_RNA|FCRL3_uc001fqy.3_RNA|FCRL3_uc001fqz.3_Silent_p.L399L|FCRL3_uc009wsn.2_RNA|FCRL3_uc009wso.2_RNA|FCRL3_uc001fra.2_Silent_p.L125L|FCRL3_uc001frc.1_Silent_p.L399L	NM_052939	NP_443171	Q96P31	FCRL3_HUMAN	Fc receptor-like 3 precursor	399	Ig-like C2-type 5.|Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(3)|breast(1)	4	all_hematologic(112;0.0378)					AGCTCCAGCAGGTCCCCCACC	0.587													20	47	---	---	---	---	PASS
CD1C	911	broad.mit.edu	37	1	158259915	158259915	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158259915G>T	uc001fru.2	+	1	353	c.61G>T	c.(61-63)GCA>TCA	p.A21S	CD1C_uc001frv.2_5'Flank	NM_001765	NP_001756	P29017	CD1C_HUMAN	CD1C antigen precursor	21	Extracellular (Potential).				antigen processing and presentation|T cell activation involved in immune response	endosome membrane|integral to plasma membrane	endogenous lipid antigen binding|exogenous lipid antigen binding|glycolipid binding|lipopeptide binding			ovary(2)|skin(1)|pancreas(1)	4	all_hematologic(112;0.0378)					CAATGCAGACGGTAAGAACAT	0.473													10	44	---	---	---	---	PASS
OR10Z1	128368	broad.mit.edu	37	1	158576522	158576522	+	Silent	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158576522T>C	uc010pio.1	+	1	294	c.294T>C	c.(292-294)GCT>GCC	p.A98A		NM_001004478	NP_001004478	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z,	98	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)|skin(1)	2	all_hematologic(112;0.0378)					TGGGCTGTGCTGCCCAGATGT	0.547													27	87	---	---	---	---	PASS
OR10Z1	128368	broad.mit.edu	37	1	158576523	158576523	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158576523G>T	uc010pio.1	+	1	295	c.295G>T	c.(295-297)GCC>TCC	p.A99S		NM_001004478	NP_001004478	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z,	99	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)|skin(1)	2	all_hematologic(112;0.0378)					GGGCTGTGCTGCCCAGATGTT	0.547													27	85	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158592826	158592826	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158592826C>G	uc001fst.1	-	43	6266	c.6067G>C	c.(6067-6069)GCC>CCC	p.A2023P		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2023	Spectrin 19.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					ACTGCCGAGGCTTCCAGCAAC	0.458													42	155	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158615329	158615329	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158615329C>A	uc001fst.1	-	28	4151	c.3952G>T	c.(3952-3954)GCC>TCC	p.A1318S		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1318	Spectrin 13.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					AAGTCTTCGGCCAGCTCCTGT	0.433													16	109	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158624460	158624460	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158624460G>T	uc001fst.1	-	21	3176	c.2977C>A	c.(2977-2979)CCC>ACC	p.P993T		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	993	SH3.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					ACTTCTCGGGGGCTGCGGGCC	0.473													9	31	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158648259	158648259	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158648259G>T	uc001fst.1	-	6	943	c.744C>A	c.(742-744)CGC>CGA	p.R248R		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	248	Spectrin 3.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					AACCACGAAGGCGCTCCCAGG	0.448													23	51	---	---	---	---	PASS
OR6N2	81442	broad.mit.edu	37	1	158747070	158747070	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158747070G>T	uc010pir.1	-	1	356	c.356C>A	c.(355-357)GCC>GAC	p.A119D		NM_001005278	NP_001005278	Q8NGY6	OR6N2_HUMAN	olfactory receptor, family 6, subfamily N,	119	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_hematologic(112;0.0378)					TCTATCATAGGCCATGGCTGT	0.498													17	84	---	---	---	---	PASS
MNDA	4332	broad.mit.edu	37	1	158813875	158813875	+	Missense_Mutation	SNP	C	A	A	rs148142374	byFrequency	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158813875C>A	uc001fsz.1	+	4	733	c.533C>A	c.(532-534)ACC>AAC	p.T178N		NM_002432	NP_002423	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	178					B cell receptor signaling pathway|cellular defense response|negative regulation of B cell proliferation|positive regulation of apoptosis|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(2)|skin(2)	4	all_hematologic(112;0.0378)					CTACCCCAGACCTCATCATCA	0.507													24	159	---	---	---	---	PASS
NCSTN	23385	broad.mit.edu	37	1	160327049	160327049	+	Intron	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160327049A>T	uc001fvx.2	+						NCSTN_uc001fvy.2_Intron|NCSTN_uc010pjf.1_Intron|NCSTN_uc001fvz.2_Intron|NCSTN_uc010pjg.1_Intron	NM_015331	NP_056146	Q92542	NICA_HUMAN	nicastrin precursor						amyloid precursor protein catabolic process|apoptosis|induction of apoptosis by extracellular signals|membrane protein ectodomain proteolysis|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|positive regulation of catalytic activity|protein processing	endoplasmic reticulum|Golgi apparatus|integral to plasma membrane|melanosome	protein binding			ovary(1)|lung(1)	2	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TTGAGGTGAGATGGGGCAGGG	0.502													8	12	---	---	---	---	PASS
SLAMF7	57823	broad.mit.edu	37	1	160719604	160719604	+	Intron	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160719604C>G	uc001fwq.2	+						SLAMF7_uc010pjn.1_Intron|SLAMF7_uc001fws.2_Intron|SLAMF7_uc001fwr.2_Intron|SLAMF7_uc010pjo.1_Intron|SLAMF7_uc010pjp.1_Intron|SLAMF7_uc010pjq.1_Intron|SLAMF7_uc010pjr.1_Intron	NM_021181	NP_067004	Q9NQ25	SLAF7_HUMAN	SLAM family member 7						cell adhesion|natural killer cell activation|natural killer cell mediated cytotoxicity	integral to membrane	receptor activity			skin(2)|ovary(1)	3	all_cancers(52;2.63e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			TTTCCTTCCTCTCACAGAGCA	0.498													31	104	---	---	---	---	PASS
OLFML2B	25903	broad.mit.edu	37	1	161967803	161967803	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161967803G>A	uc001gbu.2	-	6	1710	c.1286C>T	c.(1285-1287)CCA>CTA	p.P429L	OLFML2B_uc010pkq.1_Missense_Mutation_p.P430L	NM_015441	NP_056256	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B precursor	429										skin(1)	1	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			TGGGGCTGCTGGTTGCTGGGT	0.607													14	30	---	---	---	---	PASS
PBX1	5087	broad.mit.edu	37	1	164776878	164776878	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164776878G>T	uc001gct.2	+	5	1059	c.801G>T	c.(799-801)GAG>GAT	p.E267D	PBX1_uc010pku.1_Missense_Mutation_p.E267D|PBX1_uc010pkv.1_Missense_Mutation_p.E184D|PBX1_uc001gcs.2_Missense_Mutation_p.E267D|PBX1_uc010pkw.1_Missense_Mutation_p.E157D	NM_002585	NP_002576	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1	267	Homeobox; TALE-type.				negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding		EWSR1/PBX1(3)	soft_tissue(3)|lung(1)|skin(1)	5						AAGCCAAAGAGGAGTTAGCCA	0.542			T	TCF3|EWSR1	pre B-ALL|myoepithelioma								24	146	---	---	---	---	PASS
ILDR2	387597	broad.mit.edu	37	1	166891994	166891994	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166891994G>A	uc001gdx.1	-	8	1103	c.1047C>T	c.(1045-1047)TTC>TTT	p.F349F		NM_199351	NP_955383	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor	349	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1						AAGACTGGCGGAAATTGCTGT	0.488													32	99	---	---	---	---	PASS
ADCY10	55811	broad.mit.edu	37	1	167839660	167839660	+	Intron	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167839660A>T	uc001ger.2	-						ADCY10_uc009wvk.2_Intron|ADCY10_uc010plj.1_Intron|ADCY10_uc009wvl.2_Intron	NM_018417	NP_060887	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10						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						TGTTATTTTTAGTTTTAAAAA	0.279													3	9	---	---	---	---	PASS
C1orf9	51430	broad.mit.edu	37	1	172520690	172520690	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172520690C>T	uc001giq.3	+	2	417	c.101C>T	c.(100-102)TCA>TTA	p.S34L	C1orf9_uc010pmm.1_Missense_Mutation_p.S34L|C1orf9_uc009wwd.2_Missense_Mutation_p.S34L|C1orf9_uc010pmn.1_Missense_Mutation_p.S34L|C1orf9_uc010pmo.1_RNA	NM_014283	NP_055098	Q9UBS9	OSPT_HUMAN	chromosome 1 open reading frame 9 protein	34					multicellular organismal development|ossification	integral to membrane|rough endoplasmic reticulum membrane				ovary(2)	2		Breast(1374;0.212)		Colorectal(1306;3.98e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00544)		GAGAGTTCTTCAGCTTCAGCG	0.383													10	30	---	---	---	---	PASS
SLC9A11	284525	broad.mit.edu	37	1	173503744	173503744	+	Missense_Mutation	SNP	A	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173503744A>C	uc001giz.2	-	16	2276	c.1853T>G	c.(1852-1854)TTG>TGG	p.L618W	SLC9A11_uc009wwe.2_Missense_Mutation_p.L176W|SLC9A11_uc010pmq.1_Intron	NM_178527	NP_848622	Q5TAH2	S9A11_HUMAN	solute carrier family 9, member 11	618	Helical; (Potential).				sodium ion transport	integral to membrane	ion channel activity|solute:hydrogen antiporter activity			ovary(2)	2						AATATATATCAAATTTATAAT	0.254													6	11	---	---	---	---	PASS
SERPINC1	462	broad.mit.edu	37	1	173881102	173881102	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173881102G>C	uc001gjt.2	-	3	578	c.459C>G	c.(457-459)TTC>TTG	p.F153L		NM_000488	NP_000479	P01008	ANT3_HUMAN	serpin peptidase inhibitor, clade C, member 1	153			Missing (in AT3D; type-I).|Missing (in AT3D; type-I).		blood coagulation|regulation of proteolysis	extracellular space|plasma membrane	heparin binding|protease binding|serine-type endopeptidase inhibitor activity			ovary(1)	1					Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)	TGGCAAAGAAGAAGTGGATCT	0.408													26	56	---	---	---	---	PASS
RC3H1	149041	broad.mit.edu	37	1	173947615	173947615	+	Intron	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173947615C>G	uc001gju.3	-						RC3H1_uc010pms.1_Intron|RC3H1_uc001gjv.2_Intron|RC3H1_uc010pmt.1_Intron	NM_172071	NP_742068	Q5TC82	RC3H1_HUMAN	roquin						cytoplasmic mRNA processing body assembly|negative regulation of activated T cell proliferation|negative regulation of B cell proliferation|negative regulation of germinal center formation|negative regulation of T-helper cell differentiation|nuclear-transcribed mRNA catabolic process|regulation of mRNA stability|regulation of T cell receptor signaling pathway	cytoplasmic mRNA processing body|stress granule	mRNA 3'-UTR binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2						ATTAATTTCCCGTGGGTTTAC	0.433													42	52	---	---	---	---	PASS
TNR	7143	broad.mit.edu	37	1	175372675	175372675	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175372675C>A	uc001gkp.1	-	2	658	c.577G>T	c.(577-579)GGC>TGC	p.G193C	TNR_uc009wwu.1_Missense_Mutation_p.G193C|TNR_uc010pmz.1_Missense_Mutation_p.G193C	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor	193	EGF-like 1.|Cys-rich.				axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					CCAAACCAGCCTTCGTTGCAG	0.572													13	92	---	---	---	---	PASS
TNR	7143	broad.mit.edu	37	1	175375662	175375662	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175375662C>A	uc001gkp.1	-	1	270	c.189G>T	c.(187-189)GTG>GTT	p.V63V	TNR_uc009wwu.1_Silent_p.V63V|TNR_uc010pmz.1_Silent_p.V63V	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor	63					axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					GGTTGAAGACCACAGGCTGCT	0.552													17	71	---	---	---	---	PASS
PAPPA2	60676	broad.mit.edu	37	1	176760590	176760590	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176760590G>T	uc001gkz.2	+	19	6156	c.4992G>T	c.(4990-4992)GAG>GAT	p.E1664D	PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	1664	Sushi 5.				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						ATTCTGTGGAGTACAAATGTG	0.418													19	49	---	---	---	---	PASS
CEP350	9857	broad.mit.edu	37	1	180062650	180062650	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180062650C>T	uc001gnt.2	+	34	7793	c.7410C>T	c.(7408-7410)CGC>CGT	p.R2470R	CEP350_uc009wxl.2_Silent_p.R2469R|CEP350_uc001gnv.2_Silent_p.R605R|CEP350_uc001gnw.1_Silent_p.R227R|CEP350_uc001gnx.1_Silent_p.R227R	NM_014810	NP_055625	Q5VT06	CE350_HUMAN	centrosome-associated protein 350	2470						centrosome|nucleus|spindle				ovary(4)	4						GTAAGGAGCGCAGTGATGTGG	0.453													9	24	---	---	---	---	PASS
QSOX1	5768	broad.mit.edu	37	1	180163490	180163490	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180163490C>T	uc001gnz.2	+	11	1506	c.1431C>T	c.(1429-1431)CTC>CTT	p.L477L	QSOX1_uc001gny.2_Silent_p.L477L|QSOX1_uc001goa.2_Silent_p.L477L|QSOX1_uc001goc.2_Silent_p.L19L	NM_002826	NP_002817	O00391	QSOX1_HUMAN	quiescin Q6 sulfhydryl oxidase 1 isoform a	477	ERV/ALR sulfhydryl oxidase.				cell redox homeostasis|protein thiol-disulfide exchange	extracellular space|integral to Golgi membrane	flavin-linked sulfhydryl oxidase activity			ovary(1)|central_nervous_system(1)	2						TCCTCTGGCTCTGGTCTAGCC	0.612													7	20	---	---	---	---	PASS
CACNA1E	777	broad.mit.edu	37	1	181549846	181549846	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181549846C>A	uc001gow.2	+	6	1050	c.885C>A	c.(883-885)ATC>ATA	p.I295I	CACNA1E_uc009wxr.2_Silent_p.I202I|CACNA1E_uc009wxs.2_Silent_p.I202I	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	295	I.|Extracellular (Potential).				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6						TTGATAACATCCTTTTTGCTG	0.547													12	62	---	---	---	---	PASS
GLT25D2	23127	broad.mit.edu	37	1	183907946	183907946	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183907946G>A	uc001gqr.2	-	12	2202	c.1830C>T	c.(1828-1830)GCC>GCT	p.A610A	GLT25D2_uc010poj.1_Intron|GLT25D2_uc001gqp.2_Silent_p.A218A|GLT25D2_uc001gqq.2_Silent_p.A347A|GLT25D2_uc001gqs.2_Silent_p.A490A	NM_015101	NP_055916	Q8IYK4	GT252_HUMAN	glycosyltransferase 25 domain containing 2	610					lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen	procollagen galactosyltransferase activity			ovary(1)|breast(1)	2						GCGGTGGCAGGGCCTCTGTGT	0.562													17	38	---	---	---	---	PASS
EDEM3	80267	broad.mit.edu	37	1	184718672	184718672	+	Intron	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184718672C>A	uc010pok.1	-						EDEM3_uc010pol.1_Intron|EDEM3_uc010pom.1_Intron|EDEM3_uc001gqy.2_Intron	NM_025191	NP_079467	Q9BZQ6	EDEM3_HUMAN	ER degradation enhancer, mannosidase alpha-like						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	endoplasmic reticulum lumen|endoplasmic reticulum membrane	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding			skin(1)	1						AGATAAGCTTCCTACTTACCA	0.289													5	5	---	---	---	---	PASS
HMCN1	83872	broad.mit.edu	37	1	186010270	186010270	+	Splice_Site	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186010270T>C	uc001grq.1	+	40	6533	c.6304_splice	c.e40+2	p.V2102_splice		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						GAGTATATGGTGAGACATTTT	0.408													13	58	---	---	---	---	PASS
HMCN1	83872	broad.mit.edu	37	1	186099657	186099657	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186099657G>T	uc001grq.1	+	85	13287	c.13058G>T	c.(13057-13059)GGT>GTT	p.G4353V	HMCN1_uc001grs.1_5'UTR	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	4353	Ig-like C2-type 43.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						GTCTTCAAAGGTGATTATCCT	0.403													28	58	---	---	---	---	PASS
TPR	7175	broad.mit.edu	37	1	186326588	186326588	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186326588C>A	uc001grv.2	-	14	1962	c.1665G>T	c.(1663-1665)GTG>GTT	p.V555V	TPR_uc010pop.1_Silent_p.V631V	NM_003292	NP_003283	P12270	TPR_HUMAN	nuclear pore complex-associated protein TPR	555	Potential.				carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		CTCTAAGGGCCACTAAGAGAC	0.383			T	NTRK1	papillary thyroid								14	30	---	---	---	---	PASS
PLA2G4A	5321	broad.mit.edu	37	1	186925289	186925289	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186925289G>T	uc001gsc.2	+	14	1597	c.1392G>T	c.(1390-1392)TGG>TGT	p.W464C	PLA2G4A_uc010pos.1_Missense_Mutation_p.W404C	NM_024420	NP_077734	P47712	PA24A_HUMAN	cytosolic phospholipase A2, group IVA	464	PLA2c.				phospholipid catabolic process|platelet activating factor biosynthetic process|platelet activation	cytosol|endoplasmic reticulum membrane	calcium ion binding|calcium-dependent phospholipid binding|lysophospholipase activity			lung(2)|breast(1)	3					Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Medrysone(DB00253)|Quinacrine(DB01103)	AAGCAAGTTGGATTCATCGTA	0.408													5	34	---	---	---	---	PASS
TROVE2	6738	broad.mit.edu	37	1	193038214	193038214	+	Silent	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193038214A>T	uc001gss.2	+	2	205	c.30A>T	c.(28-30)CCA>CCT	p.P10P	TROVE2_uc001gst.1_Intron|TROVE2_uc001gsu.1_Intron|TROVE2_uc001gsv.1_Silent_p.P10P|TROVE2_uc001gsw.2_Silent_p.P10P|TROVE2_uc009wyp.2_Silent_p.P10P|TROVE2_uc009wyq.2_Silent_p.P10P|TROVE2_uc001gsx.1_Silent_p.P10P	NM_004600	NP_004591	P10155	RO60_HUMAN	TROVE domain family, member 2 isoform 2	10					transcription from RNA polymerase III promoter	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|RNA binding				0						AAATGCAGCCACTGAATGAGA	0.378													7	31	---	---	---	---	PASS
ASPM	259266	broad.mit.edu	37	1	197112698	197112698	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197112698G>A	uc001gtu.2	-	3	941	c.684C>T	c.(682-684)TTC>TTT	p.F228F	ASPM_uc001gtv.2_Silent_p.F228F|ASPM_uc001gtw.3_Intron	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	228					mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6						GGCATTCATTGAAAGCAGGGC	0.393													19	53	---	---	---	---	PASS
ZC3H11A	9877	broad.mit.edu	37	1	203798581	203798581	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203798581G>T	uc001hac.2	+	8	917	c.301G>T	c.(301-303)GTG>TTG	p.V101L	ZC3H11A_uc001had.2_Missense_Mutation_p.V101L|ZC3H11A_uc001hae.2_Missense_Mutation_p.V101L|ZC3H11A_uc001haf.2_Missense_Mutation_p.V101L|ZC3H11A_uc010pqm.1_Missense_Mutation_p.V47L|ZC3H11A_uc001hag.1_Missense_Mutation_p.V101L	NM_014827	NP_055642	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A	101							nucleic acid binding|protein binding|zinc ion binding			lung(1)|central_nervous_system(1)	2	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)			GCGTTTAGCTGTGTTGCCCAC	0.418													13	57	---	---	---	---	PASS
PPP1R15B	84919	broad.mit.edu	37	1	204380249	204380249	+	Silent	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204380249T>C	uc001hav.3	-	1	696	c.291A>G	c.(289-291)CTA>CTG	p.L97L		NM_032833	NP_116222	Q5SWA1	PR15B_HUMAN	protein phosphatase 1, regulatory subunit 15B	97					regulation of translation					ovary(1)|pancreas(1)	2	all_cancers(21;0.0032)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.179)|all_epithelial(62;0.193)|Prostate(682;0.227)		all cancers(3;1.14e-29)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.139)			CAGCAAAATCTAGCCATCTGG	0.567													32	68	---	---	---	---	PASS
LPGAT1	9926	broad.mit.edu	37	1	211952259	211952259	+	Splice_Site	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211952259C>G	uc001hiu.2	-	6	1667	c.854_splice	c.e6+1	p.R285_splice	LPGAT1_uc001hiv.2_Splice_Site_p.R285_splice	NM_014873	NP_055688	Q92604	LGAT1_HUMAN	lysophosphatidylglycerol acyltransferase 1						phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	acyltransferase activity			ovary(1)|skin(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.00773)|all cancers(67;0.0765)|Epithelial(68;0.114)		AGAATTCTTACCTGTAATGTA	0.318													10	76	---	---	---	---	PASS
CENPF	1063	broad.mit.edu	37	1	214805946	214805946	+	Splice_Site	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214805946G>T	uc001hkm.2	+	10	1620	c.1446_splice	c.e10+1	p.E482_splice		NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F						cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding			ovary(6)|central_nervous_system(4)|large_intestine(2)|skin(1)	13				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AAGCATGGAGGTAAGGGAGGA	0.438													8	19	---	---	---	---	PASS
CENPF	1063	broad.mit.edu	37	1	214816281	214816281	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214816281G>T	uc001hkm.2	+	12	4774	c.4600G>T	c.(4600-4602)GAG>TAG	p.E1534*		NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F	1630					cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding			ovary(6)|central_nervous_system(4)|large_intestine(2)|skin(1)	13				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		TCTGCAGGAGGAGAATCTGAC	0.498													8	52	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	215823956	215823956	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215823956C>T	uc001hku.1	-	65	14708	c.14321G>A	c.(14320-14322)AGC>AAC	p.S4774N		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	4774	Fibronectin type-III 33.|Extracellular (Potential).				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)		CCCATGGGCGCTGCTGGAGAA	0.483										HNSCC(13;0.011)			9	83	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	215901539	215901539	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215901539C>G	uc001hku.1	-	61	12286	c.11899G>C	c.(11899-11901)GAT>CAT	p.D3967H		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	3967	Fibronectin type-III 25.|Extracellular (Potential).				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)		GCTGGAAAATCTTGAGGTGGA	0.483										HNSCC(13;0.011)			19	36	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	215990448	215990448	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215990448G>C	uc001hku.1	-	48	9848	c.9461C>G	c.(9460-9462)GCT>GGT	p.A3154G		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	3154	Extracellular (Potential).|Fibronectin type-III 18.				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)		TTGAGTTTTAGCGCATGGATA	0.428										HNSCC(13;0.011)			25	41	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	216052200	216052200	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216052200G>C	uc001hku.1	-	42	8851	c.8464C>G	c.(8464-8466)CAG>GAG	p.Q2822E		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	2822	Extracellular (Potential).|Fibronectin type-III 15.				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)		CCAACATTCTGAGGTACGGTG	0.458										HNSCC(13;0.011)			23	67	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	216052283	216052283	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216052283A>T	uc001hku.1	-	42	8768	c.8381T>A	c.(8380-8382)GTT>GAT	p.V2794D		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	2794	Fibronectin type-III 14.|Extracellular (Potential).				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)		TGAGCAAGCAACAATGGTGAC	0.458										HNSCC(13;0.011)			24	122	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	216363668	216363668	+	Silent	SNP	T	A	A	rs142068313		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216363668T>A	uc001hku.1	-	20	4680	c.4293A>T	c.(4291-4293)GTA>GTT	p.V1431V	USH2A_uc001hkv.2_Silent_p.V1431V	NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	1431	Extracellular (Potential).|Fibronectin type-III 4.				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)		TCAGTCCTTCTACAGTGTAAG	0.348										HNSCC(13;0.011)			14	42	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	216595351	216595351	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216595351T>C	uc001hku.1	-	2	715	c.328A>G	c.(328-330)ACA>GCA	p.T110A	USH2A_uc001hkv.2_Missense_Mutation_p.T110A	NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	110	Extracellular (Potential).				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)		TTGTCTGGTGTGATGCAGCTA	0.453										HNSCC(13;0.011)			10	40	---	---	---	---	PASS
RRP15	51018	broad.mit.edu	37	1	218458684	218458684	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218458684G>T	uc001hlj.2	+	1	56	c.26G>T	c.(25-27)CGT>CTT	p.R9L		NM_016052	NP_057136	Q9Y3B9	RRP15_HUMAN	ribosomal RNA processing 15 homolog	9						mitochondrion|nucleolus	protein binding				0				all cancers(67;0.0315)|OV - Ovarian serous cystadenocarcinoma(81;0.0411)|GBM - Glioblastoma multiforme(131;0.06)|Epithelial(68;0.248)		CCGGACTCACGTGTGAGTGAG	0.547													3	20	---	---	---	---	PASS
EPRS	2058	broad.mit.edu	37	1	220152881	220152881	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220152881C>A	uc001hly.1	-	27	4058	c.3788G>T	c.(3787-3789)GGA>GTA	p.G1263V		NM_004446	NP_004437	P07814	SYEP_HUMAN	glutamyl-prolyl tRNA synthetase	1263	Prolyl-tRNA synthetase.				glutamyl-tRNA aminoacylation|prolyl-tRNA aminoacylation|protein complex assembly	cytosol|soluble fraction	ATP binding|glutamate-tRNA ligase activity|proline-tRNA ligase activity|protein binding|RNA binding			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(131;0.0735)	L-Glutamic Acid(DB00142)|L-Proline(DB00172)	TTGCTTCTCTCCTGGTATCTT	0.388													11	63	---	---	---	---	PASS
DUSP10	11221	broad.mit.edu	37	1	221912899	221912899	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221912899G>A	uc001hmy.1	-	2	370	c.188C>T	c.(187-189)TCA>TTA	p.S63L	DUSP10_uc001hmx.1_5'Flank|DUSP10_uc001hmz.1_Intron	NM_007207	NP_009138	Q9Y6W6	DUS10_HUMAN	dual specificity phosphatase 10 isoform a	63					inactivation of MAPK activity|JNK cascade|negative regulation of JNK cascade|negative regulation of JUN kinase activity|negative regulation of stress-activated MAPK cascade	Golgi apparatus|nucleus	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)|lung(1)	2				GBM - Glioblastoma multiforme(131;0.0103)		GCCGCTGGATGAGGGCATATA	0.587													10	51	---	---	---	---	PASS
DUSP10	11221	broad.mit.edu	37	1	221912900	221912900	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221912900A>T	uc001hmy.1	-	2	369	c.187T>A	c.(187-189)TCA>ACA	p.S63T	DUSP10_uc001hmx.1_5'Flank|DUSP10_uc001hmz.1_Intron	NM_007207	NP_009138	Q9Y6W6	DUS10_HUMAN	dual specificity phosphatase 10 isoform a	63					inactivation of MAPK activity|JNK cascade|negative regulation of JNK cascade|negative regulation of JUN kinase activity|negative regulation of stress-activated MAPK cascade	Golgi apparatus|nucleus	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)|lung(1)	2				GBM - Glioblastoma multiforme(131;0.0103)		CCGCTGGATGAGGGCATATAC	0.582													10	51	---	---	---	---	PASS
GUK1	2987	broad.mit.edu	37	1	228335252	228335252	+	Intron	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228335252G>C	uc001hsh.2	+						GUK1_uc001hsi.2_Intron|GUK1_uc001hsj.2_Intron|GUK1_uc010pvv.1_Intron|GJC2_uc001hsk.2_5'Flank	NM_000858	NP_000849	Q16774	KGUA_HUMAN	guanylate kinase 1 isoform b						nucleobase, nucleoside and nucleotide interconversion|purine nucleotide metabolic process	cytosol	ATP binding|guanylate kinase activity				0		Prostate(94;0.0405)				GCTGGTGTGTGCTGGGCAGGG	0.647													22	59	---	---	---	---	PASS
ACTA1	58	broad.mit.edu	37	1	229568800	229568800	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229568800G>C	uc001htm.2	-	2	168	c.63C>G	c.(61-63)GCC>GCG	p.A21A		NM_001100	NP_001091	P68133	ACTS_HUMAN	actin, alpha 1, skeletal muscle	21					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)	CGGCGAAGCCGGCTTTCACCA	0.672													6	31	---	---	---	---	PASS
DISC1	27185	broad.mit.edu	37	1	231885718	231885718	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231885718C>A	uc001huz.2	+	4	1217	c.1164C>A	c.(1162-1164)ATC>ATA	p.I388I	TSNAX-DISC1_uc010pwf.1_3'UTR|TSNAX-DISC1_uc010pwg.1_Silent_p.I377I|TSNAX-DISC1_uc010pwh.1_Silent_p.I343I|TSNAX-DISC1_uc010pwi.1_Silent_p.I343I|TSNAX-DISC1_uc010pwj.1_Silent_p.I377I|TSNAX-DISC1_uc010pwk.1_Silent_p.I377I|TSNAX-DISC1_uc010pwl.1_RNA|DISC1_uc010pwo.1_3'UTR|DISC1_uc010pwp.1_Silent_p.I388I|DISC1_uc010pwq.1_Silent_p.I388I|DISC1_uc010pwr.1_Silent_p.I388I|DISC1_uc010pws.1_Silent_p.I388I|DISC1_uc010pwt.1_Silent_p.I388I|DISC1_uc010pwu.1_Silent_p.I38I|DISC1_uc010pwv.1_RNA|DISC1_uc010pww.1_Silent_p.I388I|DISC1_uc010pwx.1_Intron|DISC1_uc010pwy.1_RNA|DISC1_uc010pwz.1_RNA|DISC1_uc010pxa.1_RNA|DISC1_uc001huy.2_Silent_p.I388I|DISC1_uc010pxb.1_Silent_p.I388I|DISC1_uc010pxc.1_Silent_p.I388I|DISC1_uc010pxd.1_Silent_p.I33I|DISC1_uc010pxe.1_Silent_p.I388I|DISC1_uc009xfr.2_Silent_p.I343I|DISC1_uc010pxf.1_Silent_p.I388I|DISC1_uc010pxg.1_Silent_p.I388I|DISC1_uc010pxh.1_Silent_p.I420I|DISC1_uc010pxi.1_Intron|DISC1_uc010pxj.1_Silent_p.I33I|DISC1_uc010pxk.1_RNA|DISC1_uc010pxl.1_RNA|DISC1_uc010pxm.1_Silent_p.I388I|DISC1_uc010pxn.1_Silent_p.I33I|DISC1_uc001hva.2_Silent_p.I388I	NM_018662	NP_061132	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1 isoform L	388	Interaction with TRAF3IP1.|Potential.				microtubule cytoskeleton organization|neuron migration|positive regulation of neuroblast proliferation|positive regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	centrosome|microtubule	protein binding			skin(1)	1		all_cancers(173;0.0208)|Prostate(94;0.0975)				AAGAGAAAATCAGCCTGCACT	0.483													32	53	---	---	---	---	PASS
SLC35F3	148641	broad.mit.edu	37	1	234041325	234041325	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234041325G>T	uc001hvy.1	+	2	249	c.104G>T	c.(103-105)AGC>ATC	p.S35I		NM_173508	NP_775779	Q8IY50	S35F3_HUMAN	solute carrier family 35, member F3	Error:Variant_position_missing_in_Q8IY50_after_alignment					transport	integral to membrane				ovary(2)	2	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)			TCCGACATCAGCCCCCAGCTC	0.667													23	30	---	---	---	---	PASS
TARBP1	6894	broad.mit.edu	37	1	234565935	234565935	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234565935C>A	uc001hwd.2	-	15	2507	c.2507G>T	c.(2506-2508)GGG>GTG	p.G836V		NM_005646	NP_005637	Q13395	TARB1_HUMAN	TAR RNA binding protein 1	836					regulation of transcription from RNA polymerase II promoter|RNA processing	nucleus	RNA binding|RNA methyltransferase activity			ovary(2)|skin(1)	3	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			TTCCAGGGGCCCAGCATGGAG	0.572													22	102	---	---	---	---	PASS
GNG4	2786	broad.mit.edu	37	1	235747031	235747031	+	Intron	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235747031C>G	uc001hxe.3	-						GNG4_uc009xfz.2_Intron|GNG4_uc001hxh.3_Intron	NM_001098722	NP_001092192	P50150	GBG4_HUMAN	guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|negative regulation of cell growth|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	signal transducer activity				0	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00168)|Prostate(94;0.0776)|Acute lymphoblastic leukemia(190;0.23)	OV - Ovarian serous cystadenocarcinoma(106;0.000882)			CTGACGCATGCATGCTTACCT	0.532													8	42	---	---	---	---	PASS
LGALS8	3964	broad.mit.edu	37	1	236702172	236702172	+	Intron	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236702172C>G	uc001hxz.1	+						LGALS8_uc001hxw.1_Intron|LGALS8_uc001hxy.1_Intron|LGALS8_uc009xgg.1_Intron|LGALS8_uc001hya.1_Intron|LGALS8_uc001hyb.1_Intron|LGALS8_uc001hyc.1_Intron	NM_201543	NP_963837	O00214	LEG8_HUMAN	galectin-8 isoform b							cytoplasm|extracellular space	sugar binding			ovary(1)	1	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			TGTCTTCCCTCATATAGATTC	0.532													9	27	---	---	---	---	PASS
LGALS8	3964	broad.mit.edu	37	1	236702237	236702237	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236702237C>A	uc001hxz.1	+	5	574	c.193C>A	c.(193-195)CAT>AAT	p.H65N	LGALS8_uc001hxw.1_Missense_Mutation_p.H65N|LGALS8_uc001hxy.1_Missense_Mutation_p.H65N|LGALS8_uc009xgg.1_RNA|LGALS8_uc001hya.1_Missense_Mutation_p.H65N|LGALS8_uc001hyb.1_Missense_Mutation_p.H65N|LGALS8_uc001hyc.1_Missense_Mutation_p.H65N	NM_201543	NP_963837	O00214	LEG8_HUMAN	galectin-8 isoform b	65	Galectin 1.					cytoplasm|extracellular space	sugar binding			ovary(1)	1	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			TGTGGCCTTTCATTTCAATCC	0.478													12	31	---	---	---	---	PASS
LGALS8	3964	broad.mit.edu	37	1	236711372	236711372	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236711372G>C	uc001hxz.1	+	11	1246	c.865G>C	c.(865-867)GAG>CAG	p.E289Q	LGALS8_uc001hxw.1_Missense_Mutation_p.E331Q|LGALS8_uc001hxy.1_Missense_Mutation_p.E331Q|LGALS8_uc009xgg.1_RNA|LGALS8_uc001hya.1_Missense_Mutation_p.E289Q|LGALS8_uc001hyb.1_Missense_Mutation_p.E289Q|LGALS8_uc001hyc.1_Missense_Mutation_p.E272Q	NM_201543	NP_963837	O00214	LEG8_HUMAN	galectin-8 isoform b	289	Galectin 2.					cytoplasm|extracellular space	sugar binding			ovary(1)	1	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			ACACAGCCTGGAGTACAAACA	0.418													23	50	---	---	---	---	PASS
HEATR1	55127	broad.mit.edu	37	1	236751300	236751300	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236751300C>A	uc001hyd.1	-	13	1699	c.1574G>T	c.(1573-1575)CGA>CTA	p.R525L		NM_018072	NP_060542	Q9H583	HEAT1_HUMAN	protein BAP28	525					rRNA processing	nucleolus|ribonucleoprotein complex	protein binding			ovary(2)|skin(1)	3	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			ATCACCTAATCGGGCTAAAAC	0.328													8	38	---	---	---	---	PASS
HEATR1	55127	broad.mit.edu	37	1	236751301	236751301	+	Nonsense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236751301G>A	uc001hyd.1	-	13	1698	c.1573C>T	c.(1573-1575)CGA>TGA	p.R525*		NM_018072	NP_060542	Q9H583	HEAT1_HUMAN	protein BAP28	525					rRNA processing	nucleolus|ribonucleoprotein complex	protein binding			ovary(2)|skin(1)	3	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			TCACCTAATCGGGCTAAAACA	0.333													9	38	---	---	---	---	PASS
ACTN2	88	broad.mit.edu	37	1	236911049	236911049	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236911049A>G	uc001hyf.2	+	13	1693	c.1489A>G	c.(1489-1491)ACT>GCT	p.T497A	ACTN2_uc001hyg.2_Missense_Mutation_p.T289A|ACTN2_uc009xgi.1_Missense_Mutation_p.T497A|ACTN2_uc010pxu.1_Missense_Mutation_p.T186A|ACTN2_uc001hyh.2_Missense_Mutation_p.T185A	NM_001103	NP_001094	P35609	ACTN2_HUMAN	actinin, alpha 2	497	Spectrin 2.				focal adhesion assembly|microspike assembly|muscle filament sliding|platelet activation|platelet degranulation|protein homotetramerization|regulation of apoptosis|synaptic transmission	actin filament|cytosol|dendritic spine|extracellular region|filopodium|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|Z disc	actin binding|calcium ion binding|FATZ 1 binding|identical protein binding|integrin binding|protein dimerization activity|structural constituent of muscle|titin binding|titin Z domain binding|ZASP binding			ovary(4)|skin(1)	5	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)			GGGAACGCTTACTCAGAAGAG	0.398													13	35	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237617764	237617764	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237617764C>A	uc001hyl.1	+	15	1486	c.1366C>A	c.(1366-1368)CTG>ATG	p.L456M		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	456	Cytoplasmic (By similarity).				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)			AAGCCTAAGTCTGCAGGATCT	0.453													10	125	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237619941	237619941	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237619941C>G	uc001hyl.1	+	16	1638	c.1518C>G	c.(1516-1518)CAC>CAG	p.H506Q		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	506	Cytoplasmic (By similarity).				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)			ACCGTTTGCACGTCTACAGCA	0.433													62	112	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237632437	237632437	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237632437G>T	uc001hyl.1	+	17	1778	c.1658G>T	c.(1657-1659)GGC>GTC	p.G553V		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	553	Cytoplasmic (By similarity).				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)			CAATTTTCTGGCTCCCTCGAC	0.373													10	77	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237730076	237730076	+	Splice_Site	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237730076G>T	uc001hyl.1	+	28	3543	c.3423_splice	c.e28+1	p.K1141_splice		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						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)			TGGCTTCAAGGTGAGTGGACT	0.537													50	191	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237778138	237778138	+	Silent	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237778138T>C	uc001hyl.1	+	37	5830	c.5710T>C	c.(5710-5712)TTG>CTG	p.L1904L		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	1904	Cytoplasmic (By similarity).|4 X approximate repeats.				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)			GCCAGTTAAATTGCAGGTAAT	0.458													9	45	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237948232	237948232	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237948232G>C	uc001hyl.1	+	90	13340	c.13220G>C	c.(13219-13221)AGC>ACC	p.S4407T	RYR2_uc010pya.1_Missense_Mutation_p.S822T	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	4407					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)			GACCTCATGAGCAACCCAGTC	0.458													7	34	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237955581	237955581	+	Silent	SNP	G	C	C	rs115854664	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237955581G>C	uc001hyl.1	+	94	13860	c.13740G>C	c.(13738-13740)ACG>ACC	p.T4580T	RYR2_uc010pyb.1_Silent_p.T13T	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	4580	Helical; Name=M6; (Potential).				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)			TTCTGCACACGGTCATTTCTT	0.393													9	95	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237982461	237982461	+	Missense_Mutation	SNP	T	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237982461T>G	uc001hyl.1	+	101	14679	c.14559T>G	c.(14557-14559)TTT>TTG	p.F4853L	RYR2_uc010pyb.1_Missense_Mutation_p.F286L	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	4853	Helical; Name=M10; (Potential).				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)			TCTTCTTCTTTGTTATTGTCA	0.408													27	140	---	---	---	---	PASS
ZP4	57829	broad.mit.edu	37	1	238050774	238050774	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238050774C>A	uc001hym.2	-	5	641	c.641G>T	c.(640-642)CGC>CTC	p.R214L	LOC100130331_uc010pyc.1_Intron	NM_021186	NP_067009	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4 preproprotein	214	ZP.|Extracellular (Potential).				acrosomal vesicle exocytosis|negative regulation of binding of sperm to zona pellucida|positive regulation of acrosome reaction|positive regulation of humoral immune response|positive regulation of protein kinase activity|positive regulation of T cell proliferation|protein kinase A signaling cascade|protein kinase C signaling cascade	integral to membrane|intracellular|plasma membrane|proteinaceous extracellular matrix	acrosin binding|receptor activity			ovary(2)|skin(1)	3	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			AAGGGCCAAGCGCACAGAATC	0.507													38	154	---	---	---	---	PASS
CEP170	9859	broad.mit.edu	37	1	243349566	243349566	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243349566C>A	uc001hzs.2	-	9	1675	c.1267G>T	c.(1267-1269)GCT>TCT	p.A423S	CEP170_uc001hzt.2_Missense_Mutation_p.A423S|CEP170_uc001hzu.2_Missense_Mutation_p.A423S	NM_014812	NP_055627	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa isoform alpha	423						centriole|microtubule|spindle				ovary(1)|haematopoietic_and_lymphoid_tissue(1)	2	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			CTTACAACAGCTTGGTCTTGA	0.413													31	172	---	---	---	---	PASS
SDCCAG8	10806	broad.mit.edu	37	1	243480191	243480191	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243480191C>A	uc001hzw.2	+	9	1220	c.1064C>A	c.(1063-1065)ACC>AAC	p.T355N	SDCCAG8_uc010pyk.1_Missense_Mutation_p.T210N|SDCCAG8_uc010pyl.1_Missense_Mutation_p.T167N|SDCCAG8_uc001hzx.2_Missense_Mutation_p.T167N	NM_006642	NP_006633	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	355	Potential.|Sufficient for homodimerization (By similarity).				establishment of cell polarity|G2/M transition of mitotic cell cycle|tube formation	cell-cell junction|centriole|cytosol	protein binding				0	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		TTTGAAAAAACCAAGGCAAGT	0.328													34	32	---	---	---	---	PASS
VN1R5	317705	broad.mit.edu	37	1	247419484	247419484	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247419484C>G	uc010pyu.1	+	1	111	c.111C>G	c.(109-111)ATC>ATG	p.I37M		NM_173858	NP_776257	Q7Z5H4	VN1R5_HUMAN	vomeronasal 1 receptor 5	37	Cytoplasmic (Potential).				response to pheromone	integral to membrane|plasma membrane	pheromone receptor activity				0	all_cancers(71;5.7e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)	all_cancers(173;0.0314)	OV - Ovarian serous cystadenocarcinoma(106;0.00854)			CTAAGATGATCAAACTTCCTG	0.343													23	104	---	---	---	---	PASS
NLRP3	114548	broad.mit.edu	37	1	247582273	247582273	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247582273C>A	uc001icr.2	+	3	315	c.177C>A	c.(175-177)ATC>ATA	p.I59I	NLRP3_uc001ics.2_Silent_p.I59I|NLRP3_uc001icu.2_Silent_p.I59I|NLRP3_uc001icw.2_Silent_p.I59I|NLRP3_uc001icv.2_Silent_p.I59I|NLRP3_uc010pyw.1_Silent_p.I57I|NLRP3_uc001ict.1_Silent_p.I57I	NM_001079821	NP_001073289	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3 isoform a	59	DAPIN.				detection of biotic stimulus|induction of apoptosis|inflammatory response|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|positive regulation of interleukin-1 beta secretion|protein oligomerization|signal transduction	cytoplasm	ATP binding|peptidoglycan binding|protein binding	p.I59M(1)		lung(8)|skin(8)|ovary(7)|upper_aerodigestive_tract(1)|breast(1)|pancreas(1)	26	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			CGCTAATGATCGACTTCAATG	0.547													11	35	---	---	---	---	PASS
OR6F1	343169	broad.mit.edu	37	1	247875361	247875361	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247875361C>A	uc001idj.1	-	1	697	c.697G>T	c.(697-699)GGC>TGC	p.G233C		NM_001005286	NP_001005286	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F,	233	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0168)			TTGCTCCGGCCACTGGCAGAG	0.517													32	120	---	---	---	---	PASS
OR1C1	26188	broad.mit.edu	37	1	247920865	247920865	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247920865C>G	uc010pza.1	-	1	844	c.844G>C	c.(844-846)GCT>CCT	p.A282P		NM_012353	NP_036485	Q15619	OR1C1_HUMAN	olfactory receptor, family 1, subfamily C,	282	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	all_cancers(71;4.34e-05)|all_epithelial(71;1.13e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)	all_cancers(173;0.0247)	OV - Ovarian serous cystadenocarcinoma(106;0.0168)			AGCATCGGAGCCACCATTGAA	0.478													24	115	---	---	---	---	PASS
OR2L13	284521	broad.mit.edu	37	1	248263520	248263520	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248263520C>A	uc001ids.2	+	3	1180	c.843C>A	c.(841-843)ACC>ACA	p.T281T		NM_175911	NP_787107	Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L,	281	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4	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;0.0132)			CCATCCTTACCCCCATGCTCA	0.463													15	82	---	---	---	---	PASS
OR2T2	401992	broad.mit.edu	37	1	248616135	248616135	+	Missense_Mutation	SNP	T	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248616135T>G	uc001iek.1	+	1	37	c.37T>G	c.(37-39)TTC>GTC	p.F13V		NM_001004136	NP_001004136	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T,	13	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CTCCACTAACTTCGTCCTCAC	0.502													14	149	---	---	---	---	PASS
OR2T3	343173	broad.mit.edu	37	1	248637586	248637586	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248637586C>A	uc001iel.1	+	1	935	c.935C>A	c.(934-936)TCA>TAA	p.S312*		NM_001005495	NP_001005495	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T,	312	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ATGATGCAGTCAAGAATGAAC	0.478													35	297	---	---	---	---	PASS
OR2G6	391211	broad.mit.edu	37	1	248685105	248685105	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248685105C>A	uc001ien.1	+	1	158	c.158C>A	c.(157-159)TCC>TAC	p.S53Y		NM_001013355	NP_001013373	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G,	53	Cytoplasmic (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)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGTCTGGACTCCAGACTCCAC	0.483													5	75	---	---	---	---	PASS
OR2G6	391211	broad.mit.edu	37	1	248685106	248685106	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248685106C>A	uc001ien.1	+	1	159	c.159C>A	c.(157-159)TCC>TCA	p.S53S		NM_001013355	NP_001013373	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G,	53	Cytoplasmic (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)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GTCTGGACTCCAGACTCCACA	0.478													7	75	---	---	---	---	PASS
OR2G6	391211	broad.mit.edu	37	1	248685110	248685110	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248685110C>G	uc001ien.1	+	1	163	c.163C>G	c.(163-165)CTC>GTC	p.L55V		NM_001013355	NP_001013373	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G,	55	Cytoplasmic (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)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GGACTCCAGACTCCACACTCC	0.468													42	38	---	---	---	---	PASS
OR2T10	127069	broad.mit.edu	37	1	248756222	248756222	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248756222G>A	uc010pzn.1	-	1	848	c.848C>T	c.(847-849)CCT>CTT	p.P283L		NM_001004693	NP_001004693	Q8NGZ9	O2T10_HUMAN	olfactory receptor, family 2, subfamily T,	283	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ATTCAAGACAGGTGTAAGGAT	0.398													8	43	---	---	---	---	PASS
OR2T10	127069	broad.mit.edu	37	1	248756589	248756589	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248756589G>T	uc010pzn.1	-	1	481	c.481C>A	c.(481-483)CCC>ACC	p.P161T		NM_001004693	NP_001004693	Q8NGZ9	O2T10_HUMAN	olfactory receptor, family 2, subfamily T,	161	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ATGGCGATGGGAGTGAGCATG	0.537													14	150	---	---	---	---	PASS
OR2T11	127077	broad.mit.edu	37	1	248790288	248790288	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248790288C>T	uc001ier.1	-	1	142	c.142G>A	c.(142-144)GTG>ATG	p.V48M		NM_001001964	NP_001001964	Q8NH01	O2T11_HUMAN	olfactory receptor, family 2, subfamily T,	48	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			lung(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CGAGAGTCCACCTGAATCAAG	0.498													19	87	---	---	---	---	PASS
TMEM18	129787	broad.mit.edu	37	2	675608	675608	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:675608C>A	uc002qwl.2	-	2	174	c.80G>T	c.(79-81)TGG>TTG	p.W27L	TMEM18_uc002qwk.2_RNA|uc002qwm.1_5'Flank	NM_152834	NP_690047	Q96B42	TMM18_HUMAN	transmembrane protein 18	27	Helical; (Potential).				cell migration	integral to membrane|nuclear membrane				ovary(1)	1	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;5.27e-05)|all_epithelial(98;2.11e-06)|Ovarian(717;0.0253)		all cancers(51;1.95e-21)|Epithelial(75;9.47e-21)|OV - Ovarian serous cystadenocarcinoma(76;8.15e-18)|GBM - Glioblastoma multiforme(21;0.0285)		CCCCATGAGCCAGGGCTCAGT	0.612													4	25	---	---	---	---	PASS
MYT1L	23040	broad.mit.edu	37	2	1926494	1926494	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1926494C>T	uc002qxe.2	-	10	1874	c.1047G>A	c.(1045-1047)AGG>AGA	p.R349R	MYT1L_uc002qxd.2_Silent_p.R349R|MYT1L_uc010ewl.1_RNA	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	349					cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		GCTGCGGATTCCTCTCCTGCG	0.567													8	33	---	---	---	---	PASS
MYT1L	23040	broad.mit.edu	37	2	1927027	1927027	+	Nonsense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1927027G>A	uc002qxe.2	-	10	1341	c.514C>T	c.(514-516)CAA>TAA	p.Q172*	MYT1L_uc002qxd.2_Nonsense_Mutation_p.Q172*|MYT1L_uc010ewl.1_RNA	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	172					cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		CAATTCATTTGATGGTCTTCT	0.313													4	12	---	---	---	---	PASS
KCNS3	3790	broad.mit.edu	37	2	18113462	18113462	+	Nonsense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18113462T>A	uc002rcv.2	+	3	1638	c.1187T>A	c.(1186-1188)TTG>TAG	p.L396*	KCNS3_uc002rcw.2_Nonsense_Mutation_p.L396*	NM_002252	NP_002243	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel	396	Helical; Name=Segment S6; (Potential).				energy reserve metabolic process|regulation of insulin secretion	Golgi apparatus|voltage-gated potassium channel complex	delayed rectifier potassium channel activity|potassium channel regulator activity			ovary(4)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TGTGGCATCTTGGTGGTGGCC	0.532													7	48	---	---	---	---	PASS
NT5C1B	93034	broad.mit.edu	37	2	18765908	18765908	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18765908G>A	uc002rcz.2	-	5	879	c.775C>T	c.(775-777)CTG>TTG	p.L259L	NT5C1B_uc002rcy.2_Silent_p.L259L|NT5C1B_uc010exr.2_Silent_p.L201L|NT5C1B_uc010yju.1_Silent_p.L199L|NT5C1B_uc002rda.2_Silent_p.L199L|NT5C1B_uc010yjv.1_Silent_p.L276L|NT5C1B_uc010yjw.1_Silent_p.L242L|NT5C1B_uc010exs.2_Silent_p.L261L|NT5C1B_uc002rdb.1_Silent_p.L51L	NM_001002006	NP_001002006	Q96P26	5NT1B_HUMAN	5' nucleotidase, cytosolic IB isoform 1	259					purine base metabolic process|purine nucleotide catabolic process	cytosol	5'-nucleotidase activity|magnesium ion binding|nucleotide binding			skin(2)|ovary(1)	3	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)	Ovarian(717;0.208)				TTGCGGTCCAGCTGGGTGGAG	0.652													4	7	---	---	---	---	PASS
APOB	338	broad.mit.edu	37	2	21234330	21234330	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21234330T>C	uc002red.2	-	26	5538	c.5410A>G	c.(5410-5412)AAT>GAT	p.N1804D		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	1804					cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|skin(9)|central_nervous_system(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)	TCCAGAGCATTGTATTTCAGG	0.393													19	104	---	---	---	---	PASS
ADCY3	109	broad.mit.edu	37	2	25061456	25061456	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25061456A>T	uc002rfs.3	-	7	1590	c.1391T>A	c.(1390-1392)CTG>CAG	p.L464Q	ADCY3_uc002rfr.3_Missense_Mutation_p.L97Q|ADCY3_uc010ykm.1_Missense_Mutation_p.L464Q	NM_004036	NP_004027	O60266	ADCY3_HUMAN	adenylate cyclase 3	464	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)					CTCCCCTTTCAGGCAGTCCAT	0.597													21	114	---	---	---	---	PASS
HADHA	3030	broad.mit.edu	37	2	26424190	26424190	+	Splice_Site	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26424190C>G	uc002rgy.2	-	13	1351	c.1221_splice	c.e13-1	p.G407_splice	HADHA_uc010yks.1_Splice_Site_p.G320_splice	NM_000182	NP_000173	P40939	ECHA_HUMAN	mitochondrial trifunctional protein, alpha						fatty acid beta-oxidation	fatty acid beta-oxidation multienzyme complex|mitochondrial nucleoid|nucleolus	3-hydroxyacyl-CoA dehydrogenase activity|acetyl-CoA C-acetyltransferase activity|coenzyme binding|enoyl-CoA hydratase activity|long-chain-3-hydroxyacyl-CoA dehydrogenase activity|protein binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				NADH(DB00157)	GTCATTCAATCTAGAAAAAAC	0.259													8	33	---	---	---	---	PASS
DPYSL5	56896	broad.mit.edu	37	2	27167686	27167686	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27167686C>A	uc002rhu.3	+	12	1761	c.1603C>A	c.(1603-1605)CTC>ATC	p.L535I	DPYSL5_uc002rhv.3_Missense_Mutation_p.L535I	NM_020134	NP_064519	Q9BPU6	DPYL5_HUMAN	dihydropyrimidinase-like 5	535					axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			ovary(2)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAGCTTCAGCCTCTCTGGTAA	0.607													11	28	---	---	---	---	PASS
GTF3C2	2976	broad.mit.edu	37	2	27552333	27552333	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27552333G>C	uc002rjv.1	-	14	2153	c.1790C>G	c.(1789-1791)TCT>TGT	p.S597C	GTF3C2_uc010eyy.1_Missense_Mutation_p.S52C|GTF3C2_uc002rju.1_Missense_Mutation_p.S608C|GTF3C2_uc002rjw.1_Missense_Mutation_p.S597C	NM_001521	NP_001512	Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide	597						transcription factor TFIIIC complex				ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGAGCCATCAGAGAGCCGTAT	0.493													29	139	---	---	---	---	PASS
IFT172	26160	broad.mit.edu	37	2	27684180	27684180	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27684180C>G	uc002rku.2	-	22	2449	c.2398G>C	c.(2398-2400)GAA>CAA	p.E800Q		NM_015662	NP_056477	Q9UG01	IF172_HUMAN	selective LIM binding factor homolog	800					cilium assembly	cilium	binding			large_intestine(1)|ovary(1)	2	Acute lymphoblastic leukemia(172;0.155)					GTGATGTGTTCTACCAGCTCT	0.557													25	65	---	---	---	---	PASS
CAPN13	92291	broad.mit.edu	37	2	30998812	30998812	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30998812C>G	uc002rnn.2	-	4	547	c.371G>C	c.(370-372)GGC>GCC	p.G124A	CAPN13_uc002rnp.1_Missense_Mutation_p.G124A	NM_144575	NP_653176	Q6MZZ7	CAN13_HUMAN	calpain 13	124	Calpain catalytic.				proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			large_intestine(1)|ovary(1)	2	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					ACGGAAAATGCCAGCATACTG	0.512													11	60	---	---	---	---	PASS
LTBP1	4052	broad.mit.edu	37	2	33500942	33500942	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33500942G>T	uc002ros.2	+	18	2947	c.2947G>T	c.(2947-2949)GAA>TAA	p.E983*	LTBP1_uc002rot.2_Nonsense_Mutation_p.E657*|LTBP1_uc002rou.2_Nonsense_Mutation_p.E656*|LTBP1_uc002rov.2_Nonsense_Mutation_p.E603*|LTBP1_uc010ymz.1_Nonsense_Mutation_p.E656*|LTBP1_uc010yna.1_Nonsense_Mutation_p.E603*	NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding	982	EGF-like 6; calcium-binding (Potential).				negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				CTTCCGGTGTGAATACTGTGA	0.557													9	63	---	---	---	---	PASS
VIT	5212	broad.mit.edu	37	2	37002155	37002155	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37002155G>A	uc002rpl.2	+	9	968	c.747G>A	c.(745-747)AGG>AGA	p.R249R	VIT_uc002rpm.2_Silent_p.R242R|VIT_uc010ezv.2_Intron|VIT_uc010ezw.2_Silent_p.R242R	NM_053276	NP_444506	Q6UXI7	VITRN_HUMAN	vitrin	249						proteinaceous extracellular matrix				ovary(1)|pancreas(1)	2		all_hematologic(82;0.248)				GTATCCAAAGGCAAGATCCTT	0.507													5	44	---	---	---	---	PASS
EIF2AK2	5610	broad.mit.edu	37	2	37374958	37374958	+	5'UTR	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37374958C>G	uc010ynh.1	-	3					EIF2AK2_uc010fab.1_5'UTR|EIF2AK2_uc010yng.1_5'UTR|EIF2AK2_uc010fac.2_5'UTR|EIF2AK2_uc010fad.2_5'UTR	NM_002759	NP_002750	P19525	E2AK2_HUMAN	eukaryotic translation initiation factor 2-alpha						evasion by virus of host immune response|modulation by virus of host cellular process|negative regulation of osteoblast proliferation|protein autophosphorylation|response to virus|viral infectious cycle	cytosol	ATP binding|double-stranded RNA binding|eukaryotic translation initiation factor 2alpha kinase activity|protein binding|protein phosphatase type 2A regulator activity			ovary(2)|lung(2)|pancreas(1)	5		all_hematologic(82;0.248)				ATTTCTTCTTCCCGTATCCTA	0.423													8	40	---	---	---	---	PASS
DHX57	90957	broad.mit.edu	37	2	39089399	39089399	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39089399C>A	uc002rrf.2	-	4	559	c.460G>T	c.(460-462)GAA>TAA	p.E154*	DHX57_uc002rre.2_5'UTR|DHX57_uc002rrg.2_Nonsense_Mutation_p.E154*	NM_198963	NP_945314	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	154							ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		all_hematologic(82;0.248)				AGGGAAGGTTCCTGTCCAGCT	0.498													6	39	---	---	---	---	PASS
SRBD1	55133	broad.mit.edu	37	2	45832512	45832512	+	Silent	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45832512T>A	uc002rus.2	-	2	145	c.69A>T	c.(67-69)TCA>TCT	p.S23S		NM_018079	NP_060549	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1	23					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		hydrolase activity, acting on ester bonds|RNA binding			central_nervous_system(1)	1		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)			ACTCAGAGAATGAAGAAAATT	0.358													11	66	---	---	---	---	PASS
EPAS1	2034	broad.mit.edu	37	2	46525084	46525084	+	Intron	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46525084G>C	uc002ruv.2	+							NM_001430	NP_001421	Q99814	EPAS1_HUMAN	endothelial PAS domain protein 1						angiogenesis|myoblast cell fate commitment|positive regulation of transcription from RNA polymerase II promoter|response to hypoxia	transcription factor complex	histone acetyltransferase binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|signal transducer activity|transcription coactivator activity|transcription factor binding			ovary(1)|skin(1)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	LUSC - Lung squamous cell carcinoma(58;0.151)			AAGGTAAGCGGGCGTCCGGGC	0.677													4	7	---	---	---	---	PASS
KLRAQ1	129285	broad.mit.edu	37	2	48713811	48713811	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48713811G>C	uc002rwm.2	+	14	1545	c.1360G>C	c.(1360-1362)GAA>CAA	p.E454Q	KLRAQ1_uc002rwj.2_Missense_Mutation_p.E454Q|KLRAQ1_uc002rwl.2_Missense_Mutation_p.E408Q|KLRAQ1_uc002rwk.2_Missense_Mutation_p.E454Q|KLRAQ1_uc010yok.1_Missense_Mutation_p.E454Q	NM_001135629	NP_001129101	Q6ZMI0	KLRAQ_HUMAN	KLRAQ motif containing 1 isoform 1	454										ovary(1)	1						AATAGAGCATGAACTTCCAAC	0.323													3	46	---	---	---	---	PASS
FSHR	2492	broad.mit.edu	37	2	49190184	49190184	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49190184G>T	uc002rww.2	-	10	1850	c.1776C>A	c.(1774-1776)GCC>GCA	p.A592A	FSHR_uc002rwx.2_Silent_p.A530A|FSHR_uc010fbn.2_Silent_p.A566A	NM_000145	NP_000136	P23945	FSHR_HUMAN	follicle stimulating hormone receptor isoform 1	592	Helical; Name=6; (Potential).				female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)|lung(2)|central_nervous_system(1)|skin(1)	8		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)	AGGCAGAAATGGCAAAGAAAG	0.527									Gonadal_Dysgenesis_46_XX				8	31	---	---	---	---	PASS
NRXN1	9378	broad.mit.edu	37	2	50699459	50699459	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50699459C>A	uc010fbq.2	-	16	4818	c.3341G>T	c.(3340-3342)GGA>GTA	p.G1114V	NRXN1_uc002rxb.3_Missense_Mutation_p.G746V|NRXN1_uc002rxe.3_Missense_Mutation_p.G1074V|NRXN1_uc002rxc.1_RNA	NM_001135659	NP_001129131	P58400	NRX1B_HUMAN	neurexin 1 isoform alpha2 precursor	Error:Variant_position_missing_in_P58400_after_alignment					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)			CTCGATCTGTCCGTTGCAGAA	0.438													9	34	---	---	---	---	PASS
GPR75	10936	broad.mit.edu	37	2	54080608	54080608	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54080608G>A	uc002rxo.3	-	2	1557	c.1286C>T	c.(1285-1287)TCT>TTT	p.S429F	ASB3_uc002rxi.3_Intron	NM_006794	NP_006785	O95800	GPR75_HUMAN	G protein-coupled receptor 75	429	Cytoplasmic (Potential).					integral to plasma membrane	G-protein coupled receptor activity			ovary(1)|skin(1)	2			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			CATGTAGGCAGAGTTTGTTTC	0.448													41	60	---	---	---	---	PASS
PAPOLG	64895	broad.mit.edu	37	2	61002258	61002258	+	Nonsense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61002258C>T	uc002sai.2	+	8	925	c.694C>T	c.(694-696)CGA>TGA	p.R232*	PAPOLG_uc002saj.2_Translation_Start_Site|PAPOLG_uc002sak.2_Translation_Start_Site	NM_022894	NP_075045	Q9BWT3	PAPOG_HUMAN	poly(A) polymerase gamma	232					mRNA processing|RNA polyadenylation|transcription, DNA-dependent	nucleus	ATP binding|metal ion binding|polynucleotide adenylyltransferase activity|RNA binding			ovary(1)|central_nervous_system(1)	2	all_hematologic(2;0.0797)		LUSC - Lung squamous cell carcinoma(5;1.19e-07)|Lung(5;2.86e-06)|Epithelial(17;0.0768)			ATGGGCAAAACGTAAGTATCC	0.318													6	21	---	---	---	---	PASS
EHBP1	23301	broad.mit.edu	37	2	63091862	63091862	+	Intron	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63091862A>T	uc002sby.2	+						EHBP1_uc010fcp.2_Intron|EHBP1_uc002sbx.2_Intron|EHBP1_uc002sbz.2_Intron|EHBP1_uc002scb.2_Intron	NM_015252	NP_056067	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1 isoform 1							cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			CTATTATTTTATAGAACCTAT	0.284									Hereditary_Prostate_Cancer				5	57	---	---	---	---	PASS
EHBP1	23301	broad.mit.edu	37	2	63176204	63176204	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63176204G>A	uc002sby.2	+	14	2810	c.2328G>A	c.(2326-2328)AAG>AAA	p.K776K	EHBP1_uc010fcp.2_Silent_p.K741K|EHBP1_uc002sbz.2_Silent_p.K741K|EHBP1_uc002scb.2_Silent_p.K741K	NM_015252	NP_056067	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1 isoform 1	776						cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			ACCTTGCTAAGAAAAAACATG	0.378									Hereditary_Prostate_Cancer				13	39	---	---	---	---	PASS
ARHGAP25	9938	broad.mit.edu	37	2	69046400	69046400	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69046400G>T	uc002seu.2	+	9	1510	c.1146G>T	c.(1144-1146)TGG>TGT	p.W382C	ARHGAP25_uc010fdg.2_Missense_Mutation_p.W383C|ARHGAP25_uc010yql.1_Missense_Mutation_p.W343C|ARHGAP25_uc002sev.2_Missense_Mutation_p.W376C|ARHGAP25_uc002sew.2_Missense_Mutation_p.W375C|ARHGAP25_uc002sex.2_Missense_Mutation_p.W376C|ARHGAP25_uc002sey.2_Missense_Mutation_p.W109C	NM_001007231	NP_001007232	P42331	RHG25_HUMAN	Rho GTPase activating protein 25 isoform a	382					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(2)|breast(2)	4						CTGTAGGCTGGGATGCCACTG	0.522													16	98	---	---	---	---	PASS
ANTXR1	84168	broad.mit.edu	37	2	69409643	69409643	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69409643G>T	uc002sfg.2	+	16	1560	c.1204G>T	c.(1204-1206)GGC>TGC	p.G402C		NM_032208	NP_115584	Q9H6X2	ANTR1_HUMAN	anthrax toxin receptor 1 isoform 1 precursor	402	Cytoplasmic (Potential).				actin cytoskeleton reorganization|substrate adhesion-dependent cell spreading	filopodium membrane|integral to membrane|lamellipodium membrane	actin filament binding|collagen binding|metal ion binding|protein binding|transmembrane receptor activity			ovary(2)|skin(2)	4						GGGAGAAAAGGGCTCCACAGA	0.413									Familial_Infantile_Hemangioma				27	45	---	---	---	---	PASS
ASPRV1	151516	broad.mit.edu	37	2	70187820	70187820	+	Nonsense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70187820G>C	uc002sfz.3	-	1	1578	c.1001C>G	c.(1000-1002)TCA>TGA	p.S334*		NM_152792	NP_690005	Q53RT3	APRV1_HUMAN	aspartic peptidase, retroviral-like 1 precursor	334	Extracellular (Potential).				protein maturation by peptide bond cleavage|skin development		aspartic-type endopeptidase activity			ovary(1)	1						CCCTTCTTCTGAGGAGGGGTC	0.552													17	97	---	---	---	---	PASS
MCEE	84693	broad.mit.edu	37	2	71351516	71351516	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71351516C>A	uc002shs.2	-	2	243	c.198G>T	c.(196-198)AAG>AAT	p.K66N		NM_032601	NP_115990	Q96PE7	MCEE_HUMAN	methylmalonyl CoA epimerase precursor	66					fatty acid beta-oxidation|L-methylmalonyl-CoA metabolic process	mitochondrial matrix	methylmalonyl-CoA epimerase activity			ovary(1)	1						CCAGAATATTCTTATAAAATG	0.478													16	119	---	---	---	---	PASS
DYSF	8291	broad.mit.edu	37	2	71838380	71838380	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71838380G>T	uc002sie.2	+	37	4285	c.3909G>T	c.(3907-3909)GAG>GAT	p.E1303D	DYSF_uc010feg.2_Missense_Mutation_p.E1334D|DYSF_uc010feh.2_Missense_Mutation_p.E1289D|DYSF_uc002sig.3_Missense_Mutation_p.E1289D|DYSF_uc010yqx.1_RNA|DYSF_uc010fee.2_Missense_Mutation_p.E1303D|DYSF_uc010fef.2_Missense_Mutation_p.E1320D|DYSF_uc010fei.2_Missense_Mutation_p.E1320D|DYSF_uc010fek.2_Missense_Mutation_p.E1321D|DYSF_uc010fej.2_Missense_Mutation_p.E1290D|DYSF_uc010fel.2_Missense_Mutation_p.E1290D|DYSF_uc010feo.2_Missense_Mutation_p.E1335D|DYSF_uc010fem.2_Missense_Mutation_p.E1304D|DYSF_uc010fen.2_Missense_Mutation_p.E1321D|DYSF_uc002sif.2_Missense_Mutation_p.E1304D|DYSF_uc010yqy.1_Missense_Mutation_p.E184D|DYSF_uc010yqz.1_Missense_Mutation_p.E43D	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8	1303	Cytoplasmic (Potential).					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7						TGCAGTCTGAGGACACAGACC	0.403													7	26	---	---	---	---	PASS
CCT7	10574	broad.mit.edu	37	2	73476157	73476157	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73476157C>G	uc002siz.2	+	8	924	c.822C>G	c.(820-822)CTC>CTG	p.L274L	CCT7_uc002sja.2_Silent_p.L70L|CCT7_uc010yrf.1_Silent_p.L230L|CCT7_uc010feu.2_Silent_p.L232L|CCT7_uc010yrg.1_Silent_p.L174L|CCT7_uc010yrh.1_Silent_p.L146L|CCT7_uc010yri.1_Silent_p.L187L	NM_006429	NP_006420	Q99832	TCPH_HUMAN	chaperonin containing TCP1, subunit 7 isoform a	274					'de novo' posttranslational protein folding		ATP binding|unfolded protein binding				0						GGAACATTCTCTATGACAAGT	0.468													20	35	---	---	---	---	PASS
ALMS1	7840	broad.mit.edu	37	2	73777572	73777572	+	Intron	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73777572G>T	uc002sje.1	+						ALMS1_uc002sjf.1_Intron|ALMS1_uc002sjg.2_Intron|ALMS1_uc002sjh.1_Intron|ALMS1_uc010fev.1_Intron	NM_015120	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1						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						CAGGTAACTGGATTGGCTTTG	0.358													14	46	---	---	---	---	PASS
STAMBP	10617	broad.mit.edu	37	2	74074506	74074506	+	Intron	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74074506C>T	uc002sjs.2	+						STAMBP_uc002sjt.2_Intron|STAMBP_uc002sju.2_Intron|STAMBP_uc002sjv.2_Intron	NM_201647	NP_964010	O95630	STABP_HUMAN	STAM binding protein						JAK-STAT cascade|positive regulation of cell proliferation	early endosome|membrane|nucleus	metal ion binding|metallopeptidase activity|protein binding			ovary(1)|lung(1)|breast(1)|pancreas(1)	4						AATTTTCTCTCTTTGTAGAAG	0.453													5	41	---	---	---	---	PASS
ACTG2	72	broad.mit.edu	37	2	74141957	74141957	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74141957G>T	uc002sjw.2	+	7	886	c.764G>T	c.(763-765)CGC>CTC	p.R255L	ACTG2_uc010fey.2_Missense_Mutation_p.R255L|ACTG2_uc010yrn.1_Missense_Mutation_p.R212L	NM_001615	NP_001606	P63267	ACTH_HUMAN	actin, gamma 2 propeptide	255					muscle contraction	cytoskeleton|cytosol	ATP binding				0						GGCAATGAGCGCTTCCGCTGC	0.567													5	37	---	---	---	---	PASS
LRRTM4	80059	broad.mit.edu	37	2	77745792	77745792	+	Silent	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77745792T>A	uc002snr.2	-	3	1618	c.1203A>T	c.(1201-1203)ACA>ACT	p.T401T	LRRTM4_uc002snq.2_Silent_p.T401T|LRRTM4_uc002sns.2_Silent_p.T401T|LRRTM4_uc002snt.2_Silent_p.T402T	NM_001134745	NP_001128217	Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	401	Extracellular (Potential).					integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)		AAGGGCTTGGTGTTTCAAAGG	0.488													24	31	---	---	---	---	PASS
REG1A	5967	broad.mit.edu	37	2	79347993	79347993	+	Silent	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79347993T>A	uc002snz.2	+	2	109	c.6T>A	c.(4-6)GCT>GCA	p.A2A	REG1A_uc010ffx.1_Silent_p.A2A|REG1A_uc010ysd.1_Silent_p.A2A	NM_002909	NP_002900	P05451	REG1A_HUMAN	regenerating islet-derived 1 alpha precursor	2					positive regulation of cell proliferation	extracellular region	growth factor activity|sugar binding				0						TCAGCATGGCTCAGACCAGCT	0.463													8	25	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	90060797	90060797	+	Intron	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90060797T>A	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		GTCAGAGCATTGGTAGTAGCT	0.527													10	24	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	90121911	90121911	+	RNA	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90121911C>A	uc010fhm.2	+	16		c.1780C>A								Parts of antibodies, mostly variable regions.																		GAGTCACCATCACTTGTCGGG	0.478													54	158	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	90249214	90249214	+	RNA	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90249214G>A	uc010fhm.2	+	28		c.3757G>A								Parts of antibodies, mostly variable regions.																		TATTTAGCCTGGTATCAGCAA	0.507													24	189	---	---	---	---	PASS
ZAP70	7535	broad.mit.edu	37	2	98351741	98351741	+	Missense_Mutation	SNP	C	A	A	rs56202620		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98351741C>A	uc002syd.1	+	10	1318	c.1111C>A	c.(1111-1113)CTG>ATG	p.L371M	ZAP70_uc010yvf.1_3'UTR|ZAP70_uc002sye.1_Missense_Mutation_p.L261M|ZAP70_uc002syf.1_Missense_Mutation_p.L64M	NM_001079	NP_001070	P43403	ZAP70_HUMAN	zeta-chain associated protein kinase 70kDa	371	Protein kinase.				immune response|intracellular protein kinase cascade|positive thymic T cell selection|T cell receptor signaling pathway	cytosol|T cell receptor complex	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(4)|upper_aerodigestive_tract(1)|ovary(1)	6						CATCAAGGTGCTGAAGCAGGG	0.672													8	62	---	---	---	---	PASS
MRPL30	51263	broad.mit.edu	37	2	99812039	99812039	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99812039C>G	uc002szu.2	+	6	519	c.357C>G	c.(355-357)ATC>ATG	p.I119M	MRPL30_uc002szl.1_RNA|MRPL30_uc002szt.1_RNA|MRPL30_uc002szv.2_Missense_Mutation_p.I119M	NM_145213	NP_660214	Q8TCC3	RM30_HUMAN	RecName: Full=39S ribosomal protein L30, mitochondrial;          Short=L30mt; AltName: Full=MRP-L30; AltName: Full=MRP-L28; Flags: Precursor;	119					translation	mitochondrion|ribosome	structural constituent of ribosome			ovary(1)	1						GTCACAGAATCAAGCCCTTGA	0.299													81	133	---	---	---	---	PASS
SLC5A7	60482	broad.mit.edu	37	2	108618456	108618456	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108618456C>T	uc002tdv.2	+	6	977	c.701C>T	c.(700-702)TCA>TTA	p.S234L	SLC5A7_uc010ywm.1_5'UTR|SLC5A7_uc010fjj.2_Missense_Mutation_p.S234L|SLC5A7_uc010ywn.1_Missense_Mutation_p.S121L	NM_021815	NP_068587	Q9GZV3	SC5A7_HUMAN	solute carrier family 5 (choline transporter),	234	Cytoplasmic (Potential).				acetylcholine biosynthetic process|neurotransmitter secretion	integral to membrane|plasma membrane	choline:sodium symporter activity			ovary(2)|central_nervous_system(1)|skin(1)	4					Choline(DB00122)	ACTGTTGACTCATCTGAAGTC	0.428													17	40	---	---	---	---	PASS
SLC5A7	60482	broad.mit.edu	37	2	108626752	108626752	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108626752C>A	uc002tdv.2	+	9	1454	c.1178C>A	c.(1177-1179)ACA>AAA	p.T393K	SLC5A7_uc010ywm.1_Missense_Mutation_p.T146K|SLC5A7_uc010fjj.2_Missense_Mutation_p.T393K|SLC5A7_uc010ywn.1_Missense_Mutation_p.T280K	NM_021815	NP_068587	Q9GZV3	SC5A7_HUMAN	solute carrier family 5 (choline transporter),	393	Helical; (Potential).				acetylcholine biosynthetic process|neurotransmitter secretion	integral to membrane|plasma membrane	choline:sodium symporter activity			ovary(2)|central_nervous_system(1)|skin(1)	4					Choline(DB00122)	GCATCTGCAACAGCCATGGCC	0.458													16	33	---	---	---	---	PASS
SH3RF3	344558	broad.mit.edu	37	2	110049062	110049062	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110049062G>C	uc010ywt.1	+	6	1509	c.1509G>C	c.(1507-1509)AAG>AAC	p.K503N		NM_001099289	NP_001092759	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	503	SH3 3.						zinc ion binding			ovary(1)	1						GCTGGTTCAAGGGGGCGTCTC	0.617													10	20	---	---	---	---	PASS
CNTNAP5	129684	broad.mit.edu	37	2	124999952	124999952	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124999952A>T	uc002tno.2	+	3	727	c.363A>T	c.(361-363)AAA>AAT	p.K121N	CNTNAP5_uc010flu.2_Missense_Mutation_p.K121N	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	121	F5/8 type C.|Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		AACAGTACAAACAAGAAGACA	0.443													19	32	---	---	---	---	PASS
CNTNAP5	129684	broad.mit.edu	37	2	125281886	125281886	+	Missense_Mutation	SNP	A	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125281886A>C	uc002tno.2	+	9	1695	c.1331A>C	c.(1330-1332)AAC>ACC	p.N444T	CNTNAP5_uc010flu.2_Missense_Mutation_p.N445T	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	444	Laminin G-like 2.|Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		GCAGGCAGCAACTTGAATGAT	0.557													21	23	---	---	---	---	PASS
CNTNAP5	129684	broad.mit.edu	37	2	125530503	125530503	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125530503C>A	uc002tno.2	+	17	3022	c.2658C>A	c.(2656-2658)ACC>ACA	p.T886T	CNTNAP5_uc010flu.2_Silent_p.T887T	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	886	Laminin G-like 3.|Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		TCAAGGAGACCTCCCTGCAGG	0.547													34	35	---	---	---	---	PASS
CNTNAP5	129684	broad.mit.edu	37	2	125669111	125669111	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125669111C>T	uc002tno.2	+	23	4084	c.3720C>T	c.(3718-3720)ATC>ATT	p.I1240I	CNTNAP5_uc010flu.2_Silent_p.I1241I	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	1240	Helical; (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		CGGCAGTCATCGGAGGTAAAC	0.413													5	7	---	---	---	---	PASS
GPR148	344561	broad.mit.edu	37	2	131487661	131487661	+	Missense_Mutation	SNP	C	T	T	rs147627830		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131487661C>T	uc002trv.1	+	1	939	c.937C>T	c.(937-939)CGT>TGT	p.R313C		NM_207364	NP_997247	Q8TDV2	GP148_HUMAN	G protein-coupled receptor 148	313	Helical; Name=7; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1	Colorectal(110;0.1)					GATGCTTCCCCGTGCCATGCT	0.587													33	23	---	---	---	---	PASS
R3HDM1	23518	broad.mit.edu	37	2	136467716	136467716	+	Missense_Mutation	SNP	C	T	T	rs145608320		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136467716C>T	uc002tuo.2	+	22	2916	c.2546C>T	c.(2545-2547)CCG>CTG	p.P849L	R3HDM1_uc010fni.2_Missense_Mutation_p.P848L|R3HDM1_uc002tup.2_Missense_Mutation_p.P794L|R3HDM1_uc010zbh.1_Missense_Mutation_p.P597L	NM_015361	NP_056176	Q15032	R3HD1_HUMAN	R3H domain containing 1	849							nucleic acid binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.127)		CACTCACCCCCGCAGTGGAAA	0.468											OREG0014997	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	47	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	142004852	142004852	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142004852T>A	uc002tvj.1	-	5	1507	c.535A>T	c.(535-537)AGT>TGT	p.S179C	LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	179	Extracellular (Potential).|EGF-like 2; calcium-binding (Potential).				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TCCACACAACTGCAAGTGTAG	0.388										TSP Lung(27;0.18)			34	33	---	---	---	---	PASS
EPC2	26122	broad.mit.edu	37	2	149539297	149539297	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149539297A>T	uc010zbt.1	+	11	1832	c.1805A>T	c.(1804-1806)CAG>CTG	p.Q602L		NM_015630	NP_056445	Q52LR7	EPC2_HUMAN	enhancer of polycomb homolog 2	602	Gln-rich.				chromatin modification|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)|breast(1)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0516)		GCCCAGCTTCAGCAGAAACAG	0.433													8	124	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152374923	152374923	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152374923T>C	uc010fnx.2	-	128	17797	c.17606A>G	c.(17605-17607)AAG>AGG	p.K5869R	NEB_uc002txr.2_Missense_Mutation_p.K2292R|NEB_uc002txt.3_Missense_Mutation_p.K374R	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	5869	Nebulin 160.				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)		CTCATACTTCTTCTTGTACTG	0.438													8	125	---	---	---	---	PASS
TANC1	85461	broad.mit.edu	37	2	160031569	160031569	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160031569G>T	uc002uag.2	+	12	1883	c.1609G>T	c.(1609-1611)GCC>TCC	p.A537S	TANC1_uc010fol.1_Missense_Mutation_p.A431S|TANC1_uc010zcm.1_Missense_Mutation_p.A529S|TANC1_uc010fom.1_Missense_Mutation_p.A343S|TANC1_uc002uai.1_5'Flank	NM_033394	NP_203752	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and	537						cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3						TCAGCTGGCCGCCTACAGAGA	0.592													5	130	---	---	---	---	PASS
TANC1	85461	broad.mit.edu	37	2	160076237	160076237	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160076237G>A	uc002uag.2	+	22	3811	c.3537G>A	c.(3535-3537)CTG>CTA	p.L1179L	TANC1_uc010zcm.1_Silent_p.L1171L|TANC1_uc010fom.1_Silent_p.L985L|TANC1_uc010fon.2_Silent_p.L23L	NM_033394	NP_203752	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and	1179	ANK 9.					cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3						AAGAGGGTCTGTCAGCATTAA	0.468													26	17	---	---	---	---	PASS
SLC4A10	57282	broad.mit.edu	37	2	162760565	162760565	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162760565G>T	uc002ubx.3	+	13	1678	c.1494G>T	c.(1492-1494)TGG>TGT	p.W498C	SLC4A10_uc010zcr.1_RNA|SLC4A10_uc002uby.3_Missense_Mutation_p.W468C|SLC4A10_uc010zcs.1_Missense_Mutation_p.W479C	NM_022058	NP_071341	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate	498	Cytoplasmic (Potential).				bicarbonate transport|chloride transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity|symporter activity			ovary(2)|lung(2)|pancreas(1)	5						CATACTTCTGGAGTGACTTCA	0.418													8	7	---	---	---	---	PASS
DPP4	1803	broad.mit.edu	37	2	162873370	162873370	+	Missense_Mutation	SNP	C	G	G	rs17848907		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162873370C>G	uc002ubz.2	-	18	2036	c.1475G>C	c.(1474-1476)AGA>ACA	p.R492T	DPP4_uc010fpb.2_Missense_Mutation_p.R168T	NM_001935	NP_001926	P27487	DPP4_HUMAN	dipeptidylpeptidase IV	492	Extracellular (Potential).				cell adhesion|endothelial cell migration|negative regulation of extracellular matrix disassembly|positive regulation of cell proliferation|proteolysis|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation|T cell costimulation	apical plasma membrane|cell surface|endocytic vesicle|extracellular region|integral to membrane|invadopodium membrane|lamellipodium membrane|membrane raft	aminopeptidase activity|dipeptidyl-peptidase activity|protease binding|protein homodimerization activity|receptor activity|receptor binding|serine-type endopeptidase activity			ovary(3)	3					Sitagliptin(DB01261)	TTCCAGGACTCTCAGCCCTAA	0.368													5	34	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	168101798	168101798	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168101798C>T	uc002udx.2	+	8	3914	c.3896C>T	c.(3895-3897)ACA>ATA	p.T1299I	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.T1124I|XIRP2_uc010fpq.2_Missense_Mutation_p.T1077I|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_5'Flank	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	1124					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						ACCAAGAAAACAATTACTGAA	0.378													15	59	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	168102608	168102608	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168102608G>T	uc002udx.2	+	8	4724	c.4706G>T	c.(4705-4707)GGA>GTA	p.G1569V	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.G1394V|XIRP2_uc010fpq.2_Missense_Mutation_p.G1347V|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_5'Flank	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	1394					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						CAGGCTCCTGGAATCATCATT	0.353													6	48	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	168106535	168106535	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168106535A>G	uc002udx.2	+	8	8651	c.8633A>G	c.(8632-8634)GAA>GGA	p.E2878G	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.E2703G|XIRP2_uc010fpq.2_Missense_Mutation_p.E2656G|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_Missense_Mutation_p.E224G	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	2703					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						CAGACCGCTGAAAGTAAAGCT	0.388													8	106	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	168106537	168106537	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168106537A>T	uc002udx.2	+	8	8653	c.8635A>T	c.(8635-8637)AGT>TGT	p.S2879C	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.S2704C|XIRP2_uc010fpq.2_Missense_Mutation_p.S2657C|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_Missense_Mutation_p.S225C	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	2704					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						GACCGCTGAAAGTAAAGCTGA	0.388													8	104	---	---	---	---	PASS
ABCB11	8647	broad.mit.edu	37	2	169814626	169814626	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169814626G>T	uc002ueo.1	-	19	2317	c.2191C>A	c.(2191-2193)CCT>ACT	p.P731T	ABCB11_uc010zda.1_Missense_Mutation_p.P173T|ABCB11_uc010zdb.1_Missense_Mutation_p.P207T	NM_003742	NP_003733	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP),	731	Cytoplasmic (Potential).				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)	TCCTGCACAGGAATGTCCTTG	0.383													28	33	---	---	---	---	PASS
LRP2	4036	broad.mit.edu	37	2	170062925	170062925	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170062925G>A	uc002ues.2	-	39	7518	c.7305C>T	c.(7303-7305)TTC>TTT	p.F2435F		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	2435	LDL-receptor class B 25.|Extracellular (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	AATTTTGTGTGAAGTAGATTC	0.433													6	42	---	---	---	---	PASS
LRP2	4036	broad.mit.edu	37	2	170062926	170062926	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170062926A>T	uc002ues.2	-	39	7517	c.7304T>A	c.(7303-7305)TTC>TAC	p.F2435Y		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	2435	LDL-receptor class B 25.|Extracellular (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	ATTTTGTGTGAAGTAGATTCT	0.433													6	43	---	---	---	---	PASS
LRP2	4036	broad.mit.edu	37	2	170135872	170135872	+	Intron	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170135872C>A	uc002ues.2	-						LRP2_uc010zdf.1_Intron	NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2						hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	TATGTTTTCACATCACTTACC	0.383													13	44	---	---	---	---	PASS
UBR3	130507	broad.mit.edu	37	2	170857932	170857932	+	Intron	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170857932G>C	uc010zdi.1	+						UBR3_uc002ufr.3_Intron|UBR3_uc010fqa.2_Intron|UBR3_uc002uft.3_Intron|UBR3_uc010zdj.1_Intron	NM_172070	NP_742067	Q6ZT12	UBR3_HUMAN	E3 ubiquitin-protein ligase UBR3						sensory perception of smell|suckling behavior|ubiquitin-dependent protein catabolic process	integral to membrane	ubiquitin-protein ligase activity|zinc ion binding				0						CGGGTAAGTTGATTGCAAAAA	0.328													13	45	---	---	---	---	PASS
GAD1	2571	broad.mit.edu	37	2	171709293	171709293	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171709293C>A	uc002ugi.2	+	13	1676	c.1254C>A	c.(1252-1254)GTC>GTA	p.V418V	GAD1_uc010fqc.2_Silent_p.V37V	NM_000817	NP_000808	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 isoform GAD67	418					glutamate decarboxylation to succinate|neurotransmitter biosynthetic process|neurotransmitter secretion|protein-pyridoxal-5-phosphate linkage	clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|plasma membrane	glutamate decarboxylase activity|protein binding|pyridoxal phosphate binding			ovary(1)	1					L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)	CCATTCTCGTCAAGGAAAAGG	0.507													21	37	---	---	---	---	PASS
SLC25A12	8604	broad.mit.edu	37	2	172712451	172712451	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172712451G>C	uc002uhh.2	-	4	307	c.218C>G	c.(217-219)TCC>TGC	p.S73C	SLC25A12_uc010fqh.2_Intron|SLC25A12_uc010zdv.1_RNA	NM_003705	NP_003696	O75746	CMC1_HUMAN	solute carrier family 25, member 12	73	1.|EF-hand 1.				gluconeogenesis|malate-aspartate shuttle|response to calcium ion	integral to membrane|mitochondrial inner membrane	calcium ion binding|L-aspartate transmembrane transporter activity|L-glutamate transmembrane transporter activity|protein binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	CTCTTGATAGGAGATCAACCT	0.259													26	107	---	---	---	---	PASS
CHN1	1123	broad.mit.edu	37	2	175665003	175665003	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175665003G>T	uc002uji.2	-	13	1751	c.1221C>A	c.(1219-1221)CAC>CAA	p.H407Q	CHN1_uc010zeq.1_Missense_Mutation_p.H381Q|CHN1_uc002ujj.2_Missense_Mutation_p.H182Q|CHN1_uc002ujg.2_Missense_Mutation_p.H282Q	NM_001822	NP_001813	P15882	CHIN_HUMAN	chimerin (chimaerin) 1 isoform a	407	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.226)			TCTCCTTTTCGTGGAGGGTCA	0.403			T	TAF15	extraskeletal myxoid chondrosarcoma								5	122	---	---	---	---	PASS
HOXD10	3236	broad.mit.edu	37	2	176982280	176982280	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176982280C>A	uc002ukj.2	+	1	789	c.719C>A	c.(718-720)CCC>CAC	p.P240H		NM_002148	NP_002139	P28358	HXD10_HUMAN	homeobox D10	240						nucleus	sequence-specific DNA binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)		GTGTCCAGTCCCGAAGTGCAG	0.672													7	31	---	---	---	---	PASS
HOXD3	3232	broad.mit.edu	37	2	177034272	177034272	+	Nonsense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177034272A>T	uc002ukt.1	+	2	606	c.430A>T	c.(430-432)AAA>TAA	p.K144*		NM_006898	NP_008829	P31249	HXD3_HUMAN	homeobox D3	144					anterior/posterior pattern formation|cartilage development|cell-matrix adhesion|embryonic skeletal system morphogenesis|Notch signaling pathway|positive regulation of gene expression|positive regulation of neuron differentiation|thyroid gland development		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.247)		CAAGAAGCCCAAAGGTGGGCC	0.418													30	63	---	---	---	---	PASS
MTX2	10651	broad.mit.edu	37	2	177202252	177202252	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177202252C>T	uc002ukx.2	+	10	887	c.652C>T	c.(652-654)CAT>TAT	p.H218Y	MTX2_uc002ukw.2_Missense_Mutation_p.H208Y	NM_006554	NP_006545	O75431	MTX2_HUMAN	metaxin 2	218					protein targeting to mitochondrion	mitochondrial outer membrane				ovary(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00365)|Epithelial(96;0.0654)|all cancers(119;0.181)			GGTATTTGGCCATCTATACAC	0.343													34	93	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179412919	179412919	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179412919A>T	uc010zfg.1	-	288	85954	c.85730T>A	c.(85729-85731)ATC>AAC	p.I28577N	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.I22272N|TTN_uc010zfi.1_Missense_Mutation_p.I22205N|TTN_uc010zfj.1_Missense_Mutation_p.I22080N	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	29504							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)			GTAGCCAGTGATCCGGCTGCC	0.493													38	124	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179443892	179443892	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179443892G>T	uc010zfg.1	-	269	60385	c.60161C>A	c.(60160-60162)ACA>AAA	p.T20054K	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.T13749K|TTN_uc010zfi.1_Missense_Mutation_p.T13682K|TTN_uc010zfj.1_Missense_Mutation_p.T13557K|uc002umv.1_Missense_Mutation_p.V40L	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	20981							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)			AAGTGTGATTGTGTATTTTCC	0.428													37	82	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179452854	179452854	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179452854C>A	uc010zfg.1	-	254	55800	c.55576G>T	c.(55576-55578)GCA>TCA	p.A18526S	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.A12221S|TTN_uc010zfi.1_Missense_Mutation_p.A12154S|TTN_uc010zfj.1_Missense_Mutation_p.A12029S	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	19453							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)			ATGATCGGTGCACCACCATCA	0.468													15	32	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179455492	179455492	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179455492G>T	uc010zfg.1	-	253	53480	c.53256C>A	c.(53254-53256)GTC>GTA	p.V17752V	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.V11447V|TTN_uc010zfi.1_Silent_p.V11380V|TTN_uc010zfj.1_Silent_p.V11255V	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	18679							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)			GTGTTTTGTTGACCCTCACCC	0.438													28	89	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179460333	179460333	+	Nonsense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179460333G>A	uc010zfg.1	-	244	50268	c.50044C>T	c.(50044-50046)CAA>TAA	p.Q16682*	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Nonsense_Mutation_p.Q10377*|TTN_uc010zfi.1_Nonsense_Mutation_p.Q10310*|TTN_uc010zfj.1_Nonsense_Mutation_p.Q10185*	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	17609							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)			GCTTTTCCTTGAATGAGACCC	0.443													7	9	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179475959	179475959	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179475959A>T	uc010zfg.1	-	219	43417	c.43193T>A	c.(43192-43194)GTT>GAT	p.V14398D	uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.V8093D|TTN_uc010zfi.1_Missense_Mutation_p.V8026D|TTN_uc010zfj.1_Missense_Mutation_p.V7901D	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	15325							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)			ACCTTCAATAACAATAATGTC	0.373													14	36	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179482066	179482066	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179482066C>T	uc010zfg.1	-	203	40266	c.40042G>A	c.(40042-40044)GAA>AAA	p.E13348K	TTN_uc010zfh.1_Missense_Mutation_p.E7043K|TTN_uc010zfi.1_Missense_Mutation_p.E6976K|TTN_uc010zfj.1_Missense_Mutation_p.E6851K	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	14275							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)			TAAGTCAGTTCAGGGACAAGT	0.333													4	8	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179534373	179534373	+	5'UTR	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179534373C>T	uc010zfk.1	-	4					TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron|TTN_uc010fre.1_Intron			Q8WZ42	TITIN_HUMAN	SubName: Full=Titin; Flags: Fragment;								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)			ACTTTTTCTTCTGGGACAATT	0.348													54	131	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179537129	179537129	+	Intron	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179537129A>G	uc010zfg.1	-						TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron|TTN_uc010fre.1_Intron|TTN_uc010zfk.1_5'Flank	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A								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)			TCTTTCCAAAAATACCTTTAG	0.328													76	110	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179575619	179575619	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179575619C>A	uc010zfg.1	-	95	24697	c.24473G>T	c.(24472-24474)CGT>CTT	p.R8158L	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.R4819L	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	9085							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)			AGGGGCAAGACGGATGTCAAA	0.493													31	67	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179595510	179595510	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179595510A>T	uc010zfg.1	-	58	14242	c.14018T>A	c.(14017-14019)ATA>AAA	p.I4673K	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.I1334K	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	5600							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)			TGAAGGAGGTATGATAAGATC	0.318													4	85	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179610930	179610930	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179610930G>C	uc002unb.2	-	46	16421	c.16197C>G	c.(16195-16197)TTC>TTG	p.F5399L	TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron	NM_133379	NP_596870	Q8WZ42	TITIN_HUMAN	titin isoform novex-3	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)			CTGAACATTTGAATACAGCAT	0.328													34	38	---	---	---	---	PASS
ZNF804A	91752	broad.mit.edu	37	2	185803014	185803014	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185803014C>A	uc002uph.2	+	4	3485	c.2891C>A	c.(2890-2892)TCA>TAA	p.S964*		NM_194250	NP_919226	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	964						intracellular	zinc ion binding			ovary(6)|skin(3)|large_intestine(1)|pancreas(1)	11						TTTAGACAGTCACAGCCTAAA	0.388													20	63	---	---	---	---	PASS
WDR75	84128	broad.mit.edu	37	2	190331241	190331241	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190331241C>G	uc002uql.1	+	13	1440	c.1380C>G	c.(1378-1380)ACC>ACG	p.T460T	WDR75_uc002uqm.1_Silent_p.T396T|WDR75_uc002uqn.1_Silent_p.T238T|WDR75_uc002uqo.1_Silent_p.T238T	NM_032168	NP_115544	Q8IWA0	WDR75_HUMAN	WD repeat domain 75	460	WD 7.					nucleolus				ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00105)|Epithelial(96;0.0129)|all cancers(119;0.0456)			AACAGCCCACCTTGGTTACAG	0.353													20	57	---	---	---	---	PASS
MSTN	2660	broad.mit.edu	37	2	190924989	190924989	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190924989G>A	uc002urp.2	-	2	679	c.546C>T	c.(544-546)GAC>GAT	p.D182D		NM_005259	NP_005250	O14793	GDF8_HUMAN	myostatin precursor	182					muscle organ development|positive regulation of transcription, DNA-dependent	extracellular space	cytokine activity|growth factor activity			lung(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.000742)|Epithelial(96;0.0121)|all cancers(119;0.0395)			ACCTTGTACCGTCTTTCATAG	0.428													17	93	---	---	---	---	PASS
PIKFYVE	200576	broad.mit.edu	37	2	209190082	209190082	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209190082G>C	uc002vcz.2	+	20	2705	c.2547G>C	c.(2545-2547)CTG>CTC	p.L849L	PIKFYVE_uc010fun.1_Silent_p.L530L|PIKFYVE_uc002vcy.1_Silent_p.L793L	NM_015040	NP_055855	Q9Y2I7	FYV1_HUMAN	phosphatidylinositol-3-phosphate 5-kinase type	849					cellular protein metabolic process|intracellular signal transduction|protein localization to nucleus|retrograde transport, endosome to Golgi	early endosome membrane|membrane raft	1-phosphatidylinositol-3-phosphate 5-kinase activity|1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|metal ion binding|protein binding			ovary(5)|kidney(2)|pancreas(1)|central_nervous_system(1)|skin(1)	10						ATTATGAGCTGGCTCGAGTTA	0.393													22	17	---	---	---	---	PASS
SPAG16	79582	broad.mit.edu	37	2	214972912	214972912	+	Intron	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214972912C>G	uc002veq.2	+						SPAG16_uc010fuz.1_Intron|SPAG16_uc002ver.2_Intron|SPAG16_uc010zjk.1_Intron	NM_024532	NP_078808	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16 isoform 1						cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		TCTGCTTTGTCTTCCTAGGGT	0.368													18	25	---	---	---	---	PASS
BCS1L	617	broad.mit.edu	37	2	219526036	219526036	+	Intron	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219526036G>A	uc002vio.2	+						ZNF142_uc002vin.2_5'Flank|ZNF142_uc010fvt.2_5'Flank|ZNF142_uc002vim.2_5'Flank|BCS1L_uc002vip.2_Intron|BCS1L_uc002viq.2_Intron|BCS1L_uc010fvu.2_Intron|BCS1L_uc010fvv.2_Intron|BCS1L_uc002vir.2_Intron|BCS1L_uc002vis.2_Intron	NM_004328	NP_004319	Q9Y276	BCS1_HUMAN	BCS1-like						mitochondrial respiratory chain complex I assembly|mitochondrial respiratory chain complex III assembly|mitochondrial respiratory chain complex IV assembly	integral to membrane|mitochondrial respiratory chain complex III	ATP binding|nucleoside-triphosphatase activity|protein binding				0		Renal(207;0.0474)		Epithelial(149;7.12e-07)|all cancers(144;0.000131)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ATCTGGTAAGGTGGGGAGCTA	0.488													4	67	---	---	---	---	PASS
TTLL4	9654	broad.mit.edu	37	2	219602602	219602602	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219602602G>T	uc002viy.2	+	3	573	c.203G>T	c.(202-204)GGC>GTC	p.G68V	TTLL4_uc010zkl.1_Intron|TTLL4_uc010fvx.2_Missense_Mutation_p.G68V	NM_014640	NP_055455	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	68					protein polyglutamylation	cilium|microtubule basal body	ATP binding|tubulin binding|tubulin-tyrosine ligase activity			ovary(2)|skin(1)	3		Renal(207;0.0915)		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)		GCAGGGTTGGGCCCAGGCCTC	0.577													37	31	---	---	---	---	PASS
SPEG	10290	broad.mit.edu	37	2	220354143	220354143	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220354143C>A	uc010fwg.2	+	36	8403	c.8403C>A	c.(8401-8403)ACC>ACA	p.T2801T		NM_005876	NP_005867	Q15772	SPEG_HUMAN	SPEG complex locus	2801	Pro-rich.				muscle organ development|negative regulation of cell proliferation	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(9)|ovary(4)|central_nervous_system(1)	14		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		ACTCTCCTACCTCACTGGCCC	0.642													9	18	---	---	---	---	PASS
EFHD1	80303	broad.mit.edu	37	2	233527618	233527618	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233527618G>T	uc002vtc.2	+	2	617	c.409G>T	c.(409-411)GAG>TAG	p.E137*	EFHD1_uc010fyf.2_Nonsense_Mutation_p.E41*|EFHD1_uc002vtd.2_Nonsense_Mutation_p.E25*	NM_025202	NP_079478	Q9BUP0	EFHD1_HUMAN	EF-hand domain family, member D1	137	EF-hand 2.						calcium ion binding|protein binding				0		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Breast(86;0.0199)|Renal(207;0.025)		Epithelial(121;2.08e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00825)|Lung(119;0.0101)		CATGATCAAGGAGGTGGATGA	0.632													15	21	---	---	---	---	PASS
INPP5D	3635	broad.mit.edu	37	2	233986827	233986827	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233986827G>T	uc010zmo.1	+	3	362	c.209G>T	c.(208-210)GGC>GTC	p.G70V	INPP5D_uc010zmp.1_Missense_Mutation_p.G70V	NM_001017915	NP_001017915	Q92835	SHIP1_HUMAN	SH2 containing inositol phosphatase isoform a	70	SH2.				apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway	cytosol	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding			ovary(1)|central_nervous_system(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)		GCATCCGAAGGCGTCTCCATG	0.522													34	40	---	---	---	---	PASS
UGT1A7	54577	broad.mit.edu	37	2	234591121	234591121	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234591121G>T	uc002vut.2	+	1	538	c.538G>T	c.(538-540)GGT>TGT	p.G180C	UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron|UGT1A9_uc010zmw.1_Intron|UGT1A9_uc002vus.2_Intron|UGT1A7_uc010zmx.1_Missense_Mutation_p.G180C	NM_019077	NP_061950	Q9HAW7	UD17_HUMAN	UDP glycosyltransferase 1 family, polypeptide A7	180					drug metabolic process|negative regulation of fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	drug binding|enzyme inhibitor activity|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|retinoic acid binding			ovary(1)	1		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;8.93e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000412)|Lung(119;0.00333)|LUSC - Lung squamous cell carcinoma(224;0.00746)		TCTTGAAGAAGGTGCACAGTG	0.483													73	66	---	---	---	---	PASS
HDAC4	9759	broad.mit.edu	37	2	240016748	240016748	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240016748C>T	uc002vyk.3	-	17	3015	c.2223G>A	c.(2221-2223)TCG>TCA	p.S741S	HDAC4_uc010fyz.1_Silent_p.S736S|HDAC4_uc010zoa.1_Silent_p.S741S|HDAC4_uc010fza.2_Silent_p.S746S|HDAC4_uc010fyy.2_Silent_p.S698S|HDAC4_uc010znz.1_Silent_p.S624S	NM_006037	NP_006028	P56524	HDAC4_HUMAN	histone deacetylase 4	741	Histone deacetylase.				B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent	histone deacetylase complex|transcriptional repressor complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding			breast(3)|skin(2)|ovary(1)	6		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		CGGAGGCGAGCGAGCCTGTGG	0.612													26	13	---	---	---	---	PASS
KIF1A	547	broad.mit.edu	37	2	241658612	241658612	+	Silent	SNP	C	A	A	rs148176695	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241658612C>A	uc002vzy.2	-	45	4868	c.4722G>T	c.(4720-4722)CCG>CCT	p.P1574P	KIF1A_uc010fzk.2_Silent_p.P1675P|KIF1A_uc002vzw.2_Silent_p.P235P|KIF1A_uc002vzx.2_Silent_p.P301P	NM_004321	NP_004312	Q12756	KIF1A_HUMAN	axonal transport of synaptic vesicles	1574					anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		TGGAAACGATCGGGCTGAAGG	0.652													29	39	---	---	---	---	PASS
HDLBP	3069	broad.mit.edu	37	2	242192394	242192394	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242192394G>C	uc002waz.2	-	11	1578	c.1350C>G	c.(1348-1350)CTC>CTG	p.L450L	HDLBP_uc002wba.2_Silent_p.L450L|HDLBP_uc002wbb.2_Silent_p.L402L	NM_203346	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	450	KH 5.				cholesterol metabolic process|lipid transport	cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane	lipid binding|protein binding|RNA binding			breast(3)|skin(1)	4		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		TCTTCCCAATGAGGTGCCTGT	0.567													36	42	---	---	---	---	PASS
IL5RA	3568	broad.mit.edu	37	3	3139615	3139615	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3139615G>T	uc011ask.1	-	8	1292	c.648C>A	c.(646-648)AAC>AAA	p.N216K	IL5RA_uc010hbq.2_Missense_Mutation_p.N216K|IL5RA_uc010hbr.2_Intron|IL5RA_uc010hbs.2_Missense_Mutation_p.N216K|IL5RA_uc011asl.1_Missense_Mutation_p.N216K|IL5RA_uc011asm.1_Missense_Mutation_p.N216K|IL5RA_uc010hbt.2_Missense_Mutation_p.N216K|IL5RA_uc011asn.1_Missense_Mutation_p.N216K|IL5RA_uc010hbu.2_Missense_Mutation_p.N216K	NM_000564	NP_000555	Q01344	IL5RA_HUMAN	interleukin 5 receptor, alpha isoform 1	216	Extracellular (Potential).				cell proliferation	extracellular space|integral to membrane|plasma membrane	interleukin-5 receptor activity			ovary(1)	1				Epithelial(13;0.00278)|all cancers(10;0.00809)|OV - Ovarian serous cystadenocarcinoma(96;0.00944)		TGCTGGAGCCGTTAACAAGCA	0.478													10	32	---	---	---	---	PASS
BRPF1	7862	broad.mit.edu	37	3	9782562	9782562	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9782562G>T	uc003bse.2	+	4	2058	c.1659G>T	c.(1657-1659)GGG>GGT	p.G553G	BRPF1_uc003bsf.2_Silent_p.G553G|BRPF1_uc003bsg.2_Silent_p.G553G|BRPF1_uc011ati.1_Silent_p.G553G	NM_004634	NP_004625	P55201	BRPF1_HUMAN	bromodomain and PHD finger-containing protein 1	553	Required for RUNX1 and RUNX2 transcriptional activation.|Interaction with MEAF6 and ING5.				histone H3 acetylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|MOZ/MORF histone acetyltransferase complex|plasma membrane	DNA binding|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Medulloblastoma(99;0.227)					CACGGAATGGGGTCCCATTGC	0.552													16	28	---	---	---	---	PASS
SLC6A11	6538	broad.mit.edu	37	3	10861482	10861482	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10861482C>A	uc003bvz.2	+	3	511	c.477C>A	c.(475-477)AGC>AGA	p.S159R	SLC6A11_uc003bvy.1_Missense_Mutation_p.S159R	NM_014229	NP_055044	P48066	S6A11_HUMAN	solute carrier family 6 (neurotransmitter	159	Extracellular (Potential).				neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity			skin(3)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.229)		TTTACCTGAGCAACTGCTTCA	0.527													14	36	---	---	---	---	PASS
ATG7	10533	broad.mit.edu	37	3	11383696	11383696	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11383696C>G	uc003bwc.2	+	11	1185	c.1068C>G	c.(1066-1068)GTC>GTG	p.V356V	ATG7_uc003bwd.2_Silent_p.V356V|ATG7_uc011aum.1_Silent_p.V317V	NM_006395	NP_006386	O95352	ATG7_HUMAN	APG7 autophagy 7-like isoform a	356					autophagy|cellular membrane fusion|positive regulation of protein modification process|protein lipidation|protein transport	cytoplasm	APG12 activating enzyme activity|protein homodimerization activity|ubiquitin activating enzyme activity			central_nervous_system(1)	1						TTGTGTCTGTCAAATGTCTGC	0.473													36	57	---	---	---	---	PASS
GALNTL2	117248	broad.mit.edu	37	3	16254180	16254180	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16254180G>A	uc003car.3	+	6	1777	c.1302G>A	c.(1300-1302)CTG>CTA	p.L434L	GALNTL2_uc003caq.3_Silent_p.L167L	NM_054110	NP_473451	Q8N3T1	GLTL2_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	434	Lumenal (Potential).					Golgi membrane|integral to membrane|transport vesicle	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(1)	1						AGGCCACCCTGAGGAACAGGG	0.547													52	27	---	---	---	---	PASS
NEK10	152110	broad.mit.edu	37	3	27244048	27244048	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27244048G>A	uc010hfk.2	-	3	256	c.27C>T	c.(25-27)CCC>CCT	p.P9P	NEK10_uc003cds.1_Silent_p.C94C|NEK10_uc010hfj.2_Silent_p.P9P			Q6ZWH5	NEK10_HUMAN	RecName: Full=Serine/threonine-protein kinase Nek10;          EC=2.7.11.1; AltName: Full=NimA-related protein kinase 10;	Error:Variant_position_missing_in_Q6ZWH5_after_alignment							ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(5)|stomach(2)|central_nervous_system(2)|lung(2)|skin(1)|pancreas(1)	13						GTACCTCGGGGCTGAAGTAAA	0.443													16	13	---	---	---	---	PASS
STAC	6769	broad.mit.edu	37	3	36422172	36422172	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36422172G>T	uc003cgh.1	+	1	76	c.37G>T	c.(37-39)GAC>TAC	p.D13Y	STAC_uc010hgd.1_RNA|STAC_uc011aya.1_Missense_Mutation_p.D13Y	NM_003149	NP_003140	Q99469	STAC_HUMAN	SH3 and cysteine rich domain	13					intracellular signal transduction	cytoplasm|soluble fraction	metal ion binding			skin(2)|ovary(1)|pancreas(1)	4						GGACGGCGTGGACGGGCTGCC	0.706													6	5	---	---	---	---	PASS
SCN10A	6336	broad.mit.edu	37	3	38770299	38770299	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38770299T>C	uc003ciq.2	-	15	2374	c.2374A>G	c.(2374-2376)ATC>GTC	p.I792V		NM_006514	NP_006505	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha	792	Helical; Name=S5 of repeat II; (Potential).|II.				sensory perception	voltage-gated sodium channel complex				ovary(5)|skin(3)|large_intestine(1)|kidney(1)	10				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dibucaine(DB00527)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)	GCCAGGATGATGGTGAGGTTC	0.517													14	74	---	---	---	---	PASS
SCN10A	6336	broad.mit.edu	37	3	38781048	38781048	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38781048C>A	uc003ciq.2	-	14	2238	c.2238G>T	c.(2236-2238)GTG>GTT	p.V746V		NM_006514	NP_006505	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha	746	Helical; Name=S3 of repeat II; (Potential).|II.				sensory perception	voltage-gated sodium channel complex				ovary(5)|skin(3)|large_intestine(1)|kidney(1)	10				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dibucaine(DB00527)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)	CCTTCTTGGCCACGCCCAGCT	0.483													28	14	---	---	---	---	PASS
SCN11A	11280	broad.mit.edu	37	3	38968411	38968411	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38968411G>A	uc011ays.1	-	4	699	c.500C>T	c.(499-501)ACT>ATT	p.T167I		NM_014139	NP_054858	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha	167	Helical; Name=S2 of repeat I; (By similarity).|I.				response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			skin(6)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)|pancreas(1)	9				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)	ATAAATCCCAGTGAAGACACA	0.363													20	43	---	---	---	---	PASS
CX3CR1	1524	broad.mit.edu	37	3	39307072	39307072	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39307072T>A	uc003cjl.2	-	2	1021	c.929A>T	c.(928-930)AAA>ATA	p.K310I		NM_001337	NP_001328	P49238	CX3C1_HUMAN	chemokine (C-X3-C motif) receptor 1	310	Cytoplasmic (Potential).				cell adhesion|cellular defense response|chemotaxis|interspecies interaction between organisms|response to wounding	integral to plasma membrane	chemokine receptor activity			lung(3)	3				KIRC - Kidney renal clear cell carcinoma(284;0.0557)|Kidney(284;0.0699)		AGCCAGGCATTTCCCATACAG	0.478													25	96	---	---	---	---	PASS
ZNF621	285268	broad.mit.edu	37	3	40571728	40571728	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40571728G>A	uc003ckm.2	+	4	396	c.180G>A	c.(178-180)CTG>CTA	p.L60L	ZNF621_uc003ckn.2_Silent_p.L60L|ZNF621_uc003cko.2_Silent_p.L25L|ZNF621_uc011aze.1_Silent_p.L52L	NM_001098414	NP_001091884	Q6ZSS3	ZN621_HUMAN	zinc finger protein 621	60	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0515)|Kidney(284;0.0648)		AACCTGCTCTGATCTCCCACC	0.522													23	30	---	---	---	---	PASS
RTP3	83597	broad.mit.edu	37	3	46541960	46541960	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46541960C>A	uc003cps.1	+	2	338	c.270C>A	c.(268-270)ACC>ACA	p.T90T		NM_031440	NP_113628	Q9BQQ7	RTP3_HUMAN	transmembrane protein 7	90	Cytoplasmic (Potential).				detection of chemical stimulus involved in sensory perception of bitter taste|protein targeting to membrane	cytoplasm|integral to membrane	protein binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;0.00114)|KIRC - Kidney renal clear cell carcinoma(197;0.0173)|Kidney(197;0.0204)		GGGTGTTTACCCAGAGATGTA	0.512													23	109	---	---	---	---	PASS
PTH1R	5745	broad.mit.edu	37	3	46945048	46945048	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46945048G>A	uc003cqm.2	+	16	1887	c.1684G>A	c.(1684-1686)GGG>AGG	p.G562R	PTH1R_uc003cqn.2_Missense_Mutation_p.G562R	NM_000316	NP_000307	Q03431	PTH1R_HUMAN	parathyroid hormone receptor 1 precursor	562	Cytoplasmic (Potential).					cytoplasm|integral to plasma membrane|nucleus	parathyroid hormone receptor activity|peptide hormone binding|protein self-association			breast(1)	1						CAAGGACGATGGGTTCCTCAA	0.662									Ollier_disease_/_Maffuci_syndrome				11	27	---	---	---	---	PASS
CCDC51	79714	broad.mit.edu	37	3	48473987	48473987	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48473987G>T	uc003csz.2	-	4	1188	c.1067C>A	c.(1066-1068)GCT>GAT	p.A356D	PLXNB1_uc003csx.2_5'Flank|CCDC51_uc003cta.2_Missense_Mutation_p.A247D|CCDC51_uc003ctb.2_Missense_Mutation_p.A247D|CCDC51_uc003ctc.2_Missense_Mutation_p.A356D|CCDC51_uc003ctd.2_Missense_Mutation_p.A247D	NM_024661	NP_078937	Q96ER9	CCD51_HUMAN	coiled-coil domain containing 51	356						integral to membrane					0				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		GCTGGGCATAGCCCCGTCTGC	0.547													7	33	---	---	---	---	PASS
CCDC66	285331	broad.mit.edu	37	3	56647606	56647606	+	Intron	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56647606C>T	uc003dhz.2	+						CCDC66_uc003dhy.2_Intron|CCDC66_uc003dhu.2_Intron|CCDC66_uc003dhx.2_Intron|CCDC66_uc003dia.2_5'Flank	NM_001141947	NP_001135419	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66 isoform 1											breast(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		TACGTGATTGCTTATGACTAG	0.279													35	26	---	---	---	---	PASS
PRICKLE2	166336	broad.mit.edu	37	3	64142967	64142967	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64142967C>A	uc003dmf.2	-	5	1057	c.471G>T	c.(469-471)CCG>CCT	p.P157P		NM_198859	NP_942559	Q7Z3G6	PRIC2_HUMAN	prickle-like 2	157	LIM zinc-binding 1.					cytoplasm|nuclear membrane	zinc ion binding			ovary(4)|skin(1)	5		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		CGAAGCACGGCGGGTGCCAGC	0.547													5	15	---	---	---	---	PASS
ADAMTS9	56999	broad.mit.edu	37	3	64547256	64547256	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64547256C>T	uc003dmg.2	-	30	4728	c.4696G>A	c.(4696-4698)GAA>AAA	p.E1566K	ADAMTS9_uc011bfo.1_Missense_Mutation_p.E1538K|ADAMTS9_uc003dmh.1_Missense_Mutation_p.E1395K|ADAMTS9_uc011bfp.1_Missense_Mutation_p.E477K|uc003dmi.1_5'Flank	NM_182920	NP_891550	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1566	TSP type-1 13.				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)		CTACTTACTTCTTGCCATTCC	0.567													23	42	---	---	---	---	PASS
LRIG1	26018	broad.mit.edu	37	3	66502051	66502051	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66502051G>C	uc003dmx.2	-	3	311	c.297C>G	c.(295-297)CTC>CTG	p.L99L	LRIG1_uc010hnz.2_5'UTR|LRIG1_uc010hoa.2_Silent_p.L99L	NM_015541	NP_056356	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like	99	Extracellular (Potential).|LRR 2.					integral to membrane				skin(3)|ovary(2)	5		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		CATTATTATTGAGGTACCTGT	0.428													28	58	---	---	---	---	PASS
EPHA6	285220	broad.mit.edu	37	3	97356890	97356890	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97356890G>C	uc010how.1	+	14	2791	c.2748G>C	c.(2746-2748)GTG>GTC	p.V916V	EPHA6_uc011bgp.1_3'UTR|EPHA6_uc003drs.3_Silent_p.V308V|EPHA6_uc003drr.3_Silent_p.V308V|EPHA6_uc003drt.2_Silent_p.V308V|EPHA6_uc010hox.1_RNA	NM_001080448	NP_001073917	Q9UF33	EPHA6_HUMAN	EPH receptor A6 isoform a	821	Protein kinase.|Cytoplasmic (Potential).					integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16						TCTCCAGAGTGCTGGAAGATG	0.368													14	44	---	---	---	---	PASS
OR5H6	79295	broad.mit.edu	37	3	97983218	97983218	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97983218C>T	uc003dsi.1	+	1	90	c.90C>T	c.(88-90)CTC>CTT	p.L30L		NM_001005479	NP_001005479	Q8NGV6	OR5H6_HUMAN	olfactory receptor, family 5, subfamily H,	30	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|large_intestine(1)	3						AGTTTGTTCTCACAGGATTTT	0.398													38	119	---	---	---	---	PASS
OR5H6	79295	broad.mit.edu	37	3	97983944	97983944	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97983944C>A	uc003dsi.1	+	1	816	c.816C>A	c.(814-816)ACC>ACA	p.T272T		NM_001005479	NP_001005479	Q8NGV6	OR5H6_HUMAN	olfactory receptor, family 5, subfamily H,	272	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|large_intestine(1)	3						GCCCCCTCACCTTCAAATATC	0.408													17	50	---	---	---	---	PASS
TMEM45A	55076	broad.mit.edu	37	3	100287758	100287758	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100287758G>T	uc003dtz.1	+	5	994	c.681G>T	c.(679-681)TGG>TGT	p.W227C	TMEM45A_uc003dua.1_Missense_Mutation_p.W243C|TMEM45A_uc003dub.1_RNA	NM_018004	NP_060474	Q9NWC5	TM45A_HUMAN	transmembrane protein 45A	227	Helical; (Potential).					integral to membrane				skin(2)|ovary(1)	3						GCTTTTGTTGGCATTATGCAG	0.393													51	96	---	---	---	---	PASS
RG9MTD1	54931	broad.mit.edu	37	3	101283908	101283908	+	Nonsense_Mutation	SNP	A	T	T	rs71684018		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101283908A>T	uc003duz.2	+	2	431	c.283A>T	c.(283-285)AGA>TGA	p.R95*		NM_017819	NP_060289	Q7L0Y3	MRRP1_HUMAN	RNA (guanine-9-) methyltransferase domain	95					tRNA processing	mitochondrion	methyltransferase activity|protein binding			ovary(1)	1						AGCTGCCACCAGAGAGTTCAT	0.418													23	66	---	---	---	---	PASS
ALCAM	214	broad.mit.edu	37	3	105252517	105252517	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105252517T>A	uc003dvx.2	+	5	1070	c.530T>A	c.(529-531)CTA>CAA	p.L177Q	ALCAM_uc003dvw.1_Missense_Mutation_p.L177Q|ALCAM_uc003dvy.2_Missense_Mutation_p.L177Q|ALCAM_uc011bhh.1_Missense_Mutation_p.L126Q|ALCAM_uc010hpp.2_5'UTR	NM_001627	NP_001618	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	177	Extracellular (Potential).|Ig-like V-type 2.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(2)|breast(1)	3						GGAAAAGTGCTACATCCCCTT	0.423													20	57	---	---	---	---	PASS
DPPA4	55211	broad.mit.edu	37	3	109047846	109047846	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109047846C>A	uc003dxq.3	-	6	824	c.769G>T	c.(769-771)GTT>TTT	p.V257F	DPPA4_uc011bho.1_Missense_Mutation_p.G158V	NM_018189	NP_060659	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	257						nucleus	protein binding			upper_aerodigestive_tract(1)	1						TTTTCTGGAACCCAGGCTTGA	0.527													5	13	---	---	---	---	PASS
SIDT1	54847	broad.mit.edu	37	3	113329854	113329854	+	Splice_Site	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113329854G>C	uc003eak.2	+	18	2372	c.1721_splice	c.e18-1	p.D574_splice	SIDT1_uc011bif.1_Splice_Site|SIDT1_uc003eaj.1_Splice_Site_p.D574_splice|SIDT1_uc011big.1_Splice_Site_p.D327_splice|SIDT1_uc011bih.1_Splice_Site|SIDT1_uc011bii.1_Splice_Site_p.D27_splice	NM_017699	NP_060169	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1 precursor							integral to membrane				ovary(3)|pancreas(1)|skin(1)	5						TGGGTCCTCAGACACCTCCTT	0.502													31	65	---	---	---	---	PASS
LSAMP	4045	broad.mit.edu	37	3	115571360	115571360	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115571360C>T	uc003ebt.2	-	4	1119	c.619G>A	c.(619-621)GAT>AAT	p.D207N	LSAMP_uc011bis.1_Missense_Mutation_p.D207N	NM_002338	NP_002329	Q13449	LSAMP_HUMAN	limbic system-associated membrane protein	207	Ig-like C2-type 2.				cell adhesion|nervous system development	anchored to membrane|plasma membrane					0		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)		TGTTTGACATCCGCCGAGGAG	0.527													5	37	---	---	---	---	PASS
STXBP5L	9515	broad.mit.edu	37	3	120977893	120977893	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120977893G>T	uc003eec.3	+	18	1976	c.1836G>T	c.(1834-1836)GTG>GTT	p.V612V	STXBP5L_uc011bji.1_Silent_p.V612V	NM_014980	NP_055795	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	612	WD 9.				exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)|skin(2)	9				GBM - Glioblastoma multiforme(114;0.0694)		CTTAAAGTGTGAAGACACGGC	0.363													23	42	---	---	---	---	PASS
POLQ	10721	broad.mit.edu	37	3	121230774	121230774	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121230774C>G	uc003eee.3	-	10	1700	c.1571G>C	c.(1570-1572)GGA>GCA	p.G524A		NM_199420	NP_955452	O75417	DPOLQ_HUMAN	DNA polymerase theta	524	Helicase C-terminal.				DNA repair|DNA replication	nucleoplasm	ATP binding|ATP-dependent helicase activity|damaged DNA binding|DNA-directed DNA polymerase activity|single-stranded DNA-dependent ATPase activity			ovary(4)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.0915)		TACTTCTTCTCCTTCTCGTCT	0.383								DNA_polymerases_(catalytic_subunits)					13	66	---	---	---	---	PASS
FBXO40	51725	broad.mit.edu	37	3	121340752	121340752	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121340752C>A	uc003eeg.2	+	3	686	c.476C>A	c.(475-477)ACT>AAT	p.T159N		NM_016298	NP_057382	Q9UH90	FBX40_HUMAN	F-box protein 40	159					muscle cell differentiation	centrosome|nucleus	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(114;0.189)		GAGGAACCAACTATGAATGGT	0.507													8	25	---	---	---	---	PASS
GOLGB1	2804	broad.mit.edu	37	3	121445853	121445853	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121445853T>C	uc003eei.3	-	5	564	c.438A>G	c.(436-438)ATA>ATG	p.I146M	GOLGB1_uc010hrc.2_Missense_Mutation_p.I146M|GOLGB1_uc003eej.3_Missense_Mutation_p.I107M|GOLGB1_uc011bjm.1_Missense_Mutation_p.I107M|GOLGB1_uc010hrd.1_Missense_Mutation_p.I146M	NM_004487	NP_004478	Q14789	GOGB1_HUMAN	golgi autoantigen, golgin subfamily b,	146	Potential.|Cytoplasmic (Potential).				Golgi organization	ER-Golgi intermediate compartment|Golgi membrane|Golgi stack|integral to membrane	protein binding			ovary(6)|breast(2)|skin(2)	10				GBM - Glioblastoma multiforme(114;0.0989)		TTATCTTTTCTATTTCCATCT	0.378													14	36	---	---	---	---	PASS
KALRN	8997	broad.mit.edu	37	3	124114075	124114075	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124114075C>A	uc003ehg.2	+	12	2177	c.2050C>A	c.(2050-2052)CAG>AAG	p.Q684K	KALRN_uc010hrv.1_Missense_Mutation_p.Q684K|KALRN_uc003ehf.1_Missense_Mutation_p.Q684K|KALRN_uc011bjy.1_Missense_Mutation_p.Q684K|KALRN_uc003ehh.1_Missense_Mutation_p.Q43K	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	684	Poly-Gln.				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						CAAGCAGTTCCAGCAGCAGCA	0.537													9	14	---	---	---	---	PASS
KALRN	8997	broad.mit.edu	37	3	124431863	124431863	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124431863G>A	uc003ehg.2	+	58	8284	c.8157G>A	c.(8155-8157)ATG>ATA	p.M2719I	KALRN_uc003ehk.2_Missense_Mutation_p.M1022I	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	2718	Protein kinase.				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						GCAAAAAAATGAAGAAGAAAG	0.473													4	42	---	---	---	---	PASS
PLXNA1	5361	broad.mit.edu	37	3	126749203	126749203	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126749203G>C	uc003ejg.2	+	28	5114	c.5110G>C	c.(5110-5112)GAC>CAC	p.D1704H	PLXNA1_uc003ejh.2_Missense_Mutation_p.D372H	NM_032242	NP_115618	Q9UIW2	PLXA1_HUMAN	plexin A1	1727	Cytoplasmic (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	semaphorin receptor activity			ovary(1)|pancreas(1)|skin(1)	3				GBM - Glioblastoma multiforme(114;0.155)		TGAGCAGGCCGACAAGCACCA	0.622													22	60	---	---	---	---	PASS
COL29A1	256076	broad.mit.edu	37	3	130188024	130188024	+	Nonsense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130188024G>A	uc010htj.1	+	38	7670	c.7176G>A	c.(7174-7176)TGG>TGA	p.W2392*	COL29A1_uc010hti.1_RNA|COL29A1_uc010htk.1_Nonsense_Mutation_p.W431*	NM_153264	NP_694996	A8TX70	CO6A5_HUMAN	collagen, type XXIX, alpha 1	2392	VWFA 10.|Nonhelical region.				axon guidance|cell adhesion	collagen					0						CCTTGCAGTGGACAATTGACA	0.383													8	62	---	---	---	---	PASS
DNAJC13	23317	broad.mit.edu	37	3	132203456	132203456	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132203456G>T	uc003eor.2	+	29	3272	c.3207G>T	c.(3205-3207)CGG>CGT	p.R1069R		NM_015268	NP_056083	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1069							heat shock protein binding			ovary(1)|breast(1)	2						CCATCATTCGGCCTCTACCCA	0.358													9	79	---	---	---	---	PASS
TMEM108	66000	broad.mit.edu	37	3	133098820	133098820	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133098820G>C	uc003eph.2	+	4	539	c.265G>C	c.(265-267)GAG>CAG	p.E89Q	TMEM108_uc003epi.2_Missense_Mutation_p.E89Q|TMEM108_uc003epj.1_Missense_Mutation_p.E89Q|TMEM108_uc003epk.2_Intron|TMEM108_uc003epm.2_Missense_Mutation_p.E40Q	NM_023943	NP_076432	Q6UXF1	TM108_HUMAN	transmembrane protein 108 precursor	89	Pro-rich.|Extracellular (Potential).					integral to membrane				ovary(2)|skin(2)	4						ACCCCGTGCAGAGGGGCACCC	0.627													13	59	---	---	---	---	PASS
SRPRB	58477	broad.mit.edu	37	3	133526599	133526599	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133526599G>T	uc003epx.1	+	3	275	c.259G>T	c.(259-261)GGC>TGC	p.G87C		NM_021203	NP_067026	Q9Y5M8	SRPRB_HUMAN	signal recognition particle receptor, beta	87						endoplasmic reticulum membrane|integral to membrane	GTP binding|protein binding|receptor activity			ovary(1)	1						GTTGTTAACAGGCCTTTATAG	0.368													17	39	---	---	---	---	PASS
CEP63	80254	broad.mit.edu	37	3	134269059	134269059	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134269059G>C	uc003eqo.1	+	12	1786	c.1337G>C	c.(1336-1338)AGA>ACA	p.R446T	CEP63_uc003eql.1_Missense_Mutation_p.R400T|CEP63_uc003eqm.2_Missense_Mutation_p.R400T|CEP63_uc003eqn.1_Missense_Mutation_p.R446T|CEP63_uc003eqp.1_Missense_Mutation_p.R75T	NM_025180	NP_079456	Q96MT8	CEP63_HUMAN	centrosomal protein 63 isoform a	446	Potential.				cell division|DNA damage checkpoint|G2/M transition of mitotic cell cycle|mitosis|signal transduction in response to DNA damage|spindle assembly	centrosome|cytosol|spindle pole	protein binding			ovary(1)	1						AAGCGACTCAGAGCAGAGATG	0.393													29	76	---	---	---	---	PASS
PRR23B	389151	broad.mit.edu	37	3	138738743	138738743	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138738743G>A	uc003esy.1	-	1	1026	c.761C>T	c.(760-762)CCT>CTT	p.P254L		NM_001013650	NP_001013672	Q6ZRT6	PR23B_HUMAN	proline rich 23B	254	Pro-rich.									breast(1)	1						CTTGCACGGAGGGCGTTCCGG	0.672													8	15	---	---	---	---	PASS
CLSTN2	64084	broad.mit.edu	37	3	140140019	140140019	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140140019G>C	uc003etn.2	+	5	880	c.690G>C	c.(688-690)GAG>GAC	p.E230D	CLSTN2_uc003etm.2_Missense_Mutation_p.E230D	NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor	230	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7						ACCAGTATGAGATCCTGGTGA	0.517										HNSCC(16;0.037)			17	99	---	---	---	---	PASS
TRIM42	287015	broad.mit.edu	37	3	140406890	140406890	+	Missense_Mutation	SNP	G	T	T	rs112034444	byFrequency	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140406890G>T	uc003eto.1	+	3	1557	c.1366G>T	c.(1366-1368)GGC>TGC	p.G456C		NM_152616	NP_689829	Q8IWZ5	TRI42_HUMAN	tripartite motif-containing 42	456	COS.					intracellular	zinc ion binding			lung(2)|skin(2)|upper_aerodigestive_tract(1)|breast(1)|central_nervous_system(1)	7						GATCGAGGACGGCATCCAGAC	0.567													10	43	---	---	---	---	PASS
GRK7	131890	broad.mit.edu	37	3	141526697	141526697	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141526697G>C	uc011bnd.1	+	3	1345	c.1261G>C	c.(1261-1263)GAG>CAG	p.E421Q		NM_139209	NP_631948	Q8WTQ7	GRK7_HUMAN	G-protein-coupled receptor kinase 7 precursor	421	Protein kinase.				visual perception	membrane	ATP binding|G-protein coupled receptor kinase activity|signal transducer activity			lung(2)|stomach(1)|ovary(1)|skin(1)	5						TAACTTCACAGAGGAAGCAAA	0.428													11	41	---	---	---	---	PASS
TRPC1	7220	broad.mit.edu	37	3	142455268	142455268	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142455268G>C	uc003evc.2	+	2	356	c.220G>C	c.(220-222)GAC>CAC	p.D74H	TRPC1_uc003evb.2_Missense_Mutation_p.D74H	NM_003304	NP_003295	P48995	TRPC1_HUMAN	transient receptor potential cation channel,	74	Cytoplasmic (Potential).|ANK 1.				axon guidance|cytosolic calcium ion homeostasis|positive regulation of release of sequestered calcium ion into cytosol|response to calcium ion	cytosol|integral to plasma membrane	protein binding|store-operated calcium channel activity			ovary(2)	2						CAGTTCAGGTGACTTGAACAT	0.333													19	50	---	---	---	---	PASS
IGSF10	285313	broad.mit.edu	37	3	151171201	151171201	+	Nonsense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151171201C>T	uc011bod.1	-	3	686	c.686G>A	c.(685-687)TGG>TAG	p.W229*		NM_178822	NP_849144	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10 precursor	229	LRRCT.				cell differentiation|multicellular organismal development|ossification	extracellular region				skin(7)|ovary(5)|central_nervous_system(1)	13			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GTCAGACAACCACTTTAAATG	0.433													14	62	---	---	---	---	PASS
GPR149	344758	broad.mit.edu	37	3	154147144	154147144	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154147144G>T	uc003faa.2	-	1	361	c.261C>A	c.(259-261)ATC>ATA	p.I87I		NM_001038705	NP_001033794	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	87	Helical; Name=2; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(6)	6			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			AAAACATGAAGATGGTCACCG	0.488													14	87	---	---	---	---	PASS
MLF1	4291	broad.mit.edu	37	3	158317862	158317862	+	Silent	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158317862T>A	uc003fcb.2	+	5	605	c.468T>A	c.(466-468)ATT>ATA	p.I156I	MLF1_uc003fbz.2_Silent_p.I131I|MLF1_uc003fca.2_Silent_p.I131I|MLF1_uc003fbx.2_Silent_p.I146I|MLF1_uc003fcc.2_Silent_p.I187I|MLF1_uc003fby.2_Silent_p.I82I|MLF1_uc010hvx.2_Silent_p.I88I	NM_022443	NP_071888	P58340	MLF1_HUMAN	myeloid leukemia factor 1 isoform 1	156					cell cycle arrest|myeloid progenitor cell differentiation|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein domain specific binding				0		Melanoma(1037;0.000458)|Prostate(884;0.0235)|all_neural(597;0.0299)	Lung(72;0.00199)|LUSC - Lung squamous cell carcinoma(72;0.00256)			AAATGGCTATTGGTCATCATA	0.313			T	NPM1	AML								21	56	---	---	---	---	PASS
SI	6476	broad.mit.edu	37	3	164712057	164712057	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164712057G>T	uc003fei.2	-	41	4891	c.4829C>A	c.(4828-4830)CCC>CAC	p.P1610H		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	1610	Sucrase.|Lumenal.				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)	ATGCAAAAGGGGTCGGATAAC	0.318										HNSCC(35;0.089)			8	39	---	---	---	---	PASS
ARPM1	84517	broad.mit.edu	37	3	169485440	169485440	+	Nonsense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169485440G>C	uc003ffs.1	-	2	1274	c.899C>G	c.(898-900)TCA>TGA	p.S300*	TERC_uc003ffr.1_5'Flank	NM_032487	NP_115876	Q9BYD9	ARPM1_HUMAN	actin related protein M1	300						cytoplasm|cytoskeleton					0	all_cancers(22;9.55e-22)|all_epithelial(15;2.04e-26)|all_lung(20;5.05e-16)|Lung NSC(18;2.19e-15)|Ovarian(172;0.000223)|Breast(254;0.197)		Epithelial(2;4.03e-64)|all cancers(2;5.01e-59)|Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)			GAAAGAGGTTGATCCCCCGGC	0.463													30	133	---	---	---	---	PASS
TBL1XR1	79718	broad.mit.edu	37	3	176769497	176769497	+	Silent	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176769497A>G	uc003fiw.3	-	5	482	c.222T>C	c.(220-222)GAT>GAC	p.D74D	TBL1XR1_uc003fix.3_Silent_p.D74D|TBL1XR1_uc011bpz.1_5'UTR|TBL1XR1_uc003fiy.2_Silent_p.D74D	NM_024665	NP_078941	Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1	74	F-box-like.				canonical Wnt receptor signaling pathway|cellular lipid metabolic process|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein N-terminus binding|transcription corepressor activity|transcription regulatory region DNA binding			ovary(1)	1	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)			TTGGTCGACCATCAAACAAGG	0.358													7	42	---	---	---	---	PASS
GNB4	59345	broad.mit.edu	37	3	179131506	179131506	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179131506G>A	uc003fjv.3	-	7	774	c.494C>T	c.(493-495)ACT>ATT	p.T165I	GNB4_uc003fju.3_Missense_Mutation_p.T76I	NM_021629	NP_067642	Q9HAV0	GBB4_HUMAN	guanine nucleotide-binding protein, beta-4	165	WD 3.				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)			AACTTACCAAGTTGTATCTCC	0.358													9	42	---	---	---	---	PASS
CCDC39	339829	broad.mit.edu	37	3	180377513	180377513	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180377513C>G	uc010hxe.2	-	5	676	c.561G>C	c.(559-561)CAG>CAC	p.Q187H	CCDC39_uc003fkn.2_RNA	NM_181426	NP_852091	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	187	Potential.				axonemal dynein complex assembly|ciliary cell motility|cilium movement involved in determination of left/right asymmetry|flagellar cell motility	cilium axoneme|cytoplasm|cytoskeleton				ovary(4)	4	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			TCTTTCTTTTCTGATTACATT	0.289													11	44	---	---	---	---	PASS
FXR1	8087	broad.mit.edu	37	3	180685922	180685922	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180685922G>A	uc003fkq.2	+	14	1304	c.1282G>A	c.(1282-1284)GAT>AAT	p.D428N	FXR1_uc003fkp.2_Missense_Mutation_p.D343N|FXR1_uc003fkr.2_Missense_Mutation_p.D428N|FXR1_uc011bqj.1_Missense_Mutation_p.D342N|FXR1_uc003fks.2_Missense_Mutation_p.D371N|FXR1_uc011bqk.1_Missense_Mutation_p.D379N|FXR1_uc011bql.1_Missense_Mutation_p.D415N	NM_005087	NP_005078	P51114	FXR1_HUMAN	fragile X mental retardation-related protein 1	428					apoptosis|cell differentiation|muscle organ development	nucleolus|polysome				breast(1)	1	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)			GGCAGGAGAAGATGATCGAGA	0.527													7	53	---	---	---	---	PASS
ABCF3	55324	broad.mit.edu	37	3	183907720	183907720	+	Splice_Site	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183907720G>A	uc003fmz.2	+	14	1524	c.1391_splice	c.e14+1	p.L464_splice	ABCF3_uc003fna.2_Splice_Site_p.L458_splice|ABCF3_uc003fnb.2_Splice_Site_p.L145_splice	NM_018358	NP_060828	Q9NUQ8	ABCF3_HUMAN	ATP-binding cassette, sub-family F (GCN20),								ATP binding|ATPase activity			ovary(3)|lung(1)	4	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.35e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TGGAGAAGCTGTGAGTACAGC	0.547													13	37	---	---	---	---	PASS
EIF4G1	1981	broad.mit.edu	37	3	184040983	184040983	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184040983G>A	uc003fnp.2	+	14	2240	c.2042G>A	c.(2041-2043)CGT>CAT	p.R681H	EIF4G1_uc003fno.1_Missense_Mutation_p.R622H|EIF4G1_uc010hxw.1_Missense_Mutation_p.R517H|EIF4G1_uc003fnt.2_Missense_Mutation_p.R392H|EIF4G1_uc003fnq.2_Missense_Mutation_p.R594H|EIF4G1_uc003fnr.2_Missense_Mutation_p.R517H|EIF4G1_uc010hxx.2_Missense_Mutation_p.R688H|EIF4G1_uc003fns.2_Missense_Mutation_p.R641H|EIF4G1_uc010hxy.2_Missense_Mutation_p.R688H|EIF4G1_uc003fnv.3_Missense_Mutation_p.R681H|EIF4G1_uc003fnu.3_Missense_Mutation_p.R681H|EIF4G1_uc003fnw.2_Missense_Mutation_p.R688H|EIF4G1_uc003fnx.2_Missense_Mutation_p.R485H|EIF4G1_uc003fny.3_Missense_Mutation_p.R485H|SNORD66_uc003fnz.2_5'Flank	NM_198241	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4	681	MIF4G.	Cleavage; by enterovirus/rhinovirus protease 2A.			insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity			lung(2)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CTTAGCACCCGTGGGCCCCCA	0.627													18	88	---	---	---	---	PASS
EIF4G1	1981	broad.mit.edu	37	3	184041675	184041675	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184041675C>G	uc003fnp.2	+	16	2580	c.2382C>G	c.(2380-2382)CTC>CTG	p.L794L	EIF4G1_uc003fno.1_Silent_p.L735L|EIF4G1_uc010hxw.1_Silent_p.L630L|EIF4G1_uc003fnt.2_Silent_p.L505L|EIF4G1_uc003fnq.2_Silent_p.L707L|EIF4G1_uc003fnr.2_Silent_p.L630L|EIF4G1_uc010hxx.2_Silent_p.L801L|EIF4G1_uc003fns.2_Silent_p.L754L|EIF4G1_uc010hxy.2_Silent_p.L801L|EIF4G1_uc003fnv.3_Silent_p.L795L|EIF4G1_uc003fnu.3_Silent_p.L794L|EIF4G1_uc003fnw.2_Silent_p.L801L|EIF4G1_uc003fnx.2_Silent_p.L599L|EIF4G1_uc003fny.3_Silent_p.L598L|SNORD66_uc003fnz.2_5'Flank	NM_198241	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4	794	eIF3/EIF4A-binding.				insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity			lung(2)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			AGGAACGCCTCAAAGGGGTCA	0.547													5	84	---	---	---	---	PASS
EIF4G1	1981	broad.mit.edu	37	3	184042714	184042714	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184042714A>G	uc003fnp.2	+	18	2866	c.2668A>G	c.(2668-2670)ATA>GTA	p.I890V	EIF4G1_uc003fno.1_Missense_Mutation_p.I831V|EIF4G1_uc010hxw.1_Missense_Mutation_p.I726V|EIF4G1_uc003fnt.2_Missense_Mutation_p.I601V|EIF4G1_uc003fnq.2_Missense_Mutation_p.I803V|EIF4G1_uc003fnr.2_Missense_Mutation_p.I726V|EIF4G1_uc010hxx.2_Missense_Mutation_p.I897V|EIF4G1_uc003fns.2_Missense_Mutation_p.I850V|EIF4G1_uc010hxy.2_Missense_Mutation_p.I897V|EIF4G1_uc003fnv.3_Missense_Mutation_p.I891V|EIF4G1_uc003fnu.3_Missense_Mutation_p.I890V|EIF4G1_uc003fnw.2_Missense_Mutation_p.I897V|EIF4G1_uc003fnx.2_Missense_Mutation_p.I695V|EIF4G1_uc003fny.3_Missense_Mutation_p.I694V|SNORD66_uc003fnz.2_5'Flank	NM_198241	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4	890	eIF3/EIF4A-binding.				insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity			lung(2)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GGCTCGGGACATAGCCCGGCG	0.493													12	62	---	---	---	---	PASS
EPHB3	2049	broad.mit.edu	37	3	184294689	184294689	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184294689G>A	uc003foz.2	+	5	1509	c.1072G>A	c.(1072-1074)GAG>AAG	p.E358K		NM_004443	NP_004434	P54753	EPHB3_HUMAN	ephrin receptor EphB3 precursor	358	Fibronectin type-III 1.|Extracellular (Potential).					integral to plasma membrane	ATP binding|ephrin receptor activity			lung(5)|breast(2)|upper_aerodigestive_tract(1)|stomach(1)|skin(1)|ovary(1)	11	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			ACTGATCCTCGAGTGGAGTGA	0.597													13	78	---	---	---	---	PASS
MASP1	5648	broad.mit.edu	37	3	186940980	186940980	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186940980C>T	uc003frh.1	-	14	2076	c.1744G>A	c.(1744-1746)GCC>ACC	p.A582T		NM_001879	NP_001870	P48740	MASP1_HUMAN	mannan-binding lectin serine protease 1 isoform	582	Peptidase S1.				complement activation, lectin pathway|negative regulation of complement activation|proteolysis	extracellular space	calcium ion binding|calcium-dependent protein binding|protein binding|protein homodimerization activity|serine-type endopeptidase activity			ovary(2)|breast(1)|liver(1)	4	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)		ATGACCATGGCTCCTGGAGGA	0.522													15	29	---	---	---	---	PASS
SST	6750	broad.mit.edu	37	3	187386958	187386958	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187386958C>T	uc003frn.2	-	2	368	c.246G>A	c.(244-246)ATG>ATA	p.M82I		NM_001048	NP_001039	P61278	SMS_HUMAN	somatostatin preproprotein	82					digestion|G-protein coupled receptor protein signaling pathway|induction of apoptosis by hormones|negative regulation of cell proliferation|response to nutrient|synaptic transmission	extracellular space	hormone activity			pancreas(1)	1	all_cancers(143;4.06e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.00444)	Bromocriptine(DB01200)|Cysteamine(DB00847)	GCTCAAGCCTCATTTCATCCT	0.522													75	201	---	---	---	---	PASS
CPN2	1370	broad.mit.edu	37	3	194062502	194062502	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194062502G>T	uc003fts.2	-	2	1020	c.930C>A	c.(928-930)GCC>GCA	p.A310A		NM_001080513	NP_001073982	P22792	CPN2_HUMAN	carboxypeptidase N, polypeptide 2	310	LRR 9.				protein stabilization	extracellular region	enzyme regulator activity			ovary(5)	5	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.65e-05)		TGGACAGGTGGGCAAAGGTGC	0.592													11	33	---	---	---	---	PASS
LSG1	55341	broad.mit.edu	37	3	194373677	194373677	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194373677C>A	uc003fui.2	-	8	1269	c.954G>T	c.(952-954)TGG>TGT	p.W318C		NM_018385	NP_060855	Q9H089	LSG1_HUMAN	large subunit GTPase 1	318					nuclear export|protein transport	Cajal body|endoplasmic reticulum	GTP binding|hydrolase activity				0	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;7.55e-06)		AGCACGTCTGCCAGTCGTCTT	0.527													25	66	---	---	---	---	PASS
TNK2	10188	broad.mit.edu	37	3	195605472	195605472	+	Intron	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195605472G>A	uc003fvu.1	-						TNK2_uc003fvs.1_Intron|TNK2_uc003fvt.1_Intron|TNK2_uc010hzw.1_Intron|TNK2_uc003fvv.1_Intron	NM_005781	NP_005772	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2 isoform 1						positive regulation of peptidyl-tyrosine phosphorylation|protein ubiquitination|small GTPase mediated signal transduction	adherens junction|cytoplasmic vesicle membrane|endosome|nucleus	ATP binding|GTPase inhibitor activity|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			ovary(3)|central_nervous_system(3)|lung(2)|stomach(1)|skin(1)	10	all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;0.000757)	Adenosine triphosphate(DB00171)	ATCTGAAGGTGAGGAGGTGCA	0.632													5	23	---	---	---	---	PASS
BDH1	622	broad.mit.edu	37	3	197239159	197239159	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197239159G>T	uc003fxr.2	-	8	1041	c.639C>A	c.(637-639)TTC>TTA	p.F213L	BDH1_uc003fxs.2_Missense_Mutation_p.F213L|BDH1_uc003fxt.2_Missense_Mutation_p.F126L|BDH1_uc003fxu.2_Missense_Mutation_p.F213L	NM_203314	NP_976059	Q02338	BDH_HUMAN	3-hydroxybutyrate dehydrogenase, type 1	213					cellular lipid metabolic process|ketone body biosynthetic process|ketone body catabolic process	mitochondrial matrix	3-hydroxybutyrate dehydrogenase activity			ovary(1)	1	all_cancers(143;3.35e-10)|Ovarian(172;0.0418)|Breast(254;0.0437)	Lung NSC(153;0.118)	Epithelial(36;3.52e-24)|all cancers(36;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-19)|LUSC - Lung squamous cell carcinoma(58;1.02e-06)|Lung(62;1.34e-06)	GBM - Glioblastoma multiforme(93;0.0977)	NADH(DB00157)	CCTCTACCCCGAACTTGGTGA	0.632													15	22	---	---	---	---	PASS
LMLN	89782	broad.mit.edu	37	3	197707242	197707242	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197707242G>T	uc011buo.1	+	6	617	c.595G>T	c.(595-597)GGT>TGT	p.G199C	LMLN_uc003fyt.2_Missense_Mutation_p.G147C|LMLN_uc010iar.2_Missense_Mutation_p.G199C|LMLN_uc010ias.2_Missense_Mutation_p.G147C|LMLN_uc003fyu.2_5'UTR	NM_033029	NP_149018	Q96KR4	LMLN_HUMAN	leishmanolysin-like isoform 2	199					cell adhesion|cell division|mitosis|proteolysis	cytoplasm|membrane	metalloendopeptidase activity|zinc ion binding			skin(1)	1	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		TGGAGCAGTGGGTGTGCCAGA	0.527													27	71	---	---	---	---	PASS
CTBP1	1487	broad.mit.edu	37	4	1207352	1207352	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1207352C>A	uc003gcv.1	-	7	1100	c.935G>T	c.(934-936)TGC>TTC	p.C312F	uc003gcs.1_Intron|CTBP1_uc003gct.1_Missense_Mutation_p.C293F|CTBP1_uc003gcu.1_Missense_Mutation_p.C301F|CTBP1_uc003gcw.2_5'UTR	NM_001328	NP_001319	Q13363	CTBP1_HUMAN	C-terminal binding protein 1 isoform 1	312	Interaction with GLIS2 2 (By similarity).				interspecies interaction between organisms|negative regulation of cell proliferation|negative regulation of histone H4 acetylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|protein phosphorylation|regulation of cell cycle|regulation of transcription by chromatin organization|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|viral genome replication|white fat cell differentiation	cytoplasm|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein C-terminus binding|protein domain specific binding|transcription factor binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(23;0.00818)	Colorectal(103;0.2)		ATGGGGGGTGCAGATGAGGTT	0.642													14	19	---	---	---	---	PASS
OTOP1	133060	broad.mit.edu	37	4	4199533	4199533	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4199533C>A	uc003ghp.1	-	5	1058	c.1028G>T	c.(1027-1029)AGC>ATC	p.S343I		NM_177998	NP_819056	Q7RTM1	OTOP1_HUMAN	otopetrin 1	343					biomineral tissue development	extracellular space|integral to membrane				ovary(2)|central_nervous_system(1)	3				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		TGCCGACTCGCTCTTGGTCTT	0.587													14	33	---	---	---	---	PASS
KIAA0232	9778	broad.mit.edu	37	4	6862821	6862821	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6862821G>C	uc003gjr.3	+	7	1175	c.712G>C	c.(712-714)GAA>CAA	p.E238Q	KIAA0232_uc003gjq.3_Missense_Mutation_p.E238Q	NM_014743	NP_055558	Q92628	K0232_HUMAN	hypothetical protein LOC9778	238							ATP binding			ovary(2)	2						AAGAAGCAGTGAAGTACCCAC	0.438													26	88	---	---	---	---	PASS
CPZ	8532	broad.mit.edu	37	4	8609035	8609035	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8609035C>A	uc003glm.2	+	7	1236	c.1110C>A	c.(1108-1110)ACC>ACA	p.T370T	CPZ_uc003gll.2_RNA|CPZ_uc003gln.2_Silent_p.T233T|CPZ_uc003glo.2_Silent_p.T359T|CPZ_uc003glp.2_RNA	NM_001014447	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z isoform 1	370					proteolysis|Wnt receptor signaling pathway	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)|pancreas(1)	3						GGATGCAGACCATACCCTTTG	0.612											OREG0016100	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	23	42	---	---	---	---	PASS
BOD1L	259282	broad.mit.edu	37	4	13602546	13602546	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13602546T>A	uc003gmz.1	-	10	6095	c.5978A>T	c.(5977-5979)AAA>ATA	p.K1993I	BOD1L_uc010idr.1_Missense_Mutation_p.K1330I	NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN	biorientation of chromosomes in cell division	1993							DNA binding			ovary(5)|breast(1)	6						ATCTTCAACTTTTTCGAGCTG	0.478													8	64	---	---	---	---	PASS
STIM2	57620	broad.mit.edu	37	4	27000893	27000893	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27000893G>A	uc003gsh.3	+	5	1026	c.810G>A	c.(808-810)TTG>TTA	p.L270L	STIM2_uc003gsg.3_Silent_p.L270L|STIM2_uc010iex.2_Silent_p.L270L	NM_020860	NP_065911	Q9P246	STIM2_HUMAN	stromal interaction molecule 2	183	SAM.|Extracellular (Potential).				activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)				TCTCCCAGTTGAAAATCAGTG	0.343													21	24	---	---	---	---	PASS
BEND4	389206	broad.mit.edu	37	4	42122315	42122315	+	Intron	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42122315G>C	uc003gwn.2	-						BEND4_uc003gwm.2_Intron|BEND4_uc011byy.1_Intron	NM_207406	NP_997289	Q6ZU67	BEND4_HUMAN	BEN domain containing 4 isoform a												0						TGCTTCCCTGGAAAAGCGAAA	0.448													11	99	---	---	---	---	PASS
GNPDA2	132789	broad.mit.edu	37	4	44713028	44713028	+	Nonsense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44713028G>C	uc003gwy.2	-	5	693	c.536C>G	c.(535-537)TCA>TGA	p.S179*	GNPDA2_uc010iga.2_Nonsense_Mutation_p.S145*|GNPDA2_uc011bzb.1_Nonsense_Mutation_p.S109*|GNPDA2_uc003gwz.1_Nonsense_Mutation_p.S179*	NM_138335	NP_612208	Q8TDQ7	GNPI2_HUMAN	glucosamine-6-phosphate deaminase 2	179					N-acetylglucosamine metabolic process	cytoplasm	glucosamine-6-phosphate deaminase activity|hydrolase activity			ovary(1)	1						TGGCACTTTTGATAAATCTCC	0.378													12	75	---	---	---	---	PASS
GABRA2	2555	broad.mit.edu	37	4	46305529	46305529	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46305529G>T	uc003gxc.3	-	7	1477	c.804C>A	c.(802-804)TCC>TCA	p.S268S	GABRA2_uc010igc.2_Silent_p.S268S|GABRA2_uc011bzc.1_Silent_p.S213S|GABRA2_uc003gxe.2_Silent_p.S268S	NM_001114175	NP_001107647	P47869	GBRA2_HUMAN	gamma-aminobutyric acid A receptor, alpha 2	268	Helical; (Probable).				gamma-aminobutyric acid signaling pathway|neurotransmitter transport|regulation of neurotransmitter levels	cell junction|chloride channel complex|integral to synaptic vesicle membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)|skin(2)	4					Alprazolam(DB00404)|Bromazepam(DB01558)|Diazepam(DB00829)|Ethchlorvynol(DB00189)|Fludiazepam(DB01567)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	ATGAAACTTGGGAGAGAATGA	0.318													36	57	---	---	---	---	PASS
CNGA1	1259	broad.mit.edu	37	4	47939827	47939827	+	Silent	SNP	C	G	G	rs149504668	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47939827C>G	uc003gxt.3	-	11	950	c.684G>C	c.(682-684)CTG>CTC	p.L228L	uc003gxr.1_Intron|CNGA1_uc003gxu.2_Silent_p.L297L	NM_000087	NP_000078	P29973	CNGA1_HUMAN	cyclic nucleotide gated channel alpha 1 isoform	228	Cytoplasmic (Potential).				response to stimulus|visual perception	integral to plasma membrane	cGMP binding|ion channel activity			ovary(2)	2						CCTTTACCAGCAGTCCTTGTT	0.284													17	69	---	---	---	---	PASS
TXK	7294	broad.mit.edu	37	4	48115301	48115301	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48115301T>A	uc003gxx.3	-	3	183	c.97A>T	c.(97-99)AGC>TGC	p.S33C	TXK_uc003gxy.1_Missense_Mutation_p.S33C	NM_003328	NP_003319	P42681	TXK_HUMAN	TXK tyrosine kinase	33						cytoplasm	ATP binding|non-membrane spanning protein tyrosine kinase activity				0						TCATCTGTGCTCAGGCTTATC	0.378													14	73	---	---	---	---	PASS
CHIC2	26511	broad.mit.edu	37	4	54930367	54930367	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54930367C>A	uc003haj.1	-	1	422	c.101G>T	c.(100-102)GGC>GTC	p.G34V	PDGFRA_uc003haa.2_Intron	NM_012110	NP_036242	Q9UKJ5	CHIC2_HUMAN	cysteine-rich hydrophobic domain 2	34						plasma membrane	protein binding			central_nervous_system(1)	1	all_cancers(7;0.0193)|all_neural(26;0.0209)|Lung NSC(11;0.0281)|Glioma(25;0.08)		LUSC - Lung squamous cell carcinoma(32;0.00216)			GTGACCGGAGCCGCGGACGAC	0.682			T	ETV6	AML								5	5	---	---	---	---	PASS
PDGFRA	5156	broad.mit.edu	37	4	55156543	55156543	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55156543G>T	uc003han.3	+	22	3275	c.2944G>T	c.(2944-2946)GTG>TTG	p.V982L	PDGFRA_uc003haa.2_Missense_Mutation_p.V742L	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	982	Cytoplasmic (Potential).				cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	ACGCATGCGTGTGGACTCAGA	0.448			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			25	266	---	---	---	---	PASS
KIT	3815	broad.mit.edu	37	4	55592146	55592146	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55592146A>T	uc010igr.2	+	9	1557	c.1470A>T	c.(1468-1470)GAA>GAT	p.E490D	KIT_uc010igs.2_Missense_Mutation_p.E490D|KIT_uc011bzw.1_5'Flank|KIT_uc010igt.1_5'Flank	NM_000222	NP_000213	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral	490	Extracellular (Potential).|Ig-like C2-type 5.				male gonad development|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular space|integral to membrane	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity	p.E490_F504>DHIVVSLTF(1)		soft_tissue(3273)|haematopoietic_and_lymphoid_tissue(1572)|skin(99)|testis(49)|bone(21)|genital_tract(18)|kidney(17)|ovary(16)|salivary_gland(15)|large_intestine(11)|thymus(6)|lung(6)|central_nervous_system(4)|NS(3)|eye(2)|endometrium(2)|breast(1)|stomach(1)|autonomic_ganglia(1)|pancreas(1)	5118	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Sorafenib(DB00398)|Sunitinib(DB01268)	GCACGGTTGAATGTAAGGCTT	0.398		1	Mis|O		GIST|AML|TGCT|mastocytosis|mucosal melanoma	GIST|epithelioma	Piebald trait		Mast_Cell_disease_Familial_Clustering_of|Piebaldism|Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Gastrointestinal_Stromal_Tumors				178	48	---	---	---	---	PASS
KIT	3815	broad.mit.edu	37	4	55599352	55599352	+	Missense_Mutation	SNP	A	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55599352A>C	uc010igr.2	+	17	2565	c.2478A>C	c.(2476-2478)AAA>AAC	p.K826N	KIT_uc010igs.2_Missense_Mutation_p.K822N	NM_000222	NP_000213	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral	826	Protein kinase.|Cytoplasmic (Potential).				male gonad development|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular space|integral to membrane	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity			soft_tissue(3273)|haematopoietic_and_lymphoid_tissue(1572)|skin(99)|testis(49)|bone(21)|genital_tract(18)|kidney(17)|ovary(16)|salivary_gland(15)|large_intestine(11)|thymus(6)|lung(6)|central_nervous_system(4)|NS(3)|eye(2)|endometrium(2)|breast(1)|stomach(1)|autonomic_ganglia(1)|pancreas(1)	5118	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Sorafenib(DB00398)|Sunitinib(DB01268)	ATGTGGTTAAAGGAAACGTGA	0.368		1	Mis|O		GIST|AML|TGCT|mastocytosis|mucosal melanoma	GIST|epithelioma	Piebald trait		Mast_Cell_disease_Familial_Clustering_of|Piebaldism|Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Gastrointestinal_Stromal_Tumors				23	368	---	---	---	---	PASS
REST	5978	broad.mit.edu	37	4	57798239	57798239	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57798239G>A	uc003hch.2	+	4	3562	c.3215G>A	c.(3214-3216)GGA>GAA	p.G1072E	REST_uc003hci.2_Missense_Mutation_p.G1072E|REST_uc010ihf.2_Missense_Mutation_p.G746E	NM_005612	NP_005603	Q13127	REST_HUMAN	RE1-silencing transcription factor	1072	C2H2-type 9.|Interaction with RCOR1.				cardiac muscle cell myoblast differentiation|cellular response to drug|cellular response to electrical stimulus|cellular response to glucocorticoid stimulus|histone H4 deacetylation|negative regulation by host of viral transcription|negative regulation of aldosterone biosynthetic process|negative regulation of calcium ion-dependent exocytosis|negative regulation of cell proliferation|negative regulation of cortisol biosynthetic process|negative regulation of dense core granule biogenesis|negative regulation of insulin secretion|negative regulation of mesenchymal stem cell differentiation|negative regulation of neurogenesis|negative regulation of neuron differentiation|positive regulation of apoptosis|positive regulation of caspase activity|positive regulation of transcription, DNA-dependent	cytoplasm|transcriptional repressor complex	calcium channel activity|chromatin binding|core promoter proximal region sequence-specific DNA binding|core promoter sequence-specific DNA binding|outward rectifier potassium channel activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|zinc ion binding			skin(5)|upper_aerodigestive_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	9	Glioma(25;0.08)|all_neural(26;0.181)					TTCAGAAAGGGAAAAGATTAC	0.408													55	32	---	---	---	---	PASS
LPHN3	23284	broad.mit.edu	37	4	62812850	62812850	+	Intron	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62812850T>C	uc010ihh.2	+						LPHN3_uc003hcq.3_Intron|LPHN3_uc003hct.2_Intron	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor						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						GGTAAGAAAATGGCATATTAG	0.289													18	19	---	---	---	---	PASS
UGT2B11	10720	broad.mit.edu	37	4	70066419	70066419	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70066419C>A	uc003heh.2	-	6	1338	c.1329G>T	c.(1327-1329)ATG>ATT	p.M443I	uc003hei.1_Intron	NM_001073	NP_001064	O75310	UDB11_HUMAN	UDP glucuronosyltransferase 2 family,	443					estrogen metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	3						TTGATAATTTCATAATATTCT	0.358													35	46	---	---	---	---	PASS
UGT2B28	54490	broad.mit.edu	37	4	70146511	70146511	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70146511C>T	uc003hej.2	+	1	295	c.293C>T	c.(292-294)TCA>TTA	p.S98L	UGT2B28_uc010ihr.2_Missense_Mutation_p.S98L	NM_053039	NP_444267	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family,	98					xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(1)	1					Flunitrazepam(DB01544)	AAGAGATGGTCAGACATTCAA	0.323													20	84	---	---	---	---	PASS
ADAMTS3	9508	broad.mit.edu	37	4	73434420	73434420	+	Silent	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73434420A>T	uc003hgk.1	-	1	97	c.60T>A	c.(58-60)GCT>GCA	p.A20A		NM_014243	NP_055058	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1	20					collagen catabolic process|collagen fibril organization|proteolysis	proteinaceous extracellular matrix	heparin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CTTGTCCATCAGCTGAAGTCC	0.443													19	14	---	---	---	---	PASS
ALB	213	broad.mit.edu	37	4	74275097	74275097	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74275097C>T	uc003hgs.3	+	5	581	c.508C>T	c.(508-510)CAT>TAT	p.H170Y	ALB_uc003hgw.3_Intron|ALB_uc011cbe.1_5'UTR|ALB_uc003hgt.3_Missense_Mutation_p.H170Y|ALB_uc010iii.2_Missense_Mutation_p.H55Y|ALB_uc003hgu.3_Missense_Mutation_p.H20Y|ALB_uc003hgv.3_5'UTR|ALB_uc011cbf.1_Missense_Mutation_p.H60Y|ALB_uc010iij.2_RNA|ALB_uc003hgx.3_5'UTR	NM_000477	NP_000468	P02768	ALBU_HUMAN	albumin preproprotein	170	Albumin 1.				bile acid and bile salt transport|bile acid metabolic process|cellular response to starvation|hemolysis by symbiont of host erythrocytes|lipoprotein metabolic process|maintenance of mitochondrion location|negative regulation of apoptosis|platelet activation|platelet degranulation|sodium-independent organic anion transport|transmembrane transport	extracellular space|platelet alpha granule lumen|protein complex	antioxidant activity|chaperone binding|copper ion binding|DNA binding|drug binding|fatty acid binding|pyridoxal phosphate binding|toxin binding			ovary(3)|skin(3)	6	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)		Acenocoumarol(DB01418)|Acitretin(DB00459)|Alfentanil(DB00802)|Aluminium(DB01370)|Auranofin(DB00995)|Bismuth(DB01402)|Captopril(DB01197)|Carboplatin(DB00958)|Cefalotin(DB00456)|Cefazolin(DB01327)|Cefonicid(DB01328)|Cefoperazone(DB01329)|Chlorpheniramine(DB01114)|Chlorpromazine(DB00477)|Ciprofloxacin(DB00537)|Clonazepam(DB01068)|Cloxacillin(DB01147)|Cytarabine(DB00987)|Dantrolene(DB01219)|Diclofenac(DB00586)|Diflunisal(DB00861)|Digitoxin(DB01396)|Estrone(DB00655)|Ethacrynic acid(DB00903)|Etodolac(DB00749)|Flurbiprofen(DB00712)|Gadobenate Dimeglumine(DB00743)|Gatifloxacin(DB01044)|Gliclazide(DB01120)|Halothane(DB01159)|Human Serum Albumin(DB00062)|Hyaluronidase(DB00070)|Ibuprofen(DB01050)|Insulin-detemir(DB01307)|Insulin-glargine(DB01308)|Iodipamide(DB04711)|Ketoprofen(DB01009)|Levamisole(DB00848)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Mefenamic acid(DB00784)|Mephenytoin(DB00532)|Methotrexate(DB00563)|Nortriptyline(DB00540)|Oxazepam(DB00842)|Paclitaxel(DB01229)|Phenprocoumon(DB00946)|Probenecid(DB01032)|Propofol(DB00818)|Pyridoxine(DB00165)|Salicyclic acid(DB00936)|Saquinavir(DB01232)|Serum albumin(DB00096)|Serum albumin iodonated(DB00064)|Sodium lauryl sulfate(DB00815)|Sucralfate(DB00364)|Sulfamethizole(DB00576)|Sulindac(DB00605)|Suprofen(DB00870)|Testosterone(DB00624)|Xanthophyll(DB00137)	TGCCAGAAGACATCCTTACTT	0.343													10	56	---	---	---	---	PASS
G3BP2	9908	broad.mit.edu	37	4	76570810	76570810	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76570810C>G	uc003hir.2	-	12	1418	c.1253G>C	c.(1252-1254)AGA>ACA	p.R418T	G3BP2_uc003his.2_Missense_Mutation_p.R418T|G3BP2_uc003hit.2_Missense_Mutation_p.R385T	NM_012297	NP_036429	Q9UN86	G3BP2_HUMAN	Ras-GTPase activating protein SH3 domain-binding	418					cytoplasmic sequestering of NF-kappaB|mRNA transport|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol	GTPase activator activity|nucleotide binding|receptor signaling complex scaffold activity|RNA binding			breast(2)|central_nervous_system(1)	3			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			ACCACCACCTCTGGTTTCTCG	0.458													36	25	---	---	---	---	PASS
STBD1	8987	broad.mit.edu	37	4	77230773	77230773	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77230773G>T	uc003hka.2	+	2	943	c.697G>T	c.(697-699)GAC>TAC	p.D233Y	STBD1_uc003hjy.2_3'UTR|STBD1_uc011cbv.1_3'UTR|STBD1_uc011cbw.1_Missense_Mutation_p.D84Y	NM_003943	NP_003934	O95210	STBD1_HUMAN	starch binding domain 1	233	Cytoplasmic (Potential).				carbohydrate metabolic process|muscle contraction	integral to plasma membrane|membrane fraction	carbohydrate binding|catalytic activity|protein binding			ovary(1)	1			Lung(101;0.196)			CCAGGGAATGGACAATGGAAG	0.517													15	16	---	---	---	---	PASS
SEPT11	55752	broad.mit.edu	37	4	77932877	77932877	+	Intron	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77932877C>G	uc003hkj.2	+						SEPT11_uc010ijh.1_Intron|SEPT11_uc011cca.1_Intron	NM_018243	NP_060713	Q9NVA2	SEP11_HUMAN	septin 11						cell cycle|cell division|protein heterooligomerization	axon|cell junction|dendritic spine|septin complex|stress fiber|synapse	GTP binding|protein binding				0						CATGCTGTTTCTGCATTCTAG	0.284													10	35	---	---	---	---	PASS
FRAS1	80144	broad.mit.edu	37	4	79353585	79353585	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79353585G>C	uc003hlb.2	+	38	5484	c.5044G>C	c.(5044-5046)GAC>CAC	p.D1682H	FRAS1_uc003hkw.2_Missense_Mutation_p.D1682H|FRAS1_uc010ijj.1_Missense_Mutation_p.D102H	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	1681	CSPG 5.|Extracellular (Potential).				cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						TACCCGGGAAGACAGCATGGA	0.478													12	7	---	---	---	---	PASS
MEPE	56955	broad.mit.edu	37	4	88766732	88766732	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88766732G>T	uc003hqy.2	+	4	751	c.712G>T	c.(712-714)GGC>TGC	p.G238C	MEPE_uc010ikn.2_Missense_Mutation_p.G125C	NM_020203	NP_064588	Q9NQ76	MEPE_HUMAN	matrix, extracellular phosphoglycoprotein with	238					skeletal system development	proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding			ovary(1)|lung(1)|skin(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000432)		TGATTTTGAAGGCAGCGGTTA	0.413													21	36	---	---	---	---	PASS
PKD2	5311	broad.mit.edu	37	4	88989210	88989210	+	Missense_Mutation	SNP	A	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88989210A>C	uc003hre.2	+	13	2585	c.2519A>C	c.(2518-2520)CAA>CCA	p.Q840P	PKD2_uc011cdf.1_Missense_Mutation_p.Q258P|PKD2_uc011cdg.1_Missense_Mutation_p.Q166P|PKD2_uc011cdh.1_Missense_Mutation_p.Q63P	NM_000297	NP_000288	Q13563	PKD2_HUMAN	polycystin 2	840	Potential.|C-terminal coiled coil domain.|Cytoplasmic (Potential).					basal cortex|basal plasma membrane|endoplasmic reticulum|integral to membrane|lamellipodium|microtubule basal body	calcium ion binding|cytoskeletal protein binding|voltage-gated chloride channel activity|voltage-gated sodium channel activity			skin(1)	1		Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221)		OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237)		GAAGAGTTTCAAGTGTAAGTA	0.458													28	38	---	---	---	---	PASS
C4orf37	285555	broad.mit.edu	37	4	98893523	98893523	+	Nonsense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98893523G>A	uc003htt.1	-	7	931	c.841C>T	c.(841-843)CAG>TAG	p.Q281*		NM_174952	NP_777612	Q8N412	CD037_HUMAN	hypothetical protein LOC285555	281											0				OV - Ovarian serous cystadenocarcinoma(123;2.27e-08)		CTTTTCTTCTGTTTCTTTGAG	0.353													34	26	---	---	---	---	PASS
MTTP	4547	broad.mit.edu	37	4	100515905	100515905	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100515905G>C	uc003hvc.3	+	8	1030	c.774G>C	c.(772-774)CTG>CTC	p.L258L	MTTP_uc011cej.1_Silent_p.L285L	NM_000253	NP_000244	P55157	MTP_HUMAN	microsomal triglyceride transfer protein large	258	Vitellogenin.				lipid metabolic process|lipoprotein metabolic process	endoplasmic reticulum lumen	lipid binding|lipid transporter activity			ovary(3)|central_nervous_system(1)	4				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)	AATTAGAGCTGAAGACAACCG	0.418													28	34	---	---	---	---	PASS
MTTP	4547	broad.mit.edu	37	4	100518389	100518389	+	Intron	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100518389C>T	uc003hvc.3	+						MTTP_uc011cej.1_Intron	NM_000253	NP_000244	P55157	MTP_HUMAN	microsomal triglyceride transfer protein large						lipid metabolic process|lipoprotein metabolic process	endoplasmic reticulum lumen	lipid binding|lipid transporter activity			ovary(3)|central_nervous_system(1)	4				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)	ATTGTAAGTTCCCCAACCTTT	0.413													40	19	---	---	---	---	PASS
CENPE	1062	broad.mit.edu	37	4	104054854	104054854	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104054854C>A	uc003hxb.1	-	41	6808	c.6718G>T	c.(6718-6720)GAG>TAG	p.E2240*	CENPE_uc003hxc.1_Nonsense_Mutation_p.E2119*	NM_001813	NP_001804	Q02224	CENPE_HUMAN	centromere protein E	2240	Kinetochore-binding domain.|Potential.				blood coagulation|cell division|kinetochore assembly|microtubule-based movement|mitotic chromosome movement towards spindle pole|mitotic metaphase|mitotic metaphase plate congression|mitotic prometaphase|multicellular organismal development|positive regulation of protein kinase activity	condensed chromosome kinetochore|cytosol|microtubule|nucleus|spindle	ATP binding|kinetochore binding|microtubule motor activity			ovary(5)|breast(4)	9				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		AATTATACCTCAATATGTAGA	0.303													6	16	---	---	---	---	PASS
COL25A1	84570	broad.mit.edu	37	4	109817873	109817873	+	Intron	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109817873G>A	uc003hze.1	-						COL25A1_uc003hzg.2_Intron|COL25A1_uc003hzd.2_Intron|COL25A1_uc003hzf.2_Intron	NM_198721	NP_942014	Q9BXS0	COPA1_HUMAN	collagen, type XXV, alpha 1 isoform 1							collagen|extracellular space	beta-amyloid binding|heparin binding			ovary(2)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		TCTCCCTGAGGAGGTGAGAAA	0.388													16	29	---	---	---	---	PASS
ALPK1	80216	broad.mit.edu	37	4	113348773	113348773	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113348773G>C	uc003iap.3	+	9	1026	c.747G>C	c.(745-747)ATG>ATC	p.M249I	ALPK1_uc003ian.3_Missense_Mutation_p.M249I|ALPK1_uc011cfx.1_Missense_Mutation_p.M171I|ALPK1_uc003iao.3_RNA|ALPK1_uc010imo.2_Missense_Mutation_p.M77I	NM_025144	NP_079420	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	249							ATP binding|protein serine/threonine kinase activity			ovary(5)	5		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		TTGTTTCCATGAGCAAGAACG	0.388													5	10	---	---	---	---	PASS
ANK2	287	broad.mit.edu	37	4	114282011	114282011	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114282011A>T	uc003ibe.3	+	39	10814	c.10714A>T	c.(10714-10716)AGG>TGG	p.R3572W	ANK2_uc003ibd.3_Missense_Mutation_p.R1478W|ANK2_uc003ibf.3_Missense_Mutation_p.R1487W|ANK2_uc011cgc.1_Missense_Mutation_p.R663W|ANK2_uc003ibg.3_Missense_Mutation_p.R471W|ANK2_uc003ibh.3_Missense_Mutation_p.R161W|ANK2_uc011cgd.1_Missense_Mutation_p.R874W	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	3539	Death.				axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		GATCGAGGAAAGGCTGGCTTA	0.463													5	2	---	---	---	---	PASS
NDST4	64579	broad.mit.edu	37	4	115891700	115891700	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115891700C>A	uc003ibu.2	-	4	1786	c.1107G>T	c.(1105-1107)CGG>CGT	p.R369R	NDST4_uc010imw.2_RNA	NM_022569	NP_072091	Q9H3R1	NDST4_HUMAN	heparan sulfate N-deacetylase/N-sulfotransferase	369	Lumenal (Potential).|Heparan sulfate N-deacetylase 4.					Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			skin(3)|ovary(1)	4		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		CATCCACAGACCGAAGTAAAA	0.393													11	26	---	---	---	---	PASS
KIAA1109	84162	broad.mit.edu	37	4	123207785	123207785	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123207785C>A	uc003ieh.2	+	51	9172	c.9127C>A	c.(9127-9129)CCT>ACT	p.P3043T	KIAA1109_uc003iel.1_Missense_Mutation_p.P978T	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	3043					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12						AACCATTCCTCCTTCTGCCAG	0.398													22	51	---	---	---	---	PASS
ADAD1	132612	broad.mit.edu	37	4	123333783	123333783	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123333783C>G	uc003ieo.2	+	10	1300	c.1068C>G	c.(1066-1068)CTC>CTG	p.L356L	ADAD1_uc003iep.2_Silent_p.L345L|ADAD1_uc003ieq.2_Silent_p.L338L	NM_139243	NP_640336	Q96M93	ADAD1_HUMAN	adenosine deaminase domain containing 1	356	A to I editase.				multicellular organismal development|RNA processing	nucleus	adenosine deaminase activity|double-stranded RNA binding				0						ATGAAGAACTCTGTCTCCACG	0.358													48	30	---	---	---	---	PASS
ANKRD50	57182	broad.mit.edu	37	4	125599908	125599908	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125599908T>C	uc003ifg.3	-	2	931	c.665A>G	c.(664-666)CAT>CGT	p.H222R	ANKRD50_uc011cgo.1_Missense_Mutation_p.H43R|ANKRD50_uc010inw.2_Missense_Mutation_p.H222R	NM_020337	NP_065070	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	222										central_nervous_system(1)	1						AAAGAACTCATGGTGACCAGC	0.428													53	93	---	---	---	---	PASS
FAT4	79633	broad.mit.edu	37	4	126412468	126412468	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126412468G>C	uc003ifj.3	+	17	14491	c.14491G>C	c.(14491-14493)GAT>CAT	p.D4831H	FAT4_uc011cgp.1_Missense_Mutation_p.D3072H|FAT4_uc003ifi.1_Missense_Mutation_p.D2308H	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	4831	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18						GAATCCAGCGGATGGCATTCC	0.488													9	43	---	---	---	---	PASS
GYPA	2993	broad.mit.edu	37	4	145041633	145041633	+	Intron	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145041633G>A	uc003ijo.3	-						GYPA_uc003ijn.2_Intron|GYPA_uc011cia.1_Intron|GYPA_uc011cib.1_Intron|GYPA_uc003ijp.3_Intron|GYPA_uc010ioq.2_Intron|GYPA_uc010ior.2_Intron|GYPA_uc010ios.1_Intron	NM_002099	NP_002090	P02724	GLPA_HUMAN	glycophorin A precursor						interspecies interaction between organisms	membrane fraction	receptor activity			central_nervous_system(2)	2	all_hematologic(180;0.15)					AAATAAAAATGAAAACAAACC	0.383													10	11	---	---	---	---	PASS
PLRG1	5356	broad.mit.edu	37	4	155459240	155459240	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155459240G>C	uc003iny.2	-	13	1235	c.1172C>G	c.(1171-1173)TCT>TGT	p.S391C	PLRG1_uc003inz.2_Missense_Mutation_p.S382C	NM_002669	NP_002660	O43660	PLRG1_HUMAN	pleiotropic regulator 1 (PRL1 homolog,	391	WD 5.					catalytic step 2 spliceosome|nuclear speck	protein binding|signal transducer activity|transcription corepressor activity				0	all_hematologic(180;0.215)	Renal(120;0.0854)				GTTATCTGGAGAACCAGATGC	0.303													4	23	---	---	---	---	PASS
TLL1	7092	broad.mit.edu	37	4	167020663	167020663	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:167020663G>C	uc003irh.1	+	20	3538	c.2891G>C	c.(2890-2892)CGA>CCA	p.R964P	TLL1_uc011cjn.1_Missense_Mutation_p.R987P|TLL1_uc011cjo.1_Missense_Mutation_p.R788P	NM_012464	NP_036596	O43897	TLL1_HUMAN	tolloid-like 1 precursor	964	CUB 5.				cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		GGGCTTGGTCGATTCTGTGGA	0.423													47	44	---	---	---	---	PASS
DDX60L	91351	broad.mit.edu	37	4	169337864	169337864	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169337864C>G	uc003irq.3	-	20	2916	c.2695G>C	c.(2695-2697)GCT>CCT	p.A899P	DDX60L_uc003irr.1_Missense_Mutation_p.A899P|DDX60L_uc003irs.1_Missense_Mutation_p.A594P	NM_001012967	NP_001012985	Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	899	Helicase ATP-binding.						ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		TTTATGGTAGCTGAAAGAACC	0.358													18	41	---	---	---	---	PASS
LOC285501	285501	broad.mit.edu	37	4	178897011	178897011	+	RNA	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178897011G>T	uc010iru.2	+	5		c.680G>T				NR_028342				Homo sapiens cDNA clone IMAGE:4828874.												0		all_lung(41;6.03e-08)|Lung NSC(41;4.26e-07)|Breast(14;0.00066)|Melanoma(52;0.00168)|Prostate(90;0.0129)|all_hematologic(60;0.0202)|Renal(120;0.0246)|Colorectal(36;0.0508)|Hepatocellular(41;0.236)		all cancers(43;9.24e-25)|Epithelial(43;6.28e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.29e-10)|LUSC - Lung squamous cell carcinoma(1;2.61e-05)|Lung(1;3.22e-05)|GBM - Glioblastoma multiforme(59;0.000185)|Colorectal(24;0.000244)|STAD - Stomach adenocarcinoma(60;0.000777)|COAD - Colon adenocarcinoma(29;0.000884)		CTGGGGCACGGGAAAGGGGTT	0.408													8	77	---	---	---	---	PASS
ING2	3622	broad.mit.edu	37	4	184431872	184431872	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184431872G>C	uc003ivs.1	+	2	739	c.610G>C	c.(610-612)GAG>CAG	p.E204Q	ING2_uc011ckk.1_Missense_Mutation_p.E164Q	NM_001564	NP_001555	Q9H160	ING2_HUMAN	inhibitor of growth family, member 2	204					chromatin modification|positive regulation of transcription, DNA-dependent|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of growth|signal transduction|transcription, DNA-dependent	CCAAT-binding factor complex|Sin3 complex	chromatin binding|DNA binding|protein complex binding|zinc ion binding			ovary(1)	1		all_lung(41;5.16e-14)|Lung NSC(41;1.33e-13)|Colorectal(36;0.00139)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|all_hematologic(60;0.0207)|Prostate(90;0.0235)|all_neural(102;0.202)		all cancers(43;1.15e-26)|Epithelial(43;2.98e-22)|OV - Ovarian serous cystadenocarcinoma(60;7.64e-10)|GBM - Glioblastoma multiforme(59;4.22e-06)|Colorectal(24;5.87e-06)|STAD - Stomach adenocarcinoma(60;2.09e-05)|COAD - Colon adenocarcinoma(29;5.15e-05)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)		TTCACCTGTTGAGTTTGCAAT	0.418													18	11	---	---	---	---	PASS
FAT1	2195	broad.mit.edu	37	4	187549470	187549470	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187549470C>T	uc003izf.2	-	9	4836	c.4648G>A	c.(4648-4650)GTC>ATC	p.V1550I		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	1550	Extracellular (Potential).|Cadherin 13.				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						CTGACATTGACCACAATCCTT	0.468										HNSCC(5;0.00058)			11	13	---	---	---	---	PASS
ZFP42	132625	broad.mit.edu	37	4	188924664	188924664	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188924664C>A	uc003izg.1	+	3	948	c.703C>A	c.(703-705)CAT>AAT	p.H235N	ZFP42_uc003izh.1_Missense_Mutation_p.H235N|ZFP42_uc003izi.1_Missense_Mutation_p.H235N	NM_174900	NP_777560	Q96MM3	ZFP42_HUMAN	zinc finger protein 42	235	C2H2-type 2.				female gonad development|male gonad development|meiosis	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)		ACTAAAGAGACATTTCCTGGT	0.507													5	44	---	---	---	---	PASS
ADAMTS16	170690	broad.mit.edu	37	5	5182170	5182170	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5182170G>T	uc003jdl.2	+	4	653	c.515G>T	c.(514-516)CGA>CTA	p.R172L	ADAMTS16_uc003jdk.1_Missense_Mutation_p.R172L|ADAMTS16_uc003jdj.1_Missense_Mutation_p.R172L	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1	172					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8						GGCATGATACGAACAGAAGAG	0.463													52	105	---	---	---	---	PASS
SRD5A1	6715	broad.mit.edu	37	5	6651984	6651984	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6651984G>C	uc003jdw.2	+	2	513	c.323G>C	c.(322-324)GGA>GCA	p.G108A	SRD5A1_uc011cml.1_RNA|SRD5A1_uc011cmm.1_Intron	NM_001047	NP_001038	P18405	S5A1_HUMAN	steroid-5-alpha-reductase 1	108					androgen biosynthetic process|cell differentiation|sex determination|sex differentiation	endoplasmic reticulum membrane|integral to membrane|microsome	3-oxo-5-alpha-steroid 4-dehydrogenase activity|electron carrier activity				0					Dutasteride(DB01126)|Finasteride(DB01216)	CTGATGCGAGGAGGAAAGCCT	0.373													31	71	---	---	---	---	PASS
SRD5A1	6715	broad.mit.edu	37	5	6668313	6668313	+	Splice_Site	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6668313A>T	uc003jdw.2	+	5	904	c.714_splice	c.e5-2	p.E238_splice	SRD5A1_uc011cml.1_Splice_Site|SRD5A1_uc011cmm.1_Splice_Site_p.E191_splice	NM_001047	NP_001038	P18405	S5A1_HUMAN	steroid-5-alpha-reductase 1						androgen biosynthetic process|cell differentiation|sex determination|sex differentiation	endoplasmic reticulum membrane|integral to membrane|microsome	3-oxo-5-alpha-steroid 4-dehydrogenase activity|electron carrier activity				0					Dutasteride(DB01126)|Finasteride(DB01216)	TTTTTTTCTTAGGTGGTACCT	0.279													20	45	---	---	---	---	PASS
ADCY2	108	broad.mit.edu	37	5	7709423	7709423	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7709423T>A	uc003jdz.1	+	10	1568	c.1501T>A	c.(1501-1503)TGG>AGG	p.W501R	ADCY2_uc011cmo.1_Missense_Mutation_p.W321R	NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2	501	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|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7						CTTGGAGTCCTGGGGGGCAGC	0.607													13	25	---	---	---	---	PASS
ADCY2	108	broad.mit.edu	37	5	7826896	7826896	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7826896T>A	uc003jdz.1	+	25	3255	c.3188T>A	c.(3187-3189)ATC>AAC	p.I1063N	ADCY2_uc011cmo.1_Missense_Mutation_p.I883N|ADCY2_uc010itm.1_Missense_Mutation_p.I259N	NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2	1063	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|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7						CGAGGAATAATCAACGTGAAA	0.522													36	100	---	---	---	---	PASS
MTRR	4552	broad.mit.edu	37	5	7869243	7869243	+	5'UTR	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7869243G>T	uc003jed.2	+	1					FASTKD3_uc011cmp.1_5'Flank|FASTKD3_uc003jeb.2_5'Flank|FASTKD3_uc003jec.2_5'Flank|MTRR_uc010itn.1_RNA|MTRR_uc003jee.3_5'UTR|MTRR_uc003jef.3_RNA|MTRR_uc003jeg.3_RNA|MTRR_uc010ito.2_RNA	NM_024010	NP_076915	Q9UBK8	MTRR_HUMAN	methionine synthase reductase isoform 2						methionine biosynthetic process	cytosol	[methionine synthase] reductase activity|flavin adenine dinucleotide binding|FMN binding|iron ion binding|NADP binding			ovary(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	CCTGGGTACCGAGCATGGGCG	0.672													40	29	---	---	---	---	PASS
TAS2R1	50834	broad.mit.edu	37	5	9629796	9629796	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9629796A>T	uc003jem.1	-	1	668	c.349T>A	c.(349-351)TGG>AGG	p.W117R		NM_019599	NP_062545	Q9NYW7	TA2R1_HUMAN	taste receptor T2R1	117	Cytoplasmic (Potential).				chemosensory behavior|sensory perception of taste	integral to membrane	taste receptor activity			ovary(3)	3						ATCTTCAACCAGATGAAGAGT	0.438													15	30	---	---	---	---	PASS
DNAH5	1767	broad.mit.edu	37	5	13830890	13830890	+	Intron	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13830890T>C	uc003jfd.2	-							NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5						microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					AACATCTGCATGGGTAGAAAC	0.493									Kartagener_syndrome				24	32	---	---	---	---	PASS
FBXL7	23194	broad.mit.edu	37	5	15935285	15935285	+	Intron	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15935285C>A	uc003jfn.1	+						MIR887_hsa-mir-887|MI0005562_5'Flank	NM_012304	NP_036436	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3						gtcagagagccccggggtgca	0.000													41	63	---	---	---	---	PASS
MYO10	4651	broad.mit.edu	37	5	16689976	16689976	+	Missense_Mutation	SNP	C	A	A	rs145872653	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16689976C>A	uc003jft.3	-	28	4321	c.3853G>T	c.(3853-3855)GAT>TAT	p.D1285Y	MYO10_uc011cnc.1_Missense_Mutation_p.D164Y|MYO10_uc011cnd.1_Missense_Mutation_p.D642Y|MYO10_uc011cne.1_Missense_Mutation_p.D642Y|MYO10_uc010itx.2_Missense_Mutation_p.D908Y	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X	1285	PH 1.				axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						AAAGTCCTATCGGCCATAATG	0.483													33	71	---	---	---	---	PASS
CDH12	1010	broad.mit.edu	37	5	21975227	21975227	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21975227C>A	uc010iuc.2	-	3	957	c.499G>T	c.(499-501)GCT>TCT	p.A167S	CDH12_uc011cno.1_Missense_Mutation_p.A167S|CDH12_uc003jgk.2_Missense_Mutation_p.A167S	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein	167	Extracellular (Potential).|Cadherin 2.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						GGAACAGTAGCAACATAAGGT	0.398										HNSCC(59;0.17)			38	95	---	---	---	---	PASS
IL7R	3575	broad.mit.edu	37	5	35867468	35867468	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35867468C>T	uc003jjs.2	+	3	371	c.282C>T	c.(280-282)ATC>ATT	p.I94I	IL7R_uc011coo.1_Silent_p.I94I|IL7R_uc011cop.1_RNA	NM_002185	NP_002176	P16871	IL7RA_HUMAN	interleukin 7 receptor precursor	94	Extracellular (Potential).				immune response|regulation of DNA recombination	extracellular region|integral to membrane	antigen binding|interleukin-7 receptor activity			ovary(3)|breast(1)|skin(1)	5	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)			TATATTTCATCGAGACAAAGA	0.388													31	68	---	---	---	---	PASS
NIPBL	25836	broad.mit.edu	37	5	37000524	37000524	+	Silent	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37000524A>G	uc003jkl.3	+	12	3853	c.3354A>G	c.(3352-3354)GAA>GAG	p.E1118E	NIPBL_uc003jkk.3_Silent_p.E1118E	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	1118					brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			GGGAATATGAAGAGCGTGACA	0.418													65	16	---	---	---	---	PASS
HEATR7B2	133558	broad.mit.edu	37	5	41057273	41057273	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41057273C>T	uc003jmj.3	-	9	1347	c.857G>A	c.(856-858)AGA>AAA	p.R286K	HEATR7B2_uc003jmi.3_Intron	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	286	HEAT 3.						binding			ovary(6)|central_nervous_system(2)	8						CTCTGGAGCTCTGCAGATCTG	0.413													31	17	---	---	---	---	PASS
HCN1	348980	broad.mit.edu	37	5	45303823	45303823	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45303823C>A	uc003jok.2	-	6	1521	c.1496G>T	c.(1495-1497)GGA>GTA	p.G499V		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	499	cAMP.|Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1						GATATAATCTCCAGGTTGAAA	0.408													40	69	---	---	---	---	PASS
HCN1	348980	broad.mit.edu	37	5	45303824	45303824	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45303824C>G	uc003jok.2	-	6	1520	c.1495G>C	c.(1495-1497)GGA>CGA	p.G499R		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	499	cAMP.|Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1						ATATAATCTCCAGGTTGAAAC	0.408													41	70	---	---	---	---	PASS
HCN1	348980	broad.mit.edu	37	5	45462083	45462083	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45462083G>A	uc003jok.2	-	3	901	c.876C>T	c.(874-876)GCC>GCT	p.A292A		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	292	Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1						CCACTGCACTGGCGAGATCAT	0.388													15	40	---	---	---	---	PASS
FST	10468	broad.mit.edu	37	5	52780903	52780903	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52780903G>T	uc003jpd.2	+	5	825	c.798G>T	c.(796-798)CGG>CGT	p.R266R	FST_uc003jpc.2_Silent_p.R266R	NM_013409	NP_037541	P19883	FST_HUMAN	follistatin isoform FST344 precursor	266	Kazal-like 3.|Follistatin-like 3.				hemopoietic progenitor cell differentiation|negative regulation of activin receptor signaling pathway|negative regulation of follicle-stimulating hormone secretion|negative regulation of transcription from RNA polymerase II promoter|positive regulation of hair follicle development	extracellular region	activin binding|protein binding|signal transducer activity				0		Ovarian(174;1.78e-06)|Lung NSC(810;3.55e-06)|Breast(144;4.08e-05)				GGAGAGGCCGGTGTTCCCTCT	0.488													24	36	---	---	---	---	PASS
BDP1	55814	broad.mit.edu	37	5	70837292	70837292	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70837292A>T	uc003kbp.1	+	29	6297	c.6034A>T	c.(6034-6036)ATA>TTA	p.I2012L	BDP1_uc003kbo.2_Missense_Mutation_p.I2012L|BDP1_uc003kbq.1_RNA|BDP1_uc003kbr.1_RNA	NM_018429	NP_060899	A6H8Y1	BDP1_HUMAN	transcription factor-like nuclear regulator	2012					regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding			skin(2)	2		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		AGGAGTATGTATAATTCCTCA	0.279													9	37	---	---	---	---	PASS
MAP1B	4131	broad.mit.edu	37	5	71493547	71493547	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71493547A>T	uc003kbw.3	+	5	4606	c.4365A>T	c.(4363-4365)CAA>CAT	p.Q1455H	MAP1B_uc010iyw.1_Missense_Mutation_p.Q1472H|MAP1B_uc010iyx.1_Missense_Mutation_p.Q1329H|MAP1B_uc010iyy.1_Missense_Mutation_p.Q1329H	NM_005909	NP_005900	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1455						microtubule|microtubule associated complex	structural molecule activity			large_intestine(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		GTCTTTACCAAGACAAACAGG	0.418													19	31	---	---	---	---	PASS
ZNF366	167465	broad.mit.edu	37	5	71756484	71756484	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71756484C>T	uc003kce.1	-	2	1026	c.840G>A	c.(838-840)CCG>CCA	p.P280P		NM_152625	NP_689838	Q8N895	ZN366_HUMAN	zinc finger protein 366	280					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)|skin(1)	2		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		TGCACGCGTGCGGCTTGATCC	0.642													13	59	---	---	---	---	PASS
CMYA5	202333	broad.mit.edu	37	5	79026607	79026607	+	Silent	SNP	A	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79026607A>C	uc003kgc.2	+	2	2091	c.2019A>C	c.(2017-2019)ACA>ACC	p.T673T		NM_153610	NP_705838	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	673						perinuclear region of cytoplasm				ovary(6)|pancreas(2)|lung(1)	9		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		CAACAGTTACACCAGAATACA	0.483													5	24	---	---	---	---	PASS
CKMT2	1160	broad.mit.edu	37	5	80559433	80559433	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80559433G>T	uc003khc.3	+	10	1380	c.1138G>T	c.(1138-1140)GAG>TAG	p.E380*	RNU5E_uc011cto.1_Intron|CKMT2_uc010jaq.2_Nonsense_Mutation_p.E380*|CKMT2_uc003khd.3_Nonsense_Mutation_p.E380*|uc003khe.1_Intron|uc003khf.1_Intron|uc003khg.1_Intron	NM_001825	NP_001816	P17540	KCRS_HUMAN	sarcomeric mitochondrial creatine kinase	380	Phosphagen kinase C-terminal.				creatine metabolic process|muscle contraction	mitochondrial inner membrane	ATP binding|creatine kinase activity				0		Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;2.29e-44)|Epithelial(54;1.05e-38)|all cancers(79;4.15e-34)	Creatine(DB00148)	TGGTCGATCAGAGGTAACGTC	0.453													4	59	---	---	---	---	PASS
GPR98	84059	broad.mit.edu	37	5	89924618	89924618	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89924618G>A	uc003kju.2	+	8	1574	c.1478G>A	c.(1477-1479)CGA>CAA	p.R493Q	GPR98_uc003kjt.2_5'UTR	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	493	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CATACAATACGAGGAGGTGCA	0.428													23	19	---	---	---	---	PASS
MCTP1	79772	broad.mit.edu	37	5	94050558	94050558	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94050558A>G	uc003kkx.2	-	20	2644	c.2644T>C	c.(2644-2646)TAT>CAT	p.Y882H	MCTP1_uc003kkv.2_Missense_Mutation_p.Y661H|MCTP1_uc003kkw.2_Missense_Mutation_p.Y575H|MCTP1_uc003kku.2_Missense_Mutation_p.Y398H	NM_024717	NP_078993	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1 isoform L	882					calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(2)	2		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		TGGATGGCATAGATTTTATTT	0.378													18	83	---	---	---	---	PASS
PAM	5066	broad.mit.edu	37	5	102363902	102363902	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102363902A>T	uc003knw.2	+	24	3076	c.2703A>T	c.(2701-2703)AAA>AAT	p.K901N	PAM_uc003kns.2_Missense_Mutation_p.K794N|PAM_uc003knt.2_Missense_Mutation_p.K902N|PAM_uc003knu.2_Missense_Mutation_p.K833N|PAM_uc003knv.2_Intron|PAM_uc011cuz.1_Missense_Mutation_p.K803N|PAM_uc003knz.2_Intron	NM_000919	NP_000910	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	901	Cytoplasmic (Potential).				peptide metabolic process|protein modification process	extracellular region|integral to membrane|stored secretory granule	L-ascorbic acid binding|peptidylamidoglycolate lyase activity|peptidylglycine monooxygenase activity|protein binding				0		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	CTGAACACAAACTCGAGACGA	0.398													27	25	---	---	---	---	PASS
FBN2	2201	broad.mit.edu	37	5	127681162	127681162	+	Missense_Mutation	SNP	G	T	T	rs145565243		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127681162G>T	uc003kuu.2	-	24	3543	c.3104C>A	c.(3103-3105)ACC>AAC	p.T1035N	FBN2_uc003kuv.2_Missense_Mutation_p.T1002N	NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	1035	TB 5.				bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		CTCACACTCGGTGCCCCAAGC	0.602													15	13	---	---	---	---	PASS
SHROOM1	134549	broad.mit.edu	37	5	132158542	132158542	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132158542C>A	uc003kxx.2	-	10	3310	c.2505G>T	c.(2503-2505)CGG>CGT	p.R835R	SHROOM1_uc003kxy.1_Silent_p.R830R	NM_133456	NP_597713	Q2M3G4	SHRM1_HUMAN	shroom family member 1	835					actin filament bundle assembly|cell morphogenesis	cytoplasm|microtubule	actin filament binding			pancreas(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCCCTGGGGGCCGCGCCGGGC	0.647													3	3	---	---	---	---	PASS
PCDHA7	56141	broad.mit.edu	37	5	140215673	140215673	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140215673C>T	uc003lhq.2	+	1	1705	c.1705C>T	c.(1705-1707)CGG>TGG	p.R569W	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.R569W	NM_018910	NP_061733	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7 isoform 1 precursor	569	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)			GCTGGCGCCTCGGGTGGGTGG	0.692													37	41	---	---	---	---	PASS
PCDHB7	56129	broad.mit.edu	37	5	140552867	140552867	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140552867G>T	uc003lit.2	+	1	625	c.451G>T	c.(451-453)GCA>TCA	p.A151S		NM_018940	NP_061763	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7 precursor	151	Extracellular (Potential).|Cadherin 2.				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|central_nervous_system(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCCAGGGGCGGCATTTCTCCT	0.448													28	22	---	---	---	---	PASS
PCDHGB1	56104	broad.mit.edu	37	5	140731747	140731747	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140731747C>A	uc003ljo.1	+	1	1920	c.1920C>A	c.(1918-1920)GTC>GTA	p.V640V	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc011daq.1_Silent_p.V640V	NM_018922	NP_061745	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1 isoform 1	640	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCTGCTGGTCGCTGTGCGTG	0.692													12	13	---	---	---	---	PASS
PCDH1	5097	broad.mit.edu	37	5	141236853	141236853	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141236853C>G	uc003llp.2	-	4	3400	c.3283G>C	c.(3283-3285)GAT>CAT	p.D1095H		NM_032420	NP_115796	Q08174	PCDH1_HUMAN	protocadherin 1 isoform 2 precursor	Error:Variant_position_missing_in_Q08174_after_alignment					cell-cell signaling|homophilic cell adhesion|nervous system development	cell-cell junction|integral to plasma membrane	calcium ion binding			ovary(5)	5		Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;1.06e-05)		ATGCTGCCATCAGGGGTGGTG	0.622													12	10	---	---	---	---	PASS
ABLIM3	22885	broad.mit.edu	37	5	148627474	148627474	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148627474G>C	uc003lpy.2	+	18	1932	c.1681G>C	c.(1681-1683)GAG>CAG	p.E561Q	ABLIM3_uc003lpz.1_Missense_Mutation_p.E561Q|ABLIM3_uc003lqa.1_Missense_Mutation_p.E458Q|ABLIM3_uc003lqb.2_Missense_Mutation_p.E450Q|ABLIM3_uc003lqc.1_Missense_Mutation_p.E528Q|ABLIM3_uc003lqd.1_Missense_Mutation_p.E466Q|ABLIM3_uc003lqf.2_Missense_Mutation_p.E450Q|ABLIM3_uc003lqe.1_Missense_Mutation_p.E450Q	NM_014945	NP_055760	O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3	561					axon guidance|cytoskeleton organization	cytoplasm	actin binding|zinc ion binding			ovary(2)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCTGGCTATGAGATGTCCCT	0.602													14	11	---	---	---	---	PASS
LARP1	23367	broad.mit.edu	37	5	154179144	154179144	+	Intron	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154179144C>T	uc003lvp.2	+						LARP1_uc003lvo.2_Intron|LARP1_uc010jie.1_Intron	NM_033551	NP_291029	Q6PKG0	LARP1_HUMAN	la related protein isoform 2								protein binding|RNA binding			ovary(2)|pancreas(1)|skin(1)	4	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CTTCTCCTCCCCTTCAGGCCC	0.488													26	18	---	---	---	---	PASS
EBF1	1879	broad.mit.edu	37	5	158204441	158204441	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158204441G>T	uc010jip.2	-	10	1318	c.1016C>A	c.(1015-1017)CCA>CAA	p.P339Q	EBF1_uc011ddw.1_Missense_Mutation_p.P207Q|EBF1_uc011ddx.1_Missense_Mutation_p.P340Q|EBF1_uc003lxl.3_Missense_Mutation_p.P308Q	NM_024007	NP_076870	Q9UH73	COE1_HUMAN	early B-cell factor	339	IPT/TIG.				multicellular organismal development	nucleus	DNA binding|metal ion binding		HMGA2/EBF1(2)	soft_tissue(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GAATCTGCCTGGTGTTCCTTT	0.498			T	HMGA2	lipoma								4	72	---	---	---	---	PASS
GABRA6	2559	broad.mit.edu	37	5	161116112	161116112	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161116112A>G	uc003lyu.2	+	4	721	c.383A>G	c.(382-384)AAC>AGC	p.N128S	GABRA6_uc003lyv.2_5'Flank	NM_000811	NP_000802	Q16445	GBRA6_HUMAN	gamma-aminobutyric acid A receptor, alpha 6	128	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity			ovary(7)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	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)		Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	ATTGCTCACAACATGACAACT	0.403										TCGA Ovarian(5;0.080)			16	14	---	---	---	---	PASS
GABRA1	2554	broad.mit.edu	37	5	161324409	161324409	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161324409C>T	uc010jiw.2	+	11	1820	c.1352C>T	c.(1351-1353)GCC>GTC	p.A451V	GABRA1_uc010jix.2_Missense_Mutation_p.A451V|GABRA1_uc010jiy.2_Missense_Mutation_p.A451V|GABRA1_uc003lyx.3_Missense_Mutation_p.A451V|GABRA1_uc010jiz.2_Missense_Mutation_p.A451V|GABRA1_uc010jja.2_Missense_Mutation_p.A451V|GABRA1_uc010jjb.2_Missense_Mutation_p.A451V	NM_000806	NP_000797	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha	451					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			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)	CAGCTAAAAGCCCCCACACCA	0.413													38	56	---	---	---	---	PASS
ODZ2	57451	broad.mit.edu	37	5	167643784	167643784	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167643784G>A	uc010jjd.2	+	22	4063	c.4063G>A	c.(4063-4065)GAC>AAC	p.D1355N	ODZ2_uc003lzr.3_Missense_Mutation_p.D1125N|ODZ2_uc003lzt.3_Missense_Mutation_p.D728N|ODZ2_uc010jje.2_Missense_Mutation_p.D619N	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		TATTGCAGTAGACAAGAATGG	0.517													5	49	---	---	---	---	PASS
SLIT3	6586	broad.mit.edu	37	5	168216618	168216618	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168216618C>T	uc003mab.2	-	11	1446	c.1026G>A	c.(1024-1026)CAG>CAA	p.Q342Q	SLIT3_uc010jjg.2_Silent_p.Q342Q|SLIT3_uc010jji.2_Silent_p.Q342Q|SLIT3_uc003mac.1_Silent_p.Q139Q	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor	342	LRR 8.				apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TATCCGATATCTGATTCTTGC	0.517													8	14	---	---	---	---	PASS
DOCK2	1794	broad.mit.edu	37	5	169506093	169506093	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169506093G>C	uc003maf.2	+	49	5189	c.5109G>C	c.(5107-5109)AAG>AAC	p.K1703N	DOCK2_uc011der.1_RNA|DOCK2_uc010jjm.2_Missense_Mutation_p.K1195N|DOCK2_uc003mah.2_Missense_Mutation_p.K259N	NM_004946	NP_004937	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1703					actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AGAGGACAAAGAGAAGCAGCG	0.587													17	35	---	---	---	---	PASS
BTNL9	153579	broad.mit.edu	37	5	180475279	180475279	+	Intron	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180475279G>T	uc003mmt.2	+						BTNL9_uc011dhi.1_Intron	NM_152547	NP_689760	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9 precursor							integral to membrane				ovary(1)|central_nervous_system(1)	2	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CAGGTGCGTGGACTGACCTAA	0.527													6	21	---	---	---	---	PASS
TRIM7	81786	broad.mit.edu	37	5	180622557	180622557	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180622557G>T	uc003mmz.1	-	7	1212	c.1145C>A	c.(1144-1146)ACC>AAC	p.T382N	TRIM7_uc003mmv.1_Missense_Mutation_p.T200N|TRIM7_uc003mmw.1_Missense_Mutation_p.T174N|TRIM7_uc003mmx.1_Missense_Mutation_p.T174N|TRIM7_uc003mmy.1_Missense_Mutation_p.T174N	NM_203293	NP_976038	Q9C029	TRIM7_HUMAN	tripartite motif-containing 7 isoform 1	382	B30.2/SPRY.					cytoplasm|nucleus	zinc ion binding			ovary(2)|skin(1)	3	all_cancers(89;6.03e-06)|all_epithelial(37;7.1e-07)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000172)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;2e-06)|Epithelial(171;1.35e-05)|OV - Ovarian serous cystadenocarcinoma(192;0.000128)|Kidney(146;0.0674)|GBM - Glioblastoma multiforme(465;0.0802)		GCGGGTGTTGGTGTCGAAGCG	0.701													6	11	---	---	---	---	PASS
F13A1	2162	broad.mit.edu	37	6	6182372	6182372	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6182372G>T	uc003mwv.2	-	11	1431	c.1308C>A	c.(1306-1308)GTC>GTA	p.V436V	F13A1_uc011dib.1_Silent_p.V373V	NM_000129	NP_000120	P00488	F13A_HUMAN	coagulation factor XIII A1 subunit precursor	436					peptide cross-linking|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)|skin(1)	6	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	GGTCGCTGTTGACCTGGAAAC	0.448													8	14	---	---	---	---	PASS
RREB1	6239	broad.mit.edu	37	6	7232080	7232080	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7232080C>T	uc003mxc.2	+	10	4138	c.3748C>T	c.(3748-3750)CAC>TAC	p.H1250Y	RREB1_uc003mxb.2_Missense_Mutation_p.H1250Y|RREB1_uc010jnx.2_Missense_Mutation_p.H1250Y	NM_001003698	NP_001003698	Q92766	RREB1_HUMAN	ras responsive element binding protein 1 isoform	1250	C2H2-type 12.				multicellular organismal development|positive regulation of transcription, DNA-dependent|Ras protein signal transduction|transcription from RNA polymerase II promoter	cytoplasm|nuclear speck	DNA binding|zinc ion binding			ovary(4)|large_intestine(2)|pancreas(2)|skin(2)|breast(1)	11	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				CACCTGTCCCCACTGTCCCCG	0.607													10	15	---	---	---	---	PASS
TFAP2A	7020	broad.mit.edu	37	6	10419691	10419691	+	5'UTR	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10419691C>A	uc003myt.2	-	1					TFAP2A_uc011dii.1_5'UTR	NM_001042425	NP_001035890	P05549	AP2A_HUMAN	transcription factor AP-2 alpha isoform c						ectoderm development|positive regulation of bone mineralization|positive regulation of tooth mineralization|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter	centrosome|Golgi apparatus|nucleus	chromatin binding|protein dimerization activity|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription regulatory region DNA binding			ovary(1)	1	Breast(50;0.0427)|Ovarian(93;0.0991)	all_hematologic(90;0.107)				CATCGCGGCTCTGCGCTCCTG	0.652													9	24	---	---	---	---	PASS
TMEM14C	51522	broad.mit.edu	37	6	10725208	10725208	+	Nonsense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10725208G>A	uc003mzh.2	+	3	216	c.35G>A	c.(34-36)TGG>TAG	p.W12*	TMEM14C_uc010joq.1_Nonsense_Mutation_p.W12*|TMEM14C_uc003mzi.2_Nonsense_Mutation_p.W12*	NM_016462	NP_057546	Q9P0S9	TM14C_HUMAN	transmembrane protein 14C	12	Helical; (Potential).				heme biosynthetic process	integral to membrane|mitochondrial membrane					0	Ovarian(93;0.107)|Breast(50;0.137)	all_hematologic(90;0.135)	Epithelial(50;0.246)			CCTTTGCATTGGTTTGGCTTT	0.433													43	70	---	---	---	---	PASS
HIVEP1	3096	broad.mit.edu	37	6	12161767	12161767	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12161767G>A	uc003nac.2	+	8	6762	c.6583G>A	c.(6583-6585)GAG>AAG	p.E2195K	HIVEP1_uc011diq.1_RNA	NM_002114	NP_002105	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer	2195					transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				AGACGATGATGAGGACAGCCA	0.473													17	22	---	---	---	---	PASS
NUP153	9972	broad.mit.edu	37	6	17637456	17637456	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17637456C>A	uc003ncd.1	-	16	2592	c.2392G>T	c.(2392-2394)GAG>TAG	p.E798*	NUP153_uc011dje.1_Nonsense_Mutation_p.E829*|NUP153_uc010jpl.1_Nonsense_Mutation_p.E756*	NM_005124	NP_005115	P49790	NU153_HUMAN	nucleoporin 153kDa	798	RanBP2-type 3.				carbohydrate metabolic process|glucose transport|interspecies interaction between organisms|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytoplasm|nuclear membrane|nuclear pore|nucleolus|nucleoplasm	DNA binding|protein binding|transporter activity|zinc ion binding			lung(4)|ovary(2)|breast(2)|skin(1)	9	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)			ACTGAACACTCCCAAGATCCA	0.408													56	76	---	---	---	---	PASS
CDKAL1	54901	broad.mit.edu	37	6	21201499	21201499	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21201499G>A	uc003ndc.1	+	15	1716	c.1542G>A	c.(1540-1542)TTG>TTA	p.L514L	CDKAL1_uc003ndd.1_Silent_p.L514L|CDKAL1_uc003nde.1_Silent_p.L423L|CDKAL1_uc003ndf.1_Intron|CDKAL1_uc003ndg.2_RNA	NM_017774	NP_060244	Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein	514					RNA modification	integral to membrane	4 iron, 4 sulfur cluster binding|metal ion binding|transferase activity			ovary(2)	2	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			TCTCGGGTTTGACAAAGGTAA	0.453													42	59	---	---	---	---	PASS
LRRC16A	55604	broad.mit.edu	37	6	25554286	25554286	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25554286G>A	uc011djw.1	+	28	2930	c.2554G>A	c.(2554-2556)GAA>AAA	p.E852K	LRRC16A_uc010jpx.2_Missense_Mutation_p.E852K|LRRC16A_uc010jpy.2_Missense_Mutation_p.E852K|LRRC16A_uc003nfa.1_Missense_Mutation_p.E206K	NM_017640	NP_060110	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	852					actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4						AATTGTGGATGAAATCCTGGA	0.448													10	17	---	---	---	---	PASS
SLC17A1	6568	broad.mit.edu	37	6	25811931	25811931	+	Nonsense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25811931G>C	uc003nfh.3	-	9	1081	c.965C>G	c.(964-966)TCA>TGA	p.S322*	SLC17A1_uc011djy.1_RNA|SLC17A1_uc010jqb.1_Nonsense_Mutation_p.S320*|SLC17A1_uc010jqc.1_Nonsense_Mutation_p.S266*	NM_005074	NP_005065	Q14916	NPT1_HUMAN	solute carrier family 17 (sodium phosphate),	322					sodium ion transport|urate metabolic process	integral to plasma membrane|membrane fraction	sodium-dependent phosphate transmembrane transporter activity|symporter activity			ovary(3)|pancreas(1)	4						GAAGAAGTCTGATAACTGACC	0.448													5	90	---	---	---	---	PASS
HIST1H3D	8351	broad.mit.edu	37	6	26197084	26197084	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26197084C>A	uc003ngv.2	-	2	792	c.395G>T	c.(394-396)CGT>CTT	p.R132L	HIST1H2BF_uc003ngx.2_5'Flank	NM_003530	NP_003521	P68431	H31_HUMAN	histone cluster 1, H3d	132					blood coagulation|nucleosome assembly|regulation of gene silencing|S phase	nucleoplasm|nucleosome	DNA binding|protein binding				0		all_hematologic(11;0.196)				CCTCTCCCCACGAATGCGGCG	0.507													25	86	---	---	---	---	PASS
HIST1H1D	3007	broad.mit.edu	37	6	26234618	26234618	+	Nonsense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26234618G>A	uc003nhd.2	-	1	599	c.544C>T	c.(544-546)CAG>TAG	p.Q182*		NM_005320	NP_005311	P16402	H13_HUMAN	histone cluster 1, H1d	182					nucleosome assembly	nucleosome|nucleus	DNA binding			skin(1)	1		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				TTTTTTGGCTGAGGTGTTTTC	0.502													40	57	---	---	---	---	PASS
BTN2A2	10385	broad.mit.edu	37	6	26393166	26393166	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26393166C>T	uc003nhq.2	+	8	1629	c.1543C>T	c.(1543-1545)CAC>TAC	p.H515Y	BTN2A2_uc011dkg.1_3'UTR|BTN2A2_uc003nhr.2_Missense_Mutation_p.H399Y|BTN2A2_uc011dkh.1_Missense_Mutation_p.H305Y|BTN2A2_uc003nhs.2_Intron|BTN2A2_uc003nht.2_Missense_Mutation_p.H515Y|BTN2A2_uc011dki.1_3'UTR	NM_006995	NP_008926	Q8WVV5	BT2A2_HUMAN	butyrophilin, subfamily 2, member A2 isoform a	515	Cytoplasmic (Potential).				negative regulation of activated T cell proliferation|negative regulation of cellular metabolic process|negative regulation of cytokine secretion	integral to membrane					0						CCTGAAACTTCACAGAGTGGG	0.572													52	49	---	---	---	---	PASS
BTN3A3	10384	broad.mit.edu	37	6	26444514	26444514	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26444514G>T	uc003nhz.2	+	4	595	c.415G>T	c.(415-417)GTG>TTG	p.V139L	BTN3A3_uc003nia.2_Missense_Mutation_p.V97L|BTN3A3_uc011dkn.1_Missense_Mutation_p.V97L	NM_006994	NP_008925	O00478	BT3A3_HUMAN	butyrophilin, subfamily 3, member A3 isoform a	139	Extracellular (Potential).|Ig-like V-type 1.					integral to membrane					0						AAAAGCCCTGGTGGAGCTGAA	0.488													23	118	---	---	---	---	PASS
BTN3A3	10384	broad.mit.edu	37	6	26445991	26445991	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26445991G>T	uc003nhz.2	+	5	673	c.493G>T	c.(493-495)GAG>TAG	p.E165*	BTN3A3_uc003nia.2_Nonsense_Mutation_p.E123*|BTN3A3_uc011dkn.1_Nonsense_Mutation_p.E123*	NM_006994	NP_008925	O00478	BT3A3_HUMAN	butyrophilin, subfamily 3, member A3 isoform a	165	Extracellular (Potential).|Ig-like V-type 2.					integral to membrane					0						GATCCATCTGGAGTGCAGGTC	0.507													7	77	---	---	---	---	PASS
HIST1H1B	3009	broad.mit.edu	37	6	27834802	27834802	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27834802T>A	uc003njx.2	-	1	558	c.506A>T	c.(505-507)AAG>ATG	p.K169M		NM_005322	NP_005313	P16401	H15_HUMAN	histone cluster 1, H1b	169					nucleosome assembly	nucleosome|nucleus	DNA binding			large_intestine(2)|lung(1)	3						CTTCGCCACCTTTTTGACGCC	0.597													53	37	---	---	---	---	PASS
HIST1H4L	8368	broad.mit.edu	37	6	27841265	27841265	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27841265C>G	uc003njz.2	-	1	25	c.24G>C	c.(22-24)GGG>GGC	p.G8G	HIST1H3I_uc003njy.2_5'Flank	NM_003546	NP_003537	P62805	H4_HUMAN	histone cluster 1, H4l	8					CenH3-containing nucleosome assembly at centromere|negative regulation of megakaryocyte differentiation|phosphatidylinositol-mediated signaling|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(1)|breast(1)	2						CCAGACccttcccgcctttgc	0.448													7	46	---	---	---	---	PASS
ZNF165	7718	broad.mit.edu	37	6	28053318	28053318	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28053318G>A	uc003nkg.2	+	3	1144	c.60G>A	c.(58-60)CTG>CTA	p.L20L	ZNF165_uc003nkh.2_Silent_p.L20L|ZNF165_uc003nki.3_Silent_p.L20L	NM_003447	NP_003438	P49910	ZN165_HUMAN	zinc finger protein 165	20					viral reproduction	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						AAGGACTTCTGATAGTGAAGA	0.448													56	163	---	---	---	---	PASS
OR2B3	442184	broad.mit.edu	37	6	29054912	29054912	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29054912G>C	uc003nlx.2	-	1	179	c.114C>G	c.(112-114)ACC>ACG	p.T38T		NM_001005226	NP_001005226			olfactory receptor, family 2, subfamily B,											skin(1)	1						TGCCAAATATGGTGATTGTGT	0.408													16	59	---	---	---	---	PASS
OR5V1	81696	broad.mit.edu	37	6	29323495	29323495	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29323495T>C	uc011dlo.1	-	1	560	c.478A>G	c.(478-480)ACA>GCA	p.T160A		NM_030876	NP_110503	Q9UGF6	OR5V1_HUMAN	olfactory receptor, family 5, subfamily V,	160	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|kidney(1)	4						GTCAACACTGTATGCACCACT	0.443													43	90	---	---	---	---	PASS
OR11A1	26531	broad.mit.edu	37	6	29395013	29395013	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29395013G>T	uc003nmg.2	-	1	497	c.406C>A	c.(406-408)CTG>ATG	p.L136M		NM_013937	NP_039225	Q9GZK7	O11A1_HUMAN	olfactory receptor, family 11, subfamily A,	136	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						GGCCCCATCAGGAGTGGGTAG	0.562													38	12	---	---	---	---	PASS
UBD	10537	broad.mit.edu	37	6	29524035	29524035	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29524035C>G	uc003nmo.2	-	2	344	c.120G>C	c.(118-120)AAG>AAC	p.K40N	GABBR1_uc003nmp.3_3'UTR	NM_006398	NP_006389	O15205	UBD_HUMAN	ubiquitin D	40	Ubiquitin 1.				aggresome assembly|myeloid dendritic cell differentiation|negative regulation of mitotic prometaphase|positive regulation of apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein ubiquitination|response to interferon-gamma|response to tumor necrosis factor|ubiquitin-dependent protein catabolic process	aggresome|cytoplasm|nucleus	proteasome binding				0						GAACCTTGGTCTTAGACCGGA	0.473													26	26	---	---	---	---	PASS
MOG	4340	broad.mit.edu	37	6	29627135	29627135	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29627135C>T	uc003nnf.2	+	2	306	c.128C>T	c.(127-129)GCT>GTT	p.A43V	MOG_uc003qzk.1_Missense_Mutation_p.A43V|MOG_uc010kle.1_Intron|MOG_uc010klf.1_Intron|MOG_uc003nmy.1_Missense_Mutation_p.A43V|MOG_uc003nmz.2_Missense_Mutation_p.A43V|MOG_uc011dlt.1_5'UTR|MOG_uc003nna.2_Intron|MOG_uc011dlu.1_Intron|MOG_uc011dlv.1_Intron|MOG_uc003nnd.2_Missense_Mutation_p.A43V|MOG_uc003nne.2_Missense_Mutation_p.A43V|MOG_uc003nng.2_Missense_Mutation_p.A43V|MOG_uc003nnh.2_Missense_Mutation_p.A43V|MOG_uc003nni.2_Missense_Mutation_p.A43V|MOG_uc003nnj.2_Missense_Mutation_p.A43V|MOG_uc003nnk.2_Missense_Mutation_p.A43V	NM_206809	NP_996532	Q16653	MOG_HUMAN	myelin oligodendrocyte glycoprotein isoform	43	Ig-like V-type.|Extracellular (Potential).				cell adhesion|central nervous system development|positive regulation of MyD88-dependent toll-like receptor signaling pathway	integral to membrane|plasma membrane				ovary(1)	1						CCTATCCGGGCTCTGGTCGGG	0.557													55	168	---	---	---	---	PASS
TNXB	7148	broad.mit.edu	37	6	32017776	32017776	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32017776C>G	uc003nzl.2	-	27	9634	c.9432G>C	c.(9430-9432)ACG>ACC	p.T3144T		NM_019105	NP_061978	P22105	TENX_HUMAN	tenascin XB isoform 1 precursor	3191					actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding				0						TTCACTCACCCGTCACCCCAA	0.602													6	71	---	---	---	---	PASS
HLA-DRB5	3127	broad.mit.edu	37	6	32497990	32497990	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32497990C>G	uc003obj.2	-	1	17	c.12G>C	c.(10-12)CTG>CTC	p.L4L	HLA-DRB1_uc011dqa.1_Intron|HLA-DRB5_uc003obk.3_Intron	NM_002125	NP_002116	Q30154	DRB5_HUMAN	major histocompatibility complex, class II, DR	4					antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0						CAGGGAGCTTCAGACACACCA	0.567													13	142	---	---	---	---	PASS
ZBTB22	9278	broad.mit.edu	37	6	33284035	33284035	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33284035G>T	uc003oeb.2	-	2	811	c.659C>A	c.(658-660)TCC>TAC	p.S220Y	TAPBP_uc003odx.1_5'Flank|TAPBP_uc010jus.1_5'Flank|TAPBP_uc003ody.2_5'Flank|TAPBP_uc003odz.2_5'Flank|TAPBP_uc010jut.1_5'Flank|TAPBP_uc011drc.1_5'Flank|ZBTB22_uc010juu.2_Missense_Mutation_p.S220Y	NM_005453	NP_005444	O15209	ZBT22_HUMAN	zinc finger and BTB domain containing 22	220					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						CTCTTGGGAGGAAGATGAGAA	0.617													8	53	---	---	---	---	PASS
ITPR3	3710	broad.mit.edu	37	6	33641418	33641418	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33641418C>G	uc011drk.1	+	23	3198	c.2979C>G	c.(2977-2979)GTC>GTG	p.V993V		NM_002224	NP_002215	Q14573	ITPR3_HUMAN	inositol 1,4,5-triphosphate receptor, type 3	993	Cytoplasmic (Potential).				activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding			ovary(6)|lung(5)|central_nervous_system(5)|breast(2)|kidney(1)	19						TGCTGTCTGTCTTCAAGAAGG	0.552													86	74	---	---	---	---	PASS
FTSJD2	23070	broad.mit.edu	37	6	37430598	37430598	+	Intron	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37430598C>T	uc003ons.2	+							NM_015050	NP_055865	Q8N1G2	MTR1_HUMAN	FtsJ methyltransferase domain containing 2						mRNA capping	cytoplasm|nucleus	mRNA (nucleoside-2'-O-)-methyltransferase activity|nucleic acid binding			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5						AGAGTATCTTCTGCCAGGTAT	0.502													25	14	---	---	---	---	PASS
LRFN2	57497	broad.mit.edu	37	6	40399677	40399677	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40399677G>T	uc003oph.1	-	2	1641	c.1176C>A	c.(1174-1176)CCC>CCA	p.P392P		NM_020737	NP_065788	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III	392	Extracellular (Potential).					cell junction|integral to membrane|postsynaptic membrane				ovary(2)|skin(1)	3	Ovarian(28;0.0418)|Colorectal(47;0.196)					GGCGGGACTTGGGGGGTGCAG	0.672													4	16	---	---	---	---	PASS
ABCC10	89845	broad.mit.edu	37	6	43403589	43403589	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43403589G>A	uc003ouy.1	+	5	1924	c.1709G>A	c.(1708-1710)CGG>CAG	p.R570Q	ABCC10_uc003ouz.1_Missense_Mutation_p.R527Q|ABCC10_uc010jyo.1_5'UTR	NM_033450	NP_258261	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C, member 10	570						integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(6)|central_nervous_system(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			TCCTTGGACCGGATCCAGCTT	0.567													13	71	---	---	---	---	PASS
YIPF3	25844	broad.mit.edu	37	6	43480033	43480033	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43480033C>A	uc003ovl.1	-	9	1082	c.925G>T	c.(925-927)GGC>TGC	p.G309C	C6orf154_uc003ovk.1_5'Flank|YIPF3_uc011dvk.1_Missense_Mutation_p.G274C|YIPF3_uc010jyr.1_Missense_Mutation_p.G315C|YIPF3_uc010jys.1_Missense_Mutation_p.G152C|YIPF3_uc003ovm.1_Missense_Mutation_p.G183C|YIPF3_uc010jyt.1_Missense_Mutation_p.G220C	NM_015388	NP_056203	Q9GZM5	YIPF3_HUMAN	natural killer cell-specific antigen KLIP1	309					cell differentiation	integral to membrane|plasma membrane|transport vesicle					0	all_cancers(18;3.79e-05)|Lung NSC(15;0.00217)|all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00736)|OV - Ovarian serous cystadenocarcinoma(102;0.0711)			ATGTTGGGGCCCTCCAGTGTG	0.612													41	37	---	---	---	---	PASS
TDRD6	221400	broad.mit.edu	37	6	46656656	46656656	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46656656G>T	uc003oyj.2	+	1	791	c.791G>T	c.(790-792)CGC>CTC	p.R264L	TDRD6_uc010jze.2_Missense_Mutation_p.R258L	NM_001010870	NP_001010870	O60522	TDRD6_HUMAN	tudor domain containing 6	264					cell differentiation|multicellular organismal development|spermatogenesis	chromatoid body	nucleic acid binding			breast(3)|ovary(2)|skin(1)	6			Lung(136;0.192)			CATCCCCACCGCATTCACTGC	0.622													5	27	---	---	---	---	PASS
C6orf138	442213	broad.mit.edu	37	6	47846520	47846520	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47846520C>G	uc011dwm.1	-	3	2094	c.2009G>C	c.(2008-2010)TGG>TCG	p.W670S	C6orf138_uc011dwn.1_Missense_Mutation_p.W434S	NM_001013732	NP_001013754	Q6ZW05	CF138_HUMAN	hypothetical protein LOC442213	687	Helical; (Potential).					integral to membrane	hedgehog receptor activity			central_nervous_system(1)	1						AAGAATTAGCCAGAAGTTTCC	0.458													13	131	---	---	---	---	PASS
C6orf138	442213	broad.mit.edu	37	6	47847511	47847511	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47847511G>T	uc011dwm.1	-	3	1103	c.1018C>A	c.(1018-1020)CCA>ACA	p.P340T	C6orf138_uc011dwn.1_Missense_Mutation_p.P104T	NM_001013732	NP_001013754	Q6ZW05	CF138_HUMAN	hypothetical protein LOC442213	357	SSD.					integral to membrane	hedgehog receptor activity			central_nervous_system(1)	1						TTTGTGAATGGGCTGGCACCC	0.453													28	43	---	---	---	---	PASS
DEFB110	245913	broad.mit.edu	37	6	49986761	49986761	+	Nonsense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49986761G>A	uc003pac.2	-	2	179	c.133C>T	c.(133-135)CAG>TAG	p.Q45*	DEFB110_uc011dwr.1_Intron	NM_001037497	NP_001032586	Q30KQ9	DB110_HUMAN	beta-defensin 110 isoform a	45					defense response to bacterium	extracellular region				ovary(1)	1	Lung NSC(77;0.042)					TCATGACACTGATTTTTACAT	0.398													39	58	---	---	---	---	PASS
PKHD1	5314	broad.mit.edu	37	6	51799118	51799118	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51799118C>T	uc003pah.1	-	37	6187	c.5911G>A	c.(5911-5913)GGC>AGC	p.G1971S	PKHD1_uc010jzn.1_5'UTR|PKHD1_uc003pai.2_Missense_Mutation_p.G1971S	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	1971	Extracellular (Potential).|G8 1.		G -> D (in ARPKD).		cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					ATCAGCTTGCCCCCTAATGGA	0.498											OREG0017491	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	71	---	---	---	---	PASS
ELOVL5	60481	broad.mit.edu	37	6	53135398	53135398	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53135398T>A	uc003pbq.1	-	7	1197	c.749A>T	c.(748-750)TAC>TTC	p.Y250F	ELOVL5_uc003pbr.1_Missense_Mutation_p.Y250F|ELOVL5_uc011dwx.1_Missense_Mutation_p.Y277F|ELOVL5_uc003pbs.1_Silent_p.L208L|ELOVL5_uc003pbt.3_RNA	NM_021814	NP_068586	Q9NYP7	ELOV5_HUMAN	elongation of very long chain fatty acids-like	250				YFGATLNSFIHVLMYSYYGLSSVPSMRPYLWWKKYITQGQL LQFVLTIIQTSCGVIWPCTFPLGWLYFQIGYMISLIALFTN FYIQTYNKKGASRR -> SVCADNHPDQLRGHLAVHIPSWL VVFPDWIHDFPDCSLHKLLHSDLQQERGLPKERPPEGPPEW VHGCCEWTHQQLFTPGKQCEAKEAAEGLKSKN (in Ref. 4; BAD93035).	fatty acid elongation, monounsaturated fatty acid|fatty acid elongation, polyunsaturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	fatty acid elongase activity|protein binding				0	Lung NSC(77;0.116)					TACCTGAATGTAGAAGTTTGT	0.403													5	56	---	---	---	---	PASS
ELOVL5	60481	broad.mit.edu	37	6	53160466	53160466	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53160466T>C	uc003pbq.1	-	2	480	c.32A>G	c.(31-33)TAT>TGT	p.Y11C	ELOVL5_uc003pbr.1_Missense_Mutation_p.Y11C|ELOVL5_uc011dwx.1_Missense_Mutation_p.Y11C|ELOVL5_uc003pbs.1_Missense_Mutation_p.Y11C|ELOVL5_uc003pbu.2_Missense_Mutation_p.Y11C|ELOVL5_uc011dwy.1_RNA	NM_021814	NP_068586	Q9NYP7	ELOV5_HUMAN	elongation of very long chain fatty acids-like	11					fatty acid elongation, monounsaturated fatty acid|fatty acid elongation, polyunsaturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	fatty acid elongase activity|protein binding				0	Lung NSC(77;0.116)					TGCCTTGAAATAGGTACTAAG	0.353													6	39	---	---	---	---	PASS
GFRAL	389400	broad.mit.edu	37	6	55196525	55196525	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55196525G>T	uc003pcm.1	+	2	121	c.35G>T	c.(34-36)AGC>ATC	p.S12I		NM_207410	NP_997293	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like precursor	12						integral to membrane	receptor activity			ovary(1)|breast(1)	2	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			ATGGGGTTAAGCTTGGAAAAT	0.323													37	47	---	---	---	---	PASS
GFRAL	389400	broad.mit.edu	37	6	55264069	55264069	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55264069C>T	uc003pcm.1	+	7	1130	c.1044C>T	c.(1042-1044)TTC>TTT	p.F348F		NM_207410	NP_997293	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like precursor	348	Extracellular (Potential).					integral to membrane	receptor activity			ovary(1)|breast(1)	2	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			ATTCCCCCTTCAATGGTCAGT	0.299													10	12	---	---	---	---	PASS
BMP5	653	broad.mit.edu	37	6	55623910	55623910	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55623910A>G	uc003pcq.2	-	6	1820	c.1108T>C	c.(1108-1110)TGG>CGG	p.W370R	BMP5_uc011dxf.1_Intron	NM_021073	NP_066551	P22003	BMP5_HUMAN	bone morphogenetic protein 5 preproprotein	370					cartilage development|cell differentiation|growth|ossification	extracellular space	BMP receptor binding|cytokine activity|growth factor activity			ovary(2)	2	Lung NSC(77;0.0462)		LUSC - Lung squamous cell carcinoma(124;0.181)			GCTATAATCCAGTCCTGacac	0.249													6	63	---	---	---	---	PASS
DST	667	broad.mit.edu	37	6	56484526	56484526	+	Intron	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56484526G>A	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron|DST_uc003pdb.2_Intron|DST_uc003pdc.3_Nonsense_Mutation_p.Q1436*	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CTGAGTTGTTGAGAATACCCT	0.408													18	131	---	---	---	---	PASS
KIAA1586	57691	broad.mit.edu	37	6	56918885	56918885	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56918885A>G	uc003pdj.2	+	4	1758	c.1588A>G	c.(1588-1590)ATT>GTT	p.I530V	KIAA1586_uc011dxm.1_Missense_Mutation_p.I503V	NM_020931	NP_065982	Q9HCI6	K1586_HUMAN	hypothetical protein LOC57691	530							nucleic acid binding				0	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			TGCTTTAATGATTGACATTCT	0.313													21	48	---	---	---	---	PASS
EYS	346007	broad.mit.edu	37	6	66112499	66112499	+	Splice_Site	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66112499C>A	uc011dxu.1	-	7	1595	c.1057_splice	c.e7-1	p.D353_splice	EYS_uc003peq.2_Splice_Site_p.D353_splice|EYS_uc003per.1_Splice_Site_p.D353_splice	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						ACATAACATCCTAGGAAAGAT	0.303													5	24	---	---	---	---	PASS
COL19A1	1310	broad.mit.edu	37	6	70778345	70778345	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70778345C>A	uc003pfc.1	+	15	1318	c.1201C>A	c.(1201-1203)CCA>ACA	p.P401T	COL19A1_uc010kam.1_Missense_Mutation_p.P297T	NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor	401	Triple-helical region 2 (COL2).				cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4						CCCCCAAGGTCCACCTGGAAA	0.438													20	28	---	---	---	---	PASS
RIMS1	22999	broad.mit.edu	37	6	72968823	72968823	+	Intron	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72968823C>A	uc003pga.2	+						RIMS1_uc011dyb.1_Intron|RIMS1_uc003pgc.2_Intron|RIMS1_uc010kaq.2_Intron|RIMS1_uc011dyc.1_Intron|RIMS1_uc010kar.2_Intron|RIMS1_uc011dyd.1_Intron|RIMS1_uc003pgf.2_Intron|RIMS1_uc003pgg.2_Intron|RIMS1_uc003pgi.2_Intron|RIMS1_uc003pgh.2_Intron|RIMS1_uc003pgd.2_Intron|RIMS1_uc003pge.2_Intron|RIMS1_uc011dye.1_Intron|RIMS1_uc011dyf.1_5'Flank|RIMS1_uc003pgb.3_Intron|RIMS1_uc010kas.1_Intron	NM_014989	NP_055804	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1						calcium ion-dependent exocytosis|cellular membrane fusion|glutamate secretion|intracellular protein transport|protein complex assembly|regulated secretory pathway|response to stimulus|synaptic vesicle exocytosis|visual perception	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(7)|pancreas(2)|breast(1)	10		all_epithelial(107;0.179)|all_hematologic(105;0.212)				AGGTATTTGTCAAAATTATGA	0.348													15	40	---	---	---	---	PASS
COL12A1	1303	broad.mit.edu	37	6	75857502	75857502	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75857502C>T	uc003phs.2	-	23	4472	c.4306G>A	c.(4306-4308)GAA>AAA	p.E1436K	COL12A1_uc003pht.2_Missense_Mutation_p.E272K	NM_004370	NP_004361	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1 long isoform	1436	Fibronectin type-III 9.				cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)|skin(1)	9						GTGCTAGTTTCCATTCGACTC	0.373													43	52	---	---	---	---	PASS
TBX18	9096	broad.mit.edu	37	6	85448296	85448296	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85448296C>T	uc003pkl.1	-	7	1018	c.1018G>A	c.(1018-1020)GCC>ACC	p.A340T	TBX18_uc010kbq.1_Missense_Mutation_p.A182T	NM_001080508	NP_001073977	O95935	TBX18_HUMAN	T-box 18	340					multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|pancreas(2)|lung(1)	5		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		TCCACCAAGGCTTCCAAACCC	0.453													44	118	---	---	---	---	PASS
C6orf165	154313	broad.mit.edu	37	6	88144698	88144698	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88144698C>A	uc003plv.2	+	11	1513	c.1421C>A	c.(1420-1422)GCC>GAC	p.A474D	SLC35A1_uc003plx.2_5'Flank|C6orf165_uc003plw.2_Missense_Mutation_p.A286D|C6orf165_uc010kbv.1_RNA|C6orf165_uc003plu.1_Missense_Mutation_p.A474D	NM_001031743	NP_001026913	Q8IYR0	CF165_HUMAN	hypothetical protein LOC154313 isoform 1	474										central_nervous_system(1)	1		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		AGAGAAAAGGCCAAAAAAAAT	0.269													11	38	---	---	---	---	PASS
MDN1	23195	broad.mit.edu	37	6	90472117	90472117	+	Silent	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90472117T>C	uc003pnn.1	-	16	2393	c.2277A>G	c.(2275-2277)AAA>AAG	p.K759K	MDN1_uc003pno.1_Silent_p.K177K	NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	759					protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CATGCCACCGTTTCTGTCTGT	0.453													32	78	---	---	---	---	PASS
MDN1	23195	broad.mit.edu	37	6	90482321	90482321	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90482321G>C	uc003pnn.1	-	14	2170	c.2054C>G	c.(2053-2055)TCT>TGT	p.S685C	MDN1_uc003pno.1_Missense_Mutation_p.S103C	NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	685					protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TTGGATGGTAGAGGTTTTGCC	0.473													36	74	---	---	---	---	PASS
MDN1	23195	broad.mit.edu	37	6	90482391	90482391	+	Nonsense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90482391G>A	uc003pnn.1	-	14	2100	c.1984C>T	c.(1984-1986)CAG>TAG	p.Q662*	MDN1_uc003pno.1_Nonsense_Mutation_p.Q80*	NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	662					protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		ACTGCAAGCTGCTCGATGAGA	0.517													41	85	---	---	---	---	PASS
GJA10	84694	broad.mit.edu	37	6	90605460	90605460	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90605460C>T	uc011eaa.1	+	1	1273	c.1273C>T	c.(1273-1275)CCA>TCA	p.P425S		NM_032602	NP_115991	Q969M2	CXA10_HUMAN	gap junction protein, alpha 10	425	Cytoplasmic (Potential).				synaptic transmission	connexon complex|integral to membrane	gap junction channel activity				0		all_cancers(76;5.71e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.0915)		CAGATCTCGCCCAGGCAGTCG	0.532													14	56	---	---	---	---	PASS
EPHA7	2045	broad.mit.edu	37	6	93964367	93964367	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93964367C>G	uc003poe.2	-	14	2771	c.2530G>C	c.(2530-2532)GAT>CAT	p.D844H	EPHA7_uc003pof.2_Missense_Mutation_p.D839H|EPHA7_uc011eac.1_Missense_Mutation_p.D840H	NM_004440	NP_004431	Q15375	EPHA7_HUMAN	ephrin receptor EphA7 precursor	844	Cytoplasmic (Potential).|Protein kinase.					integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|ovary(7)|upper_aerodigestive_tract(3)|central_nervous_system(3)|skin(3)|large_intestine(2)|stomach(1)|pancreas(1)	28		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		ACACCTACATCTTGATTTGAC	0.358													11	19	---	---	---	---	PASS
KLHL32	114792	broad.mit.edu	37	6	97489367	97489367	+	Splice_Site	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97489367G>T	uc010kcm.1	+	4	677	c.205_splice	c.e4-1	p.A69_splice	KLHL32_uc003poy.2_Splice_Site_p.A69_splice|KLHL32_uc011ead.1_Intron|KLHL32_uc003poz.2_Splice_Site|KLHL32_uc011eae.1_Intron|KLHL32_uc003ppa.2_Splice_Site	NM_052904	NP_443136	Q96NJ5	KLH32_HUMAN	kelch-like 32											ovary(3)|skin(1)	4		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		CCTCACCTCAGGCAATGTTCA	0.428													15	48	---	---	---	---	PASS
SIM1	6492	broad.mit.edu	37	6	100838631	100838631	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100838631C>G	uc003pqj.3	-	11	2114	c.1907G>C	c.(1906-1908)AGA>ACA	p.R636T	SIM1_uc010kcu.2_Missense_Mutation_p.R636T	NM_005068	NP_005059	P81133	SIM1_HUMAN	single-minded homolog 1	636	Single-minded C-terminal.				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(4)	4		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		TTTTCCCTCTCTCTGCTGGAT	0.488													44	107	---	---	---	---	PASS
LIN28B	389421	broad.mit.edu	37	6	105526586	105526586	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105526586C>A	uc003pqv.1	+	4	884	c.681C>A	c.(679-681)TCC>TCA	p.S227S	LIN28B_uc010kda.1_3'UTR	NM_001004317	NP_001004317	Q6ZN17	LN28B_HUMAN	lin-28 homolog B	227					miRNA catabolic process|pre-miRNA processing|regulation of transcription, DNA-dependent|RNA 3'-end processing	cytoplasm|nucleus	DNA binding|protein binding|RNA binding|zinc ion binding				0		all_cancers(87;0.00346)|Acute lymphoblastic leukemia(125;2.26e-08)|all_hematologic(75;2.79e-06)|all_epithelial(87;0.204)				AAGCTTCCTCCACGAAGTCAT	0.483													10	48	---	---	---	---	PASS
AIM1	202	broad.mit.edu	37	6	106989163	106989163	+	Intron	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106989163C>G	uc003prh.2	+						AIM1_uc003pri.2_Nonsense_Mutation_p.S9*	NM_001624	NP_001615	Q9Y4K1	AIM1_HUMAN	absent in melanoma 1								sugar binding			breast(4)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)	9	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		actgctttttcaagagaagta	0.080													3	8	---	---	---	---	PASS
LAMA4	3910	broad.mit.edu	37	6	112451158	112451158	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112451158C>G	uc003pvu.2	-	30	4362	c.4053G>C	c.(4051-4053)AAG>AAC	p.K1351N	LAMA4_uc003pvv.2_Missense_Mutation_p.K1344N|LAMA4_uc003pvt.2_Missense_Mutation_p.K1344N	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor	1351	Laminin G-like 3.				cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		AGTAAAACTTCTTTTCACTTG	0.358													4	21	---	---	---	---	PASS
RSPH4A	345895	broad.mit.edu	37	6	116948888	116948888	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116948888G>A	uc003pxe.2	+	3	1163	c.1018G>A	c.(1018-1020)GCC>ACC	p.A340T	RSPH4A_uc010kee.2_Missense_Mutation_p.A340T	NM_001010892	NP_001010892	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A isoform 1	340					cilium axoneme assembly|cilium movement	cytoplasm|cytoskeleton|radial spoke					0						CATATTTCTTGCCCTCAAGCA	0.438									Kartagener_syndrome				30	67	---	---	---	---	PASS
TRDN	10345	broad.mit.edu	37	6	123892185	123892185	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123892185C>A	uc003pzj.1	-	2	137	c.115G>T	c.(115-117)GAC>TAC	p.D39Y	TRDN_uc003pzk.1_Missense_Mutation_p.D39Y|TRDN_uc003pzl.1_Missense_Mutation_p.D39Y|TRDN_uc010ken.2_Missense_Mutation_p.D39Y|TRDN_uc010keo.1_Missense_Mutation_p.D39Y	NM_006073	NP_006064	Q13061	TRDN_HUMAN	triadin	39	Cytoplasmic.				muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)		GTCACTATGTCTTCTGTGACT	0.473													20	45	---	---	---	---	PASS
LAMA2	3908	broad.mit.edu	37	6	129674308	129674308	+	Splice_Site	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129674308G>T	uc003qbn.2	+	32	4629	c.4524_splice	c.e32-1	p.R1508_splice	LAMA2_uc003qbo.2_Splice_Site_p.R1508_splice	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor						cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		TTTCAATTCAGGTGTGCCCCT	0.483													5	18	---	---	---	---	PASS
MAP3K5	4217	broad.mit.edu	37	6	136888770	136888770	+	Nonsense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136888770T>A	uc003qhc.2	-	26	4121	c.3760A>T	c.(3760-3762)AGA>TGA	p.R1254*	MAP3K5_uc011edj.1_Nonsense_Mutation_p.R501*|MAP3K5_uc011edk.1_Nonsense_Mutation_p.R1100*	NM_005923	NP_005914	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase	1254					activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		AGGACTTACCTATTGGTTTCT	0.423													16	26	---	---	---	---	PASS
TNFAIP3	7128	broad.mit.edu	37	6	138198379	138198379	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138198379C>T	uc003qhr.2	+	6	1038	c.972C>T	c.(970-972)CTC>CTT	p.L324L	TNFAIP3_uc003qhs.2_Silent_p.L324L	NM_006290	NP_006281	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	324	2 X approximate repeats.|2.				anti-apoptosis|apoptosis|B-1 B cell homeostasis|negative regulation of B cell activation|negative regulation of bone resorption|negative regulation of CD40 signaling pathway|negative regulation of endothelial cell apoptosis|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of inflammatory response|negative regulation of interleukin-2 production|negative regulation of interleukin-6 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of osteoclast proliferation|negative regulation of protein ubiquitination|negative regulation of smooth muscle cell proliferation|negative regulation of toll-like receptor 2 signaling pathway|negative regulation of toll-like receptor 3 signaling pathway|negative regulation of tumor necrosis factor production|negative regulation of type I interferon production|positive regulation of protein catabolic process|protein K48-linked ubiquitination|protein K63-linked deubiquitination|protein oligomerization|regulation of defense response to virus by host|regulation of germinal center formation|regulation of vascular wound healing|tolerance induction to lipopolysaccharide	centrosome|cytosol|nucleus	caspase inhibitor activity|DNA binding|protease binding|protein self-association|ubiquitin binding|ubiquitin thiolesterase activity|ubiquitin-protein ligase activity|ubiquitin-specific protease activity|zinc ion binding	p.0?(22)|p.L324fs*7(1)		haematopoietic_and_lymphoid_tissue(133)|lung(3)|ovary(1)	137	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		CAACTCATCTCATCAATGCCG	0.463			D|N|F		marginal zone B-cell lymphomas|Hodgkin's lymphoma|primary mediastinal B cell lymphoma								20	42	---	---	---	---	PASS
UTRN	7402	broad.mit.edu	37	6	144820427	144820427	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144820427C>A	uc003qkt.2	+	33	4720	c.4628C>A	c.(4627-4629)TCA>TAA	p.S1543*		NM_007124	NP_009055	P46939	UTRO_HUMAN	utrophin	1543	Interaction with SYNM.				muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		GAAAGAGCATCACAGTTGGCC	0.463													14	46	---	---	---	---	PASS
GRM1	2911	broad.mit.edu	37	6	146720825	146720825	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146720825G>C	uc010khw.1	+	8	3120	c.2650G>C	c.(2650-2652)GGG>CGG	p.G884R	GRM1_uc010khv.1_Missense_Mutation_p.G884R|GRM1_uc003qll.2_Missense_Mutation_p.G884R|GRM1_uc011edz.1_Missense_Mutation_p.G884R|GRM1_uc011eea.1_Missense_Mutation_p.G884R	NM_000838	NP_000829	Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1 isoform alpha	884	Cytoplasmic (Potential).				synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(8)|ovary(4)|central_nervous_system(3)|large_intestine(2)|breast(2)	19		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)	GGCAGGGGCAGGGAATGCCAA	0.353													5	26	---	---	---	---	PASS
PLEKHG1	57480	broad.mit.edu	37	6	151107545	151107545	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151107545G>T	uc003qny.1	+	5	844	c.532G>T	c.(532-534)GAA>TAA	p.E178*	PLEKHG1_uc011eel.1_Nonsense_Mutation_p.E218*|PLEKHG1_uc011eem.1_Nonsense_Mutation_p.E237*|PLEKHG1_uc003qnz.2_Nonsense_Mutation_p.E178*	NM_001029884	NP_001025055	Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G	178	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)		GCAAGATTTGGAAAACTGTGA	0.378													19	31	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152782735	152782735	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152782735G>T	uc010kiw.2	-	21	2993	c.2391C>A	c.(2389-2391)ACC>ACA	p.T797T	SYNE1_uc003qot.3_Silent_p.T804T|SYNE1_uc003qou.3_Silent_p.T797T|SYNE1_uc010kjb.1_Silent_p.T780T|SYNE1_uc003qow.2_Silent_p.T92T|SYNE1_uc003qox.1_Silent_p.T313T|SYNE1_uc003qoz.2_Silent_p.T229T|SYNE1_uc003qoy.2_Silent_p.T364T	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	797	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TTCGCACCTTGGTTAGCTGCT	0.433										HNSCC(10;0.0054)			4	69	---	---	---	---	PASS
NOX3	50508	broad.mit.edu	37	6	155761279	155761279	+	Intron	SNP	A	C	C	rs140898590	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155761279A>C	uc003qqm.2	-							NM_015718	NP_056533	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3								electron carrier activity|flavin adenine dinucleotide binding|iron ion binding			ovary(1)	1		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		GTTCTaaaaaaaacaacaaca	0.323													13	34	---	---	---	---	PASS
FNDC1	84624	broad.mit.edu	37	6	159687195	159687195	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159687195G>T	uc010kjv.2	+	21	5564	c.5364G>T	c.(5362-5364)AAG>AAT	p.K1788N		NM_032532	NP_115921	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1788						extracellular region				large_intestine(4)|ovary(3)|central_nervous_system(1)	8		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		AATATGTGAAGCGCACGTGGT	0.468													34	92	---	---	---	---	PASS
AGPAT4	56895	broad.mit.edu	37	6	161574454	161574454	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161574454C>A	uc003qtr.1	-	5	815	c.588G>T	c.(586-588)GGG>GGT	p.G196G	AGPAT4_uc003qts.1_Silent_p.G56G|AGPAT4_uc011egb.1_Intron|AGPAT4_uc003qtt.1_RNA|AGPAT4_uc011egc.1_3'UTR|AGPAT4_uc011egd.1_3'UTR|AGPAT4_uc011ege.1_3'UTR	NM_020133	NP_064518	Q9NRZ5	PLCD_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 4	196					phospholipid biosynthetic process	integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity|protein binding				0		Breast(66;0.000289)|Ovarian(120;0.0266)|Prostate(117;0.0285)		OV - Ovarian serous cystadenocarcinoma(65;2.23e-17)|BRCA - Breast invasive adenocarcinoma(81;3.58e-05)		GGCGAGGCAGCCCCTTGGCCC	0.587													4	9	---	---	---	---	PASS
PACRG	135138	broad.mit.edu	37	6	163483209	163483209	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163483209C>A	uc003qua.2	+	4	543	c.319C>A	c.(319-321)CAT>AAT	p.H107N	PACRG_uc003qub.2_Missense_Mutation_p.H107N|PACRG_uc003quc.2_Missense_Mutation_p.H107N	NM_152410	NP_689623	Q96M98	PACRG_HUMAN	parkin co-regulated gene protein isoform 1	107											0		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)		GGATTACCATCATTATCTGCC	0.453													16	41	---	---	---	---	PASS
TTLL2	83887	broad.mit.edu	37	6	167753790	167753790	+	Silent	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167753790A>G	uc003qvs.1	+	3	490	c.402A>G	c.(400-402)GAA>GAG	p.E134E	TTLL2_uc011egr.1_RNA	NM_031949	NP_114155	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	134	TTL.				protein modification process		ATP binding|tubulin-tyrosine ligase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		GAATGACCGAACACAACAGTG	0.527													13	24	---	---	---	---	PASS
THBS2	7058	broad.mit.edu	37	6	169646362	169646362	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169646362G>A	uc003qwt.2	-	5	872	c.624C>T	c.(622-624)AAC>AAT	p.N208N		NM_003247	NP_003238	P35442	TSP2_HUMAN	thrombospondin 2 precursor	208	TSP N-terminal.|Heparin-binding (Potential).				cell adhesion	extracellular region	calcium ion binding|heparin binding|protein binding|structural molecule activity			ovary(5)	5		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		CTAGGTGGACGTTCTGAAGCA	0.388													10	53	---	---	---	---	PASS
THBS2	7058	broad.mit.edu	37	6	169649011	169649011	+	Missense_Mutation	SNP	C	T	T	rs150716666		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169649011C>T	uc003qwt.2	-	4	358	c.110G>A	c.(109-111)CGC>CAC	p.R37H		NM_003247	NP_003238	P35442	TSP2_HUMAN	thrombospondin 2 precursor	37	TSP N-terminal.|Heparin-binding (Potential).				cell adhesion	extracellular region	calcium ion binding|heparin binding|protein binding|structural molecule activity			ovary(5)	5		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		AATGGTCTTGCGGTTGATGTT	0.592													6	25	---	---	---	---	PASS
NUDT1	4521	broad.mit.edu	37	7	2284214	2284214	+	Missense_Mutation	SNP	G	C	C	rs144573336		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2284214G>C	uc003slp.1	+	3	176	c.74G>C	c.(73-75)GGC>GCC	p.G25A	FTSJ2_uc003slk.2_5'Flank|FTSJ2_uc003sll.2_5'Flank|FTSJ2_uc003slm.2_5'Flank|FTSJ2_uc003sln.2_5'Flank|FTSJ2_uc003slo.2_5'Flank|NUDT1_uc003slq.1_Missense_Mutation_p.G2A|NUDT1_uc003slr.1_Missense_Mutation_p.G2A|NUDT1_uc003sls.1_Missense_Mutation_p.G25A|NUDT1_uc003slt.1_Missense_Mutation_p.G2A|NUDT1_uc003slu.1_Missense_Mutation_p.G25A|NUDT1_uc003slv.1_Missense_Mutation_p.G2A	NM_198949	NP_945187	P36639	8ODP_HUMAN	nudix-type motif 1 isoform p22	43					DNA protection|DNA repair|response to oxidative stress	cytoplasm	8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity|8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity|GTPase activity|metal ion binding|protein binding				0		Ovarian(82;0.0253)|Melanoma(862;0.155)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0822)|OV - Ovarian serous cystadenocarcinoma(56;2.8e-14)|BRCA - Breast invasive adenocarcinoma(126;0.15)		GGGACCATGGGCGCCTCCAGG	0.632								Direct_reversal_of_damage|Modulation_of_nucleotide_pools					8	62	---	---	---	---	PASS
SDK1	221935	broad.mit.edu	37	7	3991404	3991404	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3991404G>T	uc003smx.2	+	7	1141	c.1002G>T	c.(1000-1002)GTG>GTT	p.V334V		NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor	334	Ig-like C2-type 3.				cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GGAATGGAGTGAGAATCACCA	0.607													11	53	---	---	---	---	PASS
SDK1	221935	broad.mit.edu	37	7	4169740	4169740	+	Intron	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4169740G>A	uc003smx.2	+						SDK1_uc010kso.2_Intron|SDK1_uc003smy.2_Intron	NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor						cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GTAGGTCCAGGGTTCGCGCCT	0.552													7	26	---	---	---	---	PASS
TNRC18	84629	broad.mit.edu	37	7	5396915	5396915	+	Intron	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5396915G>A	uc003soi.3	-						TNRC18_uc003soj.2_5'Flank	NM_001080495	NP_001073964	O15417	TNC18_HUMAN	trinucleotide repeat containing 18								DNA binding				0		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		TAGCTGGAGAGGGAAGGTGGG	0.338													4	28	---	---	---	---	PASS
PMS2	5395	broad.mit.edu	37	7	6027050	6027050	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6027050T>C	uc003spl.2	-	11	1433	c.1346A>G	c.(1345-1347)CAG>CGG	p.Q449R	PMS2_uc003spj.2_Missense_Mutation_p.Q343R|PMS2_uc003spk.2_Missense_Mutation_p.Q314R|PMS2_uc011jwl.1_Missense_Mutation_p.Q314R|PMS2_uc010ktg.2_Missense_Mutation_p.Q138R|PMS2_uc010kte.2_Intron|PMS2_uc010ktf.1_Missense_Mutation_p.Q449R	NM_000535	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 isoform	449					mismatch repair|reciprocal meiotic recombination|somatic hypermutation of immunoglobulin genes	MutLalpha complex	ATP binding|ATPase activity|endonuclease activity|protein binding|single base insertion or deletion binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		ACCCCTTTTCTGTCCTAGAGG	0.522			Mis|N|F			colorectal|endometrial|ovarian|medulloblastoma|glioma		Direct_reversal_of_damage|MMR	Lynch_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				25	63	---	---	---	---	PASS
PMS2	5395	broad.mit.edu	37	7	6048643	6048643	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6048643C>T	uc003spl.2	-	1	95	c.8G>A	c.(7-9)CGA>CAA	p.R3Q	PMS2_uc003spk.2_5'UTR|PMS2_uc011jwl.1_5'UTR|PMS2_uc010ktg.2_5'UTR|PMS2_uc010kte.2_Missense_Mutation_p.R3Q|PMS2_uc010ktf.1_Missense_Mutation_p.R3Q|AIMP2_uc003spo.2_5'Flank	NM_000535	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 isoform	3					mismatch repair|reciprocal meiotic recombination|somatic hypermutation of immunoglobulin genes	MutLalpha complex	ATP binding|ATPase activity|endonuclease activity|protein binding|single base insertion or deletion binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		GCTCTCAGCTCGCTCCATGGA	0.647			Mis|N|F			colorectal|endometrial|ovarian|medulloblastoma|glioma		Direct_reversal_of_damage|MMR	Lynch_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				17	44	---	---	---	---	PASS
ICA1	3382	broad.mit.edu	37	7	8167699	8167699	+	Missense_Mutation	SNP	C	G	G	rs144420664		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8167699C>G	uc003srm.2	-	13	1201	c.1134G>C	c.(1132-1134)GAG>GAC	p.E378D	ICA1_uc010ktr.2_Missense_Mutation_p.E407D|ICA1_uc003srl.2_Missense_Mutation_p.E366D|ICA1_uc003srn.3_Missense_Mutation_p.E304D|ICA1_uc003srp.3_Missense_Mutation_p.E377D|ICA1_uc010kts.2_RNA|ICA1_uc003srq.2_Missense_Mutation_p.E378D|ICA1_uc003srr.2_Missense_Mutation_p.E377D|ICA1_uc003sro.3_Missense_Mutation_p.E378D	NM_022307	NP_071682	Q05084	ICA69_HUMAN	islet cell autoantigen 1	378					neurotransmitter transport	cell junction|cytosol|Golgi membrane|nucleus|secretory granule membrane|synaptic vesicle membrane|transport vesicle membrane				central_nervous_system(1)	1		Ovarian(82;0.0612)		UCEC - Uterine corpus endometrioid carcinoma (126;0.246)		CATTGAAGATCTCACTCAACA	0.552													46	181	---	---	---	---	PASS
PHF14	9678	broad.mit.edu	37	7	11022091	11022091	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11022091G>T	uc003sry.1	+	3	640	c.205G>T	c.(205-207)GAA>TAA	p.E69*	PHF14_uc011jxi.1_Intron|PHF14_uc003srz.2_Nonsense_Mutation_p.E69*|PHF14_uc011jxj.1_Intron	NM_014660	NP_055475	O94880	PHF14_HUMAN	PHD finger protein 14 isoform 2	69	Glu/Lys-rich.						zinc ion binding			kidney(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)		TTTAGAAGAAGAACTGAATGA	0.318													23	24	---	---	---	---	PASS
PHF14	9678	broad.mit.edu	37	7	11078410	11078410	+	Silent	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11078410A>G	uc003sry.1	+	11	2439	c.2004A>G	c.(2002-2004)CTA>CTG	p.L668L	PHF14_uc011jxi.1_Silent_p.L383L|PHF14_uc003srz.2_Silent_p.L668L|PHF14_uc011jxj.1_Silent_p.L383L	NM_014660	NP_055475	O94880	PHF14_HUMAN	PHD finger protein 14 isoform 2	668							zinc ion binding			kidney(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)		TAGAAGAACTACAAAACCTGA	0.343													9	30	---	---	---	---	PASS
SNX13	23161	broad.mit.edu	37	7	17930043	17930043	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17930043G>C	uc003stw.1	-	5	596	c.383C>G	c.(382-384)TCT>TGT	p.S128C	SNX13_uc003stv.2_Missense_Mutation_p.S128C|SNX13_uc010kuc.2_Translation_Start_Site|SNX13_uc003stx.1_Missense_Mutation_p.S48C|SNX13_uc003sty.2_Missense_Mutation_p.S128C			Q9Y5W8	SNX13_HUMAN	SubName: Full=Putative uncharacterized protein SNX13; SubName: Full=Sorting nexin 13, isoform CRA_g;	128	PXA.				cell communication|intracellular protein transport|negative regulation of signal transduction|positive regulation of GTPase activity	early endosome membrane	phosphatidylinositol binding|signal transducer activity			central_nervous_system(2)|kidney(1)	3	Lung NSC(10;0.0261)|all_lung(11;0.0521)					AAGAAGAAAAGATTCATCATC	0.318													25	59	---	---	---	---	PASS
PRPS1L1	221823	broad.mit.edu	37	7	18066588	18066588	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18066588T>A	uc003stz.2	-	1	899	c.818A>T	c.(817-819)AAT>ATT	p.N273I		NM_175886	NP_787082	P21108	PRPS3_HUMAN	phosphoribosyl pyrophosphate synthetase 1-like	273					nucleoside metabolic process|ribonucleoside monophosphate biosynthetic process		ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity			ovary(1)	1	Lung NSC(10;0.0385)|all_lung(11;0.0736)					AGGTATGGTATTGGTGACTAC	0.438													41	151	---	---	---	---	PASS
HDAC9	9734	broad.mit.edu	37	7	18687398	18687398	+	Intron	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18687398C>A	uc003suh.2	+						HDAC9_uc003sue.2_Intron|HDAC9_uc011jyd.1_Intron|HDAC9_uc003sui.2_Intron|HDAC9_uc003suj.2_Intron|HDAC9_uc011jya.1_Intron|HDAC9_uc003sua.1_Intron|HDAC9_uc011jyb.1_Intron|HDAC9_uc003sud.1_Intron|HDAC9_uc011jyc.1_Intron|HDAC9_uc003suf.1_Intron|HDAC9_uc010kud.1_Intron|HDAC9_uc011jye.1_Intron|HDAC9_uc011jyf.1_Intron|HDAC9_uc010kue.1_Intron	NM_058176	NP_478056	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9 isoform 1						B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)	TTTGTTATTTCTCAACACAGG	0.458													19	17	---	---	---	---	PASS
HDAC9	9734	broad.mit.edu	37	7	18705919	18705919	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18705919G>C	uc003suh.2	+	11	1583	c.1542G>C	c.(1540-1542)GCG>GCC	p.A514A	HDAC9_uc003sue.2_Silent_p.A514A|HDAC9_uc011jyd.1_Silent_p.A514A|HDAC9_uc003sui.2_Silent_p.A517A|HDAC9_uc003suj.2_Silent_p.A473A|HDAC9_uc011jya.1_Silent_p.A511A|HDAC9_uc003sua.1_Silent_p.A492A|HDAC9_uc011jyb.1_Silent_p.A470A|HDAC9_uc003sud.1_Silent_p.A514A|HDAC9_uc011jyc.1_Silent_p.A473A|HDAC9_uc003suf.1_Silent_p.A545A|HDAC9_uc010kud.1_Silent_p.A517A|HDAC9_uc011jye.1_Silent_p.A486A|HDAC9_uc011jyf.1_Silent_p.A437A|HDAC9_uc010kue.1_Intron	NM_058176	NP_478056	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9 isoform 1	514					B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)	GGGACCAGGCGATGCAGGAAG	0.532											OREG0017877	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	31	102	---	---	---	---	PASS
ABCB5	340273	broad.mit.edu	37	7	20691164	20691164	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20691164G>T	uc003suw.3	+	4	665	c.119G>T	c.(118-120)GGA>GTA	p.G40V	ABCB5_uc010kuh.2_Missense_Mutation_p.G485V|ABCB5_uc003suv.3_Missense_Mutation_p.G40V|ABCB5_uc011jyi.1_Missense_Mutation_p.G40V	NM_178559	NP_848654	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B, member 5	40	ABC transporter 1.|Extracellular (Potential).				regulation of membrane potential	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus	ATP binding|ATPase activity, coupled to transmembrane movement of substances|efflux transmembrane transporter activity			skin(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|pancreas(1)	6						ATCAAGTATGGACGAGATGAT	0.433													9	164	---	---	---	---	PASS
ABCB5	340273	broad.mit.edu	37	7	20784959	20784959	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20784959G>A	uc003suw.3	+	17	2538	c.1992G>A	c.(1990-1992)GAG>GAA	p.E664E	ABCB5_uc010kuh.2_Silent_p.E1109E	NM_178559	NP_848654	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B, member 5	664	Cytoplasmic (Potential).|ABC transporter 2.				regulation of membrane potential	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus	ATP binding|ATPase activity, coupled to transmembrane movement of substances|efflux transmembrane transporter activity			skin(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|pancreas(1)	6						GCATTGCTGAGAACATCGCCT	0.458													20	91	---	---	---	---	PASS
SP4	6671	broad.mit.edu	37	7	21468913	21468913	+	Nonsense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21468913C>T	uc003sva.2	+	3	311	c.130C>T	c.(130-132)CAG>TAG	p.Q44*	SP4_uc003svb.2_Intron	NM_003112	NP_003103	Q02446	SP4_HUMAN	Sp4 transcription factor	44					regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(3)|skin(2)	5						GTAGGACTCTCAGCCCTCTCC	0.483													13	25	---	---	---	---	PASS
DNAH11	8701	broad.mit.edu	37	7	21639594	21639594	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21639594C>T	uc003svc.2	+	15	2888	c.2857C>T	c.(2857-2859)CCT>TCT	p.P953S		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	953	Stem (By similarity).				microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15						CTTGTTGCCTCCTGAGATTGT	0.398									Kartagener_syndrome				10	78	---	---	---	---	PASS
TRA2A	29896	broad.mit.edu	37	7	23561452	23561452	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23561452C>T	uc003swi.2	-	2	258	c.44G>A	c.(43-45)CGC>CAC	p.R15H	TRA2A_uc011jzb.1_RNA|TRA2A_uc011jzc.1_5'UTR|TRA2A_uc011jzd.1_5'UTR|TRA2A_uc010kuo.1_RNA	NM_013293	NP_037425	Q13595	TRA2A_HUMAN	transformer-2 alpha	15					nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|RNA binding			ovary(1)	1						TGACTGAGAGCGAGACTCCTA	0.423													44	57	---	---	---	---	PASS
HOXA3	3200	broad.mit.edu	37	7	27148264	27148264	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27148264G>C	uc011jzl.1	-	3	802	c.602C>G	c.(601-603)GCG>GGG	p.A201G	HOXA3_uc011jzk.1_Missense_Mutation_p.A43G|HOXA3_uc003syk.2_Missense_Mutation_p.A201G	NM_030661	NP_109377	O43365	HXA3_HUMAN	homeobox A3 isoform a	201	Homeobox.				angiogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(2)	2						CACCAGCTGCGCGCTCGTGTA	0.667													10	53	---	---	---	---	PASS
MIR196B	442920	broad.mit.edu	37	7	27209158	27209158	+	RNA	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27209158G>A	hsa-mir-196b|MI0001150	-			c.25G>A																				0						CCAACAACAGGAAACTACCTA	0.473											OREG0003744	type=REGULATORY REGION|Gene=HOXA9|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	9	23	---	---	---	---	PASS
ADCYAP1R1	117	broad.mit.edu	37	7	31104555	31104555	+	Intron	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31104555G>C	uc003tca.1	+						ADCYAP1R1_uc003tcb.1_Intron|ADCYAP1R1_uc003tcc.1_Intron|ADCYAP1R1_uc003tcd.1_Intron|ADCYAP1R1_uc003tce.1_Intron	NM_001118	NP_001109	P41586	PACR_HUMAN	adenylate cyclase activating polypeptide 1						activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|spermatogenesis	integral to plasma membrane	vasoactive intestinal polypeptide receptor activity			ovary(1)	1						CTCTCCAGGTGAGCGGGGCGG	0.552													6	17	---	---	---	---	PASS
PDE1C	5137	broad.mit.edu	37	7	31864492	31864492	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31864492C>A	uc003tcm.1	-	13	1864	c.1395G>T	c.(1393-1395)CAG>CAT	p.Q465H	PDE1C_uc003tcn.1_Missense_Mutation_p.Q465H|PDE1C_uc003tco.1_Missense_Mutation_p.Q525H|PDE1C_uc003tcr.2_Missense_Mutation_p.Q465H|PDE1C_uc003tcs.2_Missense_Mutation_p.Q465H	NM_005020	NP_005011	Q14123	PDE1C_HUMAN	phosphodiesterase 1C	465	Catalytic (By similarity).				activation of phospholipase C activity|nerve growth factor receptor signaling pathway	cytosol	calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(3)|central_nervous_system(1)	4			GBM - Glioblastoma multiforme(11;0.216)			TCGAACGCCTCTGTCCTGTCC	0.507													31	102	---	---	---	---	PASS
BMPER	168667	broad.mit.edu	37	7	34097706	34097706	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34097706C>A	uc011kap.1	+	10	1077	c.963C>A	c.(961-963)ATC>ATA	p.I321I		NM_133468	NP_597725	Q8N8U9	BMPER_HUMAN	BMP-binding endothelial regulator precursor	321	VWFC 5.				blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3						ATTGTACCATCTGTGCTTGTG	0.502													13	39	---	---	---	---	PASS
BMPER	168667	broad.mit.edu	37	7	34182965	34182965	+	Silent	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34182965T>C	uc011kap.1	+	14	1983	c.1869T>C	c.(1867-1869)AAT>AAC	p.N623N		NM_133468	NP_597725	Q8N8U9	BMPER_HUMAN	BMP-binding endothelial regulator precursor	623					blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3						CTCAGCAGAATTGTGCAGGTA	0.488													11	42	---	---	---	---	PASS
AMPH	273	broad.mit.edu	37	7	38516551	38516551	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38516551T>A	uc003tgu.2	-	6	484	c.415A>T	c.(415-417)AGC>TGC	p.S139C	AMPH_uc003tgv.2_Missense_Mutation_p.S139C	NM_001635	NP_001626	P49418	AMPH_HUMAN	amphiphysin isoform 1	139	BAR.				endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)|skin(1)	5						AGCTTCCTGCTGCGCTTGGCG	0.502													15	45	---	---	---	---	PASS
POU6F2	11281	broad.mit.edu	37	7	39243867	39243867	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39243867G>T	uc003thb.1	+	3	266	c.224G>T	c.(223-225)GGC>GTC	p.G75V	POU6F2_uc010kxo.2_Missense_Mutation_p.G67V	NM_007252	NP_009183	P78424	PO6F2_HUMAN	POU class 6 homeobox 2 isoform 1	75					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						TCAGACCCAGGCACTCCTGAC	0.493													15	34	---	---	---	---	PASS
GLI3	2737	broad.mit.edu	37	7	42004165	42004165	+	Silent	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42004165T>A	uc011kbh.1	-	15	4597	c.4506A>T	c.(4504-4506)GTA>GTT	p.V1502V	GLI3_uc011kbg.1_Silent_p.V1443V	NM_000168	NP_000159	P10071	GLI3_HUMAN	GLI-Kruppel family member GLI3	1502	Asp/Glu-rich (acidic).				negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1)	19						AGTCAATCTGTACCCCTTCCA	0.542									Greig_Cephalopolysyndactyly|Pallister-Hall_syndrome				9	33	---	---	---	---	PASS
GLI3	2737	broad.mit.edu	37	7	42063099	42063099	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42063099T>A	uc011kbh.1	-	10	1556	c.1465A>T	c.(1465-1467)AGG>TGG	p.R489W	GLI3_uc011kbg.1_Missense_Mutation_p.R430W	NM_000168	NP_000159	P10071	GLI3_HUMAN	GLI-Kruppel family member GLI3	489	C2H2-type 1.				negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1)	19						TCGAACTCCCTCGCGCAGCCT	0.527									Greig_Cephalopolysyndactyly|Pallister-Hall_syndrome				8	41	---	---	---	---	PASS
MRPL32	64983	broad.mit.edu	37	7	42976962	42976962	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42976962G>T	uc003tia.2	+	3	401	c.354G>T	c.(352-354)CAG>CAT	p.Q118H	MRPL32_uc003tib.2_RNA|MRPL32_uc003tic.2_Missense_Mutation_p.Q65H	NM_031903	NP_114109	Q9BYC8	RM32_HUMAN	mitochondrial ribosomal protein L32 precursor	118					translation	large ribosomal subunit|mitochondrial ribosome	structural constituent of ribosome				0						ACCTGAAACAGAAACATGTCC	0.403													17	73	---	---	---	---	PASS
GCK	2645	broad.mit.edu	37	7	44184789	44184789	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44184789G>T	uc003tkl.2	-	10	1814	c.1344C>A	c.(1342-1344)GGC>GGA	p.G448G	GCK_uc003tkh.1_Silent_p.G121G|GCK_uc003tki.1_Silent_p.G126G|GCK_uc003tkj.1_Silent_p.G447G|GCK_uc003tkk.1_Silent_p.G449G	NM_000162	NP_000153	P35557	HXK4_HUMAN	glucokinase isoform 1	448					cellular response to insulin stimulus|cellular response to leptin stimulus|detection of glucose|endocrine pancreas development|glucose homeostasis|glucose transport|glycolysis|negative regulation of gluconeogenesis|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|regulation of glucose transport|regulation of glycolysis|transmembrane transport	cytosol|nucleoplasm	ATP binding|glucokinase activity|glucose binding|protein binding			skin(3)|lung(1)	4						CCAGGGCCGCGCCCCGGCCAC	0.672													4	10	---	---	---	---	PASS
NPC1L1	29881	broad.mit.edu	37	7	44556302	44556302	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44556302C>A	uc003tlb.2	-	17	3656	c.3600G>T	c.(3598-3600)TCG>TCT	p.S1200S	NPC1L1_uc003tlc.2_Silent_p.S1173S|NPC1L1_uc011kbw.1_Silent_p.S1127S|NPC1L1_uc003tla.2_Intron	NM_013389	NP_037521	Q9UHC9	NPCL1_HUMAN	Niemann-Pick C1-like protein 1 isoform 1	1200	Helical; Name=12; (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)	GCTGGGTTACCGAGACCAGGT	0.498													3	14	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48314472	48314472	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48314472A>G	uc003toq.2	+	17	5234	c.5209A>G	c.(5209-5211)AAA>GAA	p.K1737E	ABCA13_uc010kyr.2_Missense_Mutation_p.K1240E	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	1737					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						CCTGTTTCCTAAAGATGTTGT	0.438													19	55	---	---	---	---	PASS
ZPBP	11055	broad.mit.edu	37	7	50070681	50070681	+	Intron	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50070681G>C	uc003tou.2	-						ZPBP_uc011kci.1_Intron|ZPBP_uc010kyw.2_Intron	NM_007009	NP_008940	Q9BS86	ZPBP1_HUMAN	zona pellucida binding protein isoform 1						binding of sperm to zona pellucida	extracellular region					0	Glioma(55;0.08)|all_neural(89;0.245)					AAATTGTATAGACTTACCTGA	0.299													6	59	---	---	---	---	PASS
EGFR	1956	broad.mit.edu	37	7	55233016	55233016	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55233016C>T	uc003tqk.2	+	15	2012	c.1766C>T	c.(1765-1767)CCC>CTC	p.P589L	EGFR_uc003tqi.2_Missense_Mutation_p.P589L|EGFR_uc003tqj.2_Missense_Mutation_p.P589L|EGFR_uc010kzg.1_Missense_Mutation_p.P544L|EGFR_uc011kco.1_Missense_Mutation_p.P536L|EGFR_uc011kcp.1_Intron|EGFR_uc011kcq.1_RNA|EGFR_uc003tqn.2_RNA	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	589	Approximate.|Extracellular (Potential).			DGPH->AGPA: Decreases intramolecular interactions and facilitates EGF binding.	activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)	ATTGACGGCCCCCACTGCGTC	0.532		8	A|O|Mis		glioma|NSCLC	NSCLC			Lung_Cancer_Familial_Clustering_of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			18	214	---	---	---	---	PASS
CHCHD2	51142	broad.mit.edu	37	7	56172045	56172045	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56172045C>T	uc003tsa.2	-	2	255	c.174G>A	c.(172-174)CAG>CAA	p.Q58Q	PSPH_uc003trj.2_Intron	NM_016139	NP_057223	Q9Y6H1	CHCH2_HUMAN	coiled-coil-helix-coiled-coil-helix domain	58						mitochondrion					0	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			TGGTTGCCATCTGGGCCATCA	0.647													24	53	---	---	---	---	PASS
ZNF479	90827	broad.mit.edu	37	7	57188465	57188465	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57188465G>T	uc010kzo.2	-	5	928	c.657C>A	c.(655-657)GGC>GGA	p.G219G		NM_033273	NP_150376	Q96JC4	ZN479_HUMAN	zinc finger protein 479	219	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(1)	4			GBM - Glioblastoma multiforme(1;9.18e-12)			TAAAGGATTTGCCACATTCTT	0.363													9	14	---	---	---	---	PASS
WBSCR17	64409	broad.mit.edu	37	7	70800691	70800691	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70800691C>G	uc003tvy.2	+	2	394	c.394C>G	c.(394-396)CGT>GGT	p.R132G	WBSCR17_uc003tvz.2_5'UTR	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide	132	Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				TTCACTGGACCGTTCCATTCC	0.488													19	23	---	---	---	---	PASS
MAGI2	9863	broad.mit.edu	37	7	78119166	78119166	+	Intron	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78119166A>G	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc010ldx.1_Intron|MAGI2_uc010ldy.1_Intron|MAGI2_uc011kgr.1_Intron|MAGI2_uc011kgs.1_Intron	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				GGCTGAAAAGAAAAGAGATCA	0.368													11	73	---	---	---	---	PASS
GNAI1	2770	broad.mit.edu	37	7	79846649	79846649	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79846649A>G	uc003uhb.1	+	8	1242	c.905A>G	c.(904-906)TAT>TGT	p.Y302C	GNAI1_uc011kgt.1_Missense_Mutation_p.Y250C	NM_002069	NP_002060	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein),	302					cell cycle|cell division|inhibition of adenylate cyclase activity by G-protein signaling pathway|platelet activation|synaptic transmission	centrosome|heterotrimeric G-protein complex|midbody|nucleus	G-protein beta/gamma-subunit complex binding|GTP binding|metabotropic serotonin receptor binding|signal transducer activity			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						GCAGCTGCATATATTCAATGT	0.338													5	50	---	---	---	---	PASS
PCLO	27445	broad.mit.edu	37	7	82784244	82784244	+	Silent	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82784244T>A	uc003uhx.2	-	2	2002	c.1713A>T	c.(1711-1713)ACA>ACT	p.T571T	PCLO_uc003uhv.2_Silent_p.T571T	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	517	Pro-rich.				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						ATGGAGACACTGTTGGTGGCT	0.498													176	133	---	---	---	---	PASS
PCLO	27445	broad.mit.edu	37	7	82784705	82784705	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82784705G>A	uc003uhx.2	-	2	1541	c.1252C>T	c.(1252-1254)CCA>TCA	p.P418S	PCLO_uc003uhv.2_Missense_Mutation_p.P418S	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						AGGGGTTTTGGTGTCCCCACC	0.587													12	124	---	---	---	---	PASS
ABCB4	5244	broad.mit.edu	37	7	87104757	87104757	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87104757C>G	uc003uiv.1	-	2	101	c.25G>C	c.(25-27)GGA>CGA	p.G9R	ABCB4_uc003uiw.1_Missense_Mutation_p.G9R|ABCB4_uc003uix.1_Missense_Mutation_p.G9R|ABCB4_uc003uiy.2_Missense_Mutation_p.G9R	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4	9	Cytoplasmic (By similarity).				cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|skin(1)|pancreas(1)	6	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)					CAGGCTGTTCCGTTCTTTGCC	0.632													5	29	---	---	---	---	PASS
PPP1R9A	55607	broad.mit.edu	37	7	94917904	94917904	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94917904G>T	uc003unp.2	+	15	3240	c.2958G>T	c.(2956-2958)CAG>CAT	p.Q986H	PPP1R9A_uc010lfj.2_Missense_Mutation_p.Q1262H|PPP1R9A_uc011kif.1_Missense_Mutation_p.Q1184H|PPP1R9A_uc003unq.2_Intron|PPP1R9A_uc011kig.1_Missense_Mutation_p.Q978H|PPP1R9A_uc003unr.2_Missense_Mutation_p.Q275H	NM_017650	NP_060120	Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory (inhibitor)	986	Interacts with TGN38 (By similarity).					cell junction|synapse|synaptosome	actin binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)			GGGCCGTTCAGGAATGGAGTG	0.453										HNSCC(28;0.073)			39	38	---	---	---	---	PASS
ZKSCAN5	23660	broad.mit.edu	37	7	99129345	99129345	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99129345G>T	uc003uqv.2	+	7	2117	c.1993G>T	c.(1993-1995)GAA>TAA	p.E665*	ZKSCAN5_uc010lfx.2_Nonsense_Mutation_p.E665*|ZKSCAN5_uc003uqw.2_Nonsense_Mutation_p.E665*|ZKSCAN5_uc003uqx.2_Nonsense_Mutation_p.E592*|ZKSCAN5_uc003uqy.2_Nonsense_Mutation_p.E401*	NM_145102	NP_659570	Q9Y2L8	ZKSC5_HUMAN	zinc finger with KRAB and SCAN domains 5	665	C2H2-type 9.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					TCAGTGTCGTGAATGTGGGGA	0.468													42	41	---	---	---	---	PASS
MOSPD3	64598	broad.mit.edu	37	7	100210858	100210858	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100210858G>C	uc003uvq.2	+	3	449	c.247G>C	c.(247-249)GAG>CAG	p.E83Q	MOSPD3_uc003uvr.2_Missense_Mutation_p.E83Q|MOSPD3_uc003uvs.2_Missense_Mutation_p.E83Q|MOSPD3_uc003uvt.2_Missense_Mutation_p.E83Q	NM_001040097	NP_001035186	O75425	MSPD3_HUMAN	motile sperm domain containing 3 isoform a	83	MSP.					integral to membrane	structural molecule activity			ovary(2)	2	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					GTTTGACGCAGAGGGATATGT	0.567													86	124	---	---	---	---	PASS
ORC5L	5001	broad.mit.edu	37	7	103808925	103808925	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103808925C>T	uc003vcb.2	-	9	984	c.873G>A	c.(871-873)CTG>CTA	p.L291L	ORC5L_uc011klp.1_Silent_p.L159L|ORC5L_uc003vcc.2_Silent_p.L291L	NM_002553	NP_002544	O43913	ORC5_HUMAN	origin recognition complex subunit 5 isoform 1	291					cell cycle checkpoint|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	cytoplasm|nuclear origin of replication recognition complex|nucleoplasm	ATP binding|DNA replication origin binding|identical protein binding				0						TGATACCTTTCAGTTGCCCCG	0.333													32	22	---	---	---	---	PASS
PIK3CG	5294	broad.mit.edu	37	7	106509912	106509912	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106509912T>C	uc003vdv.3	+	2	1991	c.1906T>C	c.(1906-1908)TCA>CCA	p.S636P	PIK3CG_uc003vdu.2_Missense_Mutation_p.S636P|PIK3CG_uc003vdw.2_Missense_Mutation_p.S636P	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	636					G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(16)|central_nervous_system(8)|breast(5)|pancreas(3)|stomach(2)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)	38						CTGCAACTTCTCAGATGAAAA	0.338													9	62	---	---	---	---	PASS
PIK3CG	5294	broad.mit.edu	37	7	106524666	106524666	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106524666G>T	uc003vdv.3	+	9	2912	c.2827G>T	c.(2827-2829)GGA>TGA	p.G943*	PIK3CG_uc003vdu.2_Nonsense_Mutation_p.G943*|PIK3CG_uc003vdw.2_Nonsense_Mutation_p.G943*	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	943	PI3K/PI4K.				G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(16)|central_nervous_system(8)|breast(5)|pancreas(3)|stomach(2)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)	38						CTTTGTTCTTGGAATAGGCGA	0.328													30	60	---	---	---	---	PASS
PIK3CG	5294	broad.mit.edu	37	7	106524667	106524667	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106524667G>T	uc003vdv.3	+	9	2913	c.2828G>T	c.(2827-2829)GGA>GTA	p.G943V	PIK3CG_uc003vdu.2_Missense_Mutation_p.G943V|PIK3CG_uc003vdw.2_Missense_Mutation_p.G943V	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	943	PI3K/PI4K.				G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(16)|central_nervous_system(8)|breast(5)|pancreas(3)|stomach(2)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)	38						TTTGTTCTTGGAATAGGCGAC	0.323													29	62	---	---	---	---	PASS
ST7	7982	broad.mit.edu	37	7	116739905	116739905	+	Intron	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116739905G>T	uc003vin.2	+						ST7_uc011knl.1_Intron|ST7_uc003vio.2_Intron|ST7_uc003viq.2_Intron|ST7_uc011knm.1_Intron|ST7_uc003vir.2_Intron|ST7OT2_uc003viu.2_Intron|ST7_uc011knn.1_Intron	NM_021908	NP_068708	Q9NRC1	ST7_HUMAN	suppression of tumorigenicity 7 isoform b							integral to membrane	binding			central_nervous_system(1)|skin(1)	2	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		TTTGGTAAGTGGTGGAGTCCT	0.274													22	10	---	---	---	---	PASS
AASS	10157	broad.mit.edu	37	7	121726155	121726155	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121726155C>A	uc003vka.2	-	18	2191	c.2095G>T	c.(2095-2097)GGC>TGC	p.G699C	AASS_uc011knu.1_RNA|AASS_uc011knv.1_RNA|AASS_uc003vkb.2_Missense_Mutation_p.G699C|AASS_uc011knw.1_Missense_Mutation_p.G187C	NM_005763	NP_005754	Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase precursor	699	Saccharopine dehydrogenase.				protein tetramerization	mitochondrial matrix	binding|saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity			upper_aerodigestive_tract(1)|ovary(1)	2					L-Glutamic Acid(DB00142)|NADH(DB00157)	TTAGGATAGCCTTCCAAATTT	0.438													23	34	---	---	---	---	PASS
CADPS2	93664	broad.mit.edu	37	7	122111611	122111611	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122111611C>A	uc010lkp.2	-	13	2167	c.2004G>T	c.(2002-2004)TGG>TGT	p.W668C	CADPS2_uc011knx.1_Missense_Mutation_p.W39C|CADPS2_uc003vkg.3_Missense_Mutation_p.W365C|CADPS2_uc010lkq.2_Missense_Mutation_p.W665C	NM_017954	NP_060424	Q86UW7	CAPS2_HUMAN	Ca2+-dependent activator protein for secretion 2	668					exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2						CAGGGCTAAACCATCCCTGCA	0.413													8	11	---	---	---	---	PASS
IMPDH1	3614	broad.mit.edu	37	7	128038584	128038584	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128038584G>A	uc011kol.1	-	7	809	c.703C>T	c.(703-705)CTG>TTG	p.L235L	IMPDH1_uc011kom.1_Silent_p.L230L|IMPDH1_uc003vmt.2_Silent_p.L210L|IMPDH1_uc003vmu.2_Silent_p.L320L|IMPDH1_uc003vmw.2_Silent_p.L310L|IMPDH1_uc011kon.1_Silent_p.L287L|IMPDH1_uc003vmv.2_Silent_p.L284L|IMPDH1_uc003vmx.2_Silent_p.L243L|IMPDH1_uc003vmy.2_Silent_p.L251L	NM_001142573	NP_001136045	P20839	IMDH1_HUMAN	inosine monophosphate dehydrogenase 1 isoform e	235	CBS 2.				GMP biosynthetic process|purine base metabolic process	cytosol|nucleus	DNA binding|IMP dehydrogenase activity|metal ion binding			skin(2)|lung(1)|central_nervous_system(1)	4					Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|NADH(DB00157)|Ribavirin(DB00811)|Thioguanine(DB00352)	TTGGAGGCCAGAGGGTAGTCT	0.597											OREG0018292	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	39	35	---	---	---	---	PASS
IMPDH1	3614	broad.mit.edu	37	7	128041089	128041089	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128041089C>A	uc011kol.1	-	3	335	c.229G>T	c.(229-231)GAC>TAC	p.D77Y	IMPDH1_uc011kom.1_Missense_Mutation_p.D77Y|IMPDH1_uc003vmt.2_Missense_Mutation_p.D77Y|IMPDH1_uc003vmu.2_Missense_Mutation_p.D162Y|IMPDH1_uc003vmw.2_Missense_Mutation_p.D152Y|IMPDH1_uc011kon.1_Missense_Mutation_p.D129Y|IMPDH1_uc003vmv.2_Missense_Mutation_p.D126Y|IMPDH1_uc003vmx.2_Missense_Mutation_p.D85Y|IMPDH1_uc003vmy.2_Missense_Mutation_p.D93Y	NM_001142573	NP_001136045	P20839	IMDH1_HUMAN	inosine monophosphate dehydrogenase 1 isoform e	77					GMP biosynthetic process|purine base metabolic process	cytosol|nucleus	DNA binding|IMP dehydrogenase activity|metal ion binding			skin(2)|lung(1)|central_nervous_system(1)	4					Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|NADH(DB00157)|Ribavirin(DB00811)|Thioguanine(DB00352)	ATGGCCATGTCAGCCTCTGTC	0.612													17	15	---	---	---	---	PASS
PLXNA4	91584	broad.mit.edu	37	7	131872353	131872353	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131872353G>A	uc003vra.3	-	15	3099	c.2870C>T	c.(2869-2871)TCA>TTA	p.S957L		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	957	IPT/TIG 2.|Extracellular (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1						CTTCAGATCTGAGAGAGTCAG	0.607													84	59	---	---	---	---	PASS
CNOT4	4850	broad.mit.edu	37	7	135048770	135048770	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135048770C>A	uc011kpy.1	-	10	1768	c.1676G>T	c.(1675-1677)GGG>GTG	p.G559V	CNOT4_uc003vss.2_Intron|CNOT4_uc011kpz.1_Missense_Mutation_p.G556V|CNOT4_uc003vst.2_Intron	NM_001008225	NP_001008226	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					nuclear-transcribed mRNA poly(A) tail shortening|protein autoubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	nucleotide binding|protein binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding				0						TGCCCTTAGCCCGTCCTGCCA	0.423													12	133	---	---	---	---	PASS
WEE2	494551	broad.mit.edu	37	7	141429329	141429329	+	Splice_Site	SNP	A	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141429329A>C	uc003vwn.2	+	11	1942	c.1536_splice	c.e11-2	p.R512_splice	FLJ40852_uc011krh.1_Intron|FLJ40852_uc010lnm.2_Intron|FLJ40852_uc010lnn.2_Intron|FLJ40852_uc003vwm.3_Intron|FLJ40852_uc010lno.2_Intron	NM_001105558	NP_001099028	P0C1S8	WEE2_HUMAN	WEE1 homolog 2						egg activation|female meiosis|female pronucleus assembly|meiotic metaphase II|meiotic prophase I|mitosis|negative regulation of oocyte development|regulation of meiosis I	centrosome|nucleus	ATP binding|magnesium ion binding|non-membrane spanning protein tyrosine kinase activity|protein serine/threonine kinase activity			ovary(1)|stomach(1)	2	Melanoma(164;0.0171)					CTCGCACTTCAGGGAACTGAG	0.448													14	81	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	142008651	142008651	+	Intron	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142008651T>A	uc011kro.1	+						uc011krp.1_5'Flank|uc003vxf.3_Missense_Mutation_p.C42S					SubName: Full=V_segment translation product; Flags: Fragment;																		GTCCATTAAATGTGAACAAAA	0.388													33	42	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	142223974	142223974	+	Intron	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142223974G>T	uc011krp.1	+						uc011krr.1_Intron|uc011krx.1_Intron|uc011ksa.1_Intron|uc003vyi.2_Missense_Mutation_p.L65M					Homo sapiens mRNA for T cell receptor beta variable 3, partial cds, clone: un 191.																		AATTGAACCAGAAGCTCCGGG	0.488													25	58	---	---	---	---	PASS
OR6V1	346517	broad.mit.edu	37	7	142750136	142750136	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142750136G>T	uc011ksv.1	+	1	699	c.699G>T	c.(697-699)CAG>CAT	p.Q233H		NM_001001667	NP_001001667	Q8N148	OR6V1_HUMAN	olfactory receptor, family 6, subfamily V,	233	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	Melanoma(164;0.059)					GCAGCTGCCAGAAGGCTTTCT	0.552													48	35	---	---	---	---	PASS
TAS2R41	259287	broad.mit.edu	37	7	143175872	143175872	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143175872G>T	uc003wdc.1	+	1	907	c.907G>T	c.(907-909)GGC>TGC	p.G303C	uc003wda.2_Intron	NM_176883	NP_795364	P59536	T2R41_HUMAN	taste receptor, type 2, member 41	303	Cytoplasmic (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity			pancreas(1)|skin(1)	2	Melanoma(164;0.15)					GTTGGCAAGGGGCTTCTGGGT	0.522													16	10	---	---	---	---	PASS
GIMAP1	170575	broad.mit.edu	37	7	150417175	150417175	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150417175G>A	uc003whq.2	+	3	170	c.83G>A	c.(82-84)CGG>CAG	p.R28Q	GIMAP1_uc003whp.2_Missense_Mutation_p.R36Q	NM_130759	NP_570115	Q8WWP7	GIMA1_HUMAN	GTPase, IMAP family member 1	28	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane	GTP binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GAGTCCACGCGGAGGCTCATC	0.557													83	101	---	---	---	---	PASS
ABCF2	10061	broad.mit.edu	37	7	150921165	150921165	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150921165C>T	uc003wjp.2	-	4	514	c.403G>A	c.(403-405)GAA>AAA	p.E135K	ABCF2_uc003wjo.1_Missense_Mutation_p.E135K	NM_007189	NP_009120	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F, member 2	135	ABC transporter 1.					ATP-binding cassette (ABC) transporter complex|mitochondrial envelope	ATP binding|ATPase activity|transporter activity			central_nervous_system(1)	1			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ATGGGCACTTCACGCTTCCCA	0.532													38	25	---	---	---	---	PASS
DPP6	1804	broad.mit.edu	37	7	154564582	154564582	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154564582C>T	uc003wlk.2	+	10	1195	c.1066C>T	c.(1066-1068)CTA>TTA	p.L356L	DPP6_uc003wli.2_Silent_p.L292L|DPP6_uc003wlm.2_Silent_p.L294L|DPP6_uc011kvq.1_Silent_p.L249L	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1	356	Extracellular (Potential).				cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			CAGCATTTCCCTACACGTTAT	0.468													17	27	---	---	---	---	PASS
DPP6	1804	broad.mit.edu	37	7	154564583	154564583	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154564583T>A	uc003wlk.2	+	10	1196	c.1067T>A	c.(1066-1068)CTA>CAA	p.L356Q	DPP6_uc003wli.2_Missense_Mutation_p.L292Q|DPP6_uc003wlm.2_Missense_Mutation_p.L294Q|DPP6_uc011kvq.1_Missense_Mutation_p.L249Q	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1	356	Extracellular (Potential).				cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			AGCATTTCCCTACACGTTATT	0.468													17	27	---	---	---	---	PASS
SHH	6469	broad.mit.edu	37	7	155598997	155598997	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155598997C>T	uc003wmk.1	-	2	706	c.555G>A	c.(553-555)GTG>GTA	p.V185V	SHH_uc003wmh.1_RNA|SHH_uc003wmi.1_Silent_p.V98V|SHH_uc003wmj.1_Silent_p.V98V	NM_000193	NP_000184	Q15465	SHH_HUMAN	sonic hedgehog preproprotein	185					androgen metabolic process|axon guidance|branching involved in ureteric bud morphogenesis|CD4-positive or CD8-positive, alpha-beta T cell lineage commitment|embryonic digit morphogenesis|hindbrain development|intein-mediated protein splicing|lymphoid progenitor cell differentiation|metanephric mesenchymal cell proliferation involved in metanephros development|midbrain development|negative regulation of cell migration|negative regulation of kidney smooth muscle cell differentiation|negative regulation of ureter smooth muscle cell differentiation|negative thymic T cell selection|neural crest cell migration|neuroblast proliferation|patterning of blood vessels|positive regulation of alpha-beta T cell differentiation|positive regulation of immature T cell proliferation in thymus|positive regulation of kidney smooth muscle cell differentiation|positive regulation of mesenchymal cell proliferation involved in ureter development|positive regulation of T cell differentiation in thymus|positive regulation of ureter smooth muscle cell differentiation|positive thymic T cell selection|proteolysis|sclerotome development|stem cell development|thymus development|vasculogenesis|ventral midline development	cell surface|extracellular space|membrane raft|plasma membrane	calcium ion binding|laminin-1 binding|peptidase activity|signal transducer activity|zinc ion binding			central_nervous_system(3)|lung(1)	4	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00882)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TACCTGCTTTCACCGAGCAGT	0.627													7	31	---	---	---	---	PASS
PTPRN2	5799	broad.mit.edu	37	7	157396693	157396693	+	Splice_Site	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157396693C>T	uc003wno.2	-	16	2539	c.2418_splice	c.e16+1	p.I806_splice	PTPRN2_uc003wnp.2_Splice_Site_p.I789_splice|PTPRN2_uc003wnq.2_Splice_Site_p.I777_splice|PTPRN2_uc003wnr.2_Splice_Site_p.I768_splice|PTPRN2_uc011kwa.1_Splice_Site_p.I829_splice	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		AGTGCACTTACGATGGGGCTA	0.627													10	24	---	---	---	---	PASS
DEFA5	1670	broad.mit.edu	37	8	6914043	6914043	+	Intron	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6914043C>A	uc003wra.1	-							NM_021010	NP_066290	Q01523	DEF5_HUMAN	defensin, alpha 5 preproprotein						defense response to bacterium|defense response to fungus|killing of cells of other organism	extracellular space					0				COAD - Colon adenocarcinoma(149;0.0572)|READ - Rectum adenocarcinoma(644;0.121)		ATTGATGTCTCCTACCTGAGG	0.328													25	31	---	---	---	---	PASS
DEFA5	1670	broad.mit.edu	37	8	6914138	6914138	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6914138C>A	uc003wra.1	-	1	122	c.82G>T	c.(82-84)GAG>TAG	p.E28*		NM_021010	NP_066290	Q01523	DEF5_HUMAN	defensin, alpha 5 preproprotein	28					defense response to bacterium|defense response to fungus|killing of cells of other organism	extracellular space					0				COAD - Colon adenocarcinoma(149;0.0572)|READ - Rectum adenocarcinoma(644;0.121)		GTTGTAGCCTCATCAGCTCTT	0.567													22	22	---	---	---	---	PASS
SORBS3	10174	broad.mit.edu	37	8	22421834	22421834	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22421834G>C	uc003xbv.2	+	9	1054	c.714G>C	c.(712-714)ACG>ACC	p.T238T	SORBS3_uc011kzk.1_RNA|SORBS3_uc003xbw.3_5'Flank	NM_005775	NP_005766	O60504	VINEX_HUMAN	sorbin and SH3 domain containing 3 isoform 1	238					muscle contraction|positive regulation of stress fiber assembly	cytoskeleton|cytosol|nucleus	protein binding|structural constituent of cytoskeleton|vinculin binding				0		Prostate(55;0.0421)|Breast(100;0.102)		BRCA - Breast invasive adenocarcinoma(99;0.00566)|Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)		ATGTCTGGACGGAAGAGTCCT	0.582													7	9	---	---	---	---	PASS
FZD3	7976	broad.mit.edu	37	8	28384825	28384825	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28384825G>T	uc003xgx.2	+	5	1026	c.548G>T	c.(547-549)CGT>CTT	p.R183L	FZD3_uc010lvb.2_Missense_Mutation_p.R183L	NM_017412	NP_059108	Q9NPG1	FZD3_HUMAN	frizzled 3 precursor	183	Extracellular (Potential).				canonical Wnt receptor signaling pathway|cell proliferation in midbrain|commissural neuron axon guidance|establishment of planar polarity|facial nucleus development|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|inner ear morphogenesis|neural tube closure|vasculature development	apical part of cell|axon|cytoplasm|dendrite|integral to membrane|neuron projection membrane|neuronal cell body|presynaptic active zone	G-protein coupled receptor activity|PDZ domain binding|Wnt-protein binding			ovary(1)|central_nervous_system(1)	2		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)		CTGCATGTGCGTGATTGTTCA	0.438													28	37	---	---	---	---	PASS
FZD3	7976	broad.mit.edu	37	8	28385267	28385267	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28385267G>A	uc003xgx.2	+	5	1468	c.990G>A	c.(988-990)CTG>CTA	p.L330L	FZD3_uc010lvb.2_Silent_p.L330L	NM_017412	NP_059108	Q9NPG1	FZD3_HUMAN	frizzled 3 precursor	330	Helical; Name=4; (Potential).				canonical Wnt receptor signaling pathway|cell proliferation in midbrain|commissural neuron axon guidance|establishment of planar polarity|facial nucleus development|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|inner ear morphogenesis|neural tube closure|vasculature development	apical part of cell|axon|cytoplasm|dendrite|integral to membrane|neuron projection membrane|neuronal cell body|presynaptic active zone	G-protein coupled receptor activity|PDZ domain binding|Wnt-protein binding			ovary(1)|central_nervous_system(1)	2		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)		AAGCATTGCTGTTTCACGCCA	0.448													30	28	---	---	---	---	PASS
XKR4	114786	broad.mit.edu	37	8	56436703	56436703	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56436703G>C	uc003xsf.2	+	3	1902	c.1870G>C	c.(1870-1872)GAA>CAA	p.E624Q		NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related	624						integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)			TTTAGCTTTTGAATGTTCCCC	0.438													30	14	---	---	---	---	PASS
TGS1	96764	broad.mit.edu	37	8	56699597	56699597	+	Silent	SNP	A	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56699597A>C	uc003xsj.3	+	4	1527	c.1140A>C	c.(1138-1140)ACA>ACC	p.T380T	TGS1_uc010lyh.2_Silent_p.T284T	NM_024831	NP_079107	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase homolog	380					cellular lipid metabolic process|ncRNA metabolic process|regulation of transcription, DNA-dependent|RNA capping|spliceosomal snRNP assembly|transcription, DNA-dependent	Cajal body|cytosol	RNA trimethylguanosine synthase activity			ovary(1)|lung(1)|breast(1)	3		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)			CGGGGAATACAAACACAGACC	0.413													21	20	---	---	---	---	PASS
CYP7A1	1581	broad.mit.edu	37	8	59409573	59409573	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59409573C>A	uc003xtm.3	-	3	561	c.498G>T	c.(496-498)TGG>TGT	p.W166C		NM_000780	NP_000771	P22680	CP7A1_HUMAN	cytochrome P450, family 7, subfamily A,	166					bile acid biosynthetic process|cellular lipid metabolic process|cellular response to cholesterol|cellular response to glucose stimulus|cholesterol catabolic process|cholesterol homeostasis|regulation of bile acid biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	cholesterol 7-alpha-monooxygenase activity|electron carrier activity|heme binding			ovary(1)	1		all_lung(136;0.0271)|Lung NSC(129;0.0351)|all_epithelial(80;0.0554)				CTTCTGTCACCCAGGCAGCGG	0.483									Neonatal_Giant_Cell_Hepatitis				42	41	---	---	---	---	PASS
SGK3	23678	broad.mit.edu	37	8	67726104	67726104	+	Silent	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67726104A>G	uc003xwr.2	+	5	569	c.270A>G	c.(268-270)AGA>AGG	p.R90R	SGK3_uc003xwp.2_Silent_p.R84R|SGK3_uc003xwt.2_Silent_p.R90R|SGK3_uc003xwu.2_Silent_p.R90R	NM_001033578	NP_001028750	Q96BR1	SGK3_HUMAN	serum/glucocorticoid regulated kinase 3 isoform	90	PX.			R->A: Partially localized to the membrane.	cell communication|response to stress	cytoplasmic membrane-bounded vesicle|early endosome	ATP binding|phosphatidylinositol binding|protein serine/threonine kinase activity			ovary(1)|large_intestine(1)|lung(1)|breast(1)	4	Breast(64;0.186)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206)			TTAAACAAAGACGAGCAGGAC	0.308													23	28	---	---	---	---	PASS
CPA6	57094	broad.mit.edu	37	8	68423882	68423882	+	Missense_Mutation	SNP	A	G	G	rs151119622		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68423882A>G	uc003xxq.3	-	4	582	c.326T>C	c.(325-327)ATA>ACA	p.I109T	CPA6_uc003xxr.3_5'UTR|CPA6_uc003xxs.2_Missense_Mutation_p.I109T	NM_020361	NP_065094	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6 isoform 1 precursor	109					proteolysis	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)			AAGATCTTCTATGAGGACCCT	0.378													55	42	---	---	---	---	PASS
SULF1	23213	broad.mit.edu	37	8	70501234	70501234	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70501234G>A	uc010lza.1	+	8	1309	c.592G>A	c.(592-594)GAG>AAG	p.E198K	SULF1_uc003xyd.2_Missense_Mutation_p.E198K|SULF1_uc003xye.2_Missense_Mutation_p.E198K|SULF1_uc003xyf.2_Missense_Mutation_p.E198K|SULF1_uc003xyg.2_Missense_Mutation_p.E198K	NM_015170	NP_055985	Q8IWU6	SULF1_HUMAN	sulfatase 1 precursor	198					apoptosis|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			central_nervous_system(3)|ovary(2)|pancreas(1)|skin(1)	7	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			AATCACTAACGAGAGCATTAA	0.428													14	15	---	---	---	---	PASS
SULF1	23213	broad.mit.edu	37	8	70541837	70541837	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70541837G>A	uc010lza.1	+	19	2924	c.2207G>A	c.(2206-2208)GGG>GAG	p.G736E	SULF1_uc003xyd.2_Missense_Mutation_p.G736E|SULF1_uc003xye.2_Missense_Mutation_p.G736E|SULF1_uc003xyf.2_Missense_Mutation_p.G736E|SULF1_uc003xyg.2_Missense_Mutation_p.G736E|SULF1_uc003xyh.1_RNA|SULF1_uc003xyi.1_5'UTR	NM_015170	NP_055985	Q8IWU6	SULF1_HUMAN	sulfatase 1 precursor	736					apoptosis|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			central_nervous_system(3)|ovary(2)|pancreas(1)|skin(1)	7	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			CAGAGGAAGGGGGAAGAGTGC	0.537													33	34	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77616923	77616923	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77616923C>G	uc003yav.2	+	2	987	c.600C>G	c.(598-600)TCC>TCG	p.S200S	ZFHX4_uc003yat.1_Silent_p.S200S|ZFHX4_uc003yau.1_Silent_p.S200S|ZFHX4_uc003yaw.1_Silent_p.S200S	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	200						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)			TCGCTTCATCCCTCGGGAAAC	0.493										HNSCC(33;0.089)			8	60	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77766955	77766955	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77766955G>A	uc003yav.2	+	10	8050	c.7663G>A	c.(7663-7665)GAA>AAA	p.E2555K	ZFHX4_uc003yau.1_Missense_Mutation_p.E2600K|ZFHX4_uc003yaw.1_Missense_Mutation_p.E2555K	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	2555						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)			GAATAGCGGTGAAGACCAACA	0.448										HNSCC(33;0.089)			33	67	---	---	---	---	PASS
PSKH2	85481	broad.mit.edu	37	8	87060998	87060998	+	Intron	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87060998T>A	uc011lfy.1	-							NM_033126	NP_149117	Q96QS6	KPSH2_HUMAN	protein serine kinase H2								ATP binding|protein serine/threonine kinase activity			stomach(2)|lung(2)|ovary(1)	5			STAD - Stomach adenocarcinoma(118;0.129)			TGGCCAAGGCTGAGaataaaa	0.363													13	21	---	---	---	---	PASS
CALB1	793	broad.mit.edu	37	8	91072419	91072419	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91072419G>C	uc003yel.1	-	11	950	c.768C>G	c.(766-768)CTC>CTG	p.L256L	CALB1_uc011lge.1_Silent_p.L199L	NM_004929	NP_004920	P05937	CALB1_HUMAN	calbindin 1	256						nucleus	calcium ion binding|vitamin D binding			pancreas(1)	1			BRCA - Breast invasive adenocarcinoma(11;0.00953)			CCCCAGCACAGAGAATAAGAG	0.408													48	96	---	---	---	---	PASS
KIAA1429	25962	broad.mit.edu	37	8	95538842	95538842	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95538842C>G	uc003ygo.1	-	8	1643	c.1630G>C	c.(1630-1632)GTG>CTG	p.V544L	KIAA1429_uc003ygp.2_Missense_Mutation_p.V544L|KIAA1429_uc010maz.1_RNA	NM_015496	NP_056311	Q69YN4	VIR_HUMAN	hypothetical protein LOC25962 isoform 1	544					mRNA processing|RNA splicing	nucleus				ovary(1)|skin(1)	2	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			ACAACCCTCACAGTCTGATCT	0.378													15	154	---	---	---	---	PASS
INTS8	55656	broad.mit.edu	37	8	95848775	95848775	+	Silent	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95848775A>T	uc003yhb.2	+	7	903	c.777A>T	c.(775-777)GCA>GCT	p.A259A	INTS8_uc003yha.1_Silent_p.A259A|INTS8_uc011lgq.1_RNA|INTS8_uc011lgr.1_RNA|INTS8_uc010mba.2_Silent_p.A86A	NM_017864	NP_060334	Q75QN2	INT8_HUMAN	integrator complex subunit 8	259	TPR 1.				snRNA processing	integrator complex	protein binding				0	Breast(36;1.05e-06)					TGGGCGCAGCATACTTCCAGC	0.373													39	57	---	---	---	---	PASS
KCNS2	3788	broad.mit.edu	37	8	99440426	99440426	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99440426C>A	uc003yin.2	+	2	569	c.219C>A	c.(217-219)CGC>CGA	p.R73R		NM_020697	NP_065748	Q9ULS6	KCNS2_HUMAN	potassium voltage-gated channel,	73	Cytoplasmic (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)	1	Breast(36;2.4e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.0448)			ACTTCGACCGCAACCCTGAGC	0.592													21	61	---	---	---	---	PASS
VPS13B	157680	broad.mit.edu	37	8	100133616	100133616	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100133616G>C	uc003yiv.2	+	8	1260	c.1149G>C	c.(1147-1149)TTG>TTC	p.L383F	VPS13B_uc003yiw.2_Missense_Mutation_p.L383F|VPS13B_uc003yit.2_Missense_Mutation_p.L383F|VPS13B_uc003yiu.1_Missense_Mutation_p.L383F|VPS13B_uc003yis.2_Missense_Mutation_p.L383F|VPS13B_uc011lgy.1_Missense_Mutation_p.L259F	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	383					protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			CACAGACTTTGAAGGATCCTA	0.398													12	80	---	---	---	---	PASS
PKHD1L1	93035	broad.mit.edu	37	8	110523031	110523031	+	Silent	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110523031T>A	uc003yne.2	+	71	11525	c.11421T>A	c.(11419-11421)GCT>GCA	p.A3807A		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	3807	Extracellular (Potential).				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GCTGGTGTGCTGGATATACAT	0.403										HNSCC(38;0.096)			58	43	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113317125	113317125	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113317125G>A	uc003ynu.2	-	52	8250	c.8091C>T	c.(8089-8091)ATC>ATT	p.I2697I	CSMD3_uc003yns.2_Silent_p.I1899I|CSMD3_uc003ynt.2_Silent_p.I2657I|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	2697	Extracellular (Potential).|Sushi 16.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						TAAAGGAATTGATGCTTGGAC	0.378										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			13	6	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113599332	113599332	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113599332G>C	uc003ynu.2	-	23	4007	c.3848C>G	c.(3847-3849)GCC>GGC	p.A1283G	CSMD3_uc003yns.2_Missense_Mutation_p.A555G|CSMD3_uc003ynt.2_Missense_Mutation_p.A1243G|CSMD3_uc011lhx.1_Missense_Mutation_p.A1179G	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	1283	Extracellular (Potential).|CUB 7.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						AAATGTTCTGGCTGAAATATT	0.313										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			24	28	---	---	---	---	PASS
HAS2	3037	broad.mit.edu	37	8	122641427	122641427	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122641427A>T	uc003yph.2	-	2	692	c.154T>A	c.(154-156)TTT>ATT	p.F52I		NM_005328	NP_005319	Q92819	HAS2_HUMAN	hyaluronan synthase 2	52	Helical; Name=2; (Potential).					integral to plasma membrane	hyaluronan synthase activity		HAS2/PLAG1(10)	soft_tissue(10)|ovary(5)	15	Lung NSC(37;3.12e-08)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)|all_neural(195;0.142)		STAD - Stomach adenocarcinoma(47;0.00503)			GATGCCAAAAAGGCACCATAC	0.408													50	62	---	---	---	---	PASS
FER1L6	654463	broad.mit.edu	37	8	125058105	125058105	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125058105C>A	uc003yqw.2	+	21	2893	c.2687C>A	c.(2686-2688)CCC>CAC	p.P896H		NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6	896	Cytoplasmic (Potential).|C2 3.					integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			GAGTCCCCGCCCTTAGTGGTG	0.552													20	153	---	---	---	---	PASS
TMEM71	137835	broad.mit.edu	37	8	133740110	133740110	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133740110T>A	uc003ytp.2	-	6	836	c.607A>T	c.(607-609)AGC>TGC	p.S203C	TMEM71_uc003ytm.1_Missense_Mutation_p.S25C|TMEM71_uc003ytn.2_Missense_Mutation_p.S185C|TMEM71_uc003yto.2_Intron	NM_144649	NP_653250	Q6P5X7	TMM71_HUMAN	transmembrane protein 71 isoform 1	204						integral to membrane				ovary(2)	2	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			AGAGACAAGCTATGGGAGTTT	0.473													33	64	---	---	---	---	PASS
TG	7038	broad.mit.edu	37	8	133900481	133900481	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133900481G>C	uc003ytw.2	+	10	2470	c.2429G>C	c.(2428-2430)AGA>ACA	p.R810T		NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	810	Thyroglobulin type-1 7.				hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		ATGAGCTACAGAGAAGCAGCT	0.517													8	25	---	---	---	---	PASS
TG	7038	broad.mit.edu	37	8	133905937	133905937	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133905937C>A	uc003ytw.2	+	11	2805	c.2764C>A	c.(2764-2766)CCT>ACT	p.P922T		NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	922	Thyroglobulin type-1 8.				hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		TCCCCTAGGTCCTGGCTCCTG	0.463													7	46	---	---	---	---	PASS
COL22A1	169044	broad.mit.edu	37	8	139696707	139696707	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139696707G>C	uc003yvd.2	-	39	3420	c.2973C>G	c.(2971-2973)CTC>CTG	p.L991L	COL22A1_uc011ljo.1_Silent_p.L291L	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	991	Pro-rich.|Gly-rich.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GTGATCCACGGAGTCCCTGGA	0.532										HNSCC(7;0.00092)			24	32	---	---	---	---	PASS
DENND3	22898	broad.mit.edu	37	8	142146830	142146830	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142146830G>C	uc003yvy.2	+	2	363	c.85G>C	c.(85-87)GAG>CAG	p.E29Q	DENND3_uc003yvw.1_Missense_Mutation_p.E42Q|DENND3_uc003yvx.2_Missense_Mutation_p.E109Q|DENND3_uc010mep.2_Missense_Mutation_p.E42Q	NM_014957	NP_055772	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	29	UDENN.									ovary(1)	1	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			GCCAGAGCCTGAGGATGTCGC	0.662													3	4	---	---	---	---	PASS
BAI1	575	broad.mit.edu	37	8	143570401	143570401	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143570401G>A	uc003ywm.2	+	14	2641	c.2458G>A	c.(2458-2460)GAT>AAT	p.D820N		NM_001702	NP_001693	O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	820	Extracellular (Potential).				axonogenesis|cell adhesion|negative regulation of angiogenesis|negative regulation of cell proliferation|neuropeptide signaling pathway|peripheral nervous system development	cell-cell junction|integral to plasma membrane	G-protein coupled receptor activity|protein binding			lung(3)|ovary(2)|breast(1)|central_nervous_system(1)|pancreas(1)	8	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					TCCAGAGGCCGATGAAGCATC	0.662													11	12	---	---	---	---	PASS
GLI4	2738	broad.mit.edu	37	8	144358654	144358654	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144358654G>A	uc003yxx.2	+	4	896	c.811G>A	c.(811-813)GAG>AAG	p.E271K	ZFP41_uc003yxv.2_RNA	NM_138465	NP_612474	P10075	GLI4_HUMAN	GLI-Kruppel family member GLI4	271	C2H2-type 4.					nucleus	DNA binding|zinc ion binding				0	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)			CAAGTGCGGCGAGTGCGGCCA	0.682													17	39	---	---	---	---	PASS
GSDMD	79792	broad.mit.edu	37	8	144643281	144643281	+	Intron	SNP	T	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144643281T>G	uc010mfe.2	+						uc003yye.2_5'Flank|GSDMD_uc003yyf.2_Intron|GSDMD_uc003yyi.2_3'UTR|GSDMD_uc003yyg.2_Intron|GSDMD_uc003yyh.2_Intron	NM_024736	NP_079012	P57764	GSDMD_HUMAN	gasdermin D												0						TTGGGTGAGCTGGAGTTGGGG	0.652													5	14	---	---	---	---	PASS
SCRIB	23513	broad.mit.edu	37	8	144892670	144892670	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144892670C>G	uc003yzp.1	-	13	1516	c.1509G>C	c.(1507-1509)GGG>GGC	p.G503G	SCRIB_uc003yzo.1_Silent_p.G503G	NM_015356	NP_056171	Q14160	SCRIB_HUMAN	scribble isoform b	503	Sufficient for targeting to adherens junction and to inhibit cell proliferation.				activation of Rac GTPase activity|apoptosis involved in morphogenesis|cell migration|cell proliferation|cell-cell adhesion|establishment of apical/basal cell polarity|interspecies interaction between organisms|mammary gland duct morphogenesis|negative regulation of mitotic cell cycle|positive chemotaxis|positive regulation of apoptosis|positive regulation of receptor recycling|protein localization to adherens junction	cell-cell adherens junction|Scrib-APC-beta-catenin complex	protein binding			urinary_tract(1)|ovary(1)|kidney(1)|central_nervous_system(1)|pancreas(1)	5	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			GCAAGGGCGACCCAGAGTCTG	0.697													5	38	---	---	---	---	PASS
PPAPDC2	403313	broad.mit.edu	37	9	4663258	4663258	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4663258C>G	uc003zin.2	+	1	961	c.883C>G	c.(883-885)CGA>GGA	p.R295G	C9orf68_uc003zik.2_Intron|C9orf68_uc003zil.2_Intron|C9orf68_uc010mhj.2_Intron|C9orf68_uc011lly.1_Intron|C9orf68_uc011llz.1_Intron|C9orf68_uc003zim.2_Intron	NM_203453	NP_982278	Q8IY26	PPAC2_HUMAN	phosphatidic acid phosphatase type 2 domain	295						integral to membrane	hydrolase activity				0	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.026)		GTGGAGTCAACGATGACACCA	0.483													35	51	---	---	---	---	PASS
FREM1	158326	broad.mit.edu	37	9	14842506	14842506	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14842506G>A	uc003zlm.2	-	9	2136	c.1546C>T	c.(1546-1548)CCC>TCC	p.P516S	FREM1_uc010mic.2_RNA	NM_144966	NP_659403	Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1 precursor	516	CSPG 3.				cell communication|multicellular organismal development	basement membrane|integral to membrane	metal ion binding|sugar binding			ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(50;3.53e-06)		TCATCTTTGGGCAAGACGTTG	0.502													40	58	---	---	---	---	PASS
FAM154A	158297	broad.mit.edu	37	9	18928832	18928832	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18928832G>C	uc003zni.1	-	4	921	c.643C>G	c.(643-645)CCC>GCC	p.P215A	FAM154A_uc010mip.1_Missense_Mutation_p.P23A	NM_153707	NP_714918	Q8IYX7	F154A_HUMAN	hypothetical protein LOC158297	215										pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.53e-16)		TTCTCCACGGGGTGGGCCACA	0.502													24	32	---	---	---	---	PASS
DNAJB5	25822	broad.mit.edu	37	9	34996700	34996700	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34996700G>A	uc003zvt.2	+	3	788	c.650G>A	c.(649-651)CGT>CAT	p.R217H	DNAJB5_uc003zvs.2_Missense_Mutation_p.R251H|DNAJB5_uc011los.1_Missense_Mutation_p.R289H	NM_012266	NP_036398	O75953	DNJB5_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 5	217					protein folding|response to unfolded protein		heat shock protein binding|unfolded protein binding				0			LUSC - Lung squamous cell carcinoma(32;0.00575)			GTCATCAAGCGTGGCTGGAAG	0.562													12	35	---	---	---	---	PASS
KIAA1539	80256	broad.mit.edu	37	9	35108045	35108045	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35108045G>A	uc003zwl.2	-	3	552	c.227C>T	c.(226-228)CCC>CTC	p.P76L	KIAA1539_uc003zwm.2_Missense_Mutation_p.P76L|KIAA1539_uc003zwn.2_Intron|KIAA1539_uc003zwo.2_Missense_Mutation_p.P76L|KIAA1539_uc003zwp.1_Missense_Mutation_p.P76L|KIAA1539_uc010mkk.1_Intron	NM_025182	NP_079458	Q7L5A3	K1539_HUMAN	hypothetical protein LOC80256	76						nucleus				ovary(2)	2	all_epithelial(49;0.217)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			CAGCTCCCGGGGACCCTCAGT	0.637													5	35	---	---	---	---	PASS
TRPM6	140803	broad.mit.edu	37	9	77455096	77455096	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77455096C>T	uc004ajl.1	-	5	626	c.388G>A	c.(388-390)GAG>AAG	p.E130K	TRPM6_uc004ajk.1_Missense_Mutation_p.E125K|TRPM6_uc010mpb.1_RNA|TRPM6_uc010mpc.1_Missense_Mutation_p.E130K|TRPM6_uc010mpd.1_Missense_Mutation_p.E130K|TRPM6_uc010mpe.1_Missense_Mutation_p.E130K|TRPM6_uc004ajn.1_Missense_Mutation_p.E130K	NM_017662	NP_060132	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel,	130	Cytoplasmic (Potential).				response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	8						ATTTTCCACTCTTTCAACATT	0.363													19	17	---	---	---	---	PASS
PCSK5	5125	broad.mit.edu	37	9	78686749	78686749	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78686749G>T	uc004ajz.2	+	7	1367	c.829G>T	c.(829-831)GAT>TAT	p.D277Y	PCSK5_uc004ajy.2_Missense_Mutation_p.D277Y|PCSK5_uc004aka.2_RNA	NM_006200	NP_006191	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	277	Catalytic.				anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3						CCCGGATGATGATGGCAAGAC	0.532													22	98	---	---	---	---	PASS
PCSK5	5125	broad.mit.edu	37	9	78808270	78808270	+	3'UTR	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78808270C>A	uc004ajz.2	+	21					PCSK5_uc004aka.2_RNA|PCSK5_uc004akb.2_3'UTR	NM_006200	NP_006191	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3						CAAGGCTGAGCAGCCATCTTA	0.328													13	16	---	---	---	---	PASS
PRUNE2	158471	broad.mit.edu	37	9	79322998	79322998	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79322998C>A	uc010mpk.2	-	8	4316	c.4192G>T	c.(4192-4194)GAG>TAG	p.E1398*		NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	1398					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0						AAAACTTCCTCTGGTTCCTCG	0.458													17	21	---	---	---	---	PASS
VPS13A	23230	broad.mit.edu	37	9	79999552	79999552	+	Intron	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79999552G>A	uc004akr.2	+						VPS13A_uc004akq.3_Missense_Mutation_p.D3081N|VPS13A_uc004aks.2_Intron	NM_033305	NP_150648	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13A isoform A						Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|skin(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	10						CAGTAGtgatgatgatgatga	0.274													6	36	---	---	---	---	PASS
CEP78	84131	broad.mit.edu	37	9	80856685	80856685	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80856685G>A	uc004akx.2	+	4	849	c.573G>A	c.(571-573)CAG>CAA	p.Q191Q	CEP78_uc004aky.3_Silent_p.Q191Q|CEP78_uc010mpp.2_Silent_p.Q191Q|CEP78_uc011lsp.1_Silent_p.Q104Q	NM_032171	NP_115547	Q5JTW2	CEP78_HUMAN	centrosomal protein 78kDa isoform b	191					G2/M transition of mitotic cell cycle	centrosome|cytosol				ovary(1)	1						TGACATGGCAGGGAGCAGATC	0.343													8	54	---	---	---	---	PASS
FLJ46321	389763	broad.mit.edu	37	9	84607342	84607342	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84607342C>G	uc004amn.2	+	4	2004	c.1957C>G	c.(1957-1959)CCA>GCA	p.P653A		NM_001001670	NP_001001670	Q6ZQQ2	F75D1_HUMAN	hypothetical protein LOC389763	653						integral to membrane					0						CTTTTGTCCTCCAGCTCCCAA	0.463													22	43	---	---	---	---	PASS
AGTPBP1	23287	broad.mit.edu	37	9	88203362	88203362	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88203362C>A	uc011ltd.1	-	20	2787	c.2754G>T	c.(2752-2754)CGG>CGT	p.R918R	AGTPBP1_uc004aod.3_Silent_p.R544R|AGTPBP1_uc011ltc.1_Intron|AGTPBP1_uc010mqc.2_Silent_p.R878R|AGTPBP1_uc011lte.1_Silent_p.R930R	NM_015239	NP_056054	Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	918					C-terminal protein deglutamylation|cerebellar Purkinje cell differentiation|eye photoreceptor cell differentiation|mitochondrion organization|neuromuscular process|olfactory bulb development|protein side chain deglutamylation|proteolysis	cytosol|mitochondrion|nucleus	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(4)|large_intestine(2)|skin(1)	7						CAGGATGTACCCGAGCAGACA	0.378													14	24	---	---	---	---	PASS
ASPN	54829	broad.mit.edu	37	9	95219630	95219630	+	Silent	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95219630A>G	uc004ase.1	-	8	1327	c.1083T>C	c.(1081-1083)CCT>CCC	p.P361P	CENPP_uc004arz.2_Intron|CENPP_uc010mqx.2_Intron|ASPN_uc010mqy.1_3'UTR	NM_017680	NP_060150	Q9BXN1	ASPN_HUMAN	asporin precursor	361	LRR 11.				bone mineralization|negative regulation of tooth mineralization|negative regulation of transforming growth factor beta receptor signaling pathway	proteinaceous extracellular matrix	calcium ion binding				0						GAAATGTTGCAGGTTGCATTT	0.353													12	34	---	---	---	---	PASS
FAM120AOS	158293	broad.mit.edu	37	9	96212824	96212824	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96212824G>A	uc004atu.3	-	2	1504	c.621C>T	c.(619-621)CCC>CCT	p.P207P	FAM120AOS_uc004atm.2_RNA|FAM120AOS_uc004atn.3_RNA|FAM120AOS_uc004ato.3_RNA|FAM120AOS_uc004atp.3_RNA|FAM120AOS_uc004atq.3_RNA|FAM120AOS_uc004atr.3_RNA|FAM120AOS_uc004ats.3_RNA|FAM120AOS_uc004att.3_RNA|FAM120A_uc004atv.2_5'Flank|FAM120A_uc004atw.2_5'Flank	NM_198841	NP_942138	Q5T036	F120S_HUMAN	hypothetical protein LOC158293	207											0						TCCATGTGCTGGGCAGCAGCT	0.507													9	34	---	---	---	---	PASS
HABP4	22927	broad.mit.edu	37	9	99228025	99228025	+	Silent	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99228025T>C	uc010msg.2	+	4	856	c.708T>C	c.(706-708)TGT>TGC	p.C236C	HABP4_uc010msh.2_Intron	NM_014282	NP_055097	Q5JVS0	HABP4_HUMAN	hyaluronan binding protein 4	236					platelet activation|platelet degranulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|extracellular region|nucleus	protein binding			ovary(1)	1		Acute lymphoblastic leukemia(62;0.0169)|all_hematologic(171;0.214)				TGGGTGGATGTGGAGTTCGAA	0.453													4	17	---	---	---	---	PASS
PPP3R2	5535	broad.mit.edu	37	9	104356946	104356946	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104356946G>A	uc004bbr.2	-	1	338	c.267C>T	c.(265-267)GGC>GGT	p.G89G	GRIN3A_uc004bbp.1_Intron|GRIN3A_uc004bbq.1_Intron|PPP3R2_uc010mtf.1_Intron	NM_147180	NP_671709	Q96LZ3	CANB2_HUMAN	protein phosphatase 3 regulatory subunit B, beta	86							calcium ion binding	p.G89C(1)		ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(62;0.0527)			Cyclosporine(DB00091)	GCTCCTCGTCGCCCTTGACGC	0.537													17	71	---	---	---	---	PASS
CYLC2	1539	broad.mit.edu	37	9	105767520	105767520	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105767520G>T	uc004bbs.2	+	5	677	c.607G>T	c.(607-609)GCA>TCA	p.A203S		NM_001340	NP_001331	Q14093	CYLC2_HUMAN	cylicin 2	203	3 X approximate tandem repeats.|31 X 3 AA repeats of K-K-X.|2.				cell differentiation|multicellular organismal development|spermatogenesis	cytoskeletal calyx	structural constituent of cytoskeleton			skin(1)	1		all_hematologic(171;0.125)				CAAAGACTCGGCAACAGAATC	0.239													26	67	---	---	---	---	PASS
OR13D1	286365	broad.mit.edu	37	9	107457200	107457200	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107457200C>A	uc011lvs.1	+	1	498	c.498C>A	c.(496-498)ATC>ATA	p.I166I		NM_001004484	NP_001004484	Q8NGV5	O13D1_HUMAN	olfactory receptor, family 13, subfamily D,	166	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						GGTACTCCATCATCATGAACG	0.517													15	53	---	---	---	---	PASS
ABCA1	19	broad.mit.edu	37	9	107576733	107576733	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107576733C>G	uc004bcl.2	-	26	4075	c.3762G>C	c.(3760-3762)GAG>GAC	p.E1254D		NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1	1254					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)	CCACCCCACTCTCTTCGGCCA	0.458													5	19	---	---	---	---	PASS
ACTL7A	10881	broad.mit.edu	37	9	111625099	111625099	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111625099C>T	uc004bdj.1	+	1	497	c.497C>T	c.(496-498)GCG>GTG	p.A166V		NM_006687	NP_006678	Q9Y615	ACL7A_HUMAN	actin-like 7A	166						cytoplasm|cytoskeleton|protein complex	structural constituent of cytoskeleton				0						GAGGAGCATGCGGTCTTGGTT	0.527													10	27	---	---	---	---	PASS
CTNNAL1	8727	broad.mit.edu	37	9	111741743	111741743	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111741743G>A	uc004bdo.1	-	7	961	c.919C>T	c.(919-921)CGG>TGG	p.R307W	CTNNAL1_uc010mts.1_Missense_Mutation_p.R43W|CTNNAL1_uc010mtt.1_Missense_Mutation_p.R307W|CTNNAL1_uc004bdp.1_Missense_Mutation_p.R307W	NM_003798	NP_003789	Q9UBT7	CTNL1_HUMAN	catenin, alpha-like 1	307					cell adhesion|Rho protein signal transduction	actin cytoskeleton|cytosol|plasma membrane	cadherin binding|structural molecule activity			ovary(1)	1				STAD - Stomach adenocarcinoma(157;0.0768)		AGATTCTCCCGAAGAGCTTCA	0.418													4	16	---	---	---	---	PASS
SVEP1	79987	broad.mit.edu	37	9	113308574	113308574	+	Intron	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113308574A>T	uc010mtz.2	-						SVEP1_uc010mua.1_Intron|SVEP1_uc004beu.2_Intron|SVEP1_uc004bev.2_Intron	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom						cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7						AGGTAGATCTACAAATAACAT	0.388													7	11	---	---	---	---	PASS
ASTN2	23245	broad.mit.edu	37	9	119582947	119582947	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119582947G>T	uc004bjs.1	-	12	2257	c.2156C>A	c.(2155-2157)ACG>AAG	p.T719K	ASTN2_uc004bjr.1_Missense_Mutation_p.T715K|ASTN2_uc004bjt.1_Missense_Mutation_p.T668K	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c	719	Extracellular (Potential).|EGF-like 3.					integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						CAGGGGCAGCGTCTGCTGCAG	0.577													7	30	---	---	---	---	PASS
FAM129B	64855	broad.mit.edu	37	9	130279211	130279211	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130279211C>A	uc004brh.2	-	8	1100	c.898G>T	c.(898-900)GCC>TCC	p.A300S	FAM129B_uc004bri.2_Missense_Mutation_p.A287S|FAM129B_uc004brj.3_Missense_Mutation_p.A300S	NM_022833	NP_073744	Q96TA1	NIBL1_HUMAN	hypothetical protein LOC64855 isoform 1	300							protein binding				0						GCCTGCATGGCCGGCTGCACC	0.622													27	103	---	---	---	---	PASS
FAM129B	64855	broad.mit.edu	37	9	130279214	130279214	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130279214G>C	uc004brh.2	-	8	1097	c.895C>G	c.(895-897)CCG>GCG	p.P299A	FAM129B_uc004bri.2_Missense_Mutation_p.P286A|FAM129B_uc004brj.3_Missense_Mutation_p.P299A	NM_022833	NP_073744	Q96TA1	NIBL1_HUMAN	hypothetical protein LOC64855 isoform 1	299							protein binding				0						TGCATGGCCGGCTGCACCTGC	0.622													28	103	---	---	---	---	PASS
C9orf117	286207	broad.mit.edu	37	9	130473730	130473730	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130473730G>A	uc004brn.1	+	4	850	c.810G>A	c.(808-810)GAG>GAA	p.E270E	PTRH1_uc004brm.2_Intron|C9orf117_uc010mxl.1_RNA	NM_001012502	NP_001012520	Q5JU67	CI117_HUMAN	hypothetical protein LOC286207	270	Potential.										0						AGCTGCTGGAGAACACCCAGA	0.587													45	28	---	---	---	---	PASS
ZER1	10444	broad.mit.edu	37	9	131495697	131495697	+	Intron	SNP	T	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131495697T>G	uc004bwa.1	-							NM_006336	NP_006327	Q7Z7L7	ZER1_HUMAN	zyg-11 homolog B (C. elegans)-like						ATP hydrolysis coupled proton transport|regulation of ubiquitin-protein ligase activity	Cul2-RING ubiquitin ligase complex|vacuolar proton-transporting V-type ATPase, V1 domain	protein binding|proton-transporting ATPase activity, rotational mechanism|ubiquitin-protein ligase activity			ovary(1)	1						ACACTGCTGGTCTCTTACCGG	0.562											OREG0019523	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	9	---	---	---	---	PASS
USP20	10868	broad.mit.edu	37	9	132623876	132623876	+	Missense_Mutation	SNP	A	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132623876A>C	uc004bys.2	+	8	693	c.482A>C	c.(481-483)CAG>CCG	p.Q161P	USP20_uc004byr.2_Missense_Mutation_p.Q161P|USP20_uc004byt.1_Missense_Mutation_p.Q161P	NM_001110303	NP_001103773	Q9Y2K6	UBP20_HUMAN	ubiquitin specific protease 20	161					endocytosis|protein K48-linked deubiquitination|protein K63-linked deubiquitination|regulation of G-protein coupled receptor protein signaling pathway|ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm	cysteine-type endopeptidase activity|G-protein-coupled receptor binding|ubiquitin thiolesterase activity|zinc ion binding			lung(1)|breast(1)	2		Ovarian(14;0.00556)				GCTGCCCTGCAGGCCCTGTCC	0.622													19	20	---	---	---	---	PASS
NUP214	8021	broad.mit.edu	37	9	134049561	134049561	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134049561G>C	uc004cag.2	+	22	3124	c.3013G>C	c.(3013-3015)GAT>CAT	p.D1005H	NUP214_uc004cah.2_Missense_Mutation_p.D995H|NUP214_uc004cai.2_Missense_Mutation_p.D435H|NUP214_uc004caf.1_Missense_Mutation_p.D994H|NUP214_uc010mzf.2_Missense_Mutation_p.D303H	NM_005085	NP_005076	P35658	NU214_HUMAN	nucleoporin 214kDa	1005	11 X 5 AA approximate repeats.				carbohydrate metabolic process|glucose transport|mRNA metabolic process|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore|nucleoplasm	protein binding			breast(7)|lung(3)|skin(3)|ovary(2)|central_nervous_system(1)	16	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		GTCCTGTAAAGATGACGAGGC	0.537			T	DEK|SET|ABL1	AML|T-ALL								13	53	---	---	---	---	PASS
RPL7A	6130	broad.mit.edu	37	9	136216887	136216887	+	Missense_Mutation	SNP	G	C	C	rs11549063		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136216887G>C	uc004cde.1	+	4	425	c.395G>C	c.(394-396)AGA>ACA	p.R132T	MED22_uc004cdc.2_5'Flank|MED22_uc004cdd.2_5'Flank|RPL7A_uc004cdf.1_5'UTR|SNORD36B_uc010nai.1_5'Flank|SNORD36A_uc010naj.2_5'Flank|SNORD36C_uc010nak.2_5'Flank	NM_000972	NP_000963	P62424	RL7A_HUMAN	ribosomal protein L7a	132					endocrine pancreas development|ribosome biogenesis|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|membrane fraction|polysomal ribosome	RNA binding|structural constituent of ribosome				0				OV - Ovarian serous cystadenocarcinoma(145;4.93e-07)|Epithelial(140;4.09e-06)|all cancers(34;3.78e-05)		CCAACGAAGAGACCACCTGTC	0.552													23	18	---	---	---	---	PASS
SNAPC4	6621	broad.mit.edu	37	9	139288772	139288772	+	Nonsense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139288772C>T	uc004chh.2	-	6	570	c.561G>A	c.(559-561)TGG>TGA	p.W187*		NM_003086	NP_003077	Q5SXM2	SNPC4_HUMAN	small nuclear RNA activating complex,	187					snRNA transcription from RNA polymerase II promoter|snRNA transcription from RNA polymerase III promoter	snRNA-activating protein complex	DNA binding|sequence-specific DNA binding transcription factor activity				0		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		AGGCCTTTTCCCAGTTTTTCC	0.552													22	33	---	---	---	---	PASS
FAM166A	401565	broad.mit.edu	37	9	140139971	140139971	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140139971G>A	uc004cmi.1	-	3	365	c.310C>T	c.(310-312)CTC>TTC	p.L104F		NM_001001710	NP_001001710	Q6J272	F166A_HUMAN	hypothetical protein LOC401565	104										ovary(1)	1						AAGGGTGGGAGCTGGCCCAGA	0.642													39	28	---	---	---	---	PASS
C9orf173	441476	broad.mit.edu	37	9	140146505	140146505	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140146505C>G	uc004cmk.1	+	3	330	c.318C>G	c.(316-318)ACC>ACG	p.T106T	C9orf173_uc004cmj.1_Silent_p.T107T|C9orf173_uc011meu.1_RNA|C9orf173_uc010ncd.1_Intron|C9orf173_uc011mev.1_Silent_p.T106T|C9orf173_uc004cml.1_Silent_p.T106T			Q8N7X2	CI173_HUMAN	SubName: Full=LOC441476 protein;	107										pancreas(1)	1						CCAGCCCCACCAGGTACCAGG	0.672													9	7	---	---	---	---	PASS
DHTKD1	55526	broad.mit.edu	37	10	12159705	12159705	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12159705G>T	uc001ild.3	+	14	2452	c.2353G>T	c.(2353-2355)GGA>TGA	p.G785*		NM_018706	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain	785					glycolysis	mitochondrion	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			ovary(1)|central_nervous_system(1)	2		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			AATGGCACCAGGAACAACATT	0.428													5	69	---	---	---	---	PASS
CUBN	8029	broad.mit.edu	37	10	16981039	16981039	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16981039C>A	uc001ioo.2	-	38	5708	c.5656G>T	c.(5656-5658)GCA>TCA	p.A1886S		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	1886	CUB 13.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ACGTGAGATGCATTCACATTT	0.393													13	26	---	---	---	---	PASS
ST8SIA6	338596	broad.mit.edu	37	10	17373464	17373464	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17373464C>A	uc001ipd.2	-	5	465	c.465G>T	c.(463-465)GAG>GAT	p.E155D	ST8SIA6_uc010qce.1_RNA	NM_001004470	NP_001004470	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide	155	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(1)	1						TGCTTTCCACCTCGTAACTCA	0.383													16	23	---	---	---	---	PASS
SLC39A12	221074	broad.mit.edu	37	10	18242259	18242259	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18242259C>A	uc001ipo.2	+	2	327	c.54C>A	c.(52-54)CTC>CTA	p.L18L	SLC39A12_uc001ipn.2_Silent_p.L18L|SLC39A12_uc001ipp.2_Silent_p.L18L|SLC39A12_uc010qck.1_Intron	NM_001145195	NP_001138667	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter),	18	Extracellular (Potential).				zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)|breast(1)	2						TTCTTCTACTCAGCCGTGTTT	0.527													26	46	---	---	---	---	PASS
PIP4K2A	5305	broad.mit.edu	37	10	23003205	23003205	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23003205C>G	uc001irl.3	-	1	299	c.51G>C	c.(49-51)AAG>AAC	p.K17N		NM_005028	NP_005019	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type	17							1-phosphatidylinositol-4-phosphate 5-kinase activity|1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding			ovary(1)|skin(1)	2						TCTTCTTGGTCTTGGTCTTGC	0.647													7	14	---	---	---	---	PASS
ARHGAP21	57584	broad.mit.edu	37	10	24874831	24874831	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24874831C>T	uc001isb.2	-	26	4874	c.4387G>A	c.(4387-4389)GAG>AAG	p.E1463K	ARHGAP21_uc010qdb.1_RNA	NM_020824	NP_065875	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	1462					signal transduction	cell junction|cytoplasmic vesicle membrane|cytoskeleton|Golgi membrane	GTPase activator activity|protein binding			ovary(7)|pancreas(1)	8						CCCAGTGTCTCACTTTCTTTT	0.388													28	45	---	---	---	---	PASS
CCDC7	221016	broad.mit.edu	37	10	32761397	32761397	+	Intron	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32761397G>T	uc001iwj.2	+						CCDC7_uc009xlu.1_Intron|CCDC7_uc001iwk.2_Intron|CCDC7_uc009xlv.2_Intron|CCDC7_uc009xlw.1_Intron|CCDC7_uc009xlx.1_Intron|CCDC7_uc009xly.1_Intron	NM_145023	NP_659460	Q96M83	CCDC7_HUMAN	coiled-coil domain containing 7												0		Breast(68;0.000207)|Prostate(175;0.0107)				TTCATTTATCGAACTTTAACA	0.259													3	15	---	---	---	---	PASS
PARD3	56288	broad.mit.edu	37	10	34573173	34573173	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34573173C>A	uc010qej.1	-	21	3075	c.3075G>T	c.(3073-3075)AGG>AGT	p.R1025S	PARD3_uc010qek.1_Missense_Mutation_p.R1022S|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Missense_Mutation_p.R1009S|PARD3_uc010qen.1_Missense_Mutation_p.R979S|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Missense_Mutation_p.R935S|PARD3_uc010qeq.1_Intron	NM_019619	NP_062565	Q8TEW0	PARD3_HUMAN	partitioning-defective protein 3 homolog	1025	Lys-rich.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)				GTTTGCCAAACCTGTTAATAA	0.323													11	76	---	---	---	---	PASS
CREM	1390	broad.mit.edu	37	10	35467822	35467822	+	Silent	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35467822A>T	uc001iyb.2	+	4	336	c.174A>T	c.(172-174)GCA>GCT	p.A58A	CREM_uc001ixx.2_Silent_p.A42A|CREM_uc001ixy.2_Intron|CREM_uc001ixz.2_Intron|CREM_uc001iya.2_Silent_p.A58A|CREM_uc001iyc.2_Silent_p.A42A|CREM_uc001iyd.2_Silent_p.A58A|CREM_uc001iye.2_Silent_p.A58A|CREM_uc001iyf.2_Silent_p.A28A|CREM_uc001iyg.2_Silent_p.A28A|CREM_uc001iyh.2_Silent_p.A3A|CREM_uc001iyi.2_Silent_p.A3A|CREM_uc001iyj.2_5'UTR|CREM_uc001iyk.2_5'UTR	NM_181571	NP_853549	Q03060	CREM_HUMAN	cAMP responsive element modulator isoform a	107	KID.				cell differentiation|multicellular organismal development|signal transduction|spermatogenesis	nucleus	cAMP response element binding protein binding|protein binding|protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						TATAGGTAGCAGCAATTGCAG	0.358													6	22	---	---	---	---	PASS
ZNF25	219749	broad.mit.edu	37	10	38246038	38246038	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38246038G>A	uc001ize.1	-	4	253	c.148C>T	c.(148-150)CAT>TAT	p.H50Y	ZNF25_uc001izf.1_Missense_Mutation_p.H14Y	NM_145011	NP_659448	P17030	ZNF25_HUMAN	zinc finger protein 25	50	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)|ovary(1)|central_nervous_system(1)	4		all_neural(218;0.0218)|Breast(68;0.0389)|Ovarian(717;0.0443)|Renal(717;0.157)				TTATTCACATGGTAACCTATG	0.388													6	37	---	---	---	---	PASS
ZNF33A	7581	broad.mit.edu	37	10	38343517	38343517	+	Missense_Mutation	SNP	G	T	T	rs141144828		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38343517G>T	uc001izh.2	+	5	640	c.462G>T	c.(460-462)TTG>TTT	p.L154F	ZNF33A_uc001izg.2_Missense_Mutation_p.L155F|ZNF33A_uc010qev.1_Missense_Mutation_p.L161F|ZNF33A_uc001izi.1_Intron	NM_006974	NP_008905	Q06730	ZN33A_HUMAN	zinc finger protein 33A isoform b	154						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(1)	3						TTTCAGAATTGGTTATCAGTA	0.323													13	56	---	---	---	---	PASS
ZNF33B	7582	broad.mit.edu	37	10	43088981	43088981	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43088981C>A	uc001jaf.1	-	5	1532	c.1417G>T	c.(1417-1419)GAG>TAG	p.E473*	ZNF33B_uc009xmg.1_Intron|ZNF33B_uc001jae.1_Intron|ZNF33B_uc001jag.1_Nonsense_Mutation_p.E361*|ZNF33B_uc001jad.2_Intron	NM_006955	NP_008886	Q06732	ZN33B_HUMAN	zinc finger protein 33B	473	C2H2-type 6.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						TTCCCACACTCAAGACATTCA	0.378													15	38	---	---	---	---	PASS
RASSF4	83937	broad.mit.edu	37	10	45486418	45486418	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45486418C>T	uc001jbo.2	+	9	842	c.708C>T	c.(706-708)TGC>TGT	p.C236C	RASSF4_uc001jbp.2_Silent_p.C267C|RASSF4_uc009xmn.2_Silent_p.C166C|RASSF4_uc001jbq.2_Silent_p.C133C|RASSF4_uc001jbt.2_Silent_p.C193C	NM_032023	NP_114412	Q9H2L5	RASF4_HUMAN	Ras association domain family 4	236	Ras-associating.				cell cycle|signal transduction		protein binding			large_intestine(1)	1						TAAAAGACTGCGAGTACCCGC	0.473													10	65	---	---	---	---	PASS
OR13A1	79290	broad.mit.edu	37	10	45799210	45799210	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45799210C>A	uc001jcc.1	-	4	970	c.661G>T	c.(661-663)GAT>TAT	p.D221Y	OR13A1_uc001jcd.1_Missense_Mutation_p.D217Y	NM_001004297	NP_001004297	Q8NGR1	O13A1_HUMAN	olfactory receptor, family 13, subfamily A,	221	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TAGAAAGCATCCGCCAGGACA	0.547													9	56	---	---	---	---	PASS
RBP3	5949	broad.mit.edu	37	10	48389621	48389621	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48389621C>G	uc001jez.2	-	1	1371	c.1257G>C	c.(1255-1257)GAG>GAC	p.E419D		NM_002900	NP_002891	P10745	RET3_HUMAN	retinol-binding protein 3 precursor	419	4 X approximate tandem repeats.|2.				lipid metabolic process|proteolysis|transport|visual perception	interphotoreceptor matrix	retinal binding|serine-type peptidase activity			large_intestine(1)|central_nervous_system(1)	2					Vitamin A(DB00162)	GCCGGATAGCCTCGTCCTCAG	0.637													4	27	---	---	---	---	PASS
C10orf71	118461	broad.mit.edu	37	10	50531521	50531521	+	Silent	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50531521T>C	uc010qgp.1	+	3	1270	c.931T>C	c.(931-933)TTG>CTG	p.L311L		NM_199459	NP_955629	Q711Q0	CJ071_HUMAN	hypothetical protein LOC118461 isoform 2	311											0						GGACACGACCTTGCTAAGAGA	0.572													7	51	---	---	---	---	PASS
DRGX	644168	broad.mit.edu	37	10	50574366	50574366	+	Missense_Mutation	SNP	T	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50574366T>G	uc010qgq.1	-	6	602	c.602A>C	c.(601-603)TAT>TCT	p.Y201S		NM_001080520	NP_001073989	A6NNA5	DRGX_HUMAN	dorsal root ganglia homeobox	201					multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						CTGGCAGCCATAGGTGGGAAG	0.612													11	17	---	---	---	---	PASS
A1CF	29974	broad.mit.edu	37	10	52566514	52566514	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52566514C>T	uc001jjj.2	-	13	1948	c.1760G>A	c.(1759-1761)CGA>CAA	p.R587Q	A1CF_uc010qhn.1_Missense_Mutation_p.R587Q|A1CF_uc001jji.2_Missense_Mutation_p.R579Q|A1CF_uc001jjh.2_Missense_Mutation_p.R587Q|A1CF_uc010qho.1_Missense_Mutation_p.R595Q|A1CF_uc009xov.2_Missense_Mutation_p.R579Q	NM_138932	NP_620310	Q9NQ94	A1CF_HUMAN	apobec-1 complementation factor isoform 2	587					cytidine to uridine editing|mRNA modification|mRNA processing|protein stabilization	apolipoprotein B mRNA editing enzyme complex|endoplasmic reticulum|nucleoplasm	nucleotide binding|protein binding|single-stranded RNA binding			central_nervous_system(1)	1						TCCATCCCCTCGGGCAGTCAC	0.418													10	37	---	---	---	---	PASS
PCDH15	65217	broad.mit.edu	37	10	55587246	55587246	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55587246G>C	uc001jju.1	-	32	4669	c.4274C>G	c.(4273-4275)GCA>GGA	p.A1425G	PCDH15_uc010qhq.1_Missense_Mutation_p.A1430G|PCDH15_uc010qhr.1_Missense_Mutation_p.A1425G|PCDH15_uc010qhs.1_Missense_Mutation_p.A1437G|PCDH15_uc010qht.1_Missense_Mutation_p.A1432G|PCDH15_uc010qhu.1_Missense_Mutation_p.A1425G|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Missense_Mutation_p.A1422G|PCDH15_uc010qhw.1_Missense_Mutation_p.A1385G|PCDH15_uc010qhx.1_Missense_Mutation_p.A1354G|PCDH15_uc010qhy.1_Missense_Mutation_p.A1430G|PCDH15_uc010qhz.1_Missense_Mutation_p.A1425G|PCDH15_uc010qia.1_Missense_Mutation_p.A1403G|PCDH15_uc010qib.1_Missense_Mutation_p.A1400G	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	1425	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)				AGCCGGCACTGCTGGTTTAGC	0.418										HNSCC(58;0.16)			3	25	---	---	---	---	PASS
PCDH15	65217	broad.mit.edu	37	10	55839174	55839174	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55839174G>A	uc001jju.1	-	17	2403	c.2008C>T	c.(2008-2010)CTA>TTA	p.L670L	PCDH15_uc010qhq.1_Silent_p.L675L|PCDH15_uc010qhr.1_Silent_p.L670L|PCDH15_uc010qhs.1_Silent_p.L682L|PCDH15_uc010qht.1_Silent_p.L677L|PCDH15_uc010qhu.1_Silent_p.L670L|PCDH15_uc001jjv.1_Silent_p.L648L|PCDH15_uc010qhv.1_Silent_p.L670L|PCDH15_uc010qhw.1_Silent_p.L633L|PCDH15_uc010qhx.1_Silent_p.L599L|PCDH15_uc010qhy.1_Silent_p.L675L|PCDH15_uc010qhz.1_Silent_p.L670L|PCDH15_uc010qia.1_Silent_p.L648L|PCDH15_uc010qib.1_Silent_p.L648L|PCDH15_uc001jjw.2_Silent_p.L670L	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	670	Cadherin 6.|Extracellular (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)				CCTAAGGTTAGAATCCCCGTG	0.423										HNSCC(58;0.16)			25	116	---	---	---	---	PASS
PCDH15	65217	broad.mit.edu	37	10	55973758	55973758	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55973758C>G	uc001jju.1	-	10	1431	c.1036G>C	c.(1036-1038)GAA>CAA	p.E346Q	PCDH15_uc010qhq.1_Missense_Mutation_p.E351Q|PCDH15_uc010qhr.1_Missense_Mutation_p.E346Q|PCDH15_uc010qhs.1_Missense_Mutation_p.E351Q|PCDH15_uc010qht.1_Missense_Mutation_p.E346Q|PCDH15_uc010qhu.1_Missense_Mutation_p.E346Q|PCDH15_uc001jjv.1_Missense_Mutation_p.E324Q|PCDH15_uc010qhv.1_Missense_Mutation_p.E346Q|PCDH15_uc010qhw.1_Missense_Mutation_p.E309Q|PCDH15_uc010qhx.1_Missense_Mutation_p.E346Q|PCDH15_uc010qhy.1_Missense_Mutation_p.E351Q|PCDH15_uc010qhz.1_Missense_Mutation_p.E346Q|PCDH15_uc010qia.1_Missense_Mutation_p.E324Q|PCDH15_uc010qib.1_Missense_Mutation_p.E324Q|PCDH15_uc001jjw.2_Missense_Mutation_p.E346Q	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	346	Cadherin 3.|Extracellular (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)				AGACTAAGTTCTGCTGTCCTA	0.358										HNSCC(58;0.16)			21	68	---	---	---	---	PASS
PCDH15	65217	broad.mit.edu	37	10	56106233	56106233	+	Silent	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56106233A>G	uc001jju.1	-	6	881	c.486T>C	c.(484-486)GTT>GTC	p.V162V	PCDH15_uc010qhq.1_Silent_p.V167V|PCDH15_uc010qhr.1_Silent_p.V162V|PCDH15_uc010qhs.1_Silent_p.V167V|PCDH15_uc010qht.1_Silent_p.V162V|PCDH15_uc010qhu.1_Silent_p.V162V|PCDH15_uc001jjv.1_Silent_p.V140V|PCDH15_uc010qhv.1_Silent_p.V162V|PCDH15_uc010qhw.1_Silent_p.V162V|PCDH15_uc010qhx.1_Silent_p.V162V|PCDH15_uc010qhy.1_Silent_p.V167V|PCDH15_uc010qhz.1_Silent_p.V162V|PCDH15_uc010qia.1_Silent_p.V140V|PCDH15_uc010qib.1_Silent_p.V140V|PCDH15_uc001jjw.2_Silent_p.V162V	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	162	Extracellular (Potential).|Cadherin 2.				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)				TTGTGGTACCAACTGGAGTGA	0.338										HNSCC(58;0.16)			31	95	---	---	---	---	PASS
RTKN2	219790	broad.mit.edu	37	10	63983069	63983069	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63983069C>A	uc001jlw.2	-	7	806	c.709G>T	c.(709-711)GCT>TCT	p.A237S	RTKN2_uc009xpf.1_Missense_Mutation_p.A18S	NM_145307	NP_660350	Q8IZC4	RTKN2_HUMAN	rhotekin 2	237					signal transduction	intracellular					0	Prostate(12;0.0297)|all_hematologic(501;0.215)					GTAGTGTGAGCTAGCAAATTA	0.284													5	69	---	---	---	---	PASS
JMJD1C	221037	broad.mit.edu	37	10	64943277	64943277	+	Silent	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64943277T>C	uc001jmn.2	-	22	7314	c.7014A>G	c.(7012-7014)GAA>GAG	p.E2338E	JMJD1C_uc001jml.2_Silent_p.E2101E|JMJD1C_uc001jmm.2_Silent_p.E2050E|JMJD1C_uc010qiq.1_Silent_p.E2156E|JMJD1C_uc009xpi.2_Silent_p.E2156E|JMJD1C_uc009xpj.1_RNA|JMJD1C_uc001jmo.2_Silent_p.E245E	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a	2338	JmjC.	Iron; catalytic (By similarity).			blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)					CATCAGAAACTTCAATATGGA	0.279													29	70	---	---	---	---	PASS
CTNNA3	29119	broad.mit.edu	37	10	69407282	69407282	+	Intron	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69407282C>T	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_Intron|CTNNA3_uc009xpo.1_Intron|CTNNA3_uc001jna.2_Intron	NM_001127384	NP_001120856	Q9UI47	CTNA3_HUMAN	catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8						GCTGCCTGTGCACAAACACAA	0.403													9	73	---	---	---	---	PASS
MYPN	84665	broad.mit.edu	37	10	69926318	69926318	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69926318C>T	uc001jnm.3	+	11	2053	c.1868C>T	c.(1867-1869)ACC>ATC	p.T623I	MYPN_uc001jnl.1_Missense_Mutation_p.T623I|MYPN_uc001jnn.3_Missense_Mutation_p.T348I|MYPN_uc001jno.3_Missense_Mutation_p.T623I|MYPN_uc009xps.2_Missense_Mutation_p.T623I|MYPN_uc009xpt.2_Missense_Mutation_p.T623I|MYPN_uc010qit.1_Missense_Mutation_p.T329I|MYPN_uc010qiu.1_RNA	NM_032578	NP_115967	Q86TC9	MYPN_HUMAN	myopalladin	623						nucleus|sarcomere	actin binding			ovary(3)|skin(2)	5						ACCAGACAGACCAGGCCCGAT	0.567													6	73	---	---	---	---	PASS
MYPN	84665	broad.mit.edu	37	10	69961673	69961673	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69961673G>A	uc001jnm.3	+	19	3766	c.3581G>A	c.(3580-3582)CGC>CAC	p.R1194H	MYPN_uc001jnn.3_Missense_Mutation_p.R919H|MYPN_uc001jno.3_Missense_Mutation_p.R1194H|MYPN_uc009xpt.2_Missense_Mutation_p.R1194H|MYPN_uc010qit.1_Missense_Mutation_p.R900H|MYPN_uc010qiu.1_RNA	NM_032578	NP_115967	Q86TC9	MYPN_HUMAN	myopalladin	1194	Interaction with ACTN.|Ig-like 5.					nucleus|sarcomere	actin binding			ovary(3)|skin(2)	5						CTGGAGTGCCGCGTGATAGGC	0.547													14	126	---	---	---	---	PASS
DDX21	9188	broad.mit.edu	37	10	70719870	70719870	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70719870G>A	uc001jov.1	+	2	486	c.396G>A	c.(394-396)AAG>AAA	p.K132K	DDX21_uc001jow.1_Silent_p.K64K	NM_004728	NP_004719	Q9NR30	DDX21_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 21	132						nucleolus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)	3						AGCCCAAGAAGATGAAGAAAG	0.408													16	57	---	---	---	---	PASS
SRGN	5552	broad.mit.edu	37	10	70863695	70863695	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70863695G>T	uc001joz.2	+	3	382	c.296G>T	c.(295-297)GGC>GTC	p.G99V		NM_002727	NP_002718	P10124	SRGN_HUMAN	serglycin precursor	99	3.|9 X 2 AA tandem repeats of [SF]-G.				apoptosis|biomineral tissue development|maintenance of granzyme B location in T cell secretory granule|maintenance of protease location in mast cell secretory granule|negative regulation of bone mineralization|negative regulation of cytokine secretion|platelet activation|platelet degranulation|protein maturation by peptide bond cleavage	extracellular space|mast cell granule|platelet alpha granule lumen					0						TCAGGCTTCGGCTCCGGCTCC	0.468													7	49	---	---	---	---	PASS
TYSND1	219743	broad.mit.edu	37	10	71899758	71899758	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71899758C>G	uc001jqr.2	-	4	1777	c.1623G>C	c.(1621-1623)CTG>CTC	p.L541L	TYSND1_uc001jqq.2_RNA|TYSND1_uc001jqs.2_3'UTR|TYSND1_uc001jqt.2_RNA	NM_173555	NP_775826	Q2T9J0	TYSD1_HUMAN	trypsin domain containing 1 isoform a	541					proteolysis	peroxisome	serine-type endopeptidase activity			large_intestine(1)	1						CAGCGCGGTCCAGCTCACGGA	0.652													9	59	---	---	---	---	PASS
SAR1A	56681	broad.mit.edu	37	10	71917543	71917543	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71917543C>A	uc010qjh.1	-	6	528	c.325G>T	c.(325-327)GTG>TTG	p.V109L	SAR1A_uc010qji.1_Missense_Mutation_p.V109L|SAR1A_uc010qjj.1_Missense_Mutation_p.V66L	NM_001142648	NP_001136120	Q9NR31	SAR1A_HUMAN	SAR1a gene homolog 1	109					ER to Golgi vesicle-mediated transport|intracellular protein transport	Golgi apparatus	GTP binding|GTPase activity				0						TTGGATTCCACGAGGCGAGAA	0.338													29	48	---	---	---	---	PASS
ADAMTS14	140766	broad.mit.edu	37	10	72503416	72503416	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72503416C>G	uc001jrh.2	+	13	2037	c.2037C>G	c.(2035-2037)GTC>GTG	p.V679V	ADAMTS14_uc001jrg.2_Silent_p.V682V|ADAMTS14_uc001jri.1_Silent_p.V202V	NM_080722	NP_542453	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1	679	Cys-rich.				collagen catabolic process|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|upper_aerodigestive_tract(1)	6						CATACAGCGTCTGTGCGCGTG	0.657													8	15	---	---	---	---	PASS
UNC5B	219699	broad.mit.edu	37	10	73046577	73046577	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73046577G>C	uc001jro.2	+	5	1129	c.684G>C	c.(682-684)AAG>AAC	p.K228N	UNC5B_uc001jrp.2_Missense_Mutation_p.K228N	NM_170744	NP_734465	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B precursor	228	Ig-like C2-type.|Extracellular (Potential).				apoptosis|axon guidance|regulation of apoptosis	integral to membrane				ovary(2)|lung(1)	3						GCGTGGCCAAGAACATCGTGG	0.637													42	139	---	---	---	---	PASS
CDH23	64072	broad.mit.edu	37	10	73501524	73501524	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73501524C>G	uc001jrx.3	+	36	5068	c.4691C>G	c.(4690-4692)TCC>TGC	p.S1564C	CDH23_uc001jsc.1_Missense_Mutation_p.S371C	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	1564	Cadherin 15.|Extracellular (Potential).				calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11						AGTGTTCTGTCCTACTACATC	0.617													11	27	---	---	---	---	PASS
TTC18	118491	broad.mit.edu	37	10	75013743	75013743	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75013743G>A	uc009xrc.2	-	28	3477	c.3356C>T	c.(3355-3357)CCA>CTA	p.P1119L	TTC18_uc001jty.2_Missense_Mutation_p.P1119L|MRPS16_uc010qkh.1_5'Flank|MRPS16_uc001jts.1_5'Flank|MRPS16_uc001jtt.1_5'Flank|uc001jtu.1_RNA|TTC18_uc001jtv.3_Missense_Mutation_p.P223L|TTC18_uc001jtw.3_Missense_Mutation_p.P193L|TTC18_uc001jtx.2_Missense_Mutation_p.P470L	NM_145170	NP_660153	Q5T0N1	TTC18_HUMAN	tetratricopeptide repeat domain 18	1119							binding			ovary(2)|central_nervous_system(1)	3	Prostate(51;0.0119)					TCAGAAAGATGGATTTCCAAA	0.448													7	96	---	---	---	---	PASS
KIAA0913	23053	broad.mit.edu	37	10	75550015	75550015	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75550015G>T	uc009xrl.2	+	7	938	c.906G>T	c.(904-906)CTG>CTT	p.L302L	KIAA0913_uc001jve.2_Silent_p.L302L|KIAA0913_uc001jvf.2_Silent_p.L302L|KIAA0913_uc001jvh.2_5'Flank|KIAA0913_uc001jvi.2_5'Flank|KIAA0913_uc010qkr.1_5'Flank|KIAA0913_uc001jvj.2_5'Flank	NM_015037	NP_055852	A7E2V4	K0913_HUMAN	hypothetical protein LOC23053	302							zinc ion binding			breast(1)	1	Prostate(51;0.0112)					AAAAGACACTGCACAAGTTCT	0.552													10	182	---	---	---	---	PASS
POLR3A	11128	broad.mit.edu	37	10	79777381	79777381	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79777381C>A	uc001jzn.2	-	10	1477	c.1383G>T	c.(1381-1383)CTG>CTT	p.L461L		NM_007055	NP_008986	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide	461					innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	DNA-directed RNA polymerase III complex	DNA binding|DNA-directed RNA polymerase activity|ribonucleoside binding|zinc ion binding				0	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			GCCGATTGAACAGCACCACAT	0.438													14	105	---	---	---	---	PASS
SFTPA1	653509	broad.mit.edu	37	10	81373497	81373497	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81373497C>T	uc001kap.2	+	6	496	c.375C>T	c.(373-375)CTC>CTT	p.L125L	SFTPA1_uc001kaq.2_Silent_p.L125L|SFTPA1_uc009xry.2_Silent_p.L140L|SFTPA1_uc001kar.2_Silent_p.L125L|SFTPA1_uc010qlt.1_Silent_p.L66L|SFTPA1_uc009xrz.2_Silent_p.L55L|SFTPA1_uc009xsa.2_Silent_p.L125L|SFTPA1_uc009xsf.2_5'Flank	NM_005411	NP_005402	Q8IWL2	SFTA1_HUMAN	surfactant protein A1 isoform 1	125					cell junction assembly|respiratory gaseous exchange	collagen|extracellular space	lipid transporter activity|sugar binding				0	all_cancers(46;0.197)|Breast(12;0.000326)|Prostate(51;0.00985)|all_epithelial(25;0.0149)		Epithelial(14;0.00957)|all cancers(16;0.0179)|Colorectal(32;0.229)			TCTCAGCCCTCAGTCTGCAGG	0.562													65	173	---	---	---	---	PASS
CDHR1	92211	broad.mit.edu	37	10	85968559	85968559	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85968559G>C	uc001kcv.2	+	12	1242	c.1242G>C	c.(1240-1242)CTG>CTC	p.L414L	CDHR1_uc001kcw.2_Silent_p.L414L|CDHR1_uc009xst.2_Silent_p.L173L	NM_033100	NP_149091	Q96JP9	CDHR1_HUMAN	protocadherin 21 precursor	414	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion		calcium ion binding|receptor activity			ovary(1)	1						AGACAGTCCTGAATGAAGCCC	0.478													7	29	---	---	---	---	PASS
GPR120	338557	broad.mit.edu	37	10	95347066	95347066	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95347066C>G	uc010qnt.1	+	4	890	c.834C>G	c.(832-834)CTC>CTG	p.L278L	GPR120_uc010qnu.1_Silent_p.L262L	NM_181745	NP_859529	Q5NUL3	O3FA1_HUMAN	G protein-coupled receptor 120	278	Cytoplasmic (Potential).				negative regulation of cytokine secretion|negative regulation of inflammatory response|regulation of glucose transport	integral to membrane|plasma membrane	fatty acid binding				0		Colorectal(252;0.122)				ACTTCCGGCTCTTCCGCACCC	0.552													26	35	---	---	---	---	PASS
ARHGAP19	84986	broad.mit.edu	37	10	99003889	99003889	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99003889G>A	uc001knb.2	-	8	1050	c.1021C>T	c.(1021-1023)CAT>TAT	p.H341Y	ARHGAP19_uc001kmy.2_RNA|ARHGAP19_uc001kna.2_Missense_Mutation_p.H332Y|ARHGAP19_uc009xvi.2_RNA|ARHGAP19_uc009xvj.2_Missense_Mutation_p.H312Y|ARHGAP19_uc009xvk.2_Missense_Mutation_p.H135Y	NM_032900	NP_116289	Q14CB8	RHG19_HUMAN	Rho GTPase activating protein 19	341					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|nucleus	GTPase activator activity				0		Colorectal(252;0.0854)		Epithelial(162;7.65e-09)|all cancers(201;4.49e-07)		GACTTAGTATGACATGAAGCT	0.443													10	34	---	---	---	---	PASS
DNMBP	23268	broad.mit.edu	37	10	101656026	101656026	+	Nonsense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101656026G>A	uc001kqj.2	-	10	3141	c.3049C>T	c.(3049-3051)CAG>TAG	p.Q1017*	DNMBP_uc010qpl.1_Intron|DNMBP_uc001kqg.2_Nonsense_Mutation_p.Q305*|DNMBP_uc001kqh.2_Nonsense_Mutation_p.Q649*	NM_015221	NP_056036	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	1017	BAR.				intracellular signal transduction|regulation of Rho protein signal transduction	cell junction|cytoskeleton|Golgi stack|synapse	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(5)|skin(1)	6		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		GATCTCACCTGAGGAGCAAAG	0.502													10	9	---	---	---	---	PASS
SORCS1	114815	broad.mit.edu	37	10	108336980	108336980	+	3'UTR	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108336980C>G	uc001kym.2	-	26					SORCS1_uc001kyl.2_Nonstop_Mutation_p.*1199S|SORCS1_uc009xxs.2_3'UTR|SORCS1_uc001kyn.1_3'UTR	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		GTCCTCCATTCAAACATTTAC	0.294													8	39	---	---	---	---	PASS
TDRD1	56165	broad.mit.edu	37	10	115986958	115986958	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115986958G>T	uc001lbg.1	+	23	3456	c.3303G>T	c.(3301-3303)GAG>GAT	p.E1101D	TDRD1_uc001lbf.2_Missense_Mutation_p.E978D|TDRD1_uc001lbh.1_Missense_Mutation_p.E1088D|TDRD1_uc001lbi.1_Missense_Mutation_p.E1092D|TDRD1_uc010qsc.1_Intron|TDRD1_uc001lbj.2_Missense_Mutation_p.E810D	NM_198795	NP_942090	Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	1101					DNA methylation involved in gamete generation|gene silencing by RNA|germ cell development|meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	pi-body	nucleic acid binding|protein binding|zinc ion binding				0		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		TGTCAGTTGAGAAATGTTCTG	0.348													12	31	---	---	---	---	PASS
C10orf96	374355	broad.mit.edu	37	10	118101703	118101703	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118101703G>C	uc001lck.2	+	5	689	c.438G>C	c.(436-438)ATG>ATC	p.M146I		NM_198515	NP_940917	P0C7W6	CJ096_HUMAN	hypothetical protein LOC374355	146	Potential.									ovary(2)	2		Lung NSC(174;0.204)|all_lung(145;0.248)		all cancers(201;0.014)		AAGCAAACATGTTGAAAAGTG	0.254													6	29	---	---	---	---	PASS
PNLIPRP3	119548	broad.mit.edu	37	10	118220751	118220751	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118220751G>A	uc001lcl.3	+	7	858	c.757G>A	c.(757-759)GAA>AAA	p.E253K		NM_001011709	NP_001011709	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3 precursor	253					lipid catabolic process	extracellular region	triglyceride lipase activity			ovary(1)	1				all cancers(201;0.0131)		GCCAGGATGTGAAGACTTAAT	0.353													31	14	---	---	---	---	PASS
PNLIPRP3	119548	broad.mit.edu	37	10	118231274	118231274	+	Intron	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118231274A>T	uc001lcl.3	+							NM_001011709	NP_001011709	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3 precursor						lipid catabolic process	extracellular region	triglyceride lipase activity			ovary(1)	1				all cancers(201;0.0131)		GTTTCCTTATATCTAGGTTGG	0.413													39	79	---	---	---	---	PASS
PPAPDC1A	196051	broad.mit.edu	37	10	122273500	122273500	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122273500G>T	uc001lev.1	+	3	595	c.243G>T	c.(241-243)AAG>AAT	p.K81N	PPAPDC1A_uc010qtd.1_Missense_Mutation_p.K81N|PPAPDC1A_uc009xzl.1_Missense_Mutation_p.K81N|PPAPDC1A_uc001lew.1_Intron|PPAPDC1A_uc001lex.1_Intron|PPAPDC1A_uc001ley.1_Translation_Start_Site	NM_001030059	NP_001025230	Q5VZY2	PPC1A_HUMAN	phosphatidic acid phosphatase type 2 domain	81					phospholipid dephosphorylation	integral to membrane	phosphatidate phosphatase activity			breast(1)	1		Lung NSC(174;0.1)|all_lung(145;0.132)		all cancers(201;0.0117)		CTGAAATTAAGGAAGCCTTCT	0.408													30	44	---	---	---	---	PASS
TACC2	10579	broad.mit.edu	37	10	123846008	123846008	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123846008G>A	uc001lfv.2	+	4	4353	c.3993G>A	c.(3991-3993)CGG>CGA	p.R1331R	TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Silent_p.R1331R|TACC2_uc010qtv.1_Silent_p.R1331R	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing	1331						microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				GCCTGGACCGGATGCCACTTC	0.617													6	31	---	---	---	---	PASS
GPR26	2849	broad.mit.edu	37	10	125447671	125447671	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125447671G>C	uc001lhh.2	+	3	1062	c.1009G>C	c.(1009-1011)GAG>CAG	p.E337Q		NM_153442	NP_703143	Q8NDV2	GPR26_HUMAN	G protein-coupled receptor 26	337	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1		Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)				GCCGGTGTCTGAGTGAAGGAC	0.607													12	8	---	---	---	---	PASS
C10orf90	118611	broad.mit.edu	37	10	128150052	128150052	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128150052G>T	uc001ljq.2	-	5	1758	c.1637C>A	c.(1636-1638)CCC>CAC	p.P546H	C10orf90_uc001ljp.2_Missense_Mutation_p.P402H|C10orf90_uc010qum.1_Missense_Mutation_p.P643H|C10orf90_uc001ljo.2_RNA	NM_001004298	NP_001004298	Q96M02	CJ090_HUMAN	hypothetical protein LOC118611	546										ovary(1)|skin(1)	2		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		TCCATCGCGGGGTGCTGGCGA	0.542													13	11	---	---	---	---	PASS
DOCK1	1793	broad.mit.edu	37	10	129201358	129201358	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129201358G>A	uc001ljt.2	+	39	3968	c.3904G>A	c.(3904-3906)GAG>AAG	p.E1302K	DOCK1_uc010qun.1_Missense_Mutation_p.E1323K|DOCK1_uc009yaq.2_Missense_Mutation_p.E297K	NM_001380	NP_001371	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1302	DHR-2.				apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		GGAGCTAGCCGAGCAGTATGA	0.423													5	12	---	---	---	---	PASS
MUC5B	727897	broad.mit.edu	37	11	1261425	1261425	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1261425G>A	uc009ycr.1	+	46	5995	c.5869G>A	c.(5869-5871)GAG>AAG	p.E1957K	MUC5B_uc001ltb.2_Missense_Mutation_p.E1267K|MUC5B_uc001lta.2_Missense_Mutation_p.E932K	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	1264					cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CTGCACCTATGAGGACAGGAC	0.647													10	13	---	---	---	---	PASS
KCNQ1	3784	broad.mit.edu	37	11	2604670	2604670	+	Silent	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2604670A>T	uc001lwn.2	+	7	1035	c.927A>T	c.(925-927)ACA>ACT	p.T309T	KCNQ1_uc009ydp.1_Silent_p.T93T|KCNQ1_uc001lwo.2_Silent_p.T182T	NM_000218	NP_000209	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like	309			T -> R (in LQT1).		blood circulation|membrane depolarization|muscle contraction|sensory perception of sound		delayed rectifier potassium channel activity|protein binding			ovary(1)	1		all_epithelial(84;3.26e-05)|Breast(177;0.001)|Medulloblastoma(188;0.00111)|Ovarian(85;0.00158)|all_neural(188;0.00725)|all_lung(207;0.11)|Lung NSC(207;0.159)		BRCA - Breast invasive adenocarcinoma(625;0.00251)|Lung(200;0.131)	Bepridil(DB01244)|Indapamide(DB00808)	TGCAGGTCACAGTCACCACCA	0.612													5	27	---	---	---	---	PASS
OR52I2	143502	broad.mit.edu	37	11	4608328	4608328	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4608328C>T	uc010qyh.1	+	1	286	c.286C>T	c.(286-288)CTG>TTG	p.L96L		NM_001005170	NP_001005170	Q8NH67	O52I2_HUMAN	olfactory receptor, family 52, subfamily I,	96	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCTGTGTGTTCTGGCTGCTGT	0.493													19	125	---	---	---	---	PASS
OR51S1	119692	broad.mit.edu	37	11	4869826	4869826	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4869826A>G	uc010qyo.1	-	1	613	c.613T>C	c.(613-615)TAC>CAC	p.Y205H		NM_001004758	NP_001004758	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S,	205	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		AATAGGCTGTAGGCTGCACCC	0.537													17	38	---	---	---	---	PASS
OR51S1	119692	broad.mit.edu	37	11	4869963	4869963	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4869963C>T	uc010qyo.1	-	1	476	c.476G>A	c.(475-477)CGA>CAA	p.R159Q		NM_001004758	NP_001004758	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S,	159	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		ACCCAGGCATCGAAAAGAAAT	0.542													9	50	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	5068696	5068696	+	IGR	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5068696C>G								OR52J3 (14 upstream) : OR52E2 (11185 downstream)																							AAATAAGACTCTTACCATGTT	0.373													5	16	---	---	---	---	PASS
HBB	3043	broad.mit.edu	37	11	5246869	5246869	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5246869C>A	uc001mae.1	-	3	453	c.403G>T	c.(403-405)GTG>TTG	p.V135L		NM_000518	NP_000509	P68871	HBB_HUMAN	beta globin	135			V -> E (in North Shore-Caracas; unstable).		blood coagulation|hydrogen peroxide catabolic process|nitric oxide transport|positive regulation of cell death|positive regulation of nitric oxide biosynthetic process|protein heterooligomerization|regulation of blood pressure|regulation of blood vessel size	haptoglobin-hemoglobin complex|hemoglobin complex	heme binding|hemoglobin binding|oxygen binding|oxygen transporter activity			central_nervous_system(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	Iron Dextran(DB00893)	ACACCAGCCACCACTTTCTGA	0.517									Sickle_Cell_Trait				9	24	---	---	---	---	PASS
UBQLN3	50613	broad.mit.edu	37	11	5529375	5529375	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5529375G>T	uc001may.1	-	2	1500	c.1414C>A	c.(1414-1416)CCT>ACT	p.P472T	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_5'Flank|OR51B5_uc001maq.1_5'Flank	NM_017481	NP_059509	Q9H347	UBQL3_HUMAN	ubiquilin 3	472										ovary(3)	3		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGAGGCTCAGGGATTCCAGGA	0.542													11	27	---	---	---	---	PASS
CNGA4	1262	broad.mit.edu	37	11	6261502	6261502	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6261502C>A	uc001mco.2	+	4	585	c.478C>A	c.(478-480)CGC>AGC	p.R160S	CNGA4_uc010raa.1_Intron|CNGA4_uc001mcn.2_Missense_Mutation_p.R120S	NM_001037329	NP_001032406	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	160	Extracellular (Potential).				response to stimulus|sensory perception of smell		cAMP binding			skin(1)	1		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CACAGAGACCCGCACAGCTTA	0.582													15	64	---	---	---	---	PASS
OR2D3	120775	broad.mit.edu	37	11	6942862	6942862	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6942862C>A	uc010rav.1	+	1	630	c.630C>A	c.(628-630)AGC>AGA	p.S210R		NM_001004684	NP_001004684	Q8NGH3	OR2D3_HUMAN	olfactory receptor, family 2, subfamily D,	210	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		ACACTTACAGCACAGAAATGG	0.453													11	15	---	---	---	---	PASS
ZNF215	7762	broad.mit.edu	37	11	6977732	6977732	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6977732T>A	uc001mey.2	+	7	2112	c.1524T>A	c.(1522-1524)CAT>CAA	p.H508Q	ZNF215_uc010raw.1_3'UTR|ZNF215_uc010rax.1_Missense_Mutation_p.H270Q|ZNF215_uc001mez.1_Intron	NM_013250	NP_037382	Q9UL58	ZN215_HUMAN	zinc finger protein 215	508	C2H2-type 4.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0				Epithelial(150;6.33e-08)|BRCA - Breast invasive adenocarcinoma(625;0.134)		TTGTTAAACATCAAAAACTGC	0.358													13	29	---	---	---	---	PASS
ZNF215	7762	broad.mit.edu	37	11	6977739	6977739	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6977739C>A	uc001mey.2	+	7	2119	c.1531C>A	c.(1531-1533)CTG>ATG	p.L511M	ZNF215_uc010raw.1_3'UTR|ZNF215_uc010rax.1_Missense_Mutation_p.L273M|ZNF215_uc001mez.1_Intron	NM_013250	NP_037382	Q9UL58	ZN215_HUMAN	zinc finger protein 215	511	C2H2-type 4.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0				Epithelial(150;6.33e-08)|BRCA - Breast invasive adenocarcinoma(625;0.134)		ACATCAAAAACTGCATACTCG	0.338													15	25	---	---	---	---	PASS
NLRP14	338323	broad.mit.edu	37	11	7059931	7059931	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7059931G>T	uc001mfb.1	+	2	437	c.114G>T	c.(112-114)ATG>ATT	p.M38I		NM_176822	NP_789792	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	38	DAPIN.				cell differentiation|multicellular organismal development|spermatogenesis		ATP binding			ovary(3)|breast(2)|pancreas(1)|lung(1)|skin(1)	8				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		AGGAGACCATGGAACCTGAGC	0.433													9	45	---	---	---	---	PASS
NLRP14	338323	broad.mit.edu	37	11	7059932	7059932	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7059932G>T	uc001mfb.1	+	2	438	c.115G>T	c.(115-117)GAA>TAA	p.E39*		NM_176822	NP_789792	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	39	DAPIN.				cell differentiation|multicellular organismal development|spermatogenesis		ATP binding			ovary(3)|breast(2)|pancreas(1)|lung(1)|skin(1)	8				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		GGAGACCATGGAACCTGAGCA	0.433													9	46	---	---	---	---	PASS
OR5P2	120065	broad.mit.edu	37	11	7817698	7817698	+	Silent	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7817698A>T	uc001mfp.1	-	1	792	c.792T>A	c.(790-792)ACT>ACA	p.T264T		NM_153444	NP_703145	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P,	264	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		TGTTCTGGTCAGTTGAGTAGC	0.488													9	55	---	---	---	---	PASS
ST5	6764	broad.mit.edu	37	11	8737282	8737282	+	Missense_Mutation	SNP	C	A	A	rs139182184		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8737282C>A	uc001mgt.2	-	6	1899	c.1713G>T	c.(1711-1713)AAG>AAT	p.K571N	ST5_uc009yfr.2_Missense_Mutation_p.K151N|ST5_uc001mgu.2_Missense_Mutation_p.K151N|ST5_uc001mgv.2_Missense_Mutation_p.K571N|ST5_uc010rbq.1_RNA|ST5_uc010rbp.1_Missense_Mutation_p.K84N	NM_213618	NP_998783	P78524	ST5_HUMAN	suppression of tumorigenicity 5 isoform 1	571					positive regulation of ERK1 and ERK2 cascade		protein binding			upper_aerodigestive_tract(1)	1				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		GGCTGTGCCTCTTGGGTAATC	0.617													7	25	---	---	---	---	PASS
SBF2	81846	broad.mit.edu	37	11	9861114	9861114	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9861114C>A	uc001mib.2	-	26	3524	c.3386G>T	c.(3385-3387)AGC>ATC	p.S1129I	SBF2_uc001mif.3_Missense_Mutation_p.S885I|uc001mig.2_Intron	NM_030962	NP_112224	Q86WG5	MTMRD_HUMAN	SET binding factor 2	1129	Myotubularin phosphatase.				myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		ACGGGAAGAGCTGCCACTTAT	0.473													26	61	---	---	---	---	PASS
MRGPRX3	117195	broad.mit.edu	37	11	18158752	18158752	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18158752G>C	uc001mnu.2	+	3	364	c.3G>C	c.(1-3)ATG>ATC	p.M1I		NM_054031	NP_473372	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	1	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)|pancreas(1)	2						TTCTGAGCATGGATTCAACCA	0.428													45	64	---	---	---	---	PASS
BDNF	627	broad.mit.edu	37	11	27680064	27680064	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27680064C>T	uc010rdu.1	-	2	899	c.48G>A	c.(46-48)ATG>ATA	p.M16I	BDNFOS_uc001mrm.2_Intron|BDNFOS_uc009yij.2_RNA|BDNFOS_uc009yik.2_Intron|BDNFOS_uc009yil.2_RNA|BDNFOS_uc001mrp.2_Intron|BDNFOS_uc009yim.2_RNA|BDNFOS_uc009yin.2_Intron|BDNFOS_uc009yio.2_RNA|BDNFOS_uc009yip.2_RNA|BDNFOS_uc001mrn.2_Intron|BDNFOS_uc009yiq.2_RNA|BDNFOS_uc001mro.2_Intron|BDNFOS_uc009yir.2_RNA|BDNFOS_uc009yis.2_Intron|BDNFOS_uc009yit.2_Intron|BDNFOS_uc009yiu.2_RNA|BDNFOS_uc009yiv.2_Intron|BDNFOS_uc009yiw.2_RNA|BDNFOS_uc009yix.2_Intron|BDNFOS_uc009yiy.2_RNA|BDNFOS_uc009yiz.2_RNA|BDNFOS_uc001mrq.3_Intron|BDNFOS_uc001mrr.3_Intron|BDNFOS_uc009yja.2_Intron|BDNFOS_uc009yjb.2_RNA|BDNF_uc010rdv.1_Missense_Mutation_p.M16I|BDNF_uc001mrt.2_Missense_Mutation_p.M31I|BDNF_uc010rdw.1_Missense_Mutation_p.M16I|BDNF_uc009yjd.2_Missense_Mutation_p.M16I|BDNF_uc001mru.2_Missense_Mutation_p.M16I|BDNF_uc010rdx.1_Missense_Mutation_p.M16I|BDNF_uc010rdy.1_Missense_Mutation_p.M16I|BDNF_uc009yjg.2_Missense_Mutation_p.M16I|BDNF_uc009yje.2_Missense_Mutation_p.M98I|BDNF_uc009yjf.2_Missense_Mutation_p.M45I|BDNF_uc001mrv.2_Missense_Mutation_p.M16I|BDNF_uc001mrw.3_Missense_Mutation_p.M16I|BDNF_uc001mrx.2_Missense_Mutation_p.M16I|BDNF_uc001mry.3_Missense_Mutation_p.M16I|BDNF_uc001mrz.3_Missense_Mutation_p.M16I|BDNF_uc001msa.2_Missense_Mutation_p.M24I	NM_001143816	NP_001137288	P23560	BDNF_HUMAN	brain-derived neurotrophic factor isoform a	16						extracellular region	growth factor activity				0						GGGCAGCCTTCATGCAACCAA	0.502													31	88	---	---	---	---	PASS
KCNA4	3739	broad.mit.edu	37	11	30032317	30032317	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30032317C>T	uc001msk.2	-	2	3061	c.1909G>A	c.(1909-1911)GAG>AAG	p.E637K		NM_002233	NP_002224	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related	637						voltage-gated potassium channel complex	potassium ion binding|protein binding|voltage-gated potassium channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4						TTATCTGTCTCACTGTCATCC	0.468													17	45	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	31113054	31113054	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31113054C>A	uc009yjk.1	-	5	536	c.467G>T	c.(466-468)GGA>GTA	p.G156V	uc009yjl.1_Missense_Mutation_p.G84V|DCDC1_uc001msu.1_Missense_Mutation_p.G327V					RecName: Full=Doublecortin domain-containing protein 5;																		CAGGATCATTCCAGTCTTCCA	0.428													9	11	---	---	---	---	PASS
DCDC1	341019	broad.mit.edu	37	11	31327851	31327851	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31327851C>A	uc001msv.2	-	5	721	c.519G>T	c.(517-519)GTG>GTT	p.V173V	DCDC1_uc001msu.1_5'UTR	NM_181807	NP_861523	P59894	DCDC1_HUMAN	doublecortin domain containing 1	173	Doublecortin.				intracellular signal transduction					skin(1)	1	Lung SC(675;0.225)					TTACTTTAATCACTCTTGGTT	0.383													12	42	---	---	---	---	PASS
PAX6	5080	broad.mit.edu	37	11	31811577	31811577	+	Intron	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31811577G>C	uc001mtd.3	-						PAX6_uc001mte.3_Intron|PAX6_uc001mtg.3_Intron|PAX6_uc001mtf.3_Intron|PAX6_uc001mth.3_Intron|PAX6_uc009yjr.2_Intron	NM_001127612	NP_001121084	P26367	PAX6_HUMAN	paired box gene 6 isoform a						blood vessel development|central nervous system development|cornea development in camera-type eye|glucose homeostasis|iris morphogenesis|negative regulation of neurogenesis|neuron fate commitment|pancreatic A cell development|positive regulation of transcription, DNA-dependent|response to wounding|visual perception	cytoplasm|nuclear chromatin	R-SMAD binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|ubiquitin-protein ligase activity			lung(4)|ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	9	Lung SC(675;0.225)					CCTAGAAGTGGATGAAAGAAA	0.333									Wilms_tumor-Aniridia-ambiguous_Genitals-mental_Retardation				5	36	---	---	---	---	PASS
PAX6	5080	broad.mit.edu	37	11	31815649	31815649	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31815649G>T	uc001mtd.3	-	8	1586	c.696C>A	c.(694-696)ACC>ACA	p.T232T	PAX6_uc001mte.3_Silent_p.T232T|PAX6_uc001mtg.3_Silent_p.T246T|PAX6_uc001mtf.3_Silent_p.T232T|PAX6_uc001mth.3_Silent_p.T232T|PAX6_uc009yjr.2_Silent_p.T232T	NM_001127612	NP_001121084	P26367	PAX6_HUMAN	paired box gene 6 isoform a	232	Homeobox.				blood vessel development|central nervous system development|cornea development in camera-type eye|glucose homeostasis|iris morphogenesis|negative regulation of neurogenesis|neuron fate commitment|pancreatic A cell development|positive regulation of transcription, DNA-dependent|response to wounding|visual perception	cytoplasm|nuclear chromatin	R-SMAD binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|ubiquitin-protein ligase activity			lung(4)|ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	9	Lung SC(675;0.225)					CTGGATAATGGGTTCTCTCAA	0.423									Wilms_tumor-Aniridia-ambiguous_Genitals-mental_Retardation				17	110	---	---	---	---	PASS
WT1	7490	broad.mit.edu	37	11	32417924	32417924	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32417924C>A	uc001mtn.1	-	7	1324	c.1128G>T	c.(1126-1128)CCG>CCT	p.P376P	WT1_uc001mtl.1_Silent_p.P164P|WT1_uc001mtm.1_Silent_p.P147P|WT1_uc001mto.1_Silent_p.P376P|WT1_uc001mtp.1_Silent_p.P359P|WT1_uc001mtq.1_Silent_p.P359P|WT1_uc009yjs.1_RNA	NM_024426	NP_077744	P19544	WT1_HUMAN	Wilms tumor 1 isoform D	308					adrenal cortex formation|branching involved in ureteric bud morphogenesis|camera-type eye development|cardiac muscle cell fate commitment|cellular response to cAMP|cellular response to gonadotropin stimulus|germ cell development|glomerular basement membrane development|glomerular visceral epithelial cell differentiation|induction of apoptosis|male genitalia development|male gonad development|mesenchymal to epithelial transition|metanephric epithelium development|metanephric S-shaped body morphogenesis|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of female gonad development|negative regulation of metanephric glomerular mesangial cell proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|negative regulation of translation|positive regulation of male gonad development|positive regulation of transcription, DNA-dependent|posterior mesonephric tubule development|regulation of organ formation|RNA splicing|sex determination|vasculogenesis|visceral serous pericardium development	cytoplasm|nuclear speck|nucleoplasm	C2H2 zinc finger domain binding|RNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding	p.T309fs*73(3)|p.T309fs*12(3)|p.T309fs*9(2)|p.T309fs*8(2)|p.R301fs*3(1)|p.A307fs*69(1)|p.P308fs*67(1)|p.A307fs*70(1)|p.T309fs*75(1)|p.P308fs*9(1)|p.V300fs*6(1)|p.R301fs*73(1)|p.T309fs*71(1)|p.R302fs*12(1)	EWSR1/WT1(231)	haematopoietic_and_lymphoid_tissue(318)|soft_tissue(231)|kidney(132)|pleura(2)|lung(2)|upper_aerodigestive_tract(1)|peritoneum(1)	687	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			GTACAAGAGTCGGGGCTACTC	0.517			D|Mis|N|F|S	EWSR1	Wilms|desmoplastic small round cell tumor	Wilms			Denys-Drash_syndrome|Frasier_syndrome|Familial_Wilms_tumor|Wilms_tumor-Aniridia-ambiguous_Genitals-mental_Retardation				13	26	---	---	---	---	PASS
WT1	7490	broad.mit.edu	37	11	32450097	32450097	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32450097A>G	uc001mtn.1	-	2	911	c.715T>C	c.(715-717)TTC>CTC	p.F239L	WT1_uc001mtl.1_Missense_Mutation_p.F27L|WT1_uc001mtm.1_Missense_Mutation_p.F27L|WT1_uc001mto.1_Missense_Mutation_p.F239L|WT1_uc001mtp.1_Missense_Mutation_p.F239L|WT1_uc001mtq.1_Missense_Mutation_p.F239L|WT1_uc009yjs.1_RNA	NM_024426	NP_077744	P19544	WT1_HUMAN	Wilms tumor 1 isoform D	171					adrenal cortex formation|branching involved in ureteric bud morphogenesis|camera-type eye development|cardiac muscle cell fate commitment|cellular response to cAMP|cellular response to gonadotropin stimulus|germ cell development|glomerular basement membrane development|glomerular visceral epithelial cell differentiation|induction of apoptosis|male genitalia development|male gonad development|mesenchymal to epithelial transition|metanephric epithelium development|metanephric S-shaped body morphogenesis|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of female gonad development|negative regulation of metanephric glomerular mesangial cell proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|negative regulation of translation|positive regulation of male gonad development|positive regulation of transcription, DNA-dependent|posterior mesonephric tubule development|regulation of organ formation|RNA splicing|sex determination|vasculogenesis|visceral serous pericardium development	cytoplasm|nuclear speck|nucleoplasm	C2H2 zinc finger domain binding|RNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding		EWSR1/WT1(231)	haematopoietic_and_lymphoid_tissue(318)|soft_tissue(231)|kidney(132)|pleura(2)|lung(2)|upper_aerodigestive_tract(1)|peritoneum(1)	687	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			TGGTTGGGGAACTGCGCCGCA	0.632			D|Mis|N|F|S	EWSR1	Wilms|desmoplastic small round cell tumor	Wilms			Denys-Drash_syndrome|Frasier_syndrome|Familial_Wilms_tumor|Wilms_tumor-Aniridia-ambiguous_Genitals-mental_Retardation				8	20	---	---	---	---	PASS
CCDC73	493860	broad.mit.edu	37	11	32635972	32635972	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32635972G>C	uc001mtv.2	-	16	1936	c.1892C>G	c.(1891-1893)TCG>TGG	p.S631W		NM_001008391	NP_001008392	Q6ZRK6	CCD73_HUMAN	sarcoma antigen NY-SAR-79	631										ovary(1)|central_nervous_system(1)	2	Breast(20;0.112)					ATCTAGAGACGAGTCCAAATC	0.328													9	18	---	---	---	---	PASS
QSER1	79832	broad.mit.edu	37	11	32956358	32956358	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32956358G>T	uc001mty.2	+	4	3434	c.3167G>T	c.(3166-3168)AGT>ATT	p.S1056I	QSER1_uc001mtz.1_Missense_Mutation_p.S817I|QSER1_uc001mua.2_Missense_Mutation_p.S561I	NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	1056										ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)					GATGCAGTCAGTGTCAAGATT	0.428													13	69	---	---	---	---	PASS
C11orf41	25758	broad.mit.edu	37	11	33572687	33572687	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33572687G>C	uc001mup.3	+	4	2854	c.2730G>C	c.(2728-2730)GTG>GTC	p.V910V	C11orf41_uc001mun.1_Silent_p.V910V	NM_012194	NP_036326	Q6ZVL6	CK041_HUMAN	hypothetical protein LOC25758	904						integral to membrane				ovary(2)	2						TGCTGGGTGTGTATGGAGTCA	0.493													59	86	---	---	---	---	PASS
TRAF6	7189	broad.mit.edu	37	11	36511715	36511715	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36511715C>T	uc001mwr.1	-	8	1582	c.1242G>A	c.(1240-1242)ATG>ATA	p.M414I	uc001mwq.1_5'Flank|TRAF6_uc001mws.1_Missense_Mutation_p.M414I	NM_145803	NP_665802	Q9Y4K3	TRAF6_HUMAN	TNF receptor-associated factor 6	414	MATH.				activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|innate immune response|JNK cascade|membrane protein intracellular domain proteolysis|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|ossification|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of osteoclast differentiation|positive regulation of T cell cytokine production|protein autoubiquitination|protein K63-linked ubiquitination|response to interleukin-1|stress-activated MAPK cascade|T cell receptor signaling pathway|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	CD40 receptor complex|cell cortex|cytosol|endosome membrane|internal side of plasma membrane|nuclear membrane	histone deacetylase binding|mitogen-activated protein kinase kinase kinase binding|protein kinase B binding|protein N-terminus binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1	all_lung(20;0.211)	all_hematologic(20;0.107)				ATTCTCCTTGCATTGTGTGGA	0.493													12	26	---	---	---	---	PASS
RAG1	5896	broad.mit.edu	37	11	36595604	36595604	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36595604G>T	uc001mwu.3	+	2	874	c.750G>T	c.(748-750)AAG>AAT	p.K250N	RAG1_uc001mwt.2_RNA	NM_000448	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	250	Interaction with importin alpha-1.				histone monoubiquitination|immune response|pre-B cell allelic exclusion|protein autoubiquitination|T cell differentiation in thymus|V(D)J recombination	nucleus	endonuclease activity|histone binding|protein homodimerization activity|sequence-specific DNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|pancreas(1)|lung(1)|kidney(1)|skin(1)	5	all_lung(20;0.226)	all_hematologic(20;0.107)				GTCAGCACAAGAGAAGAGCTC	0.498									Familial_Hemophagocytic_Lymphohistiocytosis				9	51	---	---	---	---	PASS
LRRC4C	57689	broad.mit.edu	37	11	40137549	40137549	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40137549G>C	uc001mxa.1	-	2	2258	c.294C>G	c.(292-294)CAC>CAG	p.H98Q	LRRC4C_uc001mxc.1_Missense_Mutation_p.H94Q|LRRC4C_uc001mxd.1_Missense_Mutation_p.H94Q|LRRC4C_uc001mxb.1_Missense_Mutation_p.H94Q	NM_020929	NP_065980	Q9HCJ2	LRC4C_HUMAN	netrin-G1 ligand precursor	98	LRR 1.				regulation of axonogenesis	integral to membrane	protein binding			ovary(4)|skin(3)|central_nervous_system(1)	8		all_lung(304;0.0575)|Lung NSC(402;0.138)				AGTGTCTCAAGTGCTTGAAGC	0.473													6	42	---	---	---	---	PASS
DDB2	1643	broad.mit.edu	37	11	47238436	47238436	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47238436C>G	uc001neb.2	+	3	487	c.292C>G	c.(292-294)CTG>GTG	p.L98V	DDB2_uc001nec.2_RNA|DDB2_uc009yli.1_Intron|DDB2_uc001ned.2_RNA|DDB2_uc001nee.2_Missense_Mutation_p.L98V|DDB2_uc001nef.2_Missense_Mutation_p.L84V|DDB2_uc001neg.2_5'UTR|DDB2_uc001neh.2_RNA	NM_000107	NP_000098	Q92466	DDB2_HUMAN	damage-specific DNA binding protein 2	98	Required for interaction with DDB1.				nucleotide-excision repair, DNA damage removal|protein autoubiquitination|protein polyubiquitination|response to UV	nucleoplasm|protein complex	damaged DNA binding|protein binding			kidney(2)|ovary(1)	3						TTTGCACACTCTGGATTCTTA	0.512			Mis|N			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				6	13	---	---	---	---	PASS
MADD	8567	broad.mit.edu	37	11	47312322	47312322	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47312322C>T	uc001ner.1	+	20	3507	c.3316C>T	c.(3316-3318)CTG>TTG	p.L1106L	MADD_uc001neq.2_Silent_p.L1086L|MADD_uc001nev.1_Silent_p.L1043L|MADD_uc001nes.1_Silent_p.L1063L|MADD_uc001net.1_Silent_p.L1106L|MADD_uc009yln.1_Silent_p.L1043L|MADD_uc001neu.1_Silent_p.L1043L|MADD_uc001nex.2_Silent_p.L1106L|MADD_uc001nez.2_Silent_p.L1043L|MADD_uc001new.2_Silent_p.L1086L|MADD_uc009ylo.2_Silent_p.L24L	NM_003682	NP_003673	Q8WXG6	MADD_HUMAN	MAP-kinase activating death domain-containing	1106					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)		TCCTAAGGAACTGGACACCAG	0.507													13	40	---	---	---	---	PASS
OR4B1	119765	broad.mit.edu	37	11	48239093	48239093	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48239093G>C	uc010rhs.1	+	1	732	c.732G>C	c.(730-732)GTG>GTC	p.V244V		NM_001005470	NP_001005470	Q8NGF8	OR4B1_HUMAN	olfactory receptor, family 4, subfamily B,	244	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)|pancreas(1)	4						ACATCACAGTGGTCATCTTGT	0.468													5	63	---	---	---	---	PASS
OR4A5	81318	broad.mit.edu	37	11	51411878	51411878	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:51411878T>C	uc001nhi.1	-	1	518	c.518A>G	c.(517-519)CAT>CGT	p.H173R		NM_001005272	NP_001005272	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A,	173	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		all_lung(304;0.236)				ACAACTGAAATGAACAATGAC	0.443													5	42	---	---	---	---	PASS
OR4C6	219432	broad.mit.edu	37	11	55433256	55433256	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55433256G>T	uc001nht.3	+	3	879	c.614G>T	c.(613-615)TGT>TTT	p.C205F	OR4C6_uc010rik.1_Missense_Mutation_p.C205F	NM_001004704	NP_001004704	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C,	205	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2						GGGATGATGTGTGTGGCCATC	0.478													14	56	---	---	---	---	PASS
OR5D18	219438	broad.mit.edu	37	11	55587261	55587261	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55587261C>G	uc010rin.1	+	1	156	c.156C>G	c.(154-156)ATC>ATG	p.I52M		NM_001001952	NP_001001952	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D,	52	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3		all_epithelial(135;0.208)				TCATCAAAATCAACCCCAAAC	0.453													14	99	---	---	---	---	PASS
OR5L2	26338	broad.mit.edu	37	11	55595417	55595417	+	Silent	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55595417T>C	uc001nhy.1	+	1	723	c.723T>C	c.(721-723)TGT>TGC	p.C241C		NM_001004739	NP_001004739	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L,	241	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		all_epithelial(135;0.208)				TCTCCACCTGTGCCTCCCACC	0.493										HNSCC(27;0.073)			29	53	---	---	---	---	PASS
OR8I2	120586	broad.mit.edu	37	11	55861081	55861081	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55861081C>G	uc010rix.1	+	1	298	c.298C>G	c.(298-300)CAA>GAA	p.Q100E		NM_001003750	NP_001003750	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I,	100	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(1)	1	Esophageal squamous(21;0.00693)					CTGCTTTGTTCAAATGTACTT	0.398													16	100	---	---	---	---	PASS
OR5J2	282775	broad.mit.edu	37	11	55944717	55944717	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55944717G>T	uc010rjb.1	+	1	624	c.624G>T	c.(622-624)ATG>ATT	p.M208I		NM_001005492	NP_001005492	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J,	208	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|large_intestine(1)|breast(1)|pancreas(1)	4	Esophageal squamous(21;0.00693)					TCATTGCCATGGCCACCTTCT	0.478													14	61	---	---	---	---	PASS
OR5M9	390162	broad.mit.edu	37	11	56230190	56230190	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56230190C>T	uc010rjj.1	-	1	688	c.688G>A	c.(688-690)GAT>AAT	p.D230N		NM_001004743	NP_001004743	Q8NGP3	OR5M9_HUMAN	olfactory receptor, family 5, subfamily M,	230	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4	Esophageal squamous(21;0.00448)					CTCCTGCCATCGGCAGAGCGC	0.498													12	9	---	---	---	---	PASS
OR5AR1	219493	broad.mit.edu	37	11	56431331	56431331	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56431331C>G	uc010rjm.1	+	1	170	c.170C>G	c.(169-171)ACA>AGA	p.T57R		NM_001004730	NP_001004730	Q8NGP9	O5AR1_HUMAN	olfactory receptor, family 5, subfamily AR,	57	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						CAGCTTCACACACCCATGTAT	0.448													33	118	---	---	---	---	PASS
OR9G9	504191	broad.mit.edu	37	11	56468215	56468215	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56468215G>C	uc010rjn.1	+	1	352	c.352G>C	c.(352-354)GCT>CCT	p.A118P		NM_001013358	NP_001013376	P0C7N8	OR9G9_HUMAN	olfactory receptor, family 9, subfamily G,	118	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						GGCTGCCGTGGCTTATGACCG	0.537													4	52	---	---	---	---	PASS
LRRC55	219527	broad.mit.edu	37	11	56949613	56949613	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56949613C>G	uc001njl.1	+	1	393	c.246C>G	c.(244-246)CCC>CCG	p.P82P		NM_001005210	NP_001005210	Q6ZSA7	LRC55_HUMAN	leucine rich repeat containing 55	52	LRRNT.					integral to membrane					0						CCAGCTGCCCCGTCCTTTGCA	0.647													7	25	---	---	---	---	PASS
OR5B12	390191	broad.mit.edu	37	11	58207465	58207465	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58207465G>C	uc010rkh.1	-	1	160	c.160C>G	c.(160-162)CAC>GAC	p.H54D		NM_001004733	NP_001004733	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B,	54	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				ATGGGGGTGTGGAGACAGGAG	0.493													16	39	---	---	---	---	PASS
GLYATL1	92292	broad.mit.edu	37	11	58715443	58715443	+	Intron	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58715443G>A	uc001nnf.2	+						uc001nng.1_Intron|GLYATL1_uc001nnh.1_Intron|GLYATL1_uc001nni.1_Intron|GLYATL1_uc001nnj.1_Intron			Q969I3	GLYL1_HUMAN	SubName: Full=Glycine acyltransferase family-C; SubName: Full=Glycine-N-acyltransferase-like 1, isoform CRA_a;							mitochondrion	glycine N-acyltransferase activity			ovary(1)	1					Glycine(DB00145)	AAGCAGGTAGGCACACAGACA	0.527													10	24	---	---	---	---	PASS
OR5A1	219982	broad.mit.edu	37	11	59211286	59211286	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59211286C>G	uc001nnx.1	+	1	645	c.645C>G	c.(643-645)CTC>CTG	p.L215L		NM_001004728	NP_001004728	Q8NGJ0	OR5A1_HUMAN	olfactory receptor, family 5, subfamily A,	215	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)	2						CATCGTTCCTCCAACTCCTTA	0.547													44	92	---	---	---	---	PASS
OR4D9	390199	broad.mit.edu	37	11	59282638	59282638	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59282638C>A	uc010rkv.1	+	1	253	c.253C>A	c.(253-255)CTT>ATT	p.L85I		NM_001004711	NP_001004711	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D,	85	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						CCTGATAGATCTTCTATCAGA	0.463													19	56	---	---	---	---	PASS
MRPL16	54948	broad.mit.edu	37	11	59574004	59574004	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59574004C>G	uc001noh.2	-	4	786	c.572G>C	c.(571-573)AGC>ACC	p.S191T		NM_017840	NP_060310	Q9NX20	RM16_HUMAN	mitochondrial ribosomal protein L16 precursor	191							rRNA binding			central_nervous_system(1)	1						AGTCCCGCGGCTCACAGCCTT	0.512													13	86	---	---	---	---	PASS
MS4A6E	245802	broad.mit.edu	37	11	60105243	60105243	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60105243G>C	uc001npd.2	+	2	191	c.177G>C	c.(175-177)CTG>CTC	p.L59L		NM_139249	NP_640342	Q96DS6	M4A6E_HUMAN	membrane-spanning 4-domains, subfamily A, member	59	Helical; (Potential).					integral to membrane	receptor activity				0						GAAGCATTCTGAGTGCTCTGT	0.483													9	67	---	---	---	---	PASS
TMEM109	79073	broad.mit.edu	37	11	60687196	60687196	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60687196G>T	uc001nqg.2	+	2	409	c.31G>T	c.(31-33)GGA>TGA	p.G11*	TMEM109_uc001nqh.2_Nonsense_Mutation_p.G11*	NM_024092	NP_076997	Q9BVC6	TM109_HUMAN	transmembrane protein 109 precursor	11						integral to membrane|nuclear outer membrane|sarcoplasmic reticulum membrane					0						TTCACCATGGGGAAAGCATGT	0.562													24	41	---	---	---	---	PASS
CD6	923	broad.mit.edu	37	11	60785239	60785239	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60785239G>A	uc001nqq.2	+	11	1814	c.1591G>A	c.(1591-1593)GAG>AAG	p.E531K	CD6_uc001nqp.2_Missense_Mutation_p.E531K|CD6_uc001nqr.2_Missense_Mutation_p.E499K|CD6_uc001nqs.2_RNA|CD6_uc001nqt.2_Missense_Mutation_p.E490K	NM_006725	NP_006716	P30203	CD6_HUMAN	CD6 molecule precursor	531	Cytoplasmic (Potential).				cell adhesion	cell surface|integral to plasma membrane	scavenger receptor activity			pancreas(1)	1						AGGACTTGAAGAGTTGCATGC	0.408													15	82	---	---	---	---	PASS
PGA3	643834	broad.mit.edu	37	11	60971058	60971058	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60971058G>C	uc001nqx.2	+	1	75	c.22G>C	c.(22-24)GGT>CGT	p.G8R	PGA3_uc010rld.1_Missense_Mutation_p.G8R	NM_001079807	NP_001073275			pepsinogen 3, group I precursor											ovary(1)|skin(1)	2						GCTGCTGCTGGGTCTGGTGGC	0.582													9	13	---	---	---	---	PASS
INCENP	3619	broad.mit.edu	37	11	61919412	61919412	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61919412C>G	uc001nsw.1	+	19	2923	c.2721C>G	c.(2719-2721)GTC>GTG	p.V907V	INCENP_uc001nsx.1_Silent_p.V903V|INCENP_uc001nsy.1_Silent_p.V321V	NM_001040694	NP_001035784	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	907					chromosome segregation|cytokinesis|mitotic prometaphase	centromeric heterochromatin|condensed chromosome kinetochore|cytosol|microtubule|spindle	protein binding			lung(1)	1						GCGCCAGGGTCCCCAGCAGCC	0.557													5	18	---	---	---	---	PASS
PYGM	5837	broad.mit.edu	37	11	64514687	64514687	+	Intron	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64514687C>G	uc001oax.3	-						RASGRP2_uc009ypv.2_5'Flank|RASGRP2_uc009ypw.2_5'Flank|RASGRP2_uc001oaw.1_5'Flank|PYGM_uc001oay.3_Intron	NM_005609	NP_005600	P11217	PYGM_HUMAN	muscle glycogen phosphorylase isoform 1						glucose metabolic process|glycogen catabolic process	cytosol	glycogen phosphorylase activity|protein binding			ovary(2)	2					Pyridoxal Phosphate(DB00114)	CCCGGGCCAACCAGCTCACCG	0.617													12	30	---	---	---	---	PASS
MALAT1	378938	broad.mit.edu	37	11	65267905	65267905	+	RNA	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65267905G>A	uc010roh.1	+	1		c.2673G>A			uc001ody.2_RNA|MALAT1_uc001odz.2_5'Flank	NR_002819				Homo sapiens clone alpha1 mRNA sequence.												0						AATCTAGGAAGACAGCAGCAG	0.448													22	40	---	---	---	---	PASS
MALAT1	378938	broad.mit.edu	37	11	65268000	65268000	+	RNA	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65268000G>C	uc010roh.1	+	1		c.2768G>C			uc001ody.2_RNA|MALAT1_uc001odz.2_5'Flank	NR_002819				Homo sapiens clone alpha1 mRNA sequence.												0						GATAGGAAAAGAGTCCAGGAG	0.507													18	59	---	---	---	---	PASS
ACY3	91703	broad.mit.edu	37	11	67413199	67413199	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67413199G>A	uc001omq.2	-	4	567	c.396C>T	c.(394-396)CAC>CAT	p.H132H		NM_080658	NP_542389	Q96HD9	ACY3_HUMAN	aspartoacylase 3	132					interspecies interaction between organisms	apical plasma membrane|cytoplasm	hydrolase activity, acting on ester bonds|metal ion binding				0					L-Aspartic Acid(DB00128)	CAAAGACTTCGTGGGAGGACT	0.652													44	31	---	---	---	---	PASS
PPFIA1	8500	broad.mit.edu	37	11	70200404	70200404	+	Intron	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70200404C>A	uc001opo.2	+						PPFIA1_uc001opn.1_Intron|PPFIA1_uc001opp.2_Intron|PPFIA1_uc001opq.1_Intron	NM_003626	NP_003617	Q13136	LIPA1_HUMAN	PTPRF interacting protein alpha 1 isoform b						cell-matrix adhesion	cytoplasm	protein binding|signal transducer activity			lung(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			TCTCACCCCTCAGTTGCCACC	0.468													35	43	---	---	---	---	PASS
KRTAP5-11	440051	broad.mit.edu	37	11	71293514	71293514	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71293514G>A	uc001oqu.2	-	1	408	c.370C>T	c.(370-372)CCC>TCC	p.P124S		NM_001005405	NP_001005405	Q6L8G4	KR511_HUMAN	keratin associated protein 5-11	124	5.|6 X 4 AA repeats of C-C-X-P.					keratin filament					0						cagcagcagggcttgcagcag	0.085													7	67	---	---	---	---	PASS
ARHGEF17	9828	broad.mit.edu	37	11	73020284	73020284	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73020284C>A	uc001otu.2	+	1	622	c.601C>A	c.(601-603)CAG>AAG	p.Q201K		NM_014786	NP_055601	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	201	Poly-Gln.				actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity				0						GCGCCGGCCGCAGCAGCAACA	0.716													12	11	---	---	---	---	PASS
C11orf30	56946	broad.mit.edu	37	11	76162994	76162994	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76162994G>C	uc001oxl.2	+	3	306	c.163G>C	c.(163-165)GTT>CTT	p.V55L	C11orf30_uc001oxj.2_Missense_Mutation_p.V55L|C11orf30_uc001oxk.2_Missense_Mutation_p.V55L|C11orf30_uc009yuj.1_Missense_Mutation_p.V55L|C11orf30_uc010rsa.1_Missense_Mutation_p.V55L|C11orf30_uc001oxm.2_Missense_Mutation_p.V55L|C11orf30_uc010rsb.1_Missense_Mutation_p.V55L|C11orf30_uc010rsc.1_Missense_Mutation_p.V55L|C11orf30_uc001oxn.2_Missense_Mutation_p.V55L|C11orf30_uc010rsd.1_Missense_Mutation_p.V55L	NM_020193	NP_064578	Q7Z589	EMSY_HUMAN	EMSY protein	55	Interaction with BRCA2.|ENT.				chromatin modification|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6						ACTATCAAAAGTTCTTAGGTA	0.348													3	30	---	---	---	---	PASS
NARS2	79731	broad.mit.edu	37	11	78285425	78285425	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78285425G>C	uc001ozi.2	-	1	485	c.109C>G	c.(109-111)CAG>GAG	p.Q37E	NARS2_uc010rsq.1_Intron	NM_024678	NP_078954	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial	37					asparaginyl-tRNA aminoacylation	mitochondrial matrix	asparagine-tRNA ligase activity|ATP binding|nucleic acid binding			ovary(2)	2	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	CTCGCGTTCTGAGCCCCGAGA	0.577													107	73	---	---	---	---	PASS
SYTL2	54843	broad.mit.edu	37	11	85447559	85447559	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85447559G>C	uc010rth.1	-	5	844	c.568C>G	c.(568-570)CAG>GAG	p.Q190E	SYTL2_uc010rtg.1_Missense_Mutation_p.Q191E|SYTL2_uc010rti.1_Missense_Mutation_p.Q190E|SYTL2_uc010rtj.1_Missense_Mutation_p.Q142E|SYTL2_uc001pbf.3_Missense_Mutation_p.Q190E|SYTL2_uc010rtf.1_Missense_Mutation_p.Q48E	NM_001162951	NP_001156423	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2 isoform g	190					intracellular protein transport|vesicle docking involved in exocytosis	exocytic vesicle|extrinsic to plasma membrane|melanosome|membrane fraction	neurexin binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding|Rab GTPase binding	p.G190V(1)		ovary(2)|large_intestine(1)	3		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		TTTGAAGTCTGAAATAAACCA	0.333													11	24	---	---	---	---	PASS
FAT3	120114	broad.mit.edu	37	11	92533735	92533735	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92533735G>C	uc001pdj.3	+	9	7573	c.7556G>C	c.(7555-7557)CGA>CCA	p.R2519P		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	2519	Cadherin 23.|Extracellular (Potential).				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)				ATTCATGTTCGAGCCACAGAT	0.493										TCGA Ovarian(4;0.039)			10	23	---	---	---	---	PASS
FAT3	120114	broad.mit.edu	37	11	92600001	92600001	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92600001A>T	uc001pdj.3	+	21	11770	c.11753A>T	c.(11752-11754)CAC>CTC	p.H3918L	FAT3_uc001pdi.3_Missense_Mutation_p.H358L	NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	3918	Laminin G-like.|Extracellular (Potential).				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)				GGGAGCTGGCACTCGGTCTTC	0.637										TCGA Ovarian(4;0.039)			12	15	---	---	---	---	PASS
SLC36A4	120103	broad.mit.edu	37	11	92881849	92881849	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92881849C>A	uc001pdn.2	-	11	1466	c.1369G>T	c.(1369-1371)GCA>TCA	p.A457S	uc001pdl.1_5'Flank|SLC36A4_uc001pdm.2_Missense_Mutation_p.A322S	NM_152313	NP_689526	Q6YBV0	S36A4_HUMAN	solute carrier family 36 (proton/amino acid	457	Helical; (Potential).				L-alanine transport|proline transport|tryptophan transport	integral to membrane	symporter activity			ovary(2)|upper_aerodigestive_tract(1)	3		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CCAGTGAATGCTATAGAAATA	0.378													15	49	---	---	---	---	PASS
MRE11A	4361	broad.mit.edu	37	11	94194214	94194214	+	Intron	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94194214G>C	uc001peu.2	-						MRE11A_uc001pev.2_Intron|MRE11A_uc009ywj.2_Intron	NM_005591	NP_005582	P49959	MRE11_HUMAN	meiotic recombination 11 homolog A isoform 1						DNA duplex unwinding|double-strand break repair via homologous recombination|double-strand break repair via nonhomologous end joining|negative regulation of DNA endoreduplication|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|sister chromatid cohesion|telomere maintenance via telomerase	Mre11 complex|nucleoplasm	3'-5' exonuclease activity|double-stranded DNA binding|manganese ion binding|protein C-terminus binding|single-stranded DNA specific endodeoxyribonuclease activity			breast(4)|lung(1)	5		Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824)				TAGAAAAAAAGAAGTATATCA	0.353								Homologous_recombination	Ataxia-Telangiectasia-Like_Disorder				4	13	---	---	---	---	PASS
ENDOD1	23052	broad.mit.edu	37	11	94861787	94861787	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94861787G>A	uc001pfh.2	+	2	622	c.547G>A	c.(547-549)GAC>AAC	p.D183N		NM_015036	NP_055851	O94919	ENDD1_HUMAN	endonuclease domain containing 1 precursor	183						extracellular region	endonuclease activity|metal ion binding|nucleic acid binding				0		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.00824)				CAGCCTAATGGACCGGGCTTT	0.517													15	32	---	---	---	---	PASS
KIAA1377	57562	broad.mit.edu	37	11	101834216	101834216	+	Missense_Mutation	SNP	A	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101834216A>C	uc001pgm.2	+	6	2720	c.2450A>C	c.(2449-2451)CAA>CCA	p.Q817P	KIAA1377_uc001pgn.2_Missense_Mutation_p.Q773P|KIAA1377_uc010run.1_Missense_Mutation_p.Q618P|KIAA1377_uc009yxa.1_Missense_Mutation_p.Q618P	NM_020802	NP_065853	Q9P2H0	K1377_HUMAN	hypothetical protein LOC57562	817							protein binding			breast(2)|ovary(1)|central_nervous_system(1)	4	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		AAAAATATACAAGTGTCTCAG	0.338													18	29	---	---	---	---	PASS
ATM	472	broad.mit.edu	37	11	108163339	108163339	+	Intron	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108163339A>G	uc001pkb.1	+						ATM_uc009yxr.1_Intron|ATM_uc001pke.1_Intron|ATM_uc001pkf.2_Intron	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1						cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		TTTTCTCCCTATATTAGGCCT	0.358			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			26	66	---	---	---	---	PASS
EXPH5	23086	broad.mit.edu	37	11	108382262	108382262	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108382262G>C	uc001pkk.2	-	6	4083	c.3972C>G	c.(3970-3972)CTC>CTG	p.L1324L	EXPH5_uc010rvy.1_Silent_p.L1136L|EXPH5_uc010rvz.1_Silent_p.L1168L|EXPH5_uc010rwa.1_Silent_p.L1248L	NM_015065	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5 isoform a	1324					intracellular protein transport		Rab GTPase binding			skin(3)|ovary(2)	5		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		TTTCAGTGGTGAGCGTCTGAT	0.438													12	18	---	---	---	---	PASS
RDX	5962	broad.mit.edu	37	11	110128828	110128828	+	Intron	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110128828T>A	uc001pku.2	-						RDX_uc009yxx.1_Intron|RDX_uc009yxy.2_Intron|RDX_uc009yxz.2_Intron|RDX_uc009yya.2_Intron|RDX_uc010rwe.1_Intron	NM_002906	NP_002897	P35241	RADI_HUMAN	radixin						actin filament capping	cleavage furrow|cytoskeleton|extrinsic to membrane|Golgi apparatus|nucleolus|plasma membrane	actin binding				0		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248)		GCTACCCAAATACCTTAACAT	0.308													17	25	---	---	---	---	PASS
ARHGAP20	57569	broad.mit.edu	37	11	110456944	110456944	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110456944G>C	uc001pkz.1	-	13	1696	c.1411C>G	c.(1411-1413)CAA>GAA	p.Q471E	ARHGAP20_uc001pky.1_Missense_Mutation_p.Q448E|ARHGAP20_uc009yyb.1_Missense_Mutation_p.Q435E|ARHGAP20_uc001pla.1_Missense_Mutation_p.Q435E|ARHGAP20_uc001plb.2_Missense_Mutation_p.Q14E	NM_020809	NP_065860	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	471	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)|kidney(2)	5		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		AATTACCTTTGAACAGTATTT	0.264													5	28	---	---	---	---	PASS
NCAM1	4684	broad.mit.edu	37	11	113075051	113075051	+	5'UTR	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113075051C>G	uc009yyq.1	+	3					NCAM1_uc001pno.2_5'UTR	NM_001076682	NP_001070150	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1 isoform 3						axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane				ovary(1)	1		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		GGTTCTCCCCCAATGGAGAAA	0.473													8	13	---	---	---	---	PASS
APOA4	337	broad.mit.edu	37	11	116693478	116693478	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116693478C>T	uc001pps.1	-	2	177	c.73G>A	c.(73-75)GAC>AAC	p.D25N		NM_000482	NP_000473			apolipoprotein A-IV precursor												0	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		GCCACCTGGTCAGCACTGACC	0.582													20	32	---	---	---	---	PASS
SORL1	6653	broad.mit.edu	37	11	121476146	121476146	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121476146C>T	uc001pxx.2	+	35	4894	c.4814C>T	c.(4813-4815)ACC>ATC	p.T1605I	SORL1_uc010rzp.1_Missense_Mutation_p.T451I|SORL1_uc010rzq.1_Missense_Mutation_p.T220I	NM_003105	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor containing LDLR class	1605	Extracellular (Potential).|Fibronectin type-III 1.				cholesterol metabolic process|lipid transport|receptor-mediated endocytosis	integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|transmembrane receptor activity			ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)|pancreas(1)	15		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		ACTCTGGAGACCCACAGCAAT	0.453													43	89	---	---	---	---	PASS
SORL1	6653	broad.mit.edu	37	11	121485651	121485651	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121485651C>G	uc001pxx.2	+	41	5571	c.5491C>G	c.(5491-5493)CTG>GTG	p.L1831V	SORL1_uc010rzp.1_Missense_Mutation_p.L677V|SORL1_uc010rzq.1_Missense_Mutation_p.L446V	NM_003105	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor containing LDLR class	1831	Extracellular (Potential).|Fibronectin type-III 3.				cholesterol metabolic process|lipid transport|receptor-mediated endocytosis	integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|transmembrane receptor activity			ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)|pancreas(1)	15		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		GGATAGCCCTCTGGCATTTGA	0.527													18	39	---	---	---	---	PASS
OR6M1	390261	broad.mit.edu	37	11	123676886	123676886	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123676886A>T	uc010rzz.1	-	1	172	c.172T>A	c.(172-174)TAC>AAC	p.Y58N		NM_001005325	NP_001005325	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M,	58	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)		AGGAAGAAGTACATTGGAGTT	0.423													13	73	---	---	---	---	PASS
OR6T1	219874	broad.mit.edu	37	11	123814316	123814316	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123814316A>T	uc010sab.1	-	1	230	c.230T>A	c.(229-231)GTG>GAG	p.V77E		NM_001005187	NP_001005187	Q8NGN1	OR6T1_HUMAN	olfactory receptor, family 6, subfamily T,	77	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		CTTGGGAACCACAACAGTTAC	0.488													38	56	---	---	---	---	PASS
OR10G9	219870	broad.mit.edu	37	11	123893820	123893820	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123893820T>A	uc010sad.1	+	1	101	c.101T>A	c.(100-102)GTG>GAG	p.V34E		NM_001001953	NP_001001953	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G,	34	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		GTGGTTTACGTGCTCACTGTG	0.572													13	68	---	---	---	---	PASS
OR8G2	26492	broad.mit.edu	37	11	124096236	124096236	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124096236C>A	uc010saf.1	+	1	839	c.839C>A	c.(838-840)TCC>TAC	p.S280Y		NM_001007249	NP_001007250	Q15614	OR8G2_HUMAN	olfactory receptor, family 8, subfamily G,	280						integral to membrane	olfactory receptor activity				0		Breast(109;0.0157)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.91e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0528)		TCTGTCAGCTCCATGGACCAG	0.478													36	68	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	124135437	124135437	+	IGR	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124135437G>T								OR8G2 (39127 upstream) : OR8D1 (44300 downstream)																							AATCTTTAGTGGAATTAACAT	0.408													36	52	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	124135727	124135727	+	IGR	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124135727C>A								OR8G2 (39417 upstream) : OR8D1 (44010 downstream)																							TCCACGTTGCCCTGAAGAAAA	0.403													16	39	---	---	---	---	PASS
HEPACAM	220296	broad.mit.edu	37	11	124793658	124793658	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124793658C>A	uc001qbk.2	-	3	1082	c.676G>T	c.(676-678)GGC>TGC	p.G226C	HEPACAM_uc009zbj.2_5'Flank|HEPACAM_uc001qbl.1_Missense_Mutation_p.G226C	NM_152722	NP_689935	Q14CZ8	HECAM_HUMAN	hepatocyte cell adhesion molecule precursor	226	Extracellular (Potential).|Ig-like C2-type.				cell adhesion|cell cycle arrest|regulation of growth	cytoplasm|integral to membrane				pancreas(1)	1	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.54e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)		AGGCTGCGGCCCTGGCTGATG	0.577													5	25	---	---	---	---	PASS
KCNJ1	3758	broad.mit.edu	37	11	128710133	128710133	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128710133G>C	uc001qeo.1	-	2	114	c.63C>G	c.(61-63)TTC>TTG	p.F21L	KCNJ1_uc001qep.1_Missense_Mutation_p.F2L|KCNJ1_uc001qeq.1_Missense_Mutation_p.F2L|KCNJ1_uc001qer.1_Missense_Mutation_p.F2L|KCNJ1_uc001qes.1_Missense_Mutation_p.F2L	NM_000220	NP_000211	P48048	IRK1_HUMAN	potassium inwardly-rectifying channel J1 isoform	21	Cytoplasmic (By similarity).				excretion	voltage-gated potassium channel complex	ATP binding|inward rectifier potassium channel activity			ovary(3)|breast(1)	4	all_hematologic(175;0.0641)	all_lung(97;4.89e-06)|Lung NSC(97;9.34e-06)|Breast(109;0.00123)|all_hematologic(192;0.00793)|Renal(330;0.0112)|all_neural(223;0.0189)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;4.05e-06)|LUSC - Lung squamous cell carcinoma(976;0.008)|Lung(977;0.00942)	Acetohexamide(DB00414)|Chlorpropamide(DB00672)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Glycodiazine(DB01382)|Minoxidil(DB00350)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolazamide(DB00839)|Tolbutamide(DB01124)	GAAGATGTTTGAACATACTTT	0.403													13	50	---	---	---	---	PASS
KDM5A	5927	broad.mit.edu	37	12	427394	427394	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:427394C>G	uc001qif.1	-	19	3138	c.2775G>C	c.(2773-2775)CTG>CTC	p.L925L	KDM5A_uc001qie.1_Silent_p.L925L|KDM5A_uc010sdn.1_Silent_p.L884L	NM_001042603	NP_001036068	P29375	KDM5A_HUMAN	retinoblastoma binding protein 2 isoform 1	925					chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3						CAGAGTCTATCAGCTTCTTCA	0.502			T 	NUP98	AML								57	39	---	---	---	---	PASS
CACNA1C	775	broad.mit.edu	37	12	2659802	2659802	+	Intron	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2659802C>A	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qka.1_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron|CACNA1C_uc009zdy.1_Missense_Mutation_p.T150K|CACNA1C_uc001qkv.1_Intron	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,						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)	GAACTGCAAACAGAGGCTCTG	0.582													20	13	---	---	---	---	PASS
CACNA1C	775	broad.mit.edu	37	12	2693757	2693757	+	Missense_Mutation	SNP	G	T	T	rs150598253	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2693757G>T	uc009zdu.1	+	16	2626	c.2313G>T	c.(2311-2313)GAG>GAT	p.E771D	CACNA1C_uc009zdv.1_Missense_Mutation_p.E768D|CACNA1C_uc001qkb.2_Missense_Mutation_p.E771D|CACNA1C_uc001qkc.2_Missense_Mutation_p.E771D|CACNA1C_uc001qke.2_Missense_Mutation_p.E771D|CACNA1C_uc001qkf.2_Missense_Mutation_p.E771D|CACNA1C_uc001qjz.2_Missense_Mutation_p.E771D|CACNA1C_uc001qkd.2_Missense_Mutation_p.E771D|CACNA1C_uc001qkg.2_Missense_Mutation_p.E771D|CACNA1C_uc009zdw.1_Missense_Mutation_p.E771D|CACNA1C_uc001qkh.2_Missense_Mutation_p.E771D|CACNA1C_uc001qkl.2_Missense_Mutation_p.E771D|CACNA1C_uc001qkn.2_Missense_Mutation_p.E771D|CACNA1C_uc001qko.2_Missense_Mutation_p.E771D|CACNA1C_uc001qkp.2_Missense_Mutation_p.E771D|CACNA1C_uc001qkr.2_Missense_Mutation_p.E771D|CACNA1C_uc001qku.2_Missense_Mutation_p.E771D|CACNA1C_uc001qkq.2_Missense_Mutation_p.E771D|CACNA1C_uc001qks.2_Missense_Mutation_p.E771D|CACNA1C_uc001qkt.2_Missense_Mutation_p.E771D|CACNA1C_uc001qka.1_Missense_Mutation_p.E306D|CACNA1C_uc001qki.1_Missense_Mutation_p.E507D|CACNA1C_uc001qkj.1_Missense_Mutation_p.E507D|CACNA1C_uc001qkk.1_Missense_Mutation_p.E507D|CACNA1C_uc001qkm.1_Missense_Mutation_p.E507D|CACNA1C_uc001qkw.2_Missense_Mutation_p.E60D	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	771	Cytoplasmic (Potential).|Poly-Glu.				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)	aggaggaagaggagaaggaga	0.468													19	45	---	---	---	---	PASS
CACNA1C	775	broad.mit.edu	37	12	2702441	2702441	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2702441C>T	uc009zdu.1	+	19	2906	c.2593C>T	c.(2593-2595)CTT>TTT	p.L865F	CACNA1C_uc009zdv.1_Missense_Mutation_p.L862F|CACNA1C_uc001qkb.2_Missense_Mutation_p.L865F|CACNA1C_uc001qkc.2_Missense_Mutation_p.L865F|CACNA1C_uc001qke.2_Missense_Mutation_p.L865F|CACNA1C_uc001qkf.2_Missense_Mutation_p.L865F|CACNA1C_uc001qjz.2_Missense_Mutation_p.L865F|CACNA1C_uc001qkd.2_Missense_Mutation_p.L865F|CACNA1C_uc001qkg.2_Missense_Mutation_p.L865F|CACNA1C_uc009zdw.1_Missense_Mutation_p.L865F|CACNA1C_uc001qkh.2_Missense_Mutation_p.L865F|CACNA1C_uc001qkl.2_Missense_Mutation_p.L865F|CACNA1C_uc001qkn.2_Missense_Mutation_p.L865F|CACNA1C_uc001qko.2_Missense_Mutation_p.L865F|CACNA1C_uc001qkp.2_Missense_Mutation_p.L865F|CACNA1C_uc001qkr.2_Missense_Mutation_p.L865F|CACNA1C_uc001qku.2_Missense_Mutation_p.L865F|CACNA1C_uc001qkq.2_Missense_Mutation_p.L865F|CACNA1C_uc001qks.2_Missense_Mutation_p.L865F|CACNA1C_uc001qkt.2_Missense_Mutation_p.L865F|CACNA1C_uc001qka.1_Missense_Mutation_p.L400F|CACNA1C_uc001qki.1_Missense_Mutation_p.L601F|CACNA1C_uc001qkj.1_Missense_Mutation_p.L601F|CACNA1C_uc001qkk.1_Missense_Mutation_p.L601F|CACNA1C_uc001qkm.1_Missense_Mutation_p.L601F|CACNA1C_uc001qkw.2_Missense_Mutation_p.L154F	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	865	Cytoplasmic (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)	ACTCTCTGAGCTTCACCTTAA	0.537													5	33	---	---	---	---	PASS
FKBP4	2288	broad.mit.edu	37	12	2906971	2906971	+	Silent	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2906971A>G	uc001qkz.2	+	3	525	c.327A>G	c.(325-327)CCA>CCG	p.P109P		NM_002014	NP_002005	Q02790	FKBP4_HUMAN	FK506 binding protein 52	109	PPIase FKBP-type 1.				negative regulation of microtubule polymerization or depolymerization|negative regulation of neuron projection development|protein folding	axonal growth cone|cytosol|membrane|microtubule|nucleus	FK506 binding|heat shock protein binding|peptidyl-prolyl cis-trans isomerase activity|protein binding, bridging				0			OV - Ovarian serous cystadenocarcinoma(31;0.00105)		Dimethyl sulfoxide(DB01093)	CCTGCAAACCAGAATATGCCT	0.532													14	111	---	---	---	---	PASS
VWF	7450	broad.mit.edu	37	12	6138553	6138553	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6138553C>A	uc001qnn.1	-	22	3172	c.2922G>T	c.(2920-2922)TGG>TGT	p.W974C	VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein	974	VWFD 3.				blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)	GGTGGCGGTCCCAGACCACGG	0.542													106	52	---	---	---	---	PASS
VWF	7450	broad.mit.edu	37	12	6138585	6138585	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6138585G>A	uc001qnn.1	-	22	3140	c.2890C>T	c.(2890-2892)CTG>TTG	p.L964L	VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein	964	VWFD 3.				blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)	CCCAGCAGCAGAATGATGTAC	0.547													80	42	---	---	---	---	PASS
IFFO1	25900	broad.mit.edu	37	12	6649720	6649720	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6649720C>A	uc001qpd.1	-	9	1643	c.1609G>T	c.(1609-1611)GAC>TAC	p.D537Y	IFFO1_uc001qoy.2_RNA|IFFO1_uc001qpa.1_Missense_Mutation_p.D177Y|IFFO1_uc001qpb.1_Missense_Mutation_p.D214Y|IFFO1_uc001qpe.1_RNA|IFFO1_uc010sfe.1_Missense_Mutation_p.D549Y|IFFO1_uc001qpf.1_Missense_Mutation_p.D540Y|IFFO1_uc001qoz.1_Missense_Mutation_p.D178Y|IFFO1_uc001qpc.1_Missense_Mutation_p.D541Y|IFFO1_uc001qpg.2_Silent_p.A176A	NM_080730	NP_542768	Q0D2I5	IFFO1_HUMAN	intermediate filament family orphan isoform 2	537						intermediate filament					0						GGCGGCGGGTCGCTAAGCGGG	0.602													3	29	---	---	---	---	PASS
CD4	920	broad.mit.edu	37	12	6925470	6925470	+	Nonsense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6925470C>T	uc001qqv.1	+	6	1101	c.856C>T	c.(856-858)CAG>TAG	p.Q286*	CD4_uc009zez.1_3'UTR|CD4_uc009zfa.1_RNA|CD4_uc009zfb.1_RNA|CD4_uc010sfj.1_Nonsense_Mutation_p.Q13*|CD4_uc009zfc.1_Nonsense_Mutation_p.Q107*|CD4_uc010sfk.1_Nonsense_Mutation_p.Q13*|CD4_uc010sfl.1_Nonsense_Mutation_p.Q13*|CD4_uc010sfm.1_Nonsense_Mutation_p.Q13*	NM_000616	NP_000607	P01730	CD4_HUMAN	CD4 antigen precursor	286	Extracellular (Potential).|Ig-like C2-type 2.				cell adhesion|entry into host cell|immune response|induction by virus of host cell-cell fusion|initiation of viral infection|maintenance of protein location in cell|positive regulation of interleukin-2 biosynthetic process|positive regulation of protein kinase activity|protein palmitoleylation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|T cell selection|transmembrane receptor protein tyrosine kinase signaling pathway	early endosome|endoplasmic reticulum membrane|integral to membrane|T cell receptor complex	coreceptor activity|extracellular matrix structural constituent|glycoprotein binding|MHC class II protein binding|protein homodimerization activity|protein kinase binding|transmembrane receptor activity|zinc ion binding				0		Myeloproliferative disorder(1001;0.0122)				CACCCTGCCCCAGGCCTTGCC	0.552													49	21	---	---	---	---	PASS
LPCAT3	10162	broad.mit.edu	37	12	7086432	7086432	+	Intron	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7086432G>A	uc001qsi.2	-						EMG1_uc010sfv.1_Intron|LPCAT3_uc010sfw.1_Intron|LPCAT3_uc009zfp.2_Intron	NM_005768	NP_005759	Q6P1A2	MBOA5_HUMAN	lysophosphatidylcholine acyltransferase 3						phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity			ovary(1)	1						CACCTGTGGAGAGAGAGGCCA	0.473													31	69	---	---	---	---	PASS
LPCAT3	10162	broad.mit.edu	37	12	7090191	7090191	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7090191C>A	uc001qsi.2	-	6	766	c.652G>T	c.(652-654)GAC>TAC	p.D218Y	EMG1_uc010sfv.1_Intron|LPCAT3_uc010sfw.1_Missense_Mutation_p.D112Y|LPCAT3_uc009zfp.2_RNA|LPCAT3_uc010sfx.1_RNA|LPCAT3_uc009zfq.1_Missense_Mutation_p.D76Y	NM_005768	NP_005759	Q6P1A2	MBOA5_HUMAN	lysophosphatidylcholine acyltransferase 3	218					phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity			ovary(1)	1						CCTGGTATGTCAATCAGCTCT	0.473													33	175	---	---	---	---	PASS
LPCAT3	10162	broad.mit.edu	37	12	7090202	7090202	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7090202C>T	uc001qsi.2	-	6	755	c.641G>A	c.(640-642)GGA>GAA	p.G214E	EMG1_uc010sfv.1_Intron|LPCAT3_uc010sfw.1_Missense_Mutation_p.G108E|LPCAT3_uc009zfp.2_RNA|LPCAT3_uc010sfx.1_RNA|LPCAT3_uc009zfq.1_Missense_Mutation_p.G72E	NM_005768	NP_005759	Q6P1A2	MBOA5_HUMAN	lysophosphatidylcholine acyltransferase 3	214					phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity			ovary(1)	1						AATCAGCTCTCCCTGCACCAG	0.478													22	161	---	---	---	---	PASS
C3AR1	719	broad.mit.edu	37	12	8212271	8212271	+	Nonsense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8212271T>A	uc001qtv.1	-	2	603	c.511A>T	c.(511-513)AGA>TGA	p.R171*		NM_004054	NP_004045	Q16581	C3AR_HUMAN	complement component 3a receptor 1	171	Extracellular (Potential).				blood circulation|chemotaxis|elevation of cytosolic calcium ion concentration|inflammatory response	integral to plasma membrane	C3a anaphylatoxin receptor activity|complement component C3a receptor activity|phosphatidylinositol phospholipase C activity			ovary(1)	1				Kidney(36;0.0893)		TAGCCACATCTATTATGGTTG	0.443													24	85	---	---	---	---	PASS
PRH2	5555	broad.mit.edu	37	12	11081921	11081921	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11081921C>A	uc009zhr.2	+	1	87	c.49C>A	c.(49-51)CAG>AAG	p.Q17K	PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRB4_uc001qzf.1_Intron|PRH2_uc001qzh.2_Missense_Mutation_p.Q17K|PRH2_uc001qzi.3_Missense_Mutation_p.Q17K	NM_001110213	NP_001103683	P02810	PRPC_HUMAN	proline-rich protein HaeIII subfamily 2	17	Inhibits hydroxyapatite formation, binds to hydroxyapatite and calcium.					extracellular space	protein binding				0						CAGCTCAGCTCAGGACTTAGA	0.517													35	74	---	---	---	---	PASS
LRP6	4040	broad.mit.edu	37	12	12303970	12303970	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12303970G>A	uc001rah.3	-	13	2936	c.2794C>T	c.(2794-2796)CCT>TCT	p.P932S	BCL2L14_uc001raf.1_Intron|LRP6_uc010shl.1_Missense_Mutation_p.P932S	NM_002336	NP_002327	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein	932	Extracellular (Potential).				cellular response to cholesterol|negative regulation of protein phosphorylation|negative regulation of protein serine/threonine kinase activity|negative regulation of smooth muscle cell apoptosis|neural crest formation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell cycle|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	cell surface|cytoplasmic vesicle|endoplasmic reticulum|integral to membrane|plasma membrane	coreceptor activity|frizzled binding|kinase inhibitor activity|low-density lipoprotein receptor activity|protein homodimerization activity|toxin transporter activity|Wnt-protein binding			lung(4)|skin(4)|ovary(2)|kidney(1)|central_nervous_system(1)	12		Prostate(47;0.0865)				AAAGTCGTAGGAGCTTAAAAG	0.348													7	36	---	---	---	---	PASS
GRIN2B	2904	broad.mit.edu	37	12	13769432	13769432	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13769432A>T	uc001rbt.2	-	5	1464	c.1285T>A	c.(1285-1287)TGC>AGC	p.C429S		NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B	429	Extracellular (Potential).				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)	TTCCTCATGCAGGTTCCACTC	0.517													16	42	---	---	---	---	PASS
ATF7IP	55729	broad.mit.edu	37	12	14577231	14577231	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14577231G>T	uc001rbw.2	+	2	540	c.382G>T	c.(382-384)GAA>TAA	p.E128*	ATF7IP_uc010shs.1_Nonsense_Mutation_p.E128*|ATF7IP_uc001rbu.2_Nonsense_Mutation_p.E128*|ATF7IP_uc001rbv.1_Nonsense_Mutation_p.E128*|ATF7IP_uc001rbx.2_Nonsense_Mutation_p.E128*|ATF7IP_uc010sht.1_Nonsense_Mutation_p.E128*|ATF7IP_uc001rby.3_Nonsense_Mutation_p.E128*|ATF7IP_uc001rbz.1_Nonsense_Mutation_p.E128*|ATF7IP_uc001rca.2_Nonsense_Mutation_p.E128*|ATF7IP_uc001rcb.2_5'Flank	NM_018179	NP_060649	Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting	128					DNA methylation|interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|regulation of RNA polymerase II transcriptional preinitiation complex assembly|transcription, DNA-dependent		protein binding			lung(3)|ovary(1)|skin(1)	5						ACTGCCTGCTGAACCAGTTTC	0.483													29	21	---	---	---	---	PASS
ABCC9	10060	broad.mit.edu	37	12	21958144	21958144	+	Missense_Mutation	SNP	A	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21958144A>C	uc001rfi.1	-	38	4634	c.4614T>G	c.(4612-4614)AAT>AAG	p.N1538K	ABCC9_uc001rfh.2_Intron|ABCC9_uc001rfj.1_Missense_Mutation_p.N1502K|ABCC9_uc001rfg.2_Intron	NM_005691	NP_005682	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	1538	Cytoplasmic (Potential).|ABC transporter 2.				defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)|skin(2)	6					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	AAAAGAGGCCATTCTTGTGGG	0.433													6	82	---	---	---	---	PASS
ARNTL2	56938	broad.mit.edu	37	12	27553476	27553476	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27553476A>G	uc001rht.1	+	10	947	c.929A>G	c.(928-930)AAA>AGA	p.K310R	ARNTL2_uc001rhw.2_Missense_Mutation_p.K273R|ARNTL2_uc010sjp.1_Missense_Mutation_p.K273R|ARNTL2_uc001rhu.1_Missense_Mutation_p.K296R|ARNTL2_uc009zji.1_Missense_Mutation_p.K276R|ARNTL2_uc001rhv.1_Missense_Mutation_p.K262R|uc001rhx.2_Intron	NM_020183	NP_064568	Q8WYA1	BMAL2_HUMAN	aryl hydrocarbon receptor nuclear	310					circadian rhythm|entrainment of circadian clock|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(1)|skin(1)	2	Colorectal(261;0.0847)|Lung SC(9;0.184)					GAGCACAGAAAATTCTATACT	0.289													11	81	---	---	---	---	PASS
REP15	387849	broad.mit.edu	37	12	27849721	27849721	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27849721C>A	uc001rig.1	+	1	294	c.226C>A	c.(226-228)CTG>ATG	p.L76M		NM_001029874	NP_001025045	Q6BDI9	REP15_HUMAN	RAB15 effector protein	76						early endosome membrane				ovary(1)	1	Lung SC(9;0.0873)					TGATGAGTGGCTGACCACCAC	0.458													47	36	---	---	---	---	PASS
PTHLH	5744	broad.mit.edu	37	12	28116594	28116594	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28116594C>T	uc001rik.2	-	3	514	c.211G>A	c.(211-213)GAA>AAA	p.E71K	PTHLH_uc001ril.2_Missense_Mutation_p.E71K|PTHLH_uc001rim.2_Missense_Mutation_p.E71K|PTHLH_uc001rin.2_Missense_Mutation_p.E71K	NM_198966	NP_945317	P12272	PTHR_HUMAN	parathyroid hormone-like hormone isoform 1	71					activation of adenylate cyclase activity by G-protein signaling pathway|cAMP metabolic process|cell-cell signaling|epidermis development|female pregnancy|negative regulation of cell proliferation|negative regulation of chondrocyte differentiation|positive regulation of cAMP biosynthetic process|positive regulation of cell proliferation	cytoplasm|extracellular space|nucleus	hormone activity|peptide hormone receptor binding			breast(1)	1	Lung SC(9;0.184)					GCTCTGATTTCAGCTGTGTGG	0.517													89	92	---	---	---	---	PASS
OVCH1	341350	broad.mit.edu	37	12	29639211	29639211	+	Silent	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29639211T>C	uc001rix.1	-	8	963	c.963A>G	c.(961-963)CAA>CAG	p.Q321Q		NM_183378	NP_899234	Q7RTY7	OVCH1_HUMAN	ovochymase 1 precursor	321	CUB 1.				proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			ovary(3)|central_nervous_system(3)|pancreas(3)|large_intestine(1)	10	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					CATTCACTTCTTGGACAGAAC	0.448													25	117	---	---	---	---	PASS
TMTC1	83857	broad.mit.edu	37	12	29659798	29659798	+	Missense_Mutation	SNP	C	G	G	rs79931373	byFrequency	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29659798C>G	uc001rjb.2	-	18	2780	c.2306G>C	c.(2305-2307)CGA>CCA	p.R769P	TMTC1_uc001riz.2_Missense_Mutation_p.R526P|TMTC1_uc001rja.2_Missense_Mutation_p.R613P|TMTC1_uc001riy.2_Missense_Mutation_p.R222P	NM_175861	NP_787057	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat	877						integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					ATCCTTTTCTCGAACTTCTTG	0.453													26	124	---	---	---	---	PASS
C12orf35	55196	broad.mit.edu	37	12	32137137	32137137	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32137137A>T	uc001rks.2	+	4	3662	c.3248A>T	c.(3247-3249)CAG>CTG	p.Q1083L	C12orf35_uc001rkt.2_5'Flank	NM_018169	NP_060639	Q9HCM1	CL035_HUMAN	hypothetical protein LOC55196	1083										ovary(1)|skin(1)	2	all_cancers(9;3.36e-11)|all_epithelial(9;2.56e-11)|all_lung(12;5.67e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0114)			ACTACATACCAGACCTCAGAA	0.408													10	127	---	---	---	---	PASS
PKP2	5318	broad.mit.edu	37	12	32974420	32974420	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32974420T>C	uc001rlj.3	-	10	2130	c.2015A>G	c.(2014-2016)AAG>AGG	p.K672R	PKP2_uc001rlk.3_Missense_Mutation_p.K628R|PKP2_uc010skj.1_Missense_Mutation_p.K625R	NM_004572	NP_004563	Q99959	PKP2_HUMAN	plakophilin 2 isoform 2b	672	ARM 5.				cell-cell adhesion	desmosome|integral to membrane|nucleus	binding			ovary(1)|pancreas(1)	2	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					CTCCACGCCCTTGGGGTTGCT	0.478													9	49	---	---	---	---	PASS
CNTN1	1272	broad.mit.edu	37	12	41327314	41327314	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41327314A>T	uc001rmm.1	+	8	868	c.755A>T	c.(754-756)TAT>TTT	p.Y252F	CNTN1_uc009zjy.1_Missense_Mutation_p.Y252F|CNTN1_uc001rmn.1_Missense_Mutation_p.Y241F|CNTN1_uc001rmo.2_Missense_Mutation_p.Y252F	NM_001843	NP_001834	Q12860	CNTN1_HUMAN	contactin 1 isoform 1 precursor	252	Ig-like C2-type 3.				axon guidance|cell adhesion|Notch signaling pathway	anchored to membrane|membrane fraction|plasma membrane				lung(4)|ovary(3)|large_intestine(1)|skin(1)	9	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				AAGGATGTATATGCATTGATG	0.303													30	35	---	---	---	---	PASS
SLC38A1	81539	broad.mit.edu	37	12	46591814	46591814	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46591814C>G	uc001rpa.2	-	15	1410	c.1152G>C	c.(1150-1152)AAG>AAC	p.K384N	SLC38A1_uc001rpb.2_Missense_Mutation_p.K384N|SLC38A1_uc001rpc.2_Missense_Mutation_p.K384N|SLC38A1_uc001rpd.2_Missense_Mutation_p.K384N|SLC38A1_uc001rpe.2_Missense_Mutation_p.K384N|SLC38A1_uc009zkj.1_Missense_Mutation_p.K384N	NM_030674	NP_109599	Q9H2H9	S38A1_HUMAN	amino acid transporter system A1	384	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process|neurotransmitter uptake	integral to membrane|plasma membrane	sodium:amino acid symporter activity			ovary(2)|skin(2)|central_nervous_system(1)	5	Lung SC(27;0.137)|Renal(347;0.236)		all cancers(1;0.00805)|OV - Ovarian serous cystadenocarcinoma(5;0.0106)|Epithelial(2;0.0344)			ACTTTGTTTTCTTAGCCAGTT	0.373													9	35	---	---	---	---	PASS
ADCY6	112	broad.mit.edu	37	12	49176824	49176824	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49176824G>A	uc001rsh.3	-	1	1054	c.394C>T	c.(394-396)CGT>TGT	p.R132C	ADCY6_uc001rsj.3_Missense_Mutation_p.R132C|ADCY6_uc001rsi.3_Missense_Mutation_p.R132C	NM_015270	NP_056085	O43306	ADCY6_HUMAN	adenylate cyclase 6 isoform a	132	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|synaptic transmission|transmembrane transport|water transport	integral to membrane	ATP binding|metal ion binding				0						TTGGCCGAACGGAACTGCTTC	0.667													24	35	---	---	---	---	PASS
DDX23	9416	broad.mit.edu	37	12	49230475	49230475	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49230475C>G	uc001rsm.2	-	10	1204	c.1113G>C	c.(1111-1113)CGG>CGC	p.R371R		NM_004818	NP_004809	Q9BUQ8	DDX23_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23	371						catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent RNA helicase activity|nucleic acid binding|protein binding			kidney(3)|ovary(1)|lung(1)|skin(1)	6						CACGGAAGATCCGCCAGTCCC	0.527													47	89	---	---	---	---	PASS
TMBIM6	7009	broad.mit.edu	37	12	50149493	50149493	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50149493G>T	uc001rux.2	+	4	373	c.241G>T	c.(241-243)GAA>TAA	p.E81*	TMBIM6_uc010sml.1_Nonsense_Mutation_p.E81*|TMBIM6_uc001ruy.2_Nonsense_Mutation_p.E139*|TMBIM6_uc001ruz.2_Nonsense_Mutation_p.E81*	NM_003217	NP_003208	P55061	BI1_HUMAN	testis enhanced gene transcript (BAX inhibitor	81					apoptosis|negative regulation of apoptosis	endoplasmic reticulum|insoluble fraction|integral to plasma membrane|nucleus					0						CCATGAAACTGAACAGAAAAG	0.438													60	85	---	---	---	---	PASS
NCKAP5L	57701	broad.mit.edu	37	12	50186285	50186285	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50186285A>T	uc009zlk.2	-	12	3938	c.3736T>A	c.(3736-3738)TCG>ACG	p.S1246T	NCKAP5L_uc001rvc.3_Missense_Mutation_p.S450T|NCKAP5L_uc001rvb.2_Missense_Mutation_p.S839T	NM_001037806	NP_001032895	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	1242	Pro-rich.									central_nervous_system(1)	1						AGAGGGTCCGAGGAGCTGCCG	0.622													10	14	---	---	---	---	PASS
SLC4A8	9498	broad.mit.edu	37	12	51851227	51851227	+	Nonsense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51851227C>T	uc001rys.1	+	6	845	c.667C>T	c.(667-669)CAG>TAG	p.Q223*	SLC4A8_uc010sni.1_Nonsense_Mutation_p.Q170*|SLC4A8_uc001rym.2_Nonsense_Mutation_p.Q170*|SLC4A8_uc001ryn.2_Nonsense_Mutation_p.Q170*|SLC4A8_uc001ryo.2_Nonsense_Mutation_p.Q170*|SLC4A8_uc001ryp.1_Nonsense_Mutation_p.Q170*|SLC4A8_uc010snj.1_Nonsense_Mutation_p.Q250*|SLC4A8_uc001ryq.3_Nonsense_Mutation_p.Q223*|SLC4A8_uc001ryr.2_Nonsense_Mutation_p.Q223*|SLC4A8_uc010snk.1_Nonsense_Mutation_p.Q170*	NM_001039960	NP_001035049	Q2Y0W8	S4A8_HUMAN	solute carrier family 4, sodium bicarbonate	223	Extracellular (Potential).				bicarbonate transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity			ovary(3)|pancreas(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.15)		GCATCATCATCAGAATGAAAA	0.448													31	74	---	---	---	---	PASS
SLC4A8	9498	broad.mit.edu	37	12	51851228	51851228	+	Missense_Mutation	SNP	A	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51851228A>C	uc001rys.1	+	6	846	c.668A>C	c.(667-669)CAG>CCG	p.Q223P	SLC4A8_uc010sni.1_Missense_Mutation_p.Q170P|SLC4A8_uc001rym.2_Missense_Mutation_p.Q170P|SLC4A8_uc001ryn.2_Missense_Mutation_p.Q170P|SLC4A8_uc001ryo.2_Missense_Mutation_p.Q170P|SLC4A8_uc001ryp.1_Missense_Mutation_p.Q170P|SLC4A8_uc010snj.1_Missense_Mutation_p.Q250P|SLC4A8_uc001ryq.3_Missense_Mutation_p.Q223P|SLC4A8_uc001ryr.2_Missense_Mutation_p.Q223P|SLC4A8_uc010snk.1_Missense_Mutation_p.Q170P	NM_001039960	NP_001035049	Q2Y0W8	S4A8_HUMAN	solute carrier family 4, sodium bicarbonate	223	Extracellular (Potential).				bicarbonate transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity			ovary(3)|pancreas(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.15)		CATCATCATCAGAATGAAAAG	0.448													31	77	---	---	---	---	PASS
KRT85	3891	broad.mit.edu	37	12	52758919	52758919	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52758919C>T	uc001sag.2	-	2	576	c.456G>A	c.(454-456)GAG>GAA	p.E152E		NM_002283	NP_002274	P78386	KRT85_HUMAN	keratin 85	152	Rod.|Coil 1A.				epidermis development	keratin filament	protein binding|structural molecule activity			ovary(1)	1	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GCCACTTGGTCTCCAGCAGCT	0.617													25	22	---	---	---	---	PASS
KRT77	374454	broad.mit.edu	37	12	53096844	53096844	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53096844C>G	uc001saw.2	-	1	404	c.375G>C	c.(373-375)GGG>GGC	p.G125G	KRT77_uc009zmi.2_5'UTR	NM_175078	NP_778253	Q7Z794	K2C1B_HUMAN	keratin 77	125	Head.					keratin filament	structural molecule activity			ovary(1)	1						GACCAAAGCCCCCAAGCCCAA	0.577													11	76	---	---	---	---	PASS
OR6C65	403282	broad.mit.edu	37	12	55794480	55794480	+	Silent	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55794480T>A	uc010spl.1	+	1	168	c.168T>A	c.(166-168)CCT>CCA	p.P56P		NM_001005518	NP_001005518	A6NJZ3	O6C65_HUMAN	olfactory receptor, family 6, subfamily C,	56	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TGAAAACTCCTATGTATTTCT	0.313													7	26	---	---	---	---	PASS
ITGA7	3679	broad.mit.edu	37	12	56094770	56094770	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56094770C>T	uc001shh.2	-	4	803	c.583G>A	c.(583-585)GGG>AGG	p.G195R	ITGA7_uc001shg.2_Missense_Mutation_p.G195R|ITGA7_uc010sps.1_Missense_Mutation_p.G98R|ITGA7_uc009znx.2_Missense_Mutation_p.G82R	NM_001144996	NP_001138468	Q13683	ITA7_HUMAN	integrin alpha 7 isoform 1 precursor	195	FG-GAP 3.|Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development|regulation of cell shape	integrin complex	receptor activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5						TGGCAGAACCCAAATTGTTCA	0.582													4	53	---	---	---	---	PASS
SMARCC2	6601	broad.mit.edu	37	12	56578034	56578034	+	Intron	SNP	T	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56578034T>G	uc001skb.2	-						SMARCC2_uc001skd.2_Intron|SMARCC2_uc001ska.2_Intron|SMARCC2_uc001skc.2_Intron|SMARCC2_uc010sqf.1_Intron	NM_003075	NP_003066	Q8TAQ2	SMRC2_HUMAN	SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			lung(2)|central_nervous_system(2)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(18;0.123)			GTTCCCTGGATGGTAAAAGGA	0.448													8	23	---	---	---	---	PASS
MARS	4141	broad.mit.edu	37	12	57910229	57910229	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57910229C>T	uc001sog.2	+	21	2591	c.2568C>T	c.(2566-2568)GTC>GTT	p.V856V	MARS_uc001sof.1_RNA|MARS_uc001soh.1_3'UTR	NM_004990	NP_004981	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	856	WHEP-TRS.				methionyl-tRNA aminoacylation	cytosol	ATP binding|methionine-tRNA ligase activity|protein binding|tRNA binding			ovary(3)|central_nervous_system(1)|pancreas(1)	5			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	GAAACATTGTCCGAGAACTGA	0.483													18	63	---	---	---	---	PASS
KIF5A	3798	broad.mit.edu	37	12	57976416	57976416	+	Intron	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57976416C>G	uc001sor.1	+						KIF5A_uc010srr.1_Intron|uc001sos.2_5'Flank	NM_004984	NP_004975	Q12840	KIF5A_HUMAN	kinesin family member 5A						blood coagulation|cell death|microtubule-based movement|synaptic transmission	cytosol|kinesin complex|membrane fraction|microtubule|perinuclear region of cytoplasm	ATP binding|microtubule motor activity			ovary(2)|skin(1)	3						ACAATAGGTACAACAGTCCCC	0.453													34	202	---	---	---	---	PASS
TBK1	29110	broad.mit.edu	37	12	64854058	64854058	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64854058G>T	uc001ssc.1	+	3	239	c.177G>T	c.(175-177)TTG>TTT	p.L59F		NM_013254	NP_037386	Q9UHD2	TBK1_HUMAN	TANK-binding kinase 1	59	Protein kinase.				I-kappaB kinase/NF-kappaB cascade|innate immune response|interspecies interaction between organisms|MyD88-independent toll-like receptor signaling pathway|negative regulation of type I interferon production|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of transcription from RNA polymerase II promoter|response to virus|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(2)|ovary(1)|large_intestine(1)|breast(1)	5				GBM - Glioblastoma multiforme(28;0.0386)		TTGAAGTGTTGAAAAAACTCA	0.284													10	42	---	---	---	---	PASS
PTPRR	5801	broad.mit.edu	37	12	71092078	71092078	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71092078C>G	uc001swi.1	-	8	1662	c.1246G>C	c.(1246-1248)GGA>CGA	p.G416R	PTPRR_uc001swh.1_Missense_Mutation_p.G171R|PTPRR_uc009zrs.2_Missense_Mutation_p.G265R|PTPRR_uc010stq.1_Missense_Mutation_p.G304R|PTPRR_uc010str.1_Missense_Mutation_p.G265R	NM_002849	NP_002840	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	416	Tyrosine-protein phosphatase.|Cytoplasmic (Potential).				in utero embryonic development	cell surface|Golgi apparatus|integral to membrane|nucleus|perinuclear region of cytoplasm|plasma membrane	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			skin(2)|ovary(1)	3			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		TTTTTAGTTCCATGACGCGGA	0.254													4	29	---	---	---	---	PASS
LRRIQ1	84125	broad.mit.edu	37	12	85432046	85432046	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85432046G>T	uc001tac.2	+	2	203	c.92G>T	c.(91-93)AGT>ATT	p.S31I	LRRIQ1_uc001tab.1_Missense_Mutation_p.S31I|TSPAN19_uc009zsj.2_5'Flank|LRRIQ1_uc001taa.1_Missense_Mutation_p.S31I|LRRIQ1_uc001tad.2_5'Flank	NM_001079910	NP_001073379	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	31										ovary(4)|central_nervous_system(1)|skin(1)	6				GBM - Glioblastoma multiforme(134;0.212)		GACATTGAGAGTGATGCAAAA	0.373													23	31	---	---	---	---	PASS
NT5DC3	51559	broad.mit.edu	37	12	104190720	104190720	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104190720G>C	uc010swe.1	-	6	746	c.705C>G	c.(703-705)CTC>CTG	p.L235L		NM_001031701	NP_001026871	Q86UY8	NT5D3_HUMAN	5'-nucleotidase domain containing 3	235							hydrolase activity|metal ion binding			ovary(2)|skin(1)	3						TGTTGTTCTTGAGGAAGTATT	0.478													26	53	---	---	---	---	PASS
APPL2	55198	broad.mit.edu	37	12	105600901	105600901	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105600901C>A	uc001tlf.1	-	8	777	c.559G>T	c.(559-561)GCG>TCG	p.A187S	APPL2_uc010swt.1_Missense_Mutation_p.A144S|APPL2_uc001tlg.1_5'UTR|APPL2_uc010swu.1_Missense_Mutation_p.A193S|APPL2_uc009zuq.2_Missense_Mutation_p.A144S	NM_018171	NP_060641	Q8NEU8	DP13B_HUMAN	adaptor protein, phosphotyrosine interaction, PH	187	Required for RAB5A binding (By similarity).				cell cycle|cell proliferation|signal transduction	early endosome membrane|nucleus	protein binding			upper_aerodigestive_tract(1)	1						TACTGCAGCGCGTTGAGGGCA	0.567													13	30	---	---	---	---	PASS
NUAK1	9891	broad.mit.edu	37	12	106460588	106460588	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106460588G>C	uc001tlj.1	-	7	3358	c.1978C>G	c.(1978-1980)CTC>GTC	p.L660V		NM_014840	NP_055655	O60285	NUAK1_HUMAN	AMPK-related protein kinase 5	660							ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)|central_nervous_system(1)	2						TGCTAGTTGAGCTTGCTGCAG	0.612													9	91	---	---	---	---	PASS
POLR3B	55703	broad.mit.edu	37	12	106824224	106824224	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106824224G>A	uc001tlp.2	+	14	1659	c.1437G>A	c.(1435-1437)CTG>CTA	p.L479L	POLR3B_uc001tlq.2_Silent_p.L421L	NM_018082	NP_060552	Q9NW08	RPC2_HUMAN	DNA-directed RNA polymerase III B isoform 1	479					innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|ribonucleoside binding			ovary(1)|central_nervous_system(1)	2						GGGGAATGCTGTGTCCTTCGG	0.522													26	43	---	---	---	---	PASS
MYO1H	283446	broad.mit.edu	37	12	109843825	109843825	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109843825C>T	uc010sxn.1	+	7	900	c.900C>T	c.(898-900)ATC>ATT	p.I300I		NM_001101421	NP_001094891	Q8N1T3	MYO1H_HUMAN	myosin 1H	Error:Variant_position_missing_in_B4DNW6_after_alignment						myosin complex	motor activity				0						CCCATGAGATCAAGTGGATAG	0.522													16	23	---	---	---	---	PASS
C12orf76	400073	broad.mit.edu	37	12	110495092	110495092	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110495092C>T	uc001tqd.1	-	4	566	c.201G>A	c.(199-201)AAG>AAA	p.K67K	C12orf76_uc001tqe.1_RNA|C12orf76_uc010sxx.1_RNA|uc001tqf.1_Intron	NM_207435	NP_997318	Q8N812	CL076_HUMAN	hypothetical protein LOC400073	67										large_intestine(1)	1						TCCTCTCCCCCTTACAGCTCC	0.522													4	12	---	---	---	---	PASS
C12orf51	283450	broad.mit.edu	37	12	112654880	112654880	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112654880G>A	uc009zwc.2	-	39	5946	c.5928C>T	c.(5926-5928)CCC>CCT	p.P1976P	C12orf51_uc001ttr.1_Silent_p.P151P	NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2						AAGTGCCCCGGGGCAGGCCTC	0.547													10	17	---	---	---	---	PASS
TBX3	6926	broad.mit.edu	37	12	115114170	115114170	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115114170G>A	uc001tvt.1	-	6	2011	c.1047C>T	c.(1045-1047)TTC>TTT	p.F349F	TBX3_uc001tvu.1_Silent_p.F329F	NM_016569	NP_057653	O15119	TBX3_HUMAN	T-box 3 protein isoform 2	349					anterior/posterior axis specification, embryo|anti-apoptosis|cell aging|embryonic arm morphogenesis|embryonic digit morphogenesis|female genitalia development|follicle-stimulating hormone secretion|luteinizing hormone secretion|male genitalia development|mesoderm morphogenesis|negative regulation of myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle|positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter|skeletal system development	nucleus	sequence-specific DNA binding			ovary(2)|skin(1)	3	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		AAGCCTGGGCGAAGCAGTTGA	0.527													15	48	---	---	---	---	PASS
TBX3	6926	broad.mit.edu	37	12	115120647	115120647	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115120647C>A	uc001tvt.1	-	1	1323	c.359G>T	c.(358-360)GGC>GTC	p.G120V	TBX3_uc001tvu.1_Missense_Mutation_p.G120V|TBX3_uc010syw.1_Missense_Mutation_p.G120V	NM_016569	NP_057653	O15119	TBX3_HUMAN	T-box 3 protein isoform 2	120	T-box; first part.				anterior/posterior axis specification, embryo|anti-apoptosis|cell aging|embryonic arm morphogenesis|embryonic digit morphogenesis|female genitalia development|follicle-stimulating hormone secretion|luteinizing hormone secretion|male genitalia development|mesoderm morphogenesis|negative regulation of myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle|positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter|skeletal system development	nucleus	sequence-specific DNA binding			ovary(2)|skin(1)	3	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		CATCTCGGTGCCCCGCTTGTG	0.547													13	30	---	---	---	---	PASS
TAOK3	51347	broad.mit.edu	37	12	118599581	118599581	+	Intron	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118599581C>A	uc001twx.2	-						TAOK3_uc001twv.2_Intron|TAOK3_uc001tww.2_Intron|TAOK3_uc001twy.3_Intron	NM_016281	NP_057365	Q9H2K8	TAOK3_HUMAN	TAO kinase 3						MAPKKK cascade|negative regulation of JNK cascade|positive regulation of JNK cascade|protein autophosphorylation	mitochondrion|plasma membrane	ATP binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			lung(5)|central_nervous_system(1)	6	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TGTCCAGCAGCACAAATCTTA	0.279													11	58	---	---	---	---	PASS
HSPB8	26353	broad.mit.edu	37	12	119624881	119624881	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119624881C>A	uc001txb.2	+	2	942	c.419C>A	c.(418-420)ACA>AAA	p.T140K	HSPB8_uc001txc.2_Intron	NM_014365	NP_055180	Q9UJY1	HSPB8_HUMAN	heat shock 22kDa protein 8	140					cell death|response to heat	cytoplasm|nucleus	identical protein binding|protein serine/threonine kinase activity			central_nervous_system(1)|skin(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AAGAACTTCACAAAGAAAATC	0.507													31	35	---	---	---	---	PASS
DNAH10	196385	broad.mit.edu	37	12	124303771	124303771	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124303771G>T	uc001uft.3	+	22	3645	c.3620G>T	c.(3619-3621)GGT>GTT	p.G1207V		NM_207437	NP_997320	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1207	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GAAGGCCCTGGTTCTGTTGGT	0.388													12	4	---	---	---	---	PASS
UBC	7316	broad.mit.edu	37	12	125397817	125397817	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125397817G>A	uc001ugs.3	-	2	949	c.501C>T	c.(499-501)CTC>CTT	p.L167L	UBC_uc001ugr.2_5'Flank|UBC_uc001ugu.1_Silent_p.L167L|UBC_uc001ugt.2_Silent_p.L167L|UBC_uc001ugv.2_Intron|UBC_uc001ugw.2_Silent_p.L15L	NM_021009	NP_066289	P0CG48	UBC_HUMAN	ubiquitin C	167	Ubiquitin-like 3.				activation of MAPK activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|anti-apoptosis|apoptosis|cellular membrane organization|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA repair|endosome transport|epidermal growth factor receptor signaling pathway|G1/S transition of mitotic cell cycle|I-kappaB kinase/NF-kappaB cascade|induction of apoptosis by extracellular signals|innate immune response|JNK cascade|M/G1 transition of mitotic cell cycle|mRNA metabolic process|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of type I interferon production|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|S phase of mitotic cell cycle|stress-activated MAPK cascade|T cell receptor signaling pathway|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|viral reproduction	cytosol|endocytic vesicle membrane|endosome membrane|nucleoplasm|plasma membrane	protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.17e-05)|Epithelial(86;0.000207)|all cancers(50;0.00308)		GCTCCACCTCGAGGGTGATGG	0.512													60	123	---	---	---	---	PASS
TMEM132B	114795	broad.mit.edu	37	12	126138695	126138695	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126138695G>C	uc001uhe.1	+	9	2684	c.2676G>C	c.(2674-2676)AGG>AGC	p.R892S	TMEM132B_uc001uhf.1_Missense_Mutation_p.R404S	NM_052907	NP_443139	Q14DG7	T132B_HUMAN	transmembrane protein 132B	892	Extracellular (Potential).					integral to membrane				skin(11)|ovary(5)|large_intestine(1)|pancreas(1)|breast(1)	19	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		TGACCTCAAGGGGGCTAACGG	0.512													14	48	---	---	---	---	PASS
TMEM132D	121256	broad.mit.edu	37	12	129559279	129559279	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129559279G>T	uc009zyl.1	-	9	2769	c.2441C>A	c.(2440-2442)GCA>GAA	p.A814E	TMEM132D_uc001uia.2_Missense_Mutation_p.A352E	NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	814	Extracellular (Potential).					integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		GTGAACCCCTGCCCCTGTGTG	0.488													9	58	---	---	---	---	PASS
IFT88	8100	broad.mit.edu	37	13	21189974	21189974	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21189974C>G	uc001unh.2	+	16	1578	c.1182C>G	c.(1180-1182)CTC>CTG	p.L394L	IFT88_uc001uni.2_Silent_p.L385L|IFT88_uc001unj.2_Silent_p.L384L|IFT88_uc010tcq.1_Silent_p.L365L|IFT88_uc001unk.2_Silent_p.L140L|IFT88_uc001unl.1_Silent_p.L12L	NM_175605	NP_783195	Q13099	IFT88_HUMAN	intraflagellar transport 88 homolog isoform 1	394					cilium morphogenesis	centriole|intraflagellar transport particle B|microtubule basal body|microtubule-based flagellum	protein binding			ovary(1)	1		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		CTGCAAAACTCATTGCTCCTG	0.284													6	19	---	---	---	---	PASS
IFT88	8100	broad.mit.edu	37	13	21219051	21219051	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21219051T>A	uc001unh.2	+	22	2326	c.1930T>A	c.(1930-1932)TTT>ATT	p.F644I	IFT88_uc001uni.2_Missense_Mutation_p.F635I|IFT88_uc001unj.2_Missense_Mutation_p.F634I|IFT88_uc010tcq.1_Missense_Mutation_p.F615I	NM_175605	NP_783195	Q13099	IFT88_HUMAN	intraflagellar transport 88 homolog isoform 1	644	TPR 11.				cilium morphogenesis	centriole|intraflagellar transport particle B|microtubule basal body|microtubule-based flagellum	protein binding			ovary(1)	1		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		TGACACCCAATTTTGGGAAAA	0.303													9	39	---	---	---	---	PASS
LATS2	26524	broad.mit.edu	37	13	21562336	21562336	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21562336G>A	uc009zzs.2	-	4	1948	c.1583C>T	c.(1582-1584)TCG>TTG	p.S528L	LATS2_uc001unr.3_Missense_Mutation_p.S528L	NM_014572	NP_055387	Q9NRM7	LATS2_HUMAN	LATS, large tumor suppressor, homolog 2	528					cell division|G1/S transition of mitotic cell cycle|hippo signaling cascade|hormone-mediated signaling pathway|intracellular protein kinase cascade|mitosis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity	microtubule organizing center|nucleus|spindle pole	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|central_nervous_system(3)|ovary(2)|breast(1)|pancreas(1)	10		all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000781)|Epithelial(112;0.00144)|OV - Ovarian serous cystadenocarcinoma(117;0.0183)|Lung(94;0.0375)|LUSC - Lung squamous cell carcinoma(192;0.104)		GTACTGCTCCGACTTGCTGCG	0.716													9	14	---	---	---	---	PASS
CENPJ	55835	broad.mit.edu	37	13	25480240	25480240	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25480240C>T	uc001upt.3	-	7	2189	c.1936G>A	c.(1936-1938)GAG>AAG	p.E646K	CENPJ_uc010tdf.1_RNA|CENPJ_uc010aae.2_RNA|CENPJ_uc010aaf.2_RNA|CENPJ_uc001upu.2_5'Flank	NM_018451	NP_060921	Q9HC77	CENPJ_HUMAN	centromere protein J	646					cell division|centriole replication|G2/M transition of mitotic cell cycle|microtubule nucleation|microtubule polymerization	centriole|cytosol|gamma-tubulin small complex|microtubule	protein domain specific binding|tubulin binding			ovary(2)	2		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)		CTCTCCTTCTCACGTGCAGTG	0.488													5	35	---	---	---	---	PASS
FLT1	2321	broad.mit.edu	37	13	29001924	29001924	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29001924A>G	uc001usb.3	-	9	1526	c.1241T>C	c.(1240-1242)GTG>GCG	p.V414A	FLT1_uc010aar.1_Missense_Mutation_p.V414A|FLT1_uc001usc.3_Missense_Mutation_p.V414A|FLT1_uc010tdp.1_Missense_Mutation_p.V414A	NM_002019	NP_002010	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1 isoform 1	414	Ig-like C2-type 4.|Extracellular (Potential).				cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)	GTTTTTAAACACATTTGACTG	0.378													12	44	---	---	---	---	PASS
MTUS2	23281	broad.mit.edu	37	13	29601047	29601047	+	Intron	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29601047G>T	uc001usl.3	+							NM_001033602	NP_001028774	Q5JR59	MTUS2_HUMAN	hypothetical protein LOC23281 isoform a							cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0						GGAGGTAAGAGAATGTCATTA	0.393													8	27	---	---	---	---	PASS
TRPC4	7223	broad.mit.edu	37	13	38213200	38213200	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38213200C>A	uc001uws.2	-	10	2423	c.2188G>T	c.(2188-2190)GGC>TGC	p.G730C	TRPC4_uc010abv.2_Missense_Mutation_p.G310C|TRPC4_uc001uwt.2_Missense_Mutation_p.G730C|TRPC4_uc010tey.1_Missense_Mutation_p.V730F|TRPC4_uc010abw.2_Missense_Mutation_p.G557C|TRPC4_uc010abx.2_Missense_Mutation_p.G735C|TRPC4_uc010aby.2_Missense_Mutation_p.G665C	NM_016179	NP_057263	Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel,	730	Binds to ITPR1, ITPR2 and ITPR3.|Cytoplasmic (Potential).				axon guidance|calcium ion import	basolateral plasma membrane|calcium channel complex|cell surface|cortical cytoskeleton	beta-catenin binding|cadherin binding|store-operated calcium channel activity			ovary(3)|skin(2)|breast(1)	6				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		TCGGTCAGGCCTTCTTCAGTT	0.398													16	88	---	---	---	---	PASS
FREM2	341640	broad.mit.edu	37	13	39264956	39264956	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39264956G>T	uc001uwv.2	+	1	3784	c.3475G>T	c.(3475-3477)GTG>TTG	p.V1159L		NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	1159	Extracellular (Potential).|CSPG 7.				cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		GGTGGAACCTGTGGAGGACCG	0.443													10	59	---	---	---	---	PASS
FREM2	341640	broad.mit.edu	37	13	39266606	39266606	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39266606C>G	uc001uwv.2	+	1	5434	c.5125C>G	c.(5125-5127)CTT>GTT	p.L1709V		NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	1709	Extracellular (Potential).|CSPG 12.				cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		ACATGGATATCTTCTCAACCT	0.423													19	73	---	---	---	---	PASS
SLC25A15	10166	broad.mit.edu	37	13	41379369	41379369	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41379369G>C	uc001uxn.2	+	4	752	c.430G>C	c.(430-432)GGG>CGG	p.G144R	SUGT1L1_uc001uxp.1_Intron|SLC25A15_uc010tfb.1_Missense_Mutation_p.G50R|SUGT1L1_uc001uxo.1_Intron	NM_014252	NP_055067	Q9Y619	ORNT1_HUMAN	mitochondrial ornithine transporter 1	144	Solcar 2.				cellular amino acid metabolic process|mitochondrial ornithine transport|urea cycle	integral to membrane|mitochondrial inner membrane	L-ornithine transmembrane transporter activity				0		Lung NSC(96;3.55e-06)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;1.48e-08)|Epithelial(112;7.51e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000191)|GBM - Glioblastoma multiforme(144;0.00231)|BRCA - Breast invasive adenocarcinoma(63;0.0704)	L-Ornithine(DB00129)	GGAGACATCAGGGAAGATAGC	0.517													6	31	---	---	---	---	PASS
ENOX1	55068	broad.mit.edu	37	13	43843595	43843595	+	Intron	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43843595C>T	uc001uza.3	-						ENOX1_uc001uzb.3_Intron|ENOX1_uc001uzc.3_Intron|ENOX1_uc001uyz.3_Intron	NM_001127615	NP_001121087	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1						electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)		AGAGCTGTTTCATTCACTTAC	0.413													13	55	---	---	---	---	PASS
PCDH17	27253	broad.mit.edu	37	13	58207038	58207038	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58207038G>T	uc001vhq.1	+	1	1250	c.358G>T	c.(358-360)GTA>TTA	p.V120L	PCDH17_uc010aec.1_Missense_Mutation_p.V120L	NM_001040429	NP_001035519	O14917	PCD17_HUMAN	protocadherin 17 precursor	120	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	7		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		CATGATCAAGGTAGAGATCCA	0.602													7	15	---	---	---	---	PASS
PCDH9	5101	broad.mit.edu	37	13	66879051	66879051	+	Silent	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66879051T>A	uc001vik.2	-	5	4142	c.3450A>T	c.(3448-3450)CCA>CCT	p.P1150P	PCDH9_uc010aei.2_RNA|PCDH9_uc001vil.2_Silent_p.P1116P|PCDH9_uc010thl.1_Silent_p.P1108P	NM_203487	NP_982354	Q9HC56	PCDH9_HUMAN	protocadherin 9 isoform 1 precursor	1150	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)|skin(1)	6		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		GGTGTTGATATGGACCCAAGC	0.517													14	44	---	---	---	---	PASS
MYCBP2	23077	broad.mit.edu	37	13	77739409	77739409	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77739409T>A	uc001vkf.2	-	43	6435	c.6344A>T	c.(6343-6345)GAG>GTG	p.E2115V	MYCBP2_uc010aev.2_Missense_Mutation_p.E1519V	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2	2115					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		CATTCTTACCTCATCAGGTCC	0.353													11	30	---	---	---	---	PASS
CLDN10	9071	broad.mit.edu	37	13	96086270	96086270	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96086270C>T	uc001vmg.2	+	1	418	c.183C>T	c.(181-183)TGC>TGT	p.C61C	CLDN10_uc010tii.1_Intron	NM_182848	NP_878268	P78369	CLD10_HUMAN	claudin 10 isoform a	63	Extracellular (Potential).				calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			ovary(1)	1	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.18)			CTTTCCATTGCCGACCGCATT	0.493													10	32	---	---	---	---	PASS
TM9SF2	9375	broad.mit.edu	37	13	100181719	100181719	+	Splice_Site	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100181719A>T	uc001voj.1	+	4	467	c.334_splice	c.e4-2	p.F112_splice	TM9SF2_uc010afz.1_Intron	NM_004800	NP_004791	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2 precursor						transport	endosome membrane|integral to plasma membrane				ovary(1)	1	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)					CTTTTAATACAGTTTACGTTT	0.303													3	19	---	---	---	---	PASS
PCCA	5095	broad.mit.edu	37	13	100925585	100925585	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100925585G>C	uc001voo.2	+	12	1088	c.1050G>C	c.(1048-1050)ATG>ATC	p.M350I	PCCA_uc010aga.2_Missense_Mutation_p.M324I|PCCA_uc010tiz.1_Missense_Mutation_p.M350I	NM_000282	NP_000273	P05165	PCCA_HUMAN	propionyl-Coenzyme A carboxylase, alpha	350	ATP-grasp.|Biotin carboxylation.				fatty acid beta-oxidation	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|enzyme binding|metal ion binding|propionyl-CoA carboxylase activity			skin(2)	2	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	TCTTGGAAATGAATACAAGAC	0.388													7	9	---	---	---	---	PASS
PROZ	8858	broad.mit.edu	37	13	113814408	113814408	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113814408G>A	uc001vta.1	+	2	158	c.151G>A	c.(151-153)GAG>AAG	p.E51K	PROZ_uc010agr.1_Missense_Mutation_p.E73K	NM_003891	NP_003882	P22891	PROZ_HUMAN	protein Z, vitamin K-dependent plasma	51	Gla.				blood coagulation|peptidyl-glutamic acid carboxylation|post-translational protein modification|proteolysis	endoplasmic reticulum lumen|extracellular region|Golgi lumen	calcium ion binding|serine-type endopeptidase activity				0	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.216)	all cancers(43;0.104)		Menadione(DB00170)	AGAACTCTTCGAGGGAAACTT	0.458													34	77	---	---	---	---	PASS
CUL4A	8451	broad.mit.edu	37	13	113893744	113893744	+	Intron	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113893744C>T	uc010tjy.1	+						CUL4A_uc010tjx.1_Intron|CUL4A_uc010agu.2_Intron|CUL4A_uc010tjz.1_Intron	NM_001008895	NP_001008895	Q13619	CUL4A_HUMAN	cullin 4A isoform 1						cell cycle arrest|DNA repair|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process	Cul4A-RING ubiquitin ligase complex	ubiquitin protein ligase binding			central_nervous_system(2)|skin(1)	3	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.112)			CTGCACATCTCAGGGCTCGAC	0.557													10	41	---	---	---	---	PASS
POTEG	404785	broad.mit.edu	37	14	19553804	19553804	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19553804G>T	uc001vuz.1	+	1	440	c.388G>T	c.(388-390)GAG>TAG	p.E130*	POTEG_uc001vva.1_RNA|POTEG_uc010ahc.1_RNA	NM_001005356	NP_001005356	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	130										ovary(1)	1						CGCTTTCATGGAGCCGAGGTA	0.592													13	317	---	---	---	---	PASS
POTEG	404785	broad.mit.edu	37	14	19563531	19563531	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19563531C>A	uc001vuz.1	+	5	1097	c.1045C>A	c.(1045-1047)CAT>AAT	p.H349N	POTEG_uc001vva.1_RNA|POTEG_uc010ahc.1_RNA|uc001vvb.2_RNA	NM_001005356	NP_001005356	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	349				H -> R (in Ref. 1; AAS58868/AAS58871).						ovary(1)	1						TGTTTCTAGTCATCATAATGT	0.353													15	174	---	---	---	---	PASS
OR4M1	441670	broad.mit.edu	37	14	20249222	20249222	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20249222C>A	uc010tku.1	+	1	741	c.741C>A	c.(739-741)ACC>ACA	p.T247T		NM_001005500	NP_001005500	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M,	247	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CCCACATTACCATTGTGGTGC	0.438													9	104	---	---	---	---	PASS
OR4N2	390429	broad.mit.edu	37	14	20296240	20296240	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20296240T>A	uc010tkv.1	+	1	633	c.633T>A	c.(631-633)TTT>TTA	p.F211L		NM_001004723	NP_001004723	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N,	211	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)|skin(1)	4	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TCCTGTGCTTTCTGGGGCTTC	0.517													9	63	---	---	---	---	PASS
OR4K15	81127	broad.mit.edu	37	14	20444459	20444459	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20444459G>T	uc010tkx.1	+	1	782	c.782G>T	c.(781-783)CGC>CTC	p.R261L		NM_001005486	NP_001005486	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K,	261	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		GCGAAGGCCCGCTCCACATTG	0.463													15	38	---	---	---	---	PASS
OR4K13	390433	broad.mit.edu	37	14	20502373	20502373	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20502373G>T	uc010tkz.1	-	1	545	c.545C>A	c.(544-546)CCC>CAC	p.P182H		NM_001004714	NP_001004714	Q8NH42	OR4KD_HUMAN	olfactory receptor, family 4, subfamily K,	182	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		AATCACAAGGGGAAGGTCACA	0.473													5	84	---	---	---	---	PASS
MYH6	4624	broad.mit.edu	37	14	23874503	23874503	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23874503C>G	uc001wjv.2	-	5	498	c.431G>C	c.(430-432)GGC>GCC	p.G144A	MYH6_uc010akp.1_Missense_Mutation_p.G144A	NM_002471	NP_002462	P13533	MYH6_HUMAN	myosin heavy chain 6	144	Myosin head-like.				adult heart development|atrial cardiac muscle tissue morphogenesis|cardiac muscle fiber development|in utero embryonic development|muscle filament sliding|regulation of ATPase activity|regulation of blood pressure|regulation of heart rate|regulation of the force of heart contraction|sarcomere organization|striated muscle contraction|ventricular cardiac muscle tissue morphogenesis|visceral muscle development	cytosol|focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|protein kinase binding|structural constituent of muscle			pancreas(2)|ovary(1)|skin(1)	4	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		CCTCTTCTTGCCCCGGTAGGC	0.612													30	35	---	---	---	---	PASS
MYH6	4624	broad.mit.edu	37	14	23874944	23874944	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23874944C>G	uc001wjv.2	-	4	304	c.237G>C	c.(235-237)CAG>CAC	p.Q79H	MYH6_uc010akp.1_Missense_Mutation_p.Q79H	NM_002471	NP_002462	P13533	MYH6_HUMAN	myosin heavy chain 6	79	Myosin head-like.				adult heart development|atrial cardiac muscle tissue morphogenesis|cardiac muscle fiber development|in utero embryonic development|muscle filament sliding|regulation of ATPase activity|regulation of blood pressure|regulation of heart rate|regulation of the force of heart contraction|sarcomere organization|striated muscle contraction|ventricular cardiac muscle tissue morphogenesis|visceral muscle development	cytosol|focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|protein kinase binding|structural constituent of muscle			pancreas(2)|ovary(1)|skin(1)	4	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		TGGGTGGGTTCTGCTGCAACA	0.602													17	85	---	---	---	---	PASS
RABGGTA	5875	broad.mit.edu	37	14	24735655	24735655	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24735655C>A	uc001wof.2	-	15	1958	c.1536G>T	c.(1534-1536)GAG>GAT	p.E512D	RABGGTA_uc001woe.2_RNA|RABGGTA_uc001wog.2_Missense_Mutation_p.E512D|RABGGTA_uc001woh.2_RNA|RABGGTA_uc001woi.2_RNA	NM_004581	NP_004572	Q92696	PGTA_HUMAN	Rab geranylgeranyltransferase alpha	512	LRR 4.				visual perception		Rab geranylgeranyltransferase activity|zinc ion binding				0				GBM - Glioblastoma multiforme(265;0.0184)		ACAGTAGCAGCTCCTGCAGCC	0.612													8	61	---	---	---	---	PASS
FOXG1	2290	broad.mit.edu	37	14	29237355	29237355	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29237355G>C	uc001wqe.2	+	1	1069	c.870G>C	c.(868-870)GCG>GCC	p.A290A		NM_005249	NP_005240	P55316	FOXG1_HUMAN	forkhead box G1	290				FKRGAR -> AFRWCA (in Ref. 1; CAA52241).	axon midline choice point recognition|central nervous system neuron development|dorsal/ventral pattern formation|embryo development ending in birth or egg hatching|hindbrain development|inner ear morphogenesis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|nonmotile primary cilium assembly|nose development|positive regulation of cell cycle|positive regulation of neuroblast proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of mitotic cell cycle|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(2)|lung(2)	4			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)		AGCGCGGTGCGCGCCTCACCT	0.716													6	37	---	---	---	---	PASS
PRKD1	5587	broad.mit.edu	37	14	30100056	30100056	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30100056T>A	uc001wqh.2	-	10	1745	c.1564A>T	c.(1564-1566)AGT>TGT	p.S522C		NM_002742	NP_002733	Q15139	KPCD1_HUMAN	protein kinase D1	522	PH.				cell proliferation|intracellular signal transduction|sphingolipid metabolic process	cytosol|integral to plasma membrane	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(3)|large_intestine(2)|ovary(2)|skin(1)	8	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		CCAACGCCACTGGTGAGAACA	0.502													51	48	---	---	---	---	PASS
EGLN3	112399	broad.mit.edu	37	14	34419656	34419656	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34419656C>A	uc001wsa.3	-	1	629	c.303G>T	c.(301-303)CTG>CTT	p.L101L	EGLN3_uc001wry.2_Intron|EGLN3_uc001wrz.2_Silent_p.L101L|EGLN3_uc001wsb.1_Silent_p.L101L	NM_022073	NP_071356	Q9H6Z9	EGLN3_HUMAN	egl nine homolog 3	101					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)	AGTAGAGGACCAGCCTGTCGA	0.667													8	23	---	---	---	---	PASS
EGLN3	112399	broad.mit.edu	37	14	34419657	34419657	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34419657A>G	uc001wsa.3	-	1	628	c.302T>C	c.(301-303)CTG>CCG	p.L101P	EGLN3_uc001wry.2_Intron|EGLN3_uc001wrz.2_Missense_Mutation_p.L101P|EGLN3_uc001wsb.1_Missense_Mutation_p.L101P	NM_022073	NP_071356	Q9H6Z9	EGLN3_HUMAN	egl nine homolog 3	101					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)	GTAGAGGACCAGCCTGTCGAT	0.667													9	22	---	---	---	---	PASS
EAPP	55837	broad.mit.edu	37	14	35008751	35008751	+	Intron	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35008751G>A	uc001wsd.1	-							NM_018453	NP_060923	Q56P03	EAPP_HUMAN	E2F-associated phosphoprotein						negative regulation of transcription elongation from RNA polymerase II promoter|positive regulation of cell proliferation|positive regulation of transcription elongation from RNA polymerase II promoter	Golgi apparatus|nucleus|plasma membrane				ovary(1)	1	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00342)|Epithelial(34;0.18)	GBM - Glioblastoma multiforme(112;0.0196)		AGGGTGGGGCGGGAGCCCACC	0.682													14	10	---	---	---	---	PASS
CFL2	1073	broad.mit.edu	37	14	35182474	35182474	+	Silent	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35182474T>C	uc001wsg.3	-	2	438	c.297A>G	c.(295-297)CTA>CTG	p.L99L	CFL2_uc010tpn.1_Silent_p.L82L|CFL2_uc001wsh.3_Silent_p.L99L|CFL2_uc001wsi.3_Intron|CFL2_uc001wsj.3_Intron	NM_021914	NP_068733	Q9Y281	COF2_HUMAN	cofilin 2	99	ADF-H.					cytoplasm|cytoskeleton|nuclear matrix	actin binding			breast(2)	2	Breast(36;0.0361)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;6.07e-06)|Lung(238;2.23e-05)|Epithelial(34;0.0387)|all cancers(34;0.0814)	GBM - Glioblastoma multiforme(112;0.0424)		ATATAAATACTAGGTCTTCTT	0.318													11	42	---	---	---	---	PASS
BAZ1A	11177	broad.mit.edu	37	14	35269419	35269419	+	Intron	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35269419C>G	uc001wsk.2	-						BAZ1A_uc001wsl.2_Intron	NM_013448	NP_038476	Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A						chromatin remodeling|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ACF complex	zinc ion binding			lung(2)|central_nervous_system(2)|ovary(1)|breast(1)|skin(1)	7	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		CTAATATACTCAAATGAATAC	0.144													4	8	---	---	---	---	PASS
KLHDC1	122773	broad.mit.edu	37	14	50201309	50201309	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50201309G>A	uc001www.2	+	10	854	c.826G>A	c.(826-828)GAT>AAT	p.D276N	SDCCAG1_uc010anj.1_Intron|KLHDC1_uc010tqg.1_Missense_Mutation_p.D231N|KLHDC1_uc010tqh.1_Missense_Mutation_p.D191N	NM_172193	NP_751943	Q8N7A1	KLDC1_HUMAN	kelch domain containing 1	276	Kelch 5.					cytoplasm				pancreas(1)	1	all_epithelial(31;0.00244)|Breast(41;0.00964)					TATTGCAGGTGATGGTTGGAT	0.313													9	18	---	---	---	---	PASS
SOS2	6655	broad.mit.edu	37	14	50626482	50626482	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50626482C>T	uc001wxs.3	-	10	1617	c.1519G>A	c.(1519-1521)GAG>AAG	p.E507K	SOS2_uc010tql.1_Missense_Mutation_p.E474K|SOS2_uc010tqm.1_RNA|SOS2_uc001wxt.2_Missense_Mutation_p.E195K	NM_006939	NP_008870	Q07890	SOS2_HUMAN	son of sevenless homolog 2	507	PH.				apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	DNA binding|protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)	2	all_epithelial(31;0.000822)|Breast(41;0.0065)					TGCTTGTGCTCACAAGTATCT	0.373													28	46	---	---	---	---	PASS
SOS2	6655	broad.mit.edu	37	14	50671113	50671113	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50671113C>A	uc001wxs.3	-	2	200	c.102G>T	c.(100-102)GTG>GTT	p.V34V	SOS2_uc010tql.1_Silent_p.V34V	NM_006939	NP_008870	Q07890	SOS2_HUMAN	son of sevenless homolog 2	34					apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	DNA binding|protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)	2	all_epithelial(31;0.000822)|Breast(41;0.0065)					GAGTGGGATGCACTTGTTCCT	0.313													23	61	---	---	---	---	PASS
NIN	51199	broad.mit.edu	37	14	51219373	51219373	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51219373C>A	uc001wym.2	-	21	5004	c.4813G>T	c.(4813-4815)GAA>TAA	p.E1605*	NIN_uc001wyi.2_Nonsense_Mutation_p.E1605*|NIN_uc001wyj.2_RNA|NIN_uc001wyk.2_Nonsense_Mutation_p.E892*|NIN_uc010tqp.1_Nonsense_Mutation_p.E1611*|NIN_uc001wyo.2_Nonsense_Mutation_p.E1605*	NM_182946	NP_891991	Q8N4C6	NIN_HUMAN	ninein isoform 5	1605	Potential.				centrosome localization	centrosome|microtubule	calcium ion binding|GTP binding|protein binding			skin(3)|ovary(1)|kidney(1)|central_nervous_system(1)	6	all_epithelial(31;0.00244)|Breast(41;0.127)					TGCAGTTTTTCCTGGTTTTGA	0.333			T	PDGFRB	MPD								20	108	---	---	---	---	PASS
DDHD1	80821	broad.mit.edu	37	14	53513567	53513567	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53513567C>A	uc001xai.2	-	13	2852	c.2622G>T	c.(2620-2622)TTG>TTT	p.L874F	DDHD1_uc001xaj.2_Missense_Mutation_p.L853F|DDHD1_uc001xah.2_Missense_Mutation_p.L846F|DDHD1_uc001xag.2_Missense_Mutation_p.L428F	NM_001160148	NP_001153620	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1 isoform c	874	DDHD.				lipid catabolic process	cytoplasm	hydrolase activity|metal ion binding			ovary(2)	2	Breast(41;0.037)					GGGCAACATCCAAGGATGACC	0.433													15	42	---	---	---	---	PASS
RTN1	6252	broad.mit.edu	37	14	60069930	60069930	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60069930C>G	uc001xen.1	-	7	2438	c.2229G>C	c.(2227-2229)CAG>CAC	p.Q743H	RTN1_uc001xem.1_Missense_Mutation_p.Q323H|RTN1_uc001xek.1_Missense_Mutation_p.Q175H|RTN1_uc001xel.1_RNA|RTN1_uc010apl.1_Missense_Mutation_p.Q160H	NM_021136	NP_066959	Q16799	RTN1_HUMAN	reticulon 1 isoform A	743	Reticulon.				neuron differentiation	integral to endoplasmic reticulum membrane	signal transducer activity			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		TAGAACTTACCTGGTGCTTAA	0.318													8	18	---	---	---	---	PASS
SYNE2	23224	broad.mit.edu	37	14	64606673	64606673	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64606673C>T	uc001xgm.2	+	80	15088	c.14858C>T	c.(14857-14859)TCG>TTG	p.S4953L	SYNE2_uc001xgl.2_Missense_Mutation_p.S4953L|SYNE2_uc010apy.2_Missense_Mutation_p.S1338L|SYNE2_uc001xgn.2_5'UTR|SYNE2_uc001xgo.2_5'Flank	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4953	Spectrin 1.|Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AACAGAGATTCGGATCAGTTA	0.378													5	48	---	---	---	---	PASS
SYNE2	23224	broad.mit.edu	37	14	64641864	64641864	+	Intron	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64641864C>T	uc001xgm.2	+						SYNE2_uc001xgl.2_Intron|SYNE2_uc010apy.2_Intron|SYNE2_uc001xgn.2_Intron|SYNE2_uc001xgo.2_Intron|SYNE2_uc010aqa.2_Intron|SYNE2_uc001xgq.2_Intron	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2						centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GAGGTAAACTCACCACTTACT	0.403													14	39	---	---	---	---	PASS
FUT8	2530	broad.mit.edu	37	14	66083914	66083914	+	Intron	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66083914G>C	uc001xin.2	+						FUT8_uc001xio.2_Intron|FUT8_uc010tsp.1_Intron|FUT8_uc001xir.3_Intron|FUT8_uc001xip.2_Intron|FUT8_uc001xiq.2_Intron	NM_178155	NP_835368	Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 isoform a						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)		ATACAAGTAAGAGATTTCATA	0.284													6	35	---	---	---	---	PASS
ZFYVE26	23503	broad.mit.edu	37	14	68251916	68251916	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68251916T>A	uc001xka.2	-	19	3522	c.3383A>T	c.(3382-3384)CAG>CTG	p.Q1128L	ZFYVE26_uc010tsz.1_RNA|ZFYVE26_uc001xkc.3_Missense_Mutation_p.Q1128L	NM_015346	NP_056161	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	1128					cell cycle|cell death|cytokinesis|double-strand break repair via homologous recombination	centrosome|midbody	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			ovary(9)|breast(2)	11				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		AGTCTGGATCTGCACAGGGTG	0.597													3	35	---	---	---	---	PASS
PCNX	22990	broad.mit.edu	37	14	71568774	71568774	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71568774A>T	uc001xmo.2	+	31	6103	c.5657A>T	c.(5656-5658)GAG>GTG	p.E1886V	PCNX_uc010are.1_Missense_Mutation_p.E1775V|PCNX_uc010arf.1_Missense_Mutation_p.E674V|PCNX_uc001xmp.2_5'UTR	NM_014982	NP_055797	Q96RV3	PCX1_HUMAN	pecanex-like 1	1886						integral to membrane				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		GTATCTCATGAGAAGAACCTC	0.418													26	58	---	---	---	---	PASS
LTBP2	4053	broad.mit.edu	37	14	74971752	74971752	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74971752C>T	uc001xqa.2	-	29	4690	c.4303G>A	c.(4303-4305)GAA>AAA	p.E1435K		NM_000428	NP_000419	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding	1435	TB 3.				protein secretion|protein targeting|transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|growth factor binding			liver(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		CAGCAGCATTCAGCCTGTGTG	0.662													21	27	---	---	---	---	PASS
DLST	1743	broad.mit.edu	37	14	75366627	75366627	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75366627G>A	uc001xqv.2	+	12	966	c.903G>A	c.(901-903)GTG>GTA	p.V301V	DLST_uc001xqu.2_Silent_p.V213V|DLST_uc001xqt.2_Silent_p.V217V|DLST_uc010tuw.1_Silent_p.V215V	NM_001933	NP_001924	P36957	ODO2_HUMAN	dihydrolipoamide S-succinyltransferase (E2	301					lysine catabolic process|tricarboxylic acid cycle	mitochondrial matrix|nucleus	dihydrolipoyllysine-residue succinyltransferase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00698)		CTCTCATAGTGATTGACGACA	0.448													6	47	---	---	---	---	PASS
TTLL5	23093	broad.mit.edu	37	14	76286427	76286427	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76286427C>T	uc001xrx.2	+	28	3454	c.3249C>T	c.(3247-3249)ATC>ATT	p.I1083I	TTLL5_uc010ask.1_Silent_p.I1098I|TTLL5_uc001xrz.2_Silent_p.I658I|TTLL5_uc001xsa.2_Silent_p.I157I	NM_015072	NP_055887	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	1083					protein modification process|transcription, DNA-dependent	centrosome|cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.029)		GACCCATCATCAGTCCTAGTG	0.517													23	24	---	---	---	---	PASS
ANGEL1	23357	broad.mit.edu	37	14	77255657	77255657	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77255657C>A	uc001xsv.2	-	10	2040	c.1927G>T	c.(1927-1929)GCT>TCT	p.A643S	uc001xsu.1_5'Flank|ANGEL1_uc010tvf.1_Intron	NM_015305	NP_056120	Q9UNK9	ANGE1_HUMAN	angel homolog 1	643										ovary(2)|central_nervous_system(1)|skin(1)	4			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0285)		CCATTGGCAGCCCAGAGTATC	0.577													29	71	---	---	---	---	PASS
GTF2A1	2957	broad.mit.edu	37	14	81670361	81670361	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81670361G>A	uc001xvf.1	-	3	652	c.220C>T	c.(220-222)CAT>TAT	p.H74Y	GTF2A1_uc010atb.1_Missense_Mutation_p.H24Y|GTF2A1_uc001xvg.1_Missense_Mutation_p.H35Y|GTF2A1_uc001xvh.1_Missense_Mutation_p.H35Y|SNORA79_uc001xvi.1_5'Flank	NM_015859	NP_056943	P52655	TF2AA_HUMAN	TFIIA alpha, p55 isoform 1	74	Poly-Gln.				regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|transcription factor TFIIA complex	DNA binding|protein binding|protein heterodimerization activity|TBP-class protein binding|transcription coactivator activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0287)		tggggttgatgctgctgttga	0.234													14	6	---	---	---	---	PASS
KIAA1409	57578	broad.mit.edu	37	14	94046632	94046632	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94046632G>T	uc001ybv.1	+	16	2123	c.2040G>T	c.(2038-2040)GAG>GAT	p.E680D	KIAA1409_uc001ybs.1_Missense_Mutation_p.E680D	NM_020818	NP_065869	Q9P2D8	UNC79_HUMAN	hypothetical protein LOC57578	857						integral to membrane				ovary(10)|skin(4)|large_intestine(3)	17		all_cancers(154;0.0354)|all_epithelial(191;0.216)		Epithelial(152;0.188)		AAGCAATCGAGTGCAACTTAT	0.468													18	52	---	---	---	---	PASS
SERPINA9	327657	broad.mit.edu	37	14	94931201	94931201	+	Intron	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94931201A>T	uc001ydf.2	-						SERPINA9_uc001yde.2_Intron|SERPINA9_uc010avc.2_Intron|SERPINA9_uc001ydg.2_Intron|SERPINA9_uc001ydh.1_Intron|SERPINA9_uc001ydi.1_Intron	NM_175739	NP_783866	Q86WD7	SPA9_HUMAN	serine (or cysteine) proteinase inhibitor, clade						regulation of proteolysis	cytoplasm|extracellular region|membrane	serine-type endopeptidase inhibitor activity			lung(1)|central_nervous_system(1)	2		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		CCTGTGGAGTAGGGAAAAGGA	0.478													8	17	---	---	---	---	PASS
SERPINA4	5267	broad.mit.edu	37	14	95033402	95033402	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95033402G>T	uc001ydk.2	+	3	811	c.745G>T	c.(745-747)GAC>TAC	p.D249Y	SERPINA4_uc010avd.2_Missense_Mutation_p.D286Y|SERPINA4_uc001ydl.2_Missense_Mutation_p.D249Y	NM_006215	NP_006206	P29622	KAIN_HUMAN	serine (or cysteine) proteinase inhibitor, clade	249					regulation of proteolysis	extracellular space	serine-type endopeptidase inhibitor activity			ovary(3)|skin(1)	4				COAD - Colon adenocarcinoma(157;0.211)		GATGCTGCAGGACCAGGAGCA	0.493													13	24	---	---	---	---	PASS
SERPINA13	388007	broad.mit.edu	37	14	95109887	95109887	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95109887C>A	uc001ydt.2	+	3	924	c.836C>A	c.(835-837)CCC>CAC	p.P279H		NR_015340				RecName: Full=Serpin A13; Flags: Precursor;											lung(1)|skin(1)	2						GTGTGGGTGCCCATGATGAAG	0.582													15	24	---	---	---	---	PASS
ATG2B	55102	broad.mit.edu	37	14	96807901	96807901	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96807901C>T	uc001yfi.2	-	6	1247	c.882G>A	c.(880-882)TTG>TTA	p.L294L		NM_018036	NP_060506	Q96BY7	ATG2B_HUMAN	ATG2 autophagy related 2 homolog B	294										ovary(1)|kidney(1)|skin(1)	3		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		ACGTGAGACTCAACTCCAACC	0.388													14	45	---	---	---	---	PASS
WARS	7453	broad.mit.edu	37	14	100801383	100801383	+	Intron	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100801383G>A	uc001yhf.1	-						WARS_uc001yhe.1_Intron|WARS_uc001yhg.1_Intron|WARS_uc001yhh.1_Intron|WARS_uc001yhi.1_Intron|WARS_uc001yhj.1_Intron|WARS_uc001yhk.1_Intron|WARS_uc001yhl.1_Intron	NM_173701	NP_776049	P23381	SYWC_HUMAN	tryptophanyl-tRNA synthetase isoform a						angiogenesis|negative regulation of cell proliferation|regulation of angiogenesis|tryptophanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|protein binding|tryptophan-tRNA ligase activity			breast(1)	1		all_cancers(154;0.00223)|all_lung(585;2.48e-06)|all_epithelial(191;0.000564)|Melanoma(154;0.152)			L-Tryptophan(DB00150)	CCTGCCCGGAGGGAGACAGCC	0.632													5	21	---	---	---	---	PASS
WARS	7453	broad.mit.edu	37	14	100808747	100808747	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100808747C>A	uc001yhf.1	-	8	1185	c.1101G>T	c.(1099-1101)CAG>CAT	p.Q367H	WARS_uc001yhe.1_Missense_Mutation_p.Q173H|WARS_uc001yhg.1_Missense_Mutation_p.Q367H|WARS_uc001yhh.1_Missense_Mutation_p.Q367H|WARS_uc001yhi.1_Missense_Mutation_p.Q326H|WARS_uc001yhj.1_Missense_Mutation_p.Q326H|WARS_uc001yhk.1_Missense_Mutation_p.Q326H|WARS_uc001yhl.1_Missense_Mutation_p.Q367H	NM_173701	NP_776049	P23381	SYWC_HUMAN	tryptophanyl-tRNA synthetase isoform a	367					angiogenesis|negative regulation of cell proliferation|regulation of angiogenesis|tryptophanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|protein binding|tryptophan-tRNA ligase activity			breast(1)	1		all_cancers(154;0.00223)|all_lung(585;2.48e-06)|all_epithelial(191;0.000564)|Melanoma(154;0.152)			L-Tryptophan(DB00150)	TGGTTTTGATCTGCTTGGCCG	0.622													14	40	---	---	---	---	PASS
WARS	7453	broad.mit.edu	37	14	100808790	100808790	+	Missense_Mutation	SNP	C	A	A	rs145597356		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100808790C>A	uc001yhf.1	-	8	1142	c.1058G>T	c.(1057-1059)AGC>ATC	p.S353I	WARS_uc001yhe.1_Missense_Mutation_p.S159I|WARS_uc001yhg.1_Missense_Mutation_p.S353I|WARS_uc001yhh.1_Missense_Mutation_p.S353I|WARS_uc001yhi.1_Missense_Mutation_p.S312I|WARS_uc001yhj.1_Missense_Mutation_p.S312I|WARS_uc001yhk.1_Missense_Mutation_p.S312I|WARS_uc001yhl.1_Missense_Mutation_p.S353I	NM_173701	NP_776049	P23381	SYWC_HUMAN	tryptophanyl-tRNA synthetase isoform a	353	KMSKS region.				angiogenesis|negative regulation of cell proliferation|regulation of angiogenesis|tryptophanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|protein binding|tryptophan-tRNA ligase activity			breast(1)	1		all_cancers(154;0.00223)|all_lung(585;2.48e-06)|all_epithelial(191;0.000564)|Melanoma(154;0.152)			L-Tryptophan(DB00150)	GTTGGGGTCGCTGGCACTCAT	0.612													42	44	---	---	---	---	PASS
BEGAIN	57596	broad.mit.edu	37	14	101010249	101010249	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101010249G>C	uc010txa.1	-	4	443	c.297C>G	c.(295-297)CTC>CTG	p.L99L	BEGAIN_uc001yhp.2_Silent_p.L35L|BEGAIN_uc001yhq.2_Silent_p.L99L	NM_001159531	NP_001153003	Q9BUH8	BEGIN_HUMAN	brain-enriched guanylate kinase-associated	99						cytoplasm|membrane	protein binding				0		Melanoma(154;0.212)				GATGGCTGTTGAGGGCAACAA	0.617													7	11	---	---	---	---	PASS
CDC42BPB	9578	broad.mit.edu	37	14	103406189	103406189	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103406189C>T	uc001ymi.1	-	33	4919	c.4687G>A	c.(4687-4689)GAA>AAA	p.E1563K		NM_006035	NP_006026	Q9Y5S2	MRCKB_HUMAN	CDC42-binding protein kinase beta	1563					actin cytoskeleton reorganization|establishment or maintenance of cell polarity|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm|cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(3)|skin(3)|lung(2)|stomach(1)|breast(1)|ovary(1)	11		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		AGTCTCTCTTCCTCTGGGACC	0.612													42	65	---	---	---	---	PASS
CDC42BPB	9578	broad.mit.edu	37	14	103406192	103406192	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103406192C>T	uc001ymi.1	-	33	4916	c.4684G>A	c.(4684-4686)GAG>AAG	p.E1562K		NM_006035	NP_006026	Q9Y5S2	MRCKB_HUMAN	CDC42-binding protein kinase beta	1562					actin cytoskeleton reorganization|establishment or maintenance of cell polarity|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm|cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(3)|skin(3)|lung(2)|stomach(1)|breast(1)|ovary(1)	11		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		CTCTCTTCCTCTGGGACCTTG	0.617													42	68	---	---	---	---	PASS
TDRD9	122402	broad.mit.edu	37	14	104470664	104470664	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104470664G>C	uc001yom.3	+	14	1603	c.1573G>C	c.(1573-1575)GAG>CAG	p.E525Q	TDRD9_uc001yon.3_Missense_Mutation_p.E263Q	NM_153046	NP_694591	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	525	Helicase C-terminal.				cell differentiation|DNA methylation involved in gamete generation|fertilization|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	nucleus|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(2)|central_nervous_system(1)	3		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				TGTTGTTCCTGAGATGTTGGT	0.323													4	12	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105410407	105410407	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105410407T>C	uc010axc.1	-	7	11501	c.11381A>G	c.(11380-11382)AAG>AGG	p.K3794R	AHNAK2_uc001ypx.2_Missense_Mutation_p.K3694R	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3794						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			AGTCACATCCTTGTCGGCCAG	0.582													100	179	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105414568	105414568	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105414568G>C	uc010axc.1	-	7	7340	c.7220C>G	c.(7219-7221)CCC>CGC	p.P2407R	AHNAK2_uc001ypx.2_Missense_Mutation_p.P2307R	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2407						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CTTGAAACTGGGCATCTGCAG	0.627													33	165	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106586427	106586427	+	RNA	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106586427C>T	uc010tyt.1	-	1286		c.27803G>A			uc001ysv.2_RNA					Parts of antibodies, mostly variable regions.												0						AGCTGCACCTCACACTGGACA	0.517													28	105	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106725423	106725423	+	RNA	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106725423G>C	uc010tyt.1	-	588		c.18124C>G								Parts of antibodies, mostly variable regions.												0						TGAATCCAGAGGCTGCACAGG	0.577													23	101	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106815779	106815779	+	RNA	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106815779C>A	uc010tyt.1	-	342		c.13380G>T								Parts of antibodies, mostly variable regions.												0						TTTGCAGATACAGCGTGTTCT	0.498													23	108	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106926233	106926233	+	RNA	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106926233G>T	uc010tyt.1	-	235		c.10322C>A			uc010tyu.1_Intron					Parts of antibodies, mostly variable regions.												0						TTCTCAGACTGTTCATTTGCA	0.488													17	136	---	---	---	---	PASS
SNRPN	6638	broad.mit.edu	37	15	25221448	25221448	+	Intron	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25221448G>T	uc001ywp.1	+						SNRPN_uc001ywq.1_Intron|SNRPN_uc001ywr.1_Intron|SNRPN_uc001yws.1_Intron|SNRPN_uc001ywt.1_Intron|SNRPN_uc001ywv.1_Intron|SNRPN_uc001yww.1_Intron|SNRPN_uc001ywx.1_Intron|SNRPN_uc001ywz.1_Intron|PAR-SN_uc001yxa.1_Intron|SNRPN_uc001ywy.1_Intron	NM_022807	NP_073718	P63162	RSMN_HUMAN	small nuclear ribonucleoprotein polypeptide N						RNA splicing	small nuclear ribonucleoprotein complex|spliceosomal complex	identical protein binding|RNA binding			ovary(1)	1		all_cancers(20;9.33e-22)|Breast(32;0.000625)		all cancers(64;3.38e-08)|Epithelial(43;3.45e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000207)|GBM - Glioblastoma multiforme(186;0.125)		ATTCTGATTTGTAGGCCAAAG	0.403									Prader-Willi_syndrome				9	19	---	---	---	---	PASS
SNORD115-11	100033448	broad.mit.edu	37	15	25432755	25432755	+	5'Flank	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25432755C>A	uc001yze.1	+						SNORD115-10_uc001yzd.1_RNA	NR_003358				Homo sapiens small nucleolar RNA, C/D box 115-11 (SNORD115-11), non-coding RNA.												0						TAGGATTACGCTGAGGCCCAG	0.483													63	91	---	---	---	---	PASS
SNORD115-11	100033448	broad.mit.edu	37	15	25434556	25434556	+	5'Flank	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25434556G>C	uc001yze.1	+						SNORD115-13_uc001yzf.1_5'Flank|SNORD115-9_uc001yzg.1_5'Flank	NR_003358				Homo sapiens small nucleolar RNA, C/D box 115-11 (SNORD115-11), non-coding RNA.												0						GGCGTGCCCTGAGTTGGGTCA	0.547													66	102	---	---	---	---	PASS
ARHGAP11B	89839	broad.mit.edu	37	15	30919108	30919108	+	Nonsense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30919108C>T	uc001zet.1	+	1	230	c.85C>T	c.(85-87)CAG>TAG	p.Q29*	ARHGAP11B_uc010azv.1_Intron|ARHGAP11B_uc001zeu.2_RNA	NM_001039841	NP_001034930	Q3KRB8	RHGBB_HUMAN	Rho GTPase activating protein 11B	29					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0		all_lung(180;2.71e-09)|Breast(32;0.00116)		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)		TGTCCGTGGGCAGTGCGATCG	0.502													4	18	---	---	---	---	PASS
ARHGAP11A	9824	broad.mit.edu	37	15	32929102	32929102	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32929102G>C	uc001zgy.1	+	12	2850	c.2128G>C	c.(2128-2130)GAT>CAT	p.D710H	ARHGAP11A_uc010ubw.1_Missense_Mutation_p.D521H|ARHGAP11A_uc010ubx.1_Missense_Mutation_p.D521H	NM_014783	NP_055598	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A isoform 1	710					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			skin(3)|breast(2)|urinary_tract(1)	6		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		TATGCCAAAAGATTATTTAAG	0.284													14	11	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	33991934	33991934	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33991934C>A	uc001zhi.2	+	41	6349	c.6279C>A	c.(6277-6279)TGC>TGA	p.C2093*	RYR3_uc010bar.2_Nonsense_Mutation_p.C2093*	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	2093	4 X approximate repeats.|Cytoplasmic (By similarity).				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)		TTGCTAGCTGCTGCCGTTTCC	0.438													8	14	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	34065783	34065783	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34065783C>A	uc001zhi.2	+	64	9174	c.9104C>A	c.(9103-9105)TCC>TAC	p.S3035Y	RYR3_uc010bar.2_Missense_Mutation_p.S3035Y	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	3035					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)		AGCCTCTACTCCCTTGGGACG	0.388													8	18	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	34131112	34131112	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34131112G>T	uc001zhi.2	+	89	13001	c.12931G>T	c.(12931-12933)GAA>TAA	p.E4311*	RYR3_uc010bar.2_Nonsense_Mutation_p.E4306*	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	4311					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)		TGGCAAGGATGAACCCCCTAC	0.453													16	30	---	---	---	---	PASS
MEIS2	4212	broad.mit.edu	37	15	37187378	37187378	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37187378T>A	uc001zjr.2	-	11	2158	c.1121A>T	c.(1120-1122)CAG>CTG	p.Q374L	MEIS2_uc001zjl.2_Missense_Mutation_p.Q361L|MEIS2_uc010ucj.1_Missense_Mutation_p.Q354L|MEIS2_uc001zjm.2_Missense_Mutation_p.Q279L|MEIS2_uc001zjn.2_Missense_Mutation_p.Q228L|MEIS2_uc001zjo.2_Missense_Mutation_p.Q374L|MEIS2_uc001zjp.2_Missense_Mutation_p.Q367L|MEIS2_uc001zjs.2_Missense_Mutation_p.Q367L|MEIS2_uc001zju.2_Missense_Mutation_p.Q354L|MEIS2_uc001zjt.2_Missense_Mutation_p.Q367L|MEIS2_uc001zjj.2_Missense_Mutation_p.Q70L|MEIS2_uc001zjk.2_Missense_Mutation_p.Q63L	NM_170675	NP_733775	O14770	MEIS2_HUMAN	Meis homeobox 2 isoform c	374					negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)	2		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)		CATGTGTTGCTGACCATCCAA	0.562													27	39	---	---	---	---	PASS
MEIS2	4212	broad.mit.edu	37	15	37390191	37390191	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37390191C>A	uc001zjr.2	-	2	1259	c.222G>T	c.(220-222)AAG>AAT	p.K74N	MEIS2_uc001zjl.2_Missense_Mutation_p.K61N|MEIS2_uc010ucj.1_Missense_Mutation_p.K61N|MEIS2_uc001zjm.2_5'UTR|MEIS2_uc001zjn.2_5'UTR|MEIS2_uc001zjo.2_Missense_Mutation_p.K74N|MEIS2_uc001zjp.2_Missense_Mutation_p.K74N|MEIS2_uc001zjs.2_Missense_Mutation_p.K74N|MEIS2_uc001zju.2_Missense_Mutation_p.K61N|MEIS2_uc001zjt.2_Missense_Mutation_p.K74N	NM_170675	NP_733775	O14770	MEIS2_HUMAN	Meis homeobox 2 isoform c	74					negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)	2		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)		CCTTGTCCCGCTTCAAGGCGT	0.627													7	14	---	---	---	---	PASS
NDUFAF1	51103	broad.mit.edu	37	15	41680695	41680695	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41680695G>C	uc001znx.2	-	4	1167	c.785C>G	c.(784-786)TCT>TGT	p.S262C	NDUFAF1_uc010bcf.2_RNA	NM_016013	NP_057097	Q9Y375	CIA30_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha	262					mitochondrial electron transport, NADH to ubiquinone|protein complex assembly	mitochondrial respiratory chain complex I	unfolded protein binding			ovary(1)	1		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;8e-17)|GBM - Glioblastoma multiforme(113;1.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.114)		TCCTCGATTAGAGAAGAAAAA	0.338													14	23	---	---	---	---	PASS
NDUFAF1	51103	broad.mit.edu	37	15	41680723	41680723	+	Intron	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41680723G>C	uc001znx.2	-						NDUFAF1_uc010bcf.2_Intron	NM_016013	NP_057097	Q9Y375	CIA30_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha						mitochondrial electron transport, NADH to ubiquinone|protein complex assembly	mitochondrial respiratory chain complex I	unfolded protein binding			ovary(1)	1		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;8e-17)|GBM - Glioblastoma multiforme(113;1.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.114)		AAAGGAATCTGAAAGAAGAAA	0.323													13	18	---	---	---	---	PASS
SPTBN5	51332	broad.mit.edu	37	15	42140831	42140831	+	Intron	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42140831T>C	uc001zos.2	-							NM_016642	NP_057726	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5						actin cytoskeleton organization|actin filament capping|axon guidance	cytosol|membrane|spectrin				ovary(1)|central_nervous_system(1)	2		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		TCAGACCTGTTGGGAAAACGG	0.542													4	79	---	---	---	---	PASS
PLA2G4F	255189	broad.mit.edu	37	15	42442310	42442310	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42442310C>A	uc001zoz.2	-	10	978	c.915G>T	c.(913-915)GTG>GTT	p.V305V	PLA2G4F_uc001zoy.2_5'Flank|PLA2G4F_uc010bcr.2_Silent_p.V56V|PLA2G4F_uc001zpa.2_Silent_p.V56V|PLA2G4F_uc010bcs.2_Silent_p.V92V	NM_213600	NP_998765	Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	305					phospholipid catabolic process	cytosol|lysosomal membrane	metal ion binding|phospholipase A2 activity			ovary(4)	4		all_cancers(109;4.82e-12)|all_epithelial(112;5.64e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.97e-07)		ACCTCATTTCCACCTTCATGC	0.592													14	9	---	---	---	---	PASS
ADAL	161823	broad.mit.edu	37	15	43641146	43641146	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43641146G>A	uc010udo.1	+	10	1168	c.594G>A	c.(592-594)CTG>CTA	p.L198L	ADAL_uc001zrh.2_Silent_p.L225L|ADAL_uc001zri.1_Silent_p.L110L	NM_001159280	NP_001152752	Q6DHV7	ADAL_HUMAN	adenosine deaminase-like isoform 1	225					adenosine catabolic process|inosine biosynthetic process|purine ribonucleoside monophosphate biosynthetic process		adenosine deaminase activity|metal ion binding				0		all_cancers(109;7.96e-11)|all_epithelial(112;2.96e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;9.31e-07)		TCCTGGATCTGCTTCCTGACA	0.458													25	26	---	---	---	---	PASS
SLC27A2	11001	broad.mit.edu	37	15	50475061	50475061	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50475061G>A	uc001zxw.2	+	1	669	c.437G>A	c.(436-438)TGC>TAC	p.C146Y	SLC27A2_uc010bes.2_Missense_Mutation_p.C146Y	NM_003645	NP_003636	O14975	S27A2_HUMAN	solute carrier family 27 (fatty acid	146	Lumenal (Potential).				bile acid biosynthetic process|fatty acid alpha-oxidation	endoplasmic reticulum membrane|integral to membrane|peroxisomal matrix|peroxisomal membrane	ATP binding|long-chain fatty acid-CoA ligase activity|phytanate-CoA ligase activity|pristanate-CoA ligase activity			ovary(1)|skin(1)	2		all_lung(180;0.00177)		all cancers(107;1.16e-06)|GBM - Glioblastoma multiforme(94;0.000113)		CTGCTGCACTGCTTCCAGTGC	0.662													41	44	---	---	---	---	PASS
SCG3	29106	broad.mit.edu	37	15	51973991	51973991	+	Silent	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51973991A>G	uc002abh.2	+	1	447	c.39A>G	c.(37-39)TTA>TTG	p.L13L	SCG3_uc010ufz.1_5'UTR	NM_013243	NP_037375	Q8WXD2	SCG3_HUMAN	secretogranin III isoform 1 precursor	13					platelet activation|platelet degranulation	extracellular region|stored secretory granule				ovary(1)	1				all cancers(107;0.00488)		TTCTGGTGTTAGTGCTCCCGA	0.522													16	11	---	---	---	---	PASS
WDR72	256764	broad.mit.edu	37	15	53998114	53998114	+	Intron	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53998114A>G	uc002acj.2	-						WDR72_uc010bfi.1_Intron	NM_182758	NP_877435	Q3MJ13	WDR72_HUMAN	WD repeat domain 72											lung(1)|skin(1)	2				all cancers(107;0.0511)		AGAAAAGGAAACTGACTTACC	0.368													19	26	---	---	---	---	PASS
UNC13C	440279	broad.mit.edu	37	15	54307002	54307002	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54307002G>C	uc002ack.2	+	1	1902	c.1902G>C	c.(1900-1902)GTG>GTC	p.V634V		NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C	634					exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		ATGGCATGGTGTGTGCATCTG	0.458													38	57	---	---	---	---	PASS
GCNT3	9245	broad.mit.edu	37	15	59910815	59910815	+	Silent	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59910815A>G	uc002age.2	+	3	827	c.378A>G	c.(376-378)AAA>AAG	p.K126K	GCNT3_uc002agd.2_Silent_p.K126K	NM_004751	NP_004742	O95395	GCNT3_HUMAN	glucosaminyl (N-acetyl) transferase 3, mucin	126	Lumenal (Potential).				protein O-linked glycosylation	Golgi membrane|integral to membrane|membrane fraction	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)	2						CACTGAGCAAAGAAGAGGTGG	0.468													21	30	---	---	---	---	PASS
RAB11A	8766	broad.mit.edu	37	15	66161914	66161914	+	5'UTR	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66161914C>T	uc002apk.2	+	1					RAB11A_uc010ujk.1_5'UTR	NM_004663	NP_004654	P62491	RB11A_HUMAN	Ras-related protein Rab-11A						cell cycle|cytokinesis|neuron projection development|plasma membrane to endosome transport|protein localization in plasma membrane|small GTPase mediated signal transduction|vesicle-mediated transport	cleavage furrow|plasma membrane|recycling endosome membrane|trans-Golgi network	GTP binding|GTPase activity|syntaxin binding				0						TTTCGCTCCTCGGCCGCGCAA	0.652													28	33	---	---	---	---	PASS
HCN4	10021	broad.mit.edu	37	15	73614857	73614857	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73614857C>G	uc002avp.2	-	8	4571	c.3577G>C	c.(3577-3579)GAG>CAG	p.E1193Q		NM_005477	NP_005468	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic	1193	Cytoplasmic (Potential).				blood circulation|muscle contraction	integral to membrane	cAMP binding|protein binding|sodium channel activity|voltage-gated potassium channel activity			ovary(5)|liver(1)	6				COAD - Colon adenocarcinoma(1;0.142)		CGCACTGGCTCAGGCCTGGCC	0.458													6	4	---	---	---	---	PASS
CCDC33	80125	broad.mit.edu	37	15	74574143	74574143	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74574143G>A	uc002axo.2	+	10	1442	c.1048G>A	c.(1048-1050)GAT>AAT	p.D350N	CCDC33_uc002axp.2_Missense_Mutation_p.D172N	NM_025055	NP_079331	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33 isoform 1	553							protein binding			ovary(3)|skin(2)	5						AACTATCAATGATGAGGCCCC	0.592													40	37	---	---	---	---	PASS
CRABP1	1381	broad.mit.edu	37	15	78635882	78635882	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78635882G>T	uc002bdp.2	+	3	396	c.291G>T	c.(289-291)ACG>ACT	p.T97T		NM_004378	NP_004369	P29762	RABP1_HUMAN	cellular retinoic acid binding protein 1	97					multicellular organismal development|signal transduction	cytoplasm	retinal binding|retinol binding|transporter activity				0					Alitretinoin(DB00523)|Etretinate(DB00926)	TCCACTGCACGCAAACTCTTC	0.512													11	28	---	---	---	---	PASS
RASGRF1	5923	broad.mit.edu	37	15	79290512	79290512	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79290512G>T	uc002beq.2	-	20	3315	c.2940C>A	c.(2938-2940)ATC>ATA	p.I980I	RASGRF1_uc002bep.2_Silent_p.I964I|RASGRF1_uc010blm.1_Silent_p.I889I|RASGRF1_uc002ber.3_Silent_p.I964I|RASGRF1_uc010unh.1_Silent_p.I375I|RASGRF1_uc002beo.2_Silent_p.I196I	NM_002891	NP_002882	Q13972	RGRF1_HUMAN	Ras protein-specific guanine	982					activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|growth cone|plasma membrane|synaptosome	Rho guanyl-nucleotide exchange factor activity			skin(4)|ovary(1)|central_nervous_system(1)	6						CCAGGAAGCCGATCACCTTGC	0.557													13	36	---	---	---	---	PASS
KIAA1024	23251	broad.mit.edu	37	15	79750590	79750590	+	Nonsense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79750590A>T	uc002bew.1	+	2	2176	c.2101A>T	c.(2101-2103)AAA>TAA	p.K701*	KIAA1024_uc010unk.1_Nonsense_Mutation_p.K701*	NM_015206	NP_056021	Q9UPX6	K1024_HUMAN	hypothetical protein LOC23251	701						integral to membrane				pancreas(2)|ovary(1)|central_nervous_system(1)	4						GGCCTTAAAAAAAAGCCTCTT	0.552													48	80	---	---	---	---	PASS
IL16	3603	broad.mit.edu	37	15	81578086	81578086	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81578086T>A	uc002bgh.3	+	10	1623	c.1247T>A	c.(1246-1248)CTG>CAG	p.L416Q	IL16_uc002bgc.2_RNA|IL16_uc010blq.1_Missense_Mutation_p.L416Q|IL16_uc002bge.3_RNA|IL16_uc010unp.1_Missense_Mutation_p.L458Q|IL16_uc002bgg.2_Missense_Mutation_p.L416Q|IL16_uc002bgi.1_5'UTR	NM_172217	NP_757366	Q14005	IL16_HUMAN	interleukin 16 isoform 2	416	PDZ 2.|Interaction with GRIN2A.				immune response|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus|plasma membrane	cytokine activity			ovary(2)|lung(1)|skin(1)	4						GTGCACTGCCTGACGCTCAAT	0.502													39	26	---	---	---	---	PASS
TMC3	342125	broad.mit.edu	37	15	81625278	81625278	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81625278C>T	uc002bgo.1	-	22	2785	c.2785G>A	c.(2785-2787)GCA>ACA	p.A929T	TMC3_uc010blr.1_RNA	NM_001080532	NP_001074001	Q7Z5M5	TMC3_HUMAN	transmembrane channel-like 3	929	Cytoplasmic (Potential).					integral to membrane				ovary(1)|liver(1)	2						ACCCGGGATGCATATTGTCGC	0.522													15	24	---	---	---	---	PASS
TMC3	342125	broad.mit.edu	37	15	81637256	81637256	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81637256G>T	uc002bgo.1	-	13	1369	c.1369C>A	c.(1369-1371)CGG>AGG	p.R457R	TMC3_uc010blr.1_RNA|TMC3_uc002bgp.2_Silent_p.R457R	NM_001080532	NP_001074001	Q7Z5M5	TMC3_HUMAN	transmembrane channel-like 3	457	Cytoplasmic (Potential).					integral to membrane				ovary(1)|liver(1)	2						ATTCCAGGCCGAGATGTGGAC	0.478													7	27	---	---	---	---	PASS
AGBL1	123624	broad.mit.edu	37	15	86697678	86697678	+	Missense_Mutation	SNP	A	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86697678A>C	uc002blz.1	+	3	222	c.142A>C	c.(142-144)AAG>CAG	p.K48Q		NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	48					C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0						GATTGGACGGAAGGCCCTAGA	0.448													5	30	---	---	---	---	PASS
MSLN	10232	broad.mit.edu	37	16	818700	818700	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:818700C>T	uc002cjw.1	+	17	1911	c.1860C>T	c.(1858-1860)GTC>GTT	p.V620V	MSLN_uc002cjt.1_Silent_p.V612V|MSLN_uc002cju.1_Silent_p.V612V|MSLN_uc010brd.1_Silent_p.V611V|MSLN_uc002cjv.1_Silent_p.V602V|MSLN_uc002cjx.1_Silent_p.V612V|MSLN_uc002cjy.1_Missense_Mutation_p.P305S|MIR662_hsa-mir-662|MI0003670_5'Flank	NM_013404	NP_037536	Q13421	MSLN_HUMAN	mesothelin isoform 2 preproprotein	620					cell adhesion	anchored to membrane|extracellular region|Golgi apparatus|plasma membrane				pancreas(1)	1		Hepatocellular(780;0.00335)				TTCTCACCGTCCTGGCACTGC	0.701													22	12	---	---	---	---	PASS
ABCA3	21	broad.mit.edu	37	16	2373534	2373534	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2373534G>T	uc002cpy.1	-	7	1315	c.603C>A	c.(601-603)GGC>GGA	p.G201G	ABCA3_uc010bsk.1_Silent_p.G201G|ABCA3_uc010bsl.1_Silent_p.G201G|ABCA3_uc002cpz.1_Silent_p.G201G	NM_001089	NP_001080	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A member 3	201					response to drug	integral to membrane|lamellar body|membrane fraction|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			breast(5)|ovary(5)|central_nervous_system(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	16		Ovarian(90;0.17)				CAGGTTCTCCGCCATCAGGGG	0.532													116	110	---	---	---	---	PASS
SEC14L5	9717	broad.mit.edu	37	16	5058478	5058478	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5058478G>T	uc002cye.2	+	14	1809	c.1629G>T	c.(1627-1629)CTG>CTT	p.L543L		NM_014692	NP_055507	O43304	S14L5_HUMAN	SEC14-like 5	543	GOLD.					integral to membrane|intracellular	transporter activity				0						TTGACATCCTGCGAGGGGACG	0.647													17	6	---	---	---	---	PASS
NOMO1	23420	broad.mit.edu	37	16	14989462	14989462	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14989462C>T	uc002dcv.2	+	31	3695	c.3629C>T	c.(3628-3630)GCA>GTA	p.A1210V		NM_014287	NP_055102	Q15155	NOMO1_HUMAN	nodal modulator 1 precursor	1210	Cytoplasmic (Potential).					integral to membrane	carbohydrate binding|carboxypeptidase activity|protein binding			ovary(1)	1						CCAGAAGATGCAAAGAGACAA	0.582													71	177	---	---	---	---	PASS
GP2	2813	broad.mit.edu	37	16	20329729	20329729	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20329729C>T	uc002dgv.2	-	8	1123	c.1040G>A	c.(1039-1041)GGG>GAG	p.G347E	GP2_uc002dgw.2_Missense_Mutation_p.G344E|GP2_uc002dgx.2_Missense_Mutation_p.G200E|GP2_uc002dgy.2_Missense_Mutation_p.G197E	NM_001007240	NP_001007241	P55259	GP2_HUMAN	zymogen granule membrane glycoprotein 2 isoform	347	ZP.					anchored to membrane|extracellular region|plasma membrane				ovary(3)|skin(1)	4						CTCTCCATTCCCGTCCACACT	0.473													29	154	---	---	---	---	PASS
DNAH3	55567	broad.mit.edu	37	16	21093016	21093016	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21093016G>A	uc010vbe.1	-	20	2910	c.2910C>T	c.(2908-2910)CCC>CCT	p.P970P		NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	970	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)		TCGTTTCGGTGGGCTTTATCT	0.368													14	108	---	---	---	---	PASS
EEF2K	29904	broad.mit.edu	37	16	22260121	22260121	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22260121C>G	uc002dki.2	+	4	878	c.393C>G	c.(391-393)ATC>ATG	p.I131M	EEF2K_uc002dkh.2_RNA	NM_013302	NP_037434	O00418	EF2K_HUMAN	elongation factor-2 kinase	131	Alpha-type protein kinase.				insulin receptor signaling pathway|translational elongation	cytosol	ATP binding|calcium ion binding|calmodulin binding|elongation factor-2 kinase activity|translation factor activity, nucleic acid binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(48;0.0223)		AAGTTCTGATCAAGATGGCAT	0.567													18	24	---	---	---	---	PASS
C16orf82	162083	broad.mit.edu	37	16	27078550	27078550	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27078550G>A	uc010vcm.1	+	1	332	c.234G>A	c.(232-234)AGG>AGA	p.R78R		NM_001145545	NP_001139017	Q7Z2V1	TNT_HUMAN	hypothetical protein LOC162083	141											0						AGCACCCGAGGCCAGAGGAGG	0.647													3	3	---	---	---	---	PASS
ITGAD	3681	broad.mit.edu	37	16	31435470	31435470	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31435470C>T	uc002ebv.1	+	28	3256	c.3207C>T	c.(3205-3207)TTC>TTT	p.F1069F	ITGAD_uc010cap.1_Silent_p.F1070F	NM_005353	NP_005344	Q13349	ITAD_HUMAN	integrin, alpha D precursor	1069	Extracellular (Potential).				cell-cell adhesion|cell-matrix adhesion|immune response|integrin-mediated signaling pathway	integrin complex	receptor activity			skin(1)	1						AAATTACGTTCGACACATCCG	0.557													7	33	---	---	---	---	PASS
ITGAD	3681	broad.mit.edu	37	16	31435806	31435806	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31435806G>A	uc002ebv.1	+	29	3329	c.3280G>A	c.(3280-3282)GAA>AAA	p.E1094K	ITGAD_uc010cap.1_Missense_Mutation_p.E1095K	NM_005353	NP_005344	Q13349	ITAD_HUMAN	integrin, alpha D precursor	1094	Extracellular (Potential).				cell-cell adhesion|cell-matrix adhesion|immune response|integrin-mediated signaling pathway	integrin complex	receptor activity			skin(1)	1						GGTGCTAGAAGAAGACGAGGT	0.542													11	22	---	---	---	---	PASS
NETO2	81831	broad.mit.edu	37	16	47117419	47117419	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47117419C>A	uc002eer.1	-	9	1676	c.1291G>T	c.(1291-1293)GCC>TCC	p.A431S	NETO2_uc002eeq.1_Missense_Mutation_p.A166S|NETO2_uc010vgf.1_Missense_Mutation_p.A288S	NM_018092	NP_060562	Q8NC67	NETO2_HUMAN	neuropilin- and tolloid-like protein 2	431	Cytoplasmic (Potential).					integral to membrane	receptor activity				0		all_cancers(37;0.00114)|all_lung(18;0.00432)|Lung NSC(13;0.0384)|Breast(268;0.174)				CAGCGGGAGGCGGTGGAGGAG	0.527										HNSCC(25;0.065)			20	36	---	---	---	---	PASS
PHKB	5257	broad.mit.edu	37	16	47581470	47581470	+	Intron	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47581470G>A	uc002eev.3	+						PHKB_uc002eeu.3_Intron	NM_000293	NP_000284	Q93100	KPBB_HUMAN	phosphorylase kinase, beta isoform a						glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity			ovary(1)|large_intestine(1)|breast(1)	3		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				GTAATTTGCTGATTTCTGAGG	0.343													13	24	---	---	---	---	PASS
CNOT1	23019	broad.mit.edu	37	16	58559117	58559117	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58559117G>C	uc002env.2	-	46	7043	c.6750C>G	c.(6748-6750)ATC>ATG	p.I2250M	CNOT1_uc002enw.2_RNA|CNOT1_uc002enu.3_Missense_Mutation_p.I2245M|CNOT1_uc002ent.2_Missense_Mutation_p.I188M|CNOT1_uc010vik.1_Missense_Mutation_p.I1207M	NM_016284	NP_057368	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	2250					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		AATTCTGGAAGATATCCATGT	0.493													27	64	---	---	---	---	PASS
CDH8	1006	broad.mit.edu	37	16	61687817	61687817	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61687817C>A	uc002eog.1	-	12	2347	c.2095G>T	c.(2095-2097)GAT>TAT	p.D699Y		NM_001796	NP_001787	P55286	CADH8_HUMAN	cadherin 8, type 2 preproprotein	699	Cytoplasmic (Potential).				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)		GGTTTAATATCCTTACGGGGT	0.428													20	75	---	---	---	---	PASS
LRRC36	55282	broad.mit.edu	37	16	67375992	67375992	+	Intron	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67375992G>A	uc002esv.2	+						LRRC36_uc002esw.2_Intron	NM_018296	NP_060766	Q1X8D7	LRC36_HUMAN	leucine rich repeat containing 36 isoform 1												0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0669)|Epithelial(162;0.161)		CTTAAGGTAAGTTATATATTC	0.363													5	18	---	---	---	---	PASS
PMFBP1	83449	broad.mit.edu	37	16	72153940	72153940	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72153940C>G	uc002fcc.3	-	20	3004	c.2832G>C	c.(2830-2832)CTG>CTC	p.L944L	PMFBP1_uc002fcd.2_Silent_p.L939L|PMFBP1_uc002fce.2_RNA|PMFBP1_uc002fcf.2_Silent_p.L814L	NM_031293	NP_112583	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	944	Potential.									ovary(2)	2		Ovarian(137;0.179)				TCTCCTTCTTCAGCTTCTTGT	0.537													25	56	---	---	---	---	PASS
NUDT7	283927	broad.mit.edu	37	16	77769814	77769814	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77769814C>A	uc010chd.2	+	3	348	c.279C>A	c.(277-279)GCC>GCA	p.A93A	NUDT7_uc010vnj.1_Intron	NM_001105663	NP_001099133	P0C024	NUDT7_HUMAN	nudix motif 7	93	Nudix hydrolase.|Nudix box.				nucleoside diphosphate metabolic process	peroxisome	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides|magnesium ion binding|manganese ion binding			ovary(1)|kidney(1)	2						TCCGGGAAGCCCAGGAGGAAG	0.542													21	63	---	---	---	---	PASS
VAT1L	57687	broad.mit.edu	37	16	77913097	77913097	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77913097G>T	uc002ffg.1	+	6	955	c.858G>T	c.(856-858)AAG>AAT	p.K286N		NM_020927	NP_065978	Q9HCJ6	VAT1L_HUMAN	vesicle amine transport protein 1 homolog (T.	286							oxidoreductase activity|zinc ion binding			central_nervous_system(1)	1						GAGAGACCAAGAGCTTCTTCA	0.368													25	84	---	---	---	---	PASS
WWOX	51741	broad.mit.edu	37	16	79245630	79245630	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79245630C>G	uc002ffk.2	+	9	1307	c.1182C>G	c.(1180-1182)GCC>GCG	p.A394A	WWOX_uc010vnk.1_Silent_p.A281A|WWOX_uc002ffl.2_Silent_p.A214A|WWOX_uc010che.2_Missense_Mutation_p.P179A	NM_016373	NP_057457	Q9NZC7	WWOX_HUMAN	WW domain-containing oxidoreductase isoform 1	394	Interaction with MAPT (By similarity).				apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		AAGAGACGGCCCGGACCCTGT	0.627													9	39	---	---	---	---	PASS
KCNG4	93107	broad.mit.edu	37	16	84271026	84271026	+	Silent	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84271026A>G	uc010voc.1	-	2	187	c.66T>C	c.(64-66)CCT>CCC	p.P22P	KCNG4_uc002fhu.1_Silent_p.P22P	NM_172347	NP_758857	Q8TDN1	KCNG4_HUMAN	potassium voltage-gated channel, subfamily G,	22	Cytoplasmic (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			breast(3)	3						GCTGACTCCAAGGGCTGTGGG	0.627													12	29	---	---	---	---	PASS
BANP	54971	broad.mit.edu	37	16	88061218	88061218	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88061218C>A	uc002fkr.2	+	8	1222	c.998C>A	c.(997-999)TCG>TAG	p.S333*	BANP_uc002fkp.2_Nonsense_Mutation_p.S303*|BANP_uc002fkq.2_Nonsense_Mutation_p.S303*|BANP_uc010vow.1_Nonsense_Mutation_p.S341*|BANP_uc002fks.3_Nonsense_Mutation_p.S302*|BANP_uc002fko.1_Nonsense_Mutation_p.S239*|BANP_uc010vov.1_Nonsense_Mutation_p.S308*	NM_079837	NP_524576	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein isoform b	334	Necessary and sufficient for TP53 activation (By similarity).|Interaction with CUX1 and HDAC1 (By similarity).				cell cycle|chromatin modification|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0				BRCA - Breast invasive adenocarcinoma(80;0.00551)		AAGAGCTTCTCGCGGAGAACG	0.677													17	41	---	---	---	---	PASS
ZC3H18	124245	broad.mit.edu	37	16	88691009	88691009	+	Splice_Site	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88691009G>C	uc002fky.2	+	12	2099	c.1899_splice	c.e12-1	p.G633_splice	ZC3H18_uc010voz.1_Splice_Site_p.G657_splice|ZC3H18_uc010chw.2_Splice_Site|ZC3H18_uc002fkz.2_5'Flank	NM_144604	NP_653205	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18							nucleus	nucleic acid binding|zinc ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0542)		CTGTCTCACAGAGAGAAGTCA	0.662													6	9	---	---	---	---	PASS
MVD	4597	broad.mit.edu	37	16	88722558	88722558	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88722558C>G	uc002flg.1	-	5	565	c.558G>C	c.(556-558)GTG>GTC	p.V186V	MVD_uc002flf.1_Silent_p.V55V	NM_002461	NP_002452	P53602	MVD1_HUMAN	diphosphomevalonate decarboxylase	186					cholesterol biosynthetic process|positive regulation of cell proliferation	cytosol	ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity				0				BRCA - Breast invasive adenocarcinoma(80;0.0478)		ACTCGGGGGCCACTTGCCGAG	0.682													11	34	---	---	---	---	PASS
PAFAH1B1	5048	broad.mit.edu	37	17	2541586	2541586	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2541586G>T	uc002fuw.3	+	2	572	c.4G>T	c.(4-6)GTG>TTG	p.V2L	PAFAH1B1_uc010ckb.1_RNA	NM_000430	NP_000421	P43034	LIS1_HUMAN	platelet-activating factor acetylhydrolase,	2	Required for self-association and interaction with PAFAH1B2 and PAFAH1B3 (By similarity).|Interaction with NDEL1 (By similarity).|Interaction with NDE1 (By similarity).				acrosome assembly|actin cytoskeleton organization|adult locomotory behavior|brain morphogenesis|corpus callosum morphogenesis|establishment of mitotic spindle orientation|G2/M transition of mitotic cell cycle|hippocampus development|layer formation in cerebral cortex|learning or memory|lipid catabolic process|microtubule organizing center organization|mitotic prometaphase|neuroblast proliferation|neuromuscular process controlling balance|neuron migration|platelet activating factor metabolic process|regulation of Rho GTPase activity|retrograde axon cargo transport|synaptic transmission|vesicle transport along microtubule	astral microtubule|cell cortex|centrosome|cytosol|kinetochore|motile primary cilium|nuclear membrane|perinuclear region of cytoplasm	dynactin binding|heparin binding|microtubule binding|phospholipase binding|phosphoprotein binding|protein homodimerization activity			skin(1)	1						AGCCAAGATGGTGCTGTCCCA	0.358													4	25	---	---	---	---	PASS
ALOX15	246	broad.mit.edu	37	17	4542274	4542274	+	Intron	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4542274G>T	uc002fyh.2	-						ALOX15_uc010vsd.1_Intron|ALOX15_uc010vse.1_Intron	NM_001140	NP_001131	P16050	LOX15_HUMAN	arachidonate 15-lipoxygenase						inflammatory response|leukotriene biosynthetic process	nucleus	arachidonate 15-lipoxygenase activity|iron ion binding|lipoxygenase activity			skin(3)|ovary(1)|lung(1)	5				READ - Rectum adenocarcinoma(115;0.0327)	Ciclopirox(DB01188)|Masoprocol(DB00179)|Zileuton(DB00744)	CCACCTGTGGGGCAGGAAGGA	0.537													23	53	---	---	---	---	PASS
CAMTA2	23125	broad.mit.edu	37	17	4877807	4877807	+	Intron	SNP	C	A	A	rs75066890	byFrequency	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4877807C>A	uc002gah.1	-						CAMTA2_uc010cku.1_Intron|CAMTA2_uc002gag.1_Intron|CAMTA2_uc002gai.1_Intron|CAMTA2_uc010ckv.1_Intron	NM_015099	NP_055914	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2						cardiac muscle hypertrophy in response to stress|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	calmodulin binding|chromatin binding|histone deacetylase binding|transcription factor binding			ovary(1)	1						TGAGGGGGAACGGGTATGGGA	0.552													13	16	---	---	---	---	PASS
SLC16A11	162515	broad.mit.edu	37	17	6946295	6946295	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6946295G>T	uc002gei.1	-	2	710	c.372C>A	c.(370-372)TTC>TTA	p.F124L		NM_153357	NP_699188	Q8NCK7	MOT11_HUMAN	solute carrier family 16, member 11	124	Helical; (Potential).					integral to membrane|plasma membrane	symporter activity			ovary(1)	1						GATCGCTGGCGAAAGCCGAGA	0.687													6	7	---	---	---	---	PASS
TMEM102	284114	broad.mit.edu	37	17	7339853	7339853	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7339853C>G	uc002ggx.1	+	3	828	c.555C>G	c.(553-555)GAC>GAG	p.D185E	FGF11_uc010vtw.1_Intron|TMEM102_uc002ggy.1_Missense_Mutation_p.D185E	NM_178518	NP_848613	Q8N9M5	TM102_HUMAN	transmembrane protein 102	185	Extracellular (Potential).				regulation of apoptosis|response to cytokine stimulus|signal transduction	cell surface|integral to membrane|intracellular	protein binding				0		Prostate(122;0.173)				GTTCCAAGGACTGGCAAAGCT	0.582													24	42	---	---	---	---	PASS
ODF4	146852	broad.mit.edu	37	17	8243550	8243550	+	Missense_Mutation	SNP	C	A	A	rs147153349		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8243550C>A	uc002gle.1	+	1	363	c.181C>A	c.(181-183)CGC>AGC	p.R61S		NM_153007	NP_694552	Q2M2E3	ODFP4_HUMAN	outer dense fiber of sperm tails 4	61					cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				ovary(1)	1						CTTGGGCCAGCGCCAGAACTC	0.592													12	22	---	---	---	---	PASS
PIK3R5	23533	broad.mit.edu	37	17	8784233	8784233	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8784233C>A	uc002glt.2	-	18	2551	c.2484G>T	c.(2482-2484)CAG>CAT	p.Q828H	PIK3R5_uc010vuz.1_Missense_Mutation_p.Q828H|PIK3R5_uc002glu.3_Missense_Mutation_p.Q442H	NM_014308	NP_055123	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5	828					platelet activation	cytosol|membrane|nucleus				breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5						TGACTACACTCTGCAGGATCT	0.577													21	20	---	---	---	---	PASS
MYH8	4626	broad.mit.edu	37	17	10298521	10298521	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10298521G>T	uc002gmm.2	-	34	4986	c.4891C>A	c.(4891-4893)CAG>AAG	p.Q1631K	uc002gml.1_Intron	NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,	1631	Potential.				muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			skin(6)|ovary(3)|breast(2)	11						TGGTTCAGCTGGATTTCCATT	0.468									Trismus-Pseudocamptodactyly_Syndrome_with_Cardiac_Myxoma_and_Freckling				31	71	---	---	---	---	PASS
MYH8	4626	broad.mit.edu	37	17	10302972	10302972	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10302972C>A	uc002gmm.2	-	28	3845	c.3750G>T	c.(3748-3750)AAG>AAT	p.K1250N	uc002gml.1_Intron	NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,	1250	Potential.				muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			skin(6)|ovary(3)|breast(2)	11						AGCGGCACATCTTTTCAAGGT	0.418									Trismus-Pseudocamptodactyly_Syndrome_with_Cardiac_Myxoma_and_Freckling				8	31	---	---	---	---	PASS
MYH4	4622	broad.mit.edu	37	17	10356530	10356530	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10356530T>A	uc002gmn.2	-	24	3161	c.3050A>T	c.(3049-3051)GAG>GTG	p.E1017V	uc002gml.1_Intron	NM_017533	NP_060003	Q9Y623	MYH4_HUMAN	myosin, heavy polypeptide 4, skeletal muscle	1017	Potential.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(10)|skin(2)|central_nervous_system(1)	13						TTTGTCCTCCTCCATCTGCAG	0.488													26	122	---	---	---	---	PASS
MYH1	4619	broad.mit.edu	37	17	10398576	10398576	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10398576C>T	uc002gmo.2	-	36	5322	c.5228G>A	c.(5227-5229)GGA>GAA	p.G1743E	uc002gml.1_Intron	NM_005963	NP_005954	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1743	Potential.					muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|skin(6)|breast(3)|upper_aerodigestive_tract(1)|kidney(1)	21						TTCCATCTCTCCCTGGATTTG	0.453													30	57	---	---	---	---	PASS
MYH1	4619	broad.mit.edu	37	17	10404776	10404776	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10404776C>G	uc002gmo.2	-	27	3483	c.3389G>C	c.(3388-3390)CGG>CCG	p.R1130P	uc002gml.1_Intron	NM_005963	NP_005954	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1130	Potential.					muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|skin(6)|breast(3)|upper_aerodigestive_tract(1)|kidney(1)	21						CCGGGAGGCCCGCTCTGCCTC	0.567													19	8	---	---	---	---	PASS
MYH1	4619	broad.mit.edu	37	17	10408626	10408626	+	Intron	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10408626G>T	uc002gmo.2	-						uc002gml.1_Intron	NM_005963	NP_005954	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult							muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|skin(6)|breast(3)|upper_aerodigestive_tract(1)|kidney(1)	21						CCTATGTGTGGGAAGAATTTC	0.438													18	53	---	---	---	---	PASS
MYH2	4620	broad.mit.edu	37	17	10432232	10432232	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10432232C>A	uc010coi.2	-	27	3647	c.3519G>T	c.(3517-3519)CGG>CGT	p.R1173R	uc002gml.1_Intron|MYH2_uc002gmp.3_Silent_p.R1173R|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	1173	Potential.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14						ACTCAGCCTCCCGCTTCTTGT	0.602													7	78	---	---	---	---	PASS
TMEM220	388335	broad.mit.edu	37	17	10628381	10628381	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10628381C>A	uc002gmx.2	-	4	712	c.234G>T	c.(232-234)GCG>GCT	p.A78A	TMEM220_uc002gmy.2_Silent_p.A68A	NM_001004313	NP_001004313	Q6QAJ8	TM220_HUMAN	transmembrane protein 220	78	Helical; (Potential).					integral to membrane					0						AGAGGTAGGACGCCAAGCCAA	0.443													9	38	---	---	---	---	PASS
TBC1D26	353149	broad.mit.edu	37	17	15640841	15640841	+	Intron	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15640841A>G	uc010cov.2	+						TBC1D26_uc010cou.1_Intron|TBC1D26_uc002gpb.3_Intron	NM_178571	NP_848666	Q86UD7	TBC26_HUMAN	TBC1 domain family, member 26							intracellular	Rab GTPase activator activity				0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.078)		GGTGAAGGTAAGAGCCTGTGC	0.647													9	44	---	---	---	---	PASS
TRPV2	51393	broad.mit.edu	37	17	16323463	16323463	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16323463C>A	uc002gpy.2	+	3	602	c.235C>A	c.(235-237)CTC>ATC	p.L79I	TRPV2_uc002gpz.2_5'UTR	NM_016113	NP_057197	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel,	79	Cytoplasmic (Potential).|Required for interaction with SLC50A1 (By similarity).|ANK 1.				sensory perception	integral to plasma membrane|melanosome	calcium channel activity			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		CCGAGATCGGCTCTTCAATGC	0.572													30	55	---	---	---	---	PASS
MAP2K3	5606	broad.mit.edu	37	17	21203906	21203906	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21203906G>T	uc002gys.2	+	4	480	c.215G>T	c.(214-216)CGT>CTT	p.R72L	MAP2K3_uc002gyt.2_Missense_Mutation_p.R43L|MAP2K3_uc002gyu.2_Missense_Mutation_p.R43L	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	72	ATP (By similarity).|Protein kinase.				activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		GAACTGGGCCGTGGAGCCTAT	0.602													4	12	---	---	---	---	PASS
SEZ6	124925	broad.mit.edu	37	17	27306729	27306729	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27306729G>A	uc002hdp.2	-	3	1021	c.827C>T	c.(826-828)TCT>TTT	p.S276F	SEZ6_uc002hdm.2_RNA|SEZ6_uc010cry.1_Missense_Mutation_p.S276F|SEZ6_uc002hdq.1_Missense_Mutation_p.S151F|SEZ6_uc010crz.1_Missense_Mutation_p.S276F	NM_178860	NP_849191	Q53EL9	SEZ6_HUMAN	seizure related 6 homolog isoform 1	276	Extracellular (Potential).					integral to membrane|plasma membrane				large_intestine(1)|central_nervous_system(1)	2	Lung NSC(42;0.0137)		Epithelial(11;4.73e-06)|all cancers(11;2.91e-05)|BRCA - Breast invasive adenocarcinoma(11;8.06e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.111)			AGGGTAGACAGAGATGTAGAA	0.547													28	13	---	---	---	---	PASS
TAOK1	57551	broad.mit.edu	37	17	27869857	27869857	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27869857C>T	uc002hdz.1	+	20	3017	c.2823C>T	c.(2821-2823)CCC>CCT	p.P941P	TAOK1_uc010wbe.1_Silent_p.P793P|TAOK1_uc010wbf.1_Silent_p.P941P	NM_020791	NP_065842	Q7L7X3	TAOK1_HUMAN	TAO kinase 1	941					mitotic prometaphase	cytosol|intracellular membrane-bounded organelle	ATP binding|protein serine/threonine kinase activity			upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)|skin(1)	4			Colorectal(6;0.198)			AAGGTGGACCCCAGCCATGGG	0.622													5	24	---	---	---	---	PASS
NF1	4763	broad.mit.edu	37	17	29684054	29684054	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29684054G>T	uc002hgg.2	+	53	8148	c.7815G>T	c.(7813-7815)TTG>TTT	p.L2605F	NF1_uc002hgh.2_Missense_Mutation_p.L2584F|NF1_uc010cso.2_Missense_Mutation_p.L793F|NF1_uc010wbt.1_Missense_Mutation_p.L83F|NF1_uc010wbu.1_RNA	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	2605					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			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)		ATGTTCTCTTGGATGAAGAAG	0.418			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)			18	84	---	---	---	---	PASS
SLFN12	55106	broad.mit.edu	37	17	33738500	33738500	+	Nonsense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33738500T>A	uc002hji.3	-	4	1971	c.1594A>T	c.(1594-1596)AAA>TAA	p.K532*	SLFN12_uc002hjj.3_Nonsense_Mutation_p.K532*|SLFN12_uc010cts.2_Nonsense_Mutation_p.K532*	NM_018042	NP_060512	Q8IYM2	SLN12_HUMAN	schlafen family member 12	532							ATP binding			skin(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		AAAAGGGCTTTCAGCAAGTAT	0.388													30	24	---	---	---	---	PASS
GAS2L2	246176	broad.mit.edu	37	17	34072205	34072205	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34072205T>A	uc002hjv.1	-	6	2339	c.2311A>T	c.(2311-2313)ATC>TTC	p.I771F		NM_139285	NP_644814	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	771					cell cycle arrest	cytoplasm|cytoskeleton				ovary(1)|skin(1)	2		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		AGCTTGTAGATGGACGGGACC	0.607													34	95	---	---	---	---	PASS
GAS2L2	246176	broad.mit.edu	37	17	34072206	34072206	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34072206G>C	uc002hjv.1	-	6	2338	c.2310C>G	c.(2308-2310)TCC>TCG	p.S770S		NM_139285	NP_644814	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	770					cell cycle arrest	cytoplasm|cytoskeleton				ovary(1)|skin(1)	2		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GCTTGTAGATGGACGGGACCC	0.607													34	92	---	---	---	---	PASS
ACACA	31	broad.mit.edu	37	17	35696814	35696814	+	Intron	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35696814G>A	uc002hnm.2	-						ACACA_uc002hnn.2_Intron|ACACA_uc002hno.2_Intron|ACACA_uc010cuz.2_Intron|ACACA_uc002hnq.2_Intron|ACACA_uc002hnp.1_Intron|ACACA_uc002hnr.1_Intron	NM_198836	NP_942133	Q13085	ACACA_HUMAN	acetyl-Coenzyme A carboxylase alpha isoform 2						acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	GAAAGACCTAGAGAGAAAAAG	0.284													37	15	---	---	---	---	PASS
TNS4	84951	broad.mit.edu	37	17	38638626	38638626	+	Missense_Mutation	SNP	G	C	C	rs142919679		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38638626G>C	uc010cxb.2	-	7	1708	c.1544C>G	c.(1543-1545)TCG>TGG	p.S515W	TNS4_uc002huu.3_5'Flank	NM_032865	NP_116254	Q8IZW8	TENS4_HUMAN	tensin 4 precursor	515	SH2.				apoptosis|protein localization	cytoplasm|cytoskeleton|focal adhesion	actin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			TTTGGCAGACGACTCGATGAG	0.522													6	61	---	---	---	---	PASS
KRT39	390792	broad.mit.edu	37	17	39116541	39116541	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39116541C>T	uc002hvo.1	-	6	1245	c.1209G>A	c.(1207-1209)TCG>TCA	p.S403S	KRT39_uc010wfm.1_Silent_p.S136S	NM_213656	NP_998821	Q6A163	K1C39_HUMAN	type I hair keratin KA35	403	Coil 2.|Rod.					intermediate filament	structural molecule activity				0		Breast(137;0.00043)|Ovarian(249;0.15)				ACTTGCCATCCGAGCTCTCCA	0.468													15	55	---	---	---	---	PASS
KRT40	125115	broad.mit.edu	37	17	39140113	39140113	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39140113C>G	uc010cxh.1	-	3	574	c.413G>C	c.(412-414)CGT>CCT	p.R138P	KRT40_uc002hvq.1_RNA	NM_182497	NP_872303	Q6A162	K1C40_HUMAN	type I hair keratin KA36	138	Rod.|Coil 1B.					intermediate filament	structural molecule activity				0		Breast(137;0.00043)				GTTGAAGTAACGCTGATAATC	0.483													85	48	---	---	---	---	PASS
KRT36	8689	broad.mit.edu	37	17	39642717	39642717	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39642717C>A	uc002hwt.2	-	7	1315	c.1315G>T	c.(1315-1317)GTT>TTT	p.V439F		NM_003771	NP_003762	O76013	KRT36_HUMAN	keratin 36	439	Tail.					intermediate filament	protein binding|structural constituent of epidermis				0		Breast(137;0.000286)				TGAGTGCCAACCTGGGGAGCC	0.622													10	26	---	---	---	---	PASS
JUP	3728	broad.mit.edu	37	17	39680252	39680252	+	Intron	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39680252G>C	uc010wfs.1	-						KRT15_uc002hxb.1_5'Flank|uc002hxc.1_5'Flank|KRT19_uc002hxd.3_Intron	NM_021991	NP_068831	P14923	PLAK_HUMAN	junction plakoglobin						adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity			ovary(2)|lung(2)|breast(1)	5		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)		GCAGCTTTCTGAGGATAGGGA	0.612													22	26	---	---	---	---	PASS
PTRF	284119	broad.mit.edu	37	17	40556972	40556972	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40556972C>A	uc002hzo.2	-	2	1065	c.906G>T	c.(904-906)ACG>ACT	p.T302T	PTRF_uc010wgi.1_Silent_p.T284T	NM_012232	NP_036364	Q6NZI2	PTRF_HUMAN	polymerase I and transcript release factor	302					regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription|transcription initiation from RNA polymerase I promoter	caveola|cytosol|endoplasmic reticulum|microsome|mitochondrion|nucleoplasm	protein binding|rRNA primary transcript binding			breast(1)	1		all_cancers(22;0.00146)|Breast(137;0.00116)|all_epithelial(22;0.0134)		BRCA - Breast invasive adenocarcinoma(366;0.193)		CGTGGTCGGGCGTGAAGGATT	0.642													12	52	---	---	---	---	PASS
RPL27	6155	broad.mit.edu	37	17	41154678	41154678	+	Intron	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41154678C>T	uc002icj.2	+						RPL27_uc002ick.2_Intron	NM_000988	NP_000979	P61353	RL27_HUMAN	ribosomal protein L27						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|ribosome	structural constituent of ribosome				0		Breast(137;0.000717)|Ovarian(249;0.0776)		BRCA - Breast invasive adenocarcinoma(366;0.157)		GCCTCTCCACCTTTGTCCCCA	0.537													5	33	---	---	---	---	PASS
BRCA1	672	broad.mit.edu	37	17	41244070	41244070	+	Nonsense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41244070T>A	uc002icq.2	-	10	3710	c.3478A>T	c.(3478-3480)AAG>TAG	p.K1160*	BRCA1_uc010whp.1_Intron|BRCA1_uc010whl.1_Intron|BRCA1_uc010whm.1_Intron|BRCA1_uc002icp.3_Nonsense_Mutation_p.K1089*|BRCA1_uc002icu.2_Intron|BRCA1_uc010cyx.2_Nonsense_Mutation_p.K1113*|BRCA1_uc002ict.2_Nonsense_Mutation_p.K1160*|BRCA1_uc010whn.1_Intron|BRCA1_uc010who.1_Intron|BRCA1_uc010whq.1_Intron|BRCA1_uc002idc.1_Intron|BRCA1_uc010whr.1_Intron|BRCA1_uc002idd.2_Nonsense_Mutation_p.K1160*|BRCA1_uc002ide.1_Nonsense_Mutation_p.K991*|BRCA1_uc010cyy.1_Nonsense_Mutation_p.K1160*|BRCA1_uc010whs.1_Nonsense_Mutation_p.K1160*|BRCA1_uc010cyz.2_Nonsense_Mutation_p.K1113*|BRCA1_uc010cza.2_Nonsense_Mutation_p.K1134*|BRCA1_uc010wht.1_Nonsense_Mutation_p.K864*	NM_007294	NP_009225	P38398	BRCA1_HUMAN	breast cancer 1, early onset isoform 1	1160					androgen receptor signaling pathway|apoptosis|cellular response to indole-3-methanol|chromosome segregation|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|DNA damage response, signal transduction resulting in induction of apoptosis|double-strand break repair via homologous recombination|fatty acid biosynthetic process|G2/M transition DNA damage checkpoint|negative regulation of centriole replication|negative regulation of fatty acid biosynthetic process|negative regulation of histone H3-K9 methylation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle arrest|positive regulation of DNA repair|positive regulation of histone acetylation|positive regulation of histone H3-K4 methylation|positive regulation of histone H4-K20 methylation|positive regulation of protein ubiquitination|positive regulation of transcription from RNA polymerase II promoter|postreplication repair|protein autoubiquitination|protein K6-linked ubiquitination|regulation of cell motility|regulation of cell proliferation|regulation of transcription from RNA polymerase III promoter|response to estrogen stimulus|response to ionizing radiation|substrate adhesion-dependent cell spreading	BRCA1-A complex|BRCA1-BARD1 complex|gamma-tubulin ring complex|nucleoplasm|plasma membrane|ribonucleoprotein complex|ruffle	androgen receptor binding|identical protein binding|protein binding|RNA binding|transcription coactivator activity|transcription regulatory region DNA binding|tubulin binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(24)|breast(21)|lung(4)|central_nervous_system(1)|endometrium(1)|urinary_tract(1)	52		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GTATCTTCCTTTATTTCACCA	0.398			D|Mis|N|F|S		ovarian	breast|ovarian		Homologous_recombination	Hereditary_Breast-Ovarian_Cancer_BRCA1_type	TCGA Ovarian(2;0.000030)			10	84	---	---	---	---	PASS
NBR1	4077	broad.mit.edu	37	17	41341074	41341074	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41341074C>G	uc010czd.2	+	7	558	c.418C>G	c.(418-420)CCA>GCA	p.P140A	NBR1_uc010diz.2_Missense_Mutation_p.P140A|NBR1_uc010whu.1_Missense_Mutation_p.P140A|NBR1_uc010whv.1_Missense_Mutation_p.P140A|NBR1_uc010whw.1_Missense_Mutation_p.P119A|NBR1_uc010whx.1_5'Flank	NM_031862	NP_114068	Q14596	NBR1_HUMAN	neighbor of BRCA1 gene 1	140					macroautophagy|protein oligomerization	autophagic vacuole|cytoplasmic vesicle|cytosol|late endosome|lysosome|sarcomere	ubiquitin binding|zinc ion binding			skin(1)	1		Breast(137;0.00086)		BRCA - Breast invasive adenocarcinoma(366;0.0934)		TCCACTTGTTCCATGTGACAC	0.448													5	67	---	---	---	---	PASS
EFTUD2	9343	broad.mit.edu	37	17	42957009	42957009	+	Intron	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42957009G>A	uc002ihn.2	-						EFTUD2_uc010wje.1_Intron|EFTUD2_uc010wjf.1_Intron	NM_004247	NP_004238	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain							Cajal body|catalytic step 2 spliceosome|cytoplasm|nuclear speck	GTP binding|GTPase activity|protein binding			ovary(1)	1		Prostate(33;0.109)				CACATGTCCTGAAAAGCAAAT	0.483													15	26	---	---	---	---	PASS
HOXB3	3213	broad.mit.edu	37	17	46628422	46628422	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46628422C>A	uc002inn.2	-	2	970	c.570G>T	c.(568-570)CGG>CGT	p.R190R	HOXB3_uc010wlm.1_Silent_p.R117R|HOXB3_uc010dbf.2_Silent_p.R190R|HOXB3_uc010dbg.2_Silent_p.R190R|HOXB3_uc002ino.2_Silent_p.R190R|HOXB3_uc010wlk.1_Silent_p.R58R|HOXB3_uc010wll.1_Silent_p.R117R	NM_002146	NP_002137	P14651	HXB3_HUMAN	homeobox B3	190	Homeobox.				angiogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						CCGTCCGCGCCCGCTTGGACG	0.488													11	34	---	---	---	---	PASS
HOXB6	3216	broad.mit.edu	37	17	46673923	46673923	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46673923C>A	uc002ins.1	-	4	852	c.527G>T	c.(526-528)CGC>CTC	p.R176L	HOXB5_uc002inr.2_5'Flank|HOXB6_uc010dbh.1_Missense_Mutation_p.R176L|HOXB6_uc002int.1_3'UTR	NM_018952	NP_061825	P17509	HXB6_HUMAN	homeobox B6	176	Homeobox.				anterior/posterior axis specification, embryo	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						GATCTCGATGCGCCGCCGCCG	0.607													45	27	---	---	---	---	PASS
SGCA	6442	broad.mit.edu	37	17	48245004	48245004	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48245004C>A	uc002iqi.2	+	3	255	c.219C>A	c.(217-219)CCC>CCA	p.P73P	SGCA_uc010wmh.1_Intron|SGCA_uc002iqj.2_Silent_p.P73P|SGCA_uc010wmi.1_RNA	NM_000023	NP_000014	Q16586	SGCA_HUMAN	sarcoglycan, alpha isoform 1 precursor	73	Extracellular (Potential).				muscle contraction|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma	calcium ion binding			ovary(2)	2						CAGACCTGCCCCGGTGGCTCC	0.662													6	28	---	---	---	---	PASS
KIF2B	84643	broad.mit.edu	37	17	51900869	51900869	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51900869C>A	uc002iua.2	+	1	631	c.475C>A	c.(475-477)CAG>AAG	p.Q159K	uc010wna.1_RNA	NM_032559	NP_115948	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	159	Potential.				blood coagulation|cell division|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|microtubule|microtubule organizing center|nucleolus|spindle	ATP binding|microtubule motor activity			ovary(5)|skin(3)	8						ACTGCAGGAGCAGCGGGAAAA	0.557													11	23	---	---	---	---	PASS
KIF2B	84643	broad.mit.edu	37	17	51901186	51901186	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51901186C>A	uc002iua.2	+	1	948	c.792C>A	c.(790-792)TTC>TTA	p.F264L	uc010wna.1_Intron	NM_032559	NP_115948	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	264	Kinesin-motor.				blood coagulation|cell division|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|microtubule|microtubule organizing center|nucleolus|spindle	ATP binding|microtubule motor activity			ovary(5)|skin(3)	8						ACCAGACCTTCTGCTTCGACC	0.557													15	19	---	---	---	---	PASS
MSI2	124540	broad.mit.edu	37	17	55693342	55693342	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55693342G>C	uc002iuz.1	+	9	722	c.549G>C	c.(547-549)AAG>AAC	p.K183N	MSI2_uc010wnm.1_Missense_Mutation_p.K161N|MSI2_uc002iva.2_Missense_Mutation_p.K179N	NM_138962	NP_620412	Q96DH6	MSI2H_HUMAN	musashi 2 isoform a	183	RRM 2.					cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)|pancreas(1)	2	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)		TAGAATGTAAGAAAGCTCAGC	0.483			T	HOXA9	CML								22	19	---	---	---	---	PASS
MKS1	54903	broad.mit.edu	37	17	56293532	56293532	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56293532G>A	uc002ivr.1	-	4	409	c.334C>T	c.(334-336)CTG>TTG	p.L112L	MKS1_uc010wnq.1_5'UTR|MKS1_uc002ivs.1_Silent_p.L112L	NM_017777	NP_060247	Q9NXB0	MKS1_HUMAN	Meckel syndrome type 1 protein isoform 1	112					cilium assembly	centrosome|cilium|microtubule basal body	protein binding			ovary(1)	1						TCCAGCTTCAGGATCTCCTGA	0.428													22	27	---	---	---	---	PASS
BZRAP1	9256	broad.mit.edu	37	17	56384158	56384158	+	Intron	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56384158T>C	uc002ivx.3	-						BZRAP1_uc002ivv.2_5'Flank|BZRAP1_uc002ivw.2_5'Flank|BZRAP1_uc010dcs.2_Intron|BZRAP1_uc010wnt.1_Intron	NM_004758	NP_004749	O95153	RIMB1_HUMAN	peripheral benzodiazepine receptor-associated							mitochondrion	benzodiazepine receptor binding			upper_aerodigestive_tract(2)|skin(1)	3	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CAGCAGGTCATACCTGAGCCC	0.592													10	7	---	---	---	---	PASS
MARCH10	162333	broad.mit.edu	37	17	60814365	60814365	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60814365G>T	uc010ddr.2	-	6	1102	c.864C>A	c.(862-864)AGC>AGA	p.S288R	MARCH10_uc002jag.3_Missense_Mutation_p.S288R|MARCH10_uc010dds.2_Missense_Mutation_p.S326R|MARCH10_uc002jah.2_Missense_Mutation_p.S287R|uc002jaj.1_RNA|uc002jak.2_RNA	NM_001100875	NP_001094345	Q8NA82	MARHA_HUMAN	ring finger protein 190	288							ligase activity|zinc ion binding				0						CAGTGTCATCGCTTTCTCTTC	0.473													75	93	---	---	---	---	PASS
SCN4A	6329	broad.mit.edu	37	17	62049739	62049739	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62049739C>A	uc002jds.1	-	2	442	c.365G>T	c.(364-366)CGC>CTC	p.R122L		NM_000334	NP_000325	P35499	SCN4A_HUMAN	voltage-gated sodium channel type 4 alpha	122					muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(1)|pancreas(1)|skin(1)	3					Lamotrigine(DB00555)	GATGGCCCCGCGCCTGACTAC	0.612													13	9	---	---	---	---	PASS
ABCA8	10351	broad.mit.edu	37	17	66878019	66878019	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66878019A>G	uc002jhp.2	-	29	3990	c.3811T>C	c.(3811-3813)TTC>CTC	p.F1271L	ABCA8_uc002jhq.2_Missense_Mutation_p.F1311L|ABCA8_uc010wqq.1_Missense_Mutation_p.F1306L	NM_007168	NP_009099	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A member 8	1271	ABC transporter 2.					integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3	Breast(10;4.56e-13)					CTAACACAGAAGGAGACATTT	0.483													24	30	---	---	---	---	PASS
ABCA9	10350	broad.mit.edu	37	17	66982358	66982358	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66982358C>A	uc002jhu.2	-	32	4298	c.4155G>T	c.(4153-4155)GTG>GTT	p.V1385V	ABCA9_uc010dez.2_Silent_p.V1347V	NM_080283	NP_525022	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A, member 9	1385	ABC transporter 2.				transport	integral to membrane	ATP binding|ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6	Breast(10;1.47e-12)					CGGCAGCGTACACCTCCAGGT	0.617													16	27	---	---	---	---	PASS
ABCA9	10350	broad.mit.edu	37	17	67029935	67029935	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67029935A>T	uc002jhu.2	-	9	1351	c.1208T>A	c.(1207-1209)CTT>CAT	p.L403H	ABCA9_uc010dez.2_Missense_Mutation_p.L403H	NM_080283	NP_525022	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A, member 9	403	Helical; (Potential).				transport	integral to membrane	ATP binding|ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6	Breast(10;1.47e-12)					CAACATGAAAAGAGTAGCTAT	0.333													22	30	---	---	---	---	PASS
GPR142	350383	broad.mit.edu	37	17	72368181	72368181	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72368181G>T	uc010wqy.1	+	4	831	c.831G>T	c.(829-831)CGG>CGT	p.R277R	GPR142_uc010wqx.1_Silent_p.R189R	NM_181790	NP_861455	Q7Z601	GP142_HUMAN	G protein-coupled receptor 142	277	Cytoplasmic (Potential).					cell junction|cytoplasm|integral to membrane	G-protein coupled receptor activity			ovary(2)|central_nervous_system(1)|skin(1)	4						GGACCCGCCGGGCCATTGCTG	0.657													4	9	---	---	---	---	PASS
ENPP7	339221	broad.mit.edu	37	17	77704931	77704931	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77704931G>C	uc002jxa.2	+	1	50	c.30G>C	c.(28-30)GTG>GTC	p.V10V		NM_178543	NP_848638	Q6UWV6	ENPP7_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	10					negative regulation of cell proliferation|negative regulation of DNA replication|sphingomyelin metabolic process	Golgi apparatus|integral to membrane|microvillus	sphingomyelin phosphodiesterase activity			central_nervous_system(2)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			TCCTCACTGTGGCTCTGGCCA	0.657													7	10	---	---	---	---	PASS
ENPP7	339221	broad.mit.edu	37	17	77711788	77711788	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77711788G>C	uc002jxa.2	+	5	1340	c.1320G>C	c.(1318-1320)AGG>AGC	p.R440S		NM_178543	NP_848638	Q6UWV6	ENPP7_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	440	Helical; (Potential).				negative regulation of cell proliferation|negative regulation of DNA replication|sphingomyelin metabolic process	Golgi apparatus|integral to membrane|microvillus	sphingomyelin phosphodiesterase activity			central_nervous_system(2)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			CCAGCAGCAGGCCCCTCCTCG	0.607													21	36	---	---	---	---	PASS
RNF213	57674	broad.mit.edu	37	17	78323667	78323667	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78323667A>G	uc002jyh.1	+	5	4491	c.4268A>G	c.(4267-4269)CAG>CGG	p.Q1423R		NM_020914	NP_065965	Q9HCF4	ALO17_HUMAN	ring finger protein 213	Error:Variant_position_missing_in_Q9HCF4_after_alignment										ovary(8)|lung(6)|breast(3)|large_intestine(2)|central_nervous_system(1)|pancreas(1)	21	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			CTGTGGCTGCAGCAGTTTGAC	0.557													18	21	---	---	---	---	PASS
SLC25A10	1468	broad.mit.edu	37	17	79686896	79686896	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79686896C>G	uc002kbi.2	+	10	827	c.741C>G	c.(739-741)CTC>CTG	p.L247L	SLC25A10_uc010wut.1_Silent_p.L402L|SLC25A10_uc010dif.2_Silent_p.L256L|SLC25A10_uc010wuu.1_Silent_p.L201L	NM_012140	NP_036272	Q9UBX3	DIC_HUMAN	solute carrier family 25 (mitochondrial carrier;	247	Solcar 3.				gluconeogenesis|mitochondrial transport	integral to membrane|mitochondrial inner membrane|nucleus	protein binding				0	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0117)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)		Succinic acid(DB00139)	CAGCGAAGCTCGGGCCTCTGG	0.582													47	50	---	---	---	---	PASS
KIAA0802	23255	broad.mit.edu	37	18	8819111	8819111	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8819111G>A	uc002knr.2	+	13	3152	c.3010G>A	c.(3010-3012)GAA>AAA	p.E1004K	KIAA0802_uc002knq.2_Missense_Mutation_p.E963K|KIAA0802_uc002kns.2_Missense_Mutation_p.E344K	NM_015210	NP_056025	Q9Y4B5	CC165_HUMAN	hypothetical protein LOC23255	1314											0						CATCCCGTTTGAAGACCGGCC	0.607													18	14	---	---	---	---	PASS
OSBPL1A	114876	broad.mit.edu	37	18	21957471	21957471	+	Silent	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21957471A>T	uc002kve.2	-	2	201	c.27T>A	c.(25-27)CTT>CTA	p.L9L		NM_080597	NP_542164	Q9BXW6	OSBL1_HUMAN	oxysterol-binding protein-like 1A isoform B	9					cholesterol metabolic process|lipid transport|vesicle-mediated transport		phospholipid binding			ovary(4)	4	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					CGTGATGGAGAAGCTGTTGCT	0.353													37	19	---	---	---	---	PASS
DSG2	1829	broad.mit.edu	37	18	29099864	29099864	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29099864G>C	uc002kwu.3	+	3	368	c.180G>C	c.(178-180)GAG>GAC	p.E60D		NM_001943	NP_001934	Q14126	DSG2_HUMAN	desmoglein 2 preproprotein	60	Extracellular (Potential).|Cadherin 1.				cellular component disassembly involved in apoptosis|homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			central_nervous_system(5)|ovary(2)|breast(1)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(10;0.0068)			CTCTTCGGGAGGGAGAGGATC	0.463													65	52	---	---	---	---	PASS
ELP2	55250	broad.mit.edu	37	18	33725955	33725955	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33725955G>T	uc002kzk.1	+	10	947	c.937G>T	c.(937-939)GAT>TAT	p.D313Y	ELP2_uc010xcg.1_Missense_Mutation_p.D378Y|ELP2_uc002kzl.1_RNA|ELP2_uc002kzm.1_Missense_Mutation_p.D287Y|ELP2_uc010xch.1_Missense_Mutation_p.D352Y|ELP2_uc002kzn.1_Missense_Mutation_p.D287Y|ELP2_uc002kzo.1_Missense_Mutation_p.D243Y	NM_018255	NP_060725	Q6IA86	ELP2_HUMAN	elongator protein 2	313	WD 6.				regulation of transcription from RNA polymerase II promoter	Golgi apparatus|transcription elongation factor complex				breast(2)|ovary(1)|skin(1)	4						TGCTTCCATGGATAAAACCAT	0.363													39	256	---	---	---	---	PASS
RIT2	6014	broad.mit.edu	37	18	40503725	40503725	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40503725C>G	uc002lav.2	-	4	411	c.238G>C	c.(238-240)GAA>CAA	p.E80Q	RIT2_uc010dnf.2_Missense_Mutation_p.E80Q	NM_002930	NP_002921	Q99578	RIT2_HUMAN	Ras-like without CAAX 2	80					nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction|synaptic transmission	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity			ovary(1)	1						GCTGTGAATTCTGCCTGCAGG	0.383													282	67	---	---	---	---	PASS
FECH	2235	broad.mit.edu	37	18	55247367	55247367	+	Silent	SNP	G	A	A	rs147500247		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55247367G>A	uc002lgq.3	-	2	249	c.132C>T	c.(130-132)GCC>GCT	p.A44A	FECH_uc002lgp.3_Silent_p.A44A|FECH_uc002lgr.3_5'UTR	NM_000140	NP_000131	P22830	HEMH_HUMAN	ferrochelatase isoform b precursor	44					generation of precursor metabolites and energy|heme biosynthetic process|protoporphyrinogen IX metabolic process|response to light stimulus	mitochondrial inner membrane|mitochondrial matrix	2 iron, 2 sulfur cluster binding|ferrochelatase activity|ferrous iron binding|protein binding			central_nervous_system(1)	1		Colorectal(73;0.227)				CTGTGGTGACGGCCGCTGCAG	0.507													5	17	---	---	---	---	PASS
SERPINB12	89777	broad.mit.edu	37	18	61226897	61226897	+	Nonsense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61226897C>G	uc010xen.1	+	3	330	c.330C>G	c.(328-330)TAC>TAG	p.Y110*	SERPINB12_uc010xeo.1_Nonsense_Mutation_p.Y130*	NM_080474	NP_536722	Q96P63	SPB12_HUMAN	serine (or cysteine) proteinase inhibitor, clade	110					negative regulation of protein catabolic process|regulation of proteolysis	cytoplasm	enzyme binding|serine-type endopeptidase inhibitor activity				0						AGACTGATTACACACTGAGTA	0.458													7	33	---	---	---	---	PASS
SERPINB4	6318	broad.mit.edu	37	18	61305083	61305083	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61305083G>C	uc002ljf.2	-	8	1129	c.1043C>G	c.(1042-1044)GCT>GGT	p.A348G	SERPINB4_uc002lje.2_Missense_Mutation_p.A327G|SERPINB4_uc002ljg.2_Missense_Mutation_p.A348G	NM_002974	NP_002965	P48594	SPB4_HUMAN	serine (or cysteine) proteinase inhibitor, clade	348					immune response|regulation of proteolysis	cytoplasm|extracellular region	protein binding|serine-type endopeptidase inhibitor activity			ovary(2)|lung(1)	3						TACTACTACAGCGGTGGCAGC	0.468													9	15	---	---	---	---	PASS
SERPINB4	6318	broad.mit.edu	37	18	61305084	61305084	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61305084C>T	uc002ljf.2	-	8	1128	c.1042G>A	c.(1042-1044)GCT>ACT	p.A348T	SERPINB4_uc002lje.2_Missense_Mutation_p.A327T|SERPINB4_uc002ljg.2_Missense_Mutation_p.A348T	NM_002974	NP_002965	P48594	SPB4_HUMAN	serine (or cysteine) proteinase inhibitor, clade	348					immune response|regulation of proteolysis	cytoplasm|extracellular region	protein binding|serine-type endopeptidase inhibitor activity			ovary(2)|lung(1)	3						ACTACTACAGCGGTGGCAGCT	0.468													8	15	---	---	---	---	PASS
SERPINB4	6318	broad.mit.edu	37	18	61306500	61306500	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61306500G>T	uc002ljf.2	-	7	773	c.687C>A	c.(685-687)GCC>GCA	p.A229A	SERPINB4_uc002lje.2_Silent_p.A208A|SERPINB4_uc002ljg.2_Intron	NM_002974	NP_002965	P48594	SPB4_HUMAN	serine (or cysteine) proteinase inhibitor, clade	229					immune response|regulation of proteolysis	cytoplasm|extracellular region	protein binding|serine-type endopeptidase inhibitor activity			ovary(2)|lung(1)	3						CCAGGACCTTGGCCTGTACAT	0.398													10	23	---	---	---	---	PASS
SERPINB7	8710	broad.mit.edu	37	18	61459629	61459629	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61459629G>T	uc002ljl.2	+	3	267	c.171G>T	c.(169-171)TTG>TTT	p.L57F	SERPINB7_uc002ljm.2_Missense_Mutation_p.L57F|SERPINB7_uc010xet.1_Intron|SERPINB7_uc010dqg.2_Missense_Mutation_p.L57F	NM_001040147	NP_001035237	O75635	SPB7_HUMAN	serine (or cysteine) proteinase inhibitor, clade	57					regulation of proteolysis	cytoplasm	serine-type endopeptidase inhibitor activity			lung(2)|central_nervous_system(1)	3		Esophageal squamous(42;0.129)				GTTTACAGTTGCTTCATGTTA	0.313													7	21	---	---	---	---	PASS
NETO1	81832	broad.mit.edu	37	18	70532107	70532107	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70532107G>T	uc002lkw.2	-	3	440	c.156C>A	c.(154-156)ATC>ATA	p.I52I	NETO1_uc002lkx.1_Silent_p.I51I|NETO1_uc002lky.1_Silent_p.I52I|NETO1_uc002lkz.2_Silent_p.I51I	NM_138966	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin- and tolloid-like protein 1 isoform 3	52	CUB 1.|Extracellular (Potential).				memory|regulation of long-term neuronal synaptic plasticity|visual learning	cell junction|excitatory synapse|extracellular region|integral to membrane|postsynaptic density|postsynaptic membrane	receptor activity			ovary(2)|skin(2)	4		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		GAGAGGTAAAGATACCTCCCT	0.423													7	31	---	---	---	---	PASS
TSHZ1	10194	broad.mit.edu	37	18	72998837	72998837	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72998837G>T	uc002lly.2	+	2	1903	c.1340G>T	c.(1339-1341)GGG>GTG	p.G447V		NM_005786	NP_005777	Q6ZSZ6	TSH1_HUMAN	teashirt family zinc finger 1	492						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		TCTCCCGCGGGGTCCACGACT	0.607													8	35	---	---	---	---	PASS
ZNF236	7776	broad.mit.edu	37	18	74622041	74622041	+	Nonsense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74622041C>T	uc002lmi.2	+	15	2761	c.2563C>T	c.(2563-2565)CAG>TAG	p.Q855*	ZNF236_uc002lmj.2_RNA	NM_007345	NP_031371	Q9UL36	ZN236_HUMAN	zinc finger protein 236	855					cellular response to glucose stimulus	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		TGTGGCTCCACAGGACCCTCT	0.512													15	54	---	---	---	---	PASS
ZNF236	7776	broad.mit.edu	37	18	74622042	74622042	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74622042A>T	uc002lmi.2	+	15	2762	c.2564A>T	c.(2563-2565)CAG>CTG	p.Q855L	ZNF236_uc002lmj.2_RNA	NM_007345	NP_031371	Q9UL36	ZN236_HUMAN	zinc finger protein 236	855					cellular response to glucose stimulus	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		GTGGCTCCACAGGACCCTCTG	0.512													15	54	---	---	---	---	PASS
ZNF236	7776	broad.mit.edu	37	18	74631815	74631815	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74631815G>T	uc002lmi.2	+	20	3550	c.3352G>T	c.(3352-3354)GAG>TAG	p.E1118*	ZNF236_uc002lmj.2_RNA	NM_007345	NP_031371	Q9UL36	ZN236_HUMAN	zinc finger protein 236	1118					cellular response to glucose stimulus	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		TTTCACGGAGGAGGAGACAGC	0.532													10	68	---	---	---	---	PASS
C18orf22	79863	broad.mit.edu	37	18	77794505	77794505	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77794505G>T	uc002lns.2	+	1	148	c.10G>T	c.(10-12)GCG>TCG	p.A4S	TXNL4A_uc010drg.2_5'Flank|C18orf22_uc010drh.2_Missense_Mutation_p.A4S|C18orf22_uc010dri.1_RNA	NM_024805	NP_079081	Q8N0V3	RBFA_HUMAN	hypothetical protein LOC79863 precursor	4					rRNA processing	mitochondrion					0		all_cancers(4;3.21e-14)|all_epithelial(4;7.11e-09)|all_lung(4;0.00366)|Lung NSC(4;0.00683)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0545)|all_hematologic(56;0.15)|Melanoma(33;0.2)		OV - Ovarian serous cystadenocarcinoma(15;6.46e-08)|BRCA - Breast invasive adenocarcinoma(31;0.00376)		CATGTGGGCTGCGGCGGGCGG	0.751													3	4	---	---	---	---	PASS
MIER2	54531	broad.mit.edu	37	19	313641	313641	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:313641A>G	uc002lok.1	-	8	667	c.658T>C	c.(658-660)TAC>CAC	p.Y220H		NM_017550	NP_060020	Q8N344	MIER2_HUMAN	mesoderm induction early response 1, family	220	ELM2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0		all_cancers(10;1.05e-30)|all_epithelial(18;3.04e-19)|Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;2.49e-05)|all_lung(49;4.36e-05)|Breast(49;0.000304)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCGTTCTCGTAGACTGCACAA	0.607													11	35	---	---	---	---	PASS
ABCA7	10347	broad.mit.edu	37	19	1043053	1043053	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1043053G>T	uc002lqw.3	+	8	824	c.593G>T	c.(592-594)CGC>CTC	p.R198L	ABCA7_uc010dsb.1_Missense_Mutation_p.R60L	NM_019112	NP_061985	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A, member 7	198	Extracellular (By similarity).				phagocytosis|transmembrane transport	ATP-binding cassette (ABC) transporter complex|endosome membrane|Golgi membrane|integral to membrane|plasma membrane	ATP binding|ATPase activity|transporter activity			pancreas(7)|ovary(1)|central_nervous_system(1)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGGCGCTGCGCAGCCTGGTG	0.667													5	18	---	---	---	---	PASS
ABCA7	10347	broad.mit.edu	37	19	1056367	1056367	+	Silent	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1056367C>G	uc002lqw.3	+	33	4686	c.4455C>G	c.(4453-4455)GCC>GCG	p.A1485A	ABCA7_uc002lqy.2_5'Flank|ABCA7_uc010dsc.2_5'Flank	NM_019112	NP_061985	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A, member 7	1485	Extracellular (By similarity).				phagocytosis|transmembrane transport	ATP-binding cassette (ABC) transporter complex|endosome membrane|Golgi membrane|integral to membrane|plasma membrane	ATP binding|ATPase activity|transporter activity			pancreas(7)|ovary(1)|central_nervous_system(1)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCATGGTGGCCTTTGTCAACC	0.612													6	20	---	---	---	---	PASS
ZNRF4	148066	broad.mit.edu	37	19	5456134	5456134	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5456134C>T	uc002mca.3	+	1	709	c.632C>T	c.(631-633)TCA>TTA	p.S211L		NM_181710	NP_859061	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4 precursor	211	Extracellular (Potential).|PA.					integral to membrane	zinc ion binding			large_intestine(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)		GCCATCCCCTCAGTGTTCGTG	0.677													11	43	---	---	---	---	PASS
SAFB2	9667	broad.mit.edu	37	19	5622569	5622569	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5622569T>A	uc002mcd.2	-	1	370	c.158A>T	c.(157-159)AAG>ATG	p.K53M	SAFB_uc010xiq.1_5'Flank|SAFB_uc002mcf.2_5'Flank|SAFB_uc002mcg.2_5'Flank|SAFB_uc002mce.3_5'Flank|SAFB_uc010xir.1_5'Flank|SAFB_uc010xis.1_5'Flank|SAFB_uc010xit.1_5'Flank|SAFB_uc010xiu.1_5'Flank|SAFB2_uc010xio.1_Missense_Mutation_p.K53M|SAFB2_uc010xip.1_RNA	NM_014649	NP_055464	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	53	SAP.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|nucleotide binding|protein binding|RNA binding				0				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		CAGGACGCTCTTGTTGCCGCC	0.726													5	8	---	---	---	---	PASS
FBN3	84467	broad.mit.edu	37	19	8175984	8175984	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8175984C>G	uc002mjf.2	-	32	4189	c.4168G>C	c.(4168-4170)GAG>CAG	p.E1390Q		NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	1390	EGF-like 21; calcium-binding.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11						AAGCCCATCTCACATTCACAG	0.642													6	16	---	---	---	---	PASS
ACTL9	284382	broad.mit.edu	37	19	8808237	8808237	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8808237G>T	uc002mkl.2	-	1	936	c.815C>A	c.(814-816)CCG>CAG	p.P272Q		NM_178525	NP_848620	Q8TC94	ACTL9_HUMAN	actin-like 9	272						cytoplasm|cytoskeleton				large_intestine(2)|pancreas(1)	3						CTCCTGCTCCGGCCGGGCCTG	0.637													6	27	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9010658	9010658	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9010658G>A	uc002mkp.2	-	38	39207	c.39003C>T	c.(39001-39003)CCC>CCT	p.P13001P	MUC16_uc010xki.1_Intron	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	13003	Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						TTGTGGGGCTGGGGAGGGAGG	0.483													16	10	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9069470	9069470	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9069470C>A	uc002mkp.2	-	3	18180	c.17976G>T	c.(17974-17976)GAG>GAT	p.E5992D		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	5994	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						AAGTGAGTATCTCACCTGAGA	0.458													21	92	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9083474	9083474	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9083474C>G	uc002mkp.2	-	1	8545	c.8341G>C	c.(8341-8343)GAG>CAG	p.E2781Q		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	2781	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GATGCCCTCTCAAGCCCAGCT	0.493													23	22	---	---	---	---	PASS
COL5A3	50509	broad.mit.edu	37	19	10076996	10076996	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10076996A>T	uc002mmq.1	-	64	4862	c.4776T>A	c.(4774-4776)TTT>TTA	p.F1592L		NM_015719	NP_056534	P25940	CO5A3_HUMAN	collagen, type V, alpha 3 preproprotein	1592	Fibrillar collagen NC1.				collagen fibril organization|skin development	collagen type V	collagen binding|extracellular matrix structural constituent			ovary(7)|lung(1)|central_nervous_system(1)|skin(1)	10			Epithelial(33;7.11e-05)			TCACGATCTCAAACTTCTTGT	0.557													27	16	---	---	---	---	PASS
SLC44A2	57153	broad.mit.edu	37	19	10753987	10753987	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10753987G>A	uc002mpf.2	+	22	2186	c.2047G>A	c.(2047-2049)GAG>AAG	p.E683K	SLC44A2_uc002mpe.3_Missense_Mutation_p.E681K|SLC44A2_uc002mpg.1_3'UTR|SLC44A2_uc002mph.2_Missense_Mutation_p.E232K|SLC44A2_uc002mpi.2_3'UTR	NM_020428	NP_065161	Q8IWA5	CTL2_HUMAN	solute carrier family 44, member 2 isoform 1	683	Cytoplasmic (Potential).				positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane|plasma membrane	choline transmembrane transporter activity|signal transducer activity			ovary(1)	1			Epithelial(33;8.7e-06)|all cancers(31;2.77e-05)		Choline(DB00122)	CGGCTCGGCCGAGAGGCCTTA	0.607													3	8	---	---	---	---	PASS
DNASE2	1777	broad.mit.edu	37	19	12989370	12989370	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12989370G>T	uc002mvn.1	-	5	681	c.535C>A	c.(535-537)CCC>ACC	p.P179T	DNASE2_uc010xmr.1_Missense_Mutation_p.P124T	NM_001375	NP_001366	O00115	DNS2A_HUMAN	deoxyribonuclease II, lysosomal precursor	179					apoptosis	lysosome	deoxyribonuclease II activity|DNA binding|protein binding				0						TAGACCCAGGGGTAGGTGTAG	0.547								Direct_reversal_of_damage					5	38	---	---	---	---	PASS
SLC1A6	6511	broad.mit.edu	37	19	15072908	15072908	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15072908C>G	uc002naa.1	-	5	849	c.841G>C	c.(841-843)GTC>CTC	p.V281L	SLC1A6_uc010dzu.1_Missense_Mutation_p.V281L|SLC1A6_uc010xod.1_Missense_Mutation_p.V217L|SLC1A6_uc002nab.2_Missense_Mutation_p.V281L|SLC1A6_uc002nac.2_Missense_Mutation_p.V281L	NM_005071	NP_005062	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity	281	Helical; (Potential).				synaptic transmission	integral to plasma membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|L-aspartate transmembrane transporter activity|sodium:dicarboxylate symporter activity			pancreas(3)|ovary(2)|skin(1)	6					L-Glutamic Acid(DB00142)	CCACCAATGACCAGCCCAAAG	0.562													36	36	---	---	---	---	PASS
CCDC105	126402	broad.mit.edu	37	19	15133834	15133834	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15133834G>A	uc002nae.2	+	7	1502	c.1403G>A	c.(1402-1404)CGG>CAG	p.R468Q		NM_173482	NP_775753	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	468					microtubule cytoskeleton organization	microtubule				ovary(1)	1						CTGCGCCAGCGGCAACCGCAC	0.687													4	9	---	---	---	---	PASS
OR10H5	284433	broad.mit.edu	37	19	15905716	15905716	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15905716C>A	uc010xos.1	+	1	858	c.858C>A	c.(856-858)CTC>CTA	p.L286L		NM_001004466	NP_001004466	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H,	286	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						CACCCTTCCTCAGCCCCATCA	0.532													8	37	---	---	---	---	PASS
MYO9B	4650	broad.mit.edu	37	19	17212909	17212909	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17212909C>A	uc010eak.2	+	2	534	c.382C>A	c.(382-384)CAG>AAG	p.Q128K	MYO9B_uc002nfi.2_Missense_Mutation_p.Q128K|MYO9B_uc002nfj.1_Missense_Mutation_p.Q128K	NM_004145	NP_004136	Q13459	MYO9B_HUMAN	myosin IXB isoform 1	128	Myosin head-like.				actin filament-based movement	cell cortex|cytosol|filamentous actin|myosin complex|perinuclear region of cytoplasm	actin binding|ADP binding|ATP binding|ATPase activity|calmodulin binding|metal ion binding|microfilament motor activity|Rho GTPase activator activity			breast(1)	1						GCTGGTGGCGCAGGCCACAGC	0.627													6	27	---	---	---	---	PASS
B3GNT3	10331	broad.mit.edu	37	19	17922653	17922653	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17922653G>A	uc002nhk.1	+	3	926	c.841G>A	c.(841-843)GCT>ACT	p.A281T	B3GNT3_uc002nhl.1_Missense_Mutation_p.A281T|B3GNT3_uc010ebd.1_Missense_Mutation_p.A281T|B3GNT3_uc010ebe.1_Missense_Mutation_p.A281T	NM_014256	NP_055071	Q9Y2A9	B3GN3_HUMAN	UDP-GlcNAc:betaGal	281	Lumenal (Potential).				protein glycosylation	Golgi membrane|integral to plasma membrane	galactosyltransferase activity			upper_aerodigestive_tract(1)	1						CTTCACGGCCGCTGCCCTGCG	0.572													28	25	---	---	---	---	PASS
ZNF208	7757	broad.mit.edu	37	19	22156135	22156135	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22156135G>T	uc002nqp.2	-	5	1550	c.1401C>A	c.(1399-1401)ACC>ACA	p.T467T	ZNF208_uc002nqo.1_Intron	NM_007153	NP_009084			zinc finger protein 208											ovary(5)|skin(2)	7		all_lung(12;0.0961)|Lung NSC(12;0.103)				GATAACTAAGGGTTGAGGACC	0.343													14	11	---	---	---	---	PASS
ZNF536	9745	broad.mit.edu	37	19	31040208	31040208	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31040208G>T	uc002nsu.1	+	4	3820	c.3682G>T	c.(3682-3684)GCA>TCA	p.A1228S	ZNF536_uc010edd.1_Missense_Mutation_p.A1228S	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	1228					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)					TTTATCCCAAGCACCGGAGAA	0.672													6	16	---	---	---	---	PASS
TSHZ3	57616	broad.mit.edu	37	19	31767965	31767965	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31767965C>A	uc002nsy.3	-	2	2799	c.2734G>T	c.(2734-2736)GCC>TCC	p.A912S		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	912	Homeobox; atypical.				negative regulation of transcription, DNA-dependent|regulation of respiratory gaseous exchange by neurological system process	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(2)|pancreas(1)|lung(1)	8	Esophageal squamous(110;0.226)					CGGAGGCTGGCGGCAAACTGG	0.627													6	16	---	---	---	---	PASS
CEBPA	1050	broad.mit.edu	37	19	33792245	33792245	+	Nonstop_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33792245C>G	uc002nun.2	-	1	1186	c.1076G>C	c.(1075-1077)TGA>TCA	p.*359S	LOC80054_uc002nuo.2_5'Flank	NM_004364	NP_004355	P49715	CEBPA_HUMAN	CCAAT/enhancer binding protein alpha	359					cytokine-mediated signaling pathway|generation of precursor metabolites and energy|interspecies interaction between organisms|positive regulation of transcription from RNA polymerase III promoter		sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding	p.?(5)		haematopoietic_and_lymphoid_tissue(728)|lung(4)|stomach(1)|prostate(1)	734	Esophageal squamous(110;0.137)					CCGCGCGCCTCACGCGCAGTT	0.706			Mis|N|F		AML|MDS				Acute_Myeloid_Leukemia_Familial_associated_with_CEBPA_germline_mutation				7	7	---	---	---	---	PASS
PEPD	5184	broad.mit.edu	37	19	33984220	33984220	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33984220C>A	uc002nur.3	-	5	552	c.417G>T	c.(415-417)CAG>CAT	p.Q139H	PEPD_uc010xrr.1_Missense_Mutation_p.Q139H|PEPD_uc010xrs.1_Missense_Mutation_p.Q75H	NM_000285	NP_000276	P12955	PEPD_HUMAN	prolidase isoform 1	139					cellular amino acid metabolic process|collagen catabolic process|proteolysis		aminopeptidase activity|dipeptidase activity|manganese ion binding|metallocarboxypeptidase activity			ovary(2)	2	Esophageal squamous(110;0.137)					CAGAGGGCTTCTGTGACGTCA	0.542													5	12	---	---	---	---	PASS
HAUS5	23354	broad.mit.edu	37	19	36110360	36110360	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36110360A>G	uc002oam.1	+	14	1265	c.1214A>G	c.(1213-1215)AAG>AGG	p.K405R		NM_015302	NP_056117	O94927	HAUS5_HUMAN	HAUS augmin-like complex, subunit 5	405					cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle					0						CTGCTCATCAAGGGAAACTCG	0.642													4	15	---	---	---	---	PASS
SARS2	54938	broad.mit.edu	37	19	39421117	39421117	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39421117G>A	uc002oka.2	-	1	420	c.260C>T	c.(259-261)CCC>CTC	p.P87L	SARS2_uc002ojz.2_5'Flank|SARS2_uc010xup.1_Missense_Mutation_p.P87L|SARS2_uc002okb.2_Missense_Mutation_p.P87L|SARS2_uc010xuq.1_Intron|SARS2_uc010xur.1_RNA|SARS2_uc010xus.1_Missense_Mutation_p.P87L|MRPS12_uc002okc.2_5'Flank|MRPS12_uc002okd.2_5'Flank|MRPS12_uc002oke.2_5'Flank	NM_017827	NP_060297	Q9NP81	SYSM_HUMAN	seryl-tRNA synthetase 2 isoform b precursor	87					seryl-tRNA aminoacylation	mitochondrial matrix	ATP binding|protein binding|serine-tRNA ligase activity			ovary(1)|pancreas(1)|skin(1)	3	all_cancers(60;2.74e-06)|all_epithelial(25;4.36e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			CACGATCGCGGGCAGGTCCGC	0.672											OREG0032101|OREG0025455	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)|type=REGULATORY REGION|TFbs=RELA|Dataset=RELA (p65) ChIP-PET Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with paired-end diTag sequencing (ChIP-PET)	4	11	---	---	---	---	PASS
SHKBP1	92799	broad.mit.edu	37	19	41083301	41083301	+	Splice_Site	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41083301G>T	uc002oob.2	+	3	190	c.141_splice	c.e3-1	p.S47_splice	SHKBP1_uc002ooc.2_Splice_Site_p.S47_splice|SHKBP1_uc002ood.2_Splice_Site_p.S47_splice|SHKBP1_uc010xvl.1_Splice_Site|SHKBP1_uc002ooe.2_5'UTR|SHKBP1_uc002oof.2_5'Flank|SHKBP1_uc010xvm.1_5'Flank|SHKBP1_uc010xvn.1_5'Flank	NM_138392	NP_612401	Q8TBC3	SHKB1_HUMAN	SH3KBP1 binding protein 1							voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|pancreas(1)	2			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CTTCCCTGCAGTCTTCTGAGC	0.617													5	16	---	---	---	---	PASS
ADCK4	79934	broad.mit.edu	37	19	41220008	41220008	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41220008G>A	uc002oor.2	-	4	555	c.253C>T	c.(253-255)CCT>TCT	p.P85S	ADCK4_uc002ooq.1_Missense_Mutation_p.P85S|ADCK4_uc002oos.2_Missense_Mutation_p.P85S|ITPKC_uc002oot.2_5'Flank	NM_024876	NP_079152	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4 isoform a	85						integral to membrane	protein serine/threonine kinase activity				0			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			CGGGAGGCAGGCACCTTGCGT	0.567													9	21	---	---	---	---	PASS
PHLDB3	653583	broad.mit.edu	37	19	44001416	44001416	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44001416C>A	uc002own.3	-	6	938	c.679G>T	c.(679-681)GAT>TAT	p.D227Y	PHLDB3_uc010eit.2_5'Flank|PHLDB3_uc002owo.2_Missense_Mutation_p.D227Y	NM_198850	NP_942147	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B,	227	Potential.										0		Prostate(69;0.0153)				TGGGCCACATCCAGTTGTTCC	0.378													6	8	---	---	---	---	PASS
PLAUR	5329	broad.mit.edu	37	19	44159726	44159726	+	Splice_Site	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44159726C>T	uc002oxf.1	-	5	703	c.473_splice	c.e5-1	p.G158_splice	PLAUR_uc002oxd.1_Splice_Site_p.G158_splice|PLAUR_uc002oxe.1_Splice_Site_p.G153_splice|PLAUR_uc002oxg.1_Intron	NM_002659	NP_002650	Q03405	UPAR_HUMAN	plasminogen activator, urokinase receptor						attachment of GPI anchor to protein|blood coagulation|C-terminal protein lipidation|cellular component movement|chemotaxis|fibrinolysis|regulation of proteolysis	anchored to membrane|cell surface|endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region|extrinsic to membrane|integral to membrane|plasma membrane	enzyme binding|U-plasminogen activator receptor activity			ovary(1)	1		Prostate(69;0.0153)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Urokinase(DB00013)	TTTGGACGCCCTATGGGGGCC	0.517													7	17	---	---	---	---	PASS
IRGC	56269	broad.mit.edu	37	19	44223323	44223323	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44223323G>C	uc002oxh.2	+	2	760	c.613G>C	c.(613-615)GCC>CCC	p.A205P		NM_019612	NP_062558	Q6NXR0	IIGP5_HUMAN	immunity-related GTPase family, cinema	205						membrane	GTP binding|hydrolase activity, acting on acid anhydrides			ovary(1)|central_nervous_system(1)|skin(1)	3		Prostate(69;0.0435)				GCTGCGGGAGGCCGGCGTGGC	0.706													7	9	---	---	---	---	PASS
ZNF222	7673	broad.mit.edu	37	19	44537160	44537160	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44537160T>C	uc002oyc.2	+	4	1516	c.1333T>C	c.(1333-1335)TCA>CCA	p.S445P	ZNF284_uc010ejd.2_Intron|ZNF222_uc002oye.2_Missense_Mutation_p.S485P|ZNF222_uc002oyd.2_Missense_Mutation_p.S391P	NM_013360	NP_037492	Q9UK12	ZN222_HUMAN	zinc finger protein 222 isoform 2	445					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Prostate(69;0.0435)				TATAATTTTATCAttattttt	0.224													9	18	---	---	---	---	PASS
MYADM	91663	broad.mit.edu	37	19	54376778	54376778	+	Intron	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54376778G>A	uc002qcl.2	+						MYADM_uc002qcm.2_Intron|MYADM_uc002qcn.2_Intron|MYADM_uc002qco.2_Intron|MYADM_uc002qcp.2_Intron	NM_001020820	NP_001018656	Q96S97	MYADM_HUMAN	myeloid-associated differentiation marker							integral to membrane				ovary(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.0488)		TCCCCTTTTTGCAGCCATGCC	0.537											OREG0003650	type=REGULATORY REGION|Gene=MYADM|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	5	16	---	---	---	---	PASS
MYADM	91663	broad.mit.edu	37	19	54377402	54377402	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54377402G>T	uc002qcl.2	+	3	767	c.619G>T	c.(619-621)GTG>TTG	p.V207L	MYADM_uc002qcm.2_Missense_Mutation_p.V207L|MYADM_uc002qcn.2_Missense_Mutation_p.V207L|MYADM_uc002qco.2_Missense_Mutation_p.V207L|MYADM_uc002qcp.2_Missense_Mutation_p.V207L	NM_001020820	NP_001018656	Q96S97	MYADM_HUMAN	myeloid-associated differentiation marker	207	MARVEL 2.|Helical; (Potential).					integral to membrane				ovary(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.0488)		GGAGTGGTGCGTGGCGGTGTA	0.627													19	26	---	---	---	---	PASS
LILRB2	10288	broad.mit.edu	37	19	54782788	54782788	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54782788C>T	uc002qfb.2	-	6	1100	c.834G>A	c.(832-834)CAG>CAA	p.Q278Q	LILRA6_uc002qew.1_Intron|LILRB2_uc010eri.2_Silent_p.Q278Q|LILRB2_uc010erj.2_RNA|LILRB2_uc002qfc.2_Silent_p.Q278Q|LILRB2_uc010yet.1_Silent_p.Q162Q|LILRB2_uc010yeu.1_RNA	NM_005874	NP_005865	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor,	278	Extracellular (Potential).|Ig-like C2-type 3.				cell surface receptor linked signaling pathway|cell-cell signaling|cellular defense response|immune response|regulation of immune response	integral to plasma membrane|membrane fraction	receptor activity			skin(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGAAGTTGGCCTGGGAGAGCC	0.637													6	19	---	---	---	---	PASS
LILRA3	11026	broad.mit.edu	37	19	54803513	54803513	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54803513G>C	uc002qfd.2	-	3	376	c.311C>G	c.(310-312)ACT>AGT	p.T104S	LILRA6_uc002qew.1_Intron|LILRA3_uc010erk.2_Missense_Mutation_p.T104S	NM_006865	NP_006856	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor,	104	Ig-like C2-type 1.				defense response	extracellular region|plasma membrane	antigen binding|receptor activity			ovary(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GAGGCCTGCAGTGTGGCTGCC	0.607													4	25	---	---	---	---	PASS
LILRA4	23547	broad.mit.edu	37	19	54848834	54848834	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54848834G>A	uc002qfj.2	-	5	846	c.789C>T	c.(787-789)CTC>CTT	p.L263L	LILRA4_uc002qfi.2_Silent_p.L197L	NM_012276	NP_036408	P59901	LIRA4_HUMAN	leukocyte immunoglobulin-like receptor subfamily	263	Extracellular (Potential).|Ig-like C2-type 3.					integral to membrane	receptor activity			upper_aerodigestive_tract(1)|central_nervous_system(1)	2	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0565)		GGCGCTGGGGGAGGCCATCGG	0.657													4	15	---	---	---	---	PASS
LILRA2	11027	broad.mit.edu	37	19	55086444	55086444	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55086444C>T	uc002qgg.3	+	4	688	c.599C>T	c.(598-600)TCG>TTG	p.S200L	LILRA2_uc010ern.2_Missense_Mutation_p.S200L|LILRA2_uc002qgf.2_Missense_Mutation_p.S200L|LILRA2_uc010yfe.1_Missense_Mutation_p.S200L|LILRA2_uc010yff.1_Missense_Mutation_p.S188L|LILRA2_uc010ero.2_Missense_Mutation_p.S188L|LILRA2_uc010yfg.1_Missense_Mutation_p.S200L	NM_001130917	NP_001124389	Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor,	200	Extracellular (Potential).|Ig-like C2-type 2.				defense response	integral to membrane	antigen binding|receptor activity			ovary(1)	1				GBM - Glioblastoma multiforme(193;0.0963)		GCTTATGACTCGAACTCTCCC	0.577													29	34	---	---	---	---	PASS
ZSCAN5B	342933	broad.mit.edu	37	19	56701752	56701752	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56701752G>T	uc010ygh.1	-	4	932	c.932C>A	c.(931-933)CCT>CAT	p.P311H		NM_001080456	NP_001073925	A6NJL1	ZSA5B_HUMAN	zinc finger and SCAN domain containing 5B	311					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2						TTCTCCTTGAGGCTCTTCTTG	0.547													12	48	---	---	---	---	PASS
PEG3	5178	broad.mit.edu	37	19	57327351	57327351	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57327351G>T	uc002qnu.2	-	7	2810	c.2459C>A	c.(2458-2460)GCT>GAT	p.A820D	ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnt.2_Missense_Mutation_p.A791D|PEG3_uc002qnv.2_Missense_Mutation_p.A820D|PEG3_uc002qnw.2_Missense_Mutation_p.A696D|PEG3_uc002qnx.2_Missense_Mutation_p.A694D|PEG3_uc010etr.2_Missense_Mutation_p.A820D	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	820					apoptosis|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		GTTCCCTCCAGCACGAACTCT	0.463													26	47	---	---	---	---	PASS
PEG3	5178	broad.mit.edu	37	19	57328094	57328094	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57328094G>C	uc002qnu.2	-	7	2067	c.1716C>G	c.(1714-1716)TTC>TTG	p.F572L	ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnt.2_Missense_Mutation_p.F543L|PEG3_uc002qnv.2_Missense_Mutation_p.F572L|PEG3_uc002qnw.2_Missense_Mutation_p.F448L|PEG3_uc002qnx.2_Missense_Mutation_p.F446L|PEG3_uc010etr.2_Missense_Mutation_p.F572L	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	572	C2H2-type 3.				apoptosis|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		AACTATGAAGGAAGGTTTCCT	0.388													6	32	---	---	---	---	PASS
ZNF749	388567	broad.mit.edu	37	19	57955212	57955212	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57955212G>A	uc002qoq.2	+	3	950	c.696G>A	c.(694-696)TTG>TTA	p.L232L	ZNF547_uc002qpm.3_Intron	NM_001023561	NP_001018855	O43361	ZN749_HUMAN	zinc finger protein 749	232	C2H2-type 3; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)|Lung(386;0.177)		GTGGGGAATTGTTTAGGTACA	0.428													21	23	---	---	---	---	PASS
ZNF530	348327	broad.mit.edu	37	19	58118382	58118382	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58118382G>A	uc002qpk.2	+	3	1709	c.1489G>A	c.(1489-1491)GGG>AGG	p.G497R	ZNF547_uc002qpm.3_Intron|ZNF530_uc002qpl.2_RNA	NM_020880	NP_065931	Q6P9A1	ZN530_HUMAN	zinc finger protein 530	497	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0443)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		CAGTGTATGTGGGAAATCTTT	0.428													22	25	---	---	---	---	PASS
PDYN	5173	broad.mit.edu	37	20	1961250	1961250	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1961250A>T	uc010gaj.2	-	3	726	c.484T>A	c.(484-486)TAT>AAT	p.Y162N	uc002wfu.1_Intron|PDYN_uc002wfv.2_Missense_Mutation_p.Y162N|PDYN_uc010zpt.1_Missense_Mutation_p.Y7N	NM_024411	NP_077722	P01213	PDYN_HUMAN	beta-neoendorphin-dynorphin preproprotein	162					cell death|neuropeptide signaling pathway|synaptic transmission	extracellular region|plasma membrane	opioid peptide activity			upper_aerodigestive_tract(1)|ovary(1)	2						TCAGCGAGATAGAGTGTGCCA	0.597													41	34	---	---	---	---	PASS
PLCB4	5332	broad.mit.edu	37	20	9401951	9401951	+	Nonsense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9401951C>G	uc002wnf.2	+	25	2262	c.2126C>G	c.(2125-2127)TCA>TGA	p.S709*	PLCB4_uc010gbw.1_Nonsense_Mutation_p.S709*|PLCB4_uc010gbx.2_Nonsense_Mutation_p.S721*|PLCB4_uc002wne.2_Nonsense_Mutation_p.S709*|PLCB4_uc002wnh.2_Nonsense_Mutation_p.S556*	NM_182797	NP_877949	Q15147	PLCB4_HUMAN	phospholipase C beta 4 isoform b	709	C2.				intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15						CAGGTTATATCAGGTCAATTC	0.413													16	13	---	---	---	---	PASS
C20orf26	26074	broad.mit.edu	37	20	20171995	20171995	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20171995C>A	uc002wru.2	+	15	1598	c.1522C>A	c.(1522-1524)CTG>ATG	p.L508M	C20orf26_uc010zse.1_Missense_Mutation_p.L488M	NM_015585	NP_056400	Q8NHU2	CT026_HUMAN	hypothetical protein LOC26074	508										ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)		GGATGGAACACTGCTGCAGGC	0.358													11	16	---	---	---	---	PASS
RALGAPA2	57186	broad.mit.edu	37	20	20621385	20621385	+	Silent	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20621385T>A	uc002wrz.2	-	6	653	c.510A>T	c.(508-510)ACA>ACT	p.T170T	RALGAPA2_uc010zsg.1_5'UTR	NM_020343	NP_065076	Q2PPJ7	RGPA2_HUMAN	akt substrate AS250	170					activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1						GTGTCTCCAGTGTGCAAGGGC	0.463													19	31	---	---	---	---	PASS
PAX1	5075	broad.mit.edu	37	20	21687608	21687608	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21687608C>A	uc002wsj.2	+	2	873	c.819C>A	c.(817-819)GTC>GTA	p.V273V	PAX1_uc010zsl.1_Silent_p.V273V|PAX1_uc010zsm.1_Silent_p.V249V	NM_006192	NP_006183	P15863	PAX1_HUMAN	paired box 1	273					regulation of transcription, DNA-dependent|skeletal system development|transcription from RNA polymerase II promoter	nucleus	DNA binding			upper_aerodigestive_tract(1)|kidney(1)	2						ACCCCGGGGTCCCGGGCACGG	0.677													6	11	---	---	---	---	PASS
NINL	22981	broad.mit.edu	37	20	25456757	25456757	+	Missense_Mutation	SNP	T	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25456757T>G	uc002wux.1	-	17	3244	c.3170A>C	c.(3169-3171)GAC>GCC	p.D1057A	NINL_uc010gdn.1_Intron	NM_025176	NP_079452	Q9Y2I6	NINL_HUMAN	ninein-like	1057	Potential.				G2/M transition of mitotic cell cycle	cytosol|microtubule|microtubule organizing center	calcium ion binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5						GGTTTCCATGTCATCCTTCTC	0.532													7	55	---	---	---	---	PASS
C20orf160	140706	broad.mit.edu	37	20	30602789	30602789	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30602789C>A	uc002wxf.2	+	2	126	c.113C>A	c.(112-114)CCC>CAC	p.P38H		NM_080625	NP_542192	Q9NUG4	CT160_HUMAN	hypothetical protein LOC140706	38										central_nervous_system(3)|ovary(1)	4						AGCCGCCGGCCCCTGCACTCG	0.637													10	42	---	---	---	---	PASS
SUN5	140732	broad.mit.edu	37	20	31590677	31590677	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31590677G>A	uc002wyi.2	-	2	219	c.126C>T	c.(124-126)TCC>TCT	p.S42S		NM_080675	NP_542406	Q8TC36	SUN5_HUMAN	sperm associated antigen 4-like	42					spermatogenesis					skin(1)	1						TCATGTTTGGGGAGGTGTCCT	0.368													5	30	---	---	---	---	PASS
BPIL1	80341	broad.mit.edu	37	20	31607502	31607502	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31607502G>T	uc002wyj.2	+	11	1220	c.1026G>T	c.(1024-1026)GAG>GAT	p.E342D		NM_025227	NP_079503	Q8N4F0	BPIL1_HUMAN	bactericidal/permeability-increasing	342						extracellular region	lipid binding			skin(2)|large_intestine(1)|ovary(1)	4						CCTTCGTGGAGGTCCTGGCCA	0.637													13	10	---	---	---	---	PASS
C20orf186	149954	broad.mit.edu	37	20	31671497	31671497	+	Missense_Mutation	SNP	C	T	T	rs143050216	byFrequency	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31671497C>T	uc010zue.1	+	3	509	c.494C>T	c.(493-495)GCG>GTG	p.A165V		NM_182519	NP_872325	P59827	LPLC4_HUMAN	antimicrobial peptide RY2G5 precursor	165	Gly-rich.					cytoplasm|extracellular region	lipid binding				0						GCCACTGGGGCGGTGGGCCCA	0.677													13	27	---	---	---	---	PASS
C20orf71	128861	broad.mit.edu	37	20	31811649	31811649	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31811649G>A	uc002wyr.2	+	2	368	c.160G>A	c.(160-162)GAA>AAA	p.E54K	C20orf71_uc002wys.2_Missense_Mutation_p.E54K	NM_178466	NP_848561	Q9BQP9	SPLC3_HUMAN	short long palate, lung and nasal epithelium	54						extracellular region	lipid binding			ovary(1)|skin(1)	2						GCACAACGCAGAAAGCCGAAT	0.423													9	83	---	---	---	---	PASS
C20orf114	92747	broad.mit.edu	37	20	31873902	31873902	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31873902C>G	uc002wyw.1	+	2	184	c.23C>G	c.(22-24)ACC>AGC	p.T8S	C20orf114_uc010gej.1_Missense_Mutation_p.T8S	NM_033197	NP_149974	Q8TDL5	LPLC1_HUMAN	LPLUNC1 protein precursor	8						extracellular space	lipid binding			central_nervous_system(2)|skin(2)	4						TGGACCTTCACCCTTCTCTGT	0.587													26	59	---	---	---	---	PASS
RBM12	10137	broad.mit.edu	37	20	34242934	34242934	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34242934C>A	uc002xdq.2	-	3	543	c.311G>T	c.(310-312)AGA>ATA	p.R104I	CPNE1_uc010zvj.1_5'Flank|CPNE1_uc002xde.2_Intron|CPNE1_uc002xdf.2_Intron|CPNE1_uc002xdg.2_Intron|CPNE1_uc010gfi.2_Intron|CPNE1_uc010gfj.2_Intron|CPNE1_uc002xdh.2_Intron|CPNE1_uc002xdi.2_Intron|CPNE1_uc002xdj.2_Intron|CPNE1_uc002xdk.2_Intron|CPNE1_uc002xdl.2_Intron|CPNE1_uc002xdm.2_Intron|CPNE1_uc010gfk.1_Intron|CPNE1_uc002xdn.1_Intron|CPNE1_uc002xdo.1_Intron|CPNE1_uc002xdp.1_Intron|RBM12_uc002xdr.2_Missense_Mutation_p.R104I|RBM12_uc002xds.2_Missense_Mutation_p.R104I	NM_152838	NP_690051	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12	104						nucleus	nucleotide binding|protein binding|RNA binding			ovary(3)	3	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			TGGTCCTGATCTACTGGCATT	0.438											OREG0004046	type=REGULATORY REGION|Gene=RBM12|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	77	84	---	---	---	---	PASS
PTPRT	11122	broad.mit.edu	37	20	41306547	41306547	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41306547C>A	uc002xkg.2	-	7	1296	c.1112G>T	c.(1111-1113)GGA>GTA	p.G371V	PTPRT_uc010ggj.2_Missense_Mutation_p.G371V	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	371	Extracellular (Potential).|Fibronectin type-III 1.				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)				CCCTGGCGGTCCCGTACCCCC	0.547													22	100	---	---	---	---	PASS
MYBL2	4605	broad.mit.edu	37	20	42315650	42315650	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42315650C>T	uc002xlb.1	+	5	653	c.438C>T	c.(436-438)ATC>ATT	p.I146I	MYBL2_uc010zwj.1_Silent_p.I122I|MYBL2_uc002xla.1_Silent_p.I146I	NM_002466	NP_002457	P10244	MYBB_HUMAN	MYB-related protein B	146	HTH myb-type 3.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			lung(3)|kidney(2)	5		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			ACCGCATCATCTGCGAGGCCC	0.627													11	24	---	---	---	---	PASS
ACOT8	10005	broad.mit.edu	37	20	44483870	44483870	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44483870G>C	uc002xqa.1	-	2	271	c.190C>G	c.(190-192)CTG>GTG	p.L64V	ACOT8_uc010zxe.1_Missense_Mutation_p.L64V|ACOT8_uc002xqc.1_Intron|ACOT8_uc010zxf.1_Intron|ZSWIM3_uc002xqd.2_5'Flank|ZSWIM3_uc010zxg.1_5'Flank	NM_005469	NP_005460	O14734	ACOT8_HUMAN	peroxisomal acyl-CoA thioesterase 1 isoform a	64					bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase|interspecies interaction between organisms|peroxisome organization	peroxisomal matrix	acetyl-CoA hydrolase activity|acyl-CoA thioesterase activity|carboxylesterase activity|choloyl-CoA hydrolase activity|protein binding			skin(1)	1		Myeloproliferative disorder(115;0.0122)				GCAGCCACCAGGGCCTGGCCC	0.592													13	73	---	---	---	---	PASS
ELMO2	63916	broad.mit.edu	37	20	45016067	45016067	+	Missense_Mutation	SNP	C	G	G	rs4992415		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45016067C>G	uc002xrt.1	-	8	645	c.435G>C	c.(433-435)GAG>GAC	p.E145D	ELMO2_uc002xru.1_Missense_Mutation_p.E145D|ELMO2_uc010zxr.1_Missense_Mutation_p.E145D|ELMO2_uc010zxs.1_Intron|ELMO2_uc002xrw.2_5'Flank|ELMO2_uc002xrx.1_Missense_Mutation_p.E145D	NM_133171	NP_573403	Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	145					apoptosis|cell chemotaxis|phagocytosis	cytoskeleton|cytosol|membrane	lyase activity|receptor tyrosine kinase binding|SH3 domain binding			ovary(1)	1		Myeloproliferative disorder(115;0.0122)				ATGCCAGCATCTCACTGTAGC	0.468													17	24	---	---	---	---	PASS
KCNB1	3745	broad.mit.edu	37	20	47990134	47990134	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47990134C>T	uc002xur.1	-	2	2127	c.1963G>A	c.(1963-1965)GAG>AAG	p.E655K	KCNB1_uc002xus.1_Missense_Mutation_p.E655K	NM_004975	NP_004966	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related	655	Cytoplasmic (Potential).				energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity			pancreas(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			TTGGGGCTCTCGATGAAGAAA	0.567													17	56	---	---	---	---	PASS
ZFP64	55734	broad.mit.edu	37	20	50776752	50776752	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50776752G>A	uc002xwl.2	-	5	1022	c.673C>T	c.(673-675)CAC>TAC	p.H225Y	ZFP64_uc002xwk.2_Missense_Mutation_p.H225Y|ZFP64_uc002xwm.2_Missense_Mutation_p.H223Y|ZFP64_uc002xwn.2_Missense_Mutation_p.H171Y	NM_018197	NP_060667	Q9NPA5	ZF64A_HUMAN	zinc finger protein 64 isoform a	225	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2						TCGTCCGAGTGGATCCTCAGG	0.617													47	51	---	---	---	---	PASS
CASS4	57091	broad.mit.edu	37	20	55027043	55027043	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55027043G>T	uc002xxp.2	+	6	1036	c.811G>T	c.(811-813)GCT>TCT	p.A271S	CASS4_uc002xxq.3_Missense_Mutation_p.A271S|CASS4_uc002xxr.2_Missense_Mutation_p.A271S|CASS4_uc010zze.1_Missense_Mutation_p.A217S|CASS4_uc010gio.2_Intron	NM_001164116	NP_001157588	Q9NQ75	CASS4_HUMAN	HEF-like protein isoform a	271					cell adhesion	cytoplasm|cytoskeleton|focal adhesion	two-component sensor activity			ovary(2)|skin(1)	3						AAGGCCCCACGCTCTCCCCAG	0.507													25	27	---	---	---	---	PASS
CTCFL	140690	broad.mit.edu	37	20	56099117	56099117	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56099117C>A	uc010gix.1	-	1	807	c.145G>T	c.(145-147)GCC>TCC	p.A49S	CTCFL_uc010giw.1_Missense_Mutation_p.A49S|CTCFL_uc002xym.2_Missense_Mutation_p.A49S|CTCFL_uc010giz.1_Intron|CTCFL_uc010giy.1_Intron|CTCFL_uc010gja.1_Missense_Mutation_p.A49S|CTCFL_uc010gjb.1_Missense_Mutation_p.A49S|CTCFL_uc010gjc.1_Missense_Mutation_p.A49S|CTCFL_uc010gjd.1_Missense_Mutation_p.A49S|CTCFL_uc010gje.2_Missense_Mutation_p.A49S|CTCFL_uc010gjf.2_Intron|CTCFL_uc010gjg.2_Intron|CTCFL_uc010gjh.1_Missense_Mutation_p.A49S|CTCFL_uc010gji.1_Intron|CTCFL_uc010gjj.1_Missense_Mutation_p.A49S|CTCFL_uc010gjk.1_Missense_Mutation_p.A49S|CTCFL_uc010gjl.1_Missense_Mutation_p.A49S	NM_080618	NP_542185	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor-like protein	49					cell cycle|DNA methylation involved in gamete generation|histone methylation|positive regulation of transcription, DNA-dependent|regulation of gene expression by genetic imprinting|regulation of histone H3-K4 methylation|transcription, DNA-dependent	cytoplasm|nucleus	histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|large_intestine(1)|skin(1)	4	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			GTACGCTCGGCCTCCAACTCA	0.577													79	121	---	---	---	---	PASS
STX16	8675	broad.mit.edu	37	20	57242623	57242623	+	Silent	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57242623A>G	uc002xzi.2	+	3	957	c.222A>G	c.(220-222)CCA>CCG	p.P74P	STX16_uc010zzq.1_5'UTR|STX16_uc002xzk.2_Silent_p.P57P|STX16_uc002xzm.2_Silent_p.P70P|STX16_uc002xzj.2_Silent_p.P53P|STX16_uc002xzl.2_5'UTR	NM_001001433	NP_001001433	O14662	STX16_HUMAN	syntaxin 16 isoform a	74	Cytoplasmic (Potential).				intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde transport, endosome to Golgi	Golgi membrane|integral to membrane|microsome|SNARE complex	SNAP receptor activity			ovary(1)	1	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;3.73e-09)|Epithelial(14;8.54e-06)|all cancers(14;6.89e-05)			CAAAACGGCCACCTCCTAAGT	0.418													10	33	---	---	---	---	PASS
CDH4	1002	broad.mit.edu	37	20	60503462	60503462	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60503462G>T	uc002ybn.1	+	12	2000	c.1986G>T	c.(1984-1986)TGG>TGT	p.W662C	CDH4_uc002ybp.1_Missense_Mutation_p.W588C	NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein	662	Extracellular (Potential).|Cadherin 5.				adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			GGAAGAACTGGACCATCACCC	0.672													16	19	---	---	---	---	PASS
C20orf200	253868	broad.mit.edu	37	20	61143700	61143700	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61143700G>T	uc002ycz.1	-	3	639	c.148C>A	c.(148-150)CCA>ACA	p.P50T	C20orf200_uc002ycy.2_RNA	NM_152757	NP_689970			hypothetical protein LOC253868												0	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;7.17e-06)			AGACCGGATGGTGTGGCCCCG	0.662													8	19	---	---	---	---	PASS
MYT1	4661	broad.mit.edu	37	20	62842683	62842683	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62842683C>T	uc002yii.2	+	8	1780	c.1416C>T	c.(1414-1416)ATC>ATT	p.I472I	MYT1_uc002yih.2_Silent_p.I174I|MYT1_uc002yij.2_Silent_p.I104I	NM_004535	NP_004526	Q01538	MYT1_HUMAN	myelin transcription factor 1	472					cell differentiation|nervous system development	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					AGGATAGGATCCCCCCAGAGA	0.587													36	56	---	---	---	---	PASS
TPTE	7179	broad.mit.edu	37	21	10910396	10910396	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10910396G>T	uc002yip.1	-	22	1728	c.1360C>A	c.(1360-1362)CTT>ATT	p.L454I	TPTE_uc002yis.1_RNA|TPTE_uc002yiq.1_Missense_Mutation_p.L436I|TPTE_uc002yir.1_Missense_Mutation_p.L416I|TPTE_uc010gkv.1_Missense_Mutation_p.L316I	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	454	C2 tensin-type.				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)		ATGTTATCAAGTACCTATGAA	0.318													12	87	---	---	---	---	PASS
TPTE	7179	broad.mit.edu	37	21	10916482	10916482	+	Intron	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10916482A>T	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)		TCTTCTGAAAAGCAACAGAAA	0.333													8	74	---	---	---	---	PASS
LIPI	149998	broad.mit.edu	37	21	15554098	15554098	+	Silent	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15554098G>C	uc002yjm.2	-	4	697	c.687C>G	c.(685-687)GTC>GTG	p.V229V	LIPI_uc010gkw.1_Silent_p.V162V	NM_198996	NP_945347	Q6XZB0	LIPI_HUMAN	lipase, member I	208					lipid catabolic process	extracellular region|extracellular space|membrane|plasma membrane	heparin binding|phospholipase activity			ovary(2)	2				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		CAGAATGGATGACATCCACAA	0.403													3	19	---	---	---	---	PASS
JAM2	58494	broad.mit.edu	37	21	27066164	27066164	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27066164C>A	uc002ylp.1	+	4	883	c.338C>A	c.(337-339)GCC>GAC	p.A113D	JAM2_uc011ace.1_Missense_Mutation_p.A113D|JAM2_uc002ylq.1_RNA|JAM2_uc011acf.1_Missense_Mutation_p.A77D|JAM2_uc010glh.1_RNA|JAM2_uc002ylr.1_Missense_Mutation_p.A113D|JAM2_uc010gli.1_Missense_Mutation_p.A113D	NM_021219	NP_067042	P57087	JAM2_HUMAN	junctional adhesion molecule 2 precursor	113	Ig-like V-type.|Extracellular (Potential).				blood coagulation|cell-cell adhesion|leukocyte migration	integral to plasma membrane|tight junction					0						GAAGTTAGTGCCCCATCTGAG	0.428													12	48	---	---	---	---	PASS
GABPA	2551	broad.mit.edu	37	21	27141330	27141330	+	Silent	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27141330G>T	uc002ylx.3	+	10	1679	c.1152G>T	c.(1150-1152)GGG>GGT	p.G384G	GABPA_uc002yly.3_Silent_p.G384G	NM_002040	NP_002031	Q06546	GABPA_HUMAN	GA binding protein transcription factor, alpha	384	ETS.				positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	protein heterodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription regulatory region DNA binding			ovary(1)|central_nervous_system(1)	2						ATTACGATGGGGACATGATTT	0.348													14	57	---	---	---	---	PASS
APP	351	broad.mit.edu	37	21	27372439	27372439	+	Nonsense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27372439G>C	uc002ylz.2	-	7	1124	c.924C>G	c.(922-924)TAC>TAG	p.Y308*	APP_uc010glk.2_Nonsense_Mutation_p.Y303*|APP_uc002yma.2_Nonsense_Mutation_p.Y308*|APP_uc011ach.1_Nonsense_Mutation_p.Y252*|APP_uc002ymb.2_Intron|APP_uc010glj.2_Intron|APP_uc011aci.1_Intron	NM_000484	NP_000475	P05067	A4_HUMAN	amyloid beta A4 protein isoform a precursor	308	Extracellular (Potential).|BPTI/Kunitz inhibitor.				adult locomotory behavior|axon cargo transport|axon midline choice point recognition|cell adhesion|cellular copper ion homeostasis|collateral sprouting in absence of injury|dendrite development|endocytosis|extracellular matrix organization|G2 phase of mitotic cell cycle|innate immune response|ionotropic glutamate receptor signaling pathway|mating behavior|mRNA polyadenylation|neuron apoptosis|neuron remodeling|Notch signaling pathway|platelet activation|platelet degranulation|positive regulation of mitotic cell cycle|protein phosphorylation|regulation of epidermal growth factor receptor activity|regulation of multicellular organism growth|regulation of synapse structure and activity|regulation of translation|visual learning	axon|cell surface|coated pit|dendritic shaft|dendritic spine|extracellular region|Golgi apparatus|integral to plasma membrane|platelet alpha granule lumen	acetylcholine receptor binding|DNA binding|heparin binding|identical protein binding|metal ion binding|protein binding|protein binding|PTB domain binding|serine-type endopeptidase inhibitor activity			ovary(1)	1		Breast(209;0.00295)				TCACATCAAAGTACCAGCGGG	0.532													4	13	---	---	---	---	PASS
KRTAP21-1	337977	broad.mit.edu	37	21	32127708	32127708	+	5'Flank	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32127708G>A	uc011adi.1	-							NM_181619	NP_853650	Q3LI58	KR211_HUMAN	keratin associated protein 21-1							intermediate filament				breast(1)	1						TTGTCAAGAGGAGAGAATTGA	0.289													25	98	---	---	---	---	PASS
SON	6651	broad.mit.edu	37	21	34924260	34924260	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34924260C>T	uc002yse.1	+	3	2772	c.2723C>T	c.(2722-2724)TCA>TTA	p.S908L	SON_uc002ysb.1_Missense_Mutation_p.S908L|SON_uc002ysc.2_Missense_Mutation_p.S908L|SON_uc002ysd.2_Intron|SON_uc002ysf.1_Intron|SON_uc002ysg.2_5'Flank	NM_138927	NP_620305	P18583	SON_HUMAN	SON DNA-binding protein isoform F	908					anti-apoptosis|cytokinesis|mRNA processing|regulation of cell cycle|regulation of RNA splicing|RNA splicing|spindle pole body separation	nuclear speck	DNA binding|double-stranded RNA binding			ovary(4)|skin(2)	6						ATGTTGGGTTCAAAATCTCCT	0.473													7	15	---	---	---	---	PASS
KRTAP10-4	386672	broad.mit.edu	37	21	45994747	45994747	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45994747C>A	uc002zfk.1	+	1	1142	c.1112C>A	c.(1111-1113)CCC>CAC	p.P371H	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198687	NP_941960	P60372	KR104_HUMAN	keratin associated protein 10-4	371	36 X 5 AA repeats of C-C-X(3).					keratin filament					0						GTGTGCAGGCCCGCCTGCTGC	0.692													17	60	---	---	---	---	PASS
COL18A1	80781	broad.mit.edu	37	21	46925829	46925829	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46925829C>T	uc011afs.1	+	37	4422	c.4401C>T	c.(4399-4401)GCC>GCT	p.A1467A	COL18A1_uc002zhg.2_Silent_p.A1052A|COL18A1_uc002zhi.2_Silent_p.A1232A|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_Silent_p.A33A|COL18A1_uc002zhk.2_5'Flank	NM_130444	NP_569711	P39060	COIA1_HUMAN	alpha 1 type XVIII collagen isoform 3 precursor	1470	Nonhelical region 11 (NC11).				cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		TCTTCGTGGCCGAGCAGGAGG	0.657													6	26	---	---	---	---	PASS
PCNT	5116	broad.mit.edu	37	21	47836082	47836082	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47836082A>T	uc002zji.3	+	30	6357	c.6250A>T	c.(6250-6252)ATG>TTG	p.M2084L	PCNT_uc002zjj.2_Missense_Mutation_p.M1966L	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin	2084					cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)					GCTGTATTCCATGACCTTCCA	0.507													6	19	---	---	---	---	PASS
DIP2A	23181	broad.mit.edu	37	21	47918562	47918562	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47918562C>A	uc002zjo.2	+	5	654	c.471C>A	c.(469-471)CTC>CTA	p.L157L	DIP2A_uc011afy.1_Silent_p.L93L|DIP2A_uc011afz.1_Silent_p.L157L|DIP2A_uc002zjl.2_Silent_p.L157L|DIP2A_uc002zjm.2_Silent_p.L157L|DIP2A_uc010gql.2_Silent_p.L157L|DIP2A_uc002zjn.2_Silent_p.L157L	NM_015151	NP_055966	Q14689	DIP2A_HUMAN	disco-interacting protein 2A isoform a	157					multicellular organismal development	nucleus	catalytic activity|transcription factor binding			ovary(2)	2	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		CCACTCCGCTCCAGAGCCATT	0.592													15	74	---	---	---	---	PASS
GAB4	128954	broad.mit.edu	37	22	17447154	17447154	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17447154G>T	uc002zlw.2	-	6	1232	c.1124C>A	c.(1123-1125)GCA>GAA	p.A375E	GAB4_uc010gqs.1_3'UTR	NM_001037814	NP_001032903	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member	375										large_intestine(1)|ovary(1)	2		all_epithelial(15;0.112)|Lung NSC(13;0.248)				ATCATCGCCTGCTTGCTTCAC	0.582													13	14	---	---	---	---	PASS
CLDN5	7122	broad.mit.edu	37	22	19511547	19511547	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19511547G>T	uc002zpu.2	-	2	702	c.487C>A	c.(487-489)CAG>AAG	p.Q163K	CLDN5_uc010grr.2_Missense_Mutation_p.Q163K	NM_003277	NP_003268	O00501	CLD5_HUMAN	claudin 5	78	Extracellular (Potential).				calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity				0	Colorectal(54;0.0993)					CGCGCCGCCTGCACCTCGGTG	0.697													10	8	---	---	---	---	PASS
PI4KA	5297	broad.mit.edu	37	22	21096603	21096603	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21096603G>A	uc002zsz.3	-	32	3711	c.3480C>T	c.(3478-3480)CCC>CCT	p.P1160P		NM_058004	NP_477352	P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase type 3 alpha	1160					phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission	Golgi-associated vesicle	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			lung(2)|upper_aerodigestive_tract(1)|salivary_gland(1)	4	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			ACATCCGGAGGGGACCCCAGC	0.587											OREG0026324	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	35	92	---	---	---	---	PASS
CRKL	1399	broad.mit.edu	37	22	21288526	21288526	+	Silent	SNP	A	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21288526A>C	uc002ztf.2	+	2	1280	c.771A>C	c.(769-771)GCA>GCC	p.A257A	CRKL_uc002ztg.1_RNA	NM_005207	NP_005198	P46109	CRKL_HUMAN	v-crk sarcoma virus CT10 oncogene homolog	257	SH3 2.				JNK cascade|Ras protein signal transduction	cytosol	protein tyrosine kinase activity|SH3/SH2 adaptor activity|signal transducer activity				0	all_cancers(11;1.16e-25)|all_epithelial(7;3.37e-24)|Lung NSC(8;7.25e-16)|all_lung(8;1.37e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.176)			CTGCCTTGGCATTAGAGGTAA	0.393													15	41	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22931056	22931056	+	Intron	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22931056C>G	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						GACCTCTTCTCAGGCTCCAAG	0.473													68	192	---	---	---	---	PASS
RTDR1	27156	broad.mit.edu	37	22	23401853	23401853	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23401853C>A	uc002zwt.2	-	7	992	c.834G>T	c.(832-834)CTG>CTT	p.L278L		NM_014433	NP_055248	Q9UHP6	RTDR1_HUMAN	rhabdoid tumor deletion region protein 1	278							binding			ovary(1)	1	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.175)		GCAGCAGCTCCAGGAGCAGGC	0.662													59	30	---	---	---	---	PASS
GAS2L1	10634	broad.mit.edu	37	22	29707967	29707967	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29707967C>T	uc003afa.1	+	7	1726	c.1527C>T	c.(1525-1527)CTC>CTT	p.L509L	GAS2L1_uc010gvm.1_Intron|GAS2L1_uc003afb.1_3'UTR|GAS2L1_uc003afc.1_Silent_p.L509L|GAS2L1_uc003afd.1_Missense_Mutation_p.S509L|GAS2L1_uc003afe.1_Missense_Mutation_p.S509L	NM_152236	NP_689422	Q99501	GA2L1_HUMAN	growth arrest-specific 2 like 1 isoform a	509					cell cycle arrest	cytoplasm|cytoskeleton					0						CCCTGCAGCTCGACCCGCAGC	0.687													15	27	---	---	---	---	PASS
NF2	4771	broad.mit.edu	37	22	30035098	30035098	+	Nonsense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30035098C>G	uc003age.3	+	3	703	c.260C>G	c.(259-261)TCA>TGA	p.S87*	NF2_uc003afy.3_Nonsense_Mutation_p.S87*|NF2_uc003afz.3_Intron|NF2_uc003agf.3_Nonsense_Mutation_p.S87*|NF2_uc003agb.3_Nonsense_Mutation_p.S10*|NF2_uc003agc.3_Nonsense_Mutation_p.S49*|NF2_uc003agd.3_Intron|NF2_uc003agg.3_Nonsense_Mutation_p.S87*|NF2_uc003aga.3_Nonsense_Mutation_p.S45*|NF2_uc003agh.3_Intron|NF2_uc003agi.3_Intron|NF2_uc003agj.3_Nonsense_Mutation_p.S87*|NF2_uc003agk.3_Nonsense_Mutation_p.S49*	NM_000268	NP_000259	P35240	MERL_HUMAN	neurofibromin 2 isoform 1	87	FERM.				actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation	cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane	cytoskeletal protein binding|protein binding	p.H84_F100del(1)|p.V86_Q111>E(1)|p.S87fs*36(1)|p.S87*(1)		meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1)	728						CATGATGTTTCAAAGGAAGAA	0.428			D|Mis|N|F|S|O		meningioma|acoustic neuroma|renal 	meningioma|acoustic neuroma			Neurofibromatosis_type_2				34	17	---	---	---	---	PASS
MYH9	4627	broad.mit.edu	37	22	36691011	36691011	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36691011C>A	uc003apg.2	-	27	3828	c.3597G>T	c.(3595-3597)GAG>GAT	p.E1199D		NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle	1199	Potential.				actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11						CCGCCAGCTCCTCCACGGCCT	0.647			T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				89	44	---	---	---	---	PASS
MYH9	4627	broad.mit.edu	37	22	36692951	36692951	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36692951C>A	uc003apg.2	-	25	3441	c.3210G>T	c.(3208-3210)CAG>CAT	p.Q1070H		NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle	1070	Potential.		Missing (in MHA and SBS).		actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11						GCTCCGCGATCTGGGCCTGGA	0.677			T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				11	31	---	---	---	---	PASS
TRIOBP	11078	broad.mit.edu	37	22	38130844	38130844	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38130844G>A	uc003atr.2	+	9	4772	c.4501G>A	c.(4501-4503)GAG>AAG	p.E1501K	TRIOBP_uc003atu.2_Missense_Mutation_p.E1329K	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6	1501					actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)					GCCCACTCATGAGCTCCCCAG	0.652													27	20	---	---	---	---	PASS
TRIOBP	11078	broad.mit.edu	37	22	38130997	38130997	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38130997G>C	uc003atr.2	+	9	4925	c.4654G>C	c.(4654-4656)GAG>CAG	p.E1552Q	TRIOBP_uc003atu.2_Missense_Mutation_p.E1380Q	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6	1552					actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)					GCGTGGCTCTGAGAGGCGACC	0.687											OREG0026548	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	25	20	---	---	---	---	PASS
TRIOBP	11078	broad.mit.edu	37	22	38131246	38131246	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38131246G>A	uc003atr.2	+	9	5174	c.4903G>A	c.(4903-4905)GAG>AAG	p.E1635K	TRIOBP_uc003atu.2_Missense_Mutation_p.E1463K	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6	1635					actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)					AGGCTGGGCCGAGGCCACCCC	0.657											OREG0026548	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	33	14	---	---	---	---	PASS
PDGFB	5155	broad.mit.edu	37	22	39629506	39629506	+	Silent	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39629506G>A	uc003axf.2	-	3	1173	c.184C>T	c.(184-186)CTG>TTG	p.L62L	PDGFB_uc003axe.2_Silent_p.L47L	NM_002608	NP_002599	P01127	PDGFB_HUMAN	platelet-derived growth factor beta isoform 1	62					activation of protein kinase B activity|cellular response to mycophenolic acid|embryonic placenta development|heart development|hemopoiesis|metanephric glomerular mesangial cell development|monocyte chemotaxis|negative regulation of phosphatidylinositol biosynthetic process|negative regulation of platelet activation|negative regulation of transcription, DNA-dependent|paracrine signaling|peptidyl-serine phosphorylation|peptidyl-tyrosine phosphorylation|platelet activation|platelet degranulation|positive regulation of blood vessel endothelial cell migration|positive regulation of calcium ion import|positive regulation of cell division|positive regulation of chemotaxis|positive regulation of cyclin-dependent protein kinase activity|positive regulation of DNA biosynthetic process|positive regulation of DNA replication|positive regulation of endothelial cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of fibroblast proliferation|positive regulation of glomerular filtration|positive regulation of glomerular mesangial cell proliferation|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 activity|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein autophosphorylation|positive regulation of protein tyrosine kinase activity|positive regulation of reactive oxygen species metabolic process|positive regulation of smooth muscle cell migration|positive regulation of smooth muscle cell proliferation|positive regulation of transcription, DNA-dependent|reactive oxygen species metabolic process|transforming growth factor beta receptor signaling pathway	basolateral plasma membrane|cell surface|endoplasmic reticulum lumen|extracellular region|Golgi membrane|platelet alpha granule lumen	collagen binding|eukaryotic cell surface binding|growth factor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein heterodimerization activity|protein homodimerization activity|superoxide-generating NADPH oxidase activator activity		COL1A1/PDGFB(372)	soft_tissue(372)|central_nervous_system(1)	373	Melanoma(58;0.04)				Becaplermin(DB00102)	GTCATGTTCAGGTCCAACTCG	0.627			T	COL1A1	DFSP								17	19	---	---	---	---	PASS
FAM116B	414918	broad.mit.edu	37	22	50750580	50750580	+	Silent	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50750580C>T	uc011aru.1	-	21	1818	c.1746G>A	c.(1744-1746)TTG>TTA	p.L582L	FAM116B_uc011arv.1_Silent_p.L582L	NM_001001794	NP_001001794	Q8NEG7	F116B_HUMAN	family with sequence similarity 116, member B	582											0		all_cancers(38;4.34e-09)|all_epithelial(38;3.03e-08)|all_lung(38;0.00141)|Breast(42;0.00387)|Lung NSC(38;0.0199)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		AGGGAGGGCACAAGACAGCCT	0.657													5	13	---	---	---	---	PASS
SHOX	6473	broad.mit.edu	37	X	591648	591648	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:591648G>C	uc004cph.1	+	2	707	c.16G>C	c.(16-18)GCT>CCT	p.A6P	SHOX_uc004cpi.2_Missense_Mutation_p.A6P	NM_000451	NP_000442	O15266	SHOX_HUMAN	short stature homeobox isoform SHOXa	6					skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				AGAGCTCACGGCTTTTGTATC	0.647													16	60	---	---	---	---	PASS
CRLF2	64109	broad.mit.edu	37	X	1314965	1314965	+	RNA	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1314965A>T	uc004cpm.1	-	6		c.878T>A						Q9HC73	CRLF2_HUMAN	Homo sapiens mRNA for IL-XR, complete cds.							extracellular region|integral to membrane|plasma membrane	receptor activity			haematopoietic_and_lymphoid_tissue(7)	7		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				AAATTAAAATAAATTTGGACA	0.488			Mis|T	P2RY8|IGH@	B-ALL|Downs associated ALL								13	32	---	---	---	---	PASS
MXRA5	25878	broad.mit.edu	37	X	3241309	3241309	+	Missense_Mutation	SNP	T	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3241309T>G	uc004crg.3	-	5	2574	c.2417A>C	c.(2416-2418)AAA>ACA	p.K806T		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	806						extracellular region				ovary(5)|lung(1)|central_nervous_system(1)|skin(1)	8		all_lung(23;0.00031)|Lung NSC(23;0.000946)				ACTTGTGGTTTTAATCAATGG	0.478													35	20	---	---	---	---	PASS
SCML2	10389	broad.mit.edu	37	X	18259479	18259479	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18259479C>A	uc004cyl.2	-	15	2152	c.1995G>T	c.(1993-1995)CTG>CTT	p.L665L	SCML2_uc004cyk.3_RNA|SCML2_uc010nfd.1_3'UTR|SCML2_uc011miz.1_3'UTR|SCML2_uc010nfc.2_3'UTR	NM_006089	NP_006080	Q9UQR0	SCML2_HUMAN	sex comb on midleg-like 2	665	SAM.				anatomical structure morphogenesis	PcG protein complex	DNA binding|sequence-specific DNA binding transcription factor activity				0	Hepatocellular(33;0.183)					TGAGTAGGAACAGAGCCTTCC	0.348													24	21	---	---	---	---	PASS
GPR64	10149	broad.mit.edu	37	X	19024151	19024151	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19024151C>G	uc004cyx.2	-	22	1972	c.1808G>C	c.(1807-1809)TGT>TCT	p.C603S	GPR64_uc004cyy.2_Missense_Mutation_p.C600S|GPR64_uc004cyz.2_Missense_Mutation_p.C589S|GPR64_uc004czb.2_Missense_Mutation_p.C603S|GPR64_uc004czc.2_Missense_Mutation_p.C587S|GPR64_uc004czd.2_Missense_Mutation_p.C579S|GPR64_uc004cze.2_Missense_Mutation_p.C573S|GPR64_uc004czf.2_Missense_Mutation_p.C565S|GPR64_uc004cza.2_Missense_Mutation_p.C581S|GPR64_uc004cyw.2_Missense_Mutation_p.C587S|GPR64_uc010nfj.2_Missense_Mutation_p.C484S	NM_001079858	NP_001073327	Q8IZP9	GPR64_HUMAN	G protein-coupled receptor 64 isoform 1	603	GPS.|Extracellular (Potential).				neuropeptide signaling pathway|spermatogenesis	cytoplasm|integral to plasma membrane	G-protein coupled receptor activity				0	Hepatocellular(33;0.183)					TAGATGGCTACAGGTACAGAT	0.502													10	21	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	X	26179751	26179751	+	IGR	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:26179751G>A								MAGEB18 (20899 upstream) : MAGEB6 (30806 downstream)																							GTGGTTTACCGGCAGGTGTGC	0.498													37	20	---	---	---	---	PASS
IL1RAPL1	11141	broad.mit.edu	37	X	29938136	29938136	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:29938136G>A	uc004dby.2	+	8	1490	c.982G>A	c.(982-984)GAC>AAC	p.D328N		NM_014271	NP_055086	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	328	Extracellular (Potential).|Ig-like C2-type 3.				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						GGAAGAAGGTGACTTGGGAAA	0.413													23	13	---	---	---	---	PASS
MAGEB2	4113	broad.mit.edu	37	X	30236723	30236723	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30236723T>A	uc004dbz.2	+	2	129	c.26T>A	c.(25-27)CTC>CAC	p.L9H		NM_002364	NP_002355	O15479	MAGB2_HUMAN	melanoma antigen family B, 2	9							protein binding			ovary(1)	1						AAGAGTAAGCTCCGTGCCCGT	0.537													14	5	---	---	---	---	PASS
CXorf59	286464	broad.mit.edu	37	X	36117869	36117869	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:36117869C>G	uc004ddk.1	+	7	911	c.725C>G	c.(724-726)TCT>TGT	p.S242C		NM_173695	NP_775966	Q8N9S7	CX059_HUMAN	hypothetical protein LOC286464	242						integral to membrane				central_nervous_system(1)	1						TTCTTAAAGTCTTCCACTAAT	0.303													22	12	---	---	---	---	PASS
CASK	8573	broad.mit.edu	37	X	41437649	41437649	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41437649C>T	uc004dfl.3	-	15	1493	c.1447G>A	c.(1447-1449)GAG>AAG	p.E483K	CASK_uc004dfj.3_Missense_Mutation_p.E46K|CASK_uc004dfk.3_Missense_Mutation_p.E298K|CASK_uc004dfm.3_Missense_Mutation_p.E483K|CASK_uc004dfn.3_Missense_Mutation_p.E477K	NM_003688	NP_003679	O14936	CSKP_HUMAN	calcium/calmodulin-dependent serine protein	483					cell adhesion	actin cytoskeleton|cytoplasm|nucleus|plasma membrane	ATP binding|calmodulin binding|guanylate kinase activity|protein serine/threonine kinase activity			ovary(3)|lung(2)|stomach(1)	6						GTCACATTCTCCATATCCATG	0.438													12	8	---	---	---	---	PASS
ZNF41	7592	broad.mit.edu	37	X	47307673	47307673	+	Missense_Mutation	SNP	T	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47307673T>G	uc004dhs.3	-	4	1689	c.1622A>C	c.(1621-1623)GAA>GCA	p.E541A	ZNF41_uc004dhu.3_Missense_Mutation_p.E533A|ZNF41_uc004dht.3_Missense_Mutation_p.E413A|ZNF41_uc004dhv.3_Missense_Mutation_p.E509A|ZNF41_uc004dhw.3_Missense_Mutation_p.E501A|ZNF41_uc004dhy.3_Missense_Mutation_p.E499A|ZNF41_uc004dhx.3_Missense_Mutation_p.E499A|ZNF41_uc011mlm.1_Missense_Mutation_p.E413A	NM_153380	NP_700359	P51814	ZNF41_HUMAN	zinc finger protein 41	541	C2H2-type 9.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3		all_lung(315;0.000129)				CTTTCCACATTCTGTACATAT	0.428													29	8	---	---	---	---	PASS
HUWE1	10075	broad.mit.edu	37	X	53661239	53661239	+	Silent	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53661239T>A	uc004dsp.2	-	8	918	c.516A>T	c.(514-516)GGA>GGT	p.G172G		NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1	172					base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17						CATTCTCCTTTCCACCCCAGC	0.299													12	15	---	---	---	---	PASS
HUWE1	10075	broad.mit.edu	37	X	53661240	53661240	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53661240C>A	uc004dsp.2	-	8	917	c.515G>T	c.(514-516)GGA>GTA	p.G172V		NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1	172					base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17						ATTCTCCTTTCCACCCCAGCT	0.294													11	15	---	---	---	---	PASS
ITIH5L	347365	broad.mit.edu	37	X	54823400	54823400	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54823400G>C	uc004dtj.2	-	2	262	c.232C>G	c.(232-234)CTT>GTT	p.L78V		NM_198510	NP_940912	Q6UXX5	ITH5L_HUMAN	inter-alpha (globulin) inhibitor H5-like	78	VIT.				hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			lung(2)|skin(2)|ovary(1)|breast(1)	6						ATAAAGGCAAGATGAGGCAGA	0.438													32	26	---	---	---	---	PASS
ZC4H2	55906	broad.mit.edu	37	X	64141826	64141826	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64141826C>A	uc004dvu.2	-	2	184	c.96G>T	c.(94-96)AAG>AAT	p.K32N	ZC4H2_uc004dvv.2_Missense_Mutation_p.K9N|ZC4H2_uc011mov.1_Missense_Mutation_p.K9N|ZC4H2_uc011mow.1_Missense_Mutation_p.K32N|ZC4H2_uc004dvw.1_Missense_Mutation_p.K32N	NM_018684	NP_061154	Q9NQZ6	ZC4H2_HUMAN	zinc finger, C4H2 domain containing	32	Potential.						metal ion binding|protein binding			ovary(1)	1						CAAACTCAGCCTTCAAACGAG	0.483													14	9	---	---	---	---	PASS
EFNB1	1947	broad.mit.edu	37	X	68059886	68059886	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:68059886G>T	uc004dxd.3	+	4	1363	c.583G>T	c.(583-585)GCC>TCC	p.A195S	EFNB1_uc004dxe.2_Missense_Mutation_p.A195S	NM_004429	NP_004420	P98172	EFNB1_HUMAN	ephrin-B1 precursor	195	Extracellular (Potential).				cell adhesion|cell-cell signaling	integral to plasma membrane|soluble fraction|synapse	ephrin receptor binding				0						GGCCACACAGGCCCCTGGTAG	0.557													6	6	---	---	---	---	PASS
OTUD6A	139562	broad.mit.edu	37	X	69282924	69282924	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69282924G>T	uc004dxu.1	+	1	584	c.550G>T	c.(550-552)GAG>TAG	p.E184*		NM_207320	NP_997203	Q7L8S5	OTU6A_HUMAN	OTU domain containing 6A	184	OTU.									lung(1)|skin(1)	2						GCACGTCGACGAGTTCCTGCC	0.602													16	5	---	---	---	---	PASS
DGAT2L6	347516	broad.mit.edu	37	X	69424174	69424174	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69424174T>A	uc004dxx.1	+	6	764	c.667T>A	c.(667-669)TAT>AAT	p.Y223N		NM_198512	NP_940914	Q6ZPD8	DG2L6_HUMAN	diacylglycerol O-acyltransferase 2-like 6	223					lipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	acyltransferase activity			ovary(1)	1						TGTCCCTTCATATTCCTTTGG	0.478													8	2	---	---	---	---	PASS
FOXO4	4303	broad.mit.edu	37	X	70321014	70321014	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70321014C>G	uc004dys.1	+	2	1287	c.934C>G	c.(934-936)CTC>GTC	p.L312V	FOXO4_uc010nkz.2_Intron|FOXO4_uc004dyt.1_Missense_Mutation_p.L257V	NM_005938	NP_005929	P98177	FOXO4_HUMAN	forkhead box O4	312					cell cycle arrest|cell differentiation|embryo development|G1 phase of mitotic cell cycle|insulin receptor signaling pathway|mitotic cell cycle G2/M transition DNA damage checkpoint|muscle organ development|negative regulation of angiogenesis|negative regulation of cell proliferation|negative regulation of smooth muscle cell differentiation|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase 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			central_nervous_system(2)|prostate(1)	3	Renal(35;0.156)					TGGGCTCAATCTCACCTCTTC	0.557											OREG0019856	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	12	7	---	---	---	---	PASS
TSIX	9383	broad.mit.edu	37	X	73047462	73047462	+	RNA	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73047462G>A	uc004ebn.2	+	1		c.35423G>A			XIST_uc004ebm.1_RNA	NR_003255				Homo sapiens XIST antisense RNA (non-protein coding) (TSIX), non-coding RNA.												0						GAACGAGAAGGGGAAGGGGTA	0.393													13	16	---	---	---	---	PASS
XIST	7503	broad.mit.edu	37	X	73053215	73053215	+	Intron	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73053215G>T	uc004ebm.1	-							NR_001564				Homo sapiens cDNA: FLJ21545 fis, clone COL06195.												0						ATGTCCTTAAGAAGAAAGACA	0.418													33	17	---	---	---	---	PASS
ATRX	546	broad.mit.edu	37	X	76938926	76938926	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76938926C>A	uc004ecp.3	-	9	2054	c.1822G>T	c.(1822-1824)GTT>TTT	p.V608F	ATRX_uc004ecq.3_Missense_Mutation_p.V570F|ATRX_uc004eco.3_Missense_Mutation_p.V393F|ATRX_uc004ecr.2_Missense_Mutation_p.V540F|ATRX_uc010nlx.1_Missense_Mutation_p.V579F|ATRX_uc010nly.1_Missense_Mutation_p.V553F	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	608					DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	TCTTGTGGAACTTCCTGACAA	0.358			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						71	75	---	---	---	---	PASS
ITM2A	9452	broad.mit.edu	37	X	78616676	78616676	+	Intron	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:78616676T>A	uc004edh.2	-						ITM2A_uc011mqr.1_Intron	NM_004867	NP_004858	O43736	ITM2A_HUMAN	integral membrane protein 2A							integral to membrane	protein binding			lung(2)	2						TGTTGAAACCTGTAAGGAAAT	0.373													6	8	---	---	---	---	PASS
KLHL4	56062	broad.mit.edu	37	X	86924368	86924368	+	3'UTR	SNP	A	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86924368A>T	uc004efb.2	+	11					KLHL4_uc004efa.2_Nonsense_Mutation_p.K713*	NM_019117	NP_061990	Q9C0H6	KLHL4_HUMAN	kelch-like 4 isoform 1							cytoplasm|microtubule cytoskeleton|nucleolus	actin binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5						TACCACACAGAAGCTGAAAGA	0.428													18	10	---	---	---	---	PASS
IL1RAPL2	26280	broad.mit.edu	37	X	104440226	104440226	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:104440226T>A	uc004elz.1	+	3	908	c.152T>A	c.(151-153)GTG>GAG	p.V51E		NM_017416	NP_059112	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	51	Ig-like C2-type 1.|Extracellular (Potential).				central nervous system development|innate immune response	integral to membrane	interleukin-1, Type II, blocking receptor activity			breast(2)|ovary(1)	3						CCAGTCCGAGTGAAATGTGCC	0.448													31	17	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	X	106840841	106840841	+	IGR	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106840841G>C								CXorf41 (353369 upstream) : PRPS1 (30813 downstream)																							GGTAGTCCCTGATGACTTTGA	0.532													59	30	---	---	---	---	PASS
GUCY2F	2986	broad.mit.edu	37	X	108636213	108636213	+	Silent	SNP	A	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108636213A>G	uc004eod.3	-	13	2772	c.2496T>C	c.(2494-2496)TCT>TCC	p.S832S	GUCY2F_uc011msq.1_RNA	NM_001522	NP_001513	P51841	GUC2F_HUMAN	guanylate cyclase 2F precursor	832	Cytoplasmic (Potential).				intracellular signal transduction|receptor guanylyl cyclase signaling pathway|visual perception	integral to plasma membrane|nuclear outer membrane	ATP binding|GTP binding|guanylate cyclase activity|protein kinase activity|receptor activity			lung(4)|breast(3)|central_nervous_system(1)	8						CCAAGTTGCTAGAATATTGCT	0.373													84	35	---	---	---	---	PASS
GPC3	2719	broad.mit.edu	37	X	132887889	132887889	+	Nonsense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132887889G>A	uc004exe.1	-	3	842	c.652C>T	c.(652-654)CAG>TAG	p.Q218*	GPC3_uc004exd.1_Nonsense_Mutation_p.Q90*|GPC3_uc010nrn.1_Nonsense_Mutation_p.Q218*|GPC3_uc011mvh.1_Nonsense_Mutation_p.Q202*|GPC3_uc010nro.1_Nonsense_Mutation_p.Q164*|GPC3_uc010nrp.1_Nonsense_Mutation_p.Q90*	NM_004484	NP_004475	P51654	GPC3_HUMAN	glypican 3 isoform 2 precursor	218						extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding|peptidyl-dipeptidase inhibitor activity			lung(2)|prostate(1)|breast(1)|skin(1)	5	Acute lymphoblastic leukemia(192;0.000127)					TTGGAAACCTGGGTCATAATA	0.473			T|D|Mis|N|F|S			Wilms tumour			Simpson-Golabi-Behmel_syndrome				61	24	---	---	---	---	PASS
MAGEC3	139081	broad.mit.edu	37	X	140983082	140983082	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140983082G>T	uc011mwp.1	+	5	937	c.937G>T	c.(937-939)GAT>TAT	p.D313Y	MAGEC3_uc004fbs.2_5'UTR|MAGEC3_uc010nsj.2_5'Flank	NM_138702	NP_619647	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3 isoform 1	313	MAGE 1.									skin(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)					AGGGTTCGCGGATGTGCTTTC	0.527													52	20	---	---	---	---	PASS
MAGEC1	9947	broad.mit.edu	37	X	140995433	140995433	+	Missense_Mutation	SNP	C	T	T	rs149394425		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140995433C>T	uc004fbt.2	+	4	2529	c.2243C>T	c.(2242-2244)TCC>TTC	p.S748F	MAGEC1_uc010nsl.1_Intron	NM_005462	NP_005453	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	748							protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)					AGTATCTGCTCCTCCTCCACT	0.572										HNSCC(15;0.026)			30	119	---	---	---	---	PASS
SPANXN2	494119	broad.mit.edu	37	X	142795489	142795489	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142795489T>C	uc004fbz.2	-	2	943	c.189A>G	c.(187-189)ATA>ATG	p.I63M		NM_001009615	NP_001009615	Q5MJ10	SPXN2_HUMAN	SPANX-N2 protein	63										ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)					GATTTGAATTTATTTTCGTAT	0.438													65	34	---	---	---	---	PASS
MIR514-1	574516	broad.mit.edu	37	X	146360837	146360837	+	RNA	SNP	G	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:146360837G>C	hsa-mir-514-1|MI0003198	-			c.26G>C																				0						TCACTCTCCAGAGTAGGGTAC	0.433													13	7	---	---	---	---	PASS
GPR50	9248	broad.mit.edu	37	X	150349889	150349889	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150349889C>T	uc010ntg.1	+	2	1969	c.1834C>T	c.(1834-1836)CCT>TCT	p.P612S		NM_004224	NP_004215	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	612	Cytoplasmic (Potential).|Pro-rich.				cell-cell signaling	integral to plasma membrane	melatonin receptor activity			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)					TGAAGATGATCCTGATGAAAT	0.458													62	40	---	---	---	---	PASS
PASD1	139135	broad.mit.edu	37	X	150842410	150842410	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150842410G>A	uc004fev.3	+	15	2259	c.1927G>A	c.(1927-1929)GAG>AAG	p.E643K		NM_173493	NP_775764	Q8IV76	PASD1_HUMAN	PAS domain containing 1	643						nucleus	signal transducer activity			ovary(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)					TTTTTATCCTGAGGCGTATCA	0.468													36	12	---	---	---	---	PASS
CNGA2	1260	broad.mit.edu	37	X	150908073	150908073	+	Missense_Mutation	SNP	C	A	A	rs144004735	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150908073C>A	uc004fey.1	+	4	467	c.243C>A	c.(241-243)AAC>AAA	p.N81K		NM_005140	NP_005131	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	81	Cytoplasmic (Potential).				response to stimulus|sensory perception of smell	intracellular cyclic nucleotide activated cation channel complex	cAMP binding|intracellular cAMP activated cation channel activity			breast(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)					AATGGGCCAACAAGAATTTCC	0.517													26	4	---	---	---	---	PASS
PNMA3	29944	broad.mit.edu	37	X	152225749	152225749	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152225749G>T	uc004fhc.2	+	2	673	c.337G>T	c.(337-339)GAG>TAG	p.E113*	PNMA5_uc004fha.3_5'Flank|PNMA3_uc004fhd.2_5'Flank	NM_013364	NP_037496	Q9UL41	PNMA3_HUMAN	paraneoplastic cancer-testis-brain antigen	113					apoptosis	nucleolus	nucleic acid binding|zinc ion binding			skin(2)|large_intestine(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)					cttagaggaggagaggcggac	0.000													35	17	---	---	---	---	PASS
FLNA	2316	broad.mit.edu	37	X	153581667	153581667	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153581667C>T	uc004fkk.2	-	37	6268	c.6019G>A	c.(6019-6021)GTG>ATG	p.V2007M	FLNA_uc004fki.2_Missense_Mutation_p.V50M|FLNA_uc011mzn.1_Missense_Mutation_p.V140M|FLNA_uc010nuu.1_Missense_Mutation_p.V1999M	NM_001110556	NP_001104026	P21333	FLNA_HUMAN	filamin A, alpha isoform 2	2007	Filamin 18.				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)					CGCTTACCCACGTGGCCATTA	0.637													26	18	---	---	---	---	PASS
TSPY1	7258	broad.mit.edu	37	Y	9305960	9305960	+	Silent	SNP	C	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9305960C>A	uc004frw.3	+	3	662	c.616C>A	c.(616-618)CGG>AGG	p.R206R	TSPY1_uc004frx.3_Silent_p.R206R|TSPY1_uc010nwp.1_Intron	NM_003308	NP_003299	Q01534	TSPY1_HUMAN	testis specific protein, Y-linked 1	206					cell differentiation|cell proliferation|gonadal mesoderm development|nucleosome assembly|spermatogenesis	cytoplasm|nucleus	identical protein binding				0						GTTGTTCTTTCGGAGTAACCC	0.478													34	142	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	822811	822813	+	IGR	DEL	AGT	-	-	rs112027111		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:822811_822813delAGT								FAM41C (10629 upstream) : FLJ39609 (30140 downstream)																							ctaccagtgaagttgtggagttt	0.153													4	2	---	---	---	---	
TMEM88B	643965	broad.mit.edu	37	1	1360108	1360108	+	5'Flank	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1360108delA	uc010nyp.1	+							NM_001146685	NP_001140157	A6NKF7	TM88B_HUMAN	transmembrane protein 88B							integral to membrane					0						cctcctcgacaaaaaaaaaag	0.174													3	3	---	---	---	---	
SLC35E2B	728661	broad.mit.edu	37	1	1661356	1661356	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1661356delA	uc001ahh.3	-						SLC35E2_uc009vkm.1_Intron|uc001ahx.1_Intron|SLC35E2_uc001ahy.2_Intron|SLC35E2_uc001ahz.2_Intron|uc001aia.1_RNA	NM_001110781	NP_001104251	P0CK96	S352B_HUMAN	similar to solute carrier family 35, member E2							integral to membrane					0						cctgggcaacaaagcgagagc	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	3835708	3835708	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3835708delC								LOC100133612 (1831 upstream) : LOC284661 (636403 downstream)																							GAGGGCTGTTCCGAGCGGCGC	0.582													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	4408070	4408070	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4408070delC								LOC100133612 (574193 upstream) : LOC284661 (64041 downstream)																							gtgtttgtgtccccagtgctg	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	5765912	5765912	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5765912delC								AJAP1 (922062 upstream) : NPHP4 (156958 downstream)																							cttcctcataccctccccctc	0.209													4	2	---	---	---	---	
CHD5	26038	broad.mit.edu	37	1	6174312	6174313	+	Intron	INS	-	A	A	rs34379729		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6174312_6174313insA	uc001amb.1	-						CHD5_uc001alz.1_Intron|CHD5_uc001ama.1_Intron	NM_015557	NP_056372	Q8TDI0	CHD5_HUMAN	chromodomain helicase DNA binding protein 5						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding|zinc ion binding			central_nervous_system(3)|breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1)	12	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		gactccgtctcaaaaaaaaaaa	0.228													5	3	---	---	---	---	
ACOT7	11332	broad.mit.edu	37	1	6425084	6425084	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6425084delA	uc001ams.2	-						ACOT7_uc010nzq.1_Intron|ACOT7_uc001amt.2_Intron|ACOT7_uc001amu.2_Intron|ACOT7_uc001amv.2_Intron	NM_181864	NP_863654	O00154	BACH_HUMAN	acyl-CoA thioesterase 7 isoform hBACHb							mitochondrion|nucleus	carboxylesterase activity|fatty-acyl-CoA binding|palmitoyl-CoA hydrolase activity				0	Ovarian(185;0.0634)|all_lung(157;0.175)	all_cancers(23;1.42e-38)|all_epithelial(116;3.96e-23)|all_lung(118;3.69e-08)|Lung NSC(185;8.52e-07)|all_hematologic(16;6.92e-06)|Colorectal(325;4.53e-05)|Acute lymphoblastic leukemia(12;5e-05)|all_neural(13;0.000164)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;9.16e-37)|GBM - Glioblastoma multiforme(13;5.89e-29)|OV - Ovarian serous cystadenocarcinoma(86;7.63e-19)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;2.06e-05)|Kidney(185;7.74e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00129)|BRCA - Breast invasive adenocarcinoma(365;0.00132)|STAD - Stomach adenocarcinoma(132;0.00195)|READ - Rectum adenocarcinoma(331;0.0481)		actccgtctcaaaaaaaaaaa	0.000													5	3	---	---	---	---	
CAMTA1	23261	broad.mit.edu	37	1	7540168	7540169	+	Intron	INS	-	GT	GT	rs151025042	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7540168_7540169insGT	uc001aoi.2	+							NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		tgtgtgagagcgtgtgtgtgtg	0.000													3	3	---	---	---	---	
ENO1	2023	broad.mit.edu	37	1	8936741	8936741	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8936741delG	uc001apj.1	-						ENO1_uc001apk.1_Intron|ENO1_uc001apl.1_Intron|ENO1_uc009vmi.1_Intron|ENO1_uc009vmj.1_Intron|ENO1_uc009vmk.1_Intron|ENO1_uc009vml.1_Intron|ENO1_uc009vmm.1_Intron	NM_001428	NP_001419	P06733	ENOA_HUMAN	enolase 1						gluconeogenesis|glycolysis|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|response to virus	phosphopyruvate hydratase complex|plasma membrane|sarcomere	DNA binding|magnesium ion binding|phosphopyruvate hydratase activity|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)|kidney(1)|central_nervous_system(1)	4	Ovarian(185;0.0661)|all_lung(157;0.127)	all_epithelial(116;2.54e-20)|all_lung(118;2.99e-06)|Lung NSC(185;6.25e-06)|Renal(390;0.000147)|Breast(348;0.00086)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;2.42e-07)|COAD - Colon adenocarcinoma(227;2.78e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00177)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|READ - Rectum adenocarcinoma(331;0.0642)		tggatcacgaggtcaggagag	0.050													4	2	---	---	---	---	
MAD2L2	10459	broad.mit.edu	37	1	11748618	11748618	+	Intron	DEL	A	-	-	rs35208427		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11748618delA	uc009vnc.2	-						MAD2L2_uc001asq.3_Intron	NM_001127325	NP_001120797	Q9UI95	MD2L2_HUMAN	MAD2 homolog						cell division|DNA damage response, signal transduction resulting in transcription|double-strand break repair|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of mitotic anaphase-promoting complex activity|positive regulation of peptidyl-serine phosphorylation|positive regulation of transcription, DNA-dependent|regulation of cell growth|transcription, DNA-dependent	cytoplasm|nucleoplasm|spindle|zeta DNA polymerase complex	JUN kinase binding				0	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.04e-06)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|Kidney(185;0.000733)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		actgcatctcaaaaaaaaaaa	0.000								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					2	4	---	---	---	---	
PRAMEF2	65122	broad.mit.edu	37	1	12920367	12920367	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12920367delG	uc001aum.1	+							NM_023014	NP_075390	O60811	PRAM2_HUMAN	PRAME family member 2												0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TCATGTACAAGCTAGTCAGTG	0.473													6	11	---	---	---	---	
KAZ	23254	broad.mit.edu	37	1	15129677	15129678	+	Intron	INS	-	C	C	rs148910385	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15129677_15129678insC	uc001avm.3	+						KAZ_uc009vog.1_Intron|KAZ_uc010obj.1_Intron	NM_201628	NP_963922	Q674X7	KAZRN_HUMAN	kazrin isoform E						keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0						ctgcgcagtgtctgctgaggaa	0.040													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	16442245	16442246	+	IGR	INS	-	C	C	rs147756990	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16442245_16442246insC								FAM131C (42118 upstream) : EPHA2 (8586 downstream)																							CCGCTGGGAGGCCCCCCAGGGC	0.644													4	2	---	---	---	---	
EPHA2	1969	broad.mit.edu	37	1	16458076	16458077	+	Intron	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16458076_16458077insA	uc001aya.1	-							NM_004431	NP_004422	P29317	EPHA2_HUMAN	ephrin receptor EphA2 precursor						activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus	focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane	ATP binding|ephrin receptor activity|protein binding			lung(3)|central_nervous_system(3)|stomach(2)|ovary(2)	10		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)	actccgtctccaaaaaaaaaaa	0.198													4	2	---	---	---	---	
CROCC	9696	broad.mit.edu	37	1	17091323	17091323	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17091323delC	uc009voy.1	+						MST1P9_uc010ock.1_5'Flank			Q5TZA2	CROCC_HUMAN	Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		TATACGTGAACTGTAAGGCCT	0.453													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	18290368	18290368	+	IGR	DEL	G	-	-	rs5772782		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18290368delG								ACTL8 (136812 upstream) : IGSF21 (143872 downstream)																							CCTTGCACACGTGCACACACA	0.537													2	6	---	---	---	---	
TMCO4	255104	broad.mit.edu	37	1	20023251	20023251	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20023251delT	uc001bcn.2	-						TMCO4_uc001bcm.2_Intron|TMCO4_uc001bco.1_Intron|TMCO4_uc001bcp.1_Intron	NM_181719	NP_859070	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4							integral to membrane					0		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)		TCCAAAATTATTTCTGTTGTA	0.358													4	2	---	---	---	---	
HP1BP3	50809	broad.mit.edu	37	1	21106205	21106205	+	Intron	DEL	A	-	-	rs34670421		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21106205delA	uc001bdw.1	-						HP1BP3_uc001bdv.1_Intron|HP1BP3_uc010odh.1_Intron|HP1BP3_uc001bdy.1_Intron|HP1BP3_uc001bdz.2_Intron|HP1BP3_uc001bea.2_Intron|HP1BP3_uc001beb.2_Intron	NM_016287	NP_057371	Q5SSJ5	HP1B3_HUMAN	HP1-BP74						nucleosome assembly	nucleosome|nucleus	DNA binding			central_nervous_system(1)|skin(1)	2		all_lung(284;6.55e-06)|Lung NSC(340;6.59e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.26e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00015)|GBM - Glioblastoma multiforme(114;0.000521)|Kidney(64;0.000529)|STAD - Stomach adenocarcinoma(196;0.00311)|KIRC - Kidney renal clear cell carcinoma(64;0.00687)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.201)		CTTAGCCATGAAAAAAAAAAA	0.338													3	3	---	---	---	---	
EPHA8	2046	broad.mit.edu	37	1	22905190	22905191	+	Intron	INS	-	TG	TG	rs146554873	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22905190_22905191insTG	uc001bfx.1	+						EPHA8_uc001bfw.2_Intron	NM_020526	NP_065387	P29322	EPHA8_HUMAN	ephrin receptor EphA8 isoform 1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity			central_nervous_system(5)|breast(3)|lung(2)|large_intestine(1)|stomach(1)|skin(1)	13		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		gtatgtgtgcctgtgtgtgtat	0.000													2	4	---	---	---	---	
MAN1C1	57134	broad.mit.edu	37	1	25977176	25977176	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25977176delT	uc001bkm.2	+						MAN1C1_uc009vry.1_Intron	NM_020379	NP_065112	Q9NR34	MA1C1_HUMAN	mannosidase, alpha, class 1C, member 1						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(1)	1		Colorectal(325;3.78e-05)|Lung NSC(340;0.000181)|all_lung(284;0.000245)|Renal(390;0.000714)|Ovarian(437;0.00159)|Breast(348;0.0156)|Myeloproliferative disorder(586;0.0257)|all_neural(195;0.0515)|Esophageal squamous(538;0.232)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0574)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.15e-07)|COAD - Colon adenocarcinoma(152;4.31e-06)|STAD - Stomach adenocarcinoma(196;0.00125)|BRCA - Breast invasive adenocarcinoma(304;0.00141)|KIRC - Kidney renal clear cell carcinoma(1967;0.00146)|GBM - Glioblastoma multiforme(114;0.0149)|READ - Rectum adenocarcinoma(331;0.0803)		GTTCTCATTCTTTCTTTCTGC	0.408													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	32888256	32888257	+	IGR	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32888256_32888257insA								BSDC1 (28194 upstream) : ZBTB8A (42401 downstream)																							ctccatctcagaaaaaaaaaaa	0.139													4	2	---	---	---	---	
CSMD2	114784	broad.mit.edu	37	1	34330530	34330531	+	Intron	INS	-	G	G	rs147096786	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34330530_34330531insG	uc001bxn.1	-						CSMD2_uc001bxm.1_Intron	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2							integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				aggggaagggaggagaggaggg	0.203													4	2	---	---	---	---	
CSMD2	114784	broad.mit.edu	37	1	34435976	34435977	+	Intron	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34435976_34435977insA	uc001bxn.1	-						CSMD2_uc001bxm.1_Intron	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2							integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				CCTGTGTCCGCAATCGCTAATC	0.545													4	2	---	---	---	---	
MEAF6	64769	broad.mit.edu	37	1	37961483	37961484	+	Splice_Site	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37961483_37961484insA	uc001cbg.1	-	6	584	c.567_splice	c.e6+1	p.A189_splice	MEAF6_uc001cbd.1_Splice_Site_p.A167_splice|MEAF6_uc001cbe.1_Splice_Site_p.A199_splice|MEAF6_uc009vvd.1_Splice_Site|MEAF6_uc001cbf.1_Splice_Site	NM_022756	NP_073593	Q9HAF1	EAF6_HUMAN	MYST/Esa1-associated factor 6						histone H2A acetylation|histone H3-K14 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|NuA4 histone acetyltransferase complex|nucleolus	protein binding				0						GGCTGATACTTACAGCTCGTGG	0.371													47	21	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	48220796	48220796	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48220796delG								FOXD2 (314434 upstream) : SKINTL (346591 downstream)																							ACTGCTGGGAGGGGAAGGGAG	0.308													4	2	---	---	---	---	
FAF1	11124	broad.mit.edu	37	1	51187186	51187187	+	Intron	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51187186_51187187insA	uc009vyx.1	-						FAF1_uc009vyw.1_Intron|FAF1_uc001cse.1_Intron	NM_007051	NP_008982	Q9UNN5	FAF1_HUMAN	FAS-associated factor 1						apoptosis|cytoplasmic sequestering of NF-kappaB|positive regulation of apoptosis|positive regulation of protein complex assembly|proteasomal ubiquitin-dependent protein catabolic process|regulation of protein catabolic process	CD95 death-inducing signaling complex|cytosol|perinuclear region of cytoplasm	heat shock protein binding|NF-kappaB binding|protein kinase binding|protein kinase regulator activity	p.0?(1)		ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		tgcccggccGGAAAAAAAAATT	0.124													4	2	---	---	---	---	
C8A	731	broad.mit.edu	37	1	57331582	57331582	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57331582delA	uc001cyo.2	+							NM_000562	NP_000553	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide						complement activation, alternative pathway|complement activation, classical pathway|cytolysis	extracellular space|membrane attack complex				ovary(1)|central_nervous_system(1)|skin(1)	3						tccaaatttcaaatgcctgat	0.000													4	2	---	---	---	---	
DAB1	1600	broad.mit.edu	37	1	58637608	58637608	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58637608delG	uc001cys.1	-						DAB1_uc001cyt.1_Intron	NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3						aaagggaccagggccctcagc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	61090897	61090898	+	IGR	INS	-	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61090897_61090898insG								C1orf87 (551471 upstream) : NFIA (452048 downstream)																							CAGAAAGGGTTGGGGGGGGAAT	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	62020512	62020512	+	IGR	DEL	T	-	-	rs66941209		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62020512delT								NFIA (92053 upstream) : TM2D1 (126207 downstream)																							AGATGGAATATTTTGTTATTG	0.214													4	2	---	---	---	---	
ROR1	4919	broad.mit.edu	37	1	64254378	64254378	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64254378delG	uc001dbj.2	+						ROR1_uc001dbi.3_Intron	NM_005012	NP_005003	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1						transmembrane receptor protein tyrosine kinase signaling pathway	cytoplasm|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			ovary(6)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|central_nervous_system(1)|skin(1)|kidney(1)	19						CAGACAAAGTGGAAGTTTTTA	0.333													7	4	---	---	---	---	
JAK1	3716	broad.mit.edu	37	1	65305083	65305084	+	Intron	INS	-	G	G	rs66907517		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65305083_65305084insG	uc001dbu.1	-						JAK1_uc009wam.1_Intron|JAK1_uc009wal.1_Intron	NM_002227	NP_002218	P23458	JAK1_HUMAN	janus kinase 1						interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|endomembrane system|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1)	61				BRCA - Breast invasive adenocarcinoma(111;0.0485)		CCCTGGATGGAGGGGCCTGGGT	0.545			Mis		ALL								7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	69692806	69692806	+	IGR	DEL	T	-	-	rs66480921		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69692806delT								DEPDC1 (730007 upstream) : LRRC7 (340062 downstream)																							TTCTTACACATTTTTTTTTTT	0.259													4	4	---	---	---	---	
SLC44A5	204962	broad.mit.edu	37	1	76084765	76084766	+	Intron	INS	-	GC	GC	rs34647299		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76084765_76084766insGC	uc010oqz.1	-						SLC44A5_uc010orb.1_Intron	NM_001130058	NP_001123530	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5 isoform B							integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4						caaaaaaaaaggggggggggaa	0.000													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	78026056	78026056	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78026056delA								AK5 (404 upstream) : ZZZ3 (4135 downstream)																							AGCAAACTGGAAAAAAAAAAG	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	78877026	78877026	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78877026delT								MGC27382 (41881 upstream) : PTGFR (79702 downstream)																							agagcacccctgcaaaattct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	78886480	78886483	+	IGR	DEL	CTTC	-	-	rs144770913		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78886480_78886483delCTTC								MGC27382 (51335 upstream) : PTGFR (70245 downstream)																							tccctgttttcttccttccttcct	0.025													4	2	---	---	---	---	
GBP1	2633	broad.mit.edu	37	1	89518866	89518866	+	3'UTR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89518866delT	uc001dmx.2	-	11						NM_002053	NP_002044	P32455	GBP1_HUMAN	guanylate binding protein 1,						interferon-gamma-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)|skin(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)		ATTTACAGTCTTTTTTTTTTT	0.318													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	91597299	91597300	+	IGR	INS	-	A	A	rs147161616	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91597299_91597300insA								ZNF644 (109628 upstream) : HFM1 (129024 downstream)																							ggcttatagataaactcccatc	0.000													7	4	---	---	---	---	
TGFBR3	7049	broad.mit.edu	37	1	92317946	92317947	+	Intron	DEL	TG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92317946_92317947delTG	uc001doh.2	-						TGFBR3_uc009wde.2_Intron|TGFBR3_uc010osy.1_Intron|TGFBR3_uc001doi.2_Intron|TGFBR3_uc001doj.2_Intron	NM_003243	NP_003234	Q03167	TGBR3_HUMAN	transforming growth factor, beta receptor III						BMP signaling pathway|cardiac epithelial to mesenchymal transition|cardiac muscle cell proliferation|cell growth|cell migration|definitive erythrocyte differentiation|heart trabecula formation|immune response|intracellular protein kinase cascade|liver development|negative regulation of cellular component movement|negative regulation of epithelial cell proliferation|palate development|pathway-restricted SMAD protein phosphorylation|response to follicle-stimulating hormone stimulus|response to luteinizing hormone stimulus|response to prostaglandin E stimulus|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis	external side of plasma membrane|extracellular space|inhibin-betaglycan-ActRII complex|integral to plasma membrane|intracellular membrane-bounded organelle	coreceptor activity|heparin binding|PDZ domain binding|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type III|type II transforming growth factor beta receptor binding			ovary(3)	3		all_lung(203;0.00719)|Lung NSC(277;0.0268)		all cancers(265;0.0108)|Epithelial(280;0.0825)		tgtgtgtgtatgtgtgtgtgtg	0.386													4	2	---	---	---	---	
BCAR3	8412	broad.mit.edu	37	1	94216168	94216171	+	Intron	DEL	CTGC	-	-	rs72422308		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94216168_94216171delCTGC	uc001dqb.2	-							NM_003567	NP_003558	O75815	BCAR3_HUMAN	breast cancer antiestrogen resistance 3						response to drug|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|lung(1)|central_nervous_system(1)	3		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)		gattctgcttctgcctgcctggtt	0.000													4	2	---	---	---	---	
TMEM56	148534	broad.mit.edu	37	1	95641755	95641756	+	Intron	DEL	TT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95641755_95641756delTT	uc001drb.2	+						RWDD3_uc001drd.3_Intron|uc001dre.1_Intron|TMEM56_uc001drc.2_Intron	NM_152487	NP_689700	Q96MV1	TMM56_HUMAN	transmembrane protein 56							integral to membrane					0		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.133)		aattttttcctttttttttttt	0.000													4	3	---	---	---	---	
DPYD	1806	broad.mit.edu	37	1	98081699	98081699	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98081699delT	uc001drv.2	-							NM_000110	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase isoform 1						'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)	taataaatgattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	102147826	102147829	+	IGR	DEL	GTGT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102147826_102147829delGTGT								S1PR1 (440750 upstream) : OLFM3 (120298 downstream)																							AGAAAGTGAGgtgtgtgtgtgtgt	0.152													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	102477865	102477865	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102477865delT								OLFM3 (15075 upstream) : COL11A1 (864159 downstream)																							gaactgtaccttttttttttt	0.000													4	2	---	---	---	---	
VAV3	10451	broad.mit.edu	37	1	108123042	108123043	+	Intron	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108123042_108123043insT	uc001dvk.1	-						VAV3_uc010ouu.1_Intron|VAV3_uc001dvj.1_Intron|VAV3_uc010ouv.1_Intron|VAV3_uc010ouw.1_Intron	NM_006113	NP_006104	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(5)|lung(2)|breast(2)	9		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		AATAACTATTATTTTTTTTTTC	0.371													4	2	---	---	---	---	
KIAA1324	57535	broad.mit.edu	37	1	109726258	109726259	+	Intron	INS	-	CTTCCTTT	CTTCCTTT	rs150843023	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109726258_109726259insCTTCCTTT	uc001dwq.2	+						KIAA1324_uc009wex.1_Intron|KIAA1324_uc009wey.2_Intron|KIAA1324_uc010ovg.1_Intron	NM_020775	NP_065826	Q6UXG2	K1324_HUMAN	hypothetical protein LOC57535 precursor						macroautophagy|positive regulation of vacuole organization|regulation of apoptosis	integral to plasma membrane				ovary(2)|haematopoietic_and_lymphoid_tissue(1)|breast(1)|skin(1)	5		all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063)		Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249)		ttccttccttcctAacagagtc	0.000													7	4	---	---	---	---	
SORT1	6272	broad.mit.edu	37	1	109888137	109888137	+	Intron	DEL	A	-	-	rs112644374		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109888137delA	uc001dxm.1	-						SORT1_uc010ovi.1_Intron	NM_002959	NP_002950	Q99523	SORT_HUMAN	sortilin 1 preproprotein						endocytosis|endosome to lysosome transport|endosome transport via multivesicular body sorting pathway|glucose import|Golgi to endosome transport|induction of apoptosis by extracellular signals|myotube differentiation|negative regulation of apoptosis|negative regulation of lipoprotein lipase activity|neuropeptide signaling pathway|ossification|plasma membrane to endosome transport|regulation of gene expression|response to insulin stimulus|vesicle organization	cell surface|coated pit|early endosome|endoplasmic reticulum membrane|endosome membrane|Golgi cisterna membrane|integral to membrane|lysosomal membrane|microsome|nuclear membrane|perinuclear region of cytoplasm|plasma membrane	enzyme binding|nerve growth factor binding|nerve growth factor receptor activity|neurotensin receptor activity, non-G-protein coupled			ovary(1)	1		all_epithelial(167;4.69e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0529)|Colorectal(144;0.142)|Epithelial(280;0.145)|Kidney(133;0.169)|all cancers(265;0.184)		actttgtttcaaaaaaaaaaa	0.174													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	111797388	111797388	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111797388delC								CHI3L2 (11328 upstream) : LOC149620 (25758 downstream)																							AGGTGTTCTTCCCCACTCCAA	0.527													2	4	---	---	---	---	
KCND3	3752	broad.mit.edu	37	1	112434602	112434603	+	Intron	INS	-	TG	TG	rs149384084	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112434602_112434603insTG	uc001ebu.1	-						KCND3_uc001ebv.1_Intron	NM_004980	NP_004971	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related							sarcolemma|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|metal ion binding			ovary(2)|large_intestine(1)	3		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)		gtgtgtgtgtctgtgtgtgtgt	0.000													3	4	---	---	---	---	
PTGFRN	5738	broad.mit.edu	37	1	117450917	117450918	+	5'Flank	INS	-	A	A	rs112240054		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117450917_117450918insA	uc001egv.1	+							NM_020440	NP_065173	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor negative regulator							endoplasmic reticulum membrane|Golgi apparatus|integral to membrane	protein binding			liver(1)	1	Lung SC(450;0.225)	all_cancers(81;0.00104)|all_lung(203;8.97e-05)|all_epithelial(167;0.000139)|Lung NSC(69;0.000446)		Lung(183;0.0704)|LUSC - Lung squamous cell carcinoma(189;0.227)|Colorectal(144;0.248)		tagcctcaaATaaaaaaaaaaa	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	118301104	118301105	+	IGR	INS	-	A	A	rs112807899		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118301104_118301105insA								FAM46C (130094 upstream) : GDAP2 (105003 downstream)																							ACTGAGTTACCAAAAAAAAAAG	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	120016646	120016646	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120016646delA								HSD3B2 (27526 upstream) : HSD3B1 (33180 downstream)																							GAGGACACACAAGGTGATTTG	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	120201820	120201820	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120201820delA								ZNF697 (11430 upstream) : PHGDH (52599 downstream)																							AAGCCTGTGTAACTACACCAA	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	120652312	120652313	+	IGR	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120652312_120652313insA								NOTCH2 (40036 upstream) : FAM72B (186692 downstream)																							aaactccatctaaaaaaaaaaa	0.203													2	4	---	---	---	---	
LOC647121	647121	broad.mit.edu	37	1	121291834	121291835	+	Intron	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:121291834_121291835insA	uc001eiu.1	+							NR_003955				Homo sapiens cDNA FLJ46881 fis, clone UTERU3015647, moderately similar to Embigin precursor.												0						GATGTATGTGTAAAAAAAAAAT	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143492170	143492171	+	IGR	INS	-	G	G	rs113259197		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143492170_143492171insG								None (None upstream) : LOC100286793 (155468 downstream)																							tggccggatttggggaggcttg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143495448	143495449	+	IGR	INS	-	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143495448_143495449insC								None (None upstream) : LOC100286793 (152190 downstream)																							CTTAGCATTTACCCCCATTTCT	0.248													4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	144596452	144596452	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144596452delG	uc010oxr.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Intron|uc001elc.2_RNA|NBPF9_uc009wif.1_Intron|uc001ele.2_RNA	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818							cytoplasm					0						ttgtagagatggggattcaac	0.000													4	3	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145289274	145289276	+	Intron	DEL	ACT	-	-	rs142911147		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145289274_145289276delACT	uc001emp.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NOTCH2NL_uc001emo.2_Intron|NOTCH2NL_uc010oyh.1_Intron	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ataCTATAGAACTAATAATAACA	0.128													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	146482252	146482253	+	IGR	INS	-	AG	AG			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146482252_146482253insAG								NBPF10 (58157 upstream) : LOC728989 (8642 downstream)																							gagaaagaaatagagccttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	146872479	146872479	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146872479delT	uc001epp.2	-											Homo sapiens cDNA clone IMAGE:5266739.																		cactaccatgtttttccatgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148848203	148848205	+	IGR	DEL	TCA	-	-	rs144912987		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148848203_148848205delTCA								NBPF16 (89892 upstream) : LOC645166 (80081 downstream)																							tcatttcatctcatcatttcatt	0.000													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148848512	148848514	+	IGR	DEL	TCA	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148848512_148848514delTCA								NBPF16 (90201 upstream) : LOC645166 (79772 downstream)																							tcatttcatctcatcatttcatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148848700	148848701	+	IGR	INS	-	TCATT	TCATT	rs143780532		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148848700_148848701insTCATT								NBPF16 (90389 upstream) : LOC645166 (79585 downstream)																							ttttcatttcctcatcatttca	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148877330	148877331	+	Intron	INS	-	T	T	rs3010988		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148877330_148877331insT	uc009wkv.1	+											Homo sapiens cDNA, FLJ17483.																		tttttttcttcttttttttttt	0.035													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149032153	149032154	+	IGR	DEL	GG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149032153_149032154delGG								LOC645166 (79099 upstream) : LOC388692 (247322 downstream)																							TTTGCAATGAGGGAGGGTGAGT	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	150759635	150759637	+	IGR	DEL	AAC	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150759635_150759637delAAC								CTSS (21330 upstream) : CTSK (9050 downstream)																							actagtctcaaacaacaacaaca	0.192													4	3	---	---	---	---	
CGN	57530	broad.mit.edu	37	1	151497466	151497466	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151497466delC	uc009wmw.2	+							NM_020770	NP_065821	Q9P2M7	CING_HUMAN	cingulin							myosin complex|tight junction	actin binding|motor activity			ovary(2)|pancreas(1)	3	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			ACTGGGAACTCCCCCTCTCCT	0.532													4	2	---	---	---	---	
S100A10	6281	broad.mit.edu	37	1	151965357	151965358	+	Intron	INS	-	G	G	rs140685377	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151965357_151965358insG	uc001ezl.2	-						uc001ezm.1_5'Flank	NM_002966	NP_002957	P60903	S10AA_HUMAN	S100 calcium binding protein A10						signal transduction		calcium ion binding|receptor binding				0	Melanoma(130;0.0648)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)			GAGGCTGGACAGGCAGCAGTGT	0.609													2	4	---	---	---	---	
TCHH	7062	broad.mit.edu	37	1	152116080	152116080	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152116080delT	uc009wne.1	-							NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin						keratinization	cytoskeleton	calcium ion binding			ovary(3)|kidney(1)|central_nervous_system(1)	5	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ccccccacaatttttttttta	0.000													4	2	---	---	---	---	
SPRR2D	6703	broad.mit.edu	37	1	153116693	153116693	+	5'Flank	DEL	T	-	-	rs78757094		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153116693delT	uc009wnz.2	-						SPRR2A_uc001fbf.2_5'Flank|SPRR2C_uc001fbj.2_5'Flank			P22532	SPR2D_HUMAN	Homo sapiens cDNA FLJ76407 complete cds, highly similar to Homo sapiens small proline-rich protein 2D (SPRR2D), mRNA.						keratinization	cornified envelope|cytoplasm					0	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCTCAATGTGTTTTTTTTCTC	0.393													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	154286062	154286063	+	IGR	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154286062_154286063insA								HAX1 (37713 upstream) : AQP10 (7529 downstream)																							ctcccaggttcaagccgattct	0.000													4	2	---	---	---	---	
SMG5	23381	broad.mit.edu	37	1	156248169	156248169	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156248169delT	uc001foc.3	-							NM_015327	NP_056142	Q9UPR3	SMG5_HUMAN	SMG5 homolog nonsense mediated mRNA decay						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|nucleus	protein phosphatase 2A binding			ovary(2)|skin(2)|pancreas(1)	5	Hepatocellular(266;0.158)					TAtttttgggttttttttttt	0.184													4	2	---	---	---	---	
NES	10763	broad.mit.edu	37	1	156645430	156645430	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156645430delG	uc001fpq.2	-							NM_006617	NP_006608	P48681	NEST_HUMAN	nestin						brain development|embryonic camera-type eye development|G2/M transition of mitotic cell cycle|negative regulation of apoptosis|positive regulation of intermediate filament depolymerization|positive regulation of neural precursor cell proliferation|stem cell proliferation	cytoplasm|intermediate filament	intermediate filament binding|structural molecule activity			ovary(6)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCCACAggaaggggaggtgag	0.318													4	2	---	---	---	---	
KCNJ9	3765	broad.mit.edu	37	1	160051023	160051023	+	5'Flank	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160051023delT	uc001fuy.1	+						KCNJ9_uc001fux.1_5'Flank|KCNJ9_uc009wte.1_5'Flank	NM_004983	NP_004974	Q92806	IRK9_HUMAN	potassium inwardly-rectifying channel subfamily						synaptic transmission	integral to membrane|plasma membrane	G-protein activated inward rectifier potassium channel activity|protein binding			ovary(1)|skin(1)	2	all_cancers(52;5.86e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			ACCTAGCACCTTATTCTCAAA	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	162912196	162912196	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162912196delG								C1orf110 (73591 upstream) : RGS4 (126200 downstream)																							GGAGAAGTAAGGAAAGAGAGT	0.398													4	2	---	---	---	---	
RGS5	8490	broad.mit.edu	37	1	163137886	163137887	+	Intron	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163137886_163137887insA	uc001gcn.2	-						RGS5_uc009wvb.2_Intron	NM_003617	NP_003608	O15539	RGS5_HUMAN	regulator of G-protein signalling 5						negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity				0			LUSC - Lung squamous cell carcinoma(543;0.187)			AGATAGTTGAGAAAAAAAAAAA	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	163771827	163771828	+	IGR	INS	-	G	G	rs143279610	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163771827_163771828insG								NUF2 (446274 upstream) : PBX1 (756974 downstream)																							GGCCTTTCTGCGGGCCCCCTTC	0.475													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	165975271	165975271	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165975271delT								UCK2 (97934 upstream) : FAM78B (54145 downstream)																							tgggtcatgcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	166391872	166391873	+	IGR	DEL	CA	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166391872_166391873delCA								FAM78B (255666 upstream) : FMO9P (181280 downstream)																							ccctagcaggcacacacacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	168186331	168186332	+	IGR	INS	-	CTT	CTT	rs143131159	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168186331_168186332insCTT								TIPRL (14982 upstream) : SFT2D2 (8923 downstream)																							TAACCACATAGCTTCCCTCAGT	0.337													4	2	---	---	---	---	
SELL	6402	broad.mit.edu	37	1	169670639	169670640	+	Intron	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169670639_169670640insT	uc001ggk.2	-						C1orf112_uc001ggj.2_Intron|SELL_uc010pls.1_Intron	NM_000655	NP_000646	P14151	LYAM1_HUMAN	selectin L precursor						blood coagulation|cell adhesion|leukocyte migration|regulation of immune response	integral to plasma membrane	glycosphingolipid binding|heparin binding|protease binding|sugar binding				0	all_hematologic(923;0.208)					CTGTGGGTTTCTTTTTTTTTTC	0.361													4	2	---	---	---	---	
RABGAP1L	9910	broad.mit.edu	37	1	174164792	174164793	+	Intron	INS	-	TCC	TCC	rs71713239		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174164792_174164793insTCC	uc001gjx.2	+						RABGAP1L_uc009wwq.1_Intron|RABGAP1L_uc001gjw.2_Intron	NM_014857	NP_055672	Q5R372	RBG1L_HUMAN	RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4						ccttccttcctttcctttcctt	0.000													4	2	---	---	---	---	
TNR	7143	broad.mit.edu	37	1	175452283	175452283	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175452283delC	uc009wwu.1	-						TNR_uc010pmz.1_Intron	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor						axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					tgaacaggctccagtccatgc	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	181093658	181093659	+	IGR	INS	-	TC	TC	rs114309731	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181093658_181093659insTC								IER5 (33681 upstream) : CACNA1E (359057 downstream)																							cctcctcctcttcctccccctc	0.094													4	2	---	---	---	---	
C1orf21	81563	broad.mit.edu	37	1	184528723	184528724	+	Intron	INS	-	CCTT	CCTT	rs141160537	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184528723_184528724insCCTT	uc001gqv.1	+							NM_030806	NP_110433	Q9H246	CA021_HUMAN	chromosome 1 open reading frame 21												0		Breast(1374;0.00262)		Colorectal(1306;4.8e-08)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)		ctctcttcctcccttccttcct	0.010													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	192024149	192024149	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192024149delC								None (None upstream) : RGS18 (103443 downstream)																							AGTAAAATTTCTTTTTTTTTT	0.209													4	2	---	---	---	---	
ZBTB41	360023	broad.mit.edu	37	1	197164727	197164727	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197164727delT	uc001gtx.1	-						ZBTB41_uc009wyz.1_Intron	NM_194314	NP_919290	Q5SVQ8	ZBT41_HUMAN	zinc finger and BTB domain containing 41						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2						ACTAGTCACATTTTTTTTTAA	0.289													4	2	---	---	---	---	
NAV1	89796	broad.mit.edu	37	1	201631624	201631624	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201631624delA	uc001gwu.2	+							NM_020443	NP_065176	Q8NEY1	NAV1_HUMAN	neuron navigator 1						cell differentiation|nervous system development	cytoplasm|microtubule	nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(3)|ovary(1)	4						ggggcgatagaaggagcacca	0.234													4	2	---	---	---	---	
ATP2B4	493	broad.mit.edu	37	1	203600063	203600063	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203600063delG	uc001gzw.2	+						ATP2B4_uc001gzv.2_Intron	NM_001684	NP_001675	P23634	AT2B4_HUMAN	plasma membrane calcium ATPase 4 isoform 4b						ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|skin(1)	3	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)			GGCTTCCTCTGCCAGTATCTC	0.473													4	2	---	---	---	---	
LEMD1	93273	broad.mit.edu	37	1	205384595	205384596	+	Intron	DEL	AG	-	-	rs145765370		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205384595_205384596delAG	uc001hcj.1	-						LEMD1_uc001hci.1_Intron|LEMD1_uc001hck.1_Intron|LEMD1_uc001hcl.1_Intron|LEMD1_uc001hcm.1_Intron|LEMD1_uc001hcn.1_Intron			Q68G75	LEMD1_HUMAN	RecName: Full=LEM domain-containing protein 1;          Short=LEMP-1; AltName: Full=Cancer/testis antigen 50;          Short=CT50;							integral to membrane|nuclear envelope					0	Breast(84;0.247)		BRCA - Breast invasive adenocarcinoma(75;0.0938)			GAATAGAAACAGAGATACAGAA	0.465													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	208516731	208516732	+	IGR	INS	-	TG	TG	rs144638505	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208516731_208516732insTG								PLXNA2 (99066 upstream) : None (None downstream)																							gtgtgtgtgcatgtgtgtgtgt	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	211727767	211727767	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211727767delA								RD3 (61508 upstream) : SLC30A1 (20614 downstream)																							AGGTGGGATCAAAAAGGCTCC	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	221533632	221533633	+	IGR	INS	-	T	T	rs149355431	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221533632_221533633insT								LOC400804 (23994 upstream) : DUSP10 (341133 downstream)																							taatttttaaattttttgtaga	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	223189183	223189183	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223189183delT								DISP1 (9848 upstream) : TLR5 (94401 downstream)																							CTTTGAtttcttttttttttt	0.254													3	3	---	---	---	---	
ITPKB	3707	broad.mit.edu	37	1	226840123	226840123	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226840123delC	uc010pvo.1	-							NM_002221	NP_002212	P27987	IP3KB_HUMAN	1D-myo-inositol-trisphosphate 3-kinase B								ATP binding|calmodulin binding|inositol trisphosphate 3-kinase activity			ovary(4)|central_nervous_system(1)	5		Prostate(94;0.0773)				CAGGCCTCATCCCCCAGATAA	0.597													4	2	---	---	---	---	
DISC1	27185	broad.mit.edu	37	1	231933859	231933860	+	Intron	INS	-	CACACACACACACA	CACACACACACACA	rs150974447	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231933859_231933860insCACACACACACACA	uc001huz.2	+						TSNAX-DISC1_uc010pwg.1_Intron|TSNAX-DISC1_uc010pwh.1_Intron|TSNAX-DISC1_uc010pwi.1_Intron|TSNAX-DISC1_uc010pwj.1_Intron|TSNAX-DISC1_uc010pwk.1_Intron|TSNAX-DISC1_uc010pwl.1_Intron|DISC1_uc010pwr.1_Intron|DISC1_uc010pws.1_Intron|DISC1_uc010pwt.1_Intron|DISC1_uc010pwu.1_Intron|DISC1_uc010pwv.1_Intron|DISC1_uc010pww.1_Intron|DISC1_uc010pwx.1_Intron|DISC1_uc010pwy.1_Intron|DISC1_uc010pwz.1_Intron|DISC1_uc010pxa.1_Intron|DISC1_uc001huy.2_Intron|DISC1_uc010pxb.1_Intron|DISC1_uc010pxc.1_Intron|DISC1_uc010pxd.1_Intron|DISC1_uc010pxe.1_Intron|DISC1_uc009xfr.2_Intron|DISC1_uc010pxf.1_Intron|DISC1_uc010pxg.1_Intron|DISC1_uc010pxh.1_Intron|DISC1_uc010pxi.1_Intron|DISC1_uc010pxj.1_Intron|DISC1_uc010pxk.1_Intron|DISC1_uc010pxl.1_Intron|DISC1_uc010pxm.1_Intron|DISC1_uc010pxn.1_Intron|DISC1_uc001hva.2_Intron	NM_018662	NP_061132	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1 isoform L						microtubule cytoskeleton organization|neuron migration|positive regulation of neuroblast proliferation|positive regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	centrosome|microtubule	protein binding			skin(1)	1		all_cancers(173;0.0208)|Prostate(94;0.0975)				GTTAGacacaccacacacacac	0.327													3	4	---	---	---	---	
KCNK1	3775	broad.mit.edu	37	1	233784309	233784310	+	Intron	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233784309_233784310insT	uc010pxo.1	+						KCNK1_uc001hvw.2_Intron|KCNK1_uc001hvx.2_Intron	NM_002245	NP_002236	O00180	KCNK1_HUMAN	potassium channel, subfamily K, member 1							voltage-gated potassium channel complex	inward rectifier potassium channel activity			central_nervous_system(1)	1		all_cancers(173;0.00217)|all_epithelial(177;0.121)|Prostate(94;0.122)|Acute lymphoblastic leukemia(190;0.175)			Ibutilide(DB00308)|Quinidine(DB00908)	tgctTGCTTGCttttttttttt	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	234893237	234893237	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234893237delA								IRF2BP2 (147966 upstream) : TOMM20 (379423 downstream)																							TGCTTGGTTCAAGATTAAGGT	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	238696127	238696128	+	IGR	DEL	TG	-	-	rs148697786		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238696127_238696128delTG								LOC339535 (46810 upstream) : CHRM3 (853737 downstream)																							TCTAGATTACtgtgtgtgtgtg	0.257													4	3	---	---	---	---	
CHRM3	1131	broad.mit.edu	37	1	239564105	239564106	+	Intron	DEL	TG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239564105_239564106delTG	uc001hyo.1	+									P20309	ACM3_HUMAN	Homo sapiens clone N10 NTera2D1 teratocarcinoma, m3 muscarinic acetylcholine receptor mRNA, partial cds.						cell proliferation|energy reserve metabolic process|nervous system development|protein modification process|regulation of insulin secretion	basolateral plasma membrane|cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(1)	5	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Cevimeline(DB00185)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Darifenacin(DB00496)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Solifenacin(DB01591)|Thiethylperazine(DB00372)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tridihexethyl(DB00505)	tccattggtctgtgtgtgtgtg	0.000													4	2	---	---	---	---	
FMN2	56776	broad.mit.edu	37	1	240342569	240342569	+	Intron	DEL	A	-	-	rs77544762		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240342569delA	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)			AATGACCAACAATGTAAAAGG	0.363													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	242995103	242995114	+	IGR	DEL	AAGGAAGGAAGG	-	-	rs71700595		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242995103_242995114delAAGGAAGGAAGG								PLD5 (307105 upstream) : CEP170 (292617 downstream)																							gaaagaaagaaaggaaggaaggaaggaagatg	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	244386680	244386683	+	IGR	DEL	TCCT	-	-	rs72765850	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244386680_244386683delTCCT								ZNF238 (165904 upstream) : C1orf100 (129254 downstream)																							ccattctccatccttccttgtctc	0.206													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	245058473	245058474	+	IGR	INS	-	T	T	rs112328486		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245058473_245058474insT								HNRNPU (30646 upstream) : EFCAB2 (74697 downstream)																							gtgaaaatgtcttttttttttt	0.000													3	3	---	---	---	---	
KIF26B	55083	broad.mit.edu	37	1	245596769	245596769	+	Intron	DEL	A	-	-	rs111335967		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245596769delA	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron	NM_018012	NP_060482	Q2KJY2	KI26B_HUMAN	kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			actctgtctcaaaaaaaaaaa	0.114													5	3	---	---	---	---	
SMYD3	64754	broad.mit.edu	37	1	246179540	246179540	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246179540delA	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron	NM_022743	NP_073580	Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		cccatcacttaaaaaaaaaaa	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	246858753	246858754	+	IGR	DEL	TC	-	-	rs144946938		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246858753_246858754delTC								CNST (26870 upstream) : SCCPDH (28624 downstream)																							TGTTTTATTTTCTTTCTTTTTG	0.104													4	3	---	---	---	---	
ZNF695	57116	broad.mit.edu	37	1	247184322	247184322	+	Intron	DEL	A	-	-	rs71922915		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247184322delA	uc001ica.2	-						ZNF695_uc001icb.1_Intron			Q8IW36	ZN695_HUMAN	Homo sapiens zinc finger protein SBZF3 mRNA, complete cds.						regulation of transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding				0	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			ccaaaaagacaaaaaaaaaaa	0.149													4	2	---	---	---	---	
ZNF496	84838	broad.mit.edu	37	1	247476052	247476052	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247476052delG	uc001ico.2	-						ZNF496_uc009xgv.2_Intron|ZNF496_uc001icp.2_Intron|ZNF496_uc001icq.1_5'Flank|ZNF496_uc010pyv.1_Intron	NM_032752	NP_116141	Q96IT1	ZN496_HUMAN	zinc finger protein 496						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)			aaaaaaaaaagaaaaagaaaa	0.000													4	2	---	---	---	---	
C1orf150	148823	broad.mit.edu	37	1	247683828	247683829	+	Intron	INS	-	CA	CA	rs145759148	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247683828_247683829insCA	uc009xgw.2	+						C1orf150_uc001ida.3_Intron|C1orf150_uc001idb.3_Intron|C1orf150_uc009xgx.2_Intron|uc001idc.2_RNA			Q5JQS6	CA150_HUMAN	Homo sapiens cDNA FLJ41804 fis, clone NOVAR2000710.												0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0241)			ccccacctcttcacacacacac	0.059													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	248824933	248824933	+	IGR	DEL	A	-	-	rs34253064		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248824933delA								OR2T27 (10748 upstream) : OR14I1 (19737 downstream)																							ccaagtggagaaaaaaaaaaa	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	248874758	248874758	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248874758delC								OR14I1 (29153 upstream) : LOC646627 (27960 downstream)																							atgcagcctaccgagatgtgc	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	597741	597741	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:597741delT								FAM150B (309433 upstream) : TMEM18 (70234 downstream)																							attcttggcctttttaaaggc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	2784659	2784659	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2784659delC								MYT1L (449614 upstream) : TSSC1 (408082 downstream)																							ACACTCTACACCCTCCCAGGA	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	2878429	2878429	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2878429delG								MYT1L (543384 upstream) : TSSC1 (314312 downstream)																							GTCCCACAGTGGGTGCAAGGC	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	4081066	4081066	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4081066delA								ALLC (330808 upstream) : None (None downstream)																							caaagaacttaaaatgaaact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	7750690	7750691	+	IGR	INS	-	TTG	TTG	rs146941205	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7750690_7750691insTTG								RNF144A (566383 upstream) : LOC339788 (311867 downstream)																							tttgttttgtttttttgtcttt	0.223													1	5	---	---	---	---	
ASAP2	8853	broad.mit.edu	37	2	9353177	9353177	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9353177delT	uc002qzh.2	+						ASAP2_uc002qzi.2_Intron	NM_003887	NP_003878	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH						regulation of ARF GTPase activity	Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|protein binding|zinc ion binding				0						ATAGGGTTGATAATCACTGat	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	10849026	10849027	+	IGR	INS	-	GTGGGGTCAGAGA	GTGGGGTCAGAGA	rs146318534	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10849026_10849027insGTGGGGTCAGAGA								NOL10 (18914 upstream) : ATP6V1C2 (12748 downstream)																							GGGGGATGGAGGTGGGGTACTT	0.574													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	12678392	12678393	+	Intron	INS	-	CA	CA	rs151238284	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12678392_12678393insCA	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																		TCTCTCTCTCTCACACACACAC	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	13415467	13415468	+	IGR	INS	-	TG	TG	rs35296952		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13415467_13415468insTG								TRIB2 (532611 upstream) : None (None downstream)																							ATCTCTCtgtctgtgtgtgtgt	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	14530699	14530700	+	Intron	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:14530699_14530700insT	uc002rby.2	-											Homo sapiens cDNA clone IMAGE:5263003.																		TTCTCTCACTCTTTTTTTTTTG	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	16953931	16953931	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16953931delC								FAM49A (106835 upstream) : RAD51AP2 (738055 downstream)																							acacctttctcaaagtcttct	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	20603679	20603680	+	IGR	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20603679_20603680insA								PUM2 (53216 upstream) : RHOB (43155 downstream)																							gcaagaaaaagaaaaaaaaatg	0.099													4	2	---	---	---	---	
C2orf39	92749	broad.mit.edu	37	2	26655473	26655474	+	Intron	INS	-	AAAG	AAAG	rs149660866	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26655473_26655474insAAAG	uc002rhg.2	+						C2orf39_uc010eym.1_Intron	NM_145038	NP_659475	Q96MC2	CC164_HUMAN	hypothetical protein LOC92749												0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					gaaagaaaaaaaaagaaaggaa	0.173													2	4	---	---	---	---	
GCKR	2646	broad.mit.edu	37	2	27723945	27723945	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27723945delG	uc002rky.2	+						GCKR_uc010ezd.2_Intron|GCKR_uc010ylu.1_Intron	NM_001486	NP_001477	Q14397	GCKR_HUMAN	glucokinase regulatory protein						carbohydrate metabolic process|glucose transport|negative regulation of glucokinase activity|positive regulation of gene expression|protein import into nucleus, translocation|regulation of glucose transport|response to fructose stimulus|transmembrane transport|triglyceride homeostasis|urate metabolic process	cytosol|nucleoplasm	fructose-6-phosphate binding|protein binding			ovary(2)	2	Acute lymphoblastic leukemia(172;0.155)					cttgagccttgggcaccacTC	0.244													80	39	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	28692865	28692867	+	IGR	DEL	AAG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28692865_28692867delAAG								FOSL2 (55351 upstream) : PLB1 (26115 downstream)																							gaggagaagaaagaggaggagga	0.084													5	3	---	---	---	---	
CAPN13	92291	broad.mit.edu	37	2	30982959	30982959	+	Intron	DEL	T	-	-	rs67222095		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30982959delT	uc002rnn.2	-						CAPN13_uc002rnp.1_Intron	NM_144575	NP_653176	Q6MZZ7	CAN13_HUMAN	calpain 13						proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			large_intestine(1)|ovary(1)	2	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					ATTGTTGTGAttttttttgag	0.269													2	4	---	---	---	---	
DHX57	90957	broad.mit.edu	37	2	39030266	39030266	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39030266delA	uc002rrf.2	-						DHX57_uc002rrd.3_Intron|DHX57_uc002rre.2_Intron	NM_198963	NP_945314	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57								ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		all_hematologic(82;0.248)				acttgtgtttaaaaAAAAAAA	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	41630902	41630905	+	IGR	DEL	AGGA	-	-	rs67267090		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41630902_41630905delAGGA								SLC8A1 (891327 upstream) : PKDCC (644256 downstream)																							gaaggaagggaggaaggaagggag	0.152													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	42300203	42300203	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42300203delG								PKDCC (14537 upstream) : EML4 (96287 downstream)																							AGGTCATCGTGGGGGTAACTC	0.562													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	42310410	42310411	+	IGR	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42310410_42310411insA								PKDCC (24744 upstream) : EML4 (86079 downstream)																							cttgcatcttcaaaaaaacctt	0.000													4	2	---	---	---	---	
LRPPRC	10128	broad.mit.edu	37	2	44225367	44225367	+	5'Flank	DEL	G	-	-	rs146248392		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44225367delG	uc002rtr.2	-						LRPPRC_uc010yob.1_5'Flank|LRPPRC_uc010faw.1_5'Flank	NM_133259	NP_573566	P42704	LPPRC_HUMAN	leucine-rich PPR motif-containing protein						mitochondrion transport along microtubule|mRNA transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed nuclear chromosome|cytoskeleton|mitochondrial nucleoid|nuclear inner membrane|nuclear outer membrane|nucleoplasm|perinuclear region of cytoplasm	beta-tubulin binding|microtubule binding|RNA binding			ovary(2)|skin(1)	3		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				gaaaagagcagggggtagaga	0.000													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	47959052	47959053	+	IGR	INS	-	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47959052_47959053insC								MSH2 (52544 upstream) : MSH6 (51168 downstream)																							caaaaaaaaaaaaaaaaaaaaa	0.158													13	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	54239373	54239373	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54239373delA								PSME4 (41396 upstream) : ACYP2 (103037 downstream)																							actccgtctcaaaaaaaaaaa	0.090													4	3	---	---	---	---	
ACYP2	98	broad.mit.edu	37	2	54377748	54377748	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54377748delG	uc002rxq.3	+							NM_138448	NP_612457	P14621	ACYP2_HUMAN	acylphosphatase 2						phosphate metabolic process		acylphosphatase activity				0						tagtagagatggggtttcacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	60881178	60881178	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60881178delA								BCL11A (100545 upstream) : PAPOLG (102205 downstream)																							caggggaggcaaaaaaaaaag	0.204													4	4	---	---	---	---	
C2orf86	51057	broad.mit.edu	37	2	63782542	63782543	+	Intron	INS	-	C	C	rs147836697	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63782542_63782543insC	uc002sch.2	-						C2orf86_uc002sci.1_Intron	NM_015910	NP_056994	O95876	FRITZ_HUMAN	hypothetical protein LOC51057 isoform 2						cilium morphogenesis|regulation of embryonic cell shape|regulation of protein localization|septin cytoskeleton organization	cilium axoneme|cytoplasm|cytoskeleton|plasma membrane					0						acttagtttttcccctgctgtc	0.000													0	7	---	---	---	---	
CLEC4F	165530	broad.mit.edu	37	2	71036190	71036190	+	3'UTR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71036190delA	uc002shf.2	-	7						NM_173535	NP_775806	Q8N1N0	CLC4F_HUMAN	C-type lectin, superfamily member 13						endocytosis	integral to membrane	receptor activity|sugar binding			ovary(5)	5						GCCAGTTGTCAGACTGATTCT	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	72193581	72193582	+	IGR	INS	-	TTCT	TTCT	rs151009969	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72193581_72193582insTTCT								DYSF (279689 upstream) : CYP26B1 (162785 downstream)																							TTCGtctttgcttctttctttc	0.188													4	2	---	---	---	---	
CTNNA2	1496	broad.mit.edu	37	2	79663764	79663764	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79663764delT	uc010yse.1	+							NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1						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						TTAAATAttcttttttttttt	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	84127340	84127340	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84127340delG								None (None upstream) : FUNDC2P2 (390466 downstream)																							tgaaatagttggtcattgttc	0.085													4	2	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87586644	87586645	+	Intron	DEL	TT	-	-	rs55885523		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87586644_87586645delTT	uc002srs.3	+									Q9H871	RMD5A_HUMAN	SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2						ataagatgacttgagatgagat	0.114													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89840267	89840267	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89840267delC								FLJ40330 (734142 upstream) : None (None downstream)																							tttgatgattccattcgagtc	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91987131	91987132	+	IGR	INS	-	AGAA	AGAA			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91987131_91987132insAGAA								GGT8P (16978 upstream) : FKSG73 (142027 downstream)																							gcaagaacgtgagaaagaaaga	0.005													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92176896	92176897	+	IGR	DEL	AA	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92176896_92176897delAA								FKSG73 (46402 upstream) : None (None downstream)																							aaatgagatgaaatgagatgaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92188404	92188405	+	IGR	INS	-	G	G	rs150975516		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92188404_92188405insG								FKSG73 (57910 upstream) : None (None downstream)																							AAAGTCtttatttttttttttt	0.218													4	2	---	---	---	---	
ARID5A	10865	broad.mit.edu	37	2	97203294	97203294	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97203294delG	uc002swe.2	+						ARID5A_uc010yuq.1_Intron|ARID5A_uc002swf.2_Intron|ARID5A_uc002swg.2_Intron	NM_212481	NP_997646	Q03989	ARI5A_HUMAN	AT rich interactive domain 5A						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding				0						TTCCCTGGTTGCTCTCCTCTC	0.647													4	3	---	---	---	---	
INPP4A	3631	broad.mit.edu	37	2	99182021	99182022	+	Intron	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99182021_99182022insT	uc002syy.2	+						INPP4A_uc010yvj.1_Intron|INPP4A_uc010yvk.1_Intron|INPP4A_uc002syx.2_Intron|INPP4A_uc010fik.2_Intron	NM_001134224	NP_001127696	Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type 1						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			kidney(1)	1						ACAGCCAGGCCTGGGCTTGGCT	0.629													9	7	---	---	---	---	
AFF3	3899	broad.mit.edu	37	2	100166045	100166046	+	3'UTR	INS	-	A	A	rs74489695		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100166045_100166046insA	uc002tag.2	-	24					AFF3_uc002taf.2_3'UTR	NM_002285	NP_002276	P51826	AFF3_HUMAN	AF4/FMR2 family, member 3 isoform 1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6						aaactcgtctcaaaaaaaaaGT	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	103681667	103681668	+	IGR	DEL	TG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103681667_103681668delTG								TMEM182 (247531 upstream) : None (None downstream)																							ATATACTAATtgtgtgtgtgtg	0.272													4	2	---	---	---	---	
SH3RF3	344558	broad.mit.edu	37	2	109963080	109963081	+	Intron	INS	-	T	T	rs142123578	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109963080_109963081insT	uc010ywt.1	+							NM_001099289	NP_001092759	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3								zinc ion binding			ovary(1)	1						GCCAGATGGACTTGATGAGACA	0.505													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	118419033	118419033	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118419033delC								None (None upstream) : DDX18 (153222 downstream)																							TGTGCAGGGGCCAGCAGGAAA	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	119024340	119024340	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119024340delC								INSIG2 (156744 upstream) : EN1 (575408 downstream)																							CGTTCTGTAGCAGGAAATTAA	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	130660460	130660460	+	IGR	DEL	G	-	-	rs11315881		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130660460delG								None (None upstream) : LOC389033 (19975 downstream)																							GGGTTAGGGTGGGGCCTAACC	0.617													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132405644	132405644	+	IGR	DEL	T	-	-	rs79519853		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132405644delT								CCDC74A (114407 upstream) : C2orf27A (74420 downstream)																							TGCCAGCCTCTAGCGTTTTGC	0.567													0	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	153779466	153779467	+	IGR	DEL	TT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153779466_153779467delTT								ARL6IP6 (161699 upstream) : RPRM (554385 downstream)																							ccttctcttcttctttcccttc	0.114													4	2	---	---	---	---	
GPD2	2820	broad.mit.edu	37	2	157303090	157303091	+	Intron	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157303090_157303091insT	uc002tzf.3	+						GPD2_uc010zch.1_Intron|GPD2_uc002tzd.3_Intron	NM_001083112	NP_001076581	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2,						cellular lipid metabolic process	glycerol-3-phosphate dehydrogenase complex|mitochondrial inner membrane	calcium ion binding|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity			ovary(1)	1						GTGTCCTTGCAttttttttttt	0.030													4	2	---	---	---	---	
TBR1	10716	broad.mit.edu	37	2	162271681	162271682	+	5'Flank	DEL	AC	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162271681_162271682delAC	uc002ubw.1	+						TBR1_uc010foy.2_5'Flank	NM_006593	NP_006584	Q16650	TBR1_HUMAN	T-box, brain, 1							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2						acacacacgtacacacacacac	0.351													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	166940728	166940729	+	Intron	INS	-	T	T	rs75658677		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166940728_166940729insT	uc002udp.2	+											Homo sapiens, clone IMAGE:3681561, mRNA.																		TCTCAATTTTCTTTTTTTTTTT	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	169777057	169777057	+	IGR	DEL	T	-	-	rs113381087		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169777057delT								G6PC2 (10548 upstream) : ABCB11 (2392 downstream)																							aatccttctattttttttttt	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	170298128	170298129	+	IGR	INS	-	G	G	rs149300431	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170298128_170298129insG								LRP2 (79006 upstream) : BBS5 (37877 downstream)																							tgaaggaaactgaaaattctga	0.000													0	7	---	---	---	---	
KLHL23	151230	broad.mit.edu	37	2	170555828	170555828	+	Intron	DEL	C	-	-	rs143881694		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170555828delC	uc002ufh.1	+						PHOSPHO2_uc002ufg.2_Intron	NM_144711	NP_653312	Q8NBE8	KLH23_HUMAN	kelch-like 23												0						ataatggcttccagatccatc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	174851320	174851323	+	IGR	DEL	TGTC	-	-	rs67158938		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174851320_174851323delTGTC								SP3 (21257 upstream) : OLA1 (85853 downstream)																							gatgtagatgtgtctgtcccctgc	0.167													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	175177634	175177634	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175177634delA								OLA1 (64269 upstream) : SP9 (22187 downstream)																							CATTGGAACCAAAAGGTGACA	0.343													4	2	---	---	---	---	
PDE1A	5136	broad.mit.edu	37	2	183209478	183209479	+	Intron	DEL	CA	-	-	rs67471209		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183209478_183209479delCA	uc002uos.2	-						PDE1A_uc010zfp.1_Intron|PDE1A_uc002uoq.1_Intron|PDE1A_uc010zfq.1_Intron|PDE1A_uc002uor.2_Intron|PDE1A_uc002uov.1_Intron	NM_001003683	NP_001003683	P54750	PDE1A_HUMAN	phosphodiesterase 1A isoform 2						activation of phospholipase C activity|nerve growth factor receptor signaling pathway|platelet activation	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(2)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.061)			ctctctctctcacacacacaca	0.243													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	186345263	186345264	+	IGR	DEL	TG	-	-	rs72125659		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186345263_186345264delTG								ZNF804A (541051 upstream) : None (None downstream)																							tatgcatgtatgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	186535215	186535215	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186535215delG								ZNF804A (731003 upstream) : ZC3H15 (815670 downstream)																							aaaagtcaaagaagtatttca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	188523917	188523917	+	IGR	DEL	C	-	-	rs1581324	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:188523917delC								TFPI (104698 upstream) : GULP1 (632687 downstream)																							ttagagggggcaatgagacag	0.000													4	2	---	---	---	---	
SATB2	23314	broad.mit.edu	37	2	200251807	200251807	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200251807delT	uc002uuy.1	-						SATB2_uc010fsq.1_Intron|SATB2_uc002uuz.1_Intron|SATB2_uc002uva.1_Intron	NM_015265	NP_056080	Q9UPW6	SATB2_HUMAN	SATB homeobox 2							cytoplasm|nuclear matrix	sequence-specific DNA binding transcription factor activity			ovary(1)	1						caaccattagtttatccttat	0.060													4	2	---	---	---	---	
ALS2	57679	broad.mit.edu	37	2	202623482	202623483	+	Intron	INS	-	GCGT	GCGT	rs143775164	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202623482_202623483insGCGT	uc002uyo.2	-						ALS2_uc002uyp.3_Intron|ALS2_uc002uyq.2_Intron	NM_020919	NP_065970	Q96Q42	ALS2_HUMAN	alsin isoform 1						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						tgtgtgtgcgcatgtgtgtgtg	0.173													1	5	---	---	---	---	
CDK15	65061	broad.mit.edu	37	2	202711958	202711958	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202711958delT	uc002uyt.2	+						CDK15_uc010ftm.2_Intron|CDK15_uc002uys.2_Intron|CDK15_uc010ftn.1_Intron|CDK15_uc010fto.1_Intron	NM_139158	NP_631897	Q96Q40	CDK15_HUMAN	PFTAIRE protein kinase 2								ATP binding|cyclin-dependent protein kinase activity|metal ion binding|protein binding			breast(2)|ovary(1)|lung(1)|kidney(1)	5					Adenosine triphosphate(DB00171)	ACATAGGGACTTTTTTTTTGG	0.363													4	2	---	---	---	---	
ABI2	10152	broad.mit.edu	37	2	204210756	204210757	+	Intron	DEL	CA	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204210756_204210757delCA	uc002vaa.2	+						ABI2_uc010zig.1_Intron|ABI2_uc002uzz.2_Intron|ABI2_uc010zih.1_Intron|ABI2_uc010zii.1_Intron|ABI2_uc010zij.1_Intron	NM_005759	NP_005750	Q9NYB9	ABI2_HUMAN	abl interactor 2						actin polymerization or depolymerization|cell migration|peptidyl-tyrosine phosphorylation	cytoskeleton|cytosol|filopodium|lamellipodium	cytoskeletal adaptor activity|DNA binding|kinase binding|proline-rich region binding|SH3 domain binding|ubiquitin protein ligase binding				0						tacacacgcgcacacacacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	206497585	206497585	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206497585delT								PARD3B (17048 upstream) : NRP2 (49639 downstream)																							CCTCTCTCTCTTTTTTTTTTC	0.269													4	2	---	---	---	---	
CPS1	1373	broad.mit.edu	37	2	211542510	211542511	+	Intron	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211542510_211542511insT	uc002vee.3	+						CPS1_uc010fur.2_Intron|CPS1_uc010fus.2_Intron	NM_001875	NP_001866	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform b						carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)|skin(1)	13				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)		TCCCATACCCCTTTGAAAACTG	0.376													42	39	---	---	---	---	
ARMC9	80210	broad.mit.edu	37	2	232183498	232183498	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232183498delG	uc002vrq.3	+						ARMC9_uc002vrp.3_Intron|ARMC9_uc002vrr.1_Intron	NM_025139	NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9								binding			ovary(1)	1		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)		ACTGTAGAGAGGAATTGCCTG	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	232590766	232590766	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232590766delT								PTMA (12518 upstream) : PDE6D (6381 downstream)																							CACCCCTCAGTTTATTTAAAG	0.313													4	2	---	---	---	---	
ESPNL	339768	broad.mit.edu	37	2	239016426	239016426	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239016426delC	uc002vxq.3	+						ESPNL_uc010fyw.2_5'Flank	NM_194312	NP_919288	Q6ZVH7	ESPNL_HUMAN	espin-like											pancreas(1)	1		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		GCCCCTCCTTCCCCAGGTCAC	0.637													6	4	---	---	---	---	
FARP2	9855	broad.mit.edu	37	2	242352633	242352634	+	Intron	INS	-	T	T	rs141753202	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242352633_242352634insT	uc002wbi.1	+						FARP2_uc010zoq.1_Intron|FARP2_uc010zor.1_Intron	NM_014808	NP_055623	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2						axon guidance|neuron remodeling|Rac protein signal transduction|regulation of Rho protein signal transduction	cytoskeleton|cytosol|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		ATTTGGGATAATTTTTTTTTAC	0.248													3	3	---	---	---	---	
ING5	84289	broad.mit.edu	37	2	242657739	242657742	+	Intron	DEL	CCTC	-	-	rs112407089		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242657739_242657742delCCTC	uc002wcd.2	+						ING5_uc002wcc.1_Intron	NM_032329	NP_115705	Q8WYH8	ING5_HUMAN	inhibitor of growth family, member 5						DNA replication|histone H3 acetylation|negative regulation of cell proliferation|negative regulation of growth|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex	protein binding|zinc ion binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.16e-33)|all cancers(36;4.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.6e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839)		ttcctcccttcctccctccctccc	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	1065219	1065219	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1065219delT								CHL1 (614124 upstream) : CNTN6 (69401 downstream)																							TCCTGAGGCCTTTTTTTCCCT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	7888494	7888495	+	IGR	INS	-	GTT	GTT	rs143325035	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7888494_7888495insGTT								GRM7 (105276 upstream) : LMCD1 (655016 downstream)																							TAAGAACAGCAGTTGGACCTGC	0.520													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	14310063	14310064	+	IGR	INS	-	TG	TG	rs147292705	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14310063_14310064insTG								LSM3 (70227 upstream) : SLC6A6 (134042 downstream)																							GCCCCATTAATtgtgtgtgtgt	0.396													6	3	---	---	---	---	
GALNTL2	117248	broad.mit.edu	37	3	16069078	16069078	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16069078delC	uc003caq.3	+							NM_054110	NP_473451	Q8N3T1	GLTL2_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane|transport vesicle	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(1)	1						gatctgcctgccttggcctcc	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	20450859	20450859	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20450859delT								SGOL1 (223176 upstream) : VENTXP7 (996359 downstream)																							gaagagtgtcttgagttggaa	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	23705200	23705200	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23705200delA								UBE2E2 (72904 upstream) : UBE2E1 (142239 downstream)																							TTACCAAAGGAAAAAAAAAAA	0.353													3	3	---	---	---	---	
UBE2E1	7324	broad.mit.edu	37	3	23929668	23929670	+	Intron	DEL	CCA	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23929668_23929670delCCA	uc003cch.2	+						UBE2E1_uc003cci.2_Intron|UBE2E1_uc011awh.1_Intron	NM_003341	NP_003332	P51965	UB2E1_HUMAN	ubiquitin-conjugating enzyme E2E 1 isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|histone H2B ubiquitination|histone monoubiquitination|ISG15-protein conjugation|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K48-linked ubiquitination	cytosol|nucleoplasm|ubiquitin ligase complex	ATP binding|ISG15 ligase activity|protein binding|ubiquitin-protein ligase activity				0						GAATCTCTTCCCAAAGCTTTGGA	0.369													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	25711605	25711605	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25711605delT								TOP2B (5774 upstream) : NGLY1 (48831 downstream)																							ATTGTGTCTCTTTAGTAGTGA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	36671960	36671960	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36671960delT								STAC (82464 upstream) : DCLK3 (81953 downstream)																							CAATCTGCAATTTTTTCCTTG	0.408													4	2	---	---	---	---	
TRAK1	22906	broad.mit.edu	37	3	42202061	42202061	+	Intron	DEL	G	-	-	rs59260540		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42202061delG	uc003cky.2	+						TRAK1_uc011azh.1_Intron|TRAK1_uc011azi.1_Intron|TRAK1_uc003ckz.3_Intron|TRAK1_uc011azj.1_Intron|TRAK1_uc003cla.2_Intron	NM_001042646	NP_001036111	Q9UPV9	TRAK1_HUMAN	OGT(O-Glc-NAc transferase)-interacting protein						endosome to lysosome transport|protein O-linked glycosylation|protein targeting|regulation of transcription from RNA polymerase II promoter	early endosome|mitochondrion|nucleus				ovary(1)	1						TTTTGTTTTTGTTTTTTTTTA	0.313													6	3	---	---	---	---	
CACNA1D	776	broad.mit.edu	37	3	53839966	53839967	+	Intron	INS	-	C	C	rs141385250	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53839966_53839967insC	uc003dgv.3	+						CACNA1D_uc003dgu.3_Intron|CACNA1D_uc003dgy.3_Intron|CACNA1D_uc003dgw.3_Intron|CACNA1D_uc011bes.1_Intron	NM_001128840	NP_001122312	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|upper_aerodigestive_tract(2)|liver(1)|central_nervous_system(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)	tccctcctcctcctccctcatc	0.000													7	5	---	---	---	---	
ARHGEF3	50650	broad.mit.edu	37	3	56937098	56937099	+	Intron	DEL	AC	-	-	rs72331472		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56937098_56937099delAC	uc003dih.2	-						ARHGEF3_uc011bew.1_Intron	NM_001128615	NP_001122087	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor 3 isoform						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)		CTCTAAacatacacacacacac	0.381													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	58284717	58284717	+	IGR	DEL	T	-	-	rs11367948		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58284717delT								ABHD6 (4258 upstream) : RPP14 (7255 downstream)																							tttccagttgttttttttttt	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	73266960	73266960	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73266960delC								PPP4R2 (151949 upstream) : PDZRN3 (164692 downstream)																							ttttcttcctccctccttccc	0.075													5	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	73381919	73381920	+	IGR	INS	-	CC	CC	rs149954246	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73381919_73381920insCC								PPP4R2 (266908 upstream) : PDZRN3 (49732 downstream)																							AGACAACGTATCTGGCTAAATG	0.391													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	82003246	82003251	+	IGR	DEL	AGAGAG	-	-	rs71108356		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82003246_82003251delAGAGAG								GBE1 (192296 upstream) : None (None downstream)																							acacacacacagagagagagagagag	0.155													2	4	---	---	---	---	
EPHA3	2042	broad.mit.edu	37	3	89192757	89192757	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89192757delA	uc003dqy.2	+						EPHA3_uc003dqx.1_Intron|EPHA3_uc010hon.1_Intron	NM_005233	NP_005224	P29320	EPHA3_HUMAN	ephrin receptor EphA3 isoform a precursor							extracellular region|integral to plasma membrane	ATP binding			lung(17)|ovary(7)|large_intestine(4)|central_nervous_system(2)|stomach(1)|skin(1)|pancreas(1)	33	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		aaataattttagatatacgga	0.114										TSP Lung(6;0.00050)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	90366618	90366619	+	IGR	DEL	AG	-	-	rs12488062		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90366618_90366619delAG								EPHA3 (835336 upstream) : None (None downstream)																							ttctacaaaaagagtgtttcaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	93986068	93986068	+	IGR	DEL	G	-	-	rs11294248		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93986068delG								NSUN3 (140438 upstream) : LOC255025 (671039 downstream)																							AATGCAGATTGGGGGGGAAAG	0.418													2	7	---	---	---	---	
ABI3BP	25890	broad.mit.edu	37	3	100700087	100700088	+	Intron	INS	-	A	A	rs145114286		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100700087_100700088insA	uc003dun.2	-						ABI3BP_uc003duo.2_Intron|ABI3BP_uc003dup.3_Intron	NM_015429	NP_056244	Q7Z7G0	TARSH_HUMAN	ABI gene family, member 3 (NESH) binding protein							extracellular space				ovary(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	4						ACTTTTGCCTTAAAAAAAAAAA	0.386													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	109662295	109662296	+	IGR	INS	-	TG	TG	rs140901843	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109662295_109662296insTG								FLJ25363 (448281 upstream) : None (None downstream)																							agttgtgtgtatgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	115529069	115529070	+	IGR	DEL	TC	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115529069_115529070delTC								LSAMP (5051 upstream) : LOC285194 (899565 downstream)																							GTCTCCCCCAtctctctctctc	0.228													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	123173598	123173598	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123173598delA								ADCY5 (6206 upstream) : PTPLB (39765 downstream)																							ctgtcactggaaaaaaaaaaa	0.005													3	3	---	---	---	---	
KALRN	8997	broad.mit.edu	37	3	124167182	124167182	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124167182delA	uc003ehg.2	+						KALRN_uc010hrv.1_Intron|KALRN_uc003ehf.1_Intron|KALRN_uc011bjy.1_Intron|KALRN_uc003ehh.1_Intron	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1						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						ATTCATCTTTAAAATGCTACT	0.398													4	2	---	---	---	---	
RPN1	6184	broad.mit.edu	37	3	128363639	128363639	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128363639delA	uc003ekr.1	-						RPN1_uc011bkq.1_Intron	NM_002950	NP_002941	P04843	RPN1_HUMAN	ribophorin I precursor						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|melanosome|oligosaccharyltransferase complex|rough microsome	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(114;0.189)		tcctctctacaaaaaaaaaaC	0.189			T	EVI1	AML								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	135054533	135054533	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135054533delT								EPHB1 (75228 upstream) : PPP2R3A (630034 downstream)																							GTGGGAGAGATTTTCCTGGGT	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	137585309	137585309	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137585309delC								SOX14 (100913 upstream) : CLDN18 (132349 downstream)																							taggattttgcttgtaacttc	0.000													2	4	---	---	---	---	
DZIP1L	199221	broad.mit.edu	37	3	137782070	137782070	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137782070delC	uc003erq.2	-							NM_173543	NP_775814	Q8IYY4	DZI1L_HUMAN	DAZ interacting protein 1-like							intracellular	zinc ion binding			ovary(1)|pancreas(1)	2						CAGGCAAGTGCCTTGGAAAGG	0.463													5	3	---	---	---	---	
COPB2	9276	broad.mit.edu	37	3	139086136	139086136	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139086136delT	uc003etf.3	-						COPB2_uc011bmv.1_Intron|COPB2_uc010hui.2_Intron	NM_004766	NP_004757	P35606	COPB2_HUMAN	coatomer protein complex, subunit beta 2 (beta						COPI coating of Golgi vesicle|intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol	protein binding|structural molecule activity			ovary(2)	2						TTCCTTGGAAttttttttttt	0.149													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	144726305	144726306	+	IGR	INS	-	GT	GT	rs150558276	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144726305_144726306insGT								None (None upstream) : None (None downstream)																							CAAGAAAAGGGgtgtgtgtgtg	0.203													7	4	---	---	---	---	
HLTF	6596	broad.mit.edu	37	3	148757290	148757291	+	Intron	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148757290_148757291insT	uc003ewq.1	-						HLTF_uc003ewr.1_Intron|HLTF_uc003ews.1_Intron|HLTF_uc010hve.1_Intron	NM_139048	NP_620636	Q14527	HLTF_HUMAN	helicase-like transcription factor						chromatin modification|transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			AACAAATTAAGTTTTTTTTTTT	0.282													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	149701114	149701114	+	IGR	DEL	G	-	-	rs34404328		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149701114delG								PFN2 (12373 upstream) : TSC22D2 (425674 downstream)																							CCAGAGAGCCGGCCCCGGTAG	0.577													4	2	---	---	---	---	
RARRES1	5918	broad.mit.edu	37	3	158448155	158448166	+	Intron	DEL	TCCTTCCTTCCT	-	-	rs75324604		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158448155_158448166delTCCTTCCTTCCT	uc003fci.2	-						RARRES1_uc003fcj.2_Intron	NM_206963	NP_996846	P49788	TIG1_HUMAN	retinoic acid receptor responder (tazarotene						negative regulation of cell proliferation	integral to membrane					0			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)		Tretinoin(DB00755)	AATAGGTTGCtccttccttccttccttccttc	0.071													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	164110524	164110524	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164110524delA								MIR720 (51286 upstream) : SI (586163 downstream)																							aataaattacaaataataatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	165488789	165488790	+	IGR	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165488789_165488790insT								SLITRK3 (574320 upstream) : BCHE (1904 downstream)																							ACAGTCTGCCCTGTAGGAAGGG	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	169910403	169910403	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169910403delT								PHC3 (10866 upstream) : PRKCI (29817 downstream)																							cacatctctcttttttttttt	0.000													4	2	---	---	---	---	
FNDC3B	64778	broad.mit.edu	37	3	171759149	171759150	+	Intron	INS	-	TTTC	TTTC	rs141385729	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171759149_171759150insTTTC	uc003fhy.2	+						FNDC3B_uc003fhz.3_Intron|FNDC3B_uc003fhx.2_Intron	NM_022763	NP_073600	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B							endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		TTAAAAATCGTtttctttcttt	0.168													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	180969669	180969669	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180969669delA								DNAJC19 (262139 upstream) : SOX2OT (311840 downstream)																							AGGAATCAGTAAGGTCTGGCA	0.333													4	2	---	---	---	---	
SOX2OT	347689	broad.mit.edu	37	3	181322083	181322084	+	Intron	DEL	TC	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181322083_181322084delTC	uc003fkv.2	+											Homo sapiens cDNA FLJ12764 fis, clone NT2RP2001506.												0						ctgccagttttctctctccttt	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184335365	184335367	+	IGR	DEL	AAG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184335365_184335367delAAG								EPHB3 (35170 upstream) : MAGEF1 (92789 downstream)																							tgagaaaagaaagaagaagaggg	0.005													4	2	---	---	---	---	
IGF2BP2	10644	broad.mit.edu	37	3	185377017	185377018	+	Intron	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185377017_185377018insA	uc003fpo.2	-						IGF2BP2_uc010hyi.2_Intron|IGF2BP2_uc010hyj.2_Intron|IGF2BP2_uc010hyk.2_Intron|IGF2BP2_uc010hyl.2_Intron|IGF2BP2_uc003fpp.2_Intron|IGF2BP2_uc003fpq.2_Intron	NM_006548	NP_006539	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding						anatomical structure morphogenesis|negative regulation of translation	cytoskeletal part|cytosol|nucleus	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity				0	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			gtctccataagaaaaaaaaaaG	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	189218913	189218913	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189218913delA								TPRG1 (177643 upstream) : TP63 (130303 downstream)																							tccttccttcacttccttcct	0.035													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	189283128	189283131	+	IGR	DEL	CTTT	-	-	rs35312733		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189283128_189283131delCTTT								TPRG1 (241858 upstream) : TP63 (66085 downstream)																							tccctccttcctttcttccttcct	0.010													6	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	190186520	190186523	+	IGR	DEL	TGTG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190186520_190186523delTGTG								TMEM207 (18855 upstream) : IL1RAP (45368 downstream)																							tttgtgtatttgtgtgtgtgtgtg	0.083													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	192820201	192820201	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192820201delC								C3orf59 (184251 upstream) : HRASLS (138717 downstream)																							tgccttgcttcccctttgcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	196359137	196359137	+	IGR	DEL	A	-	-	rs63053761		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196359137delA								FBXO45 (43209 upstream) : LRRC33 (7519 downstream)																							GAGAAGAAAGAAAAACCTACT	0.522													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197364340	197364340	+	IGR	DEL	G	-	-	rs60085265		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197364340delG								LOC220729 (9588 upstream) : KIAA0226 (33919 downstream)																							CCctcaacctgcaacactggc	0.294													4	2	---	---	---	---	
FAM157A	728262	broad.mit.edu	37	3	197900289	197900290	+	Intron	INS	-	C	C	rs148658032		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197900289_197900290insC	uc011bup.1	+						FAM157A_uc011buq.1_Intron	NM_001145248	NP_001138720	C9JC47	F157A_HUMAN	family with sequence similarity 157, member A												0						gggttagggttgggttagggtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	1552448	1552448	+	IGR	DEL	T	-	-	rs78461269		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1552448delT								CRIPAK (162666 upstream) : FAM53A (89161 downstream)																							CCTGCCCCCCTAAATGACACT	0.662													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3589447	3589448	+	Intron	INS	-	GA	GA	rs144006715		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3589447_3589448insGA	uc003ghj.1	+						uc003ghk.1_Intron					Homo sapiens cDNA FLJ35424 fis, clone SMINT2001461.																		CACTCCCAGATGAGACTTCCTG	0.550													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	4745098	4745098	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4745098delC								STX18 (201323 upstream) : MSX1 (116294 downstream)																							gtttccccatccccaccactc	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	5550718	5550721	+	IGR	DEL	TCCC	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5550718_5550721delTCCC								C4orf6 (21193 upstream) : EVC2 (13433 downstream)																							ctttcttccgtccctccctccctc	0.157													4	2	---	---	---	---	
PPP2R2C	5522	broad.mit.edu	37	4	6404225	6404227	+	Intron	DEL	CTT	-	-	rs145570132		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6404225_6404227delCTT	uc003gjc.2	-						PPP2R2C_uc003gjb.2_Intron|PPP2R2C_uc011bwd.1_Intron|PPP2R2C_uc011bwe.1_Intron	NM_020416	NP_065149	Q9Y2T4	2ABG_HUMAN	gamma isoform of regulatory subunit B55, protein						signal transduction	protein phosphatase type 2A complex	protein phosphatase type 2A regulator activity			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4						cttctccttccttctttccttct	0.251													9	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	6686841	6686842	+	IGR	INS	-	TGTG	TGTG	rs140228753	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6686841_6686842insTGTG								LOC93622 (9067 upstream) : S100P (8724 downstream)																							AGGAATCCTCTtgtgtgtgtgt	0.342													3	3	---	---	---	---	
SORCS2	57537	broad.mit.edu	37	4	7597496	7597496	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7597496delG	uc003gkb.3	+						SORCS2_uc011bwi.1_Intron	NM_020777	NP_065828	Q96PQ0	SORC2_HUMAN	VPS10 domain receptor protein SORCS 2 precursor							integral to membrane	neuropeptide receptor activity			ovary(1)|central_nervous_system(1)	2						CAACCTGGATGGGTAGGGACA	0.199													4	2	---	---	---	---	
AFAP1	60312	broad.mit.edu	37	4	7790519	7790520	+	Intron	INS	-	CCC	CCC	rs139758933	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7790519_7790520insCCC	uc003gkg.1	-						AFAP1_uc011bwk.1_Intron	NM_198595	NP_940997	Q8N556	AFAP1_HUMAN	actin filament associated protein 1							actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0						ACAGGGACCATCCCCTCCCCTG	0.554													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	9756944	9756944	+	IGR	DEL	T	-	-	rs34497276		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9756944delT								MIR548I2 (199007 upstream) : DRD5 (26314 downstream)																							TTTTGTTGTCTTTTTTTTTTT	0.403													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	10882919	10882919	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10882919delG								CLNK (196533 upstream) : MIR572 (487532 downstream)																							GGTTCACTCTGCCATCTCATG	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	13150364	13150364	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13150364delG								None (None upstream) : HSP90AB2P (184673 downstream)																							gggacagccaggaacccaaac	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	21987580	21987580	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21987580delG								KCNIP4 (37206 upstream) : GPR125 (401419 downstream)																							ATTCTCCACTGGAAATGCCAT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	24521245	24521245	+	IGR	DEL	G	-	-	rs76407152		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24521245delG								PPARGC1A (629545 upstream) : MIR573 (570 downstream)																							CAGGAGTGCAGGAAAGTCCTC	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	25712271	25712271	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25712271delA								SLC34A2 (31905 upstream) : SEL1L3 (36779 downstream)																							ccaattcatgaaaatttccta	0.000													4	2	---	---	---	---	
STIM2	57620	broad.mit.edu	37	4	27009063	27009063	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27009063delT	uc003gsh.3	+						STIM2_uc003gsg.3_Intron|STIM2_uc010iex.2_Intron|STIM2_uc010iey.2_Intron	NM_020860	NP_065911	Q9P246	STIM2_HUMAN	stromal interaction molecule 2						activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)				TTAAAATAGCTTTTTTTTTTT	0.169													5	3	---	---	---	---	
TMEM156	80008	broad.mit.edu	37	4	38998207	38998208	+	Intron	INS	-	A	A	rs149796057	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38998207_38998208insA	uc003gto.2	-						TMEM156_uc010ifj.2_Intron	NM_024943	NP_079219	Q8N614	TM156_HUMAN	transmembrane protein 156							integral to membrane				skin(1)	1						gaaaagaaaagaaaaaaaaaca	0.000													4	2	---	---	---	---	
N4BP2	55728	broad.mit.edu	37	4	40088810	40088810	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40088810delT	uc003guy.3	+						N4BP2_uc010ifq.2_Intron	NM_018177	NP_060647	Q86UW6	N4BP2_HUMAN	Nedd4 binding protein 2							cytoplasm	ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|endonuclease activity|protein binding			lung(3)|breast(2)|kidney(2)|ovary(1)	8						ttctgtgttcttactgtttCA	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	40748024	40748025	+	IGR	DEL	TT	-	-	rs35989526		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40748024_40748025delTT								RBM47 (115384 upstream) : NSUN7 (3889 downstream)																							CTCCTGAATCtttttttttttt	0.134													4	2	---	---	---	---	
GABRB1	2560	broad.mit.edu	37	4	47394355	47394356	+	Intron	INS	-	TT	TT	rs11423304		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47394355_47394356insTT	uc003gxh.2	+						GABRB1_uc011bze.1_Intron	NM_000812	NP_000803	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta						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			ovary(2)	2					Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	tcccttccaccttttttttttt	0.000													4	2	---	---	---	---	
NFXL1	152518	broad.mit.edu	37	4	47869659	47869660	+	Intron	INS	-	GGA	GGA	rs146916407	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47869659_47869660insGGA	uc010igh.2	-						NFXL1_uc003gxo.2_Intron|NFXL1_uc003gxp.2_Intron|NFXL1_uc003gxq.3_Intron|NFXL1_uc010igi.2_Intron	NM_152995	NP_694540	Q6ZNB6	NFXL1_HUMAN	nuclear transcription factor, X-box binding-like							integral to membrane|nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3						attttaaagatggaggaggagg	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	48496707	48496707	+	IGR	DEL	A	-	-	rs34211079		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48496707delA								ZAR1 (287 upstream) : FRYL (2673 downstream)																							actccatctcaaaaaaaaaaa	0.328													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49272631	49272632	+	IGR	INS	-	GC	GC	rs138265507		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49272631_49272632insGC								CWH43 (208538 upstream) : None (None downstream)																							CGGAATCGCAGGCGCGCATTCC	0.574													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49638583	49638587	+	IGR	DEL	GGAAT	-	-	rs62641032		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49638583_49638587delGGAAT								CWH43 (574490 upstream) : None (None downstream)																							ggaatggaagggaatggaatggaat	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	53136970	53136971	+	IGR	DEL	TC	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53136970_53136971delTC								SPATA18 (173513 upstream) : USP46 (320158 downstream)																							AATGACCTTTTCTCTCTCTCTC	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	53649155	53649160	+	IGR	DEL	AAAGAG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53649155_53649160delAAAGAG								KIAA0114 (68850 upstream) : RASL11B (79335 downstream)																							ATCTGCCAATAaagagaatgttcaca	0.223													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	55413588	55413593	+	IGR	DEL	TCAAAG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55413588_55413593delTCAAAG								PDGFRA (249177 upstream) : KIT (110502 downstream)																							CTAGCAGCTCTCAAAGTCAAACAGGA	0.427													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	56200483	56200483	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56200483delA								KDR (208721 upstream) : SRD5A3 (11926 downstream)																							aaaaggcaacaaaggattttt	0.000													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	57699418	57699420	+	IGR	DEL	TTG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57699418_57699420delTTG								SPINK2 (11525 upstream) : REST (74622 downstream)																							tttttgggttttgttgttgttgt	0.010													4	2	---	---	---	---	
ADAMTS3	9508	broad.mit.edu	37	4	73153062	73153063	+	Intron	DEL	GA	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73153062_73153063delGA	uc003hgk.1	-							NM_014243	NP_055058	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process|collagen fibril organization|proteolysis	proteinaceous extracellular matrix	heparin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			aagagacagggagagagagaga	0.000													4	2	---	---	---	---	
C4orf22	255119	broad.mit.edu	37	4	81816325	81816328	+	Intron	DEL	CACA	-	-	rs71664823		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81816325_81816328delCACA	uc003hmf.2	+						C4orf22_uc010ijp.2_Intron	NM_152770	NP_689983	Q6V702	CD022_HUMAN	hypothetical protein LOC255119											skin(2)	2						atgttctcaccacacacacacaca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	82409792	82409793	+	IGR	DEL	TC	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82409792_82409793delTC								RASGEF1B (16731 upstream) : HNRNPD (864674 downstream)																							ccttgcttcttctctctctctc	0.084													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	82535297	82535297	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82535297delT								RASGEF1B (142236 upstream) : HNRNPD (739170 downstream)																							AATTTGGGCATTTTTTTTTTG	0.249													4	2	---	---	---	---	
TMEM150C	441027	broad.mit.edu	37	4	83434647	83434647	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83434647delA	uc003hmy.1	-						TMEM150C_uc011ccj.1_Intron	NM_001080506	NP_001073975	B9EJG8	T150C_HUMAN	transmembrane protein 150C							integral to membrane				ovary(1)	1						taccacaattaaaaaaaAAAA	0.124													4	2	---	---	---	---	
SCD5	79966	broad.mit.edu	37	4	83700022	83700022	+	Intron	DEL	T	-	-	rs111615476		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83700022delT	uc003hna.2	-						SCD5_uc003hnb.3_Intron|SCD5_uc003hnc.2_Intron	NM_001037582	NP_001032671	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5 isoform a						fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	iron ion binding|stearoyl-CoA 9-desaturase activity			ovary(1)	1		Colorectal(4;0.0323)|Hepatocellular(203;0.115)				ctagctaatcttttttttttt	0.000													4	3	---	---	---	---	
C4orf36	132989	broad.mit.edu	37	4	87797940	87797941	+	Intron	DEL	AA	-	-	rs72349471		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87797940_87797941delAA	uc003hqe.3	-							NM_144645	NP_653246	Q96KX1	CD036_HUMAN	hypothetical protein LOC132989												0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00141)		ATTTTAAAATAAAAAAAaagag	0.163													3	3	---	---	---	---	
ATOH1	474	broad.mit.edu	37	4	94750011	94750011	+	5'Flank	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94750011delT	uc003hta.1	+							NM_005172	NP_005163	Q92858	ATOH1_HUMAN	atonal homolog 1						transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity				0		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;3.57e-07)		GGAAAGGGCCTTTTTTTTGGT	0.567													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	100954361	100954362	+	IGR	INS	-	TG	TG	rs143450943	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100954361_100954362insTG								LOC256880 (80741 upstream) : DDIT4L (152667 downstream)																							taggagatatatgtgtgtgtgt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	105006644	105006645	+	IGR	INS	-	AAG	AAG	rs149600914	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:105006644_105006645insAAG								TACR3 (365671 upstream) : CXXC4 (386700 downstream)																							aggaaagaagaaagaagaagaa	0.005													3	3	---	---	---	---	
SMAD1	4086	broad.mit.edu	37	4	146462444	146462444	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146462444delA	uc003ikc.2	+						SMAD1_uc003ikd.2_Intron|SMAD1_uc010iov.2_Intron|SMAD1_uc011cic.1_Intron	NM_005900	NP_005891	Q15797	SMAD1_HUMAN	Sma- and Mad-related protein 1						BMP signaling pathway|embryonic pattern specification|primary miRNA processing|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway	cytosol|integral to membrane|nuclear inner membrane	co-SMAD binding|I-SMAD binding|identical protein binding|protein kinase binding|sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity			ovary(1)	1	all_hematologic(180;0.151)					GGAAATATGGAAAACAGTTGC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	154783329	154783329	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154783329delT								SFRP2 (73101 upstream) : DCHS2 (372198 downstream)																							ggttttctagtttatgcacat	0.000													4	2	---	---	---	---	
TDO2	6999	broad.mit.edu	37	4	156839122	156839122	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156839122delG	uc003ipf.1	+							NM_005651	NP_005642	P48775	T23O_HUMAN	tryptophan 2,3-dioxygenase						tryptophan catabolic process to kynurenine	cytosol	tryptophan 2,3-dioxygenase activity				0	all_hematologic(180;0.24)	Renal(120;0.0854)		KIRC - Kidney renal clear cell carcinoma(143;0.0455)|Kidney(143;0.0568)|COAD - Colon adenocarcinoma(41;0.141)	L-Tryptophan(DB00150)	TGAAGCAAGTGGAGCGCTAGG	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	157013024	157013024	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157013024delG								CTSO (137976 upstream) : PDGFC (669740 downstream)																							ttttaaataaggttattaagt	0.000													4	2	---	---	---	---	
RXFP1	59350	broad.mit.edu	37	4	159494170	159494171	+	Intron	INS	-	T	T	rs149207993	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159494170_159494171insT	uc003ipz.2	+						RXFP1_uc010iqj.1_Intron|RXFP1_uc011cja.1_Intron|RXFP1_uc010iqo.2_Intron|RXFP1_uc011cjb.1_Intron|RXFP1_uc010iqk.2_Intron|RXFP1_uc011cjc.1_Intron|RXFP1_uc011cjd.1_Intron|RXFP1_uc010iql.2_Intron|RXFP1_uc011cje.1_Intron|RXFP1_uc010iqm.2_Intron|RXFP1_uc011cjf.1_Intron|RXFP1_uc010iqn.2_Intron	NM_021634	NP_067647	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1							integral to membrane|plasma membrane	G-protein coupled receptor activity|metal ion binding				0	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		tcttgtttttgtttttttttga	0.109													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	160112356	160112356	+	IGR	DEL	A	-	-	rs71993124		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160112356delA								C4orf45 (88251 upstream) : RAPGEF2 (76642 downstream)																							aaagagacagaaaaaaaaaat	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	168741275	168741276	+	IGR	DEL	TG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168741275_168741276delTG								SPOCK3 (585534 upstream) : ANXA10 (272431 downstream)																							tgtgtgtgcatgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	170832985	170832985	+	IGR	DEL	A	-	-	rs11318130		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170832985delA								C4orf27 (153892 upstream) : MFAP3L (74765 downstream)																							actccgtctcaaaaaaaaaaa	0.129													4	2	---	---	---	---	
MFAP3L	9848	broad.mit.edu	37	4	170923299	170923300	+	Intron	DEL	GG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170923299_170923300delGG	uc003isp.3	-						MFAP3L_uc003isn.3_Intron	NM_021647	NP_067679	O75121	MFA3L_HUMAN	microfibrillar-associated protein 3-like isoform							integral to membrane|plasma membrane				ovary(1)	1		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0201)|LUSC - Lung squamous cell carcinoma(193;0.116)		TCGGTAGTGAGGATGCCTTTTC	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	171496648	171496648	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:171496648delA								AADAT (485276 upstream) : None (None downstream)																							aaaaagtgagaaaaaggcatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	180073523	180073523	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180073523delC								None (None upstream) : None (None downstream)																							ACCTACGTGGCCCACATGGCA	0.269													4	2	---	---	---	---	
ODZ3	55714	broad.mit.edu	37	4	183080601	183080614	+	Intron	DEL	GTGTGTGTGTGTGT	-	-	rs112827364		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183080601_183080614delGTGTGTGTGTGTGT	uc010irv.1	+									Q9P273	TEN3_HUMAN	Homo sapiens ODZ3 (ODZ3) mRNA, partial cds.						signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		gtgtgtatgagtgtgtgtgtgtgtgtgtgtgtgt	0.192													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190076595	190076596	+	IGR	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190076595_190076596insT								None (None upstream) : FRG1 (785378 downstream)																							GGCTGCAGGGAGGGGAGGCGCA	0.703													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190546312	190546313	+	IGR	DEL	TT	-	-	rs137889406		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190546312_190546313delTT								None (None upstream) : FRG1 (315661 downstream)																							gtttaatgacttaatgcaaata	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190571940	190571940	+	IGR	DEL	C	-	-	rs67653231		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190571940delC								None (None upstream) : FRG1 (290034 downstream)																							cagacttccacaaaaatgttt	0.000													3	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190597276	190597277	+	IGR	INS	-	A	A	rs149616832		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190597276_190597277insA								None (None upstream) : FRG1 (264697 downstream)																							TGATTTTTAAGAAAAAAATCTA	0.342													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190627455	190627455	+	IGR	DEL	A	-	-	rs68065627		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190627455delA								None (None upstream) : FRG1 (234519 downstream)																							TTCAAAGCCTAAAAGCTTTGA	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190757588	190757589	+	IGR	INS	-	CAC	CAC			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190757588_190757589insCAC								None (None upstream) : FRG1 (104385 downstream)																							actagtacacacaccatcacca	0.064													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190845878	190845879	+	Intron	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190845878_190845879insA	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		atcatatatgtaaaaaacccta	0.000													4	2	---	---	---	---	
ZDHHC11	79844	broad.mit.edu	37	5	845557	845557	+	Intron	DEL	C	-	-	rs11347292		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:845557delC	uc011cma.1	-						ZDHHC11_uc003jbj.2_Intron|ZDHHC11_uc010itd.1_5'Flank|ZDHHC11_uc003jbk.2_5'Flank	NM_024786	NP_079062	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11							integral to membrane	acyltransferase activity|zinc ion binding			skin(1)|pancreas(1)	2			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			CTCCCCGCAGCCACCCAGGGA	0.607													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	1185362	1185364	+	IGR	DEL	ATG	-	-	rs66506941		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1185362_1185364delATG								SLC12A7 (73190 upstream) : SLC6A19 (16346 downstream)																							CACACGTGTCATGATGAACTTTA	0.468													4	3	---	---	---	---	
SLC6A19	340024	broad.mit.edu	37	5	1222213	1222214	+	3'UTR	DEL	TG	-	-	rs67714250		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1222213_1222214delTG	uc003jbw.3	+	12						NM_001003841	NP_001003841	Q695T7	S6A19_HUMAN	solute carrier family 6, member 19						cellular nitrogen compound metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity				0	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			gcatgggcactgtgtgagtgtg	0.000													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3970103	3970108	+	IGR	DEL	GTCCAC	-	-	rs66918854		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3970103_3970108delGTCCAC								IRX1 (368587 upstream) : None (None downstream)																							acacacacaagtccacaagtccctag	0.029													1	5	---	---	---	---	
KIAA0947	23379	broad.mit.edu	37	5	5449575	5449575	+	Intron	DEL	A	-	-	rs111912084		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5449575delA	uc003jdm.3	+							NM_015325	NP_056140	Q9Y2F5	K0947_HUMAN	hypothetical protein LOC23379											ovary(1)|central_nervous_system(1)	2						TTTCGACCGGAAAAAAAAAAA	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	10090209	10090221	+	IGR	DEL	GCAGAAGAGGGAG	-	-	rs11272394		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10090209_10090221delGCAGAAGAGGGAG								LOC285692 (186273 upstream) : FAM173B (136217 downstream)																							gtccttaaaagcagaagagggaggcagaagagg	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	12471157	12471158	+	IGR	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12471157_12471158insT								CTNND2 (567047 upstream) : None (None downstream)																							accaggagctgttttttttttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	14073170	14073170	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14073170delA								DNAH5 (128581 upstream) : TRIO (70659 downstream)																							agtctgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	16995047	16995048	+	IGR	INS	-	AGAA	AGAA	rs141924801	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16995047_16995048insAGAA								MYO10 (58662 upstream) : LOC285696 (135089 downstream)																							AAGAAAGTCAGAGGAAGTTTGC	0.441													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	18634298	18634301	+	IGR	DEL	CACA	-	-	rs71843307		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18634298_18634301delCACA								None (None upstream) : CDH18 (838856 downstream)																							ccctgtcatgcacacacacacaca	0.098													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	20782163	20782163	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20782163delA	uc003jge.1	+											Homo sapiens cDNA FLJ36043 fis, clone TESTI2017582.																		gaagatgtggaaaaagagaac	0.010													1	5	---	---	---	---	
GUSBP1	728411	broad.mit.edu	37	5	21535337	21535340	+	Intron	DEL	AAAG	-	-	rs146609299		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21535337_21535340delAAAG	uc011cnn.1	+						GUSBP1_uc003jgh.3_Intron					Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0						aatcaaagacaaagaaataatatt	0.000													2	8	---	---	---	---	
GUSBP1	728411	broad.mit.edu	37	5	21563005	21563006	+	Intron	INS	-	AA	AA	rs139587606	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21563005_21563006insAA	uc003jgh.3	+							NR_027026				Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0						ATGCTTAACTCGAGAAAGTTAA	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	23249978	23249978	+	IGR	DEL	T	-	-	rs145883373		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23249978delT								CDH12 (396247 upstream) : PRDM9 (257746 downstream)																							tactggcctattttttttttt	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	23370332	23370335	+	IGR	DEL	TGTG	-	-	rs72015611		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23370332_23370335delTGTG								CDH12 (516601 upstream) : PRDM9 (137389 downstream)																							CCCTCATAGTtgtgtgtgtgtgtg	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	24764236	24764236	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24764236delT								CDH10 (119325 upstream) : None (None downstream)																							tttttttttcttttttttttt	0.030													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	28858542	28858543	+	IGR	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28858542_28858543insT								None (None upstream) : None (None downstream)																							TCTCGTACTGCttttttttttt	0.163													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	29068022	29068031	+	IGR	DEL	CCCTCTCTTT	-	-	rs57540117		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29068022_29068031delCCCTCTCTTT								None (None upstream) : None (None downstream)																							tctcctcttcccctctctttccctctcttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	29431510	29431513	+	IGR	DEL	AAAT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29431510_29431513delAAAT								None (None upstream) : None (None downstream)																							GAGATGAGAAaaataaataaataa	0.245													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	30674056	30674056	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30674056delA								None (None upstream) : CDH6 (519740 downstream)																							aaagtataccaaaaaaaaaaa	0.015													3	3	---	---	---	---	
CDH6	1004	broad.mit.edu	37	5	31235055	31235055	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31235055delC	uc003jhe.1	+						CDH6_uc003jhc.1_Intron|CDH6_uc003jhd.1_Intron	NM_004932	NP_004923	P55285	CADH6_HUMAN	cadherin 6, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	cytoplasm|integral to membrane|nucleus|plasma membrane	calcium ion binding			ovary(4)|skin(2)|large_intestine(1)	7						AGCATCCTGTCCCCAAGCACT	0.333													2	5	---	---	---	---	
PDZD2	23037	broad.mit.edu	37	5	31741300	31741301	+	Intron	DEL	AC	-	-	rs140513180		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31741300_31741301delAC	uc003jhl.2	+							NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9						AATAGTGTGTacacacacacac	0.064													4	2	---	---	---	---	
ZFR	51663	broad.mit.edu	37	5	32433004	32433004	+	Intron	DEL	T	-	-	rs35127723		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32433004delT	uc003jhr.1	-						ZFR_uc010iun.1_Intron	NM_016107	NP_057191	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein						multicellular organismal development	chromosome|cytoplasm|nucleus	DNA binding|RNA binding|zinc ion binding				0				STAD - Stomach adenocarcinoma(35;0.19)		tggctaattgttttttttttt	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	33162897	33162897	+	RNA	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33162897delC	uc003jhx.2	+	1		c.632delC								full-length cDNA clone CS0DI021YI22 of Placenta Cot 25-normalized of Homo sapiens (human).																		AAAATCAAGGCCCGGAAAGGC	0.433													8	15	---	---	---	---	
RAI14	26064	broad.mit.edu	37	5	34817941	34817941	+	Intron	DEL	A	-	-	rs73078677	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34817941delA	uc003jir.2	+						RAI14_uc010iur.2_Intron|RAI14_uc011coj.1_Intron|RAI14_uc010ius.1_Intron|RAI14_uc003jis.2_Intron|RAI14_uc003jit.2_Intron|RAI14_uc011cok.1_Intron	NM_015577	NP_056392	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14 isoform a							cell cortex|cytoskeleton	protein binding			ovary(1)	1	all_lung(31;0.000191)					gactggttgtaatgaagcatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	35358361	35358361	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35358361delC								PRLR (127567 upstream) : SPEF2 (259628 downstream)																							ATACCCTCTGCCCCCTCCCTA	0.458													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	36489704	36489705	+	IGR	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36489704_36489705insA								RANBP3L (187693 upstream) : SLC1A3 (116752 downstream)																							ttcatcactacaaaaaaaaaaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	38655341	38655341	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38655341delT	uc003jlj.2	+											Homo sapiens cDNA clone IMAGE:4829282.																		AACGCACTGCTTTTTTTTTTT	0.274													4	2	---	---	---	---	
RICTOR	253260	broad.mit.edu	37	5	38958957	38958957	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38958957delA	uc003jlp.2	-						RICTOR_uc003jlo.2_Intron|RICTOR_uc010ivf.2_Intron	NM_152756	NP_689969	Q6R327	RICTR_HUMAN	rapamycin-insensitive companion of mTOR						actin cytoskeleton reorganization|embryo development|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|regulation of protein kinase B signaling cascade|T cell costimulation	cytosol|TORC2 complex	protein binding			ovary(3)|lung(3)|skin(2)|kidney(1)|central_nervous_system(1)	10	all_lung(31;0.000396)					TGAATACATTAAAAAAAAAAA	0.328													16	7	---	---	---	---	
RICTOR	253260	broad.mit.edu	37	5	39055439	39055439	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39055439delT	uc003jlp.2	-						RICTOR_uc003jlo.2_Intron|RICTOR_uc010ivf.2_Intron|RICTOR_uc003jlq.1_Intron|RICTOR_uc011cpk.1_Intron	NM_152756	NP_689969	Q6R327	RICTR_HUMAN	rapamycin-insensitive companion of mTOR						actin cytoskeleton reorganization|embryo development|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|regulation of protein kinase B signaling cascade|T cell costimulation	cytosol|TORC2 complex	protein binding			ovary(3)|lung(3)|skin(2)|kidney(1)|central_nervous_system(1)	10	all_lung(31;0.000396)					ttccttctacttgaagacttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	40805441	40805441	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40805441delT								PRKAA1 (7144 upstream) : RPL37 (25989 downstream)																							GGAAGGAATCttttttttttt	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	43571543	43571544	+	IGR	INS	-	T	T	rs151000710	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43571543_43571544insT								PAIP1 (14022 upstream) : NNT (31247 downstream)																							ctcgtctcgaattttttcttgc	0.010													4	5	---	---	---	---	
ITGA1	3672	broad.mit.edu	37	5	52157370	52157371	+	Frame_Shift_Ins	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52157370_52157371insT	uc003jou.2	+	3	324_325	c.272_273insT	c.(271-273)CCTfs	p.P91fs	ITGA1_uc003jov.2_RNA	NM_181501	NP_852478	P56199	ITA1_HUMAN	integrin, alpha 1 precursor	91	Extracellular (Potential).|FG-GAP 1.				axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|muscle contraction	integrin complex	collagen binding|receptor activity			ovary(2)|lung(1)	3		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				GAATCATTACCTTGTGTAAAGT	0.292													27	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	53770009	53770010	+	IGR	INS	-	TCTG	TCTG	rs141861757	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53770009_53770010insTCTG								HSPB3 (17802 upstream) : SNX18 (43579 downstream)																							gccccgccAATTCTTTTTGTTG	0.020													0	6	---	---	---	---	
PDE4D	5144	broad.mit.edu	37	5	59136061	59136064	+	Intron	DEL	CACA	-	-	rs34889262		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59136061_59136064delCACA	uc003jsa.2	-						PDE4D_uc003jsb.2_Intron	NM_001104631	NP_001098101	Q08499	PDE4D_HUMAN	phosphodiesterase 4D isoform 1						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)	cgtgcactgccacacacacacaca	0.000													4	2	---	---	---	---	
RGNEF	64283	broad.mit.edu	37	5	72951154	72951154	+	Intron	DEL	T	-	-	rs34130193		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72951154delT	uc003kcx.2	+							NM_001080479	NP_001073948	Q8N1W1	RGNEF_HUMAN	Rho-guanine nucleotide exchange factor						cell differentiation|intracellular signal transduction|regulation of Rho protein signal transduction	cytoplasm|plasma membrane	metal ion binding|Rho guanyl-nucleotide exchange factor activity|RNA binding				0		Lung NSC(167;0.0378)|all_lung(232;0.04)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.25e-51)		TTCTTGGTAGTTTTTAATGAT	0.353													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	74292360	74292361	+	IGR	INS	-	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74292360_74292361insC								FAM169A (100572 upstream) : GCNT4 (30929 downstream)																							caacctaggtgcccatcaacag	0.000													4	2	---	---	---	---	
OTP	23440	broad.mit.edu	37	5	76937234	76937235	+	5'Flank	INS	-	G	G	rs139750488	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76937234_76937235insG	uc003kfg.2	-							NM_032109	NP_115485	Q5XKR4	OTP_HUMAN	orthopedia homeobox							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)		ATAAGCATCTCGGGGGGGGGAA	0.475													4	2	---	---	---	---	
FAM151B	167555	broad.mit.edu	37	5	79796999	79797000	+	Intron	INS	-	T	T	rs76066273		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79796999_79797000insT	uc003kgv.1	+						FAM151B_uc010jal.1_Intron	NM_205548	NP_991111	Q6UXP7	F151B_HUMAN	hypothetical protein LOC167555												0		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;8.21e-47)|Epithelial(54;8.3e-42)|all cancers(79;1.97e-36)		cacctggctaattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	86199237	86199238	+	IGR	DEL	TC	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86199237_86199238delTC								COX7C (282656 upstream) : RASA1 (364913 downstream)																							CTTCACATTTTCTGTTTAGGTA	0.342													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	100994733	100994733	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100994733delG								ST8SIA4 (755746 upstream) : SLCO4C1 (574961 downstream)																							ttacaggcgtgagacaccaca	0.169													3	4	---	---	---	---	
SRP19	6728	broad.mit.edu	37	5	112198072	112198074	+	Intron	DEL	AGG	-	-	rs112093457		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112198072_112198074delAGG	uc003kqc.2	+						SRP19_uc003kqb.1_Intron|SRP19_uc011cvu.1_Intron|SRP19_uc011cvv.1_Intron	NM_003135	NP_003126	P09132	SRP19_HUMAN	signal recognition particle 19kDa						response to drug|SRP-dependent cotranslational protein targeting to membrane	cytosol|mitochondrion|nucleolus|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding				0		all_cancers(142;0.00328)|all_epithelial(76;6.39e-05)|Prostate(80;0.00174)|Colorectal(10;0.00372)|Ovarian(225;0.156)		Epithelial(69;1.7e-09)|OV - Ovarian serous cystadenocarcinoma(64;1.17e-08)|all cancers(49;3.96e-07)|Colorectal(14;0.0056)|COAD - Colon adenocarcinoma(37;0.0104)		acgcagaaaaaggaggggttgaa	0.025													1	5	---	---	---	---	
SEC24A	10802	broad.mit.edu	37	5	134023936	134023945	+	Frame_Shift_Del	DEL	GTCTTCAGGA	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134023936_134023945delGTCTTCAGGA	uc003kzs.2	+	11	1958_1967	c.1670_1679delGTCTTCAGGA	c.(1669-1680)GGTCTTCAGGAAfs	p.G557fs	SEC24A_uc011cxu.1_Frame_Shift_Del_p.G321fs	NM_021982	NP_068817	O95486	SC24A_HUMAN	SEC24 related gene family, member A	557_560					COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	zinc ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CATTTCTACGGTCTTCAGGAAAGTCTCTCT	0.310													22	14	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	134065981	134065981	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134065981delT								SEC24A (2381 upstream) : CAMLG (8225 downstream)																							TATAATTGCCTTTTCCTGACC	0.393													4	2	---	---	---	---	
TRPC7	57113	broad.mit.edu	37	5	135654532	135654533	+	Intron	INS	-	T	T	rs146859082	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135654532_135654533insT	uc003lbn.1	-						TRPC7_uc010jef.1_Intron|TRPC7_uc010jeg.1_Intron|TRPC7_uc010jeh.1_Intron|TRPC7_uc010jei.1_Intron|TRPC7_uc010jej.1_Intron	NM_020389	NP_065122	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel,						axon guidance|platelet activation	integral to membrane|plasma membrane	calcium channel activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			tttcactgttgtttttttttta	0.000													4	2	---	---	---	---	
PCDHAC1	56135	broad.mit.edu	37	5	140331679	140331679	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140331679delA	uc003lih.2	+						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_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Intron|PCDHA13_uc003lif.2_Intron	NM_018898	NP_061721	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1 isoform 1						homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			skin(3)|ovary(2)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			tctcacatccagggcacactc	0.000													4	2	---	---	---	---	
SLC36A1	206358	broad.mit.edu	37	5	150846881	150846882	+	Intron	DEL	AC	-	-	rs61191955	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150846881_150846882delAC	uc003luc.2	+						GM2A_uc011dcs.1_Intron|SLC36A1_uc003lub.1_Intron|SLC36A1_uc010jhw.1_Intron	NM_078483	NP_510968	Q7Z2H8	S36A1_HUMAN	solute carrier family 36 member 1						cellular nitrogen compound metabolic process|ion transport	endoplasmic reticulum|integral to membrane|lysosomal membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			skin(1)	1		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)|all_neural(839;0.138)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Glycine(DB00145)|L-Alanine(DB00160)	aaaaaaaaaaaCCAGAGCGAGA	0.332													6	4	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	167398373	167398374	+	Intron	INS	-	AGA	AGA	rs139472586	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167398373_167398374insAGA	uc010jjd.2	+						ODZ2_uc003lzq.2_Intron|ODZ2_uc003lzr.3_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		TAGAAAATATTAGAAGGAGTCA	0.327													4	2	---	---	---	---	
C5orf25	375484	broad.mit.edu	37	5	175669058	175669058	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175669058delA	uc003mds.3	+						C5orf25_uc003mdt.3_Intron|C5orf25_uc003mdr.3_Intron|C5orf25_uc011dfk.1_Intron			Q8NDZ2	CE025_HUMAN	RecName: Full=Uncharacterized protein C5orf25;												0	all_cancers(89;0.00381)|Renal(175;0.000269)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	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;0.000178)	Kidney(146;0.119)		gtatatgtggaaaaaaaccca	0.000													4	2	---	---	---	---	
RASGEF1C	255426	broad.mit.edu	37	5	179569353	179569353	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179569353delG	uc003mlr.2	-							NM_175062	NP_778232	Q8N431	RGF1C_HUMAN	RasGEF domain family, member 1C						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity			ovary(1)	1	all_cancers(89;3.44e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0242)|Medulloblastoma(196;0.00498)|all_neural(177;0.0137)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			acaccactgcggggaggggtg	0.030													4	2	---	---	---	---	
DUSP22	56940	broad.mit.edu	37	6	304312	304312	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:304312delG	uc003msx.2	+						DUSP22_uc011dhn.1_Intron|DUSP22_uc003msy.1_5'Flank	NM_020185	NP_064570	Q9NRW4	DUS22_HUMAN	dual specificity phosphatase 22						apoptosis|cell proliferation|inactivation of MAPK activity|multicellular organismal development|positive regulation of JNK cascade|regulation of cell proliferation|transforming growth factor beta receptor signaling pathway	cytoplasm|nucleus	protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	all_hematologic(77;0.228)	Breast(5;0.0249)|all_hematologic(90;0.0489)		OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669)		CTGCAGGGCCGCCAGGGCTGT	0.677													13	7	---	---	---	---	
C6orf105	84830	broad.mit.edu	37	6	11764778	11764778	+	Intron	DEL	T	-	-	rs150691019		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11764778delT	uc003nab.2	-						C6orf105_uc011dip.1_Intron	NM_032744	NP_116133	Q96IZ2	CF105_HUMAN	hypothetical protein LOC84830 isoform 2							integral to membrane					0	Ovarian(93;0.0848)|Breast(50;0.0871)	all_hematologic(90;0.135)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.193)			ATGAGGATTCTTTTTTTTTTT	0.333													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	12558006	12558006	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12558006delG								EDN1 (260580 upstream) : PHACTR1 (158882 downstream)																							ggttagaggtggcaggagagg	0.154													4	2	---	---	---	---	
RBM24	221662	broad.mit.edu	37	6	17282739	17282739	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17282739delC	uc003nbz.3	+						RBM24_uc003nby.3_Intron|RBM24_uc011dix.1_Intron|RBM24_uc003nca.2_5'Flank	NM_001143942	NP_001137414	Q9BX46	RBM24_HUMAN	RNA binding motif protein 24 isoform 1						cell differentiation|regulation of mRNA stability|regulation of myotube differentiation	cytoplasm|nucleus	mRNA 3'-UTR binding|nucleotide binding			ovary(1)|skin(1)	2	Breast(50;0.0615)|Ovarian(93;0.0733)	all_hematologic(90;0.062)	all cancers(50;0.131)|Epithelial(50;0.15)			ATTTAGGCTTCCAAATCTCGG	0.522													4	2	---	---	---	---	
KIF13A	63971	broad.mit.edu	37	6	17913454	17913454	+	Intron	DEL	G	-	-	rs35912032		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17913454delG	uc003ncg.3	-						KIF13A_uc003ncf.2_Intron|KIF13A_uc003nch.3_Intron|KIF13A_uc003nci.3_Intron	NM_022113	NP_071396	Q9H1H9	KI13A_HUMAN	kinesin family member 13A isoform a						cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			GATTACGGGAGGAGCAGGGAG	0.448													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	20247317	20247318	+	IGR	DEL	CA	-	-	rs34935593		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20247317_20247318delCA								MBOAT1 (34647 upstream) : E2F3 (154819 downstream)																							catacacacgcacacacacaca	0.000													4	2	---	---	---	---	
CDKAL1	54901	broad.mit.edu	37	6	20946410	20946410	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20946410delC	uc003ndc.1	+						CDKAL1_uc003ndd.1_Intron|CDKAL1_uc003nde.1_Intron	NM_017774	NP_060244	Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein						RNA modification	integral to membrane	4 iron, 4 sulfur cluster binding|metal ion binding|transferase activity			ovary(2)	2	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			ATAACAACTTCCATTAACACT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	23145298	23145299	+	IGR	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23145298_23145299insT								HDGFL1 (574549 upstream) : NRSN1 (981115 downstream)																							GTTCCCAAGCCTTTTTTTTCTG	0.391													4	2	---	---	---	---	
BTN2A2	10385	broad.mit.edu	37	6	26382994	26382995	+	5'Flank	DEL	AG	-	-	rs67857541		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26382994_26382995delAG	uc003nhq.2	+						BTN2A2_uc011dkf.1_5'Flank|BTN2A2_uc011dkg.1_5'Flank|BTN2A2_uc003nhr.2_5'Flank|BTN2A2_uc011dkh.1_5'Flank|BTN2A2_uc003nhs.2_5'Flank|BTN2A2_uc003nht.2_5'Flank	NM_006995	NP_008926	Q8WVV5	BT2A2_HUMAN	butyrophilin, subfamily 2, member A2 isoform a						negative regulation of activated T cell proliferation|negative regulation of cellular metabolic process|negative regulation of cytokine secretion	integral to membrane					0						ggaagaaaaaagaaagaaagcg	0.000													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	27665415	27665416	+	Intron	INS	-	T	T	rs73387087		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27665415_27665416insT	uc003njk.2	+											Homo sapiens cDNA clone IMAGE:5262055.																		ATGATAGAATAttttttttttt	0.188													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	28345563	28345564	+	IGR	INS	-	C	C	rs143408024	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28345563_28345564insC								ZKSCAN3 (11040 upstream) : ZSCAN12 (1206 downstream)																							aacaagcaagacccccccggaa	0.000													1	6	---	---	---	---	
LHFPL5	222662	broad.mit.edu	37	6	35791408	35791409	+	3'UTR	INS	-	G	G	rs147136847	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35791408_35791409insG	uc003olg.1	+	4						NM_182548	NP_872354	Q8TAF8	TMHS_HUMAN	lipoma HMGIC fusion partner-like 5							integral to membrane				skin(1)	1						TGCTGCTCAGAGGGGGGTAAGG	0.455													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	40640824	40640826	+	IGR	DEL	CTT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40640824_40640826delCTT								LRFN2 (85698 upstream) : UNC5CL (353946 downstream)																							ctccccccgccttcttcttcttc	0.103													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	44587610	44587611	+	IGR	INS	-	CA	CA	rs150879266	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44587610_44587611insCA								CDC5L (172831 upstream) : SUPT3H (189443 downstream)																							Tcacacacgtgcacacacacac	0.327													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	46058140	46058140	+	IGR	DEL	G	-	-	rs62399752		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46058140delG								CLIC5 (10055 upstream) : ENPP4 (39561 downstream)																							TCAACTTGATGGGTTTTTTTT	0.388											OREG0017485	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	3	---	---	---	---	
RCAN2	10231	broad.mit.edu	37	6	46326108	46326108	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46326108delG	uc003oyc.1	-						RCAN2_uc003oyd.1_Intron			Q14206	RCAN2_HUMAN	SubName: Full=cDNA, FLJ92723, highly similar to Homo sapiens Down syndrome critical region gene 1-like 1 (DSCR1L1), mRNA;						calcium-mediated signaling|central nervous system development		nucleotide binding|protein phosphatase 2B binding				0						CAGGGACAGTGGCAGGGGAGG	0.542													4	2	---	---	---	---	
MEP1A	4224	broad.mit.edu	37	6	46798699	46798699	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46798699delT	uc010jzh.1	+						MEP1A_uc011dwg.1_Intron|MEP1A_uc011dwh.1_Intron|MEP1A_uc011dwi.1_Intron	NM_005588	NP_005579	Q16819	MEP1A_HUMAN	meprin A alpha precursor						digestion|proteolysis	extracellular space|integral to plasma membrane|soluble fraction	metalloendopeptidase activity|zinc ion binding			pancreas(2)|ovary(1)	3			Lung(136;0.192)			ATGGGACCTATTATCACTCAC	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	50110072	50110073	+	IGR	DEL	AC	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50110072_50110073delAC								DEFB112 (93708 upstream) : TFAP2D (571184 downstream)																							ataaacacagacacacacacac	0.252													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	50239575	50239575	+	IGR	DEL	A	-	-	rs35540589		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50239575delA								DEFB112 (223211 upstream) : TFAP2D (441682 downstream)																							GGGAAATGATAAAAAAAAAGT	0.239													4	6	---	---	---	---	
TFAP2D	83741	broad.mit.edu	37	6	50678776	50678777	+	5'Flank	DEL	CA	-	-	rs13215781		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50678776_50678777delCA	uc003paf.2	+						TFAP2D_uc011dwt.1_5'Flank	NM_172238	NP_758438	Q7Z6R9	AP2D_HUMAN	transcription factor AP-2 beta-like 1								DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|breast(1)	7	Lung NSC(77;0.0334)					cacatcacatcacacacacaca	0.327													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	54456290	54456290	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54456290delA								TINAG (201340 upstream) : FAM83B (255279 downstream)																							cagggtcatgaaaaaaaaagc	0.015													4	2	---	---	---	---	
COL21A1	81578	broad.mit.edu	37	6	55958175	55958175	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55958175delA	uc003pcs.2	-						COL21A1_uc010jzz.2_Intron|COL21A1_uc011dxg.1_Intron|COL21A1_uc011dxh.1_Intron|COL21A1_uc003pcr.2_5'Flank	NM_030820	NP_110447	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1 precursor						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(2)	2	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			cttgttatctaaatcaggtat	0.000													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57219137	57219138	+	Intron	INS	-	TCTTA	TCTTA	rs143003076	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57219137_57219138insTCTTA	uc003pdx.2	+						PRIM2_uc003pdw.2_Intron	NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		TATTTTTCTTCTGAGTATTGTG	0.297													3	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57224536	57224536	+	Intron	DEL	T	-	-	rs11352925		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57224536delT	uc003pdx.2	+						PRIM2_uc003pdw.2_Intron	NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		CTATTAACAATTAAATAATAT	0.308													3	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57224687	57224687	+	Intron	DEL	G	-	-	rs5876538		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57224687delG	uc003pdx.2	+						PRIM2_uc003pdw.2_Intron	NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		CTGCTTAAAAGTTAGCTGAGA	0.358													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57265999	57266006	+	Intron	DEL	CTTTGGTT	-	-	rs111641104		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57265999_57266006delCTTTGGTT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		ggagttcttgctttggttctttctcatc	0.000													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57362882	57362883	+	Intron	INS	-	TGT	TGT	rs138041336	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57362882_57362883insTGT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		ACAGGATTTTCTGTTAAAATCA	0.347													3	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57391354	57391355	+	Intron	INS	-	T	T	rs5876592		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57391354_57391355insT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		CTTGCCTTGTCTTTTTCCTTTT	0.302													9	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57436081	57436082	+	Intron	INS	-	T	T	rs149176852	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57436081_57436082insT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		cttttcttttcttttctttttg	0.129													4	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57439748	57439750	+	Intron	DEL	TTC	-	-	rs78957849		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57439748_57439750delTTC	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		ATCCTCAGCTTTCTTTTTTTATT	0.281													5	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57444301	57444301	+	Intron	DEL	T	-	-	rs113862454		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57444301delT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		tcatgtctccttaatctcttc	0.000													8	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57534556	57534556	+	IGR	DEL	T	-	-	rs67039622		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57534556delT								PRIM2 (21181 upstream) : GUSBL2 (711603 downstream)																							cttattctgatgtagttacat	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57536514	57536515	+	IGR	DEL	CT	-	-	rs111477220		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57536514_57536515delCT								PRIM2 (23139 upstream) : GUSBL2 (709644 downstream)																							cagagtgatactctgtctcaaa	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57562229	57562229	+	IGR	DEL	G	-	-	rs67409233		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57562229delG								PRIM2 (48854 upstream) : GUSBL2 (683930 downstream)																							tttgttgcttgggtaaaataa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	58326516	58326517	+	IGR	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58326516_58326517insA								GUSBL2 (38792 upstream) : None (None downstream)																							ttctaaaccccaatgtggtgac	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	58327370	58327370	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58327370delC								GUSBL2 (39646 upstream) : None (None downstream)																							TCTGAGTCCTCCCCAGGCCTT	0.537													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	66480841	66480841	+	IGR	DEL	T	-	-	rs71810903		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66480841delT								EYS (63723 upstream) : MCART3P (16931 downstream)																							GTTTGTTGTGTTTTTTTTTTT	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	67764748	67764749	+	IGR	INS	-	T	T	rs142123264	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:67764748_67764749insT								None (None upstream) : None (None downstream)																							tttcttgtctgttttttttttc	0.000													4	2	---	---	---	---	
BAI3	577	broad.mit.edu	37	6	69810856	69810859	+	Intron	DEL	AGAA	-	-	rs117995213	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69810856_69810859delAGAA	uc003pev.3	+						BAI3_uc010kak.2_Intron	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3						negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)				ggagggagggagaaagggaaggaa	0.157													4	2	---	---	---	---	
RIMS1	22999	broad.mit.edu	37	6	72702336	72702337	+	Intron	INS	-	TCTTCC	TCTTCC			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72702336_72702337insTCTTCC	uc003pga.2	+							NM_014989	NP_055804	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1						calcium ion-dependent exocytosis|cellular membrane fusion|glutamate secretion|intracellular protein transport|protein complex assembly|regulated secretory pathway|response to stimulus|synaptic vesicle exocytosis|visual perception	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(7)|pancreas(2)|breast(1)	10		all_epithelial(107;0.179)|all_hematologic(105;0.212)				cttcttcctcttcttcctcttc	0.000													5	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	75737033	75737034	+	IGR	DEL	CT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75737033_75737034delCT								None (None upstream) : COL12A1 (57009 downstream)																							cccatctctactaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	77231620	77231620	+	IGR	DEL	T	-	-	rs67711717		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77231620delT								IMPG1 (449285 upstream) : HTR1B (940328 downstream)																							TATTTTTGCAttttttttttt	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	79187739	79187740	+	IGR	INS	-	T	T	rs139665624		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79187739_79187740insT								None (None upstream) : IRAK1BP1 (389449 downstream)																							tgttttttttgttttttttggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	84461250	84461251	+	IGR	DEL	GT	-	-	rs72215320		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84461250_84461251delGT								SNAP91 (42123 upstream) : RIPPLY2 (101734 downstream)																							TTATAtgtacgtgtgtgtgtgt	0.213													4	4	---	---	---	---	
TBX18	9096	broad.mit.edu	37	6	85417559	85417560	+	Intron	DEL	TG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85417559_85417560delTG	uc010kbq.1	-							NM_001080508	NP_001073977	O95935	TBX18_HUMAN	T-box 18						multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|pancreas(2)|lung(1)	5		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		tgtgtgtgtatgtgtgtgtgtg	0.272													4	2	---	---	---	---	
ZBTB24	9841	broad.mit.edu	37	6	109802814	109802816	+	In_Frame_Del	DEL	GTT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109802814_109802816delGTT	uc003ptl.1	-	2	582_584	c.414_416delAAC	c.(412-417)ACAACT>ACT	p.138_139TT>T	ZBTB24_uc011ear.1_RNA|ZBTB24_uc010kds.1_In_Frame_Del_p.138_139TT>T|ZBTB24_uc010kdt.1_RNA|ZBTB24_uc003ptm.2_In_Frame_Del_p.138_139TT>T	NM_014797	NP_055612	O43167	ZBT24_HUMAN	zinc finger and BTB domain containing 24 isoform	138_139					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0154)|all cancers(137;0.0216)|OV - Ovarian serous cystadenocarcinoma(136;0.0242)|BRCA - Breast invasive adenocarcinoma(108;0.059)		AGTGTTCAAAGTTGTTGGCTTTG	0.424													104	46	---	---	---	---	
RWDD1	51389	broad.mit.edu	37	6	116912262	116912262	+	Intron	DEL	A	-	-	rs78170063		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116912262delA	uc003pxd.2	+						RWDD1_uc003pxb.2_Intron|RWDD1_uc003pxc.2_Intron	NM_015952	NP_057036	Q9H446	RWDD1_HUMAN	RWD domain containing 1 isoform a								protein binding			ovary(2)|central_nervous_system(1)	3		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.026)|all cancers(137;0.0312)|OV - Ovarian serous cystadenocarcinoma(136;0.0689)|Epithelial(106;0.161)		tgactctattaaaaaaaaaaa	0.119													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	130207950	130207950	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130207950delC								C6orf191 (25534 upstream) : L3MBTL3 (131784 downstream)																							ACATGAACTGCCATATCTGAA	0.224													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	134976960	134976960	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134976960delG								SGK1 (337764 upstream) : ALDH8A1 (261569 downstream)																							GATTCCTCAAGGAAAGCATGA	0.363													4	2	---	---	---	---	
PDE7B	27115	broad.mit.edu	37	6	136477301	136477304	+	Intron	DEL	GTGT	-	-	rs35092466		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136477301_136477304delGTGT	uc003qgp.2	+						uc003qgq.1_Intron|PDE7B_uc003qgr.2_Intron	NM_018945	NP_061818	Q9NP56	PDE7B_HUMAN	phosphodiesterase 7B						signal transduction|synaptic transmission	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(1)	1	Colorectal(23;0.24)			OV - Ovarian serous cystadenocarcinoma(155;0.0136)|GBM - Glioblastoma multiforme(68;0.0147)	Dyphylline(DB00651)|Ketotifen(DB00920)	AATGATCCAAgtgtgtgtgtgtgt	0.191													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	138092592	138092593	+	IGR	DEL	GT	-	-	rs9484089		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138092592_138092593delGT								OLIG3 (277061 upstream) : TNFAIP3 (95988 downstream)																							AACTAAGTACgtgtgtgtgtgt	0.292													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	150272045	150272048	+	IGR	DEL	TGTT	-	-	rs10551158		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150272045_150272048delTGTT								ULBP2 (1679 upstream) : ULBP1 (13095 downstream)																							tatgtatgtgtgtttgtttgtgtg	0.054													3	3	---	---	---	---	
TIAM2	26230	broad.mit.edu	37	6	155377642	155377643	+	Intron	INS	-	T	T	rs141305321	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155377642_155377643insT	uc003qqb.2	+							NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2						apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		GAATTCAGAAATTTTTTTGCTC	0.243													3	4	---	---	---	---	
ARID1B	57492	broad.mit.edu	37	6	157249766	157249766	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157249766delC	uc003qqn.2	+						ARID1B_uc003qqo.2_Intron|ARID1B_uc003qqp.2_Intron	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)						chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		ACTTGAGGGGCCCCCATTCTT	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	158158316	158158316	+	IGR	DEL	T	-	-	rs141906900		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158158316delT								ZDHHC14 (63340 upstream) : SNX9 (85978 downstream)																							ctggtcctcattttttttttt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	159722650	159722650	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159722650delT								FNDC1 (29511 upstream) : SOD2 (377501 downstream)																							attgcaacAAttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	160329541	160329542	+	IGR	INS	-	CA	CA	rs141326570	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160329541_160329542insCA								MAS1 (436 upstream) : IGF2R (60589 downstream)																							GTTTTGTAAAGcacacacacac	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	164360710	164360710	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164360710delA								QKI (365818 upstream) : None (None downstream)																							ATCATCCCTCAGCCTCACAGC	0.582													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	165027230	165027230	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165027230delG								None (None upstream) : C6orf118 (665925 downstream)																							aggggagactgatccaccact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	166585418	166585419	+	IGR	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166585418_166585419insT								T (3287 upstream) : PRR18 (133749 downstream)																							cagatacttaattttttcaatg	0.000													4	2	---	---	---	---	
UNC93A	54346	broad.mit.edu	37	6	167725388	167725389	+	Intron	INS	-	TC	TC	rs147774750	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167725388_167725389insTC	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)		ccacggcacattcgtacagcta	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	167846747	167846749	+	IGR	DEL	GGT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167846747_167846749delGGT								TCP10 (48749 upstream) : C6orf123 (338472 downstream)																							tgtggatggaggtggtggtggca	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	168783874	168783875	+	IGR	DEL	TG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168783874_168783875delTG								DACT2 (63472 upstream) : SMOC2 (58156 downstream)																							tgtgtttgtatgtgcatgtgcg	0.094													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	169249381	169249384	+	IGR	DEL	AAAG	-	-	rs10586252		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169249381_169249384delAAAG								SMOC2 (180710 upstream) : THBS2 (366492 downstream)																							caaaaaagaaaaagaaagaagaag	0.132													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	170918572	170918573	+	IGR	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170918572_170918573insA								PDCD2 (24824 upstream) : None (None downstream)																							gagactccgtcaaaaaaaaaca	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	588884	588884	+	IGR	DEL	G	-	-	rs35268388		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:588884delG								PDGFA (29403 upstream) : PRKAR1B (503 downstream)																							GCAGAGATAAGGGGGGGGATG	0.592													4	5	---	---	---	---	
ADAP1	11033	broad.mit.edu	37	7	958418	958419	+	Intron	INS	-	A	A	rs144113910	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:958418_958419insA	uc003sjo.3	-						ADAP1_uc011jvs.1_Intron|ADAP1_uc003sjn.3_Intron|ADAP1_uc010ksc.2_Intron	NM_006869	NP_006860	O75689	ADAP1_HUMAN	centaurin, alpha 1						cell surface receptor linked signaling pathway|regulation of ARF GTPase activity	cytoplasm|nucleus|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)	1						CTGCCCTGGGGAAAAAACCACT	0.639													3	6	---	---	---	---	
C7orf50	84310	broad.mit.edu	37	7	1043982	1043983	+	Intron	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1043982_1043983insT	uc003sju.2	-						C7orf50_uc003sjs.2_Intron|C7orf50_uc011jvt.1_Intron|C7orf50_uc011jvu.1_Intron	NM_032350	NP_115726	Q9BRJ6	CG050_HUMAN	hypothetical protein LOC84310								protein binding				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0216)|OV - Ovarian serous cystadenocarcinoma(56;1.3e-15)		tttccaccagcctgtttcctcc	0.262													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	1631256	1631257	+	IGR	DEL	TC	-	-	rs141465501		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1631256_1631257delTC								KIAA1908 (1997 upstream) : TFAMP1 (22849 downstream)																							gggagggaattctctctcttcc	0.000													2	6	---	---	---	---	
SDK1	221935	broad.mit.edu	37	7	3736205	3736206	+	Intron	DEL	TG	-	-	rs150027814		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3736205_3736206delTG	uc003smx.2	+							NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor						cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		TCTCtgtgtttgtgtgtgtgtg	0.277													2	5	---	---	---	---	
SDK1	221935	broad.mit.edu	37	7	3911063	3911064	+	Intron	DEL	TG	-	-	rs146371216		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3911063_3911064delTG	uc003smx.2	+							NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor						cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		ctgaatagactgtagtacaggg	0.000													2	4	---	---	---	---	
FOXK1	221937	broad.mit.edu	37	7	4716554	4716555	+	Intron	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4716554_4716555insT	uc003sna.1	+							NM_001037165	NP_001032242	P85037	FOXK1_HUMAN	forkhead box K1						cell differentiation|embryo development|muscle organ development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion 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			upper_aerodigestive_tract(1)|skin(1)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		ctagtcTACAAttttttttttt	0.005													4	2	---	---	---	---	
TNRC18	84629	broad.mit.edu	37	7	5399459	5399460	+	Intron	DEL	CA	-	-	rs35120436		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5399459_5399460delCA	uc003soi.3	-						TNRC18_uc003soj.2_5'Flank	NM_001080495	NP_001073964	O15417	TNC18_HUMAN	trinucleotide repeat containing 18								DNA binding				0		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CGCGTACACTCACACACACACA	0.441													5	4	---	---	---	---	
ZNF853	54753	broad.mit.edu	37	7	6660196	6660197	+	Intron	INS	-	CCTTCCTTC	CCTTCCTTC	rs138713861	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6660196_6660197insCCTTCCTTC	uc011jwz.1	+							NM_017560	NP_060030	P0CG23	ZN853_HUMAN	zinc finger protein 853							intracellular	nucleic acid binding|zinc ion binding				0						CCAcctaccttccttccttccc	0.287													6	3	---	---	---	---	
DGKB	1607	broad.mit.edu	37	7	14215940	14215941	+	Intron	INS	-	AA	AA	rs139721037	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:14215940_14215941insAA	uc003ssz.2	-						DGKB_uc011jxt.1_Intron|DGKB_uc003sta.2_3'UTR|DGKB_uc011jxu.1_3'UTR	NM_004080	NP_004071	Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity|protein binding			lung(5)|ovary(4)|breast(2)|skin(1)	12					Phosphatidylserine(DB00144)	TTGAGAGGGGCAGTGTCTGCCT	0.213													1	6	---	---	---	---	
SNX13	23161	broad.mit.edu	37	7	17854575	17854576	+	Intron	INS	-	AA	AA	rs34649849		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17854575_17854576insAA	uc003stw.1	-						SNX13_uc003stv.2_Intron|SNX13_uc010kuc.2_Intron|SNX13_uc010kub.2_Intron			Q9Y5W8	SNX13_HUMAN	SubName: Full=Putative uncharacterized protein SNX13; SubName: Full=Sorting nexin 13, isoform CRA_g;						cell communication|intracellular protein transport|negative regulation of signal transduction|positive regulation of GTPase activity	early endosome membrane	phosphatidylinositol binding|signal transducer activity			central_nervous_system(2)|kidney(1)	3	Lung NSC(10;0.0261)|all_lung(11;0.0521)					TAACTAACAAGAAAAAAAAAAA	0.302													14	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	29741052	29741052	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29741052delG	uc003tah.1	+											Homo sapiens DPY-19-like 2 pseudogene 3 (DPY19L2P3) pseudogene mRNA, complete sequence.																		gggtacatgtgcaggatgtac	0.095													4	2	---	---	---	---	
EEPD1	80820	broad.mit.edu	37	7	36201064	36201065	+	Intron	INS	-	TGGG	TGGG	rs140875888	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36201064_36201065insTGGG	uc003tfa.2	+							NM_030636	NP_085139	Q7L9B9	EEPD1_HUMAN	endonuclease/exonuclease/phosphatase family						DNA repair		DNA binding				0						AGTCAGGTGGATGGGTGGTTGG	0.559													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	41545874	41545874	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41545874delC								C7orf10 (645517 upstream) : INHBA (182729 downstream)																							TTGTCTTTATCCCCTTTGAGA	0.393													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46637890	46637891	+	IGR	INS	-	GTGT	GTGT	rs143741275	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46637890_46637891insGTGT								IGFBP3 (677019 upstream) : TNS3 (676862 downstream)																							agtgactatgagtgtgtgtgtg	0.000													4	2	---	---	---	---	
VOPP1	81552	broad.mit.edu	37	7	55560961	55560961	+	Intron	DEL	G	-	-	rs35821539		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55560961delG	uc003tqs.2	-						VOPP1_uc003tqq.2_Intron|VOPP1_uc010kzh.2_Intron|VOPP1_uc010kzi.2_Intron|VOPP1_uc011kcr.1_Intron	NM_030796	NP_110423	Q96AW1	VOPP1_HUMAN	EGFR-coamplified and overexpressed protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic vesicle membrane|endosome|integral to organelle membrane	signal transducer activity				0						CTGGCAAACTGGCAAACTCTT	0.478													2	9	---	---	---	---	
GBAS	2631	broad.mit.edu	37	7	56063978	56063979	+	Intron	INS	-	A	A	rs35217666		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56063978_56063979insA	uc003tre.1	+						GBAS_uc003trf.1_Intron	NM_001483	NP_001474	O75323	NIPS2_HUMAN	nipsnap homolog 2							integral to plasma membrane|membrane fraction|mitochondrion	protein binding			central_nervous_system(1)	1	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			gactccgtctcaaaaaaaaaaa	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57393172	57393173	+	IGR	INS	-	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57393172_57393173insC								ZNF479 (185601 upstream) : ZNF716 (116710 downstream)																							tccccatgggtccccctgctcc	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57551083	57551084	+	IGR	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57551083_57551084insA								ZNF716 (17818 upstream) : None (None downstream)																							ggaatcgaatgaatcatcgaat	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	62471482	62471482	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62471482delG								None (None upstream) : LOC643955 (280190 downstream)																							tgcccaggctggtgtgcagtg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	62508102	62508103	+	IGR	INS	-	C	C	rs149477475	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62508102_62508103insC								None (None upstream) : LOC643955 (243569 downstream)																							TGGTCATTACTCTGTGCCCCTC	0.624													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	62740204	62740205	+	IGR	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62740204_62740205insT								None (None upstream) : LOC643955 (11467 downstream)																							gtgttttctagttttttttttt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	62982423	62982424	+	IGR	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62982423_62982424insT								LOC100287704 (170272 upstream) : ZNF727 (523397 downstream)																							aatctcagcactttgggaggca	0.074													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	63297133	63297133	+	IGR	DEL	T	-	-	rs35039528		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63297133delT								LOC100287704 (484982 upstream) : ZNF727 (208688 downstream)																							ccttccctgcttttggagtct	0.000													2	5	---	---	---	---	
ZNF117	51351	broad.mit.edu	37	7	64468261	64468262	+	5'Flank	INS	-	C	C	rs34168600		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64468261_64468262insC	uc011kdr.1	-						uc003tts.1_5'Flank	NM_001007253	NP_001007254	Q03924	ZN117_HUMAN	endogenous retroviral sequence 3							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1		Lung NSC(55;0.0295)|all_lung(88;0.0691)				gcacctgtggtcccagctactc	0.000													3	3	---	---	---	---	
RFC2	5982	broad.mit.edu	37	7	73655170	73655170	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73655170delG	uc003uaj.2	-						RFC2_uc011kfa.1_Intron|RFC2_uc003uak.2_Intron|RFC2_uc010lbp.2_Intron|RFC2_uc003ual.2_Intron	NM_181471	NP_852136	P35250	RFC2_HUMAN	replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|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	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2						tgcccaggctgctctcgaact	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	75373697	75373698	+	IGR	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75373697_75373698insT								HIP1 (5418 upstream) : CCL26 (25144 downstream)																							AGTTCTTGTACTTTTTTTTTTA	0.267													4	2	---	---	---	---	
MAGI2	9863	broad.mit.edu	37	7	78894176	78894177	+	Intron	DEL	AG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78894176_78894177delAG	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				agagagacacagagagagagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	79887718	79887719	+	IGR	INS	-	AC	AC	rs143989296	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79887718_79887719insAC								GNAI1 (38993 upstream) : CD36 (111172 downstream)																							TCTCTTTCTCTacacacacaca	0.193													4	3	---	---	---	---	
ADAM22	53616	broad.mit.edu	37	7	87606186	87606186	+	Intron	DEL	T	-	-	rs1637493	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87606186delT	uc003ujn.2	+						ADAM22_uc003uji.1_Intron|ADAM22_uc003ujj.1_Intron|ADAM22_uc003ujk.1_Intron|ADAM22_uc003ujl.1_Intron|ADAM22_uc003ujm.2_Intron|ADAM22_uc003ujo.2_Intron|ADAM22_uc003ujp.1_Intron	NM_021723	NP_068369	Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22 isoform 1						cell adhesion|central nervous system development|negative regulation of cell adhesion|proteolysis	integral to membrane	integrin binding|metalloendopeptidase activity|protein binding|receptor activity|zinc ion binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)			TTTTTATTTCTTTTTTTTTTT	0.418													4	2	---	---	---	---	
MTERF	7978	broad.mit.edu	37	7	91468765	91468765	+	Intron	DEL	A	-	-	rs112336728		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91468765delA	uc010let.1	-									Q99551	MTERF_HUMAN	Synthetic construct DNA, clone: pF1KB8286, Homo sapiens MTERF gene for mitochondrial transcription termination factor, without stop codon, in Flexi system.						DNA geometric change|regulation of transcription, DNA-dependent|termination of mitochondrial transcription	mitochondrial nucleoid	double-stranded DNA binding				0	all_cancers(62;2.28e-09)|all_epithelial(64;1.07e-07)|Breast(17;0.00371)|all_hematologic(106;0.091)|all_lung(186;0.178)|Lung NSC(181;0.235)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.0993)|Kidney(17;0.118)|Epithelial(20;0.136)|LUSC - Lung squamous cell carcinoma(200;0.176)			Ctttttttttatatactttaa	0.030													4	4	---	---	---	---	
ANKIB1	54467	broad.mit.edu	37	7	92027347	92027348	+	Intron	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92027347_92027348insT	uc003ulw.2	+						ANKIB1_uc010lew.1_Intron	NM_019004	NP_061877	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1								protein binding|zinc ion binding			lung(1)	1	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TTTAAGGTATGTTTTTTTTTTC	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	97134001	97134001	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97134001delG								ACN9 (322928 upstream) : TAC1 (227270 downstream)																							ATGATCCTGTGGGGttacaga	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	106074607	106074610	+	IGR	DEL	TGTG	-	-	rs143875514		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106074607_106074610delTGTG								NAMPT (148969 upstream) : FLJ36031 (224540 downstream)																							aactcaaatctgtgtgtgtgtgtg	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	115198234	115198234	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115198234delT								MDFIC (538971 upstream) : TFEC (376968 downstream)																							TGCTTATTGCTTTTTTTTCCA	0.373													4	2	---	---	---	---	
ST7	7982	broad.mit.edu	37	7	116601610	116601617	+	Intron	DEL	GTGTGTGT	-	-	rs35640208		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116601610_116601617delGTGTGTGT	uc003vin.2	+						ST7_uc011knl.1_Intron|ST7_uc003vio.2_Intron	NM_021908	NP_068708	Q9NRC1	ST7_HUMAN	suppression of tumorigenicity 7 isoform b							integral to membrane	binding			central_nervous_system(1)|skin(1)	2	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		gtattcctacgtgtgtgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
CFTR	1080	broad.mit.edu	37	7	117189072	117189072	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117189072delT	uc003vjd.2	+						CFTR_uc011knq.1_Intron	NM_000492	NP_000483	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance						respiratory gaseous exchange	apical plasma membrane|basolateral plasma membrane|chloride channel complex|early endosome membrane	ATP binding|ATP-binding and phosphorylation-dependent chloride channel activity|channel-conductance-controlling ATPase activity|chloride channel regulator activity|enzyme binding|PDZ domain binding			central_nervous_system(2)|skin(2)|ovary(1)	5	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Glibenclamide(DB01016)	CCTCATATTATTTTCAGTGGC	0.229									Cystic_Fibrosis				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	117976973	117976974	+	IGR	INS	-	T	T	rs142108499	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117976973_117976974insT								ANKRD7 (94191 upstream) : None (None downstream)																							CCTTTTATCAGTTTTTTTGATG	0.282													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	127094568	127094569	+	IGR	DEL	AA	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127094568_127094569delAA								ZNF800 (61801 upstream) : GCC1 (126114 downstream)																							ccagaggtacaaagaggagctg	0.000													4	2	---	---	---	---	
PLXNA4	91584	broad.mit.edu	37	7	131836166	131836174	+	Intron	DEL	GGAAGGAGG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131836166_131836174delGGAAGGAGG	uc003vra.3	-							NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1						aggaggaggaggaaggaggaggaggagga	0.000													3	3	---	---	---	---	
PLXNA4	91584	broad.mit.edu	37	7	132011929	132011929	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132011929delA	uc003vra.3	-							NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1						aaaggaaggcaaaaaaaaaag	0.189													4	2	---	---	---	---	
PLXNA4	91584	broad.mit.edu	37	7	132248610	132248612	+	Intron	DEL	CTC	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132248610_132248612delCTC	uc003vra.3	-						PLXNA4_uc003vrc.2_Intron|PLXNA4_uc003vrb.2_Intron	NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1						ccttctgctgctcctcctcctcc	0.000													4	2	---	---	---	---	
CNOT4	4850	broad.mit.edu	37	7	135181380	135181381	+	Intron	DEL	CT	-	-	rs112838755		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135181380_135181381delCT	uc003vsv.1	-						CNOT4_uc003vss.2_Intron|CNOT4_uc011kpz.1_Intron|CNOT4_uc003vst.2_Intron|CNOT4_uc003vsu.1_Intron	NM_001008225	NP_001008226	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4						nuclear-transcribed mRNA poly(A) tail shortening|protein autoubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	nucleotide binding|protein binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding				0						CTTCCTATTCctctctctctct	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142168221	142168222	+	Intron	INS	-	TGG	TGG			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142168221_142168222insTGG	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron|uc011krx.1_Intron					SubName: Full=V_segment translation product; Flags: Fragment;																		CTGGGCTCTGTTTGGGAGAGCT	0.530													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142448200	142448207	+	Intron	DEL	GGTGGAAA	-	-	rs112413030	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142448200_142448207delGGTGGAAA	uc011krr.1	+						uc003vzp.2_Intron|uc011ksh.1_Intron|uc011ksi.1_Intron|uc003vzw.1_Intron|uc010loj.1_Intron|uc003wad.2_Intron|uc003wag.1_Intron|uc011ksl.1_Intron					SubName: Full=V_segment translation product; Flags: Fragment;																		GTTAACACTGGGTGGAAAGGTGGAAAGA	0.457													6	8	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152099689	152099690	+	Intron	INS	-	TTAA	TTAA	rs139795813		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152099689_152099690insTTAA	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						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)		acaaatgagacttaagctaaaa	0.000			N		medulloblastoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	156829605	156829605	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156829605delA								MNX1 (26258 upstream) : UBE3C (102050 downstream)																							cccatcactcaggctcaaacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	157252960	157252960	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157252960delG								DNAJB6 (42828 upstream) : PTPRN2 (78791 downstream)																							AGATGATGGTGGGGAAGACAA	0.597													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	157317596	157317597	+	IGR	INS	-	AG	AG	rs139368030	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157317596_157317597insAG								DNAJB6 (107464 upstream) : PTPRN2 (14154 downstream)																							gagagggaggcagagagagaga	0.010													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	12438835	12438835	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12438835delA	uc003wvy.3	-											Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																		CCTCACATACACttttttttt	0.224													4	2	---	---	---	---	
DLC1	10395	broad.mit.edu	37	8	12989940	12989940	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12989940delA	uc003wwm.2	-						DLC1_uc003wwk.1_Intron|DLC1_uc003wwl.1_Intron	NM_182643	NP_872584	Q96QB1	RHG07_HUMAN	deleted in liver cancer 1 isoform 1						actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding			ovary(3)|pancreas(2)|lung(1)|kidney(1)	7						GGCAGTGATGAAAAAAAAAAA	0.408													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	21037049	21037050	+	IGR	DEL	TG	-	-	rs111608467		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21037049_21037050delTG								LZTS1 (924246 upstream) : GFRA2 (512480 downstream)																							TGCCTGCCTCtgtgtgtgtgtg	0.470													3	3	---	---	---	---	
ZMAT4	79698	broad.mit.edu	37	8	40669187	40669187	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40669187delG	uc003xnr.2	-						ZMAT4_uc003xns.2_Intron	NM_024645	NP_078921	Q9H898	ZMAT4_HUMAN	zinc finger, matrin type 4 isoform a							nucleus	DNA binding|zinc ion binding			pancreas(1)|central_nervous_system(1)|skin(1)	3	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)			ctgaaggaatgggaaagttaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	57353184	57353185	+	IGR	INS	-	TG	TG	rs149609688	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57353184_57353185insTG								SDR16C5 (119943 upstream) : PENK (328 downstream)																							AAATGCAAgtatgtgtgtgtgt	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	58144756	58144759	+	RNA	DEL	ACAC	-	-	rs72235980		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58144756_58144759delACAC	uc003xtf.2	+	8		c.1853_1856delACAC								Homo sapiens mRNA; cDNA DKFZp434D1072 (from clone DKFZp434D1072).																		CCCGacacatacacacacacacac	0.275													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	60149517	60149517	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60149517delT								TOX (117750 upstream) : CA8 (951906 downstream)																							GTTTCACTTCTTTTTTTTTTT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	76814592	76814592	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76814592delC								HNF4G (335533 upstream) : LOC100192378 (708523 downstream)																							tctccaaccacccccccaagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	77873204	77873204	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77873204delC								ZFHX4 (93684 upstream) : PEX2 (19292 downstream)																							GTATTTAAGACCACAGAAAAT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	78786397	78786398	+	IGR	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78786397_78786398insT								PEX2 (873873 upstream) : PKIA (641938 downstream)																							taatttctgtcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	81871483	81871484	+	IGR	INS	-	GT	GT	rs147587663	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81871483_81871484insGT								ZNF704 (84467 upstream) : PAG1 (8564 downstream)																							catgtatgtgcgtatgtgtgcg	0.198													4	3	---	---	---	---	
FAM82B	51115	broad.mit.edu	37	8	87515618	87515619	+	Intron	DEL	AC	-	-	rs72059042		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87515618_87515619delAC	uc003ydu.2	-						FAM82B_uc011lfz.1_Intron|FAM82B_uc011lga.1_Intron	NM_016033	NP_057117	Q96DB5	RMD1_HUMAN	regulator of microtubule dynamics 1							microtubule|spindle pole	binding			ovary(1)	1						aaaaaaaaaaacaaaaaaaaat	0.168													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	89556535	89556536	+	IGR	DEL	AC	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89556535_89556536delAC								MMP16 (216818 upstream) : None (None downstream)																							TCCAGATGAGacacacacacac	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	90690243	90690243	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90690243delA								None (None upstream) : RIPK2 (79732 downstream)																							tggcaaagacaaaaaaccaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	90907730	90907730	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90907730delG								RIPK2 (104439 upstream) : OSGIN2 (6366 downstream)																							ttaaaaagcagggagactgaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	93181307	93181308	+	IGR	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93181307_93181308insA								RUNX1T1 (73601 upstream) : C8orf83 (714557 downstream)																							GAGCTTTTGCTAATTCACAAAA	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	96621564	96621565	+	IGR	DEL	TC	-	-	rs72239058		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96621564_96621565delTC								C8orf37 (340127 upstream) : GDF6 (532995 downstream)																							TTCCTTCCTTtctctctctctc	0.064													4	4	---	---	---	---	
PGCP	10404	broad.mit.edu	37	8	97795489	97795490	+	Intron	DEL	GT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97795489_97795490delGT	uc003yhw.2	+						PGCP_uc010mbe.2_5'Flank	NM_016134	NP_057218	Q9Y646	PGCP_HUMAN	plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)					AGTtgtgtgagtgtgtgtgtgt	0.015													4	2	---	---	---	---	
POP1	10940	broad.mit.edu	37	8	99142774	99142776	+	Intron	DEL	GGA	-	-	rs34249396		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99142774_99142776delGGA	uc003yij.3	+						POP1_uc011lgv.1_Intron|POP1_uc003yik.2_Intron	NM_001145860	NP_001139332	Q99575	POP1_HUMAN	processing of precursor 1						tRNA 5'-leader removal|tRNA catabolic process	nucleolar ribonuclease P complex|ribonuclease MRP complex	identical protein binding|ribonuclease MRP activity|ribonuclease P activity			ovary(1)|breast(1)	2	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)			GGATAAGATGGGAGGAGAGGGGG	0.488													2	4	---	---	---	---	
RGS22	26166	broad.mit.edu	37	8	101101440	101101441	+	Intron	DEL	AC	-	-	rs72450766		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101101440_101101441delAC	uc003yjb.1	-						RGS22_uc003yja.1_Intron|RGS22_uc003yjc.1_Intron|RGS22_uc010mbo.1_Intron	NM_015668	NP_056483	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22						negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(3)|skin(2)|breast(1)|central_nervous_system(1)	7			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			acacacacaaacacacacacac	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	103181032	103181033	+	IGR	DEL	CA	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103181032_103181033delCA								NCALD (43897 upstream) : RRM2B (35699 downstream)																							TATGTGCATGcacacacacaca	0.252													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	105732012	105732013	+	IGR	INS	-	AGC	AGC	rs148557911		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105732012_105732013insAGC								LRP12 (130792 upstream) : ZFPM2 (599134 downstream)																							tatgaagagaaagaaagaggca	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	109438685	109438686	+	IGR	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109438685_109438686insA								EIF3E (177726 upstream) : TTC35 (17167 downstream)																							CTGAAGCCACCCCCCAAAAAAA	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	118741708	118741709	+	IGR	INS	-	C	C	rs147480855	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118741708_118741709insC								MED30 (189209 upstream) : EXT1 (69893 downstream)																							gtatggaaatgaatgcaaagct	0.000													4	2	---	---	---	---	
SAMD12	401474	broad.mit.edu	37	8	119439857	119439858	+	Intron	INS	-	T	T	rs138445027	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119439857_119439858insT	uc003yom.2	-						SAMD12_uc010mda.1_Intron|SAMD12_uc010mdb.1_Intron	NM_207506	NP_997389	Q8N8I0	SAM12_HUMAN	sterile alpha motif domain containing 12 isoform											ovary(1)	1	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		STAD - Stomach adenocarcinoma(47;0.00391)			cattgtgtgcacagtagtaggt	0.000													3	3	---	---	---	---	
SNTB1	6641	broad.mit.edu	37	8	121763715	121763715	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121763715delT	uc010mdg.2	-						SNTB1_uc003ype.2_Intron	NM_021021	NP_066301	Q13884	SNTB1_HUMAN	basic beta 1 syntrophin						muscle contraction	cell junction|cytoplasm|cytoskeleton|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|calmodulin binding			skin(5)	5	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)			TAAAGGATACTTTTTTTTTGT	0.343													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	121844442	121844442	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121844442delG								SNTB1 (20133 upstream) : HAS2 (780829 downstream)																							tcacttgcctgggtaacaatg	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	123163447	123163448	+	IGR	DEL	GT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123163447_123163448delGT								HAS2AS (506514 upstream) : ZHX2 (630453 downstream)																							GACCACGTTGGTGTGTGTGTGT	0.332													4	3	---	---	---	---	
FAM49B	51571	broad.mit.edu	37	8	130962818	130962818	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130962818delA	uc003ysw.2	-						FAM49B_uc003ysx.2_Intron|FAM49B_uc003ysy.1_Intron	NM_016623	NP_057707	Q9NUQ9	FA49B_HUMAN	hypothetical protein LOC51571												0	Ovarian(5;0.000567)|Esophageal squamous(12;0.00693)|Acute lymphoblastic leukemia(118;0.155)		LUAD - Lung adenocarcinoma(14;0.0989)			catctcaaagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	131495386	131495387	+	IGR	INS	-	T	T	rs142809011	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131495386_131495387insT								ASAP1 (81170 upstream) : ADCY8 (297161 downstream)																							gcccctgagactatagggagga	0.089													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	131669197	131669198	+	IGR	DEL	AG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131669197_131669198delAG								ASAP1 (254981 upstream) : ADCY8 (123350 downstream)																							CTCATATGTAAGAGAGAGAGAG	0.213													4	2	---	---	---	---	
PTK2	5747	broad.mit.edu	37	8	142005480	142005481	+	Intron	INS	-	A	A	rs80082021		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142005480_142005481insA	uc003yvu.2	-						PTK2_uc003yvt.2_Intron|PTK2_uc003yvv.2_Intron|PTK2_uc011ljr.1_Intron	NM_153831	NP_722560	Q05397	FAK1_HUMAN	PTK2 protein tyrosine kinase 2 isoform a						axon guidance|blood coagulation|cellular component disassembly involved in apoptosis|ephrin receptor signaling pathway|growth hormone receptor signaling pathway|integrin-mediated signaling pathway|peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of cell adhesion mediated by integrin|signal complex assembly	cytoskeleton|cytosol|focal adhesion	ATP binding|JUN kinase binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|signal transducer activity			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			gactccgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
TSNARE1	203062	broad.mit.edu	37	8	143337251	143337252	+	Intron	INS	-	CAT	CAT			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143337251_143337252insCAT	uc003ywk.2	-						TSNARE1_uc011lju.1_Intron|TSNARE1_uc003ywj.2_Intron	NM_145003	NP_659440	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1						vesicle-mediated transport	integral to membrane					0	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					atcaccaccaccaccaccactg	0.000													4	2	---	---	---	---	
LOC100133669	100133669	broad.mit.edu	37	8	144078349	144078349	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144078349delT	uc011ljz.1	-							NR_026913				Homo sapiens, clone IMAGE:3342869, mRNA.												0						TTTTTAGTCCTTTTTTTTTTT	0.333													3	3	---	---	---	---	
ZC3H3	23144	broad.mit.edu	37	8	144544146	144544146	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144544146delT	uc003yyd.2	-							NM_015117	NP_055932	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3						mRNA polyadenylation|poly(A)+ mRNA export from nucleus|regulation of mRNA export from nucleus	nucleus	nucleic acid binding|zinc ion binding			skin(1)	1	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)			GTTAAGCTGCTTTTTTTTTTT	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	144958158	144958158	+	IGR	DEL	G	-	-	rs58550695		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144958158delG								EPPK1 (10724 upstream) : PLEC (31163 downstream)																							TGCTCATGCCGCCCACAGCCT	0.741													4	2	---	---	---	---	
FLJ35024	401491	broad.mit.edu	37	9	2602433	2602433	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2602433delC	uc003zhh.1	-						FLJ35024_uc003zhi.2_Intron|FLJ35024_uc003zhj.3_Intron					Homo sapiens cDNA FLJ35024 fis, clone OCBBF2015233.												0						cctgggctcaccacagcctcc	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	11085585	11085586	+	IGR	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:11085585_11085586insA								PTPRD (472862 upstream) : None (None downstream)																							tttcaaaagagaaaaaaaaaaa	0.000													3	3	---	---	---	---	
BNC2	54796	broad.mit.edu	37	9	16769329	16769329	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16769329delA	uc003zml.2	-						BNC2_uc011lmw.1_Intron|BNC2_uc003zmm.2_Intron|BNC2_uc003zmq.1_Intron|BNC2_uc003zmr.1_Intron|BNC2_uc003zmp.1_Intron|BNC2_uc010mij.1_Intron|BNC2_uc003zmu.1_Intron|BNC2_uc010mim.1_Intron|BNC2_uc010min.1_Intron	NM_017637	NP_060107	Q6ZN30	BNC2_HUMAN	basonuclin 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	zinc ion binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(50;9.01e-08)		ataggtgtctaataaatAAca	0.000													4	2	---	---	---	---	
AQP3	360	broad.mit.edu	37	9	33442526	33442526	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33442526delG	uc003zsx.2	-						SUGT1P1_uc010mjq.1_Intron|AQP3_uc003zsv.1_3'UTR|AQP3_uc003zsw.2_Intron|AQP3_uc010mju.2_Intron	NM_004925	NP_004916	Q92482	AQP3_HUMAN	aquaporin 3						excretion|odontogenesis|positive regulation of immune system process|regulation of keratinocyte differentiation|response to calcium ion|response to retinoic acid|response to vitamin D	basolateral plasma membrane|cell-cell junction|cytoplasm	glycerol channel activity|water channel activity				0			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.0899)		ACTGGGGAGTGGGGAGAACAG	0.607													6	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	33662482	33662482	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33662482delG								ANXA2P2 (36952 upstream) : PTENP1 (11025 downstream)																							AAAATGTACTGGTCAAGATCC	0.453													34	40	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	34602966	34602966	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34602966delT								CNTFR (13244 upstream) : C9orf23 (7527 downstream)																							ccttgaagccttcagtgacgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	36701486	36701487	+	IGR	DEL	TG	-	-	rs10572618		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36701486_36701487delTG								MELK (23808 upstream) : PAX5 (137044 downstream)																							tgtgcgtgcatgtgtgtgtgtg	0.337													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66476167	66476167	+	IGR	DEL	C	-	-	rs143963246	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66476167delC								FAM74A4 (981781 upstream) : LOC442421 (20303 downstream)																							aagaatacatcatgtaaaaag	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66477358	66477358	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66477358delT								FAM74A4 (982972 upstream) : LOC442421 (19112 downstream)																							agaagaaaaatttaaaaattt	0.000													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66515952	66515952	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66515952delT	uc010mnh.1	-											Homo sapiens cDNA FLJ20444 fis, clone KAT05128.																		TTTCCACACATTTTTTTTACT	0.189													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66824412	66824412	+	IGR	DEL	T	-	-	rs113379265		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66824412delT								LOC442421 (321385 upstream) : AQP7P1 (429855 downstream)																							tgtactcaactttatagggtt	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66990579	66990579	+	IGR	DEL	T	-	-	rs140894478	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66990579delT								LOC442421 (487552 upstream) : AQP7P1 (263688 downstream)																							tgctcaatcataagaaatttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69787982	69787985	+	IGR	DEL	AACA	-	-	rs59524350		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69787982_69787985delAACA								LOC100133920 (123033 upstream) : FOXD4L5 (387724 downstream)																							AGATAGAGGTAACAAACTTAAATA	0.368													4	2	---	---	---	---	
TRPM6	140803	broad.mit.edu	37	9	77352416	77352416	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77352416delC	uc004ajl.1	-						TRPM6_uc004ajk.1_Intron|TRPM6_uc010mpb.1_Intron|TRPM6_uc010mpc.1_Intron|TRPM6_uc010mpd.1_Intron|TRPM6_uc010mpe.1_Intron|TRPM6_uc004ajj.1_Intron	NM_017662	NP_060132	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel,						response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	8						TTTAAACAAACCATAAGATGG	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	85764235	85764235	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85764235delG								RASEF (86192 upstream) : FRMD3 (93670 downstream)																							catgtttagtggcccttgatt	0.055													4	2	---	---	---	---	
HIATL1	84641	broad.mit.edu	37	9	97221855	97221855	+	3'UTR	DEL	T	-	-	rs34087557		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97221855delT	uc004aur.2	+	12					HIATL1_uc011luh.1_3'UTR	NM_032558	NP_115947	Q5SR56	HIAL1_HUMAN	hippocampus abundant transcript-like 1						transmembrane transport	integral to membrane|plasma membrane	protein binding|transporter activity			ovary(2)	2		Acute lymphoblastic leukemia(62;0.136)				CCTCCTCCTGTTTTTTTTTTT	0.403													5	3	---	---	---	---	
CORO2A	7464	broad.mit.edu	37	9	100912794	100912794	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100912794delC	uc004ayl.2	-						CORO2A_uc004aym.2_Intron	NM_003389	NP_003380	Q92828	COR2A_HUMAN	coronin, actin binding protein, 2A						actin cytoskeleton organization|intracellular signal transduction	actin cytoskeleton|transcriptional repressor complex	actin filament binding			skin(2)|ovary(1)|pancreas(1)	4		Acute lymphoblastic leukemia(62;0.0559)				agatcaccttcccaggaatgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	101035478	101035479	+	IGR	INS	-	C	C	rs138041646	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101035478_101035479insC								TBC1D2 (17475 upstream) : GABBR2 (14887 downstream)																							AGATACAGAAGCCCCCCCGGGA	0.520													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	107751624	107751624	+	IGR	DEL	C	-	-	rs34217224		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107751624delC								ABCA1 (61188 upstream) : SLC44A1 (255305 downstream)																							TCCCCATCTTCCCCCACTCCC	0.274													1	7	---	---	---	---	
SLC44A1	23446	broad.mit.edu	37	9	108129220	108129220	+	Intron	DEL	T	-	-	rs72096346		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108129220delT	uc004bcn.2	+						SLC44A1_uc010mtk.1_Intron|SLC44A1_uc004bco.1_Intron	NM_080546	NP_536856	Q8WWI5	CTL1_HUMAN	CDW92 antigen							integral to membrane|mitochondrial outer membrane|plasma membrane	choline transmembrane transporter activity			breast(3)|ovary(1)	4					Choline(DB00122)	ATGCTGATACTTTTTTTTTTT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	111186379	111186380	+	IGR	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111186379_111186380insT								KLF4 (934332 upstream) : ACTL7B (430491 downstream)																							AAATTTAGTTGTTTTGTTTGTT	0.307													4	2	---	---	---	---	
PALM2-AKAP2	445815	broad.mit.edu	37	9	112817177	112817177	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112817177delT	uc004bei.2	+						PALM2-AKAP2_uc004bek.3_Intron|PALM2-AKAP2_uc004bej.3_Intron|PALM2-AKAP2_uc004bel.1_Intron|AKAP2_uc011lwi.1_Intron|AKAP2_uc004bem.2_Intron	NM_001136562	NP_001130034	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2 isoform 2								enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6						tgtgctggccTAAAGTTAACA	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	114701247	114701248	+	IGR	INS	-	T	T	rs7021481	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114701247_114701248insT								UGCG (5816 upstream) : SUSD1 (101814 downstream)																							CTTTATTGTTGGtttttttgtt	0.243													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	118305603	118305603	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118305603delA								DEC1 (140680 upstream) : C9orf27 (344943 downstream)																							CCCaaaacagaaaaaaaaaaa	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	123008522	123008525	+	5'Flank	DEL	TTTG	-	-	rs71957252		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123008522_123008525delTTTG	uc011lxv.1	-						MIR147_hsa-mir-147|MI0000262_5'Flank					DM004233																		caggtttgtttttgtttgtttgtt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	126813824	126813824	+	IGR	DEL	T	-	-	rs113796565		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126813824delT								LHX2 (18382 upstream) : NEK6 (206062 downstream)																							GAGATGATGAttttttttttt	0.030													1	5	---	---	---	---	
FAM125B	89853	broad.mit.edu	37	9	129171579	129171588	+	Intron	DEL	TGTGTGTGTG	-	-	rs71929574		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129171579_129171588delTGTGTGTGTG	uc004bqh.1	+						FAM125B_uc011lzy.1_Intron|FAM125B_uc010mxd.2_Intron	NM_033446	NP_258257	Q9H7P6	F125B_HUMAN	hypothetical protein LOC89853 isoform 1						protein transport	late endosome membrane					0						TGAGTAACTCtgtgtgtgtgtgtgtgtgtg	0.248													4	2	---	---	---	---	
LAMC3	10319	broad.mit.edu	37	9	133916077	133916077	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133916077delC	uc004caa.1	+							NM_006059	NP_006050	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3 precursor						cell adhesion	basement membrane|membrane	structural molecule activity			ovary(2)|pancreas(1)	3	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		acacctcccacccctgccccc	0.164													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	136363481	136363482	+	IGR	DEL	GT	-	-	rs35663161		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136363481_136363482delGT								SLC2A6 (19205 upstream) : TMEM8C (16277 downstream)																							ggaacagtgcgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
CACNA1B	774	broad.mit.edu	37	9	140779418	140779419	+	Intron	INS	-	ACT	ACT	rs28409847		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140779418_140779419insACT	uc004cog.2	+						uc004cof.1_Intron	NM_000718	NP_000709	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type,						membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity			breast(3)|large_intestine(2)|ovary(1)	6	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)	ttccccccccccctcctccCAC	0.040													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	103754	103754	+	IGR	DEL	T	-	-	rs113012935		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103754delT								TUBB8 (8250 upstream) : ZMYND11 (76670 downstream)																							caacacttgctttttttttaa	0.000													4	2	---	---	---	---	
ADARB2	105	broad.mit.edu	37	10	1293848	1293848	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1293848delT	uc009xhq.2	-							NM_018702	NP_061172	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2						mRNA processing	mitochondrion|nucleus	adenosine deaminase activity|double-stranded RNA binding|metal ion binding|single-stranded RNA binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		taaaagagacttcagacagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	1914095	1914096	+	IGR	INS	-	GA	GA	rs150998753	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1914095_1914096insGA								ADARB2 (134377 upstream) : None (None downstream)																							TGGAGTGATGTgagagagagaa	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	3227407	3227408	+	IGR	INS	-	A	A	rs11449841		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3227407_3227408insA								PITRM1 (12404 upstream) : KLF6 (590781 downstream)																							gaccatggcccaagtgagaaca	0.035													4	2	---	---	---	---	
KIN	22944	broad.mit.edu	37	10	7822205	7822206	+	Intron	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7822205_7822206insA	uc001ijt.2	-						KIN_uc010qaz.1_Intron|KIN_uc009xip.2_Intron|KIN_uc010qba.1_Intron	NM_012311	NP_036443	O60870	KIN17_HUMAN	HsKin17 protein						DNA recombination|DNA repair|DNA replication|interspecies interaction between organisms|mRNA processing	cytoplasm|nuclear matrix	double-stranded DNA binding|RNA binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3						GCTGTTATTTGCACAATATTTA	0.337													34	19	---	---	---	---	
FAM171A1	221061	broad.mit.edu	37	10	15362715	15362715	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15362715delA	uc001iob.2	-							NM_001010924	NP_001010924	Q5VUB5	F1711_HUMAN	hypothetical protein LOC221061 precursor							integral to membrane				ovary(2)|breast(1)|skin(1)	4						ctctaatgataagcattttct	0.085													4	2	---	---	---	---	
ST8SIA6	338596	broad.mit.edu	37	10	17369069	17369070	+	Frame_Shift_Ins	INS	-	C	C			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17369069_17369070insC	uc001ipd.2	-	6	578_579	c.578_579insG	c.(577-579)GGAfs	p.G193fs	ST8SIA6_uc010qce.1_Intron	NM_001004470	NP_001004470	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide	193	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(1)	1						TATTCAGAATTCCCCCATTTCC	0.391													41	20	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	35860892	35860892	+	IGR	DEL	T	-	-	rs66464729		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35860892delT								CCNY (47 upstream) : GJD4 (33446 downstream)																							ACTTTTCTTATTTTTTTTTTT	0.294													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38787899	38787900	+	IGR	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38787899_38787900insT								LOC399744 (46819 upstream) : None (None downstream)																							atgcaatggaatggaagggaat	0.005													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42627698	42627698	+	IGR	DEL	T	-	-	rs9702771		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42627698delT								None (None upstream) : LOC441666 (199617 downstream)																							CACAGACCTATTAAATAAGAC	0.303													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42654253	42654255	+	IGR	DEL	TAT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42654253_42654255delTAT								None (None upstream) : LOC441666 (173060 downstream)																							caaatttgcatattattactaat	0.034													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42656644	42656645	+	IGR	INS	-	T	T	rs142739859	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42656644_42656645insT								None (None upstream) : LOC441666 (170670 downstream)																							CTAATCCTCAAAAATTTGCTTT	0.322													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	52481036	52481036	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52481036delG								SGMS1 (96113 upstream) : ASAH2B (18660 downstream)																							gatgcgatatggctggtgttg	0.000													4	2	---	---	---	---	
PCDH15	65217	broad.mit.edu	37	10	57180220	57180221	+	Intron	INS	-	T	T	rs147555336	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57180220_57180221insT	uc001jjv.1	-							NM_001142770	NP_001136242	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD2-2 precursor						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)				TAGGTATTGCATTTTTTTTCCC	0.381										HNSCC(58;0.16)			5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	57406505	57406506	+	IGR	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57406505_57406506insT								PCDH15 (18803 upstream) : ZWINT (710693 downstream)																							ACGAATTGAACTTTTTTGTGGC	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	58597595	58597596	+	IGR	INS	-	ACACAC	ACACAC	rs147403914	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58597595_58597596insACACAC								ZWINT (476561 upstream) : None (None downstream)																							gtgctcaccatacacacacaca	0.010													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	59302948	59302949	+	IGR	INS	-	AAAC	AAAC			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59302948_59302949insAAAC								None (None upstream) : IPMK (652669 downstream)																							gaaagaaagagaaagaaagaaa	0.000													5	4	---	---	---	---	
BICC1	80114	broad.mit.edu	37	10	60273190	60273193	+	Intron	DEL	CGGC	-	-	rs10571555		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60273190_60273193delCGGC	uc001jki.1	+							NM_001080512	NP_001073981	Q9H694	BICC1_HUMAN	bicaudal C homolog 1						multicellular organismal development		RNA binding			ovary(2)|lung(1)|skin(1)	4						CTCCAGCCTACGGCCGGCCGGTTT	0.667													7	4	---	---	---	---	
CCDC6	8030	broad.mit.edu	37	10	61634491	61634493	+	Intron	DEL	GAG	-	-	rs10533085		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61634491_61634493delGAG	uc001jks.3	-							NM_005436	NP_005427	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6							cytoplasm|cytoskeleton	SH3 domain binding|structural constituent of cytoskeleton			ovary(3)|breast(1)	4				Kidney(211;0.0597)		aatggaggcagagaagagatcag	0.000													5	3	---	---	---	---	
CCDC6	8030	broad.mit.edu	37	10	61641852	61641853	+	Intron	DEL	GG	-	-	rs67151745		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61641852_61641853delGG	uc001jks.3	-							NM_005436	NP_005427	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6							cytoplasm|cytoskeleton	SH3 domain binding|structural constituent of cytoskeleton			ovary(3)|breast(1)	4				Kidney(211;0.0597)		aaggaaagccggggggagaagg	0.104													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	64641168	64641169	+	IGR	DEL	TT	-	-	rs112906633		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64641168_64641169delTT								EGR2 (62241 upstream) : NRBF2 (251838 downstream)																							gcctggctaatttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	66663528	66663528	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66663528delT								ANXA2P3 (76894 upstream) : None (None downstream)																							cctcacatacttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	66736386	66736387	+	IGR	DEL	TT	-	-	rs34610191		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66736386_66736387delTT								ANXA2P3 (149752 upstream) : CTNNA3 (943338 downstream)																							tgaaggaaggtttaaactcaga	0.000													5	4	---	---	---	---	
MYPN	84665	broad.mit.edu	37	10	69971139	69971139	+	3'UTR	DEL	G	-	-	rs3217542		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69971139delG	uc001jnm.3	+	21					MYPN_uc001jnn.3_3'UTR|MYPN_uc001jno.3_3'UTR|MYPN_uc009xpt.2_3'UTR|MYPN_uc010qit.1_3'UTR|MYPN_uc010qiu.1_RNA	NM_032578	NP_115967	Q86TC9	MYPN_HUMAN	myopalladin							nucleus|sarcomere	actin binding			ovary(3)|skin(2)	5						GAGGAAGGAAGAGATACAAAC	0.443													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	71278143	71278144	+	IGR	INS	-	AG	AG	rs151188896	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71278143_71278144insAG								TSPAN15 (10720 upstream) : NEUROG3 (53648 downstream)																							GTAAAGGAAACAGGAATAAATA	0.342													5	3	---	---	---	---	
SGPL1	8879	broad.mit.edu	37	10	72624969	72624970	+	Intron	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72624969_72624970insT	uc001jrm.2	+							NM_003901	NP_003892	O95470	SGPL1_HUMAN	sphingosine-1-phosphate lyase 1						apoptosis|carboxylic acid metabolic process|ceramide metabolic process|sphingolipid catabolic process	integral to endoplasmic reticulum membrane	carboxy-lyase activity|pyridoxal phosphate binding|sphinganine-1-phosphate aldolase activity				0					Pyridoxal Phosphate(DB00114)	TTCACTGTTTCTTTTTTTTTTT	0.351													4	2	---	---	---	---	
CDH23	64072	broad.mit.edu	37	10	73158185	73158186	+	Intron	INS	-	GT	GT	rs143519061	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73158185_73158186insGT	uc001jrx.3	+						CDH23_uc001jrw.3_Intron|CDH23_uc001jrv.2_Intron|CDH23_uc009xql.2_Intron	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor						calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11						GAGACACAGGAgtgtgtgtgtg	0.401													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	74080193	74080193	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74080193delA								DDIT4 (44396 upstream) : DNAJB12 (12395 downstream)																							acctggtctcaaaaaaaaaaa	0.184													4	2	---	---	---	---	
USP54	159195	broad.mit.edu	37	10	75330462	75330462	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75330462delC	uc001juo.2	-						USP54_uc001jup.2_Intron|USP54_uc010qkl.1_Intron	NM_152586	NP_689799	Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54						ubiquitin-dependent protein catabolic process		protein binding|ubiquitin thiolesterase activity			breast(3)|lung(2)|kidney(1)	6	Prostate(51;0.0112)					tgccacctcacccgTTGTACT	0.134													3	3	---	---	---	---	
ADK	132	broad.mit.edu	37	10	76027513	76027514	+	Intron	DEL	TG	-	-	rs61863650	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76027513_76027514delTG	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron	NM_006721	NP_006712	P55263	ADK_HUMAN	adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)	TATCCTTATTtgtgtgtgtgtg	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	77531040	77531040	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77531040delT								MIR606 (218729 upstream) : C10orf11 (11479 downstream)																							catccATGCATTTTTTTTTTT	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	80500496	80500497	+	IGR	INS	-	GTGTGT	GTGTGT	rs72042765		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80500496_80500497insGTGTGT								RPS24 (683926 upstream) : LOC283050 (202587 downstream)																							CTGGATACCACgtgtgtgtgtg	0.248													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	80508267	80508268	+	IGR	INS	-	A	A	rs71883513		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80508267_80508268insA								RPS24 (691697 upstream) : LOC283050 (194816 downstream)																							CAGAAAGCAAGAAAAAAAAAAA	0.406													4	3	---	---	---	---	
LOC283050	283050	broad.mit.edu	37	10	80802069	80802070	+	Intron	INS	-	A	A	rs35414390		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80802069_80802070insA	uc001jzz.2	-						LOC283050_uc001jzx.2_Intron|LOC283050_uc001jzy.2_Intron|LOC283050_uc001kab.1_Intron	NR_024431				Homo sapiens cDNA FLJ40604 fis, clone THYMU2011806.												0						taaatggaggtaaaaaaaaaaa	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	81870315	81870315	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81870315delT								C10orf57 (18009 upstream) : PLAC9 (21943 downstream)																							cGATGTTCTGTTTTTTTTTTT	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	81909219	81909220	+	IGR	INS	-	T	T	rs148027816	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81909219_81909220insT								PLAC9 (4435 upstream) : ANXA11 (5660 downstream)																							tgttgttgttgttttctttctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	82748499	82748499	+	IGR	DEL	A	-	-	rs112135245		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82748499delA								SH2D4B (342183 upstream) : NRG3 (886571 downstream)																							CTAGGAGGTGAAGGAAGAGAG	0.423													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	82771957	82771957	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82771957delC								SH2D4B (365641 upstream) : NRG3 (863113 downstream)																							caattccattctgacactaac	0.000													4	2	---	---	---	---	
NRG3	10718	broad.mit.edu	37	10	84625387	84625388	+	Intron	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84625387_84625388insA	uc001kco.2	+						NRG3_uc010qlz.1_Intron|NRG3_uc001kcp.2_Intron|NRG3_uc001kcq.2_Intron|NRG3_uc001kcr.2_Intron	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1						regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		ATTGGAAAGGCAATTTAATGTT	0.267													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	93453661	93453662	+	IGR	INS	-	ACAC	ACAC	rs142878275	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93453661_93453662insACAC								PPP1R3C (60803 upstream) : TNKS2 (104489 downstream)																							tctgtTGGAAAacacacacaca	0.010													4	2	---	---	---	---	
NOLC1	9221	broad.mit.edu	37	10	103920996	103920996	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103920996delT	uc001kuo.2	+						NOLC1_uc001kup.2_Intron|NOLC1_uc001kuq.2_Intron|NOLC1_uc009xxb.1_Intron|NOLC1_uc001kur.2_Intron	NM_004741	NP_004732	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1						mitosis|rRNA processing	cytoplasm|nucleolus	ATP binding|GTP binding|protein binding			ovary(1)	1		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)		ACTGGTTACCttttttttttt	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	121806741	121806746	+	IGR	DEL	GTGTGT	-	-	rs10570849		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121806741_121806746delGTGTGT								SEC23IP (105496 upstream) : PPAPDC1A (409720 downstream)																							ATGTAGCTAAgtgtgtgtgtgtgtgt	0.403													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	122495624	122495624	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122495624delG								PPAPDC1A (146257 upstream) : WDR11 (115071 downstream)																							CATCATTTTTGGTAATGTAAG	0.343													3	3	---	---	---	---	
DHX32	55760	broad.mit.edu	37	10	127584491	127584491	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127584491delA	uc001ljg.1	-						FANK1_uc010quk.1_5'Flank|FANK1_uc001ljh.3_5'Flank|FANK1_uc009yan.2_5'Flank	NM_018180	NP_060650	Q7L7V1	DHX32_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32							mitochondrion|nucleus	ATP binding|helicase activity			breast(2)|ovary(1)|lung(1)	4		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				GCTTCCCGTCAGGGGGGCTCG	0.736													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	134635444	134635445	+	Intron	DEL	TG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134635444_134635445delTG	uc010qux.1	-							NM_017609	NP_060079			Homo sapiens cDNA, FLJ17989.																		tgatgtgtgctgtgtgtgcgct	0.000													5	3	---	---	---	---	
SPRN	503542	broad.mit.edu	37	10	135235404	135235405	+	3'UTR	INS	-	G	G	rs147046336	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135235404_135235405insG	uc001lnf.3	-	2						NM_001012508	NP_001012526	Q5BIV9	SPRN_HUMAN	shadow of prion protein precursor							anchored to membrane|plasma membrane					0		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		CCCAAGGCCACGGCGGGGGGCA	0.649													4	2	---	---	---	---	
TRIM66	9866	broad.mit.edu	37	11	8644563	8644566	+	Intron	DEL	CATA	-	-	rs138291059		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8644563_8644566delCATA	uc010rbo.1	-							NM_014818	NP_055633	O15016	TRI66_HUMAN	tripartite motif-containing 66							aggresome|nucleus	zinc ion binding				0						TATAGTCATTCATACATAGTGGTG	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	17045795	17045796	+	IGR	DEL	AA	-	-	rs35808573		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17045795_17045796delAA								PLEKHA7 (9832 upstream) : RPS13 (50144 downstream)																							CCCATACCCCAAAacacacaca	0.465													3	3	---	---	---	---	
ELP4	26610	broad.mit.edu	37	11	31608191	31608192	+	Intron	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31608191_31608192insT	uc001mtb.2	+						ELP4_uc001mta.1_Intron|ELP4_uc001mtc.2_Intron|ELP4_uc010rdz.1_Intron	NM_019040	NP_061913	Q96EB1	ELP4_HUMAN	elongation protein 4 homolog						histone acetylation|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|Elongator holoenzyme complex|transcription elongation factor complex	phosphorylase kinase regulator activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|prostate(1)	3	Lung SC(675;0.225)					atgttttttggttttttttttt	0.000													4	2	---	---	---	---	
PRR5L	79899	broad.mit.edu	37	11	36418697	36418697	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36418697delA	uc001mwo.3	+						PRR5L_uc001mwp.2_Intron|PRR5L_uc009ykk.2_Intron	NM_001160167	NP_001153639	Q6MZQ0	PRR5L_HUMAN	protor-2 isoform a											ovary(1)	1						ggctcactgcaacccctgcct	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	38684454	38684454	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38684454delA								None (None upstream) : None (None downstream)																							AGCATGTTAGAAGCTCTTTTT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	44285595	44285597	+	IGR	DEL	CTT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44285595_44285597delCTT								EXT2 (18616 upstream) : ALX4 (562 downstream)																							AGGACCTTTCCTTCTTCTAGCAC	0.660													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	48342432	48342433	+	IGR	INS	-	T	T	rs150320710		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48342432_48342433insT								OR4S1 (13729 upstream) : OR4C3 (4060 downstream)																							GGCCTAGGACCATGCCTAGAAT	0.426													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	48352565	48352566	+	IGR	INS	-	A	A	rs148779169	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48352565_48352566insA								OR4C3 (5085 upstream) : OR4C45 (14336 downstream)																							ttccagtcCTCATCATCTTTTc	0.094													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	49454957	49454958	+	IGR	DEL	TT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49454957_49454958delTT								FOLH1 (224735 upstream) : LOC440040 (125122 downstream)																							AAGCAACAACtttttttttttt	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	56470227	56470227	+	IGR	DEL	G	-	-	rs78375198		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56470227delG								OR9G9 (1448 upstream) : OR9G4 (40078 downstream)																							gccagtgactggggcagggtg	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	58578999	58579000	+	IGR	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58578999_58579000insT								GLYAT (79552 upstream) : GLYATL2 (22542 downstream)																							ggaagatgaggttttttttttc	0.000													4	2	---	---	---	---	
CCDC86	79080	broad.mit.edu	37	11	60615749	60615749	+	Intron	DEL	T	-	-	rs34678783		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60615749delT	uc001nqa.2	+						CCDC86_uc001nqb.2_Intron	NM_024098	NP_077003	Q9H6F5	CCD86_HUMAN	coiled-coil domain containing 86						interspecies interaction between organisms	nucleus					0						CAGTTTAGCCTGGGCTGCTGA	0.632													4	2	---	---	---	---	
FADS2	9415	broad.mit.edu	37	11	61602460	61602461	+	Intron	DEL	CA	-	-	rs149597144	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61602460_61602461delCA	uc001nsl.1	+						FADS2_uc001nsj.2_Intron|FADS2_uc010rlo.1_Intron|FADS2_uc001nsk.2_Intron	NM_004265	NP_004256	O95864	FADS2_HUMAN	fatty acid desaturase 2						electron transport chain|transport|unsaturated fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction	heme binding			ovary(1)|pancreas(1)	2					Alpha-Linolenic Acid(DB00132)	cctgcccccccaccccagccct	0.381													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	65461592	65461592	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65461592delT								RELA (31149 upstream) : KAT5 (17897 downstream)																							aagtacaggcttcctgcctta	0.000													4	2	---	---	---	---	
ALDH3B2	222	broad.mit.edu	37	11	67437413	67437414	+	Intron	DEL	GT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67437413_67437414delGT	uc001omr.2	-						ALDH3B2_uc001oms.2_Intron|ALDH3B2_uc009ysa.1_Intron	NM_000695	NP_000686	P48448	AL3B2_HUMAN	aldehyde dehydrogenase 3B2						alcohol metabolic process|cellular aldehyde metabolic process|lipid metabolic process		3-chloroallyl aldehyde dehydrogenase activity|aldehyde dehydrogenase			lung(1)|kidney(1)	2					NADH(DB00157)	ctgcgtatgggtgtgtgtgtcc	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	68412258	68412259	+	IGR	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68412258_68412259insA								SAPS3 (29459 upstream) : GAL (39724 downstream)																							aggaaggaaagaaggaaggaag	0.000													6	3	---	---	---	---	
CPT1A	1374	broad.mit.edu	37	11	68595871	68595872	+	Intron	INS	-	CC	CC	rs141375266	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68595871_68595872insCC	uc001oog.3	-						CPT1A_uc001oof.3_Intron	NM_001876	NP_001867	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A liver isoform						carnitine shuttle|fatty acid beta-oxidation	integral to membrane|mitochondrial outer membrane	carnitine O-palmitoyltransferase activity			skin(2)	2	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		L-Carnitine(DB00583)|Perhexiline(DB01074)	CTGGGTCAGGGCCCCCCACCTC	0.653													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69042784	69042795	+	IGR	DEL	TCCATCCATCTA	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69042784_69042795delTCCATCCATCTA								TPCN2 (112877 upstream) : MYEOV (18827 downstream)																							cacccacatctccatccatctatccatccatc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69714656	69714657	+	IGR	DEL	AG	-	-	rs71463652		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69714656_69714657delAG								FGF3 (80464 upstream) : ANO1 (209751 downstream)																							aaagaaagaaagagagagagag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69791960	69791960	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69791960delG								FGF3 (157768 upstream) : ANO1 (132448 downstream)																							GGGCAGAGGTGGGAGGGACAT	0.502													4	2	---	---	---	---	
ANO1	55107	broad.mit.edu	37	11	69971959	69971959	+	Intron	DEL	C	-	-	rs60749334		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69971959delC	uc001opj.2	+						ANO1_uc001opk.1_Intron|ANO1_uc001opl.1_Intron|ANO1_uc010rqk.1_Intron	NM_018043	NP_060513	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel						multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			ovary(1)|pancreas(1)	2						caaaaaaaaacaaaaaaagag	0.264													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	70941615	70941615	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70941615delA								SHANK2 (5807 upstream) : DHCR7 (203844 downstream)																							actctgtctcaaaaaaaaaaa	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	71087472	71087473	+	IGR	INS	-	AG	AG	rs76868924		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71087472_71087473insAG								SHANK2 (151664 upstream) : DHCR7 (57986 downstream)																							gctgctataacaataccacaga	0.000													3	3	---	---	---	---	
PHOX2A	401	broad.mit.edu	37	11	71953458	71953458	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71953458delC	uc001osh.3	-							NM_005169	NP_005160	O14813	PHX2A_HUMAN	paired-like homeobox 2a						noradrenergic neuron differentiation|positive regulation of transcription from RNA polymerase II promoter	nuclear chromatin	RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						AACCCTGAGTCCCCATTTCTC	0.473													4	2	---	---	---	---	
FCHSD2	9873	broad.mit.edu	37	11	72835801	72835801	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72835801delA	uc009ytl.2	-						FCHSD2_uc010rrg.1_Intron|FCHSD2_uc001oth.3_Intron|FCHSD2_uc001oti.2_Intron	NM_014824	NP_055639	O94868	FCSD2_HUMAN	FCH and double SH3 domains 2								protein binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(5;3.3e-05)			actctgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
UVRAG	7405	broad.mit.edu	37	11	75764353	75764354	+	Intron	DEL	AC	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75764353_75764354delAC	uc001oxc.2	+						UVRAG_uc010rrw.1_Intron|UVRAG_uc001oxd.2_Intron|UVRAG_uc010rrx.1_Intron	NM_003369	NP_003360	Q9P2Y5	UVRAG_HUMAN	UV radiation resistance associated						DNA repair|positive regulation of autophagy	early endosome|late endosome|lysosome	protein binding			skin(4)|lung(2)	6						ctgtctcaaaacacacacacac	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	79370233	79370238	+	IGR	DEL	CAGTAT	-	-	rs11278912		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79370233_79370238delCAGTAT								ODZ4 (218538 upstream) : None (None downstream)																							GGTCATTTTCCAGTATCATTCTTTTA	0.432													4	5	---	---	---	---	
ME3	10873	broad.mit.edu	37	11	86333430	86333430	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86333430delA	uc001pbz.2	-						ME3_uc001pca.2_Intron|ME3_uc009yvk.2_Intron|ME3_uc010rtr.1_Intron	NM_001014811	NP_001014811	Q16798	MAON_HUMAN	mitochondrial malic enzyme 3 precursor						aerobic respiration|malate metabolic process|oxygen metabolic process|pyruvate metabolic process	mitochondrial matrix	malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity|metal ion binding|NAD binding			ovary(1)	1		Acute lymphoblastic leukemia(157;4.34e-06)|all_hematologic(158;0.00252)			NADH(DB00157)	GGAGGGCATTAAAAAAAAAAA	0.393													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	91547394	91547394	+	IGR	DEL	T	-	-	rs35863465		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91547394delT								MIR1261 (945024 upstream) : FAT3 (537868 downstream)																							TCTCCATCCATTTTTTTTTTT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	101877400	101877401	+	IGR	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101877400_101877401insT								KIAA1377 (5609 upstream) : C11orf70 (40773 downstream)																							GGAACTCTGTCtttttttttta	0.178													4	2	---	---	---	---	
FAM55A	120400	broad.mit.edu	37	11	114419841	114419841	+	Intron	DEL	T	-	-	rs33961839		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114419841delT	uc001ppa.2	-						FAM55A_uc001ppb.1_Intron	NM_152315	NP_689528	Q8N323	FA55A_HUMAN	hypothetical protein LOC120400							extracellular region					0		all_cancers(61;8.53e-16)|all_epithelial(67;1.71e-08)|all_hematologic(158;3.05e-05)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0194)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;3.02e-06)|Epithelial(105;0.000144)|all cancers(92;0.00106)		tagagaatagtgaaaaaagta	0.000													4	2	---	---	---	---	
CADM1	23705	broad.mit.edu	37	11	115199579	115199579	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115199579delA	uc001ppi.3	-						CADM1_uc001ppf.3_Intron|CADM1_uc001ppk.3_Intron|CADM1_uc001ppj.3_Intron|CADM1_uc001ppl.2_Intron	NM_014333	NP_055148	Q9BY67	CADM1_HUMAN	immunoglobulin superfamily, member 4D isoform 1						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)		CATGAGAGACAAGGAAAGAAA	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	115677338	115677338	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115677338delA								CADM1 (302097 upstream) : BUD13 (941550 downstream)																							CCAGAAAGTTAATATACAAAT	0.333													4	2	---	---	---	---	
CXCR5	643	broad.mit.edu	37	11	118766356	118766357	+	3'UTR	INS	-	A	A	rs150672802	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118766356_118766357insA	uc001pue.3	+	2					CXCR5_uc001puf.2_3'UTR	NM_001716	NP_001707	P32302	CXCR5_HUMAN	Burkitt lymphoma receptor 1 isoform 1						B cell activation|cellular component movement	integral to plasma membrane	C-X-C chemokine receptor activity			breast(1)	1	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)		CGAGGAAACTCAGAGTCGGAAC	0.579													2	4	---	---	---	---	
TRIM29	23650	broad.mit.edu	37	11	119983087	119983088	+	3'UTR	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119983087_119983088insA	uc001pwz.2	-	9					TRIM29_uc001pwx.2_RNA|TRIM29_uc001pwy.2_3'UTR|TRIM29_uc010rzi.1_3'UTR|TRIM29_uc010rzj.1_3'UTR|TRIM29_uc001pxa.2_RNA	NM_012101	NP_036233	Q14134	TRI29_HUMAN	tripartite motif protein TRIM29						transcription from RNA polymerase II promoter	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|breast(1)|kidney(1)|skin(1)	4		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)		GGAGGAAGAGCAGGGGTGTGGC	0.609													19	12	---	---	---	---	
UBASH3B	84959	broad.mit.edu	37	11	122547534	122547534	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122547534delT	uc001pyi.3	+							NM_032873	NP_116262	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing,							cytoplasm|nucleus	protein tyrosine phosphatase activity			central_nervous_system(1)	1		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)		CTTCTGGCCCTTCCTGCTCAC	0.532													4	2	---	---	---	---	
ASAM	79827	broad.mit.edu	37	11	123011558	123011559	+	Intron	INS	-	GGA	GGA	rs150540303	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123011558_123011559insGGA	uc001pyt.2	-							NM_024769	NP_079045	Q9H6B4	CLMP_HUMAN	adipocyte-specific adhesion molecule precursor							integral to membrane|tight junction					0		Breast(109;0.0025)|Lung NSC(97;0.0179)|all_lung(97;0.0182)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.73e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0446)		cctctaatgttggaggtgggct	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	128019367	128019370	+	IGR	DEL	ACAC	-	-	rs150576182		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128019367_128019370delACAC								None (None upstream) : ETS1 (309286 downstream)																							acacacacatacacacacacacac	0.304													10	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	128134312	128134312	+	IGR	DEL	A	-	-	rs143965062		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128134312delA								None (None upstream) : ETS1 (194344 downstream)																							ACAAGTTTGGAAAAAAAAAAA	0.338													4	3	---	---	---	---	
ARHGAP32	9743	broad.mit.edu	37	11	128843838	128843839	+	Intron	INS	-	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128843838_128843839insG	uc009zcp.2	-						ARHGAP32_uc009zcq.1_3'UTR|ARHGAP32_uc009zco.2_5'UTR|ARHGAP32_uc001qez.2_Intron	NM_001142685	NP_001136157	A7KAX9	RHG32_HUMAN	Rho GTPase-activating protein isoform 1						cell communication|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell cortex|cell junction|cytosol|dendritic spine|endoplasmic reticulum membrane|endosome membrane|Golgi membrane|postsynaptic density|postsynaptic membrane	GTPase activator activity|phosphatidylinositol binding			lung(3)|ovary(2)	5						TTGGCCCTTTTGGGGAGTTTTG	0.436													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	133933510	133933510	+	IGR	DEL	C	-	-	rs58798142		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133933510delC								LOC100128239 (22274 upstream) : JAM3 (5310 downstream)																							AGtcttttttctttttttgag	0.174													4	2	---	---	---	---	
CACNA1C	775	broad.mit.edu	37	12	2681845	2681847	+	Intron	DEL	CTT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2681845_2681847delCTT	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qka.1_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,						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)	cttcctcctccttcttctcttcc	0.000													6	5	---	---	---	---	
TULP3	7289	broad.mit.edu	37	12	3042824	3042824	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3042824delA	uc010seh.1	+						TULP3_uc010sef.1_Intron|TULP3_uc009zec.1_Intron|TULP3_uc010seg.1_Intron|TULP3_uc001qlj.2_Intron|TULP3_uc010sei.1_Intron	NM_003324	NP_003315	O75386	TULP3_HUMAN	tubby like protein 3 isoform 1						G-protein coupled receptor protein signaling pathway|regulation of transcription, DNA-dependent	cytoplasm|extracellular region|nucleus|plasma membrane	phosphatidylinositol-4,5-bisphosphate binding				0			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			aagaaaaaggaaaaaaaaaaa	0.134													4	2	---	---	---	---	
TSPAN9	10867	broad.mit.edu	37	12	3284276	3284288	+	Intron	DEL	GGGCGAGGCTGGG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3284276_3284288delGGGCGAGGCTGGG	uc001qlp.2	+							NM_006675	NP_006666	O75954	TSN9_HUMAN	tetraspanin 9							integral to plasma membrane|membrane fraction				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(31;0.00153)|COAD - Colon adenocarcinoma(12;0.0831)			GACCCCTGCAGGGCGAGGCTGGGGGCATCATTT	0.606													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	4002952	4002955	+	IGR	DEL	CACA	-	-	rs72099216		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4002952_4002955delCACA								PARP11 (20344 upstream) : CCND2 (379947 downstream)																							tgcacgcacgcacacacacacagg	0.000													1	6	---	---	---	---	
CSDA	8531	broad.mit.edu	37	12	10857241	10857241	+	Intron	DEL	T	-	-	rs35718202		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10857241delT	uc001qyt.2	-						CSDA_uc001qyu.2_Intron	NM_003651	NP_003642	P16989	DBPA_HUMAN	cold shock domain protein A isoform a						negative regulation of transcription from RNA polymerase II promoter|response to cold	cytoplasm|nucleus	double-stranded DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)|lung(1)|large_intestine(1)	4	Glioma(1;0.155)					ttcctccccctaagagccaaa	0.104													2	5	---	---	---	---	
PRB4	5545	broad.mit.edu	37	12	11281826	11281827	+	Intron	INS	-	C	C	rs144387208	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11281826_11281827insC	uc001qzf.1	-						PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRH1_uc001qzj.2_Intron	NM_002723	NP_002714	P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4							extracellular region				ovary(1)	1						CAGTGGGAGTTTTGAAGGTCAG	0.178										HNSCC(22;0.051)			5	3	---	---	---	---	
DUSP16	80824	broad.mit.edu	37	12	12635464	12635468	+	Intron	DEL	TTAAT	-	-	rs71436716		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12635464_12635468delTTAAT	uc001rao.1	-						DUSP16_uc001ran.1_Intron	NM_030640	NP_085143	Q9BY84	DUS16_HUMAN	dual specificity phosphatase 16						inactivation of MAPK activity|MAPK export from nucleus|MAPK phosphatase export from nucleus, leptomycin B sensitive	cytoplasmic membrane-bounded vesicle|nucleus	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity				0		Prostate(47;0.0687)		BRCA - Breast invasive adenocarcinoma(232;0.0203)		AGCAAAGGAATTAATTTAACACACA	0.439													4	2	---	---	---	---	
ATF7IP	55729	broad.mit.edu	37	12	14531034	14531035	+	Intron	INS	-	T	T	rs71438312		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14531034_14531035insT	uc001rbw.2	+						ATF7IP_uc010shs.1_Intron|ATF7IP_uc001rbu.2_Intron|ATF7IP_uc001rbv.1_Intron|ATF7IP_uc001rbx.2_Intron	NM_018179	NP_060649	Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting						DNA methylation|interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|regulation of RNA polymerase II transcriptional preinitiation complex assembly|transcription, DNA-dependent		protein binding			lung(3)|ovary(1)|skin(1)	5						ttttctttttcttttttttttt	0.124													3	3	---	---	---	---	
PTPRO	5800	broad.mit.edu	37	12	15568101	15568102	+	Intron	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15568101_15568102insT	uc001rcv.1	+						PTPRO_uc001rcw.1_Intron|PTPRO_uc001rcu.1_Intron	NM_030667	NP_109592	Q16827	PTPRO_HUMAN	receptor-type protein tyrosine phosphatase O							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	9		Hepatocellular(102;0.244)				ACACCAAAAGATTTTGGAAAAT	0.460													3	4	---	---	---	---	
PDE3A	5139	broad.mit.edu	37	12	20777156	20777156	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20777156delT	uc001reh.1	+							NM_000921	NP_000912	Q14432	PDE3A_HUMAN	phosphodiesterase 3A						lipid metabolic process|platelet activation|signal transduction	cytosol|integral to membrane	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)	4	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Cilostazol(DB01166)|Enoximone(DB04880)|Milrinone(DB00235)|Theophylline(DB00277)	AACTAGGATATTTTGGGTTCT	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	25116673	25116673	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25116673delG								BCAT1 (14365 upstream) : C12orf77 (29697 downstream)																							ccccaatcccgccctgttttg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	25450052	25450053	+	IGR	INS	-	T	T	rs145772906	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25450052_25450053insT								KRAS (46189 upstream) : IFLTD1 (178963 downstream)																							AGGAAGCCATGTTTttttacag	0.035													4	2	---	---	---	---	
PPFIBP1	8496	broad.mit.edu	37	12	27842373	27842373	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27842373delA	uc001ric.1	+						PPFIBP1_uc010sjr.1_Intron|PPFIBP1_uc001rib.1_Intron|PPFIBP1_uc001ria.2_Intron|PPFIBP1_uc001rid.1_Intron|PPFIBP1_uc001rif.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)					ttgtaagaataaaaaaaaaag	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	28749169	28749169	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28749169delC								CCDC91 (46071 upstream) : FAR2 (553063 downstream)																							TCTCCTTCAACTAAGGTAAAA	0.284													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	29946795	29946796	+	IGR	INS	-	AC	AC	rs145392899	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29946795_29946796insAC								TMTC1 (9103 upstream) : IPO8 (835127 downstream)																							ACATGCTTACTATAGTTGCAAC	0.257													6	4	---	---	---	---	
BICD1	636	broad.mit.edu	37	12	32491572	32491573	+	Intron	INS	-	AA	AA	rs145615722		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32491572_32491573insAA	uc001rku.2	+						BICD1_uc001rkv.2_Intron|BICD1_uc010skd.1_Intron	NM_001714	NP_001705	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 isoform 1						anatomical structure morphogenesis|intracellular mRNA localization|microtubule anchoring at microtubule organizing center|minus-end-directed organelle transport along microtubule|positive regulation of receptor-mediated endocytosis|protein localization to organelle|RNA processing|stress granule assembly|viral reproduction	cytoplasmic vesicle|cytoskeleton|cytosol|host cell viral assembly compartment|membrane|perinuclear region of cytoplasm|trans-Golgi network	cytoskeletal adaptor activity|dynactin binding|dynein binding|proteinase activated receptor binding|Rab GTPase binding|structural constituent of cytoskeleton			large_intestine(1)|central_nervous_system(1)	2	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			ATGTGGAAACTAAAAAAAAAAA	0.282													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	32924935	32924938	+	IGR	DEL	AAGG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32924935_32924938delAAGG								YARS2 (16061 upstream) : PKP2 (18744 downstream)																							ctgtTAGAAAaaggaaggaaggaa	0.005													3	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	38127032	38127032	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38127032delG								None (None upstream) : ALG10B (583525 downstream)																							aaatttctttgtgatgtgtgc	0.000													4	2	---	---	---	---	
ADAMTS20	80070	broad.mit.edu	37	12	43837439	43837439	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43837439delA	uc010skx.1	-							NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with							proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		TTGAGTGCTTAAGAACATATG	0.303													4	2	---	---	---	---	
AQP2	359	broad.mit.edu	37	12	50351340	50351341	+	3'UTR	DEL	TG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50351340_50351341delTG	uc001rvn.2	+	4					AQP2_uc009zll.1_RNA	NM_000486	NP_000477	P41181	AQP2_HUMAN	aquaporin 2						cellular response to copper ion|cellular response to mercury ion|excretion	apical plasma membrane|integral to membrane|transport vesicle membrane	glycerol transmembrane transporter activity|water channel activity			ovary(2)	2						GGAACATCTCTGTAATTGTGTC	0.495													3	3	---	---	---	---	
KRT81	3887	broad.mit.edu	37	12	52700831	52700832	+	5'UTR	INS	-	T	T	rs150068067	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52700831_52700832insT	uc001sac.2	-	2					KRT86_uc010snq.1_Intron|KRT86_uc009zmg.2_Intron|KRT86_uc001sad.2_Intron	NM_002281	NP_002272	Q14533	KRT81_HUMAN	keratin, hair, basic, 1							keratin filament	protein binding|structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(357;0.189)		CTCGAAGCTCCTTTTTTTTTGT	0.520													6	4	---	---	---	---	
KRT85	3891	broad.mit.edu	37	12	52763107	52763107	+	5'Flank	DEL	T	-	-	rs144252538		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52763107delT	uc001sag.2	-							NM_002283	NP_002274	P78386	KRT85_HUMAN	keratin 85						epidermis development	keratin filament	protein binding|structural molecule activity			ovary(1)	1	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GCTTTTAATGTTTTTTTTTTT	0.493													1	5	---	---	---	---	
HOXC4	3221	broad.mit.edu	37	12	54426580	54426580	+	Intron	DEL	T	-	-	rs113659413		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54426580delT	uc001seu.2	+						HOXC5_uc001set.2_Intron|HOXC5_uc001sew.2_5'Flank|MIR615_hsa-mir-615|MI0003628_5'Flank	NM_014620	NP_055435	P09017	HXC4_HUMAN	homeobox C4							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						TCCAAGAACcttttttttttt	0.413											OREG0021884	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	54878487	54878487	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54878487delG								GTSF1 (11101 upstream) : NCKAP1L (13008 downstream)																							AGAAACCATTGGTTTTTTTTT	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	63022369	63022370	+	IGR	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63022369_63022370insT								MIRLET7I (24820 upstream) : PPM1H (15393 downstream)																							ccatttaagcctttttttttct	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	65104975	65104975	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65104975delA								RASSF3 (15785 upstream) : GNS (2249 downstream)																							GGGATAAGTTAAAAAAAAAAA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	65922430	65922430	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65922430delG								MSRB3 (61750 upstream) : RPSAP52 (229373 downstream)																							tgattctcccgactcagtcac	0.000													4	2	---	---	---	---	
GRIP1	23426	broad.mit.edu	37	12	66851996	66851997	+	Intron	DEL	CT	-	-	rs140154256		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66851996_66851997delCT	uc001stk.2	-						GRIP1_uc010sta.1_Intron|GRIP1_uc001stj.2_Intron|GRIP1_uc001stl.1_Intron|GRIP1_uc001stm.2_Intron	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1						androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		TGGATTccccctctctctccac	0.198													3	3	---	---	---	---	
GRIP1	23426	broad.mit.edu	37	12	67051058	67051058	+	Intron	DEL	C	-	-	rs67817466		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67051058delC	uc001stk.2	-						GRIP1_uc010sta.1_Intron|GRIP1_uc001stm.2_Intron	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1						androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		TGAAGGAGGACCCTCCCCACC	0.527													4	2	---	---	---	---	
PTPRR	5801	broad.mit.edu	37	12	71056652	71056652	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71056652delA	uc001swi.1	-						PTPRR_uc001swf.1_Intron|PTPRR_uc001swg.1_Intron|PTPRR_uc001swh.1_Intron|PTPRR_uc009zrs.2_Intron|PTPRR_uc010stq.1_Intron|PTPRR_uc010str.1_Intron	NM_002849	NP_002840	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R						in utero embryonic development	cell surface|Golgi apparatus|integral to membrane|nucleus|perinuclear region of cytoplasm|plasma membrane	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			skin(2)|ovary(1)	3			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		GGCTCCATACAAAAAAAAAAG	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	89644957	89644957	+	IGR	DEL	T	-	-	rs5799896		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89644957delT								KITLG (670719 upstream) : DUSP6 (96882 downstream)																							GCCACCACTGTtagaaaaagc	0.189													3	3	---	---	---	---	
ANKS1B	56899	broad.mit.edu	37	12	99761564	99761565	+	Intron	INS	-	TG	TG			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99761564_99761565insTG	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		gtgtgtgtgcttgtgtgtgtgt	0.045													4	2	---	---	---	---	
IGF1	3479	broad.mit.edu	37	12	102812253	102812253	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102812253delG	uc001tjp.3	-						IGF1_uc001tjn.2_Intron|IGF1_uc001tjm.2_Intron|IGF1_uc001tjo.2_Intron	NM_001111285	NP_001104755	P05019	IGF1_HUMAN	insulin-like growth factor 1 isoform 3						anti-apoptosis|bone mineralization involved in bone maturation|cellular component movement|DNA replication|glycolate metabolic process|muscle hypertrophy|myoblast differentiation|myoblast proliferation|myotube cell development|negative regulation of smooth muscle cell apoptosis|phosphatidylinositol-mediated signaling|platelet activation|platelet degranulation|positive regulation of activated T cell proliferation|positive regulation of DNA replication|positive regulation of epithelial cell proliferation|positive regulation of fibroblast proliferation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis|positive regulation of osteoblast differentiation|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of Ras protein signal transduction|positive regulation of smooth muscle cell migration|positive regulation of smooth muscle cell proliferation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tyrosine phosphorylation of Stat5 protein|Ras protein signal transduction|regulation of multicellular organism growth|satellite cell maintenance involved in skeletal muscle regeneration	platelet alpha granule lumen	growth factor activity|hormone activity|insulin receptor binding|insulin-like growth factor receptor binding|integrin binding			central_nervous_system(1)|pancreas(1)	2						AAGGTGTCATGGTGAACTTCT	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	103611309	103611310	+	IGR	DEL	AA	-	-	rs34370910		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103611309_103611310delAA								ASCL1 (257022 upstream) : C12orf42 (20060 downstream)																							accctgtctcaaaaaaaaaaaa	0.173													4	2	---	---	---	---	
RBM19	9904	broad.mit.edu	37	12	114322088	114322088	+	Intron	DEL	A	-	-	rs112733518		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114322088delA	uc009zwi.2	-						RBM19_uc001tvn.3_Intron|RBM19_uc001tvm.2_Intron	NM_001146699	NP_001140171	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19						multicellular organismal development|positive regulation of embryonic development	chromosome|cytoplasm|nucleolus|nucleoplasm	nucleotide binding|RNA binding			skin(3)|ovary(1)|liver(1)|central_nervous_system(1)	6	Medulloblastoma(191;0.163)|all_neural(191;0.178)					acaatatctcaaaaaaaaaaa	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	116885700	116885701	+	IGR	INS	-	T	T	rs74992907	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116885700_116885701insT								MED13L (170709 upstream) : NCRNA00173 (85526 downstream)																							CTCTCTCTCTCttttttttttt	0.153													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	125157148	125157149	+	IGR	DEL	CA	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125157148_125157149delCA								NCOR2 (105138 upstream) : SCARB1 (105026 downstream)																							catgtacctgcacacacacaca	0.094													2	6	---	---	---	---	
TMEM132B	114795	broad.mit.edu	37	12	126141883	126141884	+	3'UTR	DEL	GT	-	-	rs113651659		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126141883_126141884delGT	uc001uhe.1	+	9					TMEM132B_uc001uhf.1_3'UTR	NM_052907	NP_443139	Q14DG7	T132B_HUMAN	transmembrane protein 132B							integral to membrane				skin(11)|ovary(5)|large_intestine(1)|pancreas(1)|breast(1)	19	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		ACATATACCCgtgtgtgtgtgt	0.317													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	22878971	22878971	+	IGR	DEL	T	-	-	rs111500920		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22878971delT								FGF9 (600331 upstream) : SGCG (876089 downstream)																							aaaaaaaaccttttttttttt	0.085													4	2	---	---	---	---	
SPATA13	221178	broad.mit.edu	37	13	24853068	24853071	+	Intron	DEL	TTCC	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24853068_24853071delTTCC	uc001upg.1	+						SPATA13_uc001upd.1_Intron|C1QTNF9_uc001upe.2_Intron|SPATA13_uc010tcy.1_Intron|SPATA13_uc010tcz.1_Intron|SPATA13_uc010tda.1_Intron|SPATA13_uc001uph.2_Intron|SPATA13_uc010tdb.1_Intron	NM_153023	NP_694568	Q96N96	SPT13_HUMAN	spermatogenesis associated 13						cell migration|filopodium assembly|lamellipodium assembly|regulation of cell migration|regulation of Rho protein signal transduction	cytoplasm|filopodium|lamellipodium|ruffle membrane	protein binding|Rac guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		ccttccctctttccttccttcctt	0.093													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	24992928	24992928	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24992928delT								C1QTNF9 (96263 upstream) : PARP4 (2147 downstream)																							ttttgagatgtgtacgtttat	0.005													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	31740361	31740362	+	IGR	INS	-	GTGT	GTGT			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31740361_31740362insGTGT								HSPH1 (3859 upstream) : B3GALTL (33750 downstream)																							GTGATCTTGGGgtgtgtgtgtg	0.337													4	4	---	---	---	---	
FRY	10129	broad.mit.edu	37	13	32647682	32647683	+	Intron	DEL	GT	-	-	rs35631279		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32647682_32647683delGT	uc001utx.2	+						FRY_uc010tdw.1_Intron	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		atgtgggcgggtgtgtgtgtgt	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	79239719	79239719	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79239719delT								RNF219 (5019 upstream) : RBM26 (654381 downstream)																							tgtttgtttgtttgtttgcga	0.000													4	2	---	---	---	---	
FGF14	2259	broad.mit.edu	37	13	102581225	102581225	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102581225delT	uc001vpf.2	-							NM_175929	NP_787125	Q92915	FGF14_HUMAN	fibroblast growth factor 14 isoform 1B						cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			ovary(2)|lung(1)|large_intestine(1)	4	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GCACAGTCCATTTTTTTTTTC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	105177412	105177413	+	IGR	DEL	AT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:105177412_105177413delAT								None (None upstream) : DAOA (940803 downstream)																							atatgtacacatatatacacac	0.005													4	2	---	---	---	---	
FAM155A	728215	broad.mit.edu	37	13	108051803	108051804	+	Intron	INS	-	ACAC	ACAC	rs147453246	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108051803_108051804insACAC	uc001vql.2	-							NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1						cacattcacgtacacacacaca	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	21915161	21915161	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21915161delT								CHD8 (9757 upstream) : RAB2B (12019 downstream)																							attcaatgtatttttgttgaa	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	25923639	25923639	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25923639delT								STXBP6 (404468 upstream) : NOVA1 (991451 downstream)																							GCTTTAACACTTTTTTTTTTC	0.229													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	26130646	26130646	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26130646delA								STXBP6 (611475 upstream) : NOVA1 (784444 downstream)																							AATTAGGGAGAGGAAAGGGTA	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	28169731	28169732	+	IGR	INS	-	CA	CA	rs143256551	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28169731_28169732insCA								None (None upstream) : None (None downstream)																							gcgtgcacgcgcacacacacac	0.000													2	4	---	---	---	---	
NPAS3	64067	broad.mit.edu	37	14	34270285	34270285	+	Frame_Shift_Del	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34270285delG	uc001wru.2	+	12	2836	c.2772delG	c.(2770-2772)GCGfs	p.A924fs	NPAS3_uc001wrs.2_Frame_Shift_Del_p.A911fs|NPAS3_uc001wrt.2_Frame_Shift_Del_p.A892fs|NPAS3_uc001wrv.2_Frame_Shift_Del_p.A894fs	NM_173159	NP_071406	Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3 isoform 3	924					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		GCATCCACGCGGCACAGACTC	0.667													6	3	---	---	---	---	
LRFN5	145581	broad.mit.edu	37	14	42317696	42317697	+	Intron	INS	-	T	T	rs143817023	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42317696_42317697insT	uc001wvm.2	+						LRFN5_uc010ana.2_Intron	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III							integral to membrane				ovary(5)|pancreas(2)|central_nervous_system(1)	8			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		CTTCTGCATTATTTTTTTTTCG	0.411										HNSCC(30;0.082)			3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	44059473	44059473	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44059473delT								None (None upstream) : FSCB (913882 downstream)																							agttaaaacattttacaggag	0.060													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	51929503	51929504	+	IGR	DEL	AG	-	-	rs71443171		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51929503_51929504delAG								TMX1 (205133 upstream) : FRMD6 (26351 downstream)																							TAagggaggaagagagagagag	0.178													2	4	---	---	---	---	
OTX2	5015	broad.mit.edu	37	14	57272080	57272080	+	Frame_Shift_Del	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57272080delG	uc001xcp.2	-	1	266	c.95delC	c.(94-96)CCGfs	p.P32fs	OTX2_uc010aou.2_Frame_Shift_Del_p.P32fs|OTX2_uc001xcq.2_Frame_Shift_Del_p.P32fs	NM_172337	NP_758840	P32243	OTX2_HUMAN	orthodenticle homeobox 2 isoform b	32					axon guidance|forebrain development|midbrain development|positive regulation of embryonic development|positive regulation of gastrulation|primitive streak formation|protein complex assembly|regulation of fibroblast growth factor receptor signaling pathway|regulation of smoothened signaling pathway	growth cone|nucleus|protein complex	eukaryotic initiation factor 4E binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific DNA binding			ovary(1)	1	Medulloblastoma(1;0.00184)|all_neural(1;0.00414)					TCACTTACCCGGGTAGCCCAC	0.597													22	10	---	---	---	---	
C14orf37	145407	broad.mit.edu	37	14	58656263	58656263	+	Intron	DEL	T	-	-	rs35834807		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58656263delT	uc010tro.1	-							NM_001001872	NP_001001872	Q86TY3	CN037_HUMAN	hypothetical protein LOC145407 precursor							integral to membrane	binding				0						TTAGCTGTCATTTTTTTTTTT	0.224													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	66549217	66549217	+	IGR	DEL	A	-	-	rs10713127		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66549217delA								FUT8 (339256 upstream) : C14orf53 (403892 downstream)																							accatcctgcaaaaaaatatt	0.055													3	3	---	---	---	---	
GPHN	10243	broad.mit.edu	37	14	67391186	67391187	+	Intron	DEL	TT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67391186_67391187delTT	uc001xiy.2	+						GPHN_uc001xiw.2_Intron|GPHN_uc001xix.2_Intron|GPHN_uc010tss.1_Intron|GPHN_uc010tst.1_Intron|GPHN_uc010tsu.1_Intron	NM_001024218	NP_001019389	Q9NQX3	GEPH_HUMAN	gephyrin isoform 2						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		TTTAATAGAGTTTCTCCTGTGA	0.342			T	MLL	AL								3	4	---	---	---	---	
SIPA1L1	26037	broad.mit.edu	37	14	72080589	72080591	+	Intron	DEL	AGG	-	-	rs141815399		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72080589_72080591delAGG	uc001xms.2	+						SIPA1L1_uc001xmt.2_Intron|SIPA1L1_uc001xmu.2_Intron|SIPA1L1_uc001xmv.2_Intron|SIPA1L1_uc010ttm.1_Intron	NM_015556	NP_056371	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like						actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		GCCTGAAGGAAGGAGGAGACTGC	0.345													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	83444673	83444673	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:83444673delT								None (None upstream) : None (None downstream)																							CCGAATCCAATTGGTCTTGGC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	89463065	89463065	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89463065delA								TTC8 (118731 upstream) : FOXN3 (159452 downstream)																							cctctcacctaaatgacttca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	90692899	90692900	+	IGR	INS	-	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90692899_90692900insG								KCNK13 (40704 upstream) : PSMC1 (29994 downstream)																							AGTGTATGTCAGGGAAGCAATA	0.480													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	93162289	93162292	+	IGR	DEL	CTCC	-	-	rs72070486		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93162289_93162292delCTCC								RIN3 (6957 upstream) : LGMN (7865 downstream)																							ccctgcctctctccctccctccct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	95476763	95476766	+	IGR	DEL	GGAA	-	-	rs35109161		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95476763_95476766delGGAA								GSC (240264 upstream) : DICER1 (75799 downstream)																							agggaaggagggaaggaaggaagg	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	98112583	98112584	+	RNA	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98112583_98112584insT	uc001yfv.1	-	3		c.540_541insA								human full-length cDNA clone CS0DI087YB20 of Placenta of Homo sapiens (human).																		AAGCTCTGTGGTTTTTTTTTCT	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	98962170	98962172	+	IGR	DEL	AGC	-	-	rs111937821		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98962170_98962172delAGC								C14orf64 (517709 upstream) : C14orf177 (215778 downstream)																							aagagggagaagcagcagcagca	0.138													4	2	---	---	---	---	
PPP2R5C	5527	broad.mit.edu	37	14	102305803	102305803	+	Intron	DEL	C	-	-	rs118121291	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102305803delC	uc001yko.2	+						PPP2R5C_uc010txr.1_Intron|PPP2R5C_uc001ykk.2_Intron|PPP2R5C_uc010txt.1_Intron|PPP2R5C_uc001ykn.2_Intron|PPP2R5C_uc001ykp.2_Intron|PPP2R5C_uc010txs.1_Intron	NM_002719	NP_002710	Q13362	2A5G_HUMAN	gamma isoform of regulatory subunit B56, protein						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|negative regulation of cell proliferation|proteasomal ubiquitin-dependent protein catabolic process|signal transduction	chromosome, centromeric region|nucleus|protein phosphatase type 2A complex	protein binding|protein binding|protein phosphatase type 2A regulator activity|protein phosphatase type 2A regulator activity			ovary(1)|breast(1)	2						CCCATCTGTGCCCCTACTCCA	0.612													2	4	---	---	---	---	
HSP90AA1	3320	broad.mit.edu	37	14	102581473	102581474	+	Intron	INS	-	A	A	rs112143926		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102581473_102581474insA	uc001ykv.3	-							NM_001017963	NP_001017963	P07900	HS90A_HUMAN	heat shock 90kDa protein 1, alpha isoform 1						axon guidance|cellular chaperone-mediated protein complex assembly|G2/M transition of mitotic cell cycle|nitric oxide metabolic process|positive regulation of nitric oxide biosynthetic process|protein import into mitochondrial outer membrane|protein refolding|regulation of nitric-oxide synthase activity|response to unfolded protein|signal transduction	cytosol|melanosome|plasma membrane	ATP binding|ATPase activity|nitric-oxide synthase regulator activity|protein homodimerization activity|TPR domain binding|unfolded protein binding			ovary(2)|central_nervous_system(2)|prostate(1)|lung(1)|breast(1)	7					Rifabutin(DB00615)	cacagagcaagaaaaaaaaaaa	0.000													6	3	---	---	---	---	
PACS2	23241	broad.mit.edu	37	14	105814544	105814544	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105814544delC	uc001yqt.2	+						PACS2_uc001yqs.2_Intron|PACS2_uc001yqv.2_Intron|PACS2_uc001yqu.2_Intron	NM_015197	NP_056012	Q86VP3	PACS2_HUMAN	phosphofurin acidic cluster sorting protein 2						apoptosis|interspecies interaction between organisms	endoplasmic reticulum lumen|mitochondrion				pancreas(1)	1		all_cancers(154;0.0351)|all_epithelial(191;0.153)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)|Epithelial(46;0.036)	Epithelial(152;0.138)		TGTCCACAGGCCCACACTGAG	0.637													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106094606	106094607	+	Intron	INS	-	C	C	rs151095596	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106094606_106094607insC	uc010tyt.1	-						uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron					Parts of antibodies, mostly variable regions.												0						TGCTCCTCCTGCCCCCCCTCCC	0.703													10	5	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106112966	106112967	+	Intron	INS	-	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106112966_106112967insG	uc010tyt.1	-						uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron					Parts of antibodies, mostly variable regions.												0						TCTGAGCTCCAGGGGCTGTCCC	0.673													6	4	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106773997	106774002	+	Intron	DEL	CTGTCA	-	-	rs144451395		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106773997_106774002delCTGTCA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						CACGTTGTCCCTGTCACTGCCTCAGC	0.388													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20612137	20612139	+	Intron	DEL	TTG	-	-	rs150166873		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20612137_20612139delTTG	uc001ytg.2	-						uc010tyx.1_Intron					RecName: Full=Putative HERC2-like protein 3;																		atgatcaatcttgttattttatc	0.000													4	2	---	---	---	---	
LOC646214	646214	broad.mit.edu	37	15	21935593	21935593	+	RNA	DEL	A	-	-	rs111463627		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21935593delA	uc010tzj.1	-	1		c.5147delT				NR_027053				Homo sapiens mRNA for p21-activated kinase 2 variant protein.												0						AATGAAAAACAAAAAGAACAA	0.348													5	3	---	---	---	---	
POTEB	339010	broad.mit.edu	37	15	22059943	22059943	+	Intron	DEL	A	-	-	rs79395716		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22059943delA	uc010tzr.1	-						POTEB_uc010tzq.1_Intron	NM_207355	NP_997238	Q6S5H4	POTEB_HUMAN	protein expressed in prostate, ovary, testis,												0						cctgaaagccaagtgaagatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	26625634	26625635	+	IGR	DEL	TC	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26625634_26625635delTC								ATP10A (515317 upstream) : GABRB3 (163060 downstream)																							TTTCATCCTTTCTCTCTCTCTC	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	27890438	27890439	+	IGR	INS	-	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27890438_27890439insG								GABRG3 (112304 upstream) : OCA2 (109586 downstream)																							GTGAGGTGTCAAGAGGAAGAGT	0.475													39	30	---	---	---	---	
SQRDL	58472	broad.mit.edu	37	15	45965083	45965083	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45965083delA	uc001zvt.2	+						SQRDL_uc001zvu.2_Intron|SQRDL_uc001zvv.2_Intron	NM_021199	NP_067022	Q9Y6N5	SQRD_HUMAN	sulfide dehydrogenase like precursor								oxidoreductase activity			ovary(1)	1		Lung NSC(122;0.000117)|all_lung(180;0.000737)|Melanoma(134;0.0417)		all cancers(107;5.89e-18)|GBM - Glioblastoma multiforme(94;1.21e-06)|COAD - Colon adenocarcinoma(120;0.17)|Colorectal(133;0.188)		taggattctcaaacctgagtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	63298552	63298553	+	IGR	INS	-	C	C	rs148424025	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63298552_63298553insC								TLN2 (161725 upstream) : TPM1 (36285 downstream)																							acacacacacacatacacgcac	0.356													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	70581196	70581196	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70581196delG								TLE3 (190940 upstream) : UACA (365699 downstream)																							CAGTGAGTCTGAATCCAGACC	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	72676400	72676401	+	IGR	DEL	TT	-	-	rs113522246		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72676400_72676401delTT								C15orf34 (5271 upstream) : TMEM202 (14267 downstream)																							tctttctctctttttttttttt	0.248													4	2	---	---	---	---	
NEO1	4756	broad.mit.edu	37	15	73558928	73558929	+	Intron	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73558928_73558929insT	uc002avm.3	+						NEO1_uc010ukx.1_Intron|NEO1_uc010uky.1_Intron|NEO1_uc010ukz.1_Intron|NEO1_uc002avn.3_Intron	NM_002499	NP_002490	Q92859	NEO1_HUMAN	neogenin homolog 1 precursor						axon guidance|cell adhesion|positive regulation of muscle cell differentiation	Golgi apparatus|integral to plasma membrane|nucleus				pancreas(1)	1						ATTTGTTTTGCTTTTTTTTTTG	0.371													4	2	---	---	---	---	
CCDC33	80125	broad.mit.edu	37	15	74617595	74617595	+	Intron	DEL	G	-	-	rs143547599		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74617595delG	uc002axo.2	+						CCDC33_uc002axp.2_Intron|CCDC33_uc002axq.2_Intron|CCDC33_uc002axr.2_Intron	NM_025055	NP_079331	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33 isoform 1								protein binding			ovary(3)|skin(2)	5						TCCTGAGATtggccacacccc	0.274													2	5	---	---	---	---	
CRABP1	1381	broad.mit.edu	37	15	78631199	78631199	+	5'Flank	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78631199delC	uc002bdp.2	+							NM_004378	NP_004369	P29762	RABP1_HUMAN	cellular retinoic acid binding protein 1						multicellular organismal development|signal transduction	cytoplasm	retinal binding|retinol binding|transporter activity				0					Alitretinoin(DB00523)|Etretinate(DB00926)	agaatgccggccctgCCCATG	0.294													3	5	---	---	---	---	
GOLGA6L10	647042	broad.mit.edu	37	15	82818446	82818446	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82818446delA	uc010unt.1	-						uc002bhl.2_Intron|uc002bhm.2_Intron|uc002bhp.1_5'Flank			A6NI86	GG6LA_HUMAN	Homo sapiens cDNA FLJ40113 fis, clone TESTI2008621.												0						ATTGTTGATCATGAGGTGCAT	0.597													5	4	---	---	---	---	
SLCO3A1	28232	broad.mit.edu	37	15	92669754	92669754	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92669754delT	uc002bqx.2	+						SLCO3A1_uc002bqy.2_Intron|SLCO3A1_uc010boc.1_Intron|SLCO3A1_uc002bqz.1_Intron	NM_013272	NP_037404	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to membrane|plasma membrane	sodium-independent organic anion transmembrane transporter activity			skin(1)	1	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)			ATTTTTGGCATTTGACTTTAG	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	96695785	96695786	+	IGR	INS	-	T	T	rs34785295		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96695785_96695786insT								LOC145820 (644711 upstream) : NR2F2 (173371 downstream)																							TTTTTTTTCTGTTTTTTTtttt	0.020													4	2	---	---	---	---	
FAM169B	283777	broad.mit.edu	37	15	99043929	99043932	+	Intron	DEL	CCAA	-	-	rs35635096		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99043929_99043932delCCAA	uc002buk.1	-							NM_182562	NP_872368	Q8N8A8	F169B_HUMAN	hypothetical protein LOC283777												0						ggagcctgagccaaccaacagggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	102133112	102133113	+	IGR	INS	-	A	A	rs142517035	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102133112_102133113insA								PCSK6 (102925 upstream) : TM2D3 (40067 downstream)																							ggcatatacataccacatcttc	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	8252588	8252588	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8252588delT								A2BP1 (489248 upstream) : TMEM114 (366915 downstream)																							cttcacatggtttttttttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	8403422	8403422	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8403422delA								A2BP1 (640082 upstream) : TMEM114 (216081 downstream)																							CAAGACAGACAAAAAAAACTT	0.363													0	7	---	---	---	---	
GRIN2A	2903	broad.mit.edu	37	16	10172642	10172642	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10172642delC	uc002czo.3	-						GRIN2A_uc010uym.1_Intron|GRIN2A_uc002czr.3_Intron	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	GTCACCACTACCCCCTCCGAA	0.517													2	4	---	---	---	---	
C16orf62	57020	broad.mit.edu	37	16	19614227	19614227	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19614227delT	uc002dgn.1	+						C16orf62_uc002dgo.1_Intron|C16orf62_uc002dgp.1_Intron|C16orf62_uc010vas.1_Intron|C16orf62_uc002dgm.1_Intron	NM_020314	NP_064710	Q7Z3J2	CP062_HUMAN	hypothetical protein LOC57020							integral to membrane				ovary(1)	1						tgcccgtccCttttttttttt	0.015													4	2	---	---	---	---	
KIAA0556	23247	broad.mit.edu	37	16	27639266	27639266	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27639266delC	uc002dow.2	+							NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247											ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8						AAGGACCAGGCCCAAGGTGTA	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	31987336	31987336	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31987336delG								ZNF267 (58710 upstream) : HERC2P4 (175274 downstream)																							CCCAGTCCCAGGGGTCTCTGT	0.642													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32108533	32108533	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32108533delT								ZNF267 (179907 upstream) : HERC2P4 (54077 downstream)																							TCGTGTTGACTTTGCAGCCTA	0.244													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32314373	32314373	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32314373delG	uc002edb.2	-											Homo sapiens similar to protein phosphatase 2A 48 kDa regulatory subunit isoform 1; serine/threonine protein phosphatase 2A, 48kDa regulatory subunit; PP2A, subunit B, PR48 isoform; PP2A B subunit PR48; NY-REN-8 antigen, mRNA (cDNA clone IMAGE:5272051).																		ggtaaggccagggcagggtca	0.104													20	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32593167	32593167	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32593167delT								HERC2P4 (429293 upstream) : TP53TG3B (91674 downstream)																							tttcttttcattcagcagttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32846111	32846111	+	IGR	DEL	A	-	-	rs77630803		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32846111delA								TP53TG3B (157233 upstream) : SLC6A10P (42686 downstream)																							GATTTTTTTTAAAAAAGGAAA	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33042909	33042909	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33042909delA								SLC6A10P (146446 upstream) : MIR1826 (922599 downstream)																							CTGTTGTGGGAAAACAGGCTT	0.398													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33294723	33294731	+	IGR	DEL	TGGCTGGCT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33294723_33294731delTGGCTGGCT								SLC6A10P (398260 upstream) : MIR1826 (670777 downstream)																							cttgcctggctggctggcttggctggctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33543022	33543023	+	IGR	INS	-	ATT	ATT	rs138472598	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33543022_33543023insATT								SLC6A10P (646559 upstream) : MIR1826 (422485 downstream)																							ACACAATGACAATTACACTTTA	0.356													4	2	---	---	---	---	
MIR1826	100302162	broad.mit.edu	37	16	33964529	33964530	+	5'Flank	INS	-	A	A	rs76338088		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33964529_33964530insA	hsa-mir-1826|MI0008194	+																							0						GGGAGGGAGAGGGGGGGAGAGA	0.688													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33994321	33994322	+	IGR	INS	-	TG	TG	rs143364919		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33994321_33994322insTG								MIR1826 (28729 upstream) : UBE2MP1 (409480 downstream)																							agtttcaacactgagatgaatg	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46443484	46443486	+	IGR	DEL	TTA	-	-	rs75103304		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46443484_46443486delTTA								None (None upstream) : ANKRD26P1 (59763 downstream)																							tcaatgaatgttatcatcgaatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46460668	46460669	+	IGR	DEL	TT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46460668_46460669delTT								None (None upstream) : ANKRD26P1 (42580 downstream)																							tttctttctctttctttcttga	0.084													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	47098914	47098914	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47098914delG								DNAJA2 (91289 upstream) : NETO2 (16528 downstream)																							GGAAGGTGCTGGGTTAGTCCA	0.527													4	2	---	---	---	---	
N4BP1	9683	broad.mit.edu	37	16	48588085	48588085	+	Intron	DEL	A	-	-	rs10710139		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48588085delA	uc002efp.2	-							NM_153029	NP_694574	O75113	N4BP1_HUMAN	Nedd4 binding protein 1						negative regulation of proteasomal ubiquitin-dependent protein catabolic process|negative regulation of protein ubiquitination	nucleolus|PML body					0		all_cancers(37;0.179)|all_lung(18;0.11)				GAAAAAAGGtaaaaaaaaaaa	0.294													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	50025151	50025152	+	IGR	INS	-	AC	AC	rs138462892	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50025151_50025152insAC								ZNF423 (164233 upstream) : TMEM188 (34037 downstream)																							aaaccccagctacacacacaca	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	54796424	54796425	+	IGR	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54796424_54796425insT								IRX3 (476046 upstream) : IRX5 (168686 downstream)																							GAtttctttccttttttttttt	0.153													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	57724933	57724933	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57724933delA								GPR97 (1645 upstream) : CCDC135 (3780 downstream)																							ccatgtttttaaaaaaaaaaa	0.000													4	7	---	---	---	---	
TERF2	7014	broad.mit.edu	37	16	69395141	69395142	+	Intron	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69395141_69395142insA	uc002exd.2	-							NM_005652	NP_005643	Q15554	TERF2_HUMAN	telomeric repeat binding factor 2						age-dependent telomere shortening|cell cycle|cellular senescence|negative regulation of telomere maintenance via semi-conservative replication|protection from non-homologous end joining at telomere|protein localization to chromosome, telomeric region|regulation of transcription, DNA-dependent|telomeric loop formation	Golgi apparatus|nuclear telomere cap complex|nucleoplasm	double-stranded telomeric DNA binding|protein C-terminus binding|protein homodimerization activity			lung(1)	1		Ovarian(137;0.101)				tctgaaaaaggaaaaaaaaaaa	0.153													4	2	---	---	---	---	
FUK	197258	broad.mit.edu	37	16	70493709	70493710	+	Intron	DEL	TT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70493709_70493710delTT	uc002eyy.2	+						FUK_uc010vmb.1_Intron|FUK_uc010cft.2_Intron|FUK_uc002eyz.2_Intron	NM_145059	NP_659496	Q8N0W3	FUK_HUMAN	fucokinase							cytoplasm	ATP binding|fucokinase activity			ovary(1)	1		Ovarian(137;0.0694)				tttcttcatctttttttttttt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	73878753	73878754	+	IGR	INS	-	TAGG	TAGG	rs138081818	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73878753_73878754insTAGG								HTA (751083 upstream) : PSMD7 (451927 downstream)																							tgatagatggataggtaggtag	0.109													3	3	---	---	---	---	
LOC283922	283922	broad.mit.edu	37	16	74394379	74394380	+	Intron	INS	-	A	A	rs142790741	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74394379_74394380insA	uc002fcr.2	-						LOC283922_uc010vms.1_Intron					Homo sapiens cDNA FLJ39449 fis, clone PROST2008360, highly similar to Homo sapiens pyruvate dehydrogenase phosphatase regulatory subunit (PDPR), mRNA.												0						TAGTCATCCTTAAACAAAATTC	0.327													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	77694456	77694456	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77694456delA								ADAMTS18 (225445 upstream) : NUDT7 (61955 downstream)																							CTTCAAGGGGAAAAAAAAATC	0.433											OREG0023949	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	77694675	77694676	+	IGR	DEL	TC	-	-	rs67811070		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77694675_77694676delTC								ADAMTS18 (225664 upstream) : NUDT7 (61735 downstream)																							tgtgtgtgtgtctgtgtatgtg	0.139													2	5	---	---	---	---	
NUDT7	283927	broad.mit.edu	37	16	77756432	77756432	+	5'UTR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77756432delC	uc010chd.2	+	1					NUDT7_uc002fff.2_5'UTR|NUDT7_uc010vnj.1_5'UTR	NM_001105663	NP_001099133	P0C024	NUDT7_HUMAN	nudix motif 7						nucleoside diphosphate metabolic process	peroxisome	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides|magnesium ion binding|manganese ion binding			ovary(1)|kidney(1)	2						GCGCGACCGACCGAGCAGCTC	0.493													8	4	---	---	---	---	
VAT1L	57687	broad.mit.edu	37	16	77888029	77888030	+	Intron	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77888029_77888030insA	uc002ffg.1	+							NM_020927	NP_065978	Q9HCJ6	VAT1L_HUMAN	vesicle amine transport protein 1 homolog (T.								oxidoreductase activity|zinc ion binding			central_nervous_system(1)	1						tgtctcaaacgaaaaaaaaaaa	0.183													4	2	---	---	---	---	
WWOX	51741	broad.mit.edu	37	16	78146774	78146775	+	Intron	INS	-	TT	TT			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78146774_78146775insTT	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_Intron|WWOX_uc002ffj.1_Intron	NM_016373	NP_057457	Q9NZC7	WWOX_HUMAN	WW domain-containing oxidoreductase isoform 1						apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		tttttaaagactttttttttgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	79449240	79449241	+	IGR	INS	-	CAGG	CAGG	rs137919902	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79449240_79449241insCAGG								WWOX (202677 upstream) : MAF (178505 downstream)																							gggaggatgaacaggcaggcag	0.059													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86559827	86559828	+	IGR	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86559827_86559828insA								FOXF1 (11758 upstream) : MTHFSD (3955 downstream)																							CGCAAAAAGGCAAAGGCTAAAG	0.391													10	7	---	---	---	---	
SPIRE2	84501	broad.mit.edu	37	16	89893152	89893153	+	5'Flank	INS	-	AAAC	AAAC	rs145822649	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89893152_89893153insAAAC	uc002foz.1	+						SPIRE2_uc010civ.1_5'Flank|SPIRE2_uc010ciw.1_5'Flank	NM_032451	NP_115827	Q8WWL2	SPIR2_HUMAN	spire homolog 2						transport	cytoplasm|cytoskeleton	actin binding			central_nervous_system(1)	1		Lung NSC(15;5.15e-06)|all_lung(18;8.38e-06)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0286)		actctgcctcaaaacaaacaaa	0.168													4	2	---	---	---	---	
CRK	1398	broad.mit.edu	37	17	1340952	1340953	+	Intron	INS	-	T	T	rs71373999		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1340952_1340953insT	uc002fsl.2	-						CRK_uc002fsm.2_Intron	NM_016823	NP_058431	P46108	CRK_HUMAN	v-crk sarcoma virus CT10 oncogene homolog						actin cytoskeleton organization|activation of MAPKK activity|blood coagulation|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of transcription from RNA polymerase II promoter	cytosol|endosome|nucleus|plasma membrane	protein binding|SH2 domain binding			lung(2)|central_nervous_system(1)	3				UCEC - Uterine corpus endometrioid carcinoma (25;0.083)		TCTGTTGCATGttttttttttt	0.233													4	2	---	---	---	---	
TP53	7157	broad.mit.edu	37	17	7578230	7578230	+	Frame_Shift_Del	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7578230delC	uc002gim.2	-	6	813	c.619delG	c.(619-621)GATfs	p.D207fs	TP53_uc002gig.1_Frame_Shift_Del_p.D207fs|TP53_uc002gih.2_Frame_Shift_Del_p.D207fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.D75fs|TP53_uc010cng.1_Frame_Shift_Del_p.D75fs|TP53_uc002gii.1_Frame_Shift_Del_p.D75fs|TP53_uc010cnh.1_Frame_Shift_Del_p.D207fs|TP53_uc010cni.1_Frame_Shift_Del_p.D207fs|TP53_uc002gij.2_Frame_Shift_Del_p.D207fs|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_Frame_Shift_Del_p.D114fs|TP53_uc002gio.2_Frame_Shift_Del_p.D75fs|TP53_uc010vug.1_Frame_Shift_Del_p.D168fs	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	207	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		D -> E (in sporadic cancers; somatic mutation).|D -> N (in sporadic cancers; somatic mutation).|D -> V (in a sporadic cancer; somatic mutation).|D -> G (in sporadic cancers; somatic mutation).|DD -> EY (in a sporadic cancer; somatic mutation).|D -> Y (in a sporadic cancer; somatic mutation).|D -> H (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.0?(7)|p.D207fs*6(2)|p.D207G(2)|p.K164_P219del(1)|p.D207_R213delDDRNTFR(1)|p.D207A(1)|p.D207fs*2(1)|p.D207_V216del10(1)|p.D207D(1)|p.D207E(1)|p.D207Y(1)|p.E204fs*39(1)|p.E204_N210delEYLDDRN(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)		TTTCTGTCATCCAAATACTCC	0.537		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	17	---	---	---	---	
ELAC2	60528	broad.mit.edu	37	17	12908601	12908606	+	Intron	DEL	GTAACT	-	-	rs10532461		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12908601_12908606delGTAACT	uc002gnz.3	-						ELAC2_uc002gnv.3_5'Flank|ELAC2_uc002gnw.3_5'Flank|ELAC2_uc002gnx.3_Intron|ELAC2_uc010vvo.1_Intron|ELAC2_uc010vvp.1_Intron|ELAC2_uc010vvq.1_Intron|ELAC2_uc010vvr.1_Intron	NM_018127	NP_060597	Q9BQ52	RNZ2_HUMAN	elaC homolog 2 isoform 1						tRNA processing	nucleus	endonuclease activity|metal ion binding|protein binding				0						ACCTAAACAGGTAACTGTCAGGTTGA	0.466									Hereditary_Prostate_Cancer				2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	13673358	13673358	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13673358delC								HS3ST3A1 (168114 upstream) : CDRT15P (254457 downstream)																							ttccatacatcctcttaaatc	0.000													4	2	---	---	---	---	
NCOR1	9611	broad.mit.edu	37	17	16096944	16096944	+	Intron	DEL	C	-	-	rs111340641		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16096944delC	uc002gpo.2	-						NCOR1_uc002gpn.2_Intron|NCOR1_uc002gpp.1_Intron|NCOR1_uc002gpr.2_Intron|NCOR1_uc002gps.1_Intron|NCOR1_uc010coz.1_Intron|NCOR1_uc010cpb.1_Intron|NCOR1_uc010cpa.1_Intron|NCOR1_uc002gpu.2_Intron	NM_006311	NP_006302	O75376	NCOR1_HUMAN	nuclear receptor co-repressor 1						cellular lipid metabolic process|chromatin modification|negative regulation of JNK cascade|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	nuclear chromatin|spindle microtubule|transcriptional repressor complex	histone deacetylase binding|transcription corepressor activity|transcription regulatory region DNA binding			upper_aerodigestive_tract(2)|ovary(1)|central_nervous_system(1)|kidney(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		aaattcaacacccaatcatga	0.159													3	5	---	---	---	---	
C17orf76	388341	broad.mit.edu	37	17	16356663	16356670	+	Intron	DEL	CACACACA	-	-	rs72023119		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16356663_16356670delCACACACA	uc010cph.1	-						C17orf76_uc002gqh.2_Intron|NCRNA00188_uc010vwl.1_Intron|NCRNA00188_uc010vwm.1_Intron|NCRNA00188_uc010vwn.1_Intron|NCRNA00188_uc010cpe.2_Intron|NCRNA00188_uc010vwo.1_Intron|NCRNA00188_uc010vwp.1_Intron	NM_001113567	NP_001107039	Q8NAA5	CQ076_HUMAN	hypothetical protein LOC388341 isoform 1												0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0887)		cacgcacacgcacacacacacacacGAG	0.322													6	3	---	---	---	---	
CCDC144NL	339184	broad.mit.edu	37	17	20771204	20771205	+	Intron	INS	-	A	A	rs112587391		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20771204_20771205insA	uc002gyf.2	-						uc002gyg.1_5'Flank|uc002gyh.1_5'Flank	NM_001004306	NP_001004306	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family,												0						ggcaggccaggaaaactcacct	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21218954	21218954	+	IGR	DEL	C	-	-	rs5819751		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21218954delC								MAP2K3 (405 upstream) : KCNJ12 (60745 downstream)																							cagatgggaacaacagaccca	0.030													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21329072	21329072	+	IGR	DEL	C	-	-	rs73315742	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21329072delC								KCNJ12 (5893 upstream) : C17orf51 (102500 downstream)																							ttaaATTTTTCTTAAAGTGGG	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21338266	21338266	+	IGR	DEL	C	-	-	rs148232145		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21338266delC								KCNJ12 (15087 upstream) : C17orf51 (93306 downstream)																							GAGACCAGAACCTTTACATAT	0.488													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21526254	21526255	+	IGR	INS	-	A	A	rs144707550	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21526254_21526255insA								C17orf51 (48523 upstream) : FAM27L (299115 downstream)																							ATGGTTTCTTTTTTTCCTTTTC	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21548660	21548662	+	IGR	DEL	TCT	-	-	rs147918165		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21548660_21548662delTCT								C17orf51 (70929 upstream) : FAM27L (276708 downstream)																							TTAGAAGGCATCTTCTTAGATTA	0.409													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21561660	21561660	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21561660delA								C17orf51 (83929 upstream) : FAM27L (263710 downstream)																							CCGCCTGCGGACCCTCTGCCC	0.701													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21566064	21566065	+	IGR	INS	-	T	T	rs142859905	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21566064_21566065insT								C17orf51 (88333 upstream) : FAM27L (259305 downstream)																							TCTTCAAGAAATGTTCTCCTTC	0.356													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25288870	25288872	+	IGR	DEL	AAT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25288870_25288872delAAT								None (None upstream) : WSB1 (332234 downstream)																							CTGCAAATAGAATATTCATGAGC	0.345													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25319139	25319140	+	IGR	INS	-	AAG	AAG	rs144466474	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25319139_25319140insAAG								None (None upstream) : WSB1 (301966 downstream)																							CTCCACACAATAAGGTCACAGG	0.599													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25335207	25335209	+	IGR	DEL	GCT	-	-	rs147174908		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25335207_25335209delGCT								None (None upstream) : WSB1 (285897 downstream)																							AGAGGCTGAAGCTGCCTGTGTGC	0.488													3	4	---	---	---	---	
NUFIP2	57532	broad.mit.edu	37	17	27588451	27588452	+	3'UTR	DEL	CC	-	-	rs34339676		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27588451_27588452delCC	uc002hdy.3	-	4					NUFIP2_uc002hdx.3_3'UTR	NM_020772	NP_065823	Q7Z417	NUFP2_HUMAN	nuclear fragile X mental retardation protein							nucleus|polysomal ribosome	protein binding|RNA binding			skin(2)|ovary(1)|breast(1)	4			BRCA - Breast invasive adenocarcinoma(11;0.000457)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)			cacacacacacCCCTTTTTCAG	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	29877849	29877850	+	IGR	INS	-	T	T	rs142606393	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29877849_29877850insT								RAB11FIP4 (12617 upstream) : MIR193A (9165 downstream)																							ctcttcaattgtaacactccct	0.000													2	4	---	---	---	---	
MYO1D	4642	broad.mit.edu	37	17	30928485	30928485	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30928485delG	uc002hho.1	-						MYO1D_uc002hhp.1_Intron	NM_015194	NP_056009	O94832	MYO1D_HUMAN	myosin ID							myosin complex	actin binding|ATP binding|calmodulin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3			BRCA - Breast invasive adenocarcinoma(9;0.0362)			tacagtttgtggtgccctgaa	0.000													4	2	---	---	---	---	
CCL14	6358	broad.mit.edu	37	17	34311902	34311902	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34311902delC	uc010wcr.1	-						CCL14_uc010wcq.1_Intron|CCL14_uc002hkn.2_Intron|CCL14-CCL15_uc010wcs.1_Intron|CCL14-CCL15_uc010wct.1_Intron|uc002hkq.2_5'Flank	NM_032963	NP_116739	Q16627	CCL14_HUMAN	chemokine (C-C motif) ligand 14 isoform 1						cellular calcium ion homeostasis|immune response|positive regulation of cell proliferation	extracellular space	chemokine activity|signal transducer activity				0		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TGGAAGAAATCCCAATAGGGA	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	34437207	34437207	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34437207delG								CCL4 (4193 upstream) : TBC1D3B (55854 downstream)																							ATGTCTCTCAGGGAAGATGGG	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	35058676	35058677	+	IGR	DEL	GA	-	-	rs67453995		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35058676_35058677delGA								MRM1 (93270 upstream) : LHX1 (235822 downstream)																							cacacacaGTGAGAGAGAGAGA	0.327													4	3	---	---	---	---	
SRCIN1	80725	broad.mit.edu	37	17	36741517	36741518	+	Intron	DEL	CA	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36741517_36741518delCA	uc002hqd.2	-						SRCIN1_uc002hqh.1_Intron	NM_025248	NP_079524	Q9C0H9	SRCN1_HUMAN	SNAP25-interacting protein						exocytosis|negative regulation of protein tyrosine kinase activity|positive regulation of protein tyrosine kinase activity|regulation of cell migration|regulation of dendritic spine morphogenesis|substrate adhesion-dependent cell spreading	actin cytoskeleton|axon|cell junction|cytoplasm|dendrite|postsynaptic density|postsynaptic membrane	protein kinase binding				0						AGGCcacacccacacacacaca	0.554													4	2	---	---	---	---	
C17orf98	388381	broad.mit.edu	37	17	36993201	36993202	+	Intron	INS	-	A	A	rs113691927		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36993201_36993202insA	uc002hqv.2	-							NM_001080465	NP_001073934	A8MV24	CQ098_HUMAN	hypothetical protein LOC388381												0						gaccacgtctcaaaaaaaaaaa	0.223													4	2	---	---	---	---	
IKZF3	22806	broad.mit.edu	37	17	37938667	37938668	+	Intron	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37938667_37938668insA	uc002hsu.2	-						IKZF3_uc002htd.2_Intron|IKZF3_uc010cwd.2_Intron|IKZF3_uc002hsv.2_Intron|IKZF3_uc010cwe.2_Intron|IKZF3_uc010cwf.2_Intron|IKZF3_uc010cwg.2_Intron|IKZF3_uc002hsw.2_Intron|IKZF3_uc002hsx.2_Intron|IKZF3_uc002hsy.2_Intron|IKZF3_uc002hsz.2_Intron|IKZF3_uc002hta.2_Intron|IKZF3_uc002htb.2_Intron|IKZF3_uc010cwh.2_Intron|IKZF3_uc002htc.2_Intron	NM_012481	NP_036613	Q9UKT9	IKZF3_HUMAN	aiolos isoform 1						B cell activation|mesoderm development|regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(2)|kidney(2)|skin(2)	6	Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			acaacaaCAacacacacacaca	0.144													4	3	---	---	---	---	
KRT36	8689	broad.mit.edu	37	17	39644162	39644163	+	Intron	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39644162_39644163insT	uc002hwt.2	-							NM_003771	NP_003762	O76013	KRT36_HUMAN	keratin 36							intermediate filament	protein binding|structural constituent of epidermis				0		Breast(137;0.000286)				acctccttctatgggatatttg	0.163													3	7	---	---	---	---	
CDK5RAP3	80279	broad.mit.edu	37	17	46055435	46055436	+	Intron	INS	-	T	T	rs71366815		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46055435_46055436insT	uc002imr.2	+						CDK5RAP3_uc010wlc.1_Intron|CDK5RAP3_uc002imq.1_Intron|CDK5RAP3_uc002imu.2_Intron|CDK5RAP3_uc002ims.2_Intron|CDK5RAP3_uc002imv.2_Intron|CDK5RAP3_uc002imw.2_Intron|CDK5RAP3_uc002imx.2_Intron	NM_176096	NP_788276	Q96JB5	CK5P3_HUMAN	CDK5 regulatory subunit associated protein 3						brain development|regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation		neuronal Cdc2-like kinase binding				0						ACCAAGAGAGGttttttttttt	0.223													6	3	---	---	---	---	
CALCOCO2	10241	broad.mit.edu	37	17	46922683	46922692	+	Intron	DEL	GTGTGTGTGT	-	-	rs71844921		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46922683_46922692delGTGTGTGTGT	uc002iof.2	+						CALCOCO2_uc010wlp.1_Intron|CALCOCO2_uc010wlq.1_Intron|CALCOCO2_uc010wlr.1_Intron|CALCOCO2_uc010wls.1_Intron	NM_005831	NP_005822	Q13137	CACO2_HUMAN	calcium binding and coiled-coil domain 2						response to interferon-gamma|viral reproduction	cytoskeleton|Golgi apparatus|nucleus|perinuclear region of cytoplasm|soluble fraction	protein homodimerization activity			ovary(1)	1						TATGTTGAGGgtgtgtgtgtgtgtgtgtgt	0.205													5	5	---	---	---	---	
NXPH3	11248	broad.mit.edu	37	17	47655767	47655768	+	Intron	DEL	GT	-	-	rs71146917		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47655767_47655768delGT	uc002ipa.2	+						NXPH3_uc010wlw.1_Intron	NM_007225	NP_009156	O95157	NXPH3_HUMAN	neurexophilin 3 precursor						neuropeptide signaling pathway	extracellular region				pancreas(1)|skin(1)	2	all_cancers(4;7.45e-14)|Breast(4;1.08e-27)|all_epithelial(4;2.27e-17)					GGGGGGGGGGGTGACCCAACTG	0.530													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	62932555	62932556	+	IGR	DEL	GT	-	-	rs35142297		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62932555_62932556delGT								LRRC37A3 (16969 upstream) : AMZ2P1 (30112 downstream)																							gtgtgtgttcgtgtgtgtgtgt	0.238													6	3	---	---	---	---	
SEPT9	10801	broad.mit.edu	37	17	75441608	75441609	+	Intron	DEL	GT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75441608_75441609delGT	uc002jts.3	+						SEPT9_uc010wtk.1_Intron|SEPT9_uc002jtt.3_Intron|SEPT9_uc002jtu.3_Intron|SEPT9_uc002jtv.2_Intron|SEPT9_uc002jtw.2_Intron|SEPT9_uc002jtx.1_Intron|SEPT9_uc010wtl.1_Intron	NM_001113491	NP_001106963	Q9UHD8	SEPT9_HUMAN	septin 9 isoform a						cell cycle|cell division|protein heterooligomerization	microtubule|perinuclear region of cytoplasm|stress fiber	GTP binding|GTPase activity|protein binding|protein binding			breast(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(99;0.153)			gtgcacgcacgtgtgtgtgtgt	0.475													4	2	---	---	---	---	
BIRC5	332	broad.mit.edu	37	17	76209653	76209653	+	5'Flank	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76209653delC	uc002jvg.2	+						BIRC5_uc002jvc.2_5'Flank|BIRC5_uc002jve.1_5'Flank|BIRC5_uc002jvd.1_5'Flank|BIRC5_uc010dhk.1_5'Flank|BIRC5_uc010dhl.1_5'Flank|BIRC5_uc002jvf.2_5'Flank|BIRC5_uc002jvh.2_5'Flank|BIRC5_uc002jvi.2_5'Flank	NM_001168	NP_001159	O15392	BIRC5_HUMAN	baculoviral IAP repeat-containing protein 5						anti-apoptosis|apoptosis|cell division|chromosome segregation|cytokinesis|establishment of chromosome localization|G2/M transition of mitotic cell cycle|mitosis|mitotic prometaphase|positive regulation of exit from mitosis|positive regulation of mitotic cell cycle|protein complex localization|spindle checkpoint	centriole|chromosome passenger complex|chromosome, centromeric region|cytoplasm|cytoplasmic microtubule|cytosol|interphase microtubule organizing center|midbody|midbody|nuclear chromosome|spindle|spindle microtubule	caspase inhibitor activity|chaperone binding|cobalt ion binding|cofactor binding|cysteine-type endopeptidase inhibitor activity|metal ion binding|microtubule binding|protein heterodimerization activity|protein homodimerization activity|Ran GTPase binding|zinc ion binding			kidney(1)	1			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.153)			CAGTCCCTGGCCCCTGACTCC	0.617													4	2	---	---	---	---	
CANT1	124583	broad.mit.edu	37	17	77001265	77001266	+	Intron	INS	-	GA	GA			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77001265_77001266insGA	uc002jwn.2	-						CANT1_uc002jwk.2_Intron|CANT1_uc002jwj.2_Intron|CANT1_uc002jwl.2_Intron	NM_001159772	NP_001153244	Q8WVQ1	CANT1_HUMAN	calcium activated nucleotidase 1						positive regulation of I-kappaB kinase/NF-kappaB cascade	endoplasmic reticulum membrane|Golgi cisterna membrane|integral to membrane	calcium ion binding|nucleoside-diphosphatase activity|signal transducer activity				0			BRCA - Breast invasive adenocarcinoma(99;0.0362)|OV - Ovarian serous cystadenocarcinoma(97;0.139)			ggggagttagggaagggagtta	0.000			T	ETV4	prostate								4	2	---	---	---	---	
MYOM1	8736	broad.mit.edu	37	18	3156607	3156607	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3156607delT	uc002klp.2	-						MYOM1_uc002klq.2_Intron	NM_003803	NP_003794	P52179	MYOM1_HUMAN	myomesin 1 isoform a							striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5						CACttctttcttttttttttt	0.194													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	5363979	5363980	+	IGR	INS	-	TG	TG	rs147080625	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5363979_5363980insTG								ZFP161 (67940 upstream) : EPB41L3 (28408 downstream)																							ggacttaactcaatataataag	0.059													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	8691637	8691637	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8691637delA								RAB12 (52258 upstream) : KIAA0802 (15772 downstream)																							tgtcttgaagaaaaaaaaaaa	0.005													4	4	---	---	---	---	
SPIRE1	56907	broad.mit.edu	37	18	12641831	12641832	+	Intron	DEL	CT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12641831_12641832delCT	uc002kre.2	-						SPIRE1_uc010wzw.1_Intron|SPIRE1_uc010wzx.1_Intron|SPIRE1_uc010wzy.1_Intron	NM_001128626	NP_001122098	Q08AE8	SPIR1_HUMAN	spire homolog 1 isoform a							cytoskeleton|perinuclear region of cytoplasm	actin binding				0						GAATGTTATGCttttttttttt	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	14188747	14188748	+	3'UTR	INS	-	TTG	TTG	rs111398827	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14188747_14188748insTTG	uc002ksv.1	+	3										Homo sapiens cDNA FLJ34795 fis, clone NT2NE2005921.																		cattattattattgttgttgtt	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	19660355	19660355	+	IGR	DEL	T	-	-	rs33978669		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19660355delT								MIB1 (209445 upstream) : GATA6 (89061 downstream)																							AGTACAGAGATTTTTTTTTTC	0.348													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	25348377	25348377	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25348377delT								C18orf16 (577727 upstream) : CDH2 (182553 downstream)																							attgtcattattgggccagct	0.070													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	28686406	28686407	+	IGR	DEL	TT	-	-	rs34015650		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28686406_28686407delTT								DSC2 (4018 upstream) : DSC1 (22809 downstream)																							TAtttttttctttttttttttt	0.005													4	2	---	---	---	---	
C18orf34	374864	broad.mit.edu	37	18	30921179	30921180	+	Intron	INS	-	G	G	rs150970003	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30921179_30921180insG	uc002kxn.2	-						C18orf34_uc010xbr.1_Intron|C18orf34_uc010dmf.1_Intron|C18orf34_uc002kxo.2_Intron|C18orf34_uc002kxp.2_Intron	NM_001105528	NP_001098998	Q5BJE1	CR034_HUMAN	hypothetical protein LOC374864 isoform 1											ovary(1)	1						tggacttgcatggccctgtaac	0.000													1	6	---	---	---	---	
FHOD3	80206	broad.mit.edu	37	18	33910924	33910924	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33910924delC	uc002kzt.1	+						FHOD3_uc002kzr.1_Intron|FHOD3_uc002kzs.1_Intron	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				CCTGCCCCTGCCTTTAGATGA	0.537													4	2	---	---	---	---	
FHOD3	80206	broad.mit.edu	37	18	34069203	34069206	+	Intron	DEL	GTTT	-	-	rs71906409		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34069203_34069206delGTTT	uc002kzt.1	+						FHOD3_uc002kzr.1_Intron|FHOD3_uc002kzs.1_Intron	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				GAGAGAATGGGTTTGTTTGTTTGT	0.549													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	35804853	35804856	+	IGR	DEL	ACAC	-	-	rs72012957		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35804853_35804856delACAC								CELF4 (658853 upstream) : LOC647946 (982032 downstream)																							ACAATCATGAacacacacacacac	0.127													5	4	---	---	---	---	
LOC647946	647946	broad.mit.edu	37	18	36904825	36904826	+	Intron	DEL	AC	-	-	rs150152260	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:36904825_36904826delAC	uc002lak.1	-						LOC647946_uc010xcj.1_Intron|LOC647946_uc002lal.1_Intron					Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0						acatatatatacacacacacat	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	38161866	38161867	+	IGR	DEL	TG	-	-	rs111359875		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38161866_38161867delTG								LOC647946 (781584 upstream) : KC6 (898371 downstream)																							ATGATGCGTTtgtgtgtgtgtg	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	38350064	38350064	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38350064delC								LOC647946 (969782 upstream) : KC6 (710174 downstream)																							accacttaagcccaaacattt	0.035													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	38364271	38364271	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38364271delA								LOC647946 (983989 upstream) : KC6 (695967 downstream)																							AAACTTTCGGAAAATGTCTAT	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	38805462	38805463	+	IGR	INS	-	T	T	rs116613890	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38805462_38805463insT								None (None upstream) : KC6 (254775 downstream)																							ctgtacattcgttgtagctagg	0.000													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	39413587	39413588	+	IGR	INS	-	CT	CT	rs145602910	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39413587_39413588insCT								KC6 (313026 upstream) : PIK3C3 (121611 downstream)																							CAGTTTTAAAACTCATTTTCCG	0.203													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	39501872	39501872	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39501872delA								KC6 (401311 upstream) : PIK3C3 (33327 downstream)																							gttcaaggacaaaagggcaaa	0.109													4	2	---	---	---	---	
PIK3C3	5289	broad.mit.edu	37	18	39535827	39535832	+	Intron	DEL	TGGCAG	-	-	rs35557859		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39535827_39535832delTGGCAG	uc002lap.2	+						PIK3C3_uc010xcl.1_Intron|PIK3C3_uc002lao.2_Intron	NM_002647	NP_002638	Q8NEB9	PK3C3_HUMAN	catalytic phosphatidylinositol 3-kinase 3						cell cycle|cytokinesis|fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway	midbody|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|protein binding			lung(8)|ovary(1)|breast(1)	10						TTGGGTAGTATGGCAGTGTTTAGTCA	0.456										TSP Lung(28;0.18)			2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	39854554	39854554	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39854554delG	uc002las.1	+						uc002lat.2_Intron|uc002lau.2_Intron					Homo sapiens hypothetical gene supported by BC011527; BC021928; BC011527; BC021928, mRNA (cDNA clone IMAGE:3872963), with apparent retained intron.																		TAAAGGGATAGGGAGTACATA	0.388													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	39928818	39928818	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39928818delC	uc002las.1	+						uc002lat.2_Intron|uc002lau.2_Intron					Homo sapiens hypothetical gene supported by BC011527; BC021928; BC011527; BC021928, mRNA (cDNA clone IMAGE:3872963), with apparent retained intron.																		gagctcaggacccaccgagtg	0.000													4	5	---	---	---	---	
ATP5A1	498	broad.mit.edu	37	18	43664802	43664803	+	Intron	DEL	AC	-	-	rs147667560		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43664802_43664803delAC	uc002lbr.1	-						ATP5A1_uc010dnl.1_Intron|ATP5A1_uc002lbs.1_Intron|ATP5A1_uc002lbt.1_Intron	NM_004046	NP_004037	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1						ATP hydrolysis coupled proton transport|embryo development|lipid metabolic process|negative regulation of endothelial cell proliferation|respiratory electron transport chain	mitochondrial matrix|plasma membrane	ATP binding|eukaryotic cell surface binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|MHC class I protein binding|proton-transporting ATPase activity, rotational mechanism				0						CTGACAGAAAACAGTTATTTCT	0.337													1	8	---	---	---	---	
ST8SIA5	29906	broad.mit.edu	37	18	44312861	44312862	+	Intron	INS	-	CT	CT	rs139313193		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44312861_44312862insCT	uc002lcj.1	-						ST8SIA5_uc002lci.1_5'Flank|ST8SIA5_uc010xcy.1_Intron|ST8SIA5_uc010xcz.1_Intron|ST8SIA5_uc010dno.1_Intron	NM_013305	NP_037437	O15466	SIA8E_HUMAN	ST8 alpha-N-acetyl-neuraminide						glycosphingolipid biosynthetic process|protein glycosylation	integral to Golgi membrane				upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	3						CGGGAGGGCTGGTGGAAGTGGT	0.569													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	46498067	46498068	+	IGR	INS	-	T	T	rs111512825		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46498067_46498068insT								SMAD7 (20986 upstream) : DYM (72104 downstream)																							acaagatcacattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	47879362	47879363	+	IGR	INS	-	TTC	TTC	rs145675301	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47879362_47879363insTTC								CXXC1 (64670 upstream) : SKA1 (22029 downstream)																							aggtaattgctttcttcttctt	0.000													4	2	---	---	---	---	
CD226	10666	broad.mit.edu	37	18	67618380	67618380	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67618380delT	uc002lkm.3	-							NM_006566	NP_006557	Q15762	CD226_HUMAN	CD226 molecule precursor						cell adhesion|cell recognition|positive regulation of Fc receptor mediated stimulatory signaling pathway|positive regulation of immunoglobulin mediated immune response|positive regulation of mast cell activation|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target	cell surface|integral to plasma membrane|membrane raft	cell adhesion molecule binding|integrin binding|protein kinase binding|receptor activity				0		Esophageal squamous(42;0.129)				tttaaaattattttttttttg	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	69132834	69132834	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69132834delG								None (None upstream) : None (None downstream)																							CAAATCATGAGGACAACAAGC	0.209													4	2	---	---	---	---	
CTDP1	9150	broad.mit.edu	37	18	77444926	77444927	+	Intron	DEL	GG	-	-	rs113059721		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77444926_77444927delGG	uc002lnh.1	+						CTDP1_uc002lni.1_Intron|CTDP1_uc010drd.1_Intron	NM_004715	NP_004706	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II,						positive regulation of viral transcription|protein dephosphorylation|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	CTD phosphatase activity|DNA-directed RNA polymerase activity				0		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		CTGGTGAGGAGGACGGTGCAGG	0.589													6	3	---	---	---	---	
ABCA7	10347	broad.mit.edu	37	19	1049927	1049927	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1049927delC	uc002lqw.3	+						ABCA7_uc010dsb.1_Intron	NM_019112	NP_061985	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A, member 7						phagocytosis|transmembrane transport	ATP-binding cassette (ABC) transporter complex|endosome membrane|Golgi membrane|integral to membrane|plasma membrane	ATP binding|ATPase activity|transporter activity			pancreas(7)|ovary(1)|central_nervous_system(1)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ccTGTGAGTTCCCCCACCACT	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	2930257	2930257	+	IGR	DEL	C	-	-	rs34681677		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2930257delC								ZNF57 (11790 upstream) : ZNF77 (2960 downstream)																							gttgtggtggcacacacttgt	0.000													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	4272814	4272815	+	IGR	DEL	TT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4272814_4272815delTT								CCDC94 (3731 upstream) : SHD (5783 downstream)																							TTTTTATTTCTTTTTTTTTTCC	0.515													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	11822297	11822297	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11822297delT								ZNF833 (24915 upstream) : ZNF823 (9783 downstream)																							aactccccccttttttttttt	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	13093675	13093676	+	IGR	DEL	TC	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13093675_13093676delTC								DAND5 (8108 upstream) : NFIX (12908 downstream)																							tctttttctttctctctctctc	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	13744730	13744731	+	IGR	INS	-	TG	TG	rs143234949	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13744730_13744731insTG								CACNA1A (127456 upstream) : CCDC130 (97843 downstream)																							cttcctctctctcttttccttc	0.050													4	2	---	---	---	---	
MAST3	23031	broad.mit.edu	37	19	18259286	18259287	+	Intron	DEL	AA	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18259286_18259287delAA	uc002nhz.3	+							NM_015016	NP_055831	O60307	MAST3_HUMAN	microtubule associated serine/threonine kinase								ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			large_intestine(2)|ovary(2)|stomach(1)	5						aacaaaagggaaaaaaaaaaag	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	21519616	21519617	+	IGR	INS	-	T	T	rs112210648		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21519616_21519617insT								ZNF708 (7404 upstream) : ZNF738 (22118 downstream)																							ttttctttttcttttttttttt	0.000													4	3	---	---	---	---	
ZNF208	7757	broad.mit.edu	37	19	22193770	22193771	+	5'Flank	INS	-	GACA	GACA			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22193770_22193771insGACA	uc002nqp.2	-						ZNF208_uc002nqo.1_5'Flank|ZNF208_uc002nqq.2_5'Flank	NM_007153	NP_009084			zinc finger protein 208											ovary(5)|skin(2)	7		all_lung(12;0.0961)|Lung NSC(12;0.103)				GGAAGCCGACCTGTCCCCTCCA	0.594													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	23652406	23652408	+	IGR	DEL	TCG	-	-	rs56712769		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23652406_23652408delTCG								ZNF91 (74137 upstream) : ZNF675 (183301 downstream)																							ctttttctcttcgtcttctcctc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	24065129	24065130	+	IGR	INS	-	GAG	GAG	rs147613073	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24065129_24065130insGAG								RPSAP58 (54212 upstream) : ZNF254 (151117 downstream)																							gagaagagaaagaggagaagag	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	24594959	24594959	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24594959delT								LOC100101266 (248710 upstream) : None (None downstream)																							aacttctttgttatgtgtgca	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27850068	27850069	+	IGR	INS	-	AAG	AAG			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27850068_27850069insAAG								None (None upstream) : LOC148189 (431333 downstream)																							cacaaatcacaaaggagtttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	30353321	30353321	+	IGR	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30353321delG								CCNE1 (38103 upstream) : C19orf2 (61230 downstream)																							gccaggcagagggggaaatgg	0.010													4	2	---	---	---	---	
TSHZ3	57616	broad.mit.edu	37	19	31837750	31837751	+	Intron	DEL	TT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31837750_31837751delTT	uc002nsy.3	-							NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537						negative regulation of transcription, DNA-dependent|regulation of respiratory gaseous exchange by neurological system process	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(2)|pancreas(1)|lung(1)	8	Esophageal squamous(110;0.226)					AAATGTGGAGTTTTTTTTTTTT	0.416													4	2	---	---	---	---	
RHPN2	85415	broad.mit.edu	37	19	33515876	33515876	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33515876delT	uc002nuf.2	-						RHPN2_uc010xro.1_Intron|RHPN2_uc002nue.2_Intron	NM_033103	NP_149094	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2						signal transduction	perinuclear region of cytoplasm	protein binding			central_nervous_system(5)|ovary(1)	6	Esophageal squamous(110;0.137)					caggctggccttgaactcctg	0.065													4	2	---	---	---	---	
APLP1	333	broad.mit.edu	37	19	36365371	36365373	+	Intron	DEL	CTC	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36365371_36365373delCTC	uc002oce.2	+						APLP1_uc010xsz.1_Intron|APLP1_uc002ocf.2_Intron|APLP1_uc002ocg.2_Intron|APLP1_uc010xta.1_Intron	NM_005166	NP_005157	P51693	APLP1_HUMAN	amyloid precursor-like protein 1 isoform 2						apoptosis|cell adhesion|cellular response to norepinephrine stimulus|endocytosis|negative regulation of cAMP biosynthetic process|nervous system development|organ morphogenesis	basement membrane|integral to membrane|perinuclear region of cytoplasm|plasma membrane	alpha-2A adrenergic receptor binding|alpha-2B adrenergic receptor binding|alpha-2C adrenergic receptor binding|heparin binding|identical protein binding|metal ion binding			ovary(2)	2	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GACCCATCTTCTCCTCTCCTGAC	0.611													47	28	---	---	---	---	
ZNF781	163115	broad.mit.edu	37	19	38163376	38163376	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38163376delA	uc002ogy.2	-						ZNF781_uc002ogz.2_Intron	NM_152605	NP_689818	Q8N8C0	ZN781_HUMAN	zinc finger protein 781						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						ggaaggaaagaaggaaggaag	0.000													4	2	---	---	---	---	
PHLDB3	653583	broad.mit.edu	37	19	43994194	43994195	+	Intron	INS	-	AAGG	AAGG	rs143919159	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43994194_43994195insAAGG	uc002own.3	-						PHLDB3_uc010eit.2_Intron	NM_198850	NP_942147	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B,												0		Prostate(69;0.0153)				AGAGAGAGAAAaaggaaggaag	0.035													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	47131378	47131379	+	IGR	INS	-	TG	TG	rs147374918	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47131378_47131379insTG								PTGIR (3024 upstream) : GNG8 (5955 downstream)																							TTTCTCAGCATTGATTGTGTTT	0.450													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	51096130	51096152	+	IGR	DEL	TTCCTTCCTTCCTTCCCTCCTTC	-	-	rs144241755	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51096130_51096152delTTCCTTCCTTCCTTCCCTCCTTC								LRRC4B (24828 upstream) : SNAR-F (12068 downstream)																							ccttccttctttccttccttccttccctccttcctcccttctc	0.000													3	3	---	---	---	---	
ZNF615	284370	broad.mit.edu	37	19	52512443	52512444	+	5'Flank	INS	-	A	A	rs35685803		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52512443_52512444insA	uc002pye.1	-						ZNF615_uc002pyf.1_5'Flank|ZNF615_uc002pyg.1_5'Flank|ZNF615_uc002pyh.1_5'Flank|ZNF615_uc010epi.1_5'Flank|ZNF615_uc010ydg.1_5'Flank	NM_198480	NP_940882	Q8N8J6	ZN615_HUMAN	zinc finger protein 615						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		aactccatctcaaaaaaaaaac	0.000													4	2	---	---	---	---	
ZNF787	126208	broad.mit.edu	37	19	56599438	56599440	+	Splice_Site	DEL	TCG	-	-	rs72029508		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56599438_56599440delTCG	uc010eth.1	-	3	1219	c.1100_splice	c.e3+1	p.E367_splice		NM_001002836	NP_001002836	Q6DD87	ZN787_HUMAN	zinc finger protein 787						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1		Colorectal(82;3.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0559)		GCCCGCGGCCTCGTCGTCGTCGT	0.631													2	4	---	---	---	---	
SIRPB2	284759	broad.mit.edu	37	20	1459892	1459892	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1459892delG	uc002wfg.2	-						SIRPB2_uc002wfh.3_Intron|SIRPB2_uc010zpr.1_Intron	NM_001122962	NP_001116434	Q5JXA9	SIRB2_HUMAN	signal-regulatory protein beta 2 isoform 1							integral to membrane					0						TGGGGAGTGTGGTAGATGACA	0.244													4	2	---	---	---	---	
RIN2	54453	broad.mit.edu	37	20	19905133	19905134	+	Intron	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19905133_19905134insT	uc002wro.1	+						RIN2_uc010gcu.1_Intron	NM_018993	NP_061866	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2						endocytosis|small GTPase mediated signal transduction	cytoplasm	GTPase activator activity|Rab guanyl-nucleotide exchange factor activity			lung(4)|ovary(1)	5						ccttcataccccaccttcatac	0.069													9	6	---	---	---	---	
NINL	22981	broad.mit.edu	37	20	25450101	25450101	+	Intron	DEL	C	-	-	rs11477191		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25450101delC	uc002wux.1	-						NINL_uc010gdn.1_Intron	NM_025176	NP_079452	Q9Y2I6	NINL_HUMAN	ninein-like						G2/M transition of mitotic cell cycle	cytosol|microtubule|microtubule organizing center	calcium ion binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5						CTCACTGGTGCCCCCACCCCC	0.642													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25937358	25937358	+	Intron	DEL	C	-	-	rs111987729		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25937358delC	uc002wvf.2	+											Homo sapiens cDNA clone IMAGE:5298175.																		ttggctgagacagaaagaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25942650	25942650	+	Intron	DEL	A	-	-	rs75597660		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25942650delA	uc002wvf.2	+											Homo sapiens cDNA clone IMAGE:5298175.																		GACTCTGCctaaaaaaaaaaa	0.114													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26147215	26147215	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26147215delT								C20orf191 (52538 upstream) : MIR663 (41607 downstream)																							AATTTTAATCTGTTTAGATTT	0.318													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26251028	26251029	+	IGR	INS	-	A	A	rs151085511	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26251028_26251029insA								MIR663 (62114 upstream) : None (None downstream)																							acctgggaagcagagtttgcag	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29448107	29448109	+	IGR	DEL	GAA	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29448107_29448109delGAA								None (None upstream) : FRG1B (163770 downstream)																							CAGCAAAAATGAAGAATAGATAT	0.266													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29471428	29471428	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29471428delT								None (None upstream) : FRG1B (140451 downstream)																							TTGGAACTGCTTTGCTATGAA	0.348													3	4	---	---	---	---	
BCL2L1	598	broad.mit.edu	37	20	30277493	30277493	+	Intron	DEL	C	-	-	rs11167281		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30277493delC	uc002wwl.2	-						BCL2L1_uc002wwk.2_Intron|BCL2L1_uc002wwm.2_Intron|BCL2L1_uc002wwn.2_Intron	NM_138578	NP_612815	Q07817	B2CL1_HUMAN	BCL2-like 1 isoform 1						induction of apoptosis by intracellular signals|negative regulation of establishment of protein localization in plasma membrane|negative regulation of survival gene product expression|regulation of mitochondrial membrane permeability|regulation of mitochondrial membrane potential|release of cytochrome c from mitochondria|response to cytokine stimulus	integral to membrane|mitochondrial outer membrane|nuclear membrane	BH3 domain binding|identical protein binding			lung(1)|central_nervous_system(1)	2	all_cancers(5;3.47e-06)|all_epithelial(3;1.83e-06)|Lung NSC(7;2.08e-06)|all_lung(7;3.63e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;2.97e-06)|all cancers(5;3.21e-05)|OV - Ovarian serous cystadenocarcinoma(3;0.00052)|Colorectal(19;0.0055)|COAD - Colon adenocarcinoma(19;0.0264)			TAAATTGGCTCTGAAGAATAC	0.279													4	3	---	---	---	---	
FOXS1	2307	broad.mit.edu	37	20	30434245	30434246	+	5'Flank	INS	-	AG	AG	rs138357633	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30434245_30434246insAG	uc002wwt.1	-							NM_004118	NP_004109	O43638	FOXS1_HUMAN	forkhead box S1						anti-apoptosis|artery morphogenesis|blood vessel remodeling|camera-type eye development|cardiac muscle cell proliferation|collagen fibril organization|embryonic heart tube development|insulin receptor signaling pathway|lymphangiogenesis|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|neural crest cell fate commitment|neuromuscular process controlling balance|Notch signaling pathway|ossification|paraxial mesodermal cell fate commitment|patterning of blood vessels|positive regulation of multicellular organism growth|positive regulation of transcription from RNA polymerase II promoter|regulation of blood vessel size|regulation of organ growth|somitogenesis|vascular endothelial growth factor receptor signaling pathway|vasculogenesis|ventricular cardiac muscle tissue morphogenesis	transcription factor complex	chromatin DNA binding|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			ovary(1)	1						AAGGAATGAATagagagagaga	0.406													4	2	---	---	---	---	
C20orf114	92747	broad.mit.edu	37	20	31896776	31896777	+	Intron	INS	-	AC	AC	rs148963098	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31896776_31896777insAC	uc002wyw.1	+							NM_033197	NP_149974	Q8TDL5	LPLC1_HUMAN	LPLUNC1 protein precursor							extracellular space	lipid binding			central_nervous_system(2)|skin(2)	4						cacatacacatacacacacaca	0.069													3	3	---	---	---	---	
SNTA1	6640	broad.mit.edu	37	20	32006911	32006912	+	Intron	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32006911_32006912insA	uc002wzd.1	-						SNTA1_uc010zuf.1_Intron	NM_003098	NP_003089	Q13424	SNTA1_HUMAN	acidic alpha 1 syntrophin						muscle contraction	cell junction|cytoplasm|cytoskeleton|sarcolemma	actin binding|calmodulin binding			skin(1)	1						gcgactgcctcaaaaaaaaaaa	0.243													3	3	---	---	---	---	
ZHX3	23051	broad.mit.edu	37	20	39910427	39910427	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39910427delA	uc002xjs.1	-						ZHX3_uc002xjt.1_Intron|ZHX3_uc002xju.1_Intron|ZHX3_uc002xjv.1_Intron|ZHX3_uc002xjw.1_Intron	NM_015035	NP_055850	Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3						negative regulation of transcription, DNA-dependent	cytoplasm|nucleolus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3		Myeloproliferative disorder(115;0.00425)				attttatcctaagtgcaatgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	41914818	41914818	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41914818delA								PTPRT (96261 upstream) : SFRS6 (171686 downstream)																							gaacatagagaaaaaaggtat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	41959737	41959738	+	IGR	DEL	AC	-	-	rs72416190		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41959737_41959738delAC								PTPRT (141180 upstream) : SFRS6 (126766 downstream)																							atttcttcatacacacacacac	0.069													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	44800221	44800222	+	IGR	DEL	AG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44800221_44800222delAG								CD40 (41837 upstream) : CDH22 (2154 downstream)																							aagaaagaaaaggaaagaaaga	0.000													4	2	---	---	---	---	
EYA2	2139	broad.mit.edu	37	20	45816013	45816014	+	Intron	INS	-	A	A	rs55649359	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45816013_45816014insA	uc002xsm.2	+						EYA2_uc010ghp.2_Intron|EYA2_uc002xsn.2_Intron|EYA2_uc002xso.2_Intron|EYA2_uc002xsp.2_Intron|EYA2_uc002xsq.2_Intron	NM_005244	NP_005235	O00167	EYA2_HUMAN	eyes absent 2 isoform a						DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0241)				aagaaagaaagaaaaaaaaaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	46583678	46583679	+	5'Flank	INS	-	A	A	rs77852818		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46583678_46583679insA	uc002xts.1	+											Homo sapiens mRNA; cDNA DKFZp686I1537 (from clone DKFZp686I1537).																		gtctctgtctcaaaaaaaaaaa	0.228													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	47086982	47086982	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47086982delT								LOC284749 (87601 upstream) : PREX1 (153811 downstream)																							gcattctgccttctctgggaa	0.000													4	2	---	---	---	---	
TMEM189-UBE2V1	387522	broad.mit.edu	37	20	48703268	48703268	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48703268delA	uc002xvf.2	-						UBE2V1_uc002xvb.2_Intron|UBE2V1_uc002xva.2_Intron|UBE2V1_uc002xvc.2_Intron|UBE2V1_uc002xvd.2_Intron|UBE2V1_uc002xve.2_Intron	NM_199203	NP_954673	Q13404	UB2V1_HUMAN	TMEM189-UBE2V1 readthrough transcript						cell differentiation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|protein K63-linked ubiquitination|regulation of DNA repair|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleus|UBC13-UEV1A complex|ubiquitin ligase complex	acid-amino acid ligase activity|protein binding				0			BRCA - Breast invasive adenocarcinoma(9;8.29e-07)			GGAAGACAGTAAAAAAAAAAG	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	48796730	48796731	+	IGR	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48796730_48796731insT								TMEM189-UBE2V1 (26395 upstream) : CEBPB (10645 downstream)																							GGTGAATTGAGttttttttttt	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	49385817	49385818	+	IGR	INS	-	T	T	rs66512688		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49385817_49385818insT								PARD6B (15540 upstream) : BCAS4 (25649 downstream)																							GCTCAGGCGTCTTTGTTTGTGT	0.470													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	49872553	49872554	+	IGR	INS	-	AA	AA			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49872553_49872554insAA								KCNG1 (232878 upstream) : NFATC2 (135212 downstream)																							TGCCATCTTGCAATATCCCCTT	0.411													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	52138527	52138528	+	IGR	INS	-	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52138527_52138528insG								TSHZ2 (34562 upstream) : ZNF217 (45084 downstream)																							aaagaaagaaagaaaggaagaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	56469878	56469895	+	IGR	DEL	GAAGGAGGAAGGAAGGAA	-	-	rs77802920	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56469878_56469895delGAAGGAGGAAGGAAGGAA								PMEPA1 (183337 upstream) : C20orf85 (256088 downstream)																							gaaggagggggaaggaggaaggaaggaagaaggaggaa	0.101													3	3	---	---	---	---	
GMEB2	26205	broad.mit.edu	37	20	62244320	62244320	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62244320delT	uc002yfp.1	-						GMEB2_uc002yfq.1_Intron	NM_012384	NP_036516	Q9UKD1	GMEB2_HUMAN	glucocorticoid modulatory element binding						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|metal ion binding				0	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;4.79e-09)|all cancers(9;2.76e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.0114)			tttctttttcttttttttttt	0.000													4	4	---	---	---	---	
ZNF512B	57473	broad.mit.edu	37	20	62602059	62602062	+	5'Flank	DEL	CCTT	-	-	rs113164162	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62602059_62602062delCCTT	uc002yhl.1	-							NM_020713	NP_065764	Q96KM6	Z512B_HUMAN	zinc finger protein 512B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				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)					tgcctgcctgccttccttccttcc	0.230													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9829288	9829297	+	IGR	DEL	ACACACACAG	-	-	rs78132214	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9829288_9829297delACACACACAG								None (None upstream) : None (None downstream)																							ccacacacacacacacacagacactctcac	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9865833	9865834	+	IGR	INS	-	GCT	GCT	rs9286488		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9865833_9865834insGCT								None (None upstream) : None (None downstream)																							TCAGCAGCAGGGCTGCTGCTCT	0.599													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10603789	10603789	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10603789delA								None (None upstream) : TPTE (302954 downstream)																							tcgggccaccaggggtaccac	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10620009	10620010	+	IGR	INS	-	T	T			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10620009_10620010insT								None (None upstream) : TPTE (286733 downstream)																							TACTGAGCACATCCTGACTCCA	0.322													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10633109	10633109	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10633109delC								None (None upstream) : TPTE (273634 downstream)																							tccaaccccacatttccactt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10818532	10818536	+	IGR	DEL	GAAAA	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10818532_10818536delGAAAA								None (None upstream) : TPTE (88207 downstream)																							gaatggaatggaaaagaatggaatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10829388	10829397	+	IGR	DEL	GAATGGAATG	-	-	rs79950516		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10829388_10829397delGAATGGAATG								None (None upstream) : TPTE (77346 downstream)																							taatggtctcgaatggaatggaatggaatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10838038	10838042	+	IGR	DEL	TAAGA	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10838038_10838042delTAAGA								None (None upstream) : TPTE (68701 downstream)																							gactcgaatgtaagagaatggaatg	0.000													4	2	---	---	---	---	
TPTE	7179	broad.mit.edu	37	21	10938353	10938353	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10938353delT	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)		CCGACTATAATTTAGGATCTC	0.299													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11044669	11044669	+	Intron	DEL	G	-	-	rs28375420		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11044669delG	uc002yit.1	-							NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			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)		cacagcataagcttttaacca	0.119													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11063160	11063161	+	Intron	INS	-	A	A	rs149756348		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11063160_11063161insA	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			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)		aaacgctatccaaaaaatgcag	0.035													4	3	---	---	---	---	
C21orf131	387486	broad.mit.edu	37	21	22144714	22144714	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22144714delG	uc002ykz.3	-						C21orf131_uc002yky.3_Intron|C21orf131_uc002yla.3_Intron|C21orf131_uc002ylb.3_Intron|C21orf131_uc002ylc.3_Intron	NR_024090				Homo sapiens cDNA FLJ37207 fis, clone BRALZ2007576.												0						ataaatGTTTGGggctgggct	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	26614516	26614516	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26614516delT								None (None upstream) : NCRNA00158 (143618 downstream)																							atttcttacctttgttcctct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	28499850	28499850	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28499850delT								ADAMTS5 (160411 upstream) : NCRNA00113 (594848 downstream)																							attttttgtatttttttttta	0.075													4	2	---	---	---	---	
IL10RB	3588	broad.mit.edu	37	21	34666695	34666696	+	Intron	INS	-	GT	GT	rs145592012	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34666695_34666696insGT	uc002yrk.1	+						IL10RB_uc002yrl.1_Intron	NM_000628	NP_000619	Q08334	I10R2_HUMAN	interleukin 10 receptor, beta precursor						immune response|inflammatory response	interleukin-28 receptor complex	protein binding|receptor activity				0						tgtgtgtgtgcgtgtgtgtgtg	0.371													4	2	---	---	---	---	
C21orf29	54084	broad.mit.edu	37	21	45989416	45989417	+	Intron	DEL	GT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45989416_45989417delGT	uc002zfe.1	-						C21orf29_uc010gpv.1_Intron	NM_144991	NP_659428	Q8WU66	TSEAR_HUMAN	chromosome 21 open reading frame 29 precursor						cell adhesion	extracellular region	structural molecule activity				0						TGGGGCAGGGGTGTGTGTGTGT	0.594													4	2	---	---	---	---	
ADARB1	104	broad.mit.edu	37	21	46575986	46575986	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46575986delT	uc002zgy.2	+						ADARB1_uc002zgr.2_Intron|ADARB1_uc002zgs.2_Intron|ADARB1_uc002zgw.2_Intron|ADARB1_uc002zgv.2_Intron|ADARB1_uc002zgt.2_Intron|ADARB1_uc010gpx.2_Intron|ADARB1_uc002zgq.2_Intron|ADARB1_uc002zgu.2_Intron|ADARB1_uc011afo.1_Intron	NM_015833	NP_056648	P78563	RED1_HUMAN	RNA-specific adenosine deaminase B1 isoform 2						adenosine to inosine editing|mRNA modification|mRNA processing|RNA processing	nucleoplasm|nucleus	double-stranded RNA adenosine deaminase activity|double-stranded RNA adenosine deaminase activity|double-stranded RNA binding|double-stranded RNA binding|metal ion binding|mRNA binding|RNA binding			skin(1)	1				Colorectal(79;0.115)		ccatcatccattcatccatcc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16116652	16116652	+	IGR	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16116652delA								None (None upstream) : POTEH (139680 downstream)																							AAATTTATAGAAGAAGGACAC	0.274													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17034044	17034044	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17034044delC								OR11H1 (584240 upstream) : CCT8L2 (37604 downstream)																							acctcggcctcccaaagtgct	0.000													2	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17379138	17379139	+	IGR	INS	-	AA	AA	rs145734780		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17379138_17379139insAA								HSFYL1 (68913 upstream) : GAB4 (63690 downstream)																							aagaaagaggcaaaaaaaAAAT	0.040													4	2	---	---	---	---	
BCL2L13	23786	broad.mit.edu	37	22	18138192	18138192	+	Intron	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18138192delT	uc002zmw.2	+						BCL2L13_uc002zmu.2_Intron|BCL2L13_uc002zmv.2_Intron|BCL2L13_uc002zmx.2_Intron|BCL2L13_uc002zmy.2_Intron|BCL2L13_uc010gqy.2_Intron|BCL2L13_uc011agk.1_Intron|BCL2L13_uc010gqz.2_5'Flank	NM_015367	NP_056182	Q9BXK5	B2L13_HUMAN	BCL2-like 13 (apoptosis facilitator)						induction of apoptosis	integral to membrane|mitochondrial membrane|nucleus	caspase activator activity			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4		all_epithelial(15;0.123)		Lung(27;0.199)		tgtgcagtacttttttttttt	0.000													4	2	---	---	---	---	
MICAL3	57553	broad.mit.edu	37	22	18309467	18309468	+	Intron	INS	-	GAGAA	GAGAA	rs138146848	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18309467_18309468insGAGAA	uc002zng.3	-						MICAL3_uc011agl.1_Intron	NM_015241	NP_056056	Q7RTP6	MICA3_HUMAN	microtubule associated monoxygenase, calponin							cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding				0		all_epithelial(15;0.198)		Lung(27;0.0427)		AGAATCAGGATGAGAAGAGAAG	0.589													3	4	---	---	---	---	
DGCR2	9993	broad.mit.edu	37	22	19044068	19044068	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19044068delA	uc002zoq.1	-						DGCR2_uc002zor.1_Intron|DGCR2_uc011agr.1_Intron	NM_005137	NP_005128	P98153	IDD_HUMAN	integral membrane protein DGCR2 precursor						cell adhesion|organ morphogenesis	integral to membrane	receptor activity|sugar binding			large_intestine(1)	1	Colorectal(54;0.0993)					TGGCTTTAATAAAAAAAAAAA	0.498													6	4	---	---	---	---	
CDC45	8318	broad.mit.edu	37	22	19473573	19473576	+	Intron	DEL	CTCA	-	-	rs66823949		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19473573_19473576delCTCA	uc002zpr.2	+						CDC45_uc011agz.1_Intron|CDC45_uc011aha.1_Intron|CDC45_uc002zps.2_Intron|CDC45_uc002zpt.2_Intron	NM_003504	NP_003495	O75419	CDC45_HUMAN	CDC45-like						DNA replication checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle	centrosome|nucleoplasm	protein binding			lung(1)	1						gagatggagtctcactctgtcact	0.015													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	20149695	20149697	+	IGR	DEL	CAC	-	-	rs71682985		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20149695_20149697delCAC								ZDHHC8 (14166 upstream) : LOC150197 (44158 downstream)																							ccaccaccatcaccaccaccacc	0.000													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	20149872	20149873	+	IGR	INS	-	ACC	ACC	rs13057648		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20149872_20149873insACC								ZDHHC8 (14343 upstream) : LOC150197 (43982 downstream)																							ccaccatcactaccaccaccac	0.000													6	3	---	---	---	---	
MED15	51586	broad.mit.edu	37	22	20881594	20881594	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20881594delA	uc002zsp.2	+						MED15_uc002zsn.1_Intron|MED15_uc002zso.2_Intron|MED15_uc002zsq.2_Intron|MED15_uc010gso.2_Intron|MED15_uc002zsr.2_Intron|MED15_uc011ahs.1_Intron|MED15_uc011aht.1_Intron	NM_001003891	NP_001003891	Q96RN5	MED15_HUMAN	mediator complex subunit 15 isoform a						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|mediator complex	protein binding			skin(1)	1	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)			tttttctttgacctttcactg	0.000													4	2	---	---	---	---	
VPREB1	7441	broad.mit.edu	37	22	22599304	22599304	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22599304delC	uc002zvx.1	+						LOC96610_uc011aim.1_Intron	NM_007128	NP_009059	P12018	VPREB_HUMAN	immunoglobulin iota chain precursor						immune response	extracellular region	antigen binding|protein binding				0	all_hematologic(9;0.0312)|Acute lymphoblastic leukemia(84;0.155)	all_cancers(3;3.14e-14)|Acute lymphoblastic leukemia(3;2.97e-57)|all_hematologic(3;5.9e-52)		READ - Rectum adenocarcinoma(21;0.145)		AAGACTCCTGCCCCTTCCTTC	0.617													26	32	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	22641327	22641328	+	Intron	INS	-	TC	TC			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22641327_22641328insTC	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						atttcatctcatcatttcatct	0.000													4	2	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	22707222	22707223	+	Intron	INS	-	G	G	rs149766248		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22707222_22707223insG	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						CCTCCTCTGCAAGGGTGGGAAG	0.614													4	2	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	23025074	23025075	+	Intron	DEL	TG	-	-	rs148688762		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23025074_23025075delTG	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						tgcatatgcctgtgtgtgtgtg	0.025													0	8	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	23116953	23116953	+	Intron	DEL	C	-	-	rs35511743		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23116953delC	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						gacactcacacccccgcctgc	0.129													1	6	---	---	---	---	
BCR	613	broad.mit.edu	37	22	23583680	23583681	+	Intron	INS	-	C	C	rs148374007	by1000genomes	TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23583680_23583681insC	uc002zww.2	+						BCR_uc002zwx.2_Intron|BCR_uc011aiy.1_Intron	NM_004327	NP_004318	P11274	BCR_HUMAN	breakpoint cluster region isoform 1						regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	ATP binding|GTPase activator activity|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity		BCR/JAK2(6)	haematopoietic_and_lymphoid_tissue(6)|central_nervous_system(3)|urinary_tract(1)|lung(1)|skin(1)	12						CCCATGCTGCTCCCACACCAGG	0.609			T	ABL1| FGFR1|JAK2 	CML|ALL|AML								1	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	23832740	23832740	+	IGR	DEL	T	-	-	rs113337789		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23832740delT								ZDHHC8P1 (87941 upstream) : IGLL1 (82575 downstream)																							atttgtattattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	25723837	25723838	+	IGR	INS	-	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25723837_25723838insG								IGLL3 (7646 upstream) : LRP5L (23548 downstream)																							TTCCCAGGTCTGGGCATGGGGG	0.540													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	25852747	25852748	+	Intron	DEL	GT	-	-	rs140245856		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25852747_25852748delGT	uc003abt.2	+						uc003abu.2_Intron|uc003abv.2_Intron					Homo sapiens cDNA clone IMAGE:3542716, partial cds.																		gtgtgtgcacgtgtgtgtgtgc	0.188													4	5	---	---	---	---	
SRRD	402055	broad.mit.edu	37	22	26883021	26883021	+	Intron	DEL	G	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26883021delG	uc010gve.2	+						SRRD_uc003acp.3_Intron	NM_001013694	NP_001013716	Q9UH36	SRR1L_HUMAN	SRR1 domain containing						rhythmic process						0						ctgagtagctgggactacagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	34468038	34468039	+	IGR	DEL	AG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34468038_34468039delAG								LARGE (149454 upstream) : ISX (994090 downstream)																							ggagagaggcagagagagagag	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	35612942	35612943	+	IGR	INS	-	A	A			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35612942_35612943insA								ISX (129564 upstream) : HMGXB4 (40502 downstream)																							aaaactccgtcaaaaaaaaaaa	0.099													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	35873627	35873631	+	IGR	DEL	GCTGT	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35873627_35873631delGCTGT								MCM5 (53133 upstream) : RASD2 (63721 downstream)																							ACGAACATACGCTGTGTTGTTCTTT	0.293													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	36830209	36830210	+	IGR	INS	-	TTTC	TTTC			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36830209_36830210insTTTC								MYH9 (46146 upstream) : TXN2 (32883 downstream)																							gttctttcttttttctttcttt	0.000													2	4	---	---	---	---	
PPARA	5465	broad.mit.edu	37	22	46612280	46612281	+	Intron	INS	-	AA	AA	rs111225851		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46612280_46612281insAA	uc003bgw.1	+						PPARA_uc003bgx.1_Intron|PPARA_uc010hab.1_Intron|PPARA_uc003bha.2_Intron|PPARA_uc003bhb.1_Intron|PPARA_uc010hac.1_Intron	NM_005036	NP_005027	Q07869	PPARA_HUMAN	peroxisome proliferative activated receptor,						fatty acid metabolic process|fatty acid transport|negative regulation of appetite|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fatty acid beta-oxidation|regulation of cellular ketone metabolic process by positive regulation of transcription from an RNA polymerase II promoter|regulation of glycolysis by positive regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	drug binding|ligand-regulated transcription factor activity|lipid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|ubiquitin conjugating enzyme binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00522)	Atorvastatin(DB01076)|Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Simvastatin(DB00641)	aacttcatctcaaaaaaaaaaa	0.109													4	2	---	---	---	---	
GRAMD4	23151	broad.mit.edu	37	22	47035051	47035052	+	Intron	DEL	GT	-	-	rs5845762		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47035051_47035052delGT	uc003bhx.2	+						GRAMD4_uc010had.2_Intron	NM_015124	NP_055939	Q6IC98	GRAM4_HUMAN	death-inducing-protein						apoptosis	integral to membrane|mitochondrial membrane				ovary(1)	1		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|BRCA - Breast invasive adenocarcinoma(115;0.166)		gtgtgcgtgagtgtgtgtgtgt	0.356													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	1775000	1775000	+	IGR	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1775000delC								ASMT (13027 upstream) : DHRSX (362557 downstream)																							gccagtctggccagaataaaa	0.000													4	2	---	---	---	---	
ARSD	414	broad.mit.edu	37	X	2832920	2832921	+	Intron	INS	-	TA	TA			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2832920_2832921insTA	uc004cqy.2	-						ARSD_uc004cqz.1_Intron|ARSD_uc004cra.1_Intron	NM_001669	NP_001660	P51689	ARSD_HUMAN	arylsulfatase D isoform a precursor							lysosome	arylsulfatase activity|metal ion binding				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				CTTTGTACTATTATTATTATTA	0.183													15	12	---	---	---	---	
ASB9	140462	broad.mit.edu	37	X	15273107	15273107	+	Intron	DEL	A	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15273107delA	uc004cwl.2	-						ASB9_uc004cwk.2_Intron|ASB9_uc004cwm.2_Intron|ASB9_uc010ner.2_Intron|ASB9_uc004cwn.2_Intron	NM_001031739	NP_001026909	Q96DX5	ASB9_HUMAN	ankyrin repeat and SOCS box-containing 9 isoform						intracellular signal transduction						0	Hepatocellular(33;0.183)					TATTGACTTTAAaaaaaaaaa	0.224													4	2	---	---	---	---	
SYAP1	94056	broad.mit.edu	37	X	16759629	16759629	+	Intron	DEL	T	-	-	rs11364120		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16759629delT	uc004cxp.2	+						SYAP1_uc004cxo.2_Intron|SYAP1_uc011miv.1_Intron	NM_032796	NP_116185	Q96A49	SYAP1_HUMAN	SYAP1 protein											skin(1)	1	Hepatocellular(33;0.0997)					TCAAGTAGAGTTTTTTTTTTT	0.144													4	2	---	---	---	---	
FAM48B2	170067	broad.mit.edu	37	X	24331543	24331543	+	5'Flank	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24331543delC	uc011mjw.1	-							NM_001136233	NP_001129705	P0C7V6	F48B2_HUMAN	family with sequence similarity 48, member B2												0						CGCCGCAAGTCCACACTGAGT	0.557													7	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	29996711	29996711	+	IGR	DEL	T	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:29996711delT								IL1RAPL1 (22694 upstream) : MAGEB2 (236964 downstream)																							tcaaacgtgcttttttttttt	0.000													2	4	---	---	---	---	
DMD	1756	broad.mit.edu	37	X	31947973	31947973	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31947973delC	uc004dda.1	-						DMD_uc004dcr.1_Intron|DMD_uc004dcs.1_Intron|DMD_uc004dct.1_Intron|DMD_uc004dcu.1_Intron|DMD_uc004dcv.1_Intron|DMD_uc004dcw.2_Intron|DMD_uc004dcx.2_Intron|DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc010ngn.1_Intron	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform						muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				TGACCGAGGGCCCAGTGGTAC	0.393													3	4	---	---	---	---	
SYN1	6853	broad.mit.edu	37	X	47478714	47478714	+	Intron	DEL	C	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47478714delC	uc004die.2	-						SYN1_uc004did.2_Intron	NM_006950	NP_008881	P17600	SYN1_HUMAN	synapsin I isoform Ia							cell junction|Golgi apparatus	actin binding|ATP binding|ligase activity|transporter activity			ovary(1)	1						GATCTGGGGACCCAGGCCCAC	0.602													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	96865667	96865668	+	IGR	DEL	TG	-	-			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:96865667_96865668delTG								DIAPH2 (10071 upstream) : None (None downstream)																							AGTGTGCAGATGTGTGTGTGTG	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9940864	9940865	+	IGR	INS	-	AT	AT			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9940864_9940865insAT								TTTY22 (290010 upstream) : None (None downstream)																							TTTATTGTTTAATTGTTTCTTG	0.267													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	10082045	10082046	+	IGR	INS	-	G	G			TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10082045_10082046insG								TTTY22 (431191 upstream) : None (None downstream)																							tcaaaagaaatgttcaactctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	28588050	28588052	+	IGR	DEL	CAT	-	-	rs111989825		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:28588050_28588052delCAT								None (None upstream) : None (None downstream)																							tcttcttttacatcattctgtcA	0.182													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	28807588	28807589	+	IGR	INS	-	A	A	rs112875632		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:28807588_28807589insA								None (None upstream) : None (None downstream)																							tggaatgtattgggtggaatgg	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	58999857	58999858	+	IGR	INS	-	A	A	rs113244878		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:58999857_58999858insA								None (None upstream) : None (None downstream)																							cacagaattggaaaaaactact	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59002251	59002252	+	IGR	DEL	AA	-	-	rs146446459		TCGA-46-3769-01	TCGA-46-3769-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59002251_59002252delAA								None (None upstream) : None (None downstream)																							CCGATAATGCAAAAAAAAAAAA	0.381													4	2	---	---	---	---	
