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
GNB1	2782	broad.mit.edu	37	1	1749311	1749311	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1749311C>A	uc001aif.2	-	4	393	c.61G>T	c.(61-63)GCC>TCC	p.A21S	GNB1_uc009vky.2_Intron	NM_002074	NP_002065	P62873	GBB1_HUMAN	guanine nucleotide-binding protein, beta-1	21					cellular response to glucagon stimulus|energy reserve metabolic process|muscarinic acetylcholine receptor signaling pathway|platelet activation|Ras protein signal transduction|synaptic transmission	heterotrimeric G-protein complex	GTPase activity|GTPase binding|signal transducer activity				0	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;5.62e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.14e-35)|OV - Ovarian serous cystadenocarcinoma(86;7.31e-23)|GBM - Glioblastoma multiforme(42;3.1e-07)|COAD - Colon adenocarcinoma(227;0.000323)|Colorectal(212;0.000374)|Kidney(185;0.00392)|BRCA - Breast invasive adenocarcinoma(365;0.00573)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.0482)|Lung(427;0.236)		GCTTTCCTGGCGTCCTGGGAA	0.507													11	36	---	---	---	---	PASS
NPPB	4879	broad.mit.edu	37	1	11918438	11918438	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11918438G>A	uc001atj.2	-	2	323	c.221C>T	c.(220-222)ACA>ATA	p.T74I		NM_002521	NP_002512	P16860	ANFB_HUMAN	natriuretic peptide precursor B preproprotein	74					body fluid secretion|cGMP biosynthetic process|negative regulation of angiogenesis|negative regulation of cell growth|positive regulation of renal sodium excretion|positive regulation of urine volume|receptor guanylyl cyclase signaling pathway|regulation of blood pressure|regulation of blood vessel size|regulation of vascular permeability|regulation of vasodilation	extracellular space	diuretic hormone activity			ovary(2)	2	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;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)	Carvedilol(DB01136)|Nesiritide(DB04899)|Testosterone(DB00624)	CCAGACACCTGTGGGACGGGG	0.632													10	29	---	---	---	---	PASS
ECE1	1889	broad.mit.edu	37	1	21616586	21616586	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21616586C>T	uc001bek.2	-	2	190	c.115G>A	c.(115-117)GAC>AAC	p.D39N	ECE1_uc001bem.2_Missense_Mutation_p.D23N|ECE1_uc001bei.2_Missense_Mutation_p.D36N|ECE1_uc010odl.1_Missense_Mutation_p.D39N|ECE1_uc009vqa.1_Missense_Mutation_p.D39N	NM_001397	NP_001388	P42892	ECE1_HUMAN	endothelin converting enzyme 1 isoform 1	39	Cytoplasmic (Potential).				bradykinin catabolic process|calcitonin catabolic process|ear development|embryonic digit morphogenesis|endothelin maturation|heart development|positive regulation of receptor recycling|substance P catabolic process	early endosome|external side of plasma membrane|integral to membrane|intrinsic to endosome membrane|membrane fraction|perinuclear region of cytoplasm|plasma membrane|Weibel-Palade body	metal ion binding|metalloendopeptidase activity|protein homodimerization activity			ovary(2)|skin(1)	3		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)		GGGTATGCGTCGCCCTCGGAG	0.697													3	4	---	---	---	---	PASS
LUZP1	7798	broad.mit.edu	37	1	23418890	23418890	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23418890G>A	uc001bgk.2	-	4	2249	c.1865C>T	c.(1864-1866)TCA>TTA	p.S622L	LUZP1_uc010odv.1_Missense_Mutation_p.S622L|LUZP1_uc001bgl.2_Missense_Mutation_p.S622L|LUZP1_uc001bgm.1_Missense_Mutation_p.S622L	NM_033631	NP_361013	Q86V48	LUZP1_HUMAN	leucine zipper protein 1	622						nucleus					0		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Ovarian(437;0.00373)|Breast(348;0.00815)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.88e-27)|Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;4.31e-06)|GBM - Glioblastoma multiforme(114;8.64e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00176)|STAD - Stomach adenocarcinoma(196;0.0146)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0967)|LUSC - Lung squamous cell carcinoma(448;0.199)		TTCTTTATGTGAGGTTGAAAA	0.473													70	305	---	---	---	---	PASS
OPRD1	4985	broad.mit.edu	37	1	29189406	29189406	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29189406C>T	uc001brf.1	+	3	972	c.730C>T	c.(730-732)CGC>TGC	p.R244C		NM_000911	NP_000902	P41143	OPRD_HUMAN	opioid receptor, delta 1	244	Cytoplasmic (Potential).				immune response|protein import into nucleus, translocation	integral to plasma membrane	delta-opioid receptor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.000947)|all_lung(284;0.00131)|Renal(390;0.00758)|Breast(348;0.00765)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-07)|COAD - Colon adenocarcinoma(152;7.51e-06)|STAD - Stomach adenocarcinoma(196;0.00306)|BRCA - Breast invasive adenocarcinoma(304;0.0241)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)	Butorphanol(DB00611)|Codeine(DB00318)|Fentanyl(DB00813)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Loperamide(DB00836)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pimozide(DB01100)|Propoxyphene(DB00647)	GCGCAGTGTGCGCCTGCTGTC	0.642													13	26	---	---	---	---	PASS
CYP4Z2P	163720	broad.mit.edu	37	1	47333687	47333687	+	RNA	SNP	G	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47333687G>T	uc001cqo.1	-	8		c.1040C>A			CYP4Z2P_uc009vyn.1_RNA	NR_002788				Homo sapiens cDNA FLJ40054 fis, clone TBAES2000315, weakly similar to CYTOCHROME P450 4A1 (EC 1.14.15.3).												0						GATGCTCAGGGTACTTTGCCA	0.443													10	46	---	---	---	---	PASS
NEGR1	257194	broad.mit.edu	37	1	72748110	72748110	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72748110C>T	uc001dfw.2	-	1	168	c.68G>A	c.(67-69)AGC>AAC	p.S23N	NEGR1_uc010oqs.1_Missense_Mutation_p.S23N	NM_173808	NP_776169	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1 precursor	23					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)		GCAGCACAGGCTGAGGAGCAC	0.627													5	27	---	---	---	---	PASS
WDR63	126820	broad.mit.edu	37	1	85546974	85546974	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85546974G>A	uc001dkt.2	+	4	352	c.161G>A	c.(160-162)TGC>TAC	p.C54Y	WDR63_uc009wcl.2_Missense_Mutation_p.C54Y	NM_145172	NP_660155	Q8IWG1	WDR63_HUMAN	WD repeat domain 63	54										upper_aerodigestive_tract(2)|ovary(2)|skin(1)	5				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)		ATATTTAACTGCCGAATAGAT	0.363													35	125	---	---	---	---	PASS
CDC14A	8556	broad.mit.edu	37	1	100964716	100964716	+	Silent	SNP	A	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100964716A>T	uc001dtg.3	+	15	2141	c.1653A>T	c.(1651-1653)CCA>CCT	p.P551P	CDC14A_uc010oui.1_Silent_p.P493P|CDC14A_uc001dtf.2_Silent_p.P551P|CDC14A_uc009wed.1_Silent_p.P258P|CDC14A_uc009wee.2_Silent_p.P551P	NM_003672	NP_003663	Q9UNH5	CC14A_HUMAN	CDC14 homolog A isoform 1	551					cell cycle|cell division|cell proliferation	centrosome|nucleus|spindle	protein binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			large_intestine(1)	1		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)		ACAGCCCCCCAGGCCCCCACA	0.562													7	70	---	---	---	---	PASS
PRPF3	9129	broad.mit.edu	37	1	150310685	150310685	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150310685C>G	uc001eum.3	+	8	1247	c.1085C>G	c.(1084-1086)ACA>AGA	p.T362R	PRPF3_uc009wlp.2_RNA|PRPF3_uc010pca.1_Missense_Mutation_p.T321R|PRPF3_uc010pcb.1_Missense_Mutation_p.T313R|PRPF3_uc009wlq.1_RNA	NM_004698	NP_004689	O43395	PRPF3_HUMAN	PRP3 pre-mRNA processing factor 3 homolog	362					nuclear mRNA splicing, via spliceosome	Cajal body|cytoplasm|nuclear speck|spliceosomal complex	protein binding			ovary(1)	1	Lung NSC(24;5.57e-29)|Breast(34;0.000844)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)	Colorectal(1306;0.0149)		GCTCGAAAAACAGGCATCCAT	0.418													27	102	---	---	---	---	PASS
FCER1A	2205	broad.mit.edu	37	1	159277759	159277759	+	3'UTR	SNP	T	G	G			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159277759T>G	uc001ftq.2	+	6						NM_002001	NP_001992	P12319	FCERA_HUMAN	Fc fragment of IgE, high affinity I, receptor							integral to plasma membrane				lung(2)|skin(2)|prostate(1)	5	all_hematologic(112;0.0429)				Benzylpenicilloyl Polylysine(DB00895)|Omalizumab(DB00043)	CATTAGTTTTTTTCCAGCATC	0.363													12	20	---	---	---	---	PASS
ATP1A2	477	broad.mit.edu	37	1	160093040	160093040	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160093040G>T	uc001fvc.2	+	4	347	c.215G>T	c.(214-216)CGA>CTA	p.R72L	ATP1A2_uc001fvb.2_Missense_Mutation_p.R72L|ATP1A2_uc010piz.1_5'Flank	NM_000702	NP_000693	P50993	AT1A2_HUMAN	Na+/K+ -ATPase alpha 2 subunit proprotein	72	Cytoplasmic (Potential).				ATP biosynthetic process		ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			central_nervous_system(3)|ovary(2)|skin(2)	7	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			GTTCTGGCTCGAGATGGGCCC	0.642													11	110	---	---	---	---	PASS
ZNF672	79894	broad.mit.edu	37	1	249142695	249142695	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:249142695C>A	uc001iex.2	+	4	1917	c.1222C>A	c.(1222-1224)CGC>AGC	p.R408S		NM_024836	NP_079112	Q499Z4	ZN672_HUMAN	zinc finger protein 672	408	C2H2-type 14.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			CAGCCACAGCCGCTCGCTGTC	0.697													2	1	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	89339977	89339977	+	RNA	SNP	G	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89339977G>A	uc010ytr.1	-	64		c.5882C>T			uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																		TGCAGACACGGAAGATGGAGA	0.478													27	576	---	---	---	---	PASS
TBC1D8	11138	broad.mit.edu	37	2	101656644	101656644	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101656644C>A	uc010fiv.2	-	6	1162	c.1031G>T	c.(1030-1032)AGA>ATA	p.R344I	TBC1D8_uc010yvw.1_Missense_Mutation_p.R359I|TBC1D8_uc002tau.3_Missense_Mutation_p.R101I	NM_001102426	NP_001095896	O95759	TBCD8_HUMAN	TBC1 domain family, member 8	344	GRAM 2.				blood circulation|positive regulation of cell proliferation	intracellular|membrane	calcium ion binding|Rab GTPase activator activity			ovary(3)	3						GTCTACCTCTCTGAGTGGCAG	0.542													4	68	---	---	---	---	PASS
RANBP2	5903	broad.mit.edu	37	2	109365421	109365421	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109365421A>C	uc002tem.3	+	9	1235	c.1109A>C	c.(1108-1110)AAA>ACA	p.K370T		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	370					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18						GATTTTTTAAAAGAGATTGTT	0.343													124	290	---	---	---	---	PASS
AGXT	189	broad.mit.edu	37	2	241808356	241808356	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241808356T>C	uc002waa.3	+	1	195	c.74T>C	c.(73-75)CTG>CCG	p.L25P	AGXT_uc010zoi.1_Missense_Mutation_p.L25P	NM_000030	NP_000021	P21549	SPYA_HUMAN	alanine-glyoxylate aminotransferase	25					glyoxylate metabolic process|protein targeting to peroxisome	mitochondrial matrix|peroxisomal matrix	alanine-glyoxylate transaminase activity|protein homodimerization activity|pyridoxal phosphate binding|serine-pyruvate transaminase activity				0		all_epithelial(40;1.61e-15)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)	Glycine(DB00145)|L-Alanine(DB00160)|L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)	AACCAGCTCCTGCTGGGGCCT	0.647													17	44	---	---	---	---	PASS
ANO10	55129	broad.mit.edu	37	3	43474215	43474215	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43474215G>A	uc003cmv.2	-	12	1973	c.1802C>T	c.(1801-1803)GCA>GTA	p.A601V	ANO10_uc011azs.1_Intron|ANO10_uc003cmw.2_Missense_Mutation_p.A535V|ANO10_uc010hil.2_Missense_Mutation_p.A411V|ANO10_uc011azt.1_Missense_Mutation_p.A490V	NM_018075	NP_060545	Q9NW15	ANO10_HUMAN	transmembrane protein 16K	601	Helical; (Potential).				cell death	chloride channel complex	chloride channel activity			ovary(2)	2						AGCCAGGAGTGCGTGCTGAAA	0.368													4	44	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52643348	52643348	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52643348G>A	uc003des.2	-	16	2560	c.2548C>T	c.(2548-2550)CGA>TGA	p.R850*	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Nonsense_Mutation_p.R850*|PBRM1_uc003der.2_Nonsense_Mutation_p.R818*|PBRM1_uc003det.2_Nonsense_Mutation_p.R865*|PBRM1_uc003deu.2_Nonsense_Mutation_p.R865*|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Nonsense_Mutation_p.R850*|PBRM1_uc010hmk.1_Nonsense_Mutation_p.R850*|PBRM1_uc003dey.2_Nonsense_Mutation_p.R850*|PBRM1_uc003dez.1_Nonsense_Mutation_p.R850*|PBRM1_uc003dfb.1_Nonsense_Mutation_p.R763*|PBRM1_uc003dfa.1_Nonsense_Mutation_p.R196*|PBRM1_uc003dfc.2_Nonsense_Mutation_p.R217*	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	850	Bromo 6.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		CTTCTTGCTCGTTCCAATACT	0.333			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								8	67	---	---	---	---	PASS
ADCY5	111	broad.mit.edu	37	3	123005537	123005537	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123005537T>C	uc003egh.1	-	20	3652	c.3652A>G	c.(3652-3654)ATC>GTC	p.I1218V	ADCY5_uc003egg.1_Missense_Mutation_p.I876V	NM_183357	NP_899200	O95622	ADCY5_HUMAN	adenylate cyclase 5	1218	Cytoplasmic (Potential).				activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)	4				GBM - Glioblastoma multiforme(114;0.0342)		CTCACCTGGATGCGGTCGGGT	0.632											OREG0015741	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	12	52	---	---	---	---	PASS
SLITRK3	22865	broad.mit.edu	37	3	164906543	164906543	+	Silent	SNP	C	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164906543C>T	uc003fej.3	-	2	2520	c.2076G>A	c.(2074-2076)CGG>CGA	p.R692R	SLITRK3_uc003fek.2_Silent_p.R692R	NM_014926	NP_055741	O94933	SLIK3_HUMAN	slit and trk like 3 protein precursor	692	Cytoplasmic (Potential).					integral to membrane				ovary(6)|skin(3)|pancreas(1)	10						CACCTTCCTGCCGCTTGCTTC	0.443										HNSCC(40;0.11)			4	64	---	---	---	---	PASS
EIF2B5	8893	broad.mit.edu	37	3	183858287	183858287	+	Missense_Mutation	SNP	G	A	A	rs113994061		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183858287G>A	uc003fmp.2	+	7	1289	c.925G>A	c.(925-927)GTC>ATC	p.V309I	EIF2B5_uc003fmq.2_Missense_Mutation_p.V30I|EIF2B5_uc003fmr.2_5'Flank	NM_003907	NP_003898	Q13144	EI2BE_HUMAN	eukaryotic translation initiation factor 2B,	309					astrocyte development|myelination|negative regulation of translational initiation in response to stress|oligodendrocyte development|ovarian follicle development|positive regulation of translational initiation|response to glucose stimulus|response to heat|response to peptide hormone stimulus|RNA metabolic process	cytosol|eukaryotic translation initiation factor 2B complex|nucleus	guanyl-nucleotide exchange factor activity|transferase activity|translation initiation factor activity|translation initiation factor binding			ovary(5)	5	all_cancers(143;7.59e-11)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)			GTACTCAGCTGTCTGTGCTGA	0.542													9	255	---	---	---	---	PASS
PCDH10	57575	broad.mit.edu	37	4	134071517	134071517	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134071517C>A	uc003iha.2	+	1	1048	c.222C>A	c.(220-222)TAC>TAA	p.Y74*	uc003igy.2_5'Flank|PCDH10_uc003igz.2_Nonsense_Mutation_p.Y74*	NM_032961	NP_116586	Q9P2E7	PCD10_HUMAN	protocadherin 10 isoform 1 precursor	74	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2				LUSC - Lung squamous cell carcinoma(193;0.227)		GGGTGCTGTACGTGAACGAGA	0.547													34	101	---	---	---	---	PASS
FAT1	2195	broad.mit.edu	37	4	187539468	187539468	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187539468C>T	uc003izf.2	-	10	8460	c.8272G>A	c.(8272-8274)GGG>AGG	p.G2758R		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	2758	Extracellular (Potential).|Cadherin 25.				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						TTCAGTCTCCCGCTCTGTCTG	0.473										HNSCC(5;0.00058)			9	252	---	---	---	---	PASS
MCCC2	64087	broad.mit.edu	37	5	70930789	70930789	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70930789C>G	uc003kbs.3	+	9	961	c.823C>G	c.(823-825)CAC>GAC	p.H275D	MCCC2_uc010iyv.1_Missense_Mutation_p.H275D|MCCC2_uc003kbt.3_RNA|MCCC2_uc003kbu.1_Missense_Mutation_p.H144D	NM_022132	NP_071415	Q9HCC0	MCCB_HUMAN	methylcrotonoyl-Coenzyme A carboxylase 2 (beta)	275	Carboxyltransferase.				leucine catabolic process	mitochondrial inner membrane|mitochondrial matrix	ATP binding|methylcrotonoyl-CoA carboxylase activity			ovary(1)	1		Lung NSC(167;0.000697)|Prostate(74;0.0107)|Ovarian(174;0.0175)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.04e-54)	Biotin(DB00121)	AGTAAGTGACCACTGGGCTTT	0.373													41	111	---	---	---	---	PASS
SYNCRIP	10492	broad.mit.edu	37	6	86324828	86324828	+	Silent	SNP	A	G	G			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86324828A>G	uc003pla.2	-	11	2059	c.1518T>C	c.(1516-1518)GCT>GCC	p.A506A	SYNCRIP_uc003pku.2_Silent_p.A506A|SYNCRIP_uc003pkw.2_Silent_p.A471A|SYNCRIP_uc003pky.2_Silent_p.A408A|SYNCRIP_uc003pkv.2_Silent_p.A506A|SYNCRIP_uc003pkx.2_Silent_p.A354A|SYNCRIP_uc003pkz.2_Silent_p.A471A	NM_006372	NP_006363	O60506	HNRPQ_HUMAN	synaptotagmin binding, cytoplasmic RNA	506	Interaction with APOBEC1.|8 X 3 AA repeats of R-G-G.				CRD-mediated mRNA stabilization|interspecies interaction between organisms	catalytic step 2 spliceosome|CRD-mediated mRNA stability complex|endoplasmic reticulum|histone pre-mRNA 3'end processing complex|microsome|nucleoplasm	nucleotide binding|protein binding			ovary(2)	2		all_cancers(76;0.000137)|Acute lymphoblastic leukemia(125;3.66e-08)|Prostate(29;8.2e-07)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0297)		BRCA - Breast invasive adenocarcinoma(108;0.0389)		TGGATGGAGCAGCACCCCTTG	0.532													42	87	---	---	---	---	PASS
RTN4IP1	84816	broad.mit.edu	37	6	107069337	107069337	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107069337C>T	uc003prj.2	-	3	935	c.458G>A	c.(457-459)GGC>GAC	p.G153D	RTN4IP1_uc010kdd.2_Missense_Mutation_p.G153D|RTN4IP1_uc003prk.2_Missense_Mutation_p.G53D	NM_032730	NP_116119	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1 precursor	153						mitochondrion	oxidoreductase activity|zinc ion binding				0	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)	all cancers(137;0.113)|BRCA - Breast invasive adenocarcinoma(108;0.127)|Epithelial(106;0.144)		TGAAAGAGTGCCTTGTTTCCA	0.403													4	115	---	---	---	---	PASS
FIG4	9896	broad.mit.edu	37	6	110036326	110036326	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110036326G>T	uc003ptt.2	+	2	327	c.112G>T	c.(112-114)GTC>TTC	p.V38F	FIG4_uc011eau.1_5'UTR	NM_014845	NP_055660	Q92562	FIG4_HUMAN	Sac domain-containing inositol phosphatase 3	38					cell death	endosome membrane	protein binding			ovary(1)	1		all_cancers(87;8.63e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000124)|all_lung(197;0.0187)|Colorectal(196;0.0492)|Lung SC(18;0.0548)		OV - Ovarian serous cystadenocarcinoma(136;0.0355)|Epithelial(106;0.038)|all cancers(137;0.0425)|BRCA - Breast invasive adenocarcinoma(108;0.079)		GAAATATCGTGTCTTGAAGAT	0.338													9	107	---	---	---	---	PASS
OPRM1	4988	broad.mit.edu	37	6	154412549	154412549	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154412549G>A	uc003qpr.2	+	3	1343	c.1106G>A	c.(1105-1107)CGT>CAT	p.R369H	OPRM1_uc011efc.1_Missense_Mutation_p.R288H|OPRM1_uc011efd.1_Missense_Mutation_p.R269H|OPRM1_uc011efe.1_Missense_Mutation_p.R462H|OPRM1_uc003qpn.2_Missense_Mutation_p.R369H|OPRM1_uc003qpo.1_Missense_Mutation_p.R369H|OPRM1_uc011eff.1_Missense_Mutation_p.R369H|OPRM1_uc011efg.1_Missense_Mutation_p.R369H|OPRM1_uc011efh.1_Missense_Mutation_p.R369H|OPRM1_uc003qpq.1_Missense_Mutation_p.R369H|OPRM1_uc003qpt.1_Missense_Mutation_p.R369H|OPRM1_uc011efi.1_Missense_Mutation_p.R369H|OPRM1_uc003qpp.2_RNA|OPRM1_uc003qps.2_RNA|OPRM1_uc010kjg.2_Missense_Mutation_p.R269H|OPRM1_uc003qpu.2_Missense_Mutation_p.R269H	NM_000914	NP_000905	P35372	OPRM_HUMAN	opioid receptor, mu 1 isoform MOR-1	369	Cytoplasmic (Potential).				behavior|negative regulation of cell proliferation|sensory perception	endoplasmic reticulum|Golgi apparatus|integral to plasma membrane	mu-opioid receptor activity|protein binding			ovary(1)	1		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Fentanyl(DB00813)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Propoxyphene(DB00647)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tramadol(DB00193)	ACTCGAATTCGTCAGAACACT	0.438													13	69	---	---	---	---	PASS
SAMD9	54809	broad.mit.edu	37	7	92731889	92731889	+	Silent	SNP	C	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92731889C>T	uc003umf.2	-	3	3778	c.3522G>A	c.(3520-3522)GAG>GAA	p.E1174E	SAMD9_uc003umg.2_Silent_p.E1174E	NM_017654	NP_060124	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	1174						cytoplasm				ovary(3)|skin(2)|breast(1)|central_nervous_system(1)	7	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			TCACTTCATACTCTCTATCTT	0.378													30	351	---	---	---	---	PASS
CNGB3	54714	broad.mit.edu	37	8	87588236	87588236	+	Missense_Mutation	SNP	T	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87588236T>A	uc003ydx.2	-	18	2272	c.2226A>T	c.(2224-2226)AAA>AAT	p.K742N	CNGB3_uc010maj.2_Missense_Mutation_p.K599N	NM_019098	NP_061971	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	742	Cytoplasmic (Potential).				signal transduction|visual perception	integral to membrane	cGMP binding			ovary(2)|pancreas(1)	3						GCTCTCTTCCTTTATCTTTAt	0.249													17	182	---	---	---	---	PASS
LYPD2	137797	broad.mit.edu	37	8	143832568	143832568	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143832568C>G	uc003ywz.2	-	2	162	c.79G>C	c.(79-81)GTC>CTC	p.V27L		NM_205545	NP_991108	Q6UXB3	LYPD2_HUMAN	LY6/PLAUR domain containing 2 precursor	27	UPAR/Ly6.					anchored to membrane|plasma membrane					0	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					TCCGGACAGACGTAGCAGCGC	0.642													16	66	---	---	---	---	PASS
C8orf73	642475	broad.mit.edu	37	8	144654816	144654816	+	Silent	SNP	T	C	C			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144654816T>C	uc010mff.2	-	1	113	c.69A>G	c.(67-69)GCA>GCG	p.A23A	C8orf73_uc010mfg.1_Silent_p.A23A	NM_001100878	NP_001094348	A6NGR9	CH073_HUMAN	hypothetical protein LOC642475	23							binding			ovary(1)	1	all_cancers(97;6.49e-11)|all_epithelial(106;4.73e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.014)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.146)			CTTCAGTCAGTGCTGTCAGGG	0.711													3	5	---	---	---	---	PASS
FREM1	158326	broad.mit.edu	37	9	14737487	14737487	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14737487C>A	uc003zlm.2	-	37	7037	c.6447G>T	c.(6445-6447)AAG>AAT	p.K2149N	FREM1_uc010mic.2_RNA|FREM1_uc003zlk.2_RNA|FREM1_uc003zll.2_Missense_Mutation_p.K685N	NM_144966	NP_659403	Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1 precursor	2149	C-type lectin.				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)		AAACACAGCTCTTTCCAAGCT	0.473													3	53	---	---	---	---	PASS
PCSK5	5125	broad.mit.edu	37	9	78790192	78790192	+	Intron	SNP	C	G	G			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78790192C>G	uc004ajz.2	+						PCSK5_uc004ajy.2_Missense_Mutation_p.R683G|PCSK5_uc004aka.2_Intron	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						ggaatggaatcgaatcgaatc	0.129													3	11	---	---	---	---	PASS
AGTPBP1	23287	broad.mit.edu	37	9	88207597	88207597	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88207597C>T	uc011ltd.1	-	18	2479	c.2446G>A	c.(2446-2448)GTT>ATT	p.V816I	AGTPBP1_uc004aod.3_Missense_Mutation_p.V442I|AGTPBP1_uc011ltc.1_Intron|AGTPBP1_uc010mqc.2_Missense_Mutation_p.V776I|AGTPBP1_uc011lte.1_Missense_Mutation_p.V828I	NM_015239	NP_056054	Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	816					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						CCTGCAGCAACTGAACTTCTT	0.318													78	294	---	---	---	---	PASS
SYK	6850	broad.mit.edu	37	9	93624627	93624627	+	Splice_Site	SNP	G	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93624627G>A	uc004aqz.2	+	4	922	c.717_splice	c.e4+1	p.Q239_splice	SYK_uc004aqy.2_Splice_Site_p.Q239_splice|SYK_uc004ara.2_Splice_Site_p.Q239_splice|SYK_uc004arb.2_Splice_Site_p.Q239_splice|SYK_uc004arc.2_Splice_Site_p.Q239_splice|SYK_uc011ltr.1_Intron|SYK_uc011lts.1_Intron|SYK_uc011ltt.1_Splice_Site	NM_003177	NP_003168	P43405	KSYK_HUMAN	spleen tyrosine kinase isoform 1						cell proliferation|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte cell-cell adhesion|neutrophil chemotaxis|organ morphogenesis|platelet activation|protein complex assembly	cytosol|T cell receptor complex	ATP binding|integrin binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|skin(1)	5						GCTCTGGCAGGTACCCAGCCT	0.582			T	ETV6|ITK	MDS|peripheral T-cell lymphoma								4	26	---	---	---	---	PASS
SMC2	10592	broad.mit.edu	37	9	106877025	106877025	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106877025T>C	uc004bbv.2	+	13	1874	c.1586T>C	c.(1585-1587)CTG>CCG	p.L529P	SMC2_uc004bbu.1_Missense_Mutation_p.L529P|SMC2_uc004bbw.2_Missense_Mutation_p.L529P|SMC2_uc011lvl.1_Missense_Mutation_p.L529P|SMC2_uc004bbx.2_Missense_Mutation_p.L529P	NM_001042551	NP_001036016	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	529	Flexible hinge.				cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism	condensin complex|cytoplasm|nuclear chromosome	ATP binding|protein heterodimerization activity			ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1)	9						GTGGCTTCTCTGATTAGTGTG	0.353													8	69	---	---	---	---	PASS
CAMK1D	57118	broad.mit.edu	37	10	12595350	12595350	+	Silent	SNP	G	T	T	rs56079552		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12595350G>T	uc001ilo.2	+	2	454	c.219G>T	c.(217-219)CTG>CTT	p.L73L	CAMK1D_uc001iln.2_Silent_p.L73L	NM_153498	NP_705718	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID	73	Protein kinase.					calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)		TAGCCGTCCTGAGAAAGTAAG	0.577													9	82	---	---	---	---	PASS
CLRN3	119467	broad.mit.edu	37	10	129682164	129682164	+	Intron	SNP	T	C	C			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129682164T>C	uc001lka.1	-						CLRN3_uc001ljz.1_Missense_Mutation_p.M1V	NM_152311	NP_689524	Q8NCR9	CLRN3_HUMAN	clarin 3							integral to membrane				skin(1)	1		all_epithelial(44;0.00168)|all_lung(145;0.0586)|Lung NSC(174;0.0765)|all_neural(114;0.201)|Glioma(114;0.222)|Colorectal(57;0.235)				TGTGAGTGCATAGCACATAAT	0.428													24	33	---	---	---	---	PASS
NOX4	50507	broad.mit.edu	37	11	89075257	89075257	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89075257A>C	uc001pct.2	-	14	1561	c.1322T>G	c.(1321-1323)ATA>AGA	p.I441R	NOX4_uc009yvr.2_Missense_Mutation_p.I416R|NOX4_uc001pcu.2_Missense_Mutation_p.I367R|NOX4_uc001pcw.2_Missense_Mutation_p.I134R|NOX4_uc001pcx.2_Intron|NOX4_uc001pcv.2_Intron|NOX4_uc009yvo.2_RNA|NOX4_uc010rtu.1_Missense_Mutation_p.I275R|NOX4_uc009yvp.2_Intron|NOX4_uc010rtv.1_Intron|NOX4_uc009yvq.2_Missense_Mutation_p.I417R	NM_016931	NP_058627	Q9NPH5	NOX4_HUMAN	NADPH oxidase 4 isoform a	441	Helical; (Potential).|Mediates interaction with TLR4.				cell aging|cell morphogenesis|inflammatory response|negative regulation of cell proliferation|superoxide anion generation	endoplasmic reticulum membrane|focal adhesion|integral to membrane|nucleus	electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|nucleotide binding|oxygen sensor activity			ovary(1)|central_nervous_system(1)	2		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				GGTGTTGAGTATTGATGCAAA	0.368													15	62	---	---	---	---	PASS
HEPHL1	341208	broad.mit.edu	37	11	93797666	93797666	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93797666C>A	uc001pep.2	+	4	955	c.798C>A	c.(796-798)AAC>AAA	p.N266K		NM_001098672	NP_001092142	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1 precursor	266	Plastocyanin-like 2.|Extracellular (Potential).				copper ion transport	integral to membrane	copper ion binding|oxidoreductase activity			ovary(3)	3		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				AGAGGAGTAACAAAATGCATG	0.383													11	55	---	---	---	---	PASS
CD4	920	broad.mit.edu	37	12	6923323	6923323	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6923323A>T	uc001qqv.1	+	4	475	c.230A>T	c.(229-231)AAT>ATT	p.N77I	CD4_uc009zez.1_Missense_Mutation_p.N22I|CD4_uc009zfa.1_RNA|CD4_uc009zfb.1_RNA|CD4_uc010sfj.1_5'UTR|CD4_uc009zfc.1_5'UTR|CD4_uc010sfk.1_5'UTR|CD4_uc010sfl.1_5'UTR|CD4_uc010sfm.1_5'UTR	NM_000616	NP_000607	P01730	CD4_HUMAN	CD4 antigen precursor	77	Extracellular (Potential).|Ig-like V-type.				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)				TCCAAGCTGAATGATCGCGCT	0.512													23	239	---	---	---	---	PASS
GPR19	2842	broad.mit.edu	37	12	12815272	12815272	+	Silent	SNP	G	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12815272G>A	uc001rar.3	-	2	304	c.111C>T	c.(109-111)AGC>AGT	p.S37S	GPR19_uc001raq.2_Silent_p.S37S	NM_006143	NP_006134	Q15760	GPR19_HUMAN	G protein-coupled receptor 19	37	Extracellular (Potential).					integral to plasma membrane	G-protein coupled receptor activity			ovary(1)	1		Prostate(47;0.0802)		BRCA - Breast invasive adenocarcinoma(232;0.048)		TCAGGTATTGGCTTGGCAGAG	0.502													64	99	---	---	---	---	PASS
RDH5	5959	broad.mit.edu	37	12	56115013	56115013	+	Silent	SNP	G	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56115013G>A	uc001shk.2	+	2	228	c.45G>A	c.(43-45)CTG>CTA	p.L15L	BLOC1S1_uc001shj.3_Intron|RDH5_uc010spt.1_Silent_p.L15L|RDH5_uc010spu.1_Intron|RDH5_uc001shl.2_Silent_p.L15L	NM_002905	NP_002896	Q92781	RDH1_HUMAN	retinol dehydrogenase 5 (11-cis and 9-cis)	15					response to stimulus|visual perception	membrane	binding|retinol dehydrogenase activity			ovary(1)	1					NADH(DB00157)|Vitamin A(DB00162)	GGGCAGTGCTGTGGTTGCTCA	0.607											OREG0021907	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	77	---	---	---	---	PASS
CS	1431	broad.mit.edu	37	12	56668847	56668847	+	Missense_Mutation	SNP	T	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56668847T>A	uc001sks.1	-	8	1047	c.857A>T	c.(856-858)TAC>TTC	p.Y286F	CS_uc010sql.1_Missense_Mutation_p.Y273F|CS_uc001skr.1_Missense_Mutation_p.Y220F|CS_uc001skt.1_Missense_Mutation_p.Y241F|CS_uc010sqm.1_Intron	NM_004077	NP_004068	O75390	CISY_HUMAN	citrate synthase precursor	286					cellular carbohydrate metabolic process|tricarboxylic acid cycle	mitochondrial matrix	citrate (Si)-synthase activity				0		Myeloproliferative disorder(1001;0.000374)		BRCA - Breast invasive adenocarcinoma(357;6.17e-07)		AAAGGACAGGTAAGGGTCGGA	0.522													32	68	---	---	---	---	PASS
C12orf51	283450	broad.mit.edu	37	12	112673071	112673071	+	Splice_Site	SNP	C	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112673071C>A	uc009zwc.2	-	30	4478	c.4460_splice	c.e30-1	p.G1487_splice		NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2						GTCTGACATCCTTTAAGCAAA	0.403													27	51	---	---	---	---	PASS
CIT	11113	broad.mit.edu	37	12	120151395	120151395	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120151395C>A	uc001txi.1	-	33	4292	c.4239G>T	c.(4237-4239)TTG>TTT	p.L1413F	CIT_uc001txh.1_Missense_Mutation_p.L932F|CIT_uc001txj.1_Missense_Mutation_p.L1455F	NM_007174	NP_009105	O14578	CTRO_HUMAN	citron	1413					intracellular signal transduction		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity			ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1)	10	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		ATTCAGCAGGCAAGCCGCAGG	0.577													4	45	---	---	---	---	PASS
LOC284232	284232	broad.mit.edu	37	13	19435836	19435836	+	RNA	SNP	A	C	C			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19435836A>C	uc010tcj.1	-	1		c.10274T>G				NR_027995				Homo sapiens ankyrin repeat domain 20 family, member A2 pseudogene (LOC284232), non-coding RNA.												0						aagtttgagaacagcttggga	0.144													3	15	---	---	---	---	PASS
LTB4R	1241	broad.mit.edu	37	14	24785098	24785098	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24785098G>C	uc001wos.2	+	2	562	c.241G>C	c.(241-243)GGC>CGC	p.G81R	LTB4R_uc010alp.2_Missense_Mutation_p.G81R|LTB4R_uc001wou.2_Missense_Mutation_p.G81R	NM_001143919	NP_001137391	Q15722	LT4R1_HUMAN	leukotriene B4 receptor	81	Extracellular (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|cellular component movement|immune response|inflammatory response|muscle contraction	integral to plasma membrane	nucleotide binding				0				GBM - Glioblastoma multiforme(265;0.018)		CCTGGCCCAAGGCACCTGGAG	0.587													6	131	---	---	---	---	PASS
ACOT2	10965	broad.mit.edu	37	14	74036025	74036025	+	Silent	SNP	C	G	G			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74036025C>G	uc001xon.3	+	1	254	c.81C>G	c.(79-81)GTC>GTG	p.V27V	ACOT1_uc010tuc.1_Intron|ACOT2_uc001xom.2_5'UTR	NM_006821	NP_006812	P49753	ACOT2_HUMAN	acyl-CoA thioesterase 2	27					acyl-CoA metabolic process|long-chain fatty acid metabolic process|very long-chain fatty acid metabolic process	mitochondrion	carboxylesterase activity|palmitoyl-CoA hydrolase activity|protein binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0033)|OV - Ovarian serous cystadenocarcinoma(108;0.0639)		CTCCTGCTGTCCTTCGAGCGT	0.557													80	169	---	---	---	---	PASS
C14orf148	122945	broad.mit.edu	37	14	77880341	77880341	+	Silent	SNP	C	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77880341C>T	uc001xtr.2	-	2	432	c.285G>A	c.(283-285)CTG>CTA	p.L95L	C14orf148_uc010tvi.1_Silent_p.L95L	NM_001113475	NP_001106946	Q6NXP6	CN148_HUMAN	hypothetical protein LOC122945 isoform 1	95					proline biosynthetic process		binding|pyrroline-5-carboxylate reductase activity				0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0277)		CAAGCTGCAGCAGTGTGCCAG	0.572													12	18	---	---	---	---	PASS
TNFAIP2	7127	broad.mit.edu	37	14	103601714	103601714	+	3'UTR	SNP	A	C	C			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103601714A>C	uc001ymm.1	+	11					TNFAIP2_uc010awo.1_3'UTR|TNFAIP2_uc010txz.1_3'UTR|TNFAIP2_uc010tya.1_Intron	NM_006291	NP_006282	Q03169	TNAP2_HUMAN	tumor necrosis factor, alpha-induced protein 2						angiogenesis|cell differentiation	extracellular space				central_nervous_system(1)	1		Melanoma(154;0.155)	Epithelial(46;0.191)			CTGTGGCCTGACCTGCCTGTG	0.607													8	57	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106311904	106311904	+	RNA	SNP	C	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106311904C>T	uc010tyt.1	-	3608		c.57019G>A			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Intron|uc001ysf.2_Intron|uc001ysj.2_Silent_p.T50T|uc001ysk.1_Silent_p.T50T|uc001ysl.1_Silent_p.T50T|uc001ysm.1_5'UTR|uc001ysn.1_5'UTR|uc001yso.1_5'UTR					Parts of antibodies, mostly variable regions.												0						CAGTCACGGACGTTGGGTGGT	0.557													25	73	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	34113725	34113725	+	Silent	SNP	T	G	G			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34113725T>G	uc001zhi.2	+	80	10987	c.10917T>G	c.(10915-10917)GGT>GGG	p.G3639G	RYR3_uc010bar.2_Silent_p.G3634G	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	3639					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)		CCATGGCAGGTGAGATGAGCC	0.517													9	31	---	---	---	---	PASS
RPAP1	26015	broad.mit.edu	37	15	41813028	41813028	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41813028C>T	uc001zod.2	-	22	3480	c.3356G>A	c.(3355-3357)GGA>GAA	p.G1119E	RPAP1_uc001zoc.2_Missense_Mutation_p.G138E	NM_015540	NP_056355	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	1119	Leu-rich.					nucleus	DNA binding|DNA-directed RNA polymerase activity			large_intestine(1)	1		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		GGGAGAGAGTCCCGAGGGGGT	0.662													20	30	---	---	---	---	PASS
DUOXA1	90527	broad.mit.edu	37	15	45412823	45412823	+	Missense_Mutation	SNP	C	A	A	rs147223934	byFrequency	TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45412823C>A	uc001zuq.1	-	4	550	c.521G>T	c.(520-522)CGC>CTC	p.R174L	DUOXA1_uc010uem.1_Missense_Mutation_p.R129L|DUOXA1_uc001zup.2_Missense_Mutation_p.R174L|DUOXA1_uc010bec.2_Missense_Mutation_p.R174L|DUOXA1_uc001zur.1_Missense_Mutation_p.R129L|DUOXA1_uc010bed.1_Missense_Mutation_p.R129L	NM_144565	NP_653166	Q1HG43	DOXA1_HUMAN	Numb-interacting protein	174	Extracellular (Potential).				protein transport	endoplasmic reticulum membrane|integral to membrane				ovary(1)	1		all_cancers(109;6.02e-08)|all_epithelial(112;1.83e-06)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.82e-18)|GBM - Glioblastoma multiforme(94;4.39e-07)|COAD - Colon adenocarcinoma(120;0.0676)|Colorectal(133;0.0686)		TCCCGCCAGGCGGTACTGGCG	0.572													27	109	---	---	---	---	PASS
DUOXA1	90527	broad.mit.edu	37	15	45412824	45412824	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45412824G>A	uc001zuq.1	-	4	549	c.520C>T	c.(520-522)CGC>TGC	p.R174C	DUOXA1_uc010uem.1_Missense_Mutation_p.R129C|DUOXA1_uc001zup.2_Missense_Mutation_p.R174C|DUOXA1_uc010bec.2_Missense_Mutation_p.R174C|DUOXA1_uc001zur.1_Missense_Mutation_p.R129C|DUOXA1_uc010bed.1_Missense_Mutation_p.R129C	NM_144565	NP_653166	Q1HG43	DOXA1_HUMAN	Numb-interacting protein	174	Extracellular (Potential).				protein transport	endoplasmic reticulum membrane|integral to membrane				ovary(1)	1		all_cancers(109;6.02e-08)|all_epithelial(112;1.83e-06)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.82e-18)|GBM - Glioblastoma multiforme(94;4.39e-07)|COAD - Colon adenocarcinoma(120;0.0676)|Colorectal(133;0.0686)		CCCGCCAGGCGGTACTGGCGG	0.577													28	108	---	---	---	---	PASS
HERC1	8925	broad.mit.edu	37	15	64045102	64045102	+	Intron	SNP	G	C	C			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64045102G>C	uc002amp.2	-						HERC1_uc010uil.1_Intron|HERC1_uc010bgt.1_3'UTR	NM_003922	NP_003913	Q15751	HERC1_HUMAN	hect domain and RCC1-like domain 1						protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(6)|breast(6)|lung(5)|central_nervous_system(2)	19						TTACTTTTTAGTCACCTAATC	0.333													32	98	---	---	---	---	PASS
CASKIN1	57524	broad.mit.edu	37	16	2233883	2233883	+	Silent	SNP	G	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2233883G>A	uc010bsg.1	-	15	1508	c.1476C>T	c.(1474-1476)AAC>AAT	p.N492N		NM_020764	NP_065815	Q8WXD9	CSKI1_HUMAN	CASK interacting protein 1	492	SAM 1.				signal transduction	cytoplasm				skin(2)	2						CGCTGATGAAGTTGGGGGCGT	0.672													5	34	---	---	---	---	PASS
ARHGAP17	55114	broad.mit.edu	37	16	24942263	24942263	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24942263G>T	uc002dnb.2	-	19	2450	c.2357C>A	c.(2356-2358)ACT>AAT	p.T786N	ARHGAP17_uc002dmx.2_Missense_Mutation_p.T48N|ARHGAP17_uc002dmw.2_Missense_Mutation_p.T48N|ARHGAP17_uc002dmy.2_Missense_Mutation_p.T231N|ARHGAP17_uc002dmz.2_Missense_Mutation_p.T310N|ARHGAP17_uc002dna.2_Missense_Mutation_p.T513N|ARHGAP17_uc002dnc.2_Missense_Mutation_p.T708N|ARHGAP17_uc010vcf.1_Missense_Mutation_p.T529N|ARHGAP17_uc002dne.1_Missense_Mutation_p.T48N	NM_001006634	NP_001006635	Q68EM7	RHG17_HUMAN	nadrin isoform 1	786	Pro-rich.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|tight junction	GTPase activator activity|SH3 domain binding				0				GBM - Glioblastoma multiforme(48;0.0407)		TGGCTGTGCAGTTTCAGGGTT	0.637													36	88	---	---	---	---	PASS
CHD9	80205	broad.mit.edu	37	16	53308192	53308192	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53308192G>A	uc002ehb.2	+	23	5109	c.4945G>A	c.(4945-4947)GTA>ATA	p.V1649I	CHD9_uc002egy.2_Missense_Mutation_p.V1649I|CHD9_uc002ehc.2_Missense_Mutation_p.V1649I|CHD9_uc002ehf.2_Missense_Mutation_p.V763I|CHD9_uc010cbw.2_Missense_Mutation_p.V17I	NM_025134	NP_079410	Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	1649					cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleoplasm	ATP binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)				GTGTCAGAAAGTATTTGATGG	0.234													3	33	---	---	---	---	PASS
CES3	23491	broad.mit.edu	37	16	67005096	67005096	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67005096C>G	uc002eqt.2	+	10	1238	c.1165C>G	c.(1165-1167)CCC>GCC	p.P389A	CES3_uc010cdz.2_Missense_Mutation_p.P389A|CES3_uc010cea.2_Intron|CES3_uc010viw.1_Missense_Mutation_p.P28A	NM_024922	NP_079198	Q6UWW8	EST3_HUMAN	carboxylesterase 3 precursor	389						endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity			ovary(3)|central_nervous_system(2)	5		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0488)|Epithelial(162;0.127)		TGAGATGATGCCCACCGTCAT	0.562													5	69	---	---	---	---	PASS
THAP11	57215	broad.mit.edu	37	16	67877045	67877045	+	Silent	SNP	T	C	C			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67877045T>C	uc002euo.2	+	1	833	c.588T>C	c.(586-588)TTT>TTC	p.F196F	CENPT_uc002eun.3_Intron	NM_020457	NP_065190	Q96EK4	THA11_HUMAN	THAP domain containing 11	196					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|identical protein binding|metal ion binding				0		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118)		AAGTGGAGTTTGCAGCCGCAG	0.662													7	68	---	---	---	---	PASS
DULLARD	23399	broad.mit.edu	37	17	7147938	7147938	+	Silent	SNP	G	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7147938G>T	uc002gfd.2	-	7	986	c.606C>A	c.(604-606)ATC>ATA	p.I202I	GABARAP_uc002gfb.2_5'Flank|DULLARD_uc002gfe.2_Silent_p.I202I|DULLARD_uc002gff.2_Silent_p.I202I|DULLARD_uc002gfc.2_RNA	NM_001143775	NP_001137247	O95476	CNEP1_HUMAN	dullard homolog	202	FCP1 homology.				nuclear envelope organization|protein dephosphorylation	endoplasmic reticulum membrane|integral to membrane|nuclear membrane	protein serine/threonine phosphatase activity				0						ACCAGGATTTGATGGGGATGG	0.498													9	82	---	---	---	---	PASS
FXR2	9513	broad.mit.edu	37	17	7508978	7508978	+	Silent	SNP	T	C	C			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7508978T>C	uc002gia.1	-	3	440	c.213A>G	c.(211-213)GAA>GAG	p.E71E	FXR2_uc010vud.1_Silent_p.E71E	NM_004860	NP_004851	P51116	FXR2_HUMAN	fragile X mental retardation syndrome related	71						cytosolic large ribosomal subunit	protein binding|RNA binding	p.?(1)			0				READ - Rectum adenocarcinoma(115;0.17)		CTTCATCCCCTTCTGTGATCT	0.448													9	24	---	---	---	---	PASS
FAM18B	51030	broad.mit.edu	37	17	18708991	18708991	+	3'UTR	SNP	C	G	G	rs140288428	by1000genomes	TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18708991C>G	uc002gum.2	+	7					FAM18B_uc002gun.2_3'UTR	NM_016078	NP_057162	Q9NYZ1	F18B1_HUMAN	hypothetical protein LOC51030							integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (53;0.0872)|READ - Rectum adenocarcinoma(1115;0.0967)		CTTTGTTTTTCCACTTAAAAA	0.353													3	52	---	---	---	---	PASS
SLFN5	162394	broad.mit.edu	37	17	33585670	33585670	+	5'UTR	SNP	G	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33585670G>A	uc002hjf.3	+	2					SLFN5_uc002hje.2_5'UTR|SLFN5_uc010wcg.1_5'UTR	NM_144975	NP_659412	Q08AF3	SLFN5_HUMAN	schlafen family member 5						cell differentiation		ATP binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0191)		TGTTTTTCAGGAGAACATTTC	0.418													26	64	---	---	---	---	PASS
LHX1	3975	broad.mit.edu	37	17	35299577	35299577	+	Silent	SNP	C	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35299577C>T	uc002hnh.1	+	4	1752	c.756C>T	c.(754-756)TTC>TTT	p.F252F		NM_005568	NP_005559	P48742	LHX1_HUMAN	LIM homeobox protein 1	252					cerebellar Purkinje cell differentiation|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation|cervix development|comma-shaped body morphogenesis|dorsal/ventral pattern formation|ectoderm formation|embryonic pattern specification|embryonic retina morphogenesis in camera-type eye|embryonic viscerocranium morphogenesis|endoderm formation|forebrain regionalization|head development|motor axon guidance|negative regulation of transcription, DNA-dependent|nephric duct morphogenesis|nephron tubule epithelial cell differentiation|neuron migration|oviduct epithelium development|paramesonephric duct development|positive regulation of anterior head development|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of embryonic development|positive regulation of gastrulation|positive regulation of transcription, DNA-dependent|post-embryonic development|primitive streak formation|renal vesicle morphogenesis|retina layer formation|S-shaped body morphogenesis|spinal cord association neuron differentiation|transcription from RNA polymerase II promoter|ureteric bud development|uterine epithelium development|vagina development	nucleus|protein complex	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(25;0.00607)				ACGCCTTCTTCCGCAGTCCGC	0.711													2	1	---	---	---	---	PASS
ITGA3	3675	broad.mit.edu	37	17	48148238	48148238	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48148238G>T	uc010dbl.2	+	5	1159	c.695G>T	c.(694-696)TGG>TTG	p.W232L	ITGA3_uc010dbm.2_Missense_Mutation_p.W232L	NM_002204	NP_002195	P26006	ITA3_HUMAN	integrin alpha 3 isoform a precursor	232	FG-GAP 3.|Extracellular (Potential).				blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|leukocyte migration	cell surface|integrin complex	protein binding|receptor activity			ovary(2)|pancreas(1)	3						CGCAAGGAGTGGGACTTATCT	0.493													45	182	---	---	---	---	PASS
MARCH10	162333	broad.mit.edu	37	17	60802312	60802312	+	Silent	SNP	C	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60802312C>A	uc010ddr.2	-	7	2329	c.2091G>T	c.(2089-2091)GTG>GTT	p.V697V	MARCH10_uc002jag.3_Silent_p.V697V|MARCH10_uc010dds.2_Silent_p.V735V|MARCH10_uc002jah.2_Silent_p.V696V|uc002jaj.1_Intron|uc002jak.2_Intron	NM_001100875	NP_001094345	Q8NA82	MARHA_HUMAN	ring finger protein 190	697	RING-CH-type.						ligase activity|zinc ion binding				0						ATGTTATTTTCACTTTCAGCC	0.547													43	118	---	---	---	---	PASS
DDX5	1655	broad.mit.edu	37	17	62496043	62496043	+	Nonstop_Mutation	SNP	A	G	G			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62496043A>G	uc002jek.2	-	13	2090	c.1843T>C	c.(1843-1845)TAA>CAA	p.*615Q	POLG2_uc002jei.2_5'Flank|POLG2_uc010deg.1_5'Flank|DDX5_uc010deh.2_Nonstop_Mutation_p.*615Q|DDX5_uc002jej.2_Nonstop_Mutation_p.*510Q|DDX5_uc010wqa.1_Nonstop_Mutation_p.*536Q	NM_004396	NP_004387	P17844	DDX5_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5	615					cell growth|regulation of alternative nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nucleolus	ATP binding|ATP-dependent helicase activity|mRNA binding|protein binding|RNA helicase activity|transcription cofactor activity			ovary(2)|lung(1)	3	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)			CTAAAGTCTTATTGGGAATAT	0.353			T	ETV4	prostate								9	79	---	---	---	---	PASS
SPHK1	8877	broad.mit.edu	37	17	74383680	74383680	+	3'UTR	SNP	G	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74383680G>A	uc002jrf.1	+	8					SPHK1_uc002jrg.1_3'UTR|SPHK1_uc002jrh.2_3'UTR|SPHK1_uc002jrj.2_3'UTR|SPHK1_uc002jri.2_3'UTR|SPHK1_uc002jrk.3_3'UTR|uc010wtd.1_5'Flank	NM_001142602	NP_001136074	Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1 isoform 3						'de novo' posttranslational protein folding|activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|anti-apoptosis|calcium-mediated signaling|positive regulation of angiogenesis|positive regulation of cell growth|positive regulation of cell migration|positive regulation of fibroblast proliferation|positive regulation of mitotic cell cycle|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|positive regulation of smooth muscle contraction|regulation of tumor necrosis factor-mediated signaling pathway|sphingoid catabolic process|sphingosine metabolic process	cytosol|membrane fraction|nucleus|plasma membrane|soluble fraction	ATP binding|calmodulin binding|D-erythro-sphingosine kinase activity|diacylglycerol kinase activity|DNA binding|magnesium ion binding|protein phosphatase 2A binding|sphinganine kinase activity			kidney(1)	1						CCTGGGCCGCGCTGTGCCTTA	0.632													3	26	---	---	---	---	PASS
RIOK3	8780	broad.mit.edu	37	18	21059323	21059323	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21059323G>A	uc002kui.3	+	12	2004	c.1387G>A	c.(1387-1389)GAA>AAA	p.E463K	RIOK3_uc010dls.2_Missense_Mutation_p.E460K|RIOK3_uc010xas.1_Missense_Mutation_p.E447K|RIOK3_uc010xat.1_Missense_Mutation_p.E207K	NM_003831	NP_003822	O14730	RIOK3_HUMAN	sudD suppressor of bimD6 homolog	463	Protein kinase.				chromosome segregation		ATP binding|protein binding|protein serine/threonine kinase activity			ovary(2)|central_nervous_system(1)	3	all_cancers(21;0.000106)|all_epithelial(16;6.74e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TAGTGAACGAGAACTCTTCAA	0.373													7	83	---	---	---	---	PASS
ZNF532	55205	broad.mit.edu	37	18	56587466	56587466	+	Silent	SNP	T	C	C			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56587466T>C	uc002lho.2	+	4	2494	c.1947T>C	c.(1945-1947)TGT>TGC	p.C649C	ZNF532_uc002lhp.2_Silent_p.C647C|ZNF532_uc010xeg.1_Silent_p.C647C|ZNF532_uc002lhr.2_Silent_p.C647C|ZNF532_uc002lhs.2_Silent_p.C647C	NM_018181	NP_060651	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	649					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)|skin(1)	2						GCAACCATTGTACAAAGAACC	0.483													9	80	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9076252	9076252	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9076252A>T	uc002mkp.2	-	3	11398	c.11194T>A	c.(11194-11196)TCT>ACT	p.S3732T		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	3733	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						GTGGACAGAGAATCAAACAGA	0.493													27	87	---	---	---	---	PASS
LRFN3	79414	broad.mit.edu	37	19	36435683	36435683	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36435683C>A	uc002oco.2	+	3	2101	c.1649C>A	c.(1648-1650)TCG>TAG	p.S550*		NM_024509	NP_078785	Q9BTN0	LRFN3_HUMAN	leucine rich repeat and fibronectin type III	550	Helical; (Potential).				cell adhesion	axon|cell junction|dendrite|integral to membrane|postsynaptic membrane|presynaptic membrane					0	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			ATCGTAGCCTCGGTACTGGTC	0.667													3	22	---	---	---	---	PASS
ZFP112	7771	broad.mit.edu	37	19	44833609	44833609	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44833609A>G	uc010ejj.2	-	5	832	c.719T>C	c.(718-720)ATC>ACC	p.I240T	ZFP112_uc002ozc.3_Missense_Mutation_p.I234T|ZFP112_uc010xwy.1_Missense_Mutation_p.I257T|ZFP112_uc010xwz.1_Missense_Mutation_p.I239T	NM_001083335	NP_001076804	Q9UJU3	ZF112_HUMAN	zinc finger protein 228 isoform 1	240					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)	5						TACCTTCATGATATCTTCTCC	0.408													45	142	---	---	---	---	PASS
KIR3DX1	90011	broad.mit.edu	37	19	55048123	55048123	+	5'UTR	SNP	G	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55048123G>A	uc010erm.2	+	1					KIR3DX1_uc010yfa.1_RNA|KIR3DX1_uc010yfb.1_RNA|KIR3DX1_uc010yfc.1_RNA|KIR3DX1_uc010yfd.1_RNA					Homo sapiens killer cell immunoglobulin-like receptor, three domains, X1, mRNA (cDNA clone IMAGE:4849085).											ovary(1)	1				GBM - Glioblastoma multiforme(193;0.099)		CCACCCAGGTGGACCCCATGA	0.478											OREG0003665	type=REGULATORY REGION|Gene=BC033195|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	5	63	---	---	---	---	PASS
NLRP7	199713	broad.mit.edu	37	19	55450880	55450880	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55450880T>C	uc002qih.3	-	4	1383	c.1307A>G	c.(1306-1308)GAA>GGA	p.E436G	NLRP7_uc002qig.3_Missense_Mutation_p.E436G|NLRP7_uc002qii.3_Missense_Mutation_p.E436G|NLRP7_uc010esk.2_Missense_Mutation_p.E436G|NLRP7_uc010esl.2_Missense_Mutation_p.E464G	NM_206828	NP_996611	Q8WX94	NALP7_HUMAN	NACHT, leucine rich repeat and PYD containing 7	436	NACHT.						ATP binding			large_intestine(1)|breast(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(193;0.0325)		CCCGAGCCTTTCCAGGTCCTC	0.677													5	43	---	---	---	---	PASS
PANK2	80025	broad.mit.edu	37	20	3899360	3899360	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3899360A>C	uc002wkc.2	+	6	1585	c.1579A>C	c.(1579-1581)AAT>CAT	p.N527H	PANK2_uc002wkb.2_Missense_Mutation_p.N236H|PANK2_uc002wkd.2_RNA|PANK2_uc002wke.2_Missense_Mutation_p.N236H|PANK2_uc002wkf.2_Missense_Mutation_p.N91H|MIR103-2AS_hsa-mir-103-2-as|MI0007262_5'Flank	NM_153638	NP_705902	Q9BZ23	PANK2_HUMAN	pantothenate kinase 2 isoform 1 preproprotein	527					cell death|coenzyme A biosynthetic process|pantothenate metabolic process	mitochondrial intermembrane space|nucleus	ATP binding|pantothenate kinase activity|protein binding				0						CTTGAGAATTAATACGATCGC	0.378													33	292	---	---	---	---	PASS
SMOX	54498	broad.mit.edu	37	20	4164251	4164251	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4164251G>A	uc002wkm.1	+	6	1681	c.1480G>A	c.(1480-1482)GTG>ATG	p.V494M	SMOX_uc002wkk.1_Missense_Mutation_p.V441M|SMOX_uc002wkl.1_Missense_Mutation_p.V441M|SMOX_uc002wkn.1_Intron|SMOX_uc002wkp.2_Missense_Mutation_p.V494M|SMOX_uc010zqo.1_Missense_Mutation_p.V418M|SMOX_uc002wko.1_Missense_Mutation_p.V494M	NM_175839	NP_787033	Q9NWM0	SMOX_HUMAN	spermine oxidase isoform 1	494					polyamine biosynthetic process|xenobiotic metabolic process	cytosol|nucleus	polyamine oxidase activity			breast(1)	1					Spermine(DB00127)	CGGGGCGGATGTGGAGAAGCT	0.597													5	31	---	---	---	---	PASS
PAK7	57144	broad.mit.edu	37	20	9520140	9520140	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9520140A>T	uc002wnl.2	-	11	2674	c.2129T>A	c.(2128-2130)GTC>GAC	p.V710D	PAK7_uc002wnk.2_Missense_Mutation_p.V710D|PAK7_uc002wnj.2_Missense_Mutation_p.V710D|PAK7_uc010gby.1_Missense_Mutation_p.V623D	NM_020341	NP_065074	Q9P286	PAK7_HUMAN	p21-activated kinase 7	710							ATP binding|protein binding|protein serine/threonine kinase activity			lung(11)|skin(5)|central_nervous_system(3)|ovary(2)|large_intestine(1)|stomach(1)	23			COAD - Colon adenocarcinoma(9;0.194)			CATGAGGGGGACGATGCAAGA	0.493													101	208	---	---	---	---	PASS
DEFB116	245930	broad.mit.edu	37	20	29891069	29891069	+	Silent	SNP	G	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29891069G>A	uc010ztm.1	-	2	255	c.255C>T	c.(253-255)TAC>TAT	p.Y85Y		NM_001037731	NP_001032820	Q30KQ4	DB116_HUMAN	beta-defensin 116 precursor	85					defense response to bacterium	extracellular region					0	all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			AGTTAGAGTCGTAATCCTCCT	0.378													89	295	---	---	---	---	PASS
KCNB1	3745	broad.mit.edu	37	20	47989844	47989844	+	Silent	SNP	A	C	C			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47989844A>C	uc002xur.1	-	2	2417	c.2253T>G	c.(2251-2253)GGT>GGG	p.G751G	KCNB1_uc002xus.1_Silent_p.G751G	NM_004975	NP_004966	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related	751	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)			ACTGGTGGACACCCGCCTCAA	0.572													12	100	---	---	---	---	PASS
MCM3AP	8888	broad.mit.edu	37	21	47692476	47692476	+	Nonsense_Mutation	SNP	T	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47692476T>A	uc002zir.1	-	8	2500	c.2464A>T	c.(2464-2466)AGA>TGA	p.R822*		NM_003906	NP_003897	O60318	MCM3A_HUMAN	minichromosome maintenance complex component 3	822					DNA replication|protein import into nucleus	cytosol|nucleus	DNA binding|nucleotide binding			large_intestine(2)|lung(1)|ovary(1)|skin(1)	5	Breast(49;0.112)					AAAATTCACCTTAGGATGTCT	0.488													46	85	---	---	---	---	PASS
MN1	4330	broad.mit.edu	37	22	28192794	28192794	+	Silent	SNP	C	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28192794C>T	uc003adj.2	-	1	4693	c.3738G>A	c.(3736-3738)GCG>GCA	p.A1246A		NM_002430	NP_002421	Q10571	MN1_HUMAN	meningioma  1	1246							binding			central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	10						TCTCCCAGGGCGCCAACGTCT	0.622			T	ETV6	AML|meningioma								59	102	---	---	---	---	PASS
RPS19BP1	91582	broad.mit.edu	37	22	39925423	39925423	+	3'UTR	SNP	G	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39925423G>T	uc003ayb.2	-	4						NM_194326	NP_919307	Q86WX3	AROS_HUMAN	S19 binding protein							nucleolus|nucleoplasm					0	Melanoma(58;0.04)					CGCGCGGCACGGCCGGTTCCT	0.672											OREG0026578	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	2	6	---	---	---	---	PASS
MAP7D3	79649	broad.mit.edu	37	X	135314179	135314179	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135314179C>T	uc004ezt.2	-	8	1028	c.937G>A	c.(937-939)GTA>ATA	p.V313I	MAP7D3_uc004ezs.2_Missense_Mutation_p.V277I|MAP7D3_uc011mwc.1_Missense_Mutation_p.V295I|MAP7D3_uc010nsa.1_Missense_Mutation_p.V271I	NM_024597	NP_078873	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	313						cytoplasm|spindle				ovary(2)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;0.000127)					TTGCAGAATACTTCCACATTC	0.547													36	183	---	---	---	---	PASS
MAGEC1	9947	broad.mit.edu	37	X	140993825	140993825	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140993825G>C	uc004fbt.2	+	4	921	c.635G>C	c.(634-636)AGT>ACT	p.S212T	MAGEC1_uc010nsl.1_Intron	NM_005462	NP_005453	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	212							protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)					ACTTTATTGAGTATTTTCCAG	0.502										HNSCC(15;0.026)			22	211	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14033	14033	+	RNA	SNP	T	C	C			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14033T>C	uc004cox.3	+	1		c.1697T>C			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		ACCTAAAACAATTTCACAGCA	0.448													2	0	---	---	---	---	PASS
PPT1	5538	broad.mit.edu	37	1	40557538	40557538	+	Intron	DEL	A	-	-	rs11308805		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40557538delA	uc001cfb.2	-						PPT1_uc010ojf.1_Intron|PPT1_uc010ojg.1_Intron|PPT1_uc009vwa.2_Intron	NM_000310	NP_000301	P50897	PPT1_HUMAN	palmitoyl-protein thioesterase 1 isoform 1						brain development|cofactor metabolic process|cofactor transport|DNA fragmentation involved in apoptotic nuclear change|lysosomal lumen acidification|membrane raft organization|negative regulation of cell growth|negative regulation of neuron apoptosis|neuron development|pinocytosis|positive regulation of pinocytosis|positive regulation of receptor-mediated endocytosis|protein depalmitoylation|protein transport|receptor-mediated endocytosis|regulation of synapse structure and activity|sphingolipid catabolic process|visual perception	axon|cytosol|Golgi apparatus|lysosome|membrane fraction|membrane raft|nucleus|synaptic vesicle	palmitoyl-(protein) hydrolase activity|palmitoyl-CoA hydrolase activity			ovary(1)	1	Lung NSC(20;3.43e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1e-18)|Epithelial(16;3.6e-17)|all cancers(16;1.1e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			attctgtctcaaaaaaaaaaa	0.129													8	5	---	---	---	---	
CHI3L2	1117	broad.mit.edu	37	1	111772303	111772304	+	Intron	INS	-	AAAAAAA	AAAAAAA	rs61237890		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111772303_111772304insAAAAAAA	uc001eam.2	+						CHI3L2_uc001ean.2_Intron|CHI3L2_uc001eao.2_5'Flank|CHI3L2_uc009wga.2_5'Flank	NM_004000	NP_003991	Q15782	CH3L2_HUMAN	chitinase 3-like 2 isoform a						chitin catabolic process	extracellular space	cation binding|chitinase activity			central_nervous_system(1)	1		all_cancers(81;1.89e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0171)|Colorectal(144;0.0387)|all cancers(265;0.0464)|LUSC - Lung squamous cell carcinoma(189;0.0872)|Epithelial(280;0.0994)|COAD - Colon adenocarcinoma(174;0.141)		gactccgtctcaaaaaaaaaaa	0.193													10	6	---	---	---	---	
GDAP2	54834	broad.mit.edu	37	1	118429438	118429439	+	Intron	INS	-	ACA	ACA	rs143592216	by1000genomes	TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118429438_118429439insACA	uc001ehf.2	-						GDAP2_uc001ehg.2_Intron	NM_017686	NP_060156	Q9NXN4	GDAP2_HUMAN	ganglioside induced differentiation associated											ovary(2)	2		all_cancers(81;0.0156)|all_lung(203;5.81e-05)|Lung NSC(69;0.000446)|all_epithelial(167;0.00295)		Lung(183;0.0583)|LUSC - Lung squamous cell carcinoma(189;0.194)		CTACTCTGCAGACAACACCTAT	0.307													2	7	---	---	---	---	
NOTCH2	4853	broad.mit.edu	37	1	120542632	120542643	+	Intron	DEL	AAGGAAGGGAGA	-	-	rs61787008		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120542632_120542643delAAGGAAGGGAGA	uc001eik.2	-						NOTCH2_uc001eil.2_Intron|NOTCH2_uc001eim.3_Intron	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein						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)		ggaaggaaggaaggaagggagaaaggaaggaa	0.118			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				4	3	---	---	---	---	
TDRKH	11022	broad.mit.edu	37	1	151752734	151752780	+	Intron	DEL	TACTATCTATACAACCAGTCCTCAATTACTTTATATACAACCTCAGT	-	-	rs112300596		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151752734_151752780delTACTATCTATACAACCAGTCCTCAATTACTTTATATACAACCTCAGT	uc009wnb.1	-						TDRKH_uc001eyy.2_Intron|TDRKH_uc001ezb.3_Intron|TDRKH_uc001ezc.3_Intron|TDRKH_uc001eza.3_Intron|TDRKH_uc001ezd.3_Intron|TDRKH_uc010pdn.1_Intron	NM_006862	NP_006853	Q9Y2W6	TDRKH_HUMAN	tudor and KH domain containing isoform a								RNA binding			ovary(1)|pancreas(1)	2	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			AATTAGCTAATACTATCTATACAACCAGTCCTCAATTACTTTATATACAACCTCAGTTACTATCTAT	0.368													11	5	---	---	---	---	
ZNF638	27332	broad.mit.edu	37	2	71632977	71632999	+	Intron	DEL	GTGCATATTAAGTGGTCTAATAG	-	-	rs67651141		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71632977_71632999delGTGCATATTAAGTGGTCTAATAG	uc002shx.2	+						ZNF638_uc010yqw.1_Intron|ZNF638_uc002shy.2_Intron|ZNF638_uc002shz.2_Intron|ZNF638_uc002sia.2_Intron|ZNF638_uc002sib.1_Intron|ZNF638_uc010fed.2_Intron|ZNF638_uc002sic.2_Intron	NM_014497	NP_055312	Q14966	ZN638_HUMAN	zinc finger protein 638						RNA splicing	cytoplasm|nuclear speck	double-stranded DNA binding|nucleotide binding|RNA binding|zinc ion binding			pancreas(2)|ovary(1)|skin(1)	4						AGGTACTGGAGTGCATATTAAGTGGTCTAATAGGTCAATATCT	0.336													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	106984900	106984907	+	IGR	DEL	TTAATTTC	-	-	rs7570576		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106984900_106984907delTTAATTTC								UXS1 (174105 upstream) : PLGLA (17862 downstream)																							GAATGATGAATTAAtttctttttttttt	0.231													4	2	---	---	---	---	
R3HDM1	23518	broad.mit.edu	37	2	136433223	136433224	+	Intron	INS	-	TT	TT	rs72538400		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136433223_136433224insTT	uc002tuo.2	+						R3HDM1_uc010fni.2_Intron|R3HDM1_uc002tup.2_Intron|R3HDM1_uc010zbh.1_Intron	NM_015361	NP_056176	Q15032	R3HD1_HUMAN	R3H domain containing 1								nucleic acid binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.127)		ACTTTATAGTCAAGAGTTTTAT	0.277													6	3	---	---	---	---	
CYP20A1	57404	broad.mit.edu	37	2	204137273	204137274	+	Intron	INS	-	A	A	rs72103565		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204137273_204137274insA	uc002uzv.3	+						CYP20A1_uc002uzx.3_Intron|CYP20A1_uc010zif.1_Intron|CYP20A1_uc002uzy.3_Intron|CYP20A1_uc002uzw.3_Intron|CYP20A1_uc010ftw.2_Intron	NM_177538	NP_803882	Q6UW02	CP20A_HUMAN	cytochrome P450, family 20, subfamily A,							integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen				0						aaccctgactcaaaaaaaaaaa	0.104													3	3	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10191573	10191573	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191573delA	uc003bvc.2	+	3	779	c.566delA	c.(565-567)GAAfs	p.E189fs	VHL_uc003bvd.2_Frame_Shift_Del_p.E148fs	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	189					anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.E189K(3)|p.E189fs*12(2)|p.D187_N193del(1)|p.E189fs*27(1)|p.E189fs*25(1)|p.Y185fs*11(1)|p.E189fs*13(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GAAGATCTGGAAGACCACCCA	0.502		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				23	21	---	---	---	---	
ATP13A4	84239	broad.mit.edu	37	3	193180773	193180774	+	Intron	INS	-	A	A	rs9882995	by1000genomes	TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193180773_193180774insA	uc003ftd.2	-						ATP13A4_uc003fte.1_Intron|ATP13A4_uc011bsr.1_Intron|ATP13A4_uc010hzi.2_Intron|ATP13A4_uc003ftf.3_Intron	NM_032279	NP_115655	Q4VNC1	AT134_HUMAN	ATPase type 13A4						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(2)	2	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		ctccctattttaaaaaaaaaaa	0.158													4	2	---	---	---	---	
MUC4	4585	broad.mit.edu	37	3	195494493	195494495	+	Intron	DEL	CAC	-	-			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195494493_195494495delCAC	uc011bto.1	-						MUC4_uc003fuz.2_Intron|MUC4_uc003fva.2_Intron|MUC4_uc003fvb.2_Intron|MUC4_uc003fvc.2_Intron|MUC4_uc003fvd.2_Intron|MUC4_uc003fve.2_Intron|MUC4_uc010hzr.2_Intron|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a						cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ccaccaccatcaccaccatcacc	0.000													4	2	---	---	---	---	
TFRC	7037	broad.mit.edu	37	3	195789949	195789950	+	Intron	INS	-	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195789949_195789950insA	uc003fvz.3	-						TFRC_uc003fwa.3_Intron|TFRC_uc010hzy.2_Intron|TFRC_uc011btr.1_Intron	NM_003234	NP_003225	P02786	TFR1_HUMAN	transferrin receptor						cellular iron ion homeostasis|endocytosis|interspecies interaction between organisms|proteolysis|transferrin transport|transmembrane transport	coated pit|endosome|integral to plasma membrane|melanosome	peptidase activity|transferrin receptor activity			ovary(3)	3	all_cancers(143;1.94e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.36e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.17e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00233)		AGCCAAAAAAGAAAAAAAAAAC	0.307			T	BCL6	NHL								4	2	---	---	---	---	
KIAA1530	57654	broad.mit.edu	37	4	1348691	1348692	+	Intron	INS	-	G	G	rs138445940	by1000genomes	TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1348691_1348692insG	uc003gde.3	+							NM_020894	NP_065945	Q2YD98	K1530_HUMAN	hypothetical protein LOC57654												0			OV - Ovarian serous cystadenocarcinoma(23;0.0138)			GTGCCATGCATGGGGGGGGTCC	0.639													11	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	18147036	18147036	+	IGR	DEL	C	-	-			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18147036delC								LCORL (123651 upstream) : None (None downstream)																							ttccttccttccttccttcct	0.134													4	4	---	---	---	---	
ATP8A1	10396	broad.mit.edu	37	4	42557859	42557860	+	Intron	INS	-	TAAA	TAAA	rs145505019	by1000genomes	TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42557859_42557860insTAAA	uc003gwr.2	-						ATP8A1_uc003gws.2_Intron|ATP8A1_uc011byz.1_Intron	NM_006095	NP_006086	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT),						ATP biosynthetic process	chromaffin granule membrane|integral to membrane|plasma membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			skin(2)|central_nervous_system(1)	3					Phosphatidylserine(DB00144)	aactaactaactaaataaataa	0.104													4	3	---	---	---	---	
SMAD1	4086	broad.mit.edu	37	4	146479247	146479247	+	3'UTR	DEL	C	-	-	rs67615455		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146479247delC	uc003ikc.2	+	7					SMAD1_uc003ikd.2_3'UTR|SMAD1_uc010iov.2_3'UTR|SMAD1_uc011cic.1_3'UTR	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)					AAAAAAAAAACACACACACCT	0.328											OREG0016348	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	8	4	---	---	---	---	
CCT5	22948	broad.mit.edu	37	5	10250036	10250047	+	5'Flank	DEL	AAAAAAAAAAAC	-	-	rs57941186	by1000genomes	TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10250036_10250047delAAAAAAAAAAAC	uc003jeq.2	+						FAM173B_uc003jeo.2_5'Flank|FAM173B_uc003jep.2_5'Flank|FAM173B_uc010itr.2_5'Flank|CCT5_uc011cmq.1_5'Flank|CCT5_uc003jer.2_5'Flank|CCT5_uc010its.2_5'Flank|CCT5_uc011cmr.1_5'Flank|CCT5_uc011cms.1_5'Flank|CCT5_uc011cmt.1_5'Flank	NM_012073	NP_036205	P48643	TCPE_HUMAN	chaperonin containing TCP1, subunit 5 (epsilon)						'de novo' posttranslational protein folding|response to virus	microtubule organizing center|nucleolus	ATP binding|unfolded protein binding			ovary(2)	2						aaaaaaaaaaaaaaaaaaaaaCCGGAAATGGG	0.439													12	8	---	---	---	---	
MCC	4163	broad.mit.edu	37	5	112437238	112437238	+	Intron	DEL	T	-	-			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112437238delT	uc003kqj.3	-						MCC_uc003kqk.3_Intron|MCC_uc003kql.3_Intron|MCC_uc011cwb.1_Intron|MCC_uc010jcd.1_Intron	NM_002387	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers isoform 2						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		AAGTGTTTGCTTTTTTTTTTT	0.338													4	2	---	---	---	---	
DDX46	9879	broad.mit.edu	37	5	134140864	134140864	+	Intron	DEL	T	-	-			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134140864delT	uc003kzw.2	+						DDX46_uc003kzv.1_Intron	NM_014829	NP_055644	Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46						mRNA processing|RNA splicing	Cajal body|nuclear speck	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AAGAACTGTAttttttttttt	0.204													6	3	---	---	---	---	
RANBP17	64901	broad.mit.edu	37	5	170351727	170351727	+	Intron	DEL	T	-	-			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170351727delT	uc003mba.2	+						RANBP17_uc003max.1_Intron|RANBP17_uc003may.1_Intron|RANBP17_uc003maz.1_Intron|RANBP17_uc010jjr.1_Intron	NM_022897	NP_075048	Q9H2T7	RBP17_HUMAN	RAN binding protein 17						mRNA transport|protein import into nucleus|transmembrane transport	cytoplasm|nuclear pore	GTP binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TGTTGGTTGATTTTTTTTTTT	0.303			T	TRD@	ALL								4	2	---	---	---	---	
BTN3A2	11118	broad.mit.edu	37	6	26373817	26373820	+	Intron	DEL	AAAA	-	-	rs71863965		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26373817_26373820delAAAA	uc010jqh.1	+						BTN3A2_uc003nho.1_Intron|BTN3A2_uc003nhp.2_Intron|BTN3A2_uc011dkd.1_Intron|BTN3A2_uc011dke.1_Intron|BTN3A2_uc010jqi.1_Intron	NM_007047	NP_008978	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2 precursor							integral to membrane					0						TTCTCTCTAGaaaaaaaaaaaaaa	0.402													4	2	---	---	---	---	
KIAA0240	23506	broad.mit.edu	37	6	42789978	42789978	+	Intron	DEL	T	-	-			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42789978delT	uc003osn.1	+						KIAA0240_uc003osm.1_Intron|KIAA0240_uc011duw.1_Intron|KIAA0240_uc003oso.1_Intron|KIAA0240_uc003osp.1_Intron	NM_015349	NP_056164	Q6AI39	K0240_HUMAN	hypothetical protein LOC23506											ovary(1)	1	Colorectal(47;0.196)		Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00524)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.104)			TCAGTAAttcttttttttttt	0.124													9	4	---	---	---	---	
MTHFD1L	25902	broad.mit.edu	37	6	151330671	151330671	+	Intron	DEL	A	-	-	rs71780971		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151330671delA	uc003qob.2	+						MTHFD1L_uc011een.1_Intron|MTHFD1L_uc011eeo.1_Intron|MTHFD1L_uc003qoc.2_Intron	NM_015440	NP_056255	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+						folic acid-containing compound biosynthetic process|formate metabolic process|one-carbon metabolic process|tetrahydrofolate metabolic process	mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|protein homodimerization activity			ovary(3)|large_intestine(1)	4		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)		caccatctccaaaaaaaaaaG	0.254													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	56357562	56357563	+	IGR	INS	-	AAA	AAA			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56357562_56357563insAAA								PSPH (173472 upstream) : DKFZp434L192 (206353 downstream)																							gactccatctcaaaaaaaaaaa	0.158													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	101438951	101438953	+	IGR	DEL	ACT	-	-	rs151175364		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101438951_101438953delACT								RNF19A (116624 upstream) : ANKRD46 (83034 downstream)																							caccaccaccactaccatcacca	0.000													4	4	---	---	---	---	
KCNQ3	3786	broad.mit.edu	37	8	133146759	133146761	+	Intron	DEL	GAG	-	-			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133146759_133146761delGAG	uc003ytj.2	-						KCNQ3_uc010mdt.2_Intron	NM_004519	NP_004510	O43525	KCNQ3_HUMAN	potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)			gaggagaggagaggagaagtgag	0.172													3	3	---	---	---	---	
RECK	8434	broad.mit.edu	37	9	36100673	36100684	+	Intron	DEL	CCACTTTTTCCT	-	-	rs35712498		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36100673_36100684delCCACTTTTTCCT	uc003zyv.2	+						RECK_uc003zyw.2_Intron|RECK_uc003zyx.2_Intron	NM_021111	NP_066934	O95980	RECK_HUMAN	RECK protein precursor							anchored to membrane|peripheral to membrane of membrane fraction|plasma membrane	metalloendopeptidase inhibitor activity|serine-type endopeptidase inhibitor activity			skin(2)|ovary(1)	3			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)			AAATGCTTTCCCACTTTTTCCTCCTCTAGTTG	0.472													4	6	---	---	---	---	
SCAI	286205	broad.mit.edu	37	9	127765212	127765212	+	Intron	DEL	A	-	-	rs79884030		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127765212delA	uc004bpe.2	-						SCAI_uc004bpd.2_Intron|SCAI_uc010mwu.2_Intron	NM_001144877	NP_001138349	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion isoform 2						negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|integral to membrane|nucleus	protein binding|transcription corepressor activity			ovary(2)|breast(2)|central_nervous_system(1)	5						CCAGGAGTACaaaaaaaaaaa	0.254													4	2	---	---	---	---	
FAM102A	399665	broad.mit.edu	37	9	130705357	130705357	+	3'UTR	DEL	G	-	-			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130705357delG	uc004bsx.1	-	11					FAM102A_uc004bsw.1_3'UTR|FAM102A_uc004bsy.1_3'UTR	NM_001035254	NP_001030331	Q5T9C2	F102A_HUMAN	early estrogen-induced gene 1 protein isoform a											ovary(1)	1						GCATGGAGGAGGCATGGATGA	0.582											OREG0019513	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	12	8	---	---	---	---	
LCN10	414332	broad.mit.edu	37	9	139635199	139635200	+	Intron	INS	-	TCCTGGG	TCCTGGG	rs145287279	by1000genomes	TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139635199_139635200insTCCTGGG	uc010nbq.2	-						LCN10_uc004civ.2_Intron|LCN10_uc011med.1_Intron|LCN10_uc011mee.1_Intron|LCN10_uc011mef.1_Intron|LCN10_uc004ciw.2_Intron			Q6JVE6	LCN10_HUMAN	SubName: Full=LCN10 protein;						transport	extracellular region	binding			large_intestine(1)	1	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.32e-06)|Epithelial(140;7.83e-05)		cccgcctcacctcctgcccggc	0.257													4	2	---	---	---	---	
APBB1IP	54518	broad.mit.edu	37	10	26828336	26828337	+	Intron	INS	-	A	A	rs113271338		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26828336_26828337insA	uc001iss.2	+						APBB1IP_uc009xks.1_Intron	NM_019043	NP_061916	Q7Z5R6	AB1IP_HUMAN	amyloid beta (A4) precursor protein-binding,						blood coagulation|signal transduction	cytoskeleton|cytosol|focal adhesion|lamellipodium				lung(4)|skin(2)|central_nervous_system(1)	7						atgagatcctgaaaaaaaaaaa	0.025													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	32541474	32541475	+	IGR	INS	-	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32541474_32541475insA								KIF5B (196103 upstream) : EPC1 (16384 downstream)																							aggaaggaaggaaggaaggaag	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	49319126	49319126	+	Intron	DEL	A	-	-			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49319126delA	uc009xny.1	-											Homo sapiens cDNA, FLJ99963.																		GGTATTAGCCAAAATTAGTAG	0.388													30	41	---	---	---	---	
PRKG1	5592	broad.mit.edu	37	10	53387680	53387680	+	Intron	DEL	C	-	-			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53387680delC	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	NM_001098512	NP_001091982	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		tcccttccttcccttcctttc	0.015													3	3	---	---	---	---	
MYPN	84665	broad.mit.edu	37	10	69921273	69921274	+	Intron	DEL	AA	-	-			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69921273_69921274delAA	uc001jnm.3	+						MYPN_uc001jnl.1_Intron|MYPN_uc001jnn.3_Intron|MYPN_uc001jno.3_Intron|MYPN_uc001jnp.1_Intron|MYPN_uc009xps.2_Intron|MYPN_uc009xpt.2_Intron|MYPN_uc010qit.1_Intron|MYPN_uc010qiu.1_Intron	NM_032578	NP_115967	Q86TC9	MYPN_HUMAN	myopalladin							nucleus|sarcomere	actin binding			ovary(3)|skin(2)	5						actcagtctcaaaaaaaaaaaa	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	79897407	79897407	+	IGR	DEL	T	-	-	rs78604103	by1000genomes	TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79897407delT								RPS24 (80837 upstream) : LOC283050 (805677 downstream)																							ccttccttcctttccttcctt	0.164													4	2	---	---	---	---	
SH3PXD2A	9644	broad.mit.edu	37	10	105561300	105561301	+	Intron	INS	-	ACACAC	ACACAC	rs148335179	by1000genomes	TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105561300_105561301insACACAC	uc001kxj.1	-							NM_014631	NP_055446	Q5TCZ1	SPD2A_HUMAN	SH3 multiple domains 1						cell communication|superoxide metabolic process	cell junction|cell projection|cytoplasm|podosome	phosphatidylinositol binding|protein binding				0		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)		tatgtctAAATacacacacaca	0.139													4	4	---	---	---	---	
MRE11A	4361	broad.mit.edu	37	11	94170172	94170173	+	Intron	INS	-	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94170172_94170173insA	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)				GAGCAACCAAGAAAAAAAAAAT	0.104								Homologous_recombination	Ataxia-Telangiectasia-Like_Disorder				4	2	---	---	---	---	
GRIA4	2893	broad.mit.edu	37	11	105781021	105781021	+	Intron	DEL	T	-	-	rs113570660		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105781021delT	uc001pix.2	+						GRIA4_uc001piu.1_Intron|GRIA4_uc001piw.2_Intron|GRIA4_uc009yxk.1_Intron	NM_000829	NP_000820	P48058	GRIA4_HUMAN	glutamate receptor, ionotrophic, AMPA 4 isoform						glutamate signaling pathway|synaptic transmission	cell junction|endocytic vesicle membrane|integral to membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)	L-Glutamic Acid(DB00142)	TTCTGAACACTTTTTTTTTTT	0.328													4	2	---	---	---	---	
CACNA2D4	93589	broad.mit.edu	37	12	1909657	1909657	+	Intron	DEL	C	-	-	rs111637110		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1909657delC	uc001qjp.2	-						CACNA2D4_uc009zds.1_Intron|CACNA2D4_uc001qjo.2_Intron|CACNA2D4_uc001qjs.1_Intron|CACNA2D4_uc010sdw.1_Intron|CACNA2D4_uc009zdr.1_Intron	NM_172364	NP_758952	Q7Z3S7	CA2D4_HUMAN	voltage-gated calcium channel alpha(2)delta-4							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			ovary(1)	1	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		GGTGAGGGTGCCCCCCCCCCA	0.667											OREG0021569	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	4	---	---	---	---	
ETNK1	55500	broad.mit.edu	37	12	22796574	22796574	+	Intron	DEL	T	-	-			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22796574delT	uc001rft.2	+						ETNK1_uc009ziz.2_Intron|ETNK1_uc001rfs.2_Intron	NM_018638	NP_061108	Q9HBU6	EKI1_HUMAN	ethanolamine kinase 1 isoform A						phosphatidylethanolamine biosynthetic process	cytoplasm	ATP binding|ethanolamine kinase activity				0						AAGATGGTTCTTTTATGTGAA	0.249													5	3	---	---	---	---	
PDZRN4	29951	broad.mit.edu	37	12	41961406	41961407	+	Intron	INS	-	T	T	rs34848026		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41961406_41961407insT	uc010skn.1	+						PDZRN4_uc001rmq.3_Intron|PDZRN4_uc009zjz.2_Intron|PDZRN4_uc001rmr.2_Intron	NM_013377	NP_037509	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing RING finger 4 isoform 2								ubiquitin-protein ligase activity|zinc ion binding			lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	11	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				CATAAGAGTCCTTTTTTTTTTT	0.361													5	3	---	---	---	---	
CCT2	10576	broad.mit.edu	37	12	69986093	69986094	+	Intron	INS	-	A	A			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69986093_69986094insA	uc001svb.1	+						CCT2_uc009zrm.1_Intron|CCT2_uc009zrn.1_Intron|CCT2_uc010stl.1_Intron	NM_006431	NP_006422	P78371	TCPB_HUMAN	chaperonin containing TCP1, subunit 2						'de novo' posttranslational protein folding	nucleus	ATP binding|unfolded protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(2;7.7e-106)|Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.72e-18)|GBM - Glioblastoma multiforme(2;2.58e-10)|Lung(24;0.000185)|OV - Ovarian serous cystadenocarcinoma(12;0.00126)|STAD - Stomach adenocarcinoma(21;0.00501)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)			ctgtctctactaaaaaaaaaaa	0.000													9	4	---	---	---	---	
ZDHHC17	23390	broad.mit.edu	37	12	77243103	77243104	+	Intron	INS	-	AAA	AAA	rs34062414		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77243103_77243104insAAA	uc001syk.1	+							NM_015336	NP_056151	Q8IUH5	ZDH17_HUMAN	huntingtin interacting protein 14						lipoprotein transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi-associated vesicle membrane|integral to membrane	magnesium ion transmembrane transporter activity|protein binding|protein-cysteine S-palmitoleyltransferase activity|signal transducer activity|zinc ion binding				0						ggtcctgtctcaaaaaaaaaaa	0.119													5	3	---	---	---	---	
IKBIP	121457	broad.mit.edu	37	12	99028313	99028313	+	Intron	DEL	T	-	-			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99028313delT	uc001tfv.2	-						IKBIP_uc001tfw.2_Intron|IKBIP_uc001tfx.2_Intron	NM_201612	NP_963906	Q70UQ0	IKIP_HUMAN	IKK interacting protein isoform 2						induction of apoptosis|response to X-ray	endoplasmic reticulum membrane|integral to membrane	protein binding				0						TAGCTGTAGGttttttttttt	0.169													11	5	---	---	---	---	
FAM48A	55578	broad.mit.edu	37	13	37622887	37622888	+	Intron	INS	-	AA	AA	rs140526539	by1000genomes	TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37622887_37622888insAA	uc001uwg.2	-						FAM48A_uc010abt.2_Intron|FAM48A_uc001uwh.2_Intron|FAM48A_uc001uwi.2_Intron|FAM48A_uc001uwj.2_Intron|FAM48A_uc001uwk.2_Intron|FAM48A_uc010tes.1_Intron|FAM48A_uc001uwl.1_Intron	NM_001014286	NP_001014308	Q8NEM7	FA48A_HUMAN	family with sequence similarity 48, member A						autophagy|gastrulation	SAGA-type complex	protein binding				0		Lung NSC(96;2.09e-06)|Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.0959)		all cancers(112;6.06e-07)|Epithelial(112;1.87e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00794)|BRCA - Breast invasive adenocarcinoma(63;0.0128)|GBM - Glioblastoma multiforme(144;0.0477)		AATATATATATAACAAAGAAAA	0.297													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	30384348	30384349	+	5'Flank	INS	-	C	C			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30384348_30384349insC	uc001zcx.1	-						uc010uau.1_5'Flank					DQ595055																		TGAGCCTGACTCCCCCTGCACC	0.604													6	7	---	---	---	---	
FSIP1	161835	broad.mit.edu	37	15	40018751	40018752	+	Intron	DEL	CA	-	-			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40018751_40018752delCA	uc001zki.2	-							NM_152597	NP_689810	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1											ovary(2)|skin(1)	3		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		ACAGCTTTAGCACACATTAACT	0.371													58	25	---	---	---	---	
RNF111	54778	broad.mit.edu	37	15	59341562	59341564	+	Intron	DEL	TTT	-	-			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59341562_59341564delTTT	uc002afv.2	+						RNF111_uc002afs.2_Intron|RNF111_uc002aft.2_Intron|RNF111_uc002afu.2_Intron|RNF111_uc002afw.2_Intron	NM_017610	NP_060080	Q6ZNA4	RN111_HUMAN	ring finger protein 111						multicellular organismal development|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2				all cancers(107;0.194)		GTGTCTTTGAttttttttttttt	0.232													6	3	---	---	---	---	
ZNF646	9726	broad.mit.edu	37	16	31094274	31094275	+	Intron	DEL	CT	-	-			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31094274_31094275delCT	uc002eap.2	+							NM_014699	NP_055514	O15015	ZN646_HUMAN	zinc finger protein 646						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			breast(2)	2						TGGTGACCTCCTCTCTCTCTCC	0.683													4	2	---	---	---	---	
VAT1L	57687	broad.mit.edu	37	16	77850682	77850683	+	Intron	INS	-	A	A	rs71884745		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77850682_77850683insA	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						TTGCCAAaaagaaaaaaaaaag	0.243													4	2	---	---	---	---	
LRRC50	123872	broad.mit.edu	37	16	84193579	84193579	+	Intron	DEL	T	-	-	rs11292642		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84193579delT	uc002fhl.3	+						LRRC50_uc010vnw.1_Intron	NM_178452	NP_848547	Q8NEP3	DAAF1_HUMAN	leucine rich repeat containing 50						axonemal dynein complex assembly|cilium morphogenesis	cilium axoneme|cytoplasm|spindle pole	dynein binding				0						TATTCATAGATTTTTTTatat	0.154									Kartagener_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	6561456	6561456	+	IGR	DEL	C	-	-			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6561456delC								C17orf100 (4839 upstream) : SLC13A5 (26585 downstream)																							AAACCCTTTGCCCCATTCTGT	0.418													30	13	---	---	---	---	
SNF8	11267	broad.mit.edu	37	17	47013394	47013394	+	Intron	DEL	T	-	-			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47013394delT	uc002ioj.2	-						SNF8_uc002iok.2_Intron	NM_007241	NP_009172	Q96H20	SNF8_HUMAN	EAP30 subunit of ELL complex						cellular membrane organization|endosome transport|protein transport|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytosol|late endosome membrane|transcription factor complex	transcription factor binding				0						TTGTTTTTTGTTTTTTTTTTT	0.184													5	3	---	---	---	---	
FAM59A	64762	broad.mit.edu	37	18	29973144	29973144	+	Intron	DEL	T	-	-	rs10708225		TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29973144delT	uc002kxl.2	-						FAM59A_uc002kxk.1_Intron	NM_022751	NP_073588	Q9H706	FA59A_HUMAN	family with sequence similarity 59, member A											ovary(1)|skin(1)	2						CTCTGAATTGttttttttttt	0.308													9	4	---	---	---	---	
ADAMTS1	9510	broad.mit.edu	37	21	28215162	28215167	+	Intron	DEL	TTATTT	-	-			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28215162_28215167delTTATTT	uc002ymf.2	-							NM_006988	NP_008919	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1						integrin-mediated signaling pathway|negative regulation of cell proliferation|proteolysis		heparin binding|zinc ion binding			lung(3)|large_intestine(2)|central_nervous_system(1)	6		Breast(209;0.000962)		Lung(58;0.215)		ACTCCAAGTGTTATTTTTAAAGTTCT	0.359													4	2	---	---	---	---	
SSX3	10214	broad.mit.edu	37	X	48217953	48217953	+	5'Flank	DEL	A	-	-			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48217953delA	uc004djd.1	-						SSX3_uc004dje.2_5'Flank|SSX3_uc010nic.2_5'Flank	NM_021014	NP_066294	Q99909	SSX3_HUMAN	synovial sarcoma, X breakpoint 3 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding				0						agcaagactgaaaaaaaaaaa	0.015													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13466354	13466354	+	IGR	DEL	G	-	-			TCGA-BP-4993-01A-02D-1421-08	TCGA-BP-4993-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13466354delG								None (None upstream) : None (None downstream)																							atatagacaagagttacatca	0.000													4	2	---	---	---	---	
