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
UTS2	10911	broad.mit.edu	37	1	7913405	7913405	+	5'Flank	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7913405G>T	uc001aor.2	-						UTS2_uc001aoq.2_5'UTR|UTS2_uc001aos.2_Missense_Mutation_p.N29K	NM_006786	NP_006777	O95399	UTS2_HUMAN	urotensin 2 isoform b preproprotein						muscle contraction|regulation of blood pressure|synaptic transmission	extracellular space	hormone activity				0	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;1.38e-20)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.26e-71)|GBM - Glioblastoma multiforme(8;5.15e-36)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000386)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|STAD - Stomach adenocarcinoma(132;0.000951)|READ - Rectum adenocarcinoma(331;0.0642)		TTGGATATGAGTTGAAGTGGC	0.358													22	32	---	---	---	---	PASS
PRAMEF2	65122	broad.mit.edu	37	1	12921337	12921337	+	Silent	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12921337C>T	uc001aum.1	+	4	1215	c.1128C>T	c.(1126-1128)TGC>TGT	p.C376C		NM_023014	NP_075390	O60811	PRAM2_HUMAN	PRAME family member 2	376											0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TGAGCTGCTGCTCCCAGCTCA	0.562													47	179	---	---	---	---	PASS
ARHGEF10L	55160	broad.mit.edu	37	1	17991036	17991036	+	Nonsense_Mutation	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17991036G>A	uc001ban.2	+	26	3114	c.2955G>A	c.(2953-2955)TGG>TGA	p.W985*	ARHGEF10L_uc009vpe.1_Nonsense_Mutation_p.W946*|ARHGEF10L_uc001bao.2_Nonsense_Mutation_p.W946*|ARHGEF10L_uc001bap.2_Nonsense_Mutation_p.W941*|ARHGEF10L_uc001baq.2_Nonsense_Mutation_p.W746*|ARHGEF10L_uc010ocs.1_Nonsense_Mutation_p.W758*|ARHGEF10L_uc001bar.2_Nonsense_Mutation_p.W688*|ARHGEF10L_uc009vpf.2_RNA	NM_018125	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF)	985					regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)|ovary(1)|pancreas(1)	3		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		ATGCCGTGTGGGCCAGCTGTG	0.667													15	9	---	---	---	---	PASS
TAS1R2	80834	broad.mit.edu	37	1	19180803	19180803	+	Silent	SNP	G	A	A	rs139739080		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19180803G>A	uc001bba.1	-	3	1162	c.1161C>T	c.(1159-1161)AGC>AGT	p.S387S		NM_152232	NP_689418	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2 precursor	387	Extracellular (Potential).				detection of chemical stimulus involved in sensory perception of sweet taste	plasma membrane	protein heterodimerization activity|taste receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	CAGAGTACACGCTGTAGACGA	0.592													10	27	---	---	---	---	PASS
HMGN2	3151	broad.mit.edu	37	1	26801131	26801131	+	Silent	SNP	A	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26801131A>T	uc001bmp.3	+	5	412	c.210A>T	c.(208-210)GCA>GCT	p.A70A	HMGN2_uc009vsk.2_Silent_p.A55A|HMGN2_uc001bmq.3_Missense_Mutation_p.Q104L	NM_005517	NP_005508	P05204	HMGN2_HUMAN	high-mobility group nucleosomal binding domain	70					chromatin organization|regulation of transcription, DNA-dependent	chromatin|cytoplasm|nucleus	DNA binding|protein binding				0		all_cancers(24;1.9e-24)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.38e-49)|OV - Ovarian serous cystadenocarcinoma(117;5.38e-28)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.026)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.153)|LUSC - Lung squamous cell carcinoma(448;0.227)		ATAACCCTGCAGAAAATGGAG	0.408													4	17	---	---	---	---	PASS
UTP11L	51118	broad.mit.edu	37	1	38483404	38483404	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38483404G>T	uc001ccn.3	+	3	281	c.190G>T	c.(190-192)GAT>TAT	p.D64Y	UTP11L_uc009vvm.2_5'UTR|UTP11L_uc010oil.1_RNA|UTP11L_uc001cco.3_5'UTR	NM_016037	NP_057121	Q9Y3A2	UTP11_HUMAN	UTP11-like, U3 small nucleolar	64					induction of apoptosis|nerve growth factor receptor signaling pathway|nervous system development|rRNA processing	cytoplasm|extracellular space|nucleolus|small-subunit processome	protein binding				0	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				AAAAAATCCAGATGAATTCTA	0.403													17	26	---	---	---	---	PASS
DPH2	1802	broad.mit.edu	37	1	44435860	44435860	+	Missense_Mutation	SNP	T	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44435860T>C	uc001ckz.2	+	1	208	c.13T>C	c.(13-15)TTT>CTT	p.F5L	DPH2_uc001cla.2_Missense_Mutation_p.F5L|DPH2_uc010okk.1_5'UTR|DPH2_uc001clb.2_5'UTR	NM_001384	NP_001375	Q9BQC3	DPH2_HUMAN	diphthamide biosynthesis protein 2 isoform a	5					peptidyl-diphthamide biosynthetic process from peptidyl-histidine	cytoplasm				ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)				GGAGTCGATGTTTAGCAGCCC	0.657													19	32	---	---	---	---	PASS
LRRC7	57554	broad.mit.edu	37	1	70303969	70303969	+	Intron	SNP	A	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70303969A>T	uc001dep.2	+						LRRC7_uc001deo.1_Intron|LRRC7_uc009wbg.2_Intron	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7							centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14						CTACCAAAGTAAGTGACTGTG	0.299													16	34	---	---	---	---	PASS
ELTD1	64123	broad.mit.edu	37	1	79474666	79474666	+	5'Flank	SNP	A	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79474666A>T	uc001diq.3	-							NM_022159	NP_071442	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain						neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(1)|skin(1)	2				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		AAAATAAACTATGAAGAGTTT	0.348													22	38	---	---	---	---	PASS
GBP6	163351	broad.mit.edu	37	1	89845989	89845989	+	Missense_Mutation	SNP	A	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89845989A>T	uc001dnf.2	+	6	944	c.670A>T	c.(670-672)ATC>TTC	p.I224F	GBP6_uc010ost.1_Missense_Mutation_p.I94F	NM_198460	NP_940862	Q6ZN66	GBP6_HUMAN	guanylate binding protein family, member 6	224							GTP binding|GTPase activity			ovary(2)	2		Lung NSC(277;0.0908)		all cancers(265;0.0108)|Epithelial(280;0.0398)		CAGGGAGTGCATCAGGCGTTT	0.413													35	52	---	---	---	---	PASS
DPYD	1806	broad.mit.edu	37	1	98293701	98293701	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98293701C>A	uc001drv.2	-	3	339	c.202G>T	c.(202-204)GGT>TGT	p.G68C	DPYD_uc010oub.1_RNA|DPYD_uc001drw.2_Missense_Mutation_p.G68C	NM_000110	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase isoform 1	68					'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)	CCTCGCTCACCAAGAGTCGTG	0.393													22	34	---	---	---	---	PASS
EXTL2	2135	broad.mit.edu	37	1	101339863	101339863	+	Missense_Mutation	SNP	T	C	C	rs141823466	by1000genomes	TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101339863T>C	uc001dtk.1	-	5	965	c.628A>G	c.(628-630)ATG>GTG	p.M210V	EXTL2_uc001dtl.1_Missense_Mutation_p.M210V|EXTL2_uc010ouk.1_Missense_Mutation_p.M197V|EXTL2_uc001dtm.1_Missense_Mutation_p.M209V	NM_001439	NP_001430	Q9UBQ6	EXTL2_HUMAN	exostoses-like 2	210	Lumenal (Potential).				N-acetylglucosamine metabolic process|UDP-N-acetylgalactosamine metabolic process	extracellular region|integral to membrane|intrinsic to endoplasmic reticulum membrane	alpha-1,4-N-acetylgalactosaminyltransferase activity|glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|metal ion binding			skin(1)	1		all_epithelial(167;2.48e-06)|all_lung(203;0.000414)|Lung NSC(277;0.000946)		Epithelial(280;0.0425)|all cancers(265;0.0628)|COAD - Colon adenocarcinoma(174;0.148)|Colorectal(144;0.167)|Lung(183;0.195)		ATCAGCACCATAGAGTACTGG	0.408													22	45	---	---	---	---	PASS
PROK1	84432	broad.mit.edu	37	1	110998843	110998843	+	Intron	SNP	T	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110998843T>G	uc001dzs.2	+							NM_032414	NP_115790	P58294	PROK1_HUMAN	prokineticin 1 precursor						angiogenesis|positive regulation of cell division	extracellular region	growth factor activity				0		all_cancers(81;6.23e-06)|all_epithelial(167;2.12e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0239)|all cancers(265;0.0699)|Epithelial(280;0.0753)|Colorectal(144;0.105)|LUSC - Lung squamous cell carcinoma(189;0.135)		GTTGATTTCTTCTCTCCTTAG	0.597													38	45	---	---	---	---	PASS
CHIA	27159	broad.mit.edu	37	1	111857928	111857928	+	Silent	SNP	G	A	A	rs150698600	byFrequency	TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111857928G>A	uc001eas.2	+	6	454	c.351G>A	c.(349-351)CAG>CAA	p.Q117Q	CHIA_uc001ear.2_Silent_p.Q9Q|CHIA_uc001eaq.2_Silent_p.Q9Q|CHIA_uc009wgc.2_Silent_p.Q9Q|CHIA_uc001eat.2_Intron|CHIA_uc001eav.2_5'UTR|CHIA_uc001eau.2_Intron|CHIA_uc009wgd.2_Intron	NM_201653	NP_970615	Q9BZP6	CHIA_HUMAN	acidic chitinase isoform c	117					apoptosis|cell wall chitin metabolic process|chitin catabolic process|digestion|immune response|positive regulation of chemokine secretion|production of molecular mediator involved in inflammatory response|response to acid|response to fungus	cytoplasm|extracellular space	cation binding|chitin binding|chitinase activity|kinase binding|lysozyme activity|sugar binding			ovary(1)	1		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		AGAACCGCCAGACTTTCATCA	0.537													61	129	---	---	---	---	PASS
MRPL9	65005	broad.mit.edu	37	1	151732535	151732535	+	Silent	SNP	G	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151732535G>C	uc001eyv.2	-	7	880	c.795C>G	c.(793-795)CCC>CCG	p.P265P	MRPL9_uc009wmz.2_RNA	NM_031420	NP_113608	Q9BYD2	RM09_HUMAN	mitochondrial ribosomal protein L9 precursor	265					translation	mitochondrial ribosome	structural constituent of ribosome			ovary(1)	1	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			TTTAGATCTGGGGGCTGGTGG	0.527													33	32	---	---	---	---	PASS
RPTN	126638	broad.mit.edu	37	1	152129212	152129212	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152129212G>T	uc001ezs.1	-	3	428	c.363C>A	c.(361-363)CAC>CAA	p.H121Q		NM_001122965	NP_001116437	Q6XPR3	RPTN_HUMAN	repetin	121	Gln-rich.					proteinaceous extracellular matrix	calcium ion binding				0						GCCTCTGTCTGTGTTGTCTGC	0.532													103	228	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152283417	152283417	+	Missense_Mutation	SNP	G	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152283417G>C	uc001ezu.1	-	3	3981	c.3945C>G	c.(3943-3945)GAC>GAG	p.D1315E	uc001ezv.2_5'Flank	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1315	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GACTGGCTCTGTCTTCTTGAT	0.373									Ichthyosis				93	222	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152287908	152287908	+	Missense_Mutation	SNP	A	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152287908A>C	uc001ezu.1	-	2	61	c.25T>G	c.(25-27)TTT>GTT	p.F9V	uc001ezv.2_Intron	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	9	EF-hand 1.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ATTATGGCAAAGATGTTTTCC	0.299									Ichthyosis				13	79	---	---	---	---	PASS
ARHGEF2	9181	broad.mit.edu	37	1	155921325	155921325	+	Splice_Site	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155921325C>T	uc001fmt.2	-	19	2327	c.2209_splice	c.e19-1	p.E737_splice	ARHGEF2_uc001fmq.2_5'Flank|ARHGEF2_uc001fmr.2_Splice_Site_p.E709_splice|ARHGEF2_uc001fms.2_Splice_Site_p.E736_splice|ARHGEF2_uc001fmu.2_Splice_Site_p.E781_splice	NM_001162383	NP_001155855	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor 2						actin filament organization|apoptosis|cell division|cell morphogenesis|induction of apoptosis by extracellular signals|intracellular protein transport|mitosis|negative regulation of microtubule depolymerization|nerve growth factor receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|regulation of cell proliferation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|Golgi apparatus|microtubule|ruffle membrane|spindle|tight junction	microtubule binding|Rac GTPase binding|Rac guanyl-nucleotide exchange factor activity|zinc ion binding			ovary(1)	1	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					GTAACGCCTCCTGAGGACAGA	0.557													102	98	---	---	---	---	PASS
SLAMF6	114836	broad.mit.edu	37	1	160465906	160465906	+	Silent	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160465906G>T	uc001fwe.1	-	2	387	c.327C>A	c.(325-327)GCC>GCA	p.A109A	SLAMF6_uc001fwd.1_Silent_p.A109A|SLAMF6_uc010pjh.1_Silent_p.A60A|SLAMF6_uc010pji.1_Intron|SLAMF6_uc010pjj.1_Intron|SLAMF6_uc009wtm.1_Silent_p.A60A	NM_052931	NP_443163	Q96DU3	SLAF6_HUMAN	activating NK receptor precursor	109	Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(1)|skin(1)	2	all_cancers(52;1.05e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0923)			TGGATATCTGGGCTCTGTAAG	0.438													125	105	---	---	---	---	PASS
BAT2L2	23215	broad.mit.edu	37	1	171548569	171548569	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171548569G>T	uc010pmg.1	+	27	7496	c.7230G>T	c.(7228-7230)TTG>TTT	p.L2410F	BAT2L2_uc010pmh.1_Missense_Mutation_p.L1322F|BAT2L2_uc010pmi.1_Missense_Mutation_p.L247F|BAT2L2_uc010pmj.1_5'Flank	NM_015172	NP_055987	Q9Y520	PRC2C_HUMAN	HBxAg transactivated protein 2	2410	Gln-rich.						protein C-terminus binding				0						CGCCATCCTTGGCTCAACAAC	0.423													11	48	---	---	---	---	PASS
BAT2L2	23215	broad.mit.edu	37	1	171548570	171548570	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171548570G>T	uc010pmg.1	+	27	7497	c.7231G>T	c.(7231-7233)GCT>TCT	p.A2411S	BAT2L2_uc010pmh.1_Missense_Mutation_p.A1323S|BAT2L2_uc010pmi.1_Missense_Mutation_p.A248S|BAT2L2_uc010pmj.1_5'Flank	NM_015172	NP_055987	Q9Y520	PRC2C_HUMAN	HBxAg transactivated protein 2	2411	Gln-rich.						protein C-terminus binding				0						GCCATCCTTGGCTCAACAACA	0.418													11	46	---	---	---	---	PASS
PAPPA2	60676	broad.mit.edu	37	1	176740254	176740254	+	Missense_Mutation	SNP	C	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176740254C>G	uc001gkz.2	+	17	5817	c.4653C>G	c.(4651-4653)ATC>ATG	p.I1551M	PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	1551	Sushi 3.				cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16						TGGGCACCATCTGCAAATATG	0.483													28	74	---	---	---	---	PASS
RASAL2	9462	broad.mit.edu	37	1	178442279	178442279	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178442279C>T	uc001glr.2	+	16	3450	c.3325C>T	c.(3325-3327)CGG>TGG	p.R1109W	RASAL2_uc001glq.2_Missense_Mutation_p.R1250W|RASAL2_uc009wxc.2_Missense_Mutation_p.A633V	NM_004841	NP_004832	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2 isoform 1	1109					negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity			ovary(2)|breast(2)|large_intestine(1)	5						AGTGAAGGAGCGGTACAGCAT	0.537													27	83	---	---	---	---	PASS
SRGAP2	23380	broad.mit.edu	37	1	206634572	206634572	+	Missense_Mutation	SNP	T	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206634572T>C	uc001hdy.2	+	20	3095	c.2762T>C	c.(2761-2763)TTC>TCC	p.F921S	SRGAP2_uc010pru.1_Missense_Mutation_p.F844S	NM_015326	NP_056141	O75044	FNBP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2	1008					axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding				0	Breast(84;0.137)					GAGCCCGCCTTCCAGCGCAGC	0.672													21	15	---	---	---	---	PASS
SMYD2	56950	broad.mit.edu	37	1	214501018	214501018	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214501018G>T	uc010ptx.1	+	7	689	c.656G>T	c.(655-657)GGG>GTG	p.G219V	SMYD2_uc009xdj.2_Missense_Mutation_p.G127V|SMYD2_uc010ptw.1_RNA|SMYD2_uc009xdl.1_RNA	NM_020197	NP_064582	Q9NRG4	SMYD2_HUMAN	SET and MYND domain containing 2	219	SET.				negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation|regulation of DNA damage response, signal transduction by p53 class mediator|transcription, DNA-dependent	cytosol|nucleus	histone methyltransferase activity (H3-K36 specific)|p53 binding|RNA polymerase II core binding|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0122)|all cancers(67;0.0209)|GBM - Glioblastoma multiforme(131;0.106)|Epithelial(68;0.144)		ACCTACAAAGGGACCCTGGCA	0.488											OREG0004276	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	32	113	---	---	---	---	PASS
HLX	3142	broad.mit.edu	37	1	221053501	221053501	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221053501C>T	uc001hmv.3	+	1	759	c.302C>T	c.(301-303)CCC>CTC	p.P101L		NM_021958	NP_068777	Q14774	HLX_HUMAN	H2.0-like homeobox	101	Pro-rich.				cell differentiation	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2				GBM - Glioblastoma multiforme(131;0.00914)		GTGGTGGCGCCCTCCGAAGTC	0.607													3	12	---	---	---	---	PASS
PARP1	142	broad.mit.edu	37	1	226567672	226567672	+	Silent	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226567672C>T	uc001hqd.3	-	10	1665	c.1494G>A	c.(1492-1494)AAG>AAA	p.K498K		NM_001618	NP_001609	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase family, member 1	498	Automodification domain.				cellular response to insulin stimulus|protein ADP-ribosylation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nuclear envelope|nucleolus|transcription factor complex	DNA binding|identical protein binding|NAD+ ADP-ribosyltransferase activity|protein N-terminus binding|transcription factor binding|zinc ion binding			lung(3)|ovary(2)|breast(2)|skin(2)|upper_aerodigestive_tract(1)	10	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		CAGCCCCTGACTTCCCTCTTG	0.597								Direct_reversal_of_damage|PARP_enzymes_that_bind_to_DNA					52	113	---	---	---	---	PASS
URB2	9816	broad.mit.edu	37	1	229770893	229770893	+	Missense_Mutation	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229770893G>A	uc001hts.1	+	4	669	c.533G>A	c.(532-534)GGC>GAC	p.G178D	URB2_uc009xfd.1_Missense_Mutation_p.G178D	NM_014777	NP_055592	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog	178						nucleolus				central_nervous_system(2)|ovary(1)	3						CTGGCCCTTGGCCATTATCTC	0.592													27	79	---	---	---	---	PASS
NID1	4811	broad.mit.edu	37	1	236154191	236154191	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236154191C>A	uc001hxo.2	-	14	3025	c.2923G>T	c.(2923-2925)GTC>TTC	p.V975F	NID1_uc009xgd.2_Missense_Mutation_p.V842F|NID1_uc009xgc.2_Missense_Mutation_p.V61F	NM_002508	NP_002499	P14543	NID1_HUMAN	nidogen 1 precursor	975					cell-matrix adhesion	basement membrane	calcium ion binding			large_intestine(1)|pancreas(1)	2	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Becaplermin(DB00102)|Urokinase(DB00013)	CTCACCGGGACATGAAGGAAC	0.537													24	104	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237777617	237777617	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237777617C>T	uc001hyl.1	+	37	5309	c.5189C>T	c.(5188-5190)ACG>ATG	p.T1730M		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	1730	Cytoplasmic (By similarity).|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GTCCCCATGACGGAGGAGACG	0.547													13	50	---	---	---	---	PASS
FMN2	56776	broad.mit.edu	37	1	240497231	240497231	+	Silent	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240497231C>T	uc010pyd.1	+	12	4854	c.4629C>T	c.(4627-4629)CTC>CTT	p.L1543L	FMN2_uc010pye.1_Silent_p.L1547L|FMN2_uc010pyf.1_Silent_p.L189L|FMN2_uc010pyg.1_Silent_p.L139L	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	1543	FH2.				actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CGTATTATCTCCGAAATTTTG	0.279													15	17	---	---	---	---	PASS
OR2C3	81472	broad.mit.edu	37	1	247695527	247695527	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247695527C>A	uc009xgy.2	-	2	649	c.287G>T	c.(286-288)GGA>GTA	p.G96V	C1orf150_uc009xgw.2_Intron|C1orf150_uc001ida.3_Intron|C1orf150_uc001idb.3_Intron|C1orf150_uc009xgx.2_Intron|LOC148824_uc001idd.2_5'Flank	NM_198074	NP_932340	Q8N628	OR2C3_HUMAN	olfactory receptor, family 2, subfamily C,	96	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0242)	OV - Ovarian serous cystadenocarcinoma(106;0.0241)			CACACACCCTCCATAGCTTAT	0.562													30	19	---	---	---	---	PASS
C1orf150	148823	broad.mit.edu	37	1	247719780	247719780	+	Intron	SNP	G	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247719780G>C	uc001idf.2	+						C1orf150_uc009xgw.2_Intron|C1orf150_uc001ida.3_Intron|C1orf150_uc001idb.3_Intron|C1orf150_uc009xgx.2_Intron	NM_145278	NP_660321	Q5JQS6	CA150_HUMAN	hypothetical protein LOC148823												0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0241)			TAAGAACAGAGCATCTCAGAG	0.373													8	15	---	---	---	---	PASS
OR6F1	343169	broad.mit.edu	37	1	247875412	247875412	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247875412C>A	uc001idj.1	-	1	646	c.646G>T	c.(646-648)GTC>TTC	p.V216F		NM_001005286	NP_001005286	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F,	216	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0168)			ACATAGGAGACAAAGGTGATG	0.552													84	65	---	---	---	---	PASS
OR1C1	26188	broad.mit.edu	37	1	247921568	247921568	+	Silent	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247921568C>T	uc010pza.1	-	1	141	c.141G>A	c.(139-141)GCG>GCA	p.A47A		NM_012353	NP_036485	Q15619	OR1C1_HUMAN	olfactory receptor, family 1, subfamily C,	47	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	all_cancers(71;4.34e-05)|all_epithelial(71;1.13e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)	all_cancers(173;0.0247)	OV - Ovarian serous cystadenocarcinoma(106;0.0168)			AGCCAATCGTCGCAATGATGA	0.488													15	29	---	---	---	---	PASS
OR2L2	26246	broad.mit.edu	37	1	248201674	248201674	+	Silent	SNP	A	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248201674A>T	uc001idw.2	+	1	201	c.105A>T	c.(103-105)CTA>CTT	p.L35L	OR2L13_uc001ids.2_Intron	NM_001004686	NP_001004686	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L,	35	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			TCATTTTCCTAATGGCTCTAA	0.373													172	108	---	---	---	---	PASS
OR2L3	391192	broad.mit.edu	37	1	248224524	248224524	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248224524C>A	uc001idx.1	+	1	541	c.541C>A	c.(541-543)CCA>ACA	p.P181T	OR2L13_uc001ids.2_Intron	NM_001004687	NP_001004687	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L,	181	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			CTGTGATGTCCCAGCAATGGT	0.463													102	114	---	---	---	---	PASS
CAPN13	92291	broad.mit.edu	37	2	30998886	30998886	+	Silent	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30998886C>A	uc002rnn.2	-	4	473	c.297G>T	c.(295-297)CTG>CTT	p.L99L	CAPN13_uc002rnp.1_Silent_p.L99L	NM_144575	NP_653176	Q6MZZ7	CAN13_HUMAN	calpain 13	99	Calpain catalytic.				proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			large_intestine(1)|ovary(1)	2	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					TCAAGGATCCCAGTGCTGCCA	0.517													38	11	---	---	---	---	PASS
CD207	50489	broad.mit.edu	37	2	71060081	71060081	+	Missense_Mutation	SNP	A	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71060081A>G	uc002shg.2	-	4	714	c.667T>C	c.(667-669)TGT>CGT	p.C223R		NM_015717	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 antigen, langerin	223	C-type lectin.|Extracellular (Potential).				defense response to virus	endocytic vesicle|integral to membrane	mannose binding			ovary(1)|lung(1)	2						CTGGACACACAGAACTGCTCG	0.507													52	48	---	---	---	---	PASS
DCTN1	1639	broad.mit.edu	37	2	74597355	74597355	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74597355C>A	uc002skx.2	-	12	1556	c.1245G>T	c.(1243-1245)GAG>GAT	p.E415D	DCTN1_uc002skv.2_Missense_Mutation_p.E281D|DCTN1_uc002sku.2_Missense_Mutation_p.E281D|DCTN1_uc002skw.1_Missense_Mutation_p.E391D|DCTN1_uc010ffd.2_Missense_Mutation_p.E395D|DCTN1_uc002sky.2_Missense_Mutation_p.E378D	NM_004082	NP_004073	Q14203	DCTN1_HUMAN	dynactin 1 isoform 1	415	Potential.				cell death|G2/M transition of mitotic cell cycle|mitosis|nervous system development	centrosome|cytosol|kinetochore|microtubule|spindle pole	motor activity|protein binding			ovary(3)|skin(2)	5						CCTGGCTTAGCTCCTCCTGCA	0.562													52	83	---	---	---	---	PASS
REG3A	5068	broad.mit.edu	37	2	79385837	79385837	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79385837C>A	uc002sod.1	-	2	390	c.135G>T	c.(133-135)AAG>AAT	p.K45N	REG3A_uc002soe.1_Missense_Mutation_p.K45N|REG3A_uc002sof.1_Missense_Mutation_p.K45N	NM_138938	NP_620355	Q06141	REG3A_HUMAN	pancreatitis-associated protein precursor	45	C-type lectin.				acute-phase response|cell proliferation|heterophilic cell-cell adhesion|multicellular organismal development	cytoplasm|extracellular space|soluble fraction	sugar binding			skin(1)	1						AGCCATAGGCCTTGGAGCCTT	0.547													21	47	---	---	---	---	PASS
MAP4K4	9448	broad.mit.edu	37	2	102460599	102460599	+	Silent	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102460599C>T	uc002tbg.2	+	12	1114	c.1059C>T	c.(1057-1059)CGC>CGT	p.R353R	MAP4K4_uc002tbc.2_Silent_p.R353R|MAP4K4_uc002tbd.2_Silent_p.R353R|MAP4K4_uc002tbe.2_Silent_p.R353R|MAP4K4_uc002tbf.2_Silent_p.R353R|MAP4K4_uc010yvy.1_Silent_p.R353R|MAP4K4_uc002tbh.2_Silent_p.R353R|MAP4K4_uc002tbi.2_Silent_p.R206R|MAP4K4_uc010yvz.1_Silent_p.R333R|MAP4K4_uc002tbk.2_5'UTR|MAP4K4_uc002tbj.1_Silent_p.R249R	NM_145687	NP_663720	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase	353					intracellular protein kinase cascade|regulation of JNK cascade|response to stress	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	4						CTACTCTTCGCCGAGATTTCC	0.512													17	23	---	---	---	---	PASS
RANBP2	5903	broad.mit.edu	37	2	109398838	109398838	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109398838G>T	uc002tem.3	+	27	9141	c.9015G>T	c.(9013-9015)TGG>TGT	p.W3005C		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	3005	RanBD1 4.				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						CTTTAGTTTGGACTGCCTCAG	0.303													65	112	---	---	---	---	PASS
SCTR	6344	broad.mit.edu	37	2	120221813	120221813	+	Silent	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120221813G>A	uc002tma.2	-	6	748	c.522C>T	c.(520-522)CGC>CGT	p.R174R	SCTR_uc002tlz.2_5'UTR	NM_002980	NP_002971	P47872	SCTR_HUMAN	secretin receptor precursor	174	Cytoplasmic (Potential).				digestion|excretion	integral to plasma membrane	secretin receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3					Secretin(DB00021)	GGATGTAGTTGCGAGTGCAGT	0.577													42	45	---	---	---	---	PASS
PTPN4	5775	broad.mit.edu	37	2	120723183	120723183	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120723183G>T	uc002tmf.1	+	25	3291	c.2520G>T	c.(2518-2520)AAG>AAT	p.K840N	PTPN4_uc010flj.1_Missense_Mutation_p.K553N|PTPN4_uc010yyr.1_Missense_Mutation_p.K473N	NM_002830	NP_002821	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type	840	Tyrosine-protein phosphatase.					cytoplasm|cytoskeleton|internal side of plasma membrane	cytoskeletal protein binding|non-membrane spanning protein tyrosine phosphatase activity			ovary(2)	2					Alendronate(DB00630)	TACGAAACAAGAGGGCTGGCA	0.443													54	111	---	---	---	---	PASS
THSD7B	80731	broad.mit.edu	37	2	138375955	138375955	+	Intron	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138375955C>A	uc002tva.1	+						THSD7B_uc010zbj.1_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		TGATCCTATGCCTGTAGAGTG	0.483													24	46	---	---	---	---	PASS
SLC4A10	57282	broad.mit.edu	37	2	162762167	162762167	+	Silent	SNP	A	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162762167A>C	uc002ubx.3	+	15	1951	c.1767A>C	c.(1765-1767)TCA>TCC	p.S589S	SLC4A10_uc002uby.3_Silent_p.S559S|SLC4A10_uc010zcs.1_Silent_p.S570S	NM_022058	NP_071341	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate	589	Extracellular (Potential).				bicarbonate transport|chloride transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity|symporter activity			ovary(2)|lung(2)|pancreas(1)	5						ATGGGCTGTCATACCTATCTT	0.403													92	116	---	---	---	---	PASS
SCN1A	6323	broad.mit.edu	37	2	166870302	166870302	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166870302C>A	uc010zcz.1	-	18	3642	c.3624G>T	c.(3622-3624)TGG>TGT	p.W1208C	SCN1A_uc002udo.3_Missense_Mutation_p.W1088C|SCN1A_uc010fpk.2_Missense_Mutation_p.W1060C	NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha	1219	III.|Helical; Name=S1 of repeat III; (By similarity).					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|skin(6)|large_intestine(1)	13					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)	AGGTCTCAAACCAGTTATGTT	0.383													50	60	---	---	---	---	PASS
SCN1A	6323	broad.mit.edu	37	2	166870303	166870303	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166870303C>A	uc010zcz.1	-	18	3641	c.3623G>T	c.(3622-3624)TGG>TTG	p.W1208L	SCN1A_uc002udo.3_Missense_Mutation_p.W1088L|SCN1A_uc010fpk.2_Missense_Mutation_p.W1060L	NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha	1219	III.|Helical; Name=S1 of repeat III; (By similarity).					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|skin(6)|large_intestine(1)	13					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)	GGTCTCAAACCAGTTATGTTC	0.388													50	61	---	---	---	---	PASS
KIAA1715	80856	broad.mit.edu	37	2	176829140	176829140	+	Silent	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176829140C>T	uc002ukc.1	-	8	646	c.453G>A	c.(451-453)CCG>CCA	p.P151P	KIAA1715_uc010zer.1_Silent_p.P151P|KIAA1715_uc010fqw.1_Silent_p.P217P|KIAA1715_uc010zes.1_Silent_p.P153P|KIAA1715_uc002ukd.1_Silent_p.P28P|KIAA1715_uc010zet.1_RNA	NM_030650	NP_085153	Q9C0E8	LNP_HUMAN	Lunapark	151	Cytoplasmic (Potential).					integral to membrane	protein binding			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.0793)			CAGCAGATGGCGGCTCACACT	0.378													46	86	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179456980	179456980	+	Missense_Mutation	SNP	A	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179456980A>T	uc010zfg.1	-	251	52171	c.51947T>A	c.(51946-51948)CTG>CAG	p.L17316Q	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.L11011Q|TTN_uc010zfi.1_Missense_Mutation_p.L10944Q|TTN_uc010zfj.1_Missense_Mutation_p.L10819Q	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	18243							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACTGACTTCCAGATCTCTAGG	0.323													16	24	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179612491	179612491	+	Missense_Mutation	SNP	A	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179612491A>G	uc002unb.2	-	46	14860	c.14636T>C	c.(14635-14637)ATA>ACA	p.I4879T	TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron	NM_133379	NP_596870	Q8WZ42	TITIN_HUMAN	titin isoform novex-3	1002							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACTAGTTTCTATCATTTCTCC	0.358													48	44	---	---	---	---	PASS
SSFA2	6744	broad.mit.edu	37	2	182780263	182780263	+	Silent	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182780263G>A	uc002uoi.2	+	11	2218	c.1896G>A	c.(1894-1896)GAG>GAA	p.E632E	SSFA2_uc002uoh.2_Silent_p.E632E|SSFA2_uc002uoj.2_Silent_p.E632E|SSFA2_uc002uok.2_RNA|SSFA2_uc010zfo.1_Silent_p.E479E|SSFA2_uc002uol.2_Silent_p.E479E|SSFA2_uc002uom.2_Silent_p.E100E	NM_001130445	NP_001123917	P28290	SSFA2_HUMAN	sperm specific antigen 2 isoform 1	632						cytoplasm|plasma membrane	actin binding			breast(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			TTCCAGCAGAGACAGTAGAGC	0.413													40	69	---	---	---	---	PASS
COL3A1	1281	broad.mit.edu	37	2	189859285	189859285	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189859285G>T	uc002uqj.1	+	19	1429	c.1312G>T	c.(1312-1314)GGT>TGT	p.G438C		NM_000090	NP_000081	P02461	CO3A1_HUMAN	collagen type III alpha 1 preproprotein	438	Triple-helical region.				axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway	collagen type III|extracellular space	extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding			central_nervous_system(7)|ovary(4)|large_intestine(2)	13			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)|Palifermin(DB00039)	TGGTAAGAATGGTGCCAAAGG	0.393													30	57	---	---	---	---	PASS
GLS	2744	broad.mit.edu	37	2	191792047	191792047	+	Missense_Mutation	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191792047G>A	uc002usf.2	+	12	1528	c.1264G>A	c.(1264-1266)GTG>ATG	p.V422M	GLS_uc002use.2_Missense_Mutation_p.V422M|GLS_uc002usg.1_Missense_Mutation_p.V83M|GLS_uc002ush.2_Missense_Mutation_p.V83M|GLS_uc010zgi.1_Translation_Start_Site|GLS_uc010zgj.1_5'Flank	NM_014905	NP_055720	O94925	GLSK_HUMAN	glutaminase precursor	422					cellular amino acid biosynthetic process|glutamate secretion|glutamine catabolic process|neurotransmitter secretion	mitochondrial matrix	glutaminase activity			ovary(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00625)|Epithelial(96;0.0744)|all cancers(119;0.181)		L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	CTCCATTGAAGTGACTTGTGA	0.383													27	39	---	---	---	---	PASS
ALS2CR11	151254	broad.mit.edu	37	2	202400736	202400736	+	Intron	SNP	A	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202400736A>G	uc002uye.2	-						ALS2CR11_uc002uyf.2_Intron|ALS2CR11_uc010fti.2_Intron	NM_152525	NP_689738	Q53TS8	AL2SA_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)											large_intestine(1)|ovary(1)|skin(1)	3						GATACTCCTCAAATTTACCTC	0.318													29	37	---	---	---	---	PASS
MPP4	58538	broad.mit.edu	37	2	202547600	202547600	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202547600C>A	uc002uyk.3	-	8	822	c.614G>T	c.(613-615)GGA>GTA	p.G205V	MPP4_uc010ftj.2_Missense_Mutation_p.G205V|MPP4_uc010zhq.1_Missense_Mutation_p.G205V|MPP4_uc010zhr.1_Missense_Mutation_p.G205V|MPP4_uc010zhs.1_Missense_Mutation_p.G161V|MPP4_uc002uyj.3_Missense_Mutation_p.G161V|MPP4_uc010zht.1_Missense_Mutation_p.G178V|MPP4_uc002uyl.3_RNA|MPP4_uc010ftk.2_Missense_Mutation_p.G205V|MPP4_uc002uym.1_Missense_Mutation_p.G174V|MPP4_uc002uyn.2_Missense_Mutation_p.G161V	NM_033066	NP_149055	Q96JB8	MPP4_HUMAN	membrane protein, palmitoylated 4	205	PDZ.					cytoplasm	protein binding				0						AACTGAAACTCCATTCACTTC	0.383													70	91	---	---	---	---	PASS
PARD3B	117583	broad.mit.edu	37	2	206165256	206165256	+	Missense_Mutation	SNP	T	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206165256T>A	uc002var.1	+	17	2395	c.2188T>A	c.(2188-2190)TCT>ACT	p.S730T	PARD3B_uc010fub.1_Missense_Mutation_p.S730T|PARD3B_uc002vao.1_Missense_Mutation_p.S730T|PARD3B_uc002vap.1_Missense_Mutation_p.S668T|PARD3B_uc002vaq.1_Intron	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform	730					cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		TTTTCCAGAATCTCCAAGCAA	0.458													83	146	---	---	---	---	PASS
ZNF142	7701	broad.mit.edu	37	2	219507362	219507362	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219507362C>T	uc002vin.2	-	8	4313	c.3877G>A	c.(3877-3879)GCC>ACC	p.A1293T	ZNF142_uc002vil.2_Missense_Mutation_p.A1254T|ZNF142_uc010fvt.2_Missense_Mutation_p.A1130T|ZNF142_uc002vim.2_Missense_Mutation_p.A1130T	NM_001105537	NP_001099007	P52746	ZN142_HUMAN	zinc finger protein 142	1293	C2H2-type 20.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)|ovary(1)|skin(1)	4		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		CTGAACTGGGCTTCACACTGG	0.592													49	72	---	---	---	---	PASS
ANKMY1	51281	broad.mit.edu	37	2	241468618	241468618	+	Silent	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241468618C>A	uc002vyz.1	-	4	751	c.522G>T	c.(520-522)TCG>TCT	p.S174S	ANKMY1_uc002vza.1_Intron|ANKMY1_uc010fzd.1_Silent_p.S263S|ANKMY1_uc002vzb.1_Intron|ANKMY1_uc002vzc.1_Intron|ANKMY1_uc002vzd.1_Intron|ANKMY1_uc010fze.1_Intron|ANKMY1_uc002vze.2_Intron	NM_016552	NP_057636	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	174							zinc ion binding			central_nervous_system(1)	1		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		CACTGTTGGTCGAGTAGACAT	0.502													45	53	---	---	---	---	PASS
KCNH8	131096	broad.mit.edu	37	3	19492675	19492675	+	Missense_Mutation	SNP	G	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19492675G>C	uc003cbk.1	+	10	1799	c.1604G>C	c.(1603-1605)CGT>CCT	p.R535P	KCNH8_uc011awe.1_3'UTR|KCNH8_uc010hex.1_5'UTR|KCNH8_uc011awf.1_3'UTR	NM_144633	NP_653234	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H,	535	Cytoplasmic (Potential).					integral to membrane	two-component sensor activity			lung(4)|ovary(1)	5						GATGAACTGCGTTCTGACATC	0.438													135	29	---	---	---	---	PASS
SCN10A	6336	broad.mit.edu	37	3	38805051	38805051	+	Silent	SNP	T	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38805051T>G	uc003ciq.2	-	5	636	c.636A>C	c.(634-636)TCA>TCC	p.S212S		NM_006514	NP_006505	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha	212	I.				sensory perception	voltage-gated sodium channel complex				ovary(5)|skin(3)|large_intestine(1)|kidney(1)	10				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dibucaine(DB00527)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)	TCCGCAGGCCTGAGATCCCAC	0.428													70	12	---	---	---	---	PASS
DHFRL1	200895	broad.mit.edu	37	3	93779797	93779797	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93779797C>T	uc003dri.2	-	2	725	c.559G>A	c.(559-561)GAT>AAT	p.D187N	DHFRL1_uc003drj.2_Missense_Mutation_p.D187N|NSUN3_uc003drk.2_5'Flank|NSUN3_uc003drl.1_5'Flank	NM_176815	NP_789785	Q86XF0	DYRL1_HUMAN	dihydrofolate reductase-like 1	187					glycine biosynthetic process|nucleotide biosynthetic process|one-carbon metabolic process		dihydrofolate reductase activity|NADP binding				0						TCATATTAATCATCCTTCTCA	0.383													52	12	---	---	---	---	PASS
CBLB	868	broad.mit.edu	37	3	105377809	105377809	+	3'UTR	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105377809G>A	uc003dwc.2	-	19					CBLB_uc003dwa.2_3'UTR|CBLB_uc011bhi.1_3'UTR	NM_170662	NP_733762	Q13191	CBLB_HUMAN	Cas-Br-M (murine) ecotropic retroviral						cell surface receptor linked signaling pathway|NLS-bearing substrate import into nucleus	cytoplasm|nucleus	calcium ion binding|ligase activity|signal transducer activity|zinc ion binding			lung(4)|ovary(3)|breast(1)|skin(1)	9						CTACAGTTCTGGCTGCTATAG	0.463			Mis S		AML								61	17	---	---	---	---	PASS
ZNF80	7634	broad.mit.edu	37	3	113955305	113955305	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113955305C>T	uc010hqo.2	-	1	1121	c.617G>A	c.(616-618)CGA>CAA	p.R206Q	ZNF80_uc003ebf.2_RNA	NM_007136	NP_009067	P51504	ZNF80_HUMAN	zinc finger protein 80	206	C2H2-type 6.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Lung NSC(201;0.0233)|all_neural(597;0.0837)				CATACTATGTCGGAAGAAAAC	0.493													59	14	---	---	---	---	PASS
CCDC48	79825	broad.mit.edu	37	3	128757707	128757707	+	Silent	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128757707C>T	uc011bkt.1	+	7	1624	c.1624C>T	c.(1624-1626)CTG>TTG	p.L542L		NM_024768	NP_079044	Q9HA90	CCD48_HUMAN	coiled-coil domain containing 48	542											0						GAAGATTTTGCTGAGCACGCT	0.547													94	13	---	---	---	---	PASS
SLC9A9	285195	broad.mit.edu	37	3	143551032	143551032	+	Silent	SNP	A	G	G	rs112237207		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143551032A>G	uc003evn.2	-	2	389	c.207T>C	c.(205-207)GCT>GCC	p.A69A	SLC9A9_uc011bnk.1_Intron	NM_173653	NP_775924	Q8IVB4	SL9A9_HUMAN	solute carrier family 9 (sodium/hydrogen	69					regulation of pH	integral to membrane|late endosome membrane|recycling endosome	sodium:hydrogen antiporter activity			ovary(2)|skin(1)	3						TTGGTGCTGTAGCATATCGTA	0.348													20	41	---	---	---	---	PASS
MME	4311	broad.mit.edu	37	3	154802012	154802012	+	Missense_Mutation	SNP	A	T	T	rs148334392		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154802012A>T	uc010hvr.1	+	2	267	c.56A>T	c.(55-57)AAG>ATG	p.K19M	MME_uc003fab.1_Missense_Mutation_p.K19M|MME_uc003fac.1_Missense_Mutation_p.K19M|MME_uc003fad.1_Missense_Mutation_p.K19M|MME_uc003fae.1_Missense_Mutation_p.K19M	NM_007289	NP_009220	P08473	NEP_HUMAN	membrane metallo-endopeptidase	19	Cytoplasmic (Potential).|Stop-transfer sequence (Potential).				cell-cell signaling|proteolysis	integral to plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(2)|central_nervous_system(1)	3		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)	CCAAAGCCAAAGAAGAAACAG	0.418													140	27	---	---	---	---	PASS
GOLIM4	27333	broad.mit.edu	37	3	167764795	167764795	+	Intron	SNP	A	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167764795A>T	uc003ffe.2	-						GOLIM4_uc011bpe.1_Intron|GOLIM4_uc011bpf.1_Intron|GOLIM4_uc011bpg.1_Intron	NM_014498	NP_055313	O00461	GOLI4_HUMAN	golgi integral membrane protein 4						transport	cis-Golgi network|endocytic vesicle|endosome membrane|Golgi cisterna membrane|Golgi lumen|integral to membrane|nucleus				breast(4)|skin(1)	5						AATCTAGAAAATACAAGATGG	0.274													82	19	---	---	---	---	PASS
MAP3K13	9175	broad.mit.edu	37	3	185155322	185155322	+	Missense_Mutation	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185155322G>A	uc010hyf.2	+	4	829	c.563G>A	c.(562-564)CGG>CAG	p.R188Q	MAP3K13_uc011brt.1_Intron|MAP3K13_uc003fph.3_5'UTR|MAP3K13_uc011bru.1_Missense_Mutation_p.R44Q|MAP3K13_uc003fpi.2_Missense_Mutation_p.R188Q|MAP3K13_uc010hyg.2_Intron	NM_004721	NP_004712	O43283	M3K13_HUMAN	mitogen-activated protein kinase kinase kinase	188	Protein kinase.				activation of MAPKK activity|JNK cascade|positive regulation of NF-kappaB transcription factor activity|protein autophosphorylation	cytoplasm|membrane|membrane fraction	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding			ovary(2)|skin(1)	3	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			GGCAAGTTCCGGGCGGAAGAG	0.507													40	527	---	---	---	---	PASS
MAP3K13	9175	broad.mit.edu	37	3	185184616	185184616	+	Missense_Mutation	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185184616G>A	uc010hyf.2	+	11	1774	c.1508G>A	c.(1507-1509)CGT>CAT	p.R503H	MAP3K13_uc011brt.1_Missense_Mutation_p.R296H|MAP3K13_uc011bru.1_Missense_Mutation_p.R359H|MAP3K13_uc003fpi.2_Missense_Mutation_p.R503H|MAP3K13_uc010hyg.2_Missense_Mutation_p.R193H	NM_004721	NP_004712	O43283	M3K13_HUMAN	mitogen-activated protein kinase kinase kinase	503	Leucine-zipper 2.				activation of MAPKK activity|JNK cascade|positive regulation of NF-kappaB transcription factor activity|protein autophosphorylation	cytoplasm|membrane|membrane fraction	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding			ovary(2)|skin(1)	3	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			TTCTGCAGGCGTGAGCAAGCA	0.458													30	395	---	---	---	---	PASS
ZNF721	170960	broad.mit.edu	37	4	435561	435561	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:435561C>T	uc003gag.2	-	3	3386	c.2695G>A	c.(2695-2697)GGC>AGC	p.G899S	ABCA11P_uc003gac.2_Intron|ABCA11P_uc003gad.2_Intron|ABCA11P_uc011buv.1_Intron|ABCA11P_uc003gae.2_Intron|ABCA11P_uc010ibd.1_Intron|ZNF721_uc003gaf.3_Missense_Mutation_p.G931S|ZNF721_uc010ibe.2_Missense_Mutation_p.G887S	NM_133474	NP_597731	D9N162	D9N162_HUMAN	zinc finger protein 721	899						intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1						AAGGTTTTGCCACAGTCTCCA	0.383													6	25	---	---	---	---	PASS
LDB2	9079	broad.mit.edu	37	4	16504484	16504484	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16504484C>A	uc003goz.2	-	8	1220	c.904G>T	c.(904-906)GTA>TTA	p.V302L	LDB2_uc003gpa.2_3'UTR|LDB2_uc003gpb.2_Missense_Mutation_p.V300L|LDB2_uc011bxh.1_Missense_Mutation_p.V274L|LDB2_uc010iee.2_3'UTR|LDB2_uc003goy.2_Missense_Mutation_p.V177L|LDB2_uc011bxi.1_3'UTR	NM_001290	NP_001281	O43679	LDB2_HUMAN	LIM domain binding 2 isoform a	302	LIM-binding domain (LID) (By similarity).						LIM domain binding|transcription cofactor activity				0						GGCTCTCCTACCACCATCACA	0.488													13	116	---	---	---	---	PASS
SLIT2	9353	broad.mit.edu	37	4	20258373	20258373	+	Intron	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20258373G>T	uc003gpr.1	+						SLIT2_uc003gps.1_Intron	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11						TTCTGTAAGTGCATCCTCTGt	0.308													9	56	---	---	---	---	PASS
KCNIP4	80333	broad.mit.edu	37	4	20852181	20852181	+	Nonsense_Mutation	SNP	G	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20852181G>C	uc003gqe.2	-	2	306	c.222C>G	c.(220-222)TAC>TAG	p.Y74*	KCNIP4_uc003gqf.1_Nonsense_Mutation_p.Y70*|KCNIP4_uc003gqg.1_Nonsense_Mutation_p.Y29*|KCNIP4_uc003gqh.1_Nonsense_Mutation_p.Y66*|KCNIP4_uc003gqi.1_Nonsense_Mutation_p.Y29*|KCNIP4_uc010iel.2_Nonsense_Mutation_p.Y71*|KCNIP4_uc003gqd.3_Nonsense_Mutation_p.Y54*	NM_147182	NP_671711	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4 isoform 3	91	EF-hand 1; degenerate.					plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)				TAAATCCTCTGTAAAGGATCT	0.438													121	62	---	---	---	---	PASS
GPR125	166647	broad.mit.edu	37	4	22389781	22389781	+	Silent	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22389781G>A	uc003gqm.1	-	19	3778	c.3513C>T	c.(3511-3513)CAC>CAT	p.H1171H	GPR125_uc010ieo.1_Silent_p.H1027H|GPR125_uc003gql.1_Silent_p.H298H	NM_145290	NP_660333	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125 precursor	1171	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity			skin(1)	1		Breast(46;0.198)				TGTTTTTATGGTGGCGGCTTG	0.463													15	65	---	---	---	---	PASS
CORIN	10699	broad.mit.edu	37	4	47605631	47605631	+	Silent	SNP	A	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47605631A>G	uc003gxm.2	-	20	2688	c.2595T>C	c.(2593-2595)CAT>CAC	p.H865H	CORIN_uc011bzf.1_Silent_p.H726H|CORIN_uc011bzg.1_Silent_p.H798H	NM_006587	NP_006578	Q9Y5Q5	CORIN_HUMAN	corin	865	Extracellular (Potential).|Peptidase S1.				peptide hormone processing|regulation of systemic arterial blood pressure by atrial natriuretic peptide	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity|serine-type exopeptidase activity			ovary(1)|central_nervous_system(1)	2						ACACTGATGGATGGTCTAGAT	0.443													43	43	---	---	---	---	PASS
CCDC158	339965	broad.mit.edu	37	4	77290572	77290572	+	Intron	SNP	C	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77290572C>G	uc003hkb.3	-							NM_001042784	NP_001036249	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158											skin(3)|ovary(2)|pancreas(1)	6						CCTGTGCAGGCACTGACCTGC	0.493													21	49	---	---	---	---	PASS
CNOT6L	246175	broad.mit.edu	37	4	78695839	78695839	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78695839C>A	uc011ccd.1	-	3	290	c.159G>T	c.(157-159)TGG>TGT	p.W53C	CNOT6L_uc003hks.2_Missense_Mutation_p.W53C|CNOT6L_uc011cce.1_Missense_Mutation_p.W53C	NM_144571	NP_653172	Q96LI5	CNO6L_HUMAN	CCR4-NOT transcription complex, subunit 6-like	53					nuclear-transcribed mRNA poly(A) tail shortening	cytosol	exonuclease activity|protein binding			large_intestine(1)	1						GTGTCAATGACCAAAGTGATG	0.428													25	22	---	---	---	---	PASS
PPA2	27068	broad.mit.edu	37	4	106359127	106359127	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106359127C>T	uc003hxl.2	-	6	528	c.508G>A	c.(508-510)GTT>ATT	p.V170I	PPA2_uc003hxm.2_Missense_Mutation_p.V152I|PPA2_uc003hxn.2_Intron|PPA2_uc003hxo.2_Intron|PPA2_uc003hxp.2_Intron|PPA2_uc003hxq.2_Missense_Mutation_p.V77I|PPA2_uc003hxr.2_Missense_Mutation_p.V77I|PPA2_uc011cfa.1_Missense_Mutation_p.V77I	NM_176869	NP_789845	Q9H2U2	IPYR2_HUMAN	inorganic pyrophosphatase 2 isoform 1 precursor	170					diphosphate metabolic process|tRNA aminoacylation for protein translation	mitochondrial matrix	inorganic diphosphatase activity|magnesium ion binding			pancreas(1)	1		Myeloproliferative disorder(5;0.0255)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.03e-07)		ATTTCGCAAACATCAATAGGA	0.313													29	9	---	---	---	---	PASS
PDE5A	8654	broad.mit.edu	37	4	120474846	120474846	+	Missense_Mutation	SNP	T	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120474846T>C	uc003idh.2	-	8	1410	c.1255A>G	c.(1255-1257)ATG>GTG	p.M419V	PDE5A_uc003idf.2_Missense_Mutation_p.M377V|PDE5A_uc003idg.2_Missense_Mutation_p.M367V	NM_001083	NP_001074	O76074	PDE5A_HUMAN	phosphodiesterase 5A isoform 1	419	GAF 2.				platelet activation|signal transduction	cytosol	3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|zinc ion binding				0					Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Vardenafil(DB00862)	AGTGGTTCCATAGTATTTTTG	0.353													63	94	---	---	---	---	PASS
LRBA	987	broad.mit.edu	37	4	151509200	151509200	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151509200C>A	uc010ipj.2	-	41	6837	c.6363G>T	c.(6361-6363)AAG>AAT	p.K2121N	LRBA_uc003ilt.3_Missense_Mutation_p.K769N|LRBA_uc003ilu.3_Missense_Mutation_p.K2110N	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and	2121						endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)					ATCTTCTCACCTTGGGGTCGA	0.438													154	261	---	---	---	---	PASS
DCHS2	54798	broad.mit.edu	37	4	155253927	155253927	+	Missense_Mutation	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155253927G>A	uc003inw.2	-	9	1936	c.1936C>T	c.(1936-1938)CGG>TGG	p.R646W	DCHS2_uc003inx.2_Missense_Mutation_p.R1145W	NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1	646	Cadherin 5.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		AACTGTCGCCGCAAATAAATC	0.502													4	93	---	---	---	---	PASS
ANP32C	23520	broad.mit.edu	37	4	165118456	165118456	+	Silent	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165118456C>A	uc011cjk.1	-	1	408	c.408G>T	c.(406-408)CTG>CTT	p.L136L	MARCH1_uc003iqs.1_Intron	NM_012403	NP_036535	O43423	AN32C_HUMAN	acidic nuclear phosphoprotein 32C	136											0	all_hematologic(180;0.203)	Prostate(90;0.0138)|Melanoma(52;0.18)|all_neural(102;0.223)		KIRC - Kidney renal clear cell carcinoma(143;0.242)		ATGTGAGTTGCAGGAGAAGCT	0.502													57	21	---	---	---	---	PASS
CMBL	134147	broad.mit.edu	37	5	10290792	10290792	+	Missense_Mutation	SNP	T	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10290792T>C	uc003jes.2	-	2	534	c.83A>G	c.(82-84)GAG>GGG	p.E28G		NM_138809	NP_620164	Q96DG6	CMBL_HUMAN	carboxymethylenebutenolidase	28						cytosol	hydrolase activity|protein binding			skin(1)	1						CTTGATGTGCTCGACTTGAAC	0.473													156	368	---	---	---	---	PASS
ROPN1L	83853	broad.mit.edu	37	5	10450186	10450186	+	Missense_Mutation	SNP	G	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10450186G>C	uc003jex.3	+	3	649	c.378G>C	c.(376-378)TGG>TGC	p.W126C		NM_031916	NP_114122	Q96C74	ROP1L_HUMAN	ropporin 1-like	126					ciliary or flagellar motility|signal transduction	cytoplasm|motile cilium	cAMP-dependent protein kinase regulator activity|protein binding			ovary(1)	1						AAATCAAGTGGATAAACTTTT	0.388													80	191	---	---	---	---	PASS
CTNND2	1501	broad.mit.edu	37	5	11082963	11082963	+	Intron	SNP	A	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11082963A>G	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron|CTNND2_uc011cmx.1_Intron	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8						TGACCACTGCAAAAACAGGGA	0.517													32	70	---	---	---	---	PASS
CDH18	1016	broad.mit.edu	37	5	19483655	19483655	+	Missense_Mutation	SNP	G	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19483655G>C	uc003jgc.2	-	11	2014	c.1637C>G	c.(1636-1638)ACA>AGA	p.T546R	CDH18_uc003jgd.2_Missense_Mutation_p.T546R|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	546	Extracellular (Potential).|Cadherin 5.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)					AATGCTGGCTGTGTTATCTAT	0.408													38	79	---	---	---	---	PASS
CDH10	1008	broad.mit.edu	37	5	24535924	24535924	+	Silent	SNP	A	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24535924A>G	uc003jgr.1	-	4	866	c.534T>C	c.(532-534)TCT>TCC	p.S178S	CDH10_uc011cnu.1_RNA	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein	178	Cadherin 2.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)		CTTGCACCACAGAAGTACCTG	0.458										HNSCC(23;0.051)			37	55	---	---	---	---	PASS
CAPSL	133690	broad.mit.edu	37	5	35921087	35921087	+	Missense_Mutation	SNP	T	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35921087T>C	uc003jjt.1	-	2	231	c.136A>G	c.(136-138)AGA>GGA	p.R46G	CAPSL_uc003jju.1_Missense_Mutation_p.R46G	NM_001042625	NP_001036090	Q8WWF8	CAPSL_HUMAN	calcyphosine-like	46	EF-hand 1.					cytoplasm	calcium ion binding			skin(1)	1	all_lung(31;0.000268)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.167)|Colorectal(62;0.202)			GGGTCCTACCTGCCAAGTCCT	0.433													48	84	---	---	---	---	PASS
LMBRD2	92255	broad.mit.edu	37	5	36114583	36114583	+	Missense_Mutation	SNP	C	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36114583C>G	uc003jkb.1	-	13	1998	c.1583G>C	c.(1582-1584)GGA>GCA	p.G528A		NM_001007527	NP_001007528	Q68DH5	LMBD2_HUMAN	LMBR1 domain containing 2	528	Helical; (Potential).					integral to membrane					0	all_lung(31;0.000146)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TATATAGAATCCATCTGCAAT	0.303													66	95	---	---	---	---	PASS
HEATR7B2	133558	broad.mit.edu	37	5	41052595	41052595	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41052595G>T	uc003jmj.3	-	12	1692	c.1202C>A	c.(1201-1203)TCC>TAC	p.S401Y	HEATR7B2_uc003jmi.3_Intron	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	401							binding			ovary(6)|central_nervous_system(2)	8						TGCAAACTGGGAGAAGACATA	0.398													52	70	---	---	---	---	PASS
IQGAP2	10788	broad.mit.edu	37	5	75950761	75950761	+	Silent	SNP	T	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75950761T>C	uc003kek.2	+	20	2475	c.2253T>C	c.(2251-2253)AAT>AAC	p.N751N	IQGAP2_uc010izv.2_Silent_p.N304N|IQGAP2_uc011csv.1_Silent_p.N247N|IQGAP2_uc003kel.2_Silent_p.N247N	NM_006633	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	751	IQ 3.				small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity			ovary(6)|central_nervous_system(1)	7		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		TTTTGCAGAATAATGAAATTG	0.358													3	66	---	---	---	---	PASS
KLHL3	26249	broad.mit.edu	37	5	136961565	136961565	+	Missense_Mutation	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136961565G>A	uc010jek.2	-	14	2056	c.1612C>T	c.(1612-1614)CTC>TTC	p.L538F	KLHL3_uc011cyc.1_Missense_Mutation_p.L273F|KLHL3_uc003lbr.3_Missense_Mutation_p.L456F|KLHL3_uc011cyd.1_RNA	NM_017415	NP_059111	Q9UH77	KLHL3_HUMAN	kelch-like 3	538						cytoplasm|cytoskeleton	actin binding|structural molecule activity				0		all_hematologic(541;3.67e-07)|Breast(839;7.61e-05)|Prostate(281;0.000825)|Ovarian(839;0.0481)|all_lung(232;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	GBM - Glioblastoma multiforme(465;0.0223)		ACATACAGGAGCCCATTTACT	0.483													46	17	---	---	---	---	PASS
KDM3B	51780	broad.mit.edu	37	5	137708464	137708464	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137708464G>T	uc003lcy.1	+	2	494	c.294G>T	c.(292-294)TGG>TGT	p.W98C	KDM3B_uc010jew.1_5'UTR	NM_016604	NP_057688	Q7LBC6	KDM3B_HUMAN	jumonji domain containing 1B	98					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(3)|upper_aerodigestive_tract(2)|lung(2)|kidney(2)|central_nervous_system(1)|skin(1)	11						CTCTTGTATGGGCGCCCCGTG	0.517													5	75	---	---	---	---	PASS
PCDHB2	56133	broad.mit.edu	37	5	140475752	140475752	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140475752C>A	uc003lil.2	+	1	1516	c.1378C>A	c.(1378-1380)CTG>ATG	p.L460M	PCDHB2_uc003lim.1_Missense_Mutation_p.L121M	NM_018936	NP_061759	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2 precursor	460	Extracellular (Potential).|Cadherin 5.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			ovary(3)|upper_aerodigestive_tract(2)|pancreas(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTCCTACACCCTGTTCGTCCG	0.622													38	129	---	---	---	---	PASS
PCDHB10	56126	broad.mit.edu	37	5	140573497	140573497	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140573497C>A	uc003lix.2	+	1	1546	c.1372C>A	c.(1372-1374)CTG>ATG	p.L458M		NM_018930	NP_061753	Q9UN67	PCDBA_HUMAN	protocadherin beta 10 precursor	458	Cadherin 5.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTCCTACACCCTGTTCGTCCG	0.617													47	11	---	---	---	---	PASS
TIMD4	91937	broad.mit.edu	37	5	156378594	156378594	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156378594C>T	uc003lwh.2	-	3	665	c.608G>A	c.(607-609)AGC>AAC	p.S203N	TIMD4_uc010jii.2_Missense_Mutation_p.S203N	NM_138379	NP_612388	Q96H15	TIMD4_HUMAN	T-cell immunoglobulin and mucin domain	203	Extracellular (Potential).|Thr-rich.					integral to membrane				ovary(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CGGAAGGGTGCTTGGGGTTAG	0.537													72	15	---	---	---	---	PASS
HIST1H1C	3006	broad.mit.edu	37	6	26056542	26056542	+	Missense_Mutation	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26056542G>A	uc003nfw.2	-	1	158	c.115C>T	c.(115-117)CCG>TCG	p.P39S		NM_005319	NP_005310	P16403	H12_HUMAN	histone cluster 1, H1c	39	H15.				nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(3)|skin(2)	5						TCTGACACCGGGGGACCAGAC	0.627													22	86	---	---	---	---	PASS
HIST1H1C	3006	broad.mit.edu	37	6	26056543	26056543	+	Silent	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26056543G>A	uc003nfw.2	-	1	157	c.114C>T	c.(112-114)CCC>CCT	p.P38P		NM_005319	NP_005310	P16403	H12_HUMAN	histone cluster 1, H1c	38	H15.				nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(3)|skin(2)	5						CTGACACCGGGGGACCAGACG	0.632													22	85	---	---	---	---	PASS
BTN3A3	10384	broad.mit.edu	37	6	26446185	26446185	+	Silent	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26446185G>T	uc003nhz.2	+	5	867	c.687G>T	c.(685-687)CTG>CTT	p.L229L	BTN3A3_uc003nia.2_Silent_p.L187L|BTN3A3_uc011dkn.1_Silent_p.L187L	NM_006994	NP_008925	O00478	BT3A3_HUMAN	butyrophilin, subfamily 3, member A3 isoform a	229	Extracellular (Potential).|Ig-like V-type 2.					integral to membrane					0						TCCTCGGCCTGGAAAAGACAG	0.547													95	85	---	---	---	---	PASS
HIST1H1B	3009	broad.mit.edu	37	6	27835194	27835194	+	Silent	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27835194C>A	uc003njx.2	-	1	166	c.114G>T	c.(112-114)GCG>GCT	p.A38A		NM_005322	NP_005313	P16401	H15_HUMAN	histone cluster 1, H1b	38					nucleosome assembly	nucleosome|nucleus	DNA binding			large_intestine(2)|lung(1)	3						GGGGCCCCGTCGCTTTGCGCT	0.627													85	63	---	---	---	---	PASS
ZFP57	346171	broad.mit.edu	37	6	29640508	29640508	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29640508C>A	uc011dlw.1	-	4	1531	c.1380G>T	c.(1378-1380)AGG>AGT	p.R460S	ZFP57_uc003nnl.3_Missense_Mutation_p.R440S	NM_001109809	NP_001103279	Q9NU63	ZFP57_HUMAN	zinc finger protein 57 homolog	376	C2H2-type 7; degenerate.				DNA methylation involved in embryo development|regulation of gene expression by genetic imprinting|transcription, DNA-dependent		DNA binding|zinc ion binding			ovary(3)|skin(2)	5						CTTTATAGCCCCTCCAGTGAT	0.557													42	82	---	---	---	---	PASS
C6orf136	221545	broad.mit.edu	37	6	30619233	30619233	+	Missense_Mutation	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30619233G>A	uc003nqw.3	+	4	947	c.754G>A	c.(754-756)GAG>AAG	p.E252K	C6orf136_uc003nqx.3_Missense_Mutation_p.E433K|C6orf136_uc011dmn.1_Missense_Mutation_p.E118K	NM_001109938	NP_001103408	Q5SQH8	CF136_HUMAN	hypothetical protein LOC221545 isoform 1	252											0						TGACAAAGACGAGCATTACCG	0.408													188	172	---	---	---	---	PASS
BTNL2	56244	broad.mit.edu	37	6	32372966	32372966	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32372966C>T	uc003obg.1	-	2	177	c.177G>A	c.(175-177)ATG>ATA	p.M59I	BTNL2_uc010jty.1_5'UTR|BTNL2_uc010jtz.1_RNA|BTNL2_uc010jua.1_Intron	NM_019602	NP_062548	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2	59	Ig-like V-type 1.|Extracellular (Potential).					integral to membrane				central_nervous_system(1)	1						CCTCCACGTGCATTGTGGTCC	0.562													77	109	---	---	---	---	PASS
MOCS1	4337	broad.mit.edu	37	6	39881098	39881098	+	Silent	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39881098G>T	uc003opb.2	-	5	858	c.720C>A	c.(718-720)CCC>CCA	p.P240P	MOCS1_uc003opa.2_Silent_p.P240P|MOCS1_uc003opc.2_Silent_p.P240P|MOCS1_uc003opd.2_Silent_p.P240P|MOCS1_uc003ope.2_Silent_p.P153P	NM_005942	NP_005933	Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis-step 1 protein	240	Molybdenum cofactor biosynthesis protein A.				Mo-molybdopterin cofactor biosynthetic process|Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol|molybdopterin synthase complex|nucleus	4 iron, 4 sulfur cluster binding|4 iron, 4 sulfur cluster binding|catalytic activity|GTP binding|metal ion binding			ovary(1)|liver(1)|central_nervous_system(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)					GCACATCCAGGGGGAGGCCCT	0.572													19	72	---	---	---	---	PASS
RUNX2	860	broad.mit.edu	37	6	45405763	45405763	+	Silent	SNP	A	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45405763A>C	uc011dvx.1	+	5	870	c.660A>C	c.(658-660)ACA>ACC	p.T220T	RUNX2_uc011dvy.1_Silent_p.T220T|RUNX2_uc003oxt.2_Silent_p.T206T	NM_001024630	NP_001019801	Q13950	RUNX2_HUMAN	runt-related transcription factor 2 isoform a	220	Runt.		T -> I (in CLCD; has severely impaired DNA binding and transactivation).		negative regulation of transcription, DNA-dependent|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3						TTAAAGTTACAGTAGATGGAC	0.408													89	144	---	---	---	---	PASS
ENPP5	59084	broad.mit.edu	37	6	46135373	46135373	+	Silent	SNP	T	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46135373T>A	uc003oxz.1	-	2	835	c.627A>T	c.(625-627)TCA>TCT	p.S209S	ENPP5_uc003oya.1_Silent_p.S209S|ENPP5_uc011dvz.1_Silent_p.S115S|ENPP5_uc010jzc.1_Silent_p.S209S	NM_021572	NP_067547	Q9UJA9	ENPP5_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	209						extracellular region|integral to membrane	hydrolase activity				0						TGTCAATATCTGAAATGACAG	0.443													75	71	---	---	---	---	PASS
DST	667	broad.mit.edu	37	6	56468740	56468740	+	Intron	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56468740C>A	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron|DST_uc003pdb.2_Missense_Mutation_p.L3025F	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CATCTCTTGGCAATGTTGATG	0.393													22	38	---	---	---	---	PASS
SIM1	6492	broad.mit.edu	37	6	100895281	100895281	+	Missense_Mutation	SNP	C	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100895281C>G	uc003pqj.3	-	8	1068	c.861G>C	c.(859-861)AAG>AAC	p.K287N	SIM1_uc010kcu.2_Missense_Mutation_p.K287N	NM_005068	NP_005059	P81133	SIM1_HUMAN	single-minded homolog 1	287	PAS 2.				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(4)	4		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		TCACCTGTCCCTTCACCAGCA	0.592													30	36	---	---	---	---	PASS
AHI1	54806	broad.mit.edu	37	6	135811852	135811852	+	Missense_Mutation	SNP	C	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135811852C>G	uc003qgi.2	-	5	428	c.44G>C	c.(43-45)CGC>CCC	p.R15P	AHI1_uc003qgh.2_Missense_Mutation_p.R15P|AHI1_uc003qgj.2_Missense_Mutation_p.R15P|AHI1_uc003qgk.3_RNA|AHI1_uc003qgl.3_Missense_Mutation_p.R15P	NM_001134831	NP_001128303	Q8N157	AHI1_HUMAN	Abelson helper integration site 1 isoform a	15	Potential.					adherens junction|cilium|microtubule basal body				ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		TTCTTCAAAGCGAACTTTGGT	0.353													112	124	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152718077	152718077	+	Silent	SNP	A	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152718077A>G	uc010kiw.2	-	50	7991	c.7389T>C	c.(7387-7389)CTT>CTC	p.L2463L	SYNE1_uc003qot.3_Silent_p.L2470L|SYNE1_uc003qou.3_Silent_p.L2463L|SYNE1_uc010kjb.1_Silent_p.L2446L	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2463	Spectrin 4.|Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TCACTGCATCAAGTTTGCTCT	0.388										HNSCC(10;0.0054)			76	65	---	---	---	---	PASS
SYNJ2	8871	broad.mit.edu	37	6	158497822	158497822	+	Intron	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158497822G>T	uc003qqx.1	+						SYNJ2_uc003qqw.1_Intron|SYNJ2_uc003qqy.1_Intron|SYNJ2_uc003qqz.1_Intron|SYNJ2_uc003qra.1_Intron	NM_003898	NP_003889	O15056	SYNJ2_HUMAN	synaptojanin 2								nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		CAGGTGAGGGGGCCGTGCCCG	0.562													24	21	---	---	---	---	PASS
SLC22A1	6580	broad.mit.edu	37	6	160551242	160551242	+	Intron	SNP	A	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160551242A>T	uc003qtc.2	+						SLC22A1_uc003qtd.2_Intron	NM_003057	NP_003048	O15245	S22A1_HUMAN	solute carrier family 22 member 1 isoform a							basolateral plasma membrane|integral to plasma membrane|membrane fraction	organic cation transmembrane transporter activity|protein binding				0		Breast(66;0.000776)|Ovarian(120;0.00556)		OV - Ovarian serous cystadenocarcinoma(65;2.73e-17)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)		GCAGACAGGTATGTAAAGGCC	0.348													78	65	---	---	---	---	PASS
SP4	6671	broad.mit.edu	37	7	21469180	21469180	+	Missense_Mutation	SNP	G	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21469180G>C	uc003sva.2	+	3	578	c.397G>C	c.(397-399)GGG>CGG	p.G133R	SP4_uc003svb.2_5'UTR	NM_003112	NP_003103	Q02446	SP4_HUMAN	Sp4 transcription factor	133					regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(3)|skin(2)	5						CAGTAATAACGGGAGTGCATC	0.428													45	11	---	---	---	---	PASS
SCRN1	9805	broad.mit.edu	37	7	29966073	29966073	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29966073C>A	uc010kvp.2	-	6	1285	c.1081G>T	c.(1081-1083)GAC>TAC	p.D361Y	SCRN1_uc011jzy.1_Missense_Mutation_p.D293Y|SCRN1_uc003tak.2_Missense_Mutation_p.D361Y|SCRN1_uc011jzz.1_Missense_Mutation_p.D361Y|SCRN1_uc011kaa.1_Missense_Mutation_p.D381Y|SCRN1_uc011jzw.1_Missense_Mutation_p.D228Y|SCRN1_uc011jzx.1_Missense_Mutation_p.D184Y	NM_001145515	NP_001138987	Q12765	SCRN1_HUMAN	secernin 1 isoform c	361					exocytosis|proteolysis	cytoplasm|nuclear membrane	dipeptidase activity			ovary(2)	2						CTCACCTGGTCACTTTCGATG	0.622													95	21	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48285534	48285534	+	Silent	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48285534C>A	uc003toq.2	+	13	1591	c.1566C>A	c.(1564-1566)TCC>TCA	p.S522S	ABCA13_uc010kyr.2_Silent_p.S25S	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	522					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						CTGGAAACTCCAGCATATGGG	0.463													41	5	---	---	---	---	PASS
ZNF479	90827	broad.mit.edu	37	7	57188389	57188389	+	Nonsense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57188389C>A	uc010kzo.2	-	5	1004	c.733G>T	c.(733-735)GAA>TAA	p.E245*		NM_033273	NP_150376	Q96JC4	ZN479_HUMAN	zinc finger protein 479	245	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(1)	4			GBM - Glioblastoma multiforme(1;9.18e-12)			TTGCCACATTCCTCACATCTA	0.408													28	15	---	---	---	---	PASS
WBSCR17	64409	broad.mit.edu	37	7	71130455	71130455	+	Missense_Mutation	SNP	G	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71130455G>C	uc003tvy.2	+	7	1140	c.1140G>C	c.(1138-1140)GAG>GAC	p.E380D	WBSCR17_uc003tvz.2_Missense_Mutation_p.E79D	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide	380	Catalytic subdomain B.|Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				CCCACATTGAGCGGAAGAAGA	0.493													76	118	---	---	---	---	PASS
PCLO	27445	broad.mit.edu	37	7	82455955	82455955	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82455955C>T	uc003uhx.2	-	18	14654	c.14365G>A	c.(14365-14367)GTG>ATG	p.V4789M	PCLO_uc003uhv.2_Missense_Mutation_p.V4789M|PCLO_uc003uht.1_Missense_Mutation_p.V231M|PCLO_uc003uhu.1_Missense_Mutation_p.V210M	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	4651	C2 1.				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						CAAACTGTCACCTCCAGTGTT	0.363													41	94	---	---	---	---	PASS
ZNF804B	219578	broad.mit.edu	37	7	88965803	88965803	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88965803G>T	uc011khi.1	+	4	4045	c.3507G>T	c.(3505-3507)ATG>ATT	p.M1169I		NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	1169						intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			AGCAGCATATGCAGAAGCAAC	0.458										HNSCC(36;0.09)			39	68	---	---	---	---	PASS
ZNF804B	219578	broad.mit.edu	37	7	88965804	88965804	+	Nonsense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88965804C>T	uc011khi.1	+	4	4046	c.3508C>T	c.(3508-3510)CAG>TAG	p.Q1170*		NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	1170						intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			GCAGCATATGCAGAAGCAACT	0.458										HNSCC(36;0.09)			39	66	---	---	---	---	PASS
CYP3A43	64816	broad.mit.edu	37	7	99457596	99457596	+	Missense_Mutation	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99457596G>A	uc003urx.1	+	10	1112	c.1009G>A	c.(1009-1011)GCA>ACA	p.A337T	CYP3A43_uc003ury.1_Missense_Mutation_p.A337T|CYP3A43_uc003urz.1_Missense_Mutation_p.A337T|CYP3A43_uc003usa.1_RNA|CYP3A43_uc010lgi.1_Missense_Mutation_p.A227T|CYP3A43_uc003usb.1_Missense_Mutation_p.A197T	NM_057095	NP_476436	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A,	337			Missing (in allele CYP3A43*2).		xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding			ovary(1)|skin(1)	2	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)				Cetirizine(DB00341)|Doxycycline(DB00254)	GGAGATTGACGCAGTTTTACC	0.498													60	69	---	---	---	---	PASS
ZNF425	155054	broad.mit.edu	37	7	148801240	148801240	+	Missense_Mutation	SNP	T	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148801240T>C	uc003wfj.2	-	4	1796	c.1723A>G	c.(1723-1725)ATG>GTG	p.M575V		NM_001001661	NP_001001661	Q6IV72	ZN425_HUMAN	zinc finger protein 425	575	C2H2-type 13.				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			breast(2)|ovary(1)	3	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			TCCCTGTGCATCCGCTGGTGG	0.597													29	50	---	---	---	---	PASS
KRBA1	84626	broad.mit.edu	37	7	149421860	149421860	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149421860C>T	uc003wfz.2	+	9	1445	c.1046C>T	c.(1045-1047)CCT>CTT	p.P349L	KRBA1_uc010lpj.2_RNA|KRBA1_uc003wga.2_RNA|KRBA1_uc003wgb.2_Missense_Mutation_p.P17L	NM_032534	NP_115923	A5PL33	KRBA1_HUMAN	KRAB A domain containing 1	349										ovary(1)|central_nervous_system(1)	2	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			TCCTGTCAGCCTGGCAGGCAG	0.567													4	0	---	---	---	---	PASS
MLL3	58508	broad.mit.edu	37	7	151944982	151944982	+	Intron	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151944982C>A	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		TTAAAATCACCCTACCTGTTT	0.373			N		medulloblastoma								43	154	---	---	---	---	PASS
MLL3	58508	broad.mit.edu	37	7	151962204	151962204	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151962204C>A	uc003wla.2	-	8	1322	c.1103G>T	c.(1102-1104)GGA>GTA	p.G368V		NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	368	PHD-type 1.|RING-type.				intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		CAGGCACATTCCATGATAGTG	0.438			N		medulloblastoma								37	497	---	---	---	---	PASS
CNPY1	285888	broad.mit.edu	37	7	155301605	155301605	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155301605C>A	uc003wmc.1	-	2	273	c.128G>T	c.(127-129)AGA>ATA	p.R43I		NM_001103176	NP_001096646	Q3B7I2	CNPY1_HUMAN	canopy 1 homolog	43											0	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)		TTTCAAAGGTCTGTAAGCATC	0.358													36	6	---	---	---	---	PASS
CSGALNACT1	55790	broad.mit.edu	37	8	19362938	19362938	+	Silent	SNP	G	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19362938G>C	uc011kyn.1	-	4	1472	c.408C>G	c.(406-408)GGC>GGG	p.G136G	CSGALNACT1_uc011kyo.1_Silent_p.G136G|CSGALNACT1_uc003wzg.2_RNA|CSGALNACT1_uc011kyp.1_Silent_p.G135G|CSGALNACT1_uc003wzh.2_RNA	NM_001130518	NP_001123990	Q8TDX6	CGAT1_HUMAN	chondroitin sulfate	136	Lumenal (Potential).				anatomical structure morphogenesis|cell proliferation|cell recognition|chondroitin sulfate biosynthetic process|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process|extracellular matrix organization|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|heparin biosynthetic process|nervous system development|UDP-glucuronate metabolic process|UDP-N-acetylgalactosamine metabolic process	Golgi cisterna membrane|integral to Golgi membrane|soluble fraction	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|glucuronosyltransferase activity|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|peptidoglycan glycosyltransferase activity			central_nervous_system(2)|ovary(1)	3				Colorectal(111;0.182)		CCAGCTTGACGCCAGCATTCA	0.607													59	11	---	---	---	---	PASS
ADAM2	2515	broad.mit.edu	37	8	39627070	39627070	+	Silent	SNP	A	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39627070A>G	uc003xnj.2	-	12	1128	c.1053T>C	c.(1051-1053)TTT>TTC	p.F351F	ADAM2_uc003xnk.2_Silent_p.F332F|ADAM2_uc011lck.1_Silent_p.F351F|ADAM2_uc003xnl.2_Silent_p.F225F	NM_001464	NP_001455	Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2 proprotein	351	Extracellular (Potential).|Peptidase M12B.				cell adhesion|fusion of sperm to egg plasma membrane|proteolysis	integral to plasma membrane	integrin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)		TGCAGTTACTAAAGATCTTCA	0.368													27	54	---	---	---	---	PASS
SNTG1	54212	broad.mit.edu	37	8	51449231	51449231	+	Intron	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51449231C>T	uc010lxy.1	+						SNTG1_uc003xqs.1_Intron|SNTG1_uc010lxz.1_Intron|SNTG1_uc011ldl.1_Intron	NM_018967	NP_061840	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1						cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding			ovary(5)	5		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				ATTTATCTTCCTTTCAGGACA	0.438													103	333	---	---	---	---	PASS
C8orf38	137682	broad.mit.edu	37	8	96070046	96070046	+	Missense_Mutation	SNP	G	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96070046G>C	uc003yhj.2	+	9	899	c.883G>C	c.(883-885)GAG>CAG	p.E295Q	C8orf38_uc003yhf.2_Missense_Mutation_p.E203Q|C8orf38_uc011lgs.1_Intron|C8orf38_uc003yhi.2_Missense_Mutation_p.E243Q|C8orf38_uc003yhk.2_RNA|C8orf38_uc003yhl.2_Missense_Mutation_p.E203Q	NM_152416	NP_689629	Q330K2	CH038_HUMAN	hypothetical protein LOC137682 precursor	295					biosynthetic process	mitochondrion	transferase activity				0	Breast(36;3.32e-06)					GGTTTCTCTAGAGGACTTTCT	0.284													40	98	---	---	---	---	PASS
DPYS	1807	broad.mit.edu	37	8	105393524	105393524	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105393524C>A	uc003yly.3	-	9	1591	c.1462G>T	c.(1462-1464)GTG>TTG	p.V488L	DPYS_uc010mcf.1_Missense_Mutation_p.V58L	NM_001385	NP_001376	Q14117	DPYS_HUMAN	dihydropyrimidinase	488					protein homotetramerization|pyrimidine nucleoside catabolic process|thymine catabolic process|uracil catabolic process	cytosol	dihydropyrimidinase activity|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)			GCACGCTCCACAGGGGTAGGT	0.468													163	15	---	---	---	---	PASS
TRPS1	7227	broad.mit.edu	37	8	116631873	116631873	+	Missense_Mutation	SNP	T	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116631873T>A	uc003ynz.2	-	2	872	c.413A>T	c.(412-414)GAT>GTT	p.D138V	TRPS1_uc011lhy.1_Missense_Mutation_p.D142V|TRPS1_uc003yny.2_Missense_Mutation_p.D151V|TRPS1_uc010mcy.2_Missense_Mutation_p.D138V	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	138					negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			GCAGGCCATATCTTGAGGGTC	0.527									Langer-Giedion_syndrome				77	142	---	---	---	---	PASS
TRPS1	7227	broad.mit.edu	37	8	116631874	116631874	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116631874C>A	uc003ynz.2	-	2	871	c.412G>T	c.(412-414)GAT>TAT	p.D138Y	TRPS1_uc011lhy.1_Missense_Mutation_p.D142Y|TRPS1_uc003yny.2_Missense_Mutation_p.D151Y|TRPS1_uc010mcy.2_Missense_Mutation_p.D138Y	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	138					negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			CAGGCCATATCTTGAGGGTCA	0.532									Langer-Giedion_syndrome				76	143	---	---	---	---	PASS
NDUFB9	4715	broad.mit.edu	37	8	125551427	125551427	+	5'UTR	SNP	A	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125551427A>G	uc003yrg.3	+	1					NDUFB9_uc011lim.1_5'UTR|TATDN1_uc003yre.2_5'Flank|TATDN1_uc003yrd.2_5'Flank|TATDN1_uc010mdm.2_5'Flank|TATDN1_uc003yrf.2_5'Flank	NM_005005	NP_004996	Q9Y6M9	NDUB9_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta						mitochondrial electron transport, NADH to ubiquinone|sensory perception of sound|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity			ovary(1)|skin(1)	2	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)		NADH(DB00157)	TCAGCGCCGTAATGGCGTTCT	0.677													61	76	---	---	---	---	PASS
FAM135B	51059	broad.mit.edu	37	8	139164914	139164914	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139164914G>T	uc003yuy.2	-	13	1975	c.1804C>A	c.(1804-1806)CAA>AAA	p.Q602K	FAM135B_uc003yux.2_Missense_Mutation_p.Q503K|FAM135B_uc003yuz.2_RNA|FAM135B_uc003yva.2_Missense_Mutation_p.Q164K|FAM135B_uc003yvb.2_Missense_Mutation_p.Q164K	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	602										ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			ATGGCATTTTGGTGGCTTCCA	0.453										HNSCC(54;0.14)			477	37	---	---	---	---	PASS
FAM135B	51059	broad.mit.edu	37	8	139164915	139164915	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139164915G>T	uc003yuy.2	-	13	1974	c.1803C>A	c.(1801-1803)CAC>CAA	p.H601Q	FAM135B_uc003yux.2_Missense_Mutation_p.H502Q|FAM135B_uc003yuz.2_RNA|FAM135B_uc003yva.2_Missense_Mutation_p.H163Q|FAM135B_uc003yvb.2_Missense_Mutation_p.H163Q	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	601										ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			TGGCATTTTGGTGGCTTCCAC	0.458										HNSCC(54;0.14)			480	36	---	---	---	---	PASS
FAM135B	51059	broad.mit.edu	37	8	139165094	139165094	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139165094C>A	uc003yuy.2	-	13	1795	c.1624G>T	c.(1624-1626)GGT>TGT	p.G542C	FAM135B_uc003yux.2_Missense_Mutation_p.G443C|FAM135B_uc003yuz.2_RNA|FAM135B_uc003yva.2_Missense_Mutation_p.G104C|FAM135B_uc003yvb.2_Missense_Mutation_p.G104C	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	542										ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			TCCTCTGGACCTGGACTCCTT	0.502										HNSCC(54;0.14)			238	10	---	---	---	---	PASS
COL22A1	169044	broad.mit.edu	37	8	139610959	139610959	+	Intron	SNP	T	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139610959T>C	uc003yvd.2	-						COL22A1_uc011ljo.1_Intron	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			TTAGCATCCTTACCCTCAGTC	0.488										HNSCC(7;0.00092)			286	15	---	---	---	---	PASS
UNC13B	10497	broad.mit.edu	37	9	35295836	35295836	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35295836C>A	uc003zwq.2	+	8	962	c.670C>A	c.(670-672)CAG>AAG	p.Q224K	UNC13B_uc010mkl.1_Missense_Mutation_p.Q224K|UNC13B_uc003zwr.2_Missense_Mutation_p.Q224K	NM_006377	NP_006368	O14795	UN13B_HUMAN	UNC13 (C. elegans)-like	224					excretion|induction of apoptosis|intracellular signal transduction	cell junction|Golgi apparatus|synapse	metal ion binding|receptor activity			ovary(3)|large_intestine(1)|skin(1)	5	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			GCGATCGCCACAGCAGCTGCT	0.542													22	6	---	---	---	---	PASS
C9orf128	392307	broad.mit.edu	37	9	35825345	35825345	+	Silent	SNP	A	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35825345A>T	uc010mlc.2	-	3	909	c.624T>A	c.(622-624)CCT>CCA	p.P208P	C9orf128_uc003zyj.2_RNA|C9orf128_uc011lpg.1_Silent_p.P208P	NM_001012446	NP_001012448	A6H8Z2	CI128_HUMAN	hypothetical protein LOC392307	208											0	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)			TCTGCCTAGCAGGGAACACTG	0.532													62	26	---	---	---	---	PASS
NIPSNAP3B	55335	broad.mit.edu	37	9	107535353	107535353	+	Nonstop_Mutation	SNP	A	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107535353A>T	uc004bci.2	+	6	814	c.743A>T	c.(742-744)TAG>TTG	p.*248L	NIPSNAP3B_uc004bcj.1_RNA|LOC286367_uc004bck.3_5'Flank	NM_018376	NP_060846	Q9BS92	NPS3B_HUMAN	nipsnap homolog 3B	248										pancreas(1)|skin(1)	2						CCATTGAAATAGTTTTCTACT	0.363													57	14	---	---	---	---	PASS
ABCA1	19	broad.mit.edu	37	9	107560766	107560766	+	Missense_Mutation	SNP	T	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107560766T>A	uc004bcl.2	-	37	5370	c.5057A>T	c.(5056-5058)CAC>CTC	p.H1686L		NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1	1686					Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	GAACTGCAGGTGTTTTGCTTT	0.488													84	13	---	---	---	---	PASS
WDR31	114987	broad.mit.edu	37	9	116082637	116082637	+	Silent	SNP	C	G	G	rs148709910		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116082637C>G	uc004bhe.2	-	9	1032	c.780G>C	c.(778-780)ACG>ACC	p.T260T	WDR31_uc004bhc.2_Silent_p.T259T|WDR31_uc004bhd.2_Silent_p.T135T|WDR31_uc004bhf.2_RNA	NM_001012361	NP_001012361	Q8NA23	WDR31_HUMAN	WD repeat domain 31 isoform 1	260											0						AGTCTCCTACCGTGGCTTCAC	0.517													75	19	---	---	---	---	PASS
CEP110	11064	broad.mit.edu	37	9	123903707	123903707	+	Silent	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123903707G>A	uc004bkx.1	+	16	2563	c.2532G>A	c.(2530-2532)CAG>CAA	p.Q844Q	CEP110_uc004bky.1_Silent_p.Q448Q|CEP110_uc004bkz.1_Silent_p.Q292Q|CEP110_uc004bla.1_Silent_p.Q292Q|CEP110_uc010mvo.1_5'Flank	NM_007018	NP_008949	Q7Z7A1	CNTRL_HUMAN	centrosomal protein 110kDa	844					cell division|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding				0						CTGATTTACAGAAACAATTCA	0.393													76	10	---	---	---	---	PASS
OR1J1	347168	broad.mit.edu	37	9	125240093	125240093	+	Missense_Mutation	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125240093G>A	uc011lyu.1	-	1	113	c.113C>T	c.(112-114)ACG>ATG	p.T38M	OR1J2_uc004bmj.1_Intron	NM_001004451	NP_001004451	Q8NGS3	OR1J1_HUMAN	olfactory receptor, family 1, subfamily J,	38	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2						CCCCAGCACCGTGGTCAGGTA	0.597													11	186	---	---	---	---	PASS
GARNL3	84253	broad.mit.edu	37	9	130106616	130106616	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130106616C>A	uc011mae.1	+	15	1755	c.1354C>A	c.(1354-1356)CAG>AAG	p.Q452K	GARNL3_uc011mad.1_Missense_Mutation_p.Q430K|GARNL3_uc004bqt.1_Missense_Mutation_p.Q233K	NM_032293	NP_115669	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3	452					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity|small GTPase regulator activity			ovary(1)|central_nervous_system(1)|skin(1)	3						TAGAATAGGGCAGGTGGGTTT	0.483													141	26	---	---	---	---	PASS
SPTAN1	6709	broad.mit.edu	37	9	131337068	131337068	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131337068G>T	uc004bvl.3	+	4	591	c.478G>T	c.(478-480)GAC>TAC	p.D160Y	SPTAN1_uc011mbg.1_Missense_Mutation_p.D160Y|SPTAN1_uc011mbh.1_Missense_Mutation_p.D172Y|SPTAN1_uc004bvm.3_Missense_Mutation_p.D160Y|SPTAN1_uc004bvn.3_Missense_Mutation_p.D160Y	NM_003127	NP_003118	Q13813	SPTA2_HUMAN	spectrin, alpha, non-erythrocytic 1	160	Spectrin 3.				actin filament capping|axon guidance|cellular component disassembly involved in apoptosis	cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin	actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton			breast(5)|ovary(4)|pancreas(1)	10						AGAATGTGAGGACGTGATGGA	0.473													56	7	---	---	---	---	PASS
ADARB2	105	broad.mit.edu	37	10	1230902	1230902	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1230902G>T	uc009xhq.2	-	9	2316	c.1942C>A	c.(1942-1944)CTG>ATG	p.L648M	ADARB2_uc009xhp.2_Missense_Mutation_p.L32M|ADARB2_uc001igl.3_Missense_Mutation_p.L10M|ADARB2_uc001igm.3_Missense_Mutation_p.L157M	NM_018702	NP_061172	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2	648	A to I editase.				mRNA processing	mitochondrion|nucleus	adenosine deaminase activity|double-stranded RNA binding|metal ion binding|single-stranded RNA binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		ATAATCTCCAGGTCCGCGCTG	0.687													25	8	---	---	---	---	PASS
PTCHD3	374308	broad.mit.edu	37	10	27703066	27703066	+	Silent	SNP	C	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27703066C>G	uc001itu.2	-	1	232	c.114G>C	c.(112-114)TCG>TCC	p.S38S		NM_001034842	NP_001030014	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	38					spermatid development	integral to membrane	hedgehog receptor activity			ovary(2)|pancreas(1)|skin(1)	4						GCTTGCCTTCCGACTCCGATT	0.692													98	129	---	---	---	---	PASS
RASSF4	83937	broad.mit.edu	37	10	45486409	45486409	+	Silent	SNP	A	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45486409A>G	uc001jbo.2	+	9	833	c.699A>G	c.(697-699)TTA>TTG	p.L233L	RASSF4_uc001jbp.2_Silent_p.L264L|RASSF4_uc009xmn.2_Silent_p.L163L|RASSF4_uc001jbq.2_Silent_p.L130L|RASSF4_uc001jbt.2_Silent_p.L190L	NM_032023	NP_114412	Q9H2L5	RASF4_HUMAN	Ras association domain family 4	233	Ras-associating.				cell cycle|signal transduction		protein binding			large_intestine(1)	1						GGACAAAATTAAAAGACTGCG	0.468													54	21	---	---	---	---	PASS
FRMPD2	143162	broad.mit.edu	37	10	49381129	49381129	+	Missense_Mutation	SNP	C	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49381129C>G	uc001jgi.2	-	25	3190	c.3083G>C	c.(3082-3084)AGA>ACA	p.R1028T	FRMPD2_uc001jgh.2_Missense_Mutation_p.R996T|FRMPD2_uc001jgj.2_Missense_Mutation_p.R1006T|FRMPD2L1_uc001jgf.2_Missense_Mutation_p.R39T|FRMPD2_uc001jgg.2_5'UTR|FRMPD2_uc001jgk.2_5'UTR	NM_001018071	NP_001018081	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2 isoform 3	1028	PDZ 2.				tight junction assembly	basolateral plasma membrane|cytoplasm|cytoskeleton|tight junction	1-phosphatidylinositol binding|protein binding			large_intestine(1)	1				Kidney(211;0.201)		TAAGACCAGTCTTGCAACCTA	0.473													8	6	---	---	---	---	PASS
GLUD1	2746	broad.mit.edu	37	10	88835729	88835729	+	Missense_Mutation	SNP	T	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88835729T>C	uc001keh.2	-	3	675	c.578A>G	c.(577-579)TAT>TGT	p.Y193C	GLUD1_uc001keg.2_Missense_Mutation_p.Y26C|GLUD1_uc010qmp.1_Missense_Mutation_p.Y60C	NM_005271	NP_005262	P00367	DHE3_HUMAN	glutamate dehydrogenase 1 precursor	193					glutamate biosynthetic process|glutamate catabolic process|positive regulation of insulin secretion	mitochondrial matrix	ADP binding|ATP binding|glutamate dehydrogenase|glutamate dehydrogenase activity|GTP binding|identical protein binding|leucine binding|NAD+ binding				0					L-Glutamic Acid(DB00142)|NADH(DB00157)	ACTTACAGTATAGTTCTTGGG	0.234													73	13	---	---	---	---	PASS
MUC5B	727897	broad.mit.edu	37	11	1253773	1253773	+	Nonsense_Mutation	SNP	C	A	A	rs147470207	by1000genomes	TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1253773C>A	uc009ycr.1	+	32	4040	c.3914C>A	c.(3913-3915)TCG>TAG	p.S1305*	MUC5B_uc009yct.1_Nonsense_Mutation_p.S646*|MUC5B_uc001ltb.2_Nonsense_Mutation_p.S649*|MUC5B_uc001lta.2_Nonsense_Mutation_p.S314*	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	646					cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CCCTTCCACTCGGTGAGAGGC	0.687													8	3	---	---	---	---	PASS
OR51A4	401666	broad.mit.edu	37	11	4967983	4967983	+	Silent	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4967983G>T	uc010qys.1	-	1	348	c.348C>A	c.(346-348)GTC>GTA	p.V116V		NM_001005329	NP_001005329	Q8NGJ6	O51A4_HUMAN	olfactory receptor, family 51, subfamily A,	116	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGATCAGGAGGACTGAGGACT	0.438													144	118	---	---	---	---	PASS
LDHAL6A	160287	broad.mit.edu	37	11	18497181	18497181	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18497181C>T	uc001mop.1	+	5	848	c.587C>T	c.(586-588)TCA>TTA	p.S196L	LDHAL6A_uc001moq.2_Missense_Mutation_p.S196L	NM_001144071	NP_001137543	Q6ZMR3	LDH6A_HUMAN	lactate dehydrogenase A-like 6A	196					glycolysis	cytoplasm	binding|L-lactate dehydrogenase activity				0					NADH(DB00157)	CATGGCGACTCAAGTGGTAAG	0.453													273	77	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	31113001	31113001	+	Missense_Mutation	SNP	T	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31113001T>C	uc009yjk.1	-	5	589	c.520A>G	c.(520-522)ATC>GTC	p.I174V	uc009yjl.1_Missense_Mutation_p.I102V|DCDC1_uc001msu.1_Missense_Mutation_p.I345V					RecName: Full=Doublecortin domain-containing protein 5;																		TTGACTCTGATAGGATGACCA	0.393													11	12	---	---	---	---	PASS
FOLH1	2346	broad.mit.edu	37	11	49179538	49179538	+	Missense_Mutation	SNP	T	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49179538T>C	uc001ngy.2	-	14	1759	c.1498A>G	c.(1498-1500)AAA>GAA	p.K500E	FOLH1_uc001ngz.2_Missense_Mutation_p.K500E|FOLH1_uc009yly.2_Missense_Mutation_p.K485E|FOLH1_uc009ylz.2_Missense_Mutation_p.K485E|FOLH1_uc009yma.2_Missense_Mutation_p.K192E	NM_004476	NP_004467	Q04609	FOLH1_HUMAN	folate hydrolase 1 isoform 1	500	NAALADase.|Extracellular (Probable).				proteolysis	cytoplasm|integral to plasma membrane|membrane fraction|nucleus	carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity			large_intestine(1)|ovary(1)|skin(1)	3					Capromab(DB00089)|L-Glutamic Acid(DB00142)	GAAGGACTTTTTTTAGTCCAA	0.353													73	80	---	---	---	---	PASS
OR5D14	219436	broad.mit.edu	37	11	55563598	55563598	+	Silent	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55563598G>T	uc010rim.1	+	1	567	c.567G>T	c.(565-567)GTG>GTT	p.V189V		NM_001004735	NP_001004735	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D,	189	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3		all_epithelial(135;0.196)				TCATCTCTGTGTCTGGCTCTG	0.448													159	209	---	---	---	---	PASS
SPRYD5	84767	broad.mit.edu	37	11	55655539	55655539	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55655539G>T	uc010rip.1	+	4	631	c.539G>T	c.(538-540)AGA>ATA	p.R180I	SPRYD5_uc010riq.1_Missense_Mutation_p.R37I	NM_032681	NP_116070	Q9BSJ1	SPRY5_HUMAN	SPRY domain containing 5	180						intracellular	zinc ion binding				0		all_epithelial(135;0.226)				GAAGCAATCAGAGCTGAATAT	0.393													27	41	---	---	---	---	PASS
OR8K5	219453	broad.mit.edu	37	11	55926908	55926908	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55926908C>T	uc010rja.1	-	1	886	c.886G>A	c.(886-888)GAG>AAG	p.E296K		NM_001004058	NP_001004058	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K,	296	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|pancreas(1)|skin(1)	4	Esophageal squamous(21;0.00693)	Lung NSC(402;0.197)|all_epithelial(135;0.236)				TTTTTCACCTCTTCGTTTCTT	0.274													31	53	---	---	---	---	PASS
OR5T3	390154	broad.mit.edu	37	11	56019795	56019795	+	Silent	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56019795C>A	uc010rjd.1	+	1	120	c.120C>A	c.(118-120)ACC>ACA	p.T40T		NM_001004747	NP_001004747	Q8NGG3	OR5T3_HUMAN	olfactory receptor, family 5, subfamily T,	40	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Esophageal squamous(21;0.00448)					CTGAAGTCACCATGTTTATAT	0.348													59	90	---	---	---	---	PASS
OR9Q1	219956	broad.mit.edu	37	11	57885969	57885969	+	Intron	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57885969G>A	uc001nmj.2	+							NM_001005212	NP_001005212	Q8NGQ5	OR9Q1_HUMAN	olfactory receptor, family 9, subfamily Q,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(21;0.222)				CTCTTACTTAGATCTACATGC	0.413													53	169	---	---	---	---	PASS
OR9Q2	219957	broad.mit.edu	37	11	57958903	57958903	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57958903C>A	uc010rka.1	+	1	941	c.941C>A	c.(940-942)CCC>CAC	p.P314H		NM_001005283	NP_001005283	Q8NGE9	OR9Q2_HUMAN	olfactory receptor, family 9, subfamily Q,	314	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|breast(1)|central_nervous_system(1)	4		Breast(21;0.0589)				GCTAGAAGACCCTAAATGGAC	0.299													13	51	---	---	---	---	PASS
OR9Q2	219957	broad.mit.edu	37	11	57958904	57958904	+	Silent	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57958904C>A	uc010rka.1	+	1	942	c.942C>A	c.(940-942)CCC>CCA	p.P314P		NM_001005283	NP_001005283	Q8NGE9	OR9Q2_HUMAN	olfactory receptor, family 9, subfamily Q,	314	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|breast(1)|central_nervous_system(1)	4		Breast(21;0.0589)				CTAGAAGACCCTAAATGGACC	0.294													13	49	---	---	---	---	PASS
MS4A10	341116	broad.mit.edu	37	11	60565996	60565996	+	Intron	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60565996G>T	uc001npz.1	+							NM_206893	NP_996776	Q96PG2	M4A10_HUMAN	membrane-spanning 4-domains, subfamily A, member							integral to membrane	receptor activity			ovary(1)|skin(1)	2						AGGTGAAGAGGTTTGGCCCTG	0.587													18	94	---	---	---	---	PASS
BEST1	7439	broad.mit.edu	37	11	61730083	61730083	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61730083C>A	uc001nss.2	+	10	2037	c.1457C>A	c.(1456-1458)CCG>CAG	p.P486Q	BEST1_uc010rlq.1_3'UTR|BEST1_uc010rlr.1_3'UTR|BEST1_uc010rls.1_Missense_Mutation_p.P114Q|BEST1_uc001nsr.2_Missense_Mutation_p.P426Q|BEST1_uc009ynt.2_RNA|BEST1_uc010rlt.1_Missense_Mutation_p.P426Q|BEST1_uc001nst.2_Missense_Mutation_p.P399Q|BEST1_uc010rlu.1_3'UTR|BEST1_uc010rlv.1_Missense_Mutation_p.P380Q	NM_004183	NP_004174	O76090	BEST1_HUMAN	bestrophin 1 isoform 1	486	Cytoplasmic (Potential).				response to stimulus|transepithelial chloride transport|visual perception	basolateral plasma membrane|chloride channel complex|cytosol|membrane fraction	chloride channel activity			central_nervous_system(1)	1						CCATCAGCGCCGTCAAAGCTT	0.522													54	38	---	---	---	---	PASS
DPP3	10072	broad.mit.edu	37	11	66252646	66252646	+	Silent	SNP	G	A	A	rs146040863	byFrequency	TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66252646G>A	uc001oig.1	+	3	335	c.273G>A	c.(271-273)GCG>GCA	p.A91A	DPP3_uc001oif.1_Silent_p.A91A|DPP3_uc010rpe.1_Intron	NM_005700	NP_005691	Q9NY33	DPP3_HUMAN	dipeptidyl peptidase III	91					proteolysis	cytoplasm	aminopeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity			ovary(1)|skin(1)	2						CCCCTCAGGCGTTCCTGGTCT	0.587													38	26	---	---	---	---	PASS
DGAT2	84649	broad.mit.edu	37	11	75509352	75509352	+	Missense_Mutation	SNP	G	T	T	rs140793537	byFrequency	TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75509352G>T	uc001oxa.2	+	7	1149	c.890G>T	c.(889-891)CGA>CTA	p.R297L	DGAT2_uc001oxb.2_Missense_Mutation_p.R254L	NM_032564	NP_115953	Q96PD7	DGAT2_HUMAN	diacylglycerol O-acyltransferase 2	297	Cytoplasmic (Potential).				glycerol metabolic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	diacylglycerol O-acyltransferase activity				0	Ovarian(111;0.103)					TCCTGGGGCCGATGGGTCCAG	0.572													61	171	---	---	---	---	PASS
TRIM49	57093	broad.mit.edu	37	11	89531515	89531515	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89531515C>A	uc001pdb.2	-	8	1471	c.1142G>T	c.(1141-1143)GGG>GTG	p.G381V		NM_020358	NP_065091	P0CI25	TRI49_HUMAN	ring finger protein 18	381	B30.2/SPRY.					intracellular	zinc ion binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				CTTAACACACCCAAGAAGAAA	0.438													30	102	---	---	---	---	PASS
ARCN1	372	broad.mit.edu	37	11	118451966	118451966	+	Silent	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118451966G>T	uc001ptq.2	+	2	170	c.9G>T	c.(7-9)CTG>CTT	p.L3L	ARCN1_uc009zah.2_Silent_p.L3L|ARCN1_uc010ryg.1_Intron|ARCN1_uc009zag.2_Silent_p.L44L	NM_001655	NP_001646	P48444	COPD_HUMAN	archain isoform 1	3					COPI coating of Golgi vesicle|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	clathrin adaptor complex|COPI vesicle coat|cytosol					0	all_hematologic(175;0.0349)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		GGCAGGTGCTGTTGGCAGCAG	0.413													40	68	---	---	---	---	PASS
FOXRED1	55572	broad.mit.edu	37	11	126145236	126145236	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126145236G>T	uc001qdi.2	+	6	693	c.646G>T	c.(646-648)GGT>TGT	p.G216C	FOXRED1_uc010sbn.1_Missense_Mutation_p.G46C|FOXRED1_uc010sbo.1_RNA|FOXRED1_uc010sbp.1_Missense_Mutation_p.G29C|FOXRED1_uc010sbq.1_Missense_Mutation_p.G83C|FOXRED1_uc001qdj.2_Missense_Mutation_p.G5C|FOXRED1_uc010sbr.1_Missense_Mutation_p.G202C|FOXRED1_uc001qdk.2_Missense_Mutation_p.G5C	NM_017547	NP_060017	Q96CU9	FXRD1_HUMAN	FAD-dependent oxidoreductase domain containing	216						integral to membrane|mitochondrion	oxidoreductase activity|protein binding				0	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0729)		GGAGGACGAAGGTTGGTTTGA	0.537													39	143	---	---	---	---	PASS
IQSEC3	440073	broad.mit.edu	37	12	176411	176411	+	5'UTR	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:176411G>A	uc001qht.1	+	1						NM_015232	NP_056047	Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3						regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity			central_nervous_system(2)|large_intestine(1)|skin(1)	4	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		GACAGCTCCTGGAGCAGCCCC	0.701													5	15	---	---	---	---	PASS
SCNN1A	6337	broad.mit.edu	37	12	6458148	6458148	+	Silent	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6458148C>T	uc001qnx.2	-	11	1810	c.1521G>A	c.(1519-1521)TCG>TCA	p.S507S	SCNN1A_uc001qnv.2_Silent_p.S207S|SCNN1A_uc001qnw.2_Silent_p.S566S|SCNN1A_uc010sfb.1_Silent_p.S530S	NM_001038	NP_001029	P37088	SCNNA_HUMAN	sodium channel, nonvoltage-gated 1 alpha isoform	507	Extracellular (By similarity).				excretion|response to stimulus|sensory perception of taste	apical plasma membrane	WW domain binding				0					Amiloride(DB00594)|Triamterene(DB00384)	TGTTCTGTCGCGATAGCATCT	0.493													403	392	---	---	---	---	PASS
EPS8	2059	broad.mit.edu	37	12	15822599	15822599	+	Missense_Mutation	SNP	T	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15822599T>A	uc009zif.2	-	5	459	c.365A>T	c.(364-366)AAG>ATG	p.K122M	EPS8_uc001rdb.2_Missense_Mutation_p.K122M|EPS8_uc009zig.2_Translation_Start_Site	NM_004447	NP_004438	Q12929	EPS8_HUMAN	epidermal growth factor receptor pathway	122	PH; first part.				cell proliferation|epidermal growth factor receptor signaling pathway		SH3/SH2 adaptor activity			ovary(2)|upper_aerodigestive_tract(1)|skin(1)	4		all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244)		BRCA - Breast invasive adenocarcinoma(232;4.29e-05)|GBM - Glioblastoma multiforme(207;0.0264)		CACACTTGCCTTTGATTCTAA	0.328													46	73	---	---	---	---	PASS
OVCH1	341350	broad.mit.edu	37	12	29649181	29649181	+	Missense_Mutation	SNP	A	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29649181A>G	uc001rix.1	-	3	214	c.214T>C	c.(214-216)TGT>CGT	p.C72R		NM_183378	NP_899234	Q7RTY7	OVCH1_HUMAN	ovochymase 1 precursor	72	Peptidase S1 1.				proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			ovary(3)|central_nervous_system(3)|pancreas(3)|large_intestine(1)	10	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					CTTCCTCCACAGAAGTGGTGC	0.458													8	17	---	---	---	---	PASS
LRRK2	120892	broad.mit.edu	37	12	40757299	40757299	+	Missense_Mutation	SNP	T	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40757299T>C	uc001rmg.3	+	48	7245	c.7124T>C	c.(7123-7125)GTG>GCG	p.V2375A	LRRK2_uc009zjw.2_Missense_Mutation_p.V1213A|LRRK2_uc001rmi.2_Missense_Mutation_p.V1208A	NM_198578	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2375					activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb	external side of mitochondrial outer membrane	ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding			ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1)	24	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				GTTGTGGAAGTGTGGGATAAG	0.363													86	12	---	---	---	---	PASS
KRT6A	3853	broad.mit.edu	37	12	52884675	52884675	+	Silent	SNP	G	A	A	rs398542		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52884675G>A	uc001sam.2	-	4	1088	c.879C>T	c.(877-879)GAC>GAT	p.D293D		NM_005554	NP_005545	P02538	K2C6A_HUMAN	keratin 6A	293	Coil 1B.|Rod.				cell differentiation|ectoderm development|positive regulation of cell proliferation	keratin filament	protein binding|structural constituent of cytoskeleton			ovary(4)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.189)		AGTTGATCTCGTCTGTGAGAG	0.498													4	127	---	---	---	---	PASS
WIF1	11197	broad.mit.edu	37	12	65461474	65461474	+	Splice_Site	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65461474C>T	uc001ssk.2	-	5	779	c.634_splice	c.e5+1	p.A212_splice		NM_007191	NP_009122	Q9Y5W5	WIF1_HUMAN	WNT inhibitory factor 1 precursor						multicellular organismal development|Wnt receptor signaling pathway	extracellular region	protein tyrosine kinase activity			ovary(2)|lung(1)|skin(1)	4			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0231)		CCATGTCTTACCTTTCTCACA	0.488			T	HMGA2	pleomorphic salivary gland adenoma								60	53	---	---	---	---	PASS
PTPRB	5787	broad.mit.edu	37	12	70986093	70986093	+	Silent	SNP	C	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70986093C>G	uc001swb.3	-	5	1125	c.1095G>C	c.(1093-1095)CTG>CTC	p.L365L	PTPRB_uc010sto.1_Silent_p.L365L|PTPRB_uc010stp.1_Silent_p.L365L|PTPRB_uc001swc.3_Silent_p.L583L|PTPRB_uc001swa.3_Silent_p.L583L|PTPRB_uc001swd.3_Silent_p.L582L|PTPRB_uc009zrr.1_Silent_p.L462L|PTPRB_uc001swe.2_Silent_p.L583L	NM_002837	NP_002828	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	365	Fibronectin type-III 4.|Extracellular (Potential).				angiogenesis	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(2)|skin(1)	3	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			TCTGAGCAGACAGTTCACCAG	0.448													81	102	---	---	---	---	PASS
CCDC38	120935	broad.mit.edu	37	12	96292356	96292356	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96292356C>T	uc001tek.1	-	6	757	c.523G>A	c.(523-525)GCT>ACT	p.A175T		NM_182496	NP_872302	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	175	Potential.									skin(1)	1						ATTTTCAGAGCGTCTACAGAT	0.363													76	9	---	---	---	---	PASS
APPL2	55198	broad.mit.edu	37	12	105582189	105582189	+	Missense_Mutation	SNP	A	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105582189A>C	uc001tlf.1	-	17	1714	c.1496T>G	c.(1495-1497)TTG>TGG	p.L499W	APPL2_uc010swt.1_Missense_Mutation_p.L456W|APPL2_uc001tlg.1_Missense_Mutation_p.L253W|APPL2_uc010swu.1_Missense_Mutation_p.L505W|APPL2_uc009zuq.2_Missense_Mutation_p.L456W	NM_018171	NP_060641	Q8NEU8	DP13B_HUMAN	adaptor protein, phosphotyrosine interaction, PH	499	PID.				cell cycle|cell proliferation|signal transduction	early endosome membrane|nucleus	protein binding			upper_aerodigestive_tract(1)	1						CATTGATCCCAAAAACCGAAC	0.423													63	7	---	---	---	---	PASS
RBM19	9904	broad.mit.edu	37	12	114397945	114397945	+	Silent	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114397945G>T	uc009zwi.2	-	3	402	c.258C>A	c.(256-258)CCC>CCA	p.P86P	RBM19_uc001tvn.3_Silent_p.P86P|RBM19_uc001tvm.2_Silent_p.P86P	NM_001146699	NP_001140171	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	86					multicellular organismal development|positive regulation of embryonic development	chromosome|cytoplasm|nucleolus|nucleoplasm	nucleotide binding|RNA binding			skin(3)|ovary(1)|liver(1)|central_nervous_system(1)	6	Medulloblastoma(191;0.163)|all_neural(191;0.178)					TCCAGGCTCTGGGTTTGGCCG	0.532													48	10	---	---	---	---	PASS
TBX3	6926	broad.mit.edu	37	12	115112350	115112350	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115112350G>T	uc001tvt.1	-	7	2354	c.1390C>A	c.(1390-1392)CCG>ACG	p.P464T	TBX3_uc001tvu.1_Missense_Mutation_p.P444T	NM_016569	NP_057653	O15119	TBX3_HUMAN	T-box 3 protein isoform 2	464					anterior/posterior axis specification, embryo|anti-apoptosis|cell aging|embryonic arm morphogenesis|embryonic digit morphogenesis|female genitalia development|follicle-stimulating hormone secretion|luteinizing hormone secretion|male genitalia development|mesoderm morphogenesis|negative regulation of myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle|positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter|skeletal system development	nucleus	sequence-specific DNA binding			ovary(2)|skin(1)	3	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		ACCTTGGCCGGCGCTGTGCCC	0.766													5	1	---	---	---	---	PASS
IL31	386653	broad.mit.edu	37	12	122658483	122658483	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122658483G>T	uc001ubv.2	-	2	100	c.73C>A	c.(73-75)CAC>AAC	p.H25N	LRRC43_uc001ubw.3_Intron|LRRC43_uc009zxl.1_Intron	NM_001014336	NP_001014358	Q6EBC2	IL31_HUMAN	interleukin 31 precursor	25						extracellular space	cytokine activity			central_nervous_system(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;6.93e-05)|Breast(359;0.0544)		OV - Ovarian serous cystadenocarcinoma(86;3.27e-29)|Epithelial(86;4.86e-27)|BRCA - Breast invasive adenocarcinoma(302;0.223)		GGCAACGTGTGGGAGGCCAGC	0.532													77	12	---	---	---	---	PASS
FRY	10129	broad.mit.edu	37	13	32783211	32783211	+	Missense_Mutation	SNP	C	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32783211C>G	uc001utx.2	+	32	4736	c.4240C>G	c.(4240-4242)CTG>GTG	p.L1414V	FRY_uc010tdw.1_RNA	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog	1414					regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		AGCCACGTCACTGGTCCTGAA	0.537													54	10	---	---	---	---	PASS
NBEA	26960	broad.mit.edu	37	13	35692566	35692566	+	Missense_Mutation	SNP	A	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35692566A>C	uc001uvb.2	+	17	2404	c.2198A>C	c.(2197-2199)CAC>CCC	p.H733P		NM_015678	NP_056493	Q8NFP9	NBEA_HUMAN	neurobeachin	733						cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		ATGTCGGAACACCCAGCCTCA	0.333													10	3	---	---	---	---	PASS
LCP1	3936	broad.mit.edu	37	13	46725138	46725138	+	Missense_Mutation	SNP	C	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46725138C>G	uc001vaz.3	-	8	941	c.815G>C	c.(814-816)AGG>ACG	p.R272T	LCP1_uc001vba.3_Missense_Mutation_p.R272T	NM_002298	NP_002289	P13796	PLSL_HUMAN	L-plastin	272	CH 2.|Actin-binding 1.				regulation of intracellular protein transport|T cell activation involved in immune response	cell junction|cytosol|ruffle membrane	calcium ion binding			lung(4)|ovary(3)	7		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.39e-05)		ATTAGCCCACCTCAGCAAGAG	0.463			T	BCL6	NHL 								95	17	---	---	---	---	PASS
RB1	5925	broad.mit.edu	37	13	48953748	48953748	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48953748C>T	uc001vcb.2	+	14	1517	c.1351C>T	c.(1351-1353)CGC>TGC	p.R451C		NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1	451	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.?(7)		lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	ACTTGGAGTTCGCTTGTATTA	0.204		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			4	24	---	---	---	---	PASS
DIAPH3	81624	broad.mit.edu	37	13	60566228	60566228	+	Silent	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60566228G>A	uc001vht.2	-	11	1437	c.1218C>T	c.(1216-1218)CGC>CGT	p.R406R	DIAPH3_uc001vhu.2_Silent_p.R143R|DIAPH3_uc001vhv.2_5'Flank|DIAPH3_uc001vhw.1_Silent_p.R395R|DIAPH3_uc010aed.1_Silent_p.R360R|DIAPH3_uc010aee.1_Silent_p.R336R	NM_001042517	NP_001035982	Q9NSV4	DIAP3_HUMAN	diaphanous homolog 3 isoform a	406	GBD/FH3.				actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		TATCTTCAAGGCGATGGGATA	0.313													51	10	---	---	---	---	PASS
KLHL1	57626	broad.mit.edu	37	13	70514310	70514310	+	Silent	SNP	A	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:70514310A>C	uc001vip.2	-	4	1670	c.876T>G	c.(874-876)CTT>CTG	p.L292L	KLHL1_uc010thm.1_Silent_p.L231L	NM_020866	NP_065917	Q9NR64	KLHL1_HUMAN	kelch-like 1 protein	292					actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding				0		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)		GTGGAAGCTGAAGAAGGCACG	0.428													13	27	---	---	---	---	PASS
COL4A1	1282	broad.mit.edu	37	13	110818651	110818651	+	Splice_Site	SNP	C	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110818651C>G	uc001vqw.3	-	45	4072	c.3950_splice	c.e45-1	p.G1317_splice	COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein						angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			CCTTTTGGACCTAAAAGCAGA	0.423													71	12	---	---	---	---	PASS
UPF3A	65110	broad.mit.edu	37	13	115047559	115047559	+	Silent	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115047559C>T	uc001vup.2	+	2	308	c.271C>T	c.(271-273)CTG>TTG	p.L91L	UPF3A_uc010tkn.1_Silent_p.L91L|UPF3A_uc001vuq.2_Silent_p.L91L|UPF3A_uc001vus.2_RNA|UPF3A_uc001vur.2_RNA	NM_023011	NP_075387	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A	91	Required for interaction with UPF2.				mRNA transport|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation	cytoplasm|nucleus|plasma membrane	nucleocytoplasmic transporter activity|nucleotide binding|protein binding|RNA binding			skin(1)	1	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)		GCTGCGCCCGCTGCCAGCACA	0.731													2	2	---	---	---	---	PASS
NID2	22795	broad.mit.edu	37	14	52520919	52520919	+	Silent	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52520919C>A	uc001wzo.2	-	4	1122	c.888G>T	c.(886-888)CTG>CTT	p.L296L	NID2_uc010tqs.1_Silent_p.L296L|NID2_uc010tqt.1_Silent_p.L296L|NID2_uc001wzp.2_Silent_p.L296L	NM_007361	NP_031387	Q14112	NID2_HUMAN	nidogen 2 precursor	296						basement membrane	calcium ion binding|collagen binding			pancreas(2)|breast(2)|ovary(1)|liver(1)|skin(1)	7	Breast(41;0.0639)|all_epithelial(31;0.123)					AGGAACGTCCCAGGGGAACAG	0.522													24	37	---	---	---	---	PASS
SERPINA5	5104	broad.mit.edu	37	14	95054021	95054021	+	Missense_Mutation	SNP	C	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95054021C>G	uc001ydm.2	+	3	532	c.322C>G	c.(322-324)CAC>GAC	p.H108D	SERPINA5_uc010ave.2_Missense_Mutation_p.H108D|SERPINA5_uc001ydn.1_Missense_Mutation_p.H108D	NM_000624	NP_000615	P05154	IPSP_HUMAN	serine (or cysteine) proteinase inhibitor, clade	108					fusion of sperm to egg plasma membrane|regulation of proteolysis|spermatogenesis	extracellular region|membrane|protein complex	acrosin binding|heparin binding|protease binding|serine-type endopeptidase inhibitor activity			ovary(2)	2				COAD - Colon adenocarcinoma(157;0.21)	Drotrecogin alfa(DB00055)|Urokinase(DB00013)	GAAGGAGCTGCACAGAGGCTT	0.597													33	40	---	---	---	---	PASS
EML1	2009	broad.mit.edu	37	14	100375748	100375748	+	Nonsense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100375748G>T	uc001ygs.2	+	11	1240	c.1171G>T	c.(1171-1173)GGA>TGA	p.G391*	EML1_uc010avt.1_Nonsense_Mutation_p.G378*|EML1_uc010tww.1_Nonsense_Mutation_p.G379*|EML1_uc001ygq.2_Nonsense_Mutation_p.G410*|EML1_uc001ygr.2_Nonsense_Mutation_p.G410*	NM_004434	NP_004425	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	391	WD 3.					cytoplasm|microtubule|microtubule associated complex	calcium ion binding|protein binding			large_intestine(2)|pancreas(1)|ovary(1)|skin(1)	5		Melanoma(154;0.0879)|all_epithelial(191;0.216)				AGTTACTTGTGGAAAATCACA	0.393													99	134	---	---	---	---	PASS
PPP1R13B	23368	broad.mit.edu	37	14	104202520	104202520	+	Silent	SNP	A	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104202520A>G	uc001yof.1	-	16	3334	c.3051T>C	c.(3049-3051)GGT>GGC	p.G1017G	PPP1R13B_uc010awv.1_RNA	NM_015316	NP_056131	Q96KQ4	ASPP1_HUMAN	apoptosis-stimulating protein of p53, 1	1017					apoptosis|induction of apoptosis|negative regulation of cell cycle	cytoplasm|nucleus|plasma membrane	protein binding			ovary(1)	1		all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155)				TGTTCATCACACCCAGCTTTT	0.607													61	125	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105415305	105415305	+	Silent	SNP	C	G	G	rs74090124	by1000genomes	TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105415305C>G	uc010axc.1	-	7	6603	c.6483G>C	c.(6481-6483)CCG>CCC	p.P2161P	AHNAK2_uc001ypx.2_Silent_p.P2061P	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2161						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CCCCAAACGACGGCATCTTGA	0.592													2	1	---	---	---	---	PASS
SNORD116-4	100033416	broad.mit.edu	37	15	25344752	25344752	+	Intron	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25344752C>A	uc001yxh.1	+						SNORD116-4_uc001yxm.1_Intron|IPW_uc001yxn.3_Intron|SNORD116-28_uc001yxy.2_Intron|IPW_uc001yyb.3_Intron|uc001yyd.2_Intron|SNORD116-27_uc001yym.2_5'Flank					Homo sapiens clone kid4 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.												0						AGCACTGGGACCATGCCAGGC	0.413													36	7	---	---	---	---	PASS
HERC2	8924	broad.mit.edu	37	15	28459024	28459024	+	Missense_Mutation	SNP	A	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28459024A>T	uc001zbj.2	-	42	6756	c.6650T>A	c.(6649-6651)CTG>CAG	p.L2217Q		NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	2217					DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		GCCCAGGCGCAGGCGACCATC	0.582													30	10	---	---	---	---	PASS
TJP1	7082	broad.mit.edu	37	15	30000933	30000933	+	Missense_Mutation	SNP	T	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30000933T>A	uc001zcr.2	-	25	5155	c.4680A>T	c.(4678-4680)AAA>AAT	p.K1560N	TJP1_uc010azl.2_Missense_Mutation_p.K1548N|TJP1_uc001zcq.2_Missense_Mutation_p.K1484N|TJP1_uc001zcs.2_Missense_Mutation_p.K1480N	NM_003257	NP_003248	Q07157	ZO1_HUMAN	tight junction protein 1 isoform a	1560					cell-cell junction assembly|cellular component disassembly involved in apoptosis	basolateral plasma membrane|cell-cell adherens junction|Golgi apparatus|tight junction				ovary(4)|central_nervous_system(1)|pancreas(1)	6		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		ACAAGTCAGGTTTATGTGCAG	0.413													178	39	---	---	---	---	PASS
GJD2	57369	broad.mit.edu	37	15	35044963	35044963	+	Silent	SNP	A	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35044963A>G	uc001zis.1	-	2	682	c.682T>C	c.(682-684)TTG>CTG	p.L228L	uc001zit.1_5'Flank	NM_020660	NP_065711	Q9UKL4	CXD2_HUMAN	gap junction protein, delta 2, 36kDa	228	Extracellular (Potential).				synaptic transmission	connexon complex|integral to membrane	gap junction channel activity				0		all_lung(180;9.67e-07)		all cancers(64;2.75e-18)|GBM - Glioblastoma multiforme(113;1.9e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		CACTCATACAACCCTGGGACA	0.473													34	5	---	---	---	---	PASS
MYEF2	50804	broad.mit.edu	37	15	48460929	48460929	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48460929C>A	uc001zwi.3	-	2	393	c.269G>T	c.(268-270)GGC>GTC	p.G90V	MYEF2_uc001zwj.3_Missense_Mutation_p.G90V|MYEF2_uc001zwl.2_5'UTR	NM_016132	NP_057216	Q9P2K5	MYEF2_HUMAN	myelin expression factor 2	90					transcription, DNA-dependent	Golgi apparatus|nucleus	DNA binding|nucleotide binding|RNA binding			lung(2)|ovary(1)	3		all_lung(180;0.00217)		all cancers(107;3.73e-10)|GBM - Glioblastoma multiforme(94;7.81e-07)		TTCTCCAGCGCCCGAATTCTT	0.363													48	129	---	---	---	---	PASS
DMXL2	23312	broad.mit.edu	37	15	51828999	51828999	+	Missense_Mutation	SNP	T	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51828999T>C	uc002abf.2	-	12	1903	c.1678A>G	c.(1678-1680)AAA>GAA	p.K560E	DMXL2_uc010ufy.1_Missense_Mutation_p.K560E|DMXL2_uc010bfa.2_Missense_Mutation_p.K560E	NM_015263	NP_056078	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	560						cell junction|synaptic vesicle membrane	Rab GTPase binding			ovary(6)|skin(3)	9				all cancers(107;0.00494)		ATGATATTTTTACTAAGAGAG	0.403													23	58	---	---	---	---	PASS
UNC13C	440279	broad.mit.edu	37	15	54916021	54916021	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54916021G>T	uc002ack.2	+	30	6228	c.6228G>T	c.(6226-6228)CAG>CAT	p.Q2076H	UNC13C_uc002acm.2_5'UTR	NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C	2076	C2 2.				exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TAAACTGGCAGACCACAGCAA	0.363													29	22	---	---	---	---	PASS
NEDD4	4734	broad.mit.edu	37	15	56142732	56142732	+	Intron	SNP	A	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56142732A>G	uc002adj.2	-						NEDD4_uc002adl.2_Intron|NEDD4_uc002adi.2_Intron|NEDD4_uc010ugj.1_Intron|NEDD4_uc010bfm.2_Intron|NEDD4_uc002adk.2_Intron	NM_198400	NP_006145	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally						development involved in symbiotic interaction|glucocorticoid receptor signaling pathway|negative regulation of sodium ion transport|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage|negative regulation of vascular endothelial growth factor receptor signaling pathway|neuron projection development|positive regulation of nucleocytoplasmic transport|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein catabolic process|progesterone receptor signaling pathway|protein K63-linked ubiquitination|protein targeting to lysosome|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|receptor internalization|regulation of dendrite morphogenesis|response to calcium ion|transmission of virus	apicolateral plasma membrane|cell cortex|chromatin|cytosol|perinuclear region of cytoplasm|ubiquitin ligase complex	beta-2 adrenergic receptor binding|phosphoserine binding|phosphothreonine binding|proline-rich region binding|protein domain specific binding|RNA polymerase binding|sodium channel inhibitor activity|ubiquitin binding|ubiquitin-protein ligase activity			skin(2)|ovary(1)|breast(1)	4				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)		GAAAAGTATCAAAGTTACCCA	0.353													68	217	---	---	---	---	PASS
USP3	9960	broad.mit.edu	37	15	63883009	63883009	+	Missense_Mutation	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63883009G>A	uc002amf.2	+	15	1676	c.1547G>A	c.(1546-1548)GGA>GAA	p.G516E	USP3_uc002amg.2_Missense_Mutation_p.G431E|USP3_uc002amh.2_Missense_Mutation_p.G494E|USP3_uc010uij.1_Missense_Mutation_p.G472E|USP3_uc010uik.1_Missense_Mutation_p.G267E|USP3_uc010bgs.2_Missense_Mutation_p.G499E|USP3_uc002ami.2_Missense_Mutation_p.G347E|uc002amj.2_Intron|uc002amk.2_Intron|uc002aml.2_Intron	NM_006537	NP_006528	Q9Y6I4	UBP3_HUMAN	ubiquitin thiolesterase 3	516					DNA repair|histone deubiquitination|mitotic cell cycle|regulation of protein stability|ubiquitin-dependent protein catabolic process	nuclear chromatin	histone binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)	1				GBM - Glioblastoma multiforme(80;0.0187)		GCCAAAGCTGGATCGGATAAA	0.418													44	145	---	---	---	---	PASS
ITGA11	22801	broad.mit.edu	37	15	68605181	68605181	+	Missense_Mutation	SNP	T	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68605181T>C	uc002ari.2	-	24	2990	c.2903A>G	c.(2902-2904)TAC>TGC	p.Y968C	ITGA11_uc010bib.2_Missense_Mutation_p.Y968C	NM_001004439	NP_001004439	Q9UKX5	ITA11_HUMAN	integrin, alpha 11 precursor	968	Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development	integrin complex	collagen binding|receptor activity			kidney(2)|pancreas(1)	3					Tirofiban(DB00775)	CTTGACCTCGTAGTGGCTCAG	0.617													11	33	---	---	---	---	PASS
ADAMTSL3	57188	broad.mit.edu	37	15	84373179	84373179	+	Silent	SNP	C	T	T	rs140402380		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84373179C>T	uc002bjz.3	+	3	332	c.108C>T	c.(106-108)CCC>CCT	p.P36P	ADAMTSL3_uc002bjy.1_Silent_p.P36P|ADAMTSL3_uc010bmt.1_Silent_p.P36P|ADAMTSL3_uc010bmu.1_Silent_p.P36P	NM_207517	NP_997400	P82987	ATL3_HUMAN	ADAMTS-like 3 precursor	36						proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)			ATTTCCTTCCCGAGTTTGCAC	0.468													15	267	---	---	---	---	PASS
OR4F6	390648	broad.mit.edu	37	15	102346017	102346017	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102346017C>T	uc010utr.1	+	1	95	c.95C>T	c.(94-96)TCA>TTA	p.S32L		NM_001005326	NP_001005326	Q8NGB9	OR4F6_HUMAN	olfactory receptor, family 4, subfamily F,	32	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00039)|Lung(145;0.17)|LUSC - Lung squamous cell carcinoma(107;0.187)			CTCTTTTTCTCAGTGTTCTAT	0.507													93	251	---	---	---	---	PASS
PKD1	5310	broad.mit.edu	37	16	2150202	2150202	+	Missense_Mutation	SNP	T	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2150202T>G	uc002cos.1	-	28	9886	c.9677A>C	c.(9676-9678)AAC>ACC	p.N3226T	PKD1_uc002cot.1_Missense_Mutation_p.N3226T|PKD1_uc010bse.1_RNA	NM_001009944	NP_001009944	P98161	PKD1_HUMAN	polycystin 1 isoform 1 precursor	3226	PLAT.|Cytoplasmic (Potential).				calcium-independent cell-matrix adhesion|homophilic cell adhesion|neuropeptide signaling pathway	basolateral plasma membrane|integral to plasma membrane	protein domain specific binding|sugar binding			central_nervous_system(2)|skin(1)	3						CAGGCCCCCGTTGGCCTCCGT	0.657													30	7	---	---	---	---	PASS
CORO7	79585	broad.mit.edu	37	16	4407255	4407255	+	Nonsense_Mutation	SNP	G	A	A	rs142694458		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4407255G>A	uc002cwh.3	-	26	2719	c.2599C>T	c.(2599-2601)CAA>TAA	p.Q867*	CORO7_uc002cwe.2_RNA|CORO7_uc002cwf.2_Nonsense_Mutation_p.Q867*|CORO7_uc002cwg.3_Nonsense_Mutation_p.Q647*|CORO7_uc010uxh.1_Nonsense_Mutation_p.Q849*|CORO7_uc010uxi.1_Nonsense_Mutation_p.Q782*	NM_024535	NP_078811	P57737	CORO7_HUMAN	coronin 7	867						cytoplasmic membrane-bounded vesicle|cytosol|Golgi membrane|integral to membrane of membrane fraction|soluble fraction					0						CGGGGGGCTTGGCTCACTGGG	0.552													42	6	---	---	---	---	PASS
ABCC1	4363	broad.mit.edu	37	16	16232425	16232425	+	Intron	SNP	C	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16232425C>G	uc010bvi.2	+						ABCC1_uc010bvj.2_Intron|ABCC1_uc010bvk.2_Intron|ABCC1_uc010bvl.2_Intron|ABCC1_uc010bvm.2_Intron|ABCC1_uc002del.3_Intron	NM_004996	NP_004987	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C, member 1						hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|response to drug	Golgi apparatus|integral to plasma membrane|membrane fraction|nucleus	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)	4					Daunorubicin(DB00694)|Glibenclamide(DB01016)|Probenecid(DB01032)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)	GGTGATGCCACTGGCACAGTG	0.522													18	25	---	---	---	---	PASS
PDILT	204474	broad.mit.edu	37	16	20373796	20373796	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20373796G>T	uc002dhc.1	-	10	1569	c.1346C>A	c.(1345-1347)GCA>GAA	p.A449E		NM_174924	NP_777584	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis	449	Thioredoxin.				cell differentiation|cell redox homeostasis|multicellular organismal development|spermatogenesis	endoplasmic reticulum	isomerase activity			large_intestine(1)	1						AATGTCATTTGCTGTGACATC	0.488													57	72	---	---	---	---	PASS
HS3ST4	9951	broad.mit.edu	37	16	26147026	26147026	+	Silent	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26147026C>T	uc002dof.2	+	2	1220	c.828C>T	c.(826-828)TCC>TCT	p.S276S		NM_006040	NP_006031	Q9Y661	HS3S4_HUMAN	heparan sulfate D-glucosaminyl	276	Lumenal (Potential).				heparan sulfate proteoglycan metabolic process	extracellular region|Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity			large_intestine(1)|breast(1)	2				GBM - Glioblastoma multiforme(48;0.0988)		GCATTCACTCCATGGCCAAGG	0.498													78	97	---	---	---	---	PASS
RUNDC2C	440352	broad.mit.edu	37	16	29376097	29376097	+	Missense_Mutation	SNP	A	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29376097A>G	uc002dsj.1	+	5	836	c.439A>G	c.(439-441)ATG>GTG	p.M147V	uc010vct.1_Intron|RUNDC2C_uc010bys.1_RNA|RUNDC2C_uc010vdo.1_Missense_Mutation_p.M128V	NM_001012391	NP_001012391			RecName: Full=RUN domain-containing protein 2A;												0						CTCTGGGGACATGTTTAAAAA	0.478													4	113	---	---	---	---	PASS
ABCC12	94160	broad.mit.edu	37	16	48121987	48121987	+	Nonsense_Mutation	SNP	G	T	T	rs144720520	byFrequency	TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48121987G>T	uc002efc.1	-	25	3831	c.3485C>A	c.(3484-3486)TCG>TAG	p.S1162*	ABCC12_uc002eey.1_RNA|ABCC12_uc002eez.1_RNA|ABCC12_uc002efa.1_RNA|ABCC12_uc002efb.1_RNA|ABCC12_uc002efd.1_RNA	NM_033226	NP_150229	Q96J65	MRP9_HUMAN	ATP-binding cassette protein C12	1162	ABC transporter 2.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3		all_cancers(37;0.0474)|all_lung(18;0.047)				CATTCCTAACGATGACTTTCC	0.413													23	23	---	---	---	---	PASS
CDH8	1006	broad.mit.edu	37	16	61689506	61689506	+	Missense_Mutation	SNP	A	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61689506A>T	uc002eog.1	-	11	2026	c.1774T>A	c.(1774-1776)TTG>ATG	p.L592M		NM_001796	NP_001787	P55286	CADH8_HUMAN	cadherin 8, type 2 preproprotein	592	Extracellular (Potential).|Cadherin 5.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		CTGATTGTCAAGGTGCTAGTG	0.468													56	92	---	---	---	---	PASS
CDH11	1009	broad.mit.edu	37	16	65038624	65038624	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65038624C>A	uc002eoi.2	-	3	583	c.149G>T	c.(148-150)CGC>CTC	p.R50L	CDH11_uc010cdn.2_RNA|CDH11_uc002eoj.2_Missense_Mutation_p.R50L|CDH11_uc010vin.1_Intron|CDH11_uc010vio.1_Missense_Mutation_p.R50L	NM_001797	NP_001788	P55287	CAD11_HUMAN	cadherin 11, type 2 preproprotein	50					adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development	integral to membrane|plasma membrane	calcium ion binding|protein binding			lung(10)|ovary(3)|skin(1)	14		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		ACGCTTGGAGCGCTGTAGCAC	0.642			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			34	28	---	---	---	---	PASS
AARS	16	broad.mit.edu	37	16	70293019	70293019	+	Missense_Mutation	SNP	A	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70293019A>G	uc002eyn.1	-	14	1966	c.1856T>C	c.(1855-1857)CTT>CCT	p.L619P	AARS_uc010vlu.1_Missense_Mutation_p.L449P	NM_001605	NP_001596	P49588	SYAC_HUMAN	alanyl-tRNA synthetase	619					alanyl-tRNA aminoacylation|tRNA processing	cytosol|soluble fraction	alanine-tRNA ligase activity|ATP binding|metal ion binding|tRNA binding			pancreas(1)	1		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)	L-Alanine(DB00160)	AGCTTCCCCAAGCACTGAGCG	0.562													105	169	---	---	---	---	PASS
PKD1L2	114780	broad.mit.edu	37	16	81161404	81161404	+	Silent	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81161404G>A	uc002fgh.1	-	38	6312	c.6312C>T	c.(6310-6312)TAC>TAT	p.Y2104Y	PKD1L2_uc002fgf.1_Translation_Start_Site|PKD1L2_uc002fgg.1_RNA	NM_052892	NP_443124	Q7Z442	PK1L2_HUMAN	polycystin 1-like 2 isoform a	2104	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3						AGGGGACCACGTAGCCTCCTC	0.522													25	39	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7574017	7574017	+	Missense_Mutation	SNP	C	A	A	rs121912664		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7574017C>A	uc002gim.2	-	10	1204	c.1010G>T	c.(1009-1011)CGC>CTC	p.R337L	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Intron|TP53_uc010cne.1_Intron|TP53_uc010cnf.1_3'UTR|TP53_uc010cng.1_3'UTR|TP53_uc002gii.1_Missense_Mutation_p.R205L|TP53_uc010cnh.1_3'UTR|TP53_uc010cni.1_3'UTR|TP53_uc002gij.2_Missense_Mutation_p.R337L	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	337	Oligomerization.|Interaction with HIPK1 (By similarity).|Interaction with CARM1.|Interaction with HIPK2.		R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.R337C(12)|p.0?(7)|p.R337L(5)|p.R337H(2)|p.?(1)|p.I332fs*5(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		CATCTCGAAGCGCTCACGCCC	0.453		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			25	8	---	---	---	---	PASS
MYH13	8735	broad.mit.edu	37	17	10214458	10214458	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10214458C>T	uc002gmk.1	-	33	4708	c.4618G>A	c.(4618-4620)GAA>AAA	p.E1540K		NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	1540	Potential.				muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|skin(2)	6						TCTGACTTTTCCTGCTCCACT	0.473													62	10	---	---	---	---	PASS
MYH2	4620	broad.mit.edu	37	17	10447295	10447295	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10447295C>A	uc010coi.2	-	7	700	c.572G>T	c.(571-573)CGT>CTT	p.R191L	uc002gml.1_Intron|MYH2_uc002gmp.3_Missense_Mutation_p.R191L|MYH2_uc010coj.2_Missense_Mutation_p.R191L	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	191	Myosin head-like.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14						CTGGATGACACGCTTGGTGTT	0.428													61	19	---	---	---	---	PASS
SYNRG	11276	broad.mit.edu	37	17	35921348	35921348	+	Missense_Mutation	SNP	T	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35921348T>G	uc002hoa.2	-	13	1695	c.1612A>C	c.(1612-1614)AAA>CAA	p.K538Q	SYNRG_uc010wde.1_Missense_Mutation_p.K460Q|SYNRG_uc010wdf.1_Missense_Mutation_p.K460Q|SYNRG_uc002hoc.2_Missense_Mutation_p.K459Q|SYNRG_uc002hoe.2_Missense_Mutation_p.K460Q|SYNRG_uc002hod.2_Missense_Mutation_p.K460Q|SYNRG_uc010wdg.1_Missense_Mutation_p.K377Q|SYNRG_uc002hob.2_Missense_Mutation_p.K538Q|SYNRG_uc002hof.2_Missense_Mutation_p.K250Q|SYNRG_uc010cvd.1_Missense_Mutation_p.K338Q	NM_007247	NP_009178	Q9UMZ2	SYNRG_HUMAN	synergin, gamma isoform 1	538	Interaction with A1P1G1 and A1P1G2.				endocytosis|intracellular protein transport	AP-1 adaptor complex	calcium ion binding			ovary(2)	2						GCACTATATTTATCACCAGGA	0.353													52	94	---	---	---	---	PASS
KIAA1267	284058	broad.mit.edu	37	17	44110445	44110445	+	Splice_Site	SNP	C	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44110445C>G	uc002ikb.2	-	12	2922	c.2837_splice	c.e12+1	p.R946_splice	KIAA1267_uc002ikc.2_Splice_Site_p.R946_splice|KIAA1267_uc002ikd.2_Splice_Site_p.R946_splice|KIAA1267_uc010dav.2_Splice_Site_p.R945_splice|KIAA1267_uc010wkb.1_Splice_Site_p.R277_splice|KIAA1267_uc010wkc.1_Splice_Site_p.R214_splice	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058							MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)				TGCCCCATCACCTGCTGCCCC	0.647													6	6	---	---	---	---	PASS
PPP1R9B	84687	broad.mit.edu	37	17	48226576	48226576	+	Missense_Mutation	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48226576G>A	uc002iqh.3	-	3	1306	c.1303C>T	c.(1303-1305)CCG>TCG	p.P435S		NM_032595	NP_115984	Q96SB3	NEB2_HUMAN	protein phosphatase 1, regulatory subunit 9B	433	Interacts with protein phosphatase 1 (By similarity).				cell cycle arrest|cell differentiation|cell migration|filopodium assembly|negative regulation of cell growth|nervous system development|regulation of cell growth by extracellular stimulus|regulation of cell proliferation|regulation of exit from mitosis|RNA splicing	adherens junction|cytoskeleton|dendritic spine|filopodium|lamellipodium|nucleoplasm|protein phosphatase type 1 complex|ruffle membrane|synapse	actin binding|protein phosphatase 1 binding|protein phosphatase inhibitor activity				0						GACAGCCCCGGGATCTCCACG	0.597													6	17	---	---	---	---	PASS
GPRC5C	55890	broad.mit.edu	37	17	72443115	72443115	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72443115C>T	uc002jks.2	+	3	1313	c.1274C>T	c.(1273-1275)CCG>CTG	p.P425L	GPRC5C_uc002jkp.2_Missense_Mutation_p.P470L|GPRC5C_uc002jkq.2_3'UTR|GPRC5C_uc002jkr.2_Missense_Mutation_p.P437L|GPRC5C_uc002jkt.2_Missense_Mutation_p.P425L|GPRC5C_uc002jku.2_Missense_Mutation_p.P180L	NM_018653	NP_061123	Q9NQ84	GPC5C_HUMAN	G protein-coupled receptor family C, group 5,	425	Cytoplasmic (Potential).					cytoplasmic vesicle membrane|integral to plasma membrane	G-protein coupled receptor activity|protein binding			ovary(2)|prostate(1)|central_nervous_system(1)|pancreas(1)	5						GCCACACCGCCGAAAGACGGC	0.652													69	100	---	---	---	---	PASS
SAP30BP	29115	broad.mit.edu	37	17	73702489	73702489	+	Missense_Mutation	SNP	T	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73702489T>G	uc002jpe.2	+	11	869	c.815T>G	c.(814-816)CTC>CGC	p.L272R	SAP30BP_uc002jpc.1_RNA|SAP30BP_uc010wsf.1_RNA|SAP30BP_uc010wsg.1_RNA|SAP30BP_uc002jpf.2_Missense_Mutation_p.L256R	NM_013260	NP_037392	Q9UHR5	S30BP_HUMAN	transcriptional regulator protein	272	Thr-rich.				apoptosis|induction of apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			ovary(1)	1	all_cancers(13;6.42e-08)		all cancers(21;4.25e-07)|Epithelial(20;9.57e-07)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			CCCACCATCCTCACCACCACA	0.557													106	199	---	---	---	---	PASS
DNAH17	8632	broad.mit.edu	37	17	76435203	76435203	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76435203G>T	uc010dhp.1	-	18	2996	c.2774C>A	c.(2773-2775)GCT>GAT	p.A925D	DNAH17_uc002jvq.2_Missense_Mutation_p.A210D|DNAH17_uc002jvs.2_RNA					SubName: Full=DNAH17 variant protein; Flags: Fragment;											ovary(6)|breast(2)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			TTTCTCTGCAGCCACGTCCAG	0.562													40	31	---	---	---	---	PASS
KIAA0802	23255	broad.mit.edu	37	18	8825138	8825138	+	Silent	SNP	T	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8825138T>C	uc002knr.2	+	15	3772	c.3630T>C	c.(3628-3630)GGT>GGC	p.G1210G	KIAA0802_uc002knq.2_Silent_p.G1169G|KIAA0802_uc002kns.2_Silent_p.G550G	NM_015210	NP_056025	Q9Y4B5	CC165_HUMAN	hypothetical protein LOC23255	1520											0						CGGCAGGTGGTGAGGGTCCCT	0.677													33	12	---	---	---	---	PASS
C18orf34	374864	broad.mit.edu	37	18	30672775	30672775	+	Missense_Mutation	SNP	T	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30672775T>C	uc002kxn.2	-	20	2480	c.2338A>G	c.(2338-2340)ATA>GTA	p.I780V	C18orf34_uc010xbq.1_Intron|C18orf34_uc010dme.1_Intron|C18orf34_uc010xbr.1_Missense_Mutation_p.I780V|C18orf34_uc010dmf.1_Intron|C18orf34_uc002kxo.2_Missense_Mutation_p.I742V|C18orf34_uc002kxp.2_Missense_Mutation_p.I780V	NM_001105528	NP_001098998	Q5BJE1	CR034_HUMAN	hypothetical protein LOC374864 isoform 1	780										ovary(1)	1						TTATCATATATATTGAAATAA	0.284													68	12	---	---	---	---	PASS
CELF4	56853	broad.mit.edu	37	18	34850747	34850747	+	Silent	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34850747G>A	uc002lae.2	-	8	1479	c.1083C>T	c.(1081-1083)GGC>GGT	p.G361G	CELF4_uc010dnd.1_Silent_p.G359G|CELF4_uc002lag.2_Silent_p.G351G|CELF4_uc002laf.2_Silent_p.G356G|CELF4_uc002lai.2_Silent_p.G346G|CELF4_uc002lah.1_Silent_p.G86G	NM_020180	NP_064565	Q9BZC1	CELF4_HUMAN	bruno-like 4, RNA binding protein isoform 1	361					embryo development|germ cell development|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	BRE binding|nucleotide binding|translation repressor activity, nucleic acid binding			ovary(2)	2						AGGGGTGGATGCCATTGGCGA	0.557													59	15	---	---	---	---	PASS
CDH20	28316	broad.mit.edu	37	18	59195329	59195329	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59195329G>T	uc010dps.1	+	6	1159	c.1147G>T	c.(1147-1149)GTG>TTG	p.V383L	CDH20_uc002lif.2_Missense_Mutation_p.V377L	NM_031891	NP_114097	Q9HBT6	CAD20_HUMAN	cadherin 20, type 2 preproprotein	383	Extracellular (Potential).|Cadherin 3.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)				TGTGGAAGACGTGGACGAGCC	0.512													86	24	---	---	---	---	PASS
CD226	10666	broad.mit.edu	37	18	67563044	67563044	+	Missense_Mutation	SNP	A	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67563044A>G	uc010dqo.2	-	3	1067	c.620T>C	c.(619-621)ATC>ACC	p.I207T	CD226_uc002lkm.3_Missense_Mutation_p.I207T	NM_006566	NP_006557	Q15762	CD226_HUMAN	CD226 molecule precursor	207	Ig-like C2-type 2.|Extracellular (Potential).				cell adhesion|cell recognition|positive regulation of Fc receptor mediated stimulatory signaling pathway|positive regulation of immunoglobulin mediated immune response|positive regulation of mast cell activation|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target	cell surface|integral to plasma membrane|membrane raft	cell adhesion molecule binding|integrin binding|protein kinase binding|receptor activity				0		Esophageal squamous(42;0.129)				GGGGATGACGATGACGCTCCA	0.512													74	19	---	---	---	---	PASS
ABCA7	10347	broad.mit.edu	37	19	1056426	1056426	+	Missense_Mutation	SNP	G	T	T	rs113269196	byFrequency	TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1056426G>T	uc002lqw.3	+	33	4745	c.4514G>T	c.(4513-4515)CGC>CTC	p.R1505L	ABCA7_uc002lqy.2_5'Flank|ABCA7_uc010dsc.2_5'Flank	NM_019112	NP_061985	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A, member 7	1505	Extracellular (By similarity).				phagocytosis|transmembrane transport	ATP-binding cassette (ABC) transporter complex|endosome membrane|Golgi membrane|integral to membrane|plasma membrane	ATP binding|ATPase activity|transporter activity			pancreas(7)|ovary(1)|central_nervous_system(1)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCCCGGCCCGCCACGCCCAC	0.612													12	19	---	---	---	---	PASS
VAV1	7409	broad.mit.edu	37	19	6854071	6854071	+	Missense_Mutation	SNP	G	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6854071G>C	uc002mfu.1	+	26	2543	c.2446G>C	c.(2446-2448)GGA>CGA	p.G816R	VAV1_uc010xjh.1_Missense_Mutation_p.G784R|VAV1_uc010dva.1_Missense_Mutation_p.G794R|VAV1_uc002mfv.1_Missense_Mutation_p.G761R	NM_005428	NP_005419	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	816	SH3 2.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|T cell costimulation	cytosol|plasma membrane	metal ion binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(4)|ovary(4)|breast(3)|central_nervous_system(2)|kidney(2)|skin(1)	16						TAACAAGAAGGGACAGCAAGG	0.602													60	46	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9061509	9061509	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9061509G>T	uc002mkp.2	-	3	26141	c.25937C>A	c.(25936-25938)CCT>CAT	p.P8646H		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	8648	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						ATTGACTACAGGTGTGTTTGA	0.438													15	81	---	---	---	---	PASS
PDE4A	5141	broad.mit.edu	37	19	10572296	10572296	+	Silent	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10572296C>T	uc002moj.2	+	12	1668	c.1560C>T	c.(1558-1560)GAC>GAT	p.D520D	PDE4A_uc002mok.2_Silent_p.D494D|PDE4A_uc002mol.2_Silent_p.D459D|PDE4A_uc002mom.2_Silent_p.D281D|PDE4A_uc002mon.2_5'UTR|PDE4A_uc002moo.2_Silent_p.D186D	NM_001111307	NP_001104777	P27815	PDE4A_HUMAN	phosphodiesterase 4A isoform 1	520	Catalytic.				signal transduction	cytosol|membrane fraction|perinuclear region of cytoplasm|ruffle membrane|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Cilostazol(DB01166)|Dipyridamole(DB00975)|Dyphylline(DB00651)|Enprofylline(DB00824)|Iloprost(DB01088)|Milrinone(DB00235)|Pentoxifylline(DB00806)|Phentolamine(DB00692)|Tadalafil(DB00820)|Theophylline(DB00277)	ACAACTGCGACATCTTCCAGA	0.622													26	60	---	---	---	---	PASS
ZNF625	90589	broad.mit.edu	37	19	12256966	12256966	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12256966C>A	uc002mth.2	-	4	417	c.67G>T	c.(67-69)GAT>TAT	p.D23Y	ZNF20_uc002mtg.1_Intron|ZNF625_uc010dyn.1_RNA|ZNF625_uc010dyo.1_Missense_Mutation_p.D57Y	NM_145233	NP_660276	Q96I27	ZN625_HUMAN	zinc finger protein 625	23					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						AGCATGTCATCTGGAACCTGG	0.433													45	45	---	---	---	---	PASS
TNPO2	30000	broad.mit.edu	37	19	12816128	12816128	+	Nonsense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12816128C>A	uc002muo.2	-	17	2133	c.1948G>T	c.(1948-1950)GAG>TAG	p.E650*	TNPO2_uc002mup.2_Nonsense_Mutation_p.E742*|TNPO2_uc002muq.2_Nonsense_Mutation_p.E650*|TNPO2_uc002mur.2_Nonsense_Mutation_p.E650*	NM_001136196	NP_001129668	O14787	TNPO2_HUMAN	transportin 2 (importin 3, karyopherin beta 2b)	650					intracellular protein transport	cytoplasm|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			ovary(1)	1						CCCAGGCCCTCGGCCAGGCCG	0.602													6	7	---	---	---	---	PASS
NANOS3	342977	broad.mit.edu	37	19	13988533	13988533	+	Silent	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13988533G>A	uc002mxj.3	+	1	584	c.471G>A	c.(469-471)GCG>GCA	p.A157A		NM_001098622	NP_001092092	P60323	NANO3_HUMAN	nanos homolog 3	138					anti-apoptosis|germ cell development|multicellular organismal development|oogenesis|regulation of cell cycle|regulation of translation|spermatogenesis	cytoplasmic mRNA processing body|nucleus|stress granule	RNA binding|zinc ion binding			skin(1)	1			OV - Ovarian serous cystadenocarcinoma(19;2e-21)			CTGACAAGGCGAAGACACAGG	0.667													3	9	---	---	---	---	PASS
RYR1	6261	broad.mit.edu	37	19	38942422	38942422	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38942422G>T	uc002oit.2	+	12	1271	c.1141G>T	c.(1141-1143)GGC>TGC	p.G381C	RYR1_uc002oiu.2_Missense_Mutation_p.G381C	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	381	Cytoplasmic.|MIR 5.				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)	GCACCAGGAGGGCCACATGGA	0.627													49	108	---	---	---	---	PASS
LRFN1	57622	broad.mit.edu	37	19	39805146	39805146	+	Silent	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39805146C>T	uc002okw.2	-	1	831	c.831G>A	c.(829-831)ACG>ACA	p.T277T		NM_020862	NP_065913	Q9P244	LRFN1_HUMAN	leucine rich repeat and fibronectin type III	277	LRRCT.|Extracellular (Potential).					cell junction|integral to membrane|postsynaptic density|postsynaptic membrane				ovary(2)	2	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.96e-27)|all cancers(26;2.05e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			GGTGTTCGGGCGTGGCGCAGG	0.697													3	7	---	---	---	---	PASS
ZNF234	10780	broad.mit.edu	37	19	44661166	44661166	+	Missense_Mutation	SNP	A	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44661166A>G	uc002oym.2	+	6	1304	c.997A>G	c.(997-999)ATC>GTC	p.I333V	ZNF234_uc002oyl.3_Missense_Mutation_p.I333V	NM_006630	NP_006621	Q14588	ZN234_HUMAN	zinc finger protein 234	333	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0435)				AAACCTTCGTATCCATCAAAG	0.428													39	60	---	---	---	---	PASS
SYNGR4	23546	broad.mit.edu	37	19	48878904	48878904	+	Nonsense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48878904C>A	uc002piz.2	+	4	611	c.366C>A	c.(364-366)TGC>TGA	p.C122*		NM_012451	NP_036583	O95473	SNG4_HUMAN	synaptogyrin 4	122	MARVEL.|Helical; (Potential).					integral to membrane					0		all_epithelial(76;5.08e-07)|all_lung(116;5.76e-06)|Lung NSC(112;1.18e-05)|Prostate(7;0.0143)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000138)|all cancers(93;0.00017)|Epithelial(262;0.0138)|GBM - Glioblastoma multiforme(486;0.0146)		TGGGTTTCTGCTTCCTGGCCA	0.592													95	81	---	---	---	---	PASS
VPS16	64601	broad.mit.edu	37	20	2843947	2843947	+	Missense_Mutation	SNP	G	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2843947G>C	uc002whe.2	+	15	1427	c.1379G>C	c.(1378-1380)CGG>CCG	p.R460P	VPS16_uc002whh.2_RNA|PTPRA_uc002whj.2_5'Flank|VPS16_uc002whf.2_Missense_Mutation_p.R316P|VPS16_uc002whd.2_RNA|VPS16_uc002whg.2_Missense_Mutation_p.R146P|VPS16_uc002whi.2_5'Flank	NM_022575	NP_072097	Q9H269	VPS16_HUMAN	vacuolar protein sorting 16 isoform 1	460					intracellular protein transport	early endosome|HOPS complex|late endosome membrane|lysosomal membrane|recycling endosome				ovary(2)|pancreas(1)|skin(1)	4						CTCGTGTTGCGGAGACTTTAC	0.597													90	100	---	---	---	---	PASS
TMX4	56255	broad.mit.edu	37	20	7980436	7980436	+	Missense_Mutation	SNP	T	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7980436T>A	uc002wmx.1	-	4	543	c.410A>T	c.(409-411)GAG>GTG	p.E137V		NM_021156	NP_066979	Q9H1E5	TMX4_HUMAN	thioredoxin-related transmembrane protein 4	137	Thioredoxin.				cell redox homeostasis|electron transport chain|transport	integral to membrane					0						CCATTTCTTCTCTAAGATATA	0.408													63	35	---	---	---	---	PASS
TOX2	84969	broad.mit.edu	37	20	42683148	42683148	+	Silent	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42683148G>T	uc002xlf.3	+	5	905	c.888G>T	c.(886-888)CTG>CTT	p.L296L	TOX2_uc010ggo.2_Silent_p.L287L|TOX2_uc002xle.3_Silent_p.L245L|TOX2_uc010ggp.2_Silent_p.L245L|TOX2_uc002xlg.2_Silent_p.L245L|TOX2_uc010zwk.1_Silent_p.L165L	NM_001098798	NP_001092268	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2	296	HMG box.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)			GGGACAGCCTGGGAGAGGAAC	0.562													27	22	---	---	---	---	PASS
WFDC8	90199	broad.mit.edu	37	20	44190741	44190741	+	Intron	SNP	G	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44190741G>C	uc002xow.2	-						WFDC8_uc002xox.2_Intron	NM_181510	NP_852611	Q8IUA0	WFDC8_HUMAN	WAP four-disulfide core domain 8 precursor							extracellular region	serine-type endopeptidase inhibitor activity				0		Myeloproliferative disorder(115;0.0122)				CAGCTTTTTTGAACTCACGTT	0.502													48	26	---	---	---	---	PASS
MMP9	4318	broad.mit.edu	37	20	44640921	44640921	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44640921C>A	uc002xqz.2	+	7	1162	c.1143C>A	c.(1141-1143)AGC>AGA	p.S381R		NM_004994	NP_004985	P14780	MMP9_HUMAN	matrix metalloproteinase 9 preproprotein	381	Fibronectin type-II 3.				collagen catabolic process|macrophage differentiation|positive regulation of keratinocyte migration|proteolysis	extracellular space|proteinaceous extracellular matrix	collagen binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		Myeloproliferative disorder(115;0.0122)			Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)|Simvastatin(DB00641)	ACTTTGACAGCGACAAGAAGT	0.662													88	101	---	---	---	---	PASS
NTSR1	4923	broad.mit.edu	37	20	61386239	61386239	+	Splice_Site	SNP	G	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61386239G>C	uc002ydf.2	+	2	1287	c.916_splice	c.e2+1	p.R306_splice		NM_002531	NP_002522	P30989	NTR1_HUMAN	neurotensin receptor 1							endoplasmic reticulum|Golgi apparatus|integral to plasma membrane	neurotensin receptor activity, G-protein coupled			skin(2)|lung(1)|central_nervous_system(1)	4	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;3.63e-06)			CGCGTCCTACGTACGTAACCT	0.662													9	24	---	---	---	---	PASS
BIRC7	79444	broad.mit.edu	37	20	61869312	61869312	+	Missense_Mutation	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61869312G>A	uc002yej.2	+	2	580	c.407G>A	c.(406-408)CGC>CAC	p.R136H	BIRC7_uc010gkc.1_Missense_Mutation_p.R136H|BIRC7_uc002yei.2_Missense_Mutation_p.R136H|hsa-mir-3196|MI0014241_5'Flank	NM_139317	NP_647478	Q96CA5	BIRC7_HUMAN	livin inhibitor of apoptosis isoform alpha	136	BIR.				activation of JUN kinase activity|anti-apoptosis|DNA fragmentation involved in apoptotic nuclear change	cytoplasm|nucleus	enzyme binding|zinc ion binding			ovary(1)|lung(1)|kidney(1)	3	all_cancers(38;2.72e-09)					AGCTGGAAGCGCGGGGACGAC	0.682													33	25	---	---	---	---	PASS
CHRNA4	1137	broad.mit.edu	37	20	61981226	61981226	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61981226G>T	uc002yes.2	-	5	1715	c.1537C>A	c.(1537-1539)CGC>AGC	p.R513S	CHRNA4_uc002yet.1_Missense_Mutation_p.R337S|CHRNA4_uc011aaw.1_RNA|CHRNA4_uc010gke.1_Missense_Mutation_p.R442S|CHRNA4_uc002yev.1_Missense_Mutation_p.R337S|CHRNA4_uc010gkf.1_Missense_Mutation_p.R337S	NM_000744	NP_000735	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 subunit	513	Cytoplasmic (Potential).				B cell activation|behavioral response to nicotine|calcium ion transport|cognition|DNA repair|membrane depolarization|regulation of action potential|regulation of dopamine secretion|regulation of inhibitory postsynaptic membrane potential|response to hypoxia|response to oxidative stress|sensory perception of pain|synaptic transmission, cholinergic	cell junction|dendrite|external side of plasma membrane|membrane fraction|neuronal cell body|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			central_nervous_system(1)|skin(1)	2	all_cancers(38;1.71e-10)				Nicotine(DB00184)|Varenicline(DB01273)	TGGGTGTTGCGAGAGGCCAGG	0.687													6	19	---	---	---	---	PASS
ARFRP1	10139	broad.mit.edu	37	20	62337709	62337709	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62337709C>A	uc002yga.2	-	3	831	c.264G>T	c.(262-264)AAG>AAT	p.K88N	ARFRP1_uc002ygc.2_Missense_Mutation_p.K88N|ARFRP1_uc002ygh.3_Missense_Mutation_p.K88N|ARFRP1_uc011abf.1_Missense_Mutation_p.K88N|ARFRP1_uc011abg.1_Missense_Mutation_p.K88N|ARFRP1_uc002yge.2_RNA|ARFRP1_uc002ygd.2_RNA|ARFRP1_uc002ygf.2_Missense_Mutation_p.K88N|ARFRP1_uc002ygg.2_RNA|ARFRP1_uc011abh.1_RNA|ZGPAT_uc002ygi.2_5'Flank|ZGPAT_uc002ygj.2_5'Flank|ZGPAT_uc002ygk.2_5'Flank|ZGPAT_uc010gkk.1_5'Flank|ZGPAT_uc010gkl.1_5'Flank|ZGPAT_uc002ygm.2_5'Flank|ZGPAT_uc002ygn.3_5'Flank	NM_003224	NP_003215	Q13795	ARFRP_HUMAN	ADP-ribosylation factor related protein 1	88					small GTPase mediated signal transduction	Golgi apparatus|membrane fraction	GTP binding|GTPase activity			breast(1)|skin(1)	2	all_cancers(38;9.53e-13)|all_epithelial(29;2.64e-14)|Lung NSC(23;7e-10)|all_lung(23;2.53e-09)		Epithelial(9;4.09e-08)|all cancers(9;1.7e-07)|OV - Ovarian serous cystadenocarcinoma(5;0.0102)			GGAGTCTTACCTTGTCCCACA	0.592													114	204	---	---	---	---	PASS
TPTE	7179	broad.mit.edu	37	21	10908860	10908860	+	Silent	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10908860G>A	uc002yip.1	-	23	1853	c.1485C>T	c.(1483-1485)TAC>TAT	p.Y495Y	TPTE_uc002yis.1_RNA|TPTE_uc002yiq.1_Silent_p.Y477Y|TPTE_uc002yir.1_Silent_p.Y457Y|TPTE_uc010gkv.1_Silent_p.Y357Y	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	495	C2 tensin-type.				signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GCAACCAGAAGTAAAATGAGC	0.284													9	38	---	---	---	---	PASS
LIPI	149998	broad.mit.edu	37	21	15554171	15554171	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15554171G>T	uc002yjm.2	-	4	624	c.614C>A	c.(613-615)CCT>CAT	p.P205H	LIPI_uc010gkw.1_Missense_Mutation_p.P138H	NM_198996	NP_945347	Q6XZB0	LIPI_HUMAN	lipase, member I	184					lipid catabolic process	extracellular region|extracellular space|membrane|plasma membrane	heparin binding|phospholipase activity			ovary(2)	2				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		TGGCCCAGCAGGGTCAAGACC	0.398													36	78	---	---	---	---	PASS
TMPRSS15	5651	broad.mit.edu	37	21	19737446	19737446	+	Intron	SNP	T	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19737446T>A	uc002ykw.2	-							NM_002772	NP_002763	P98073	ENTK_HUMAN	enterokinase precursor						proteolysis	brush border|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(5)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	8						AAATATAAGATCTTGTATTAC	0.333													18	224	---	---	---	---	PASS
TMPRSS15	5651	broad.mit.edu	37	21	19737474	19737474	+	Silent	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19737474G>T	uc002ykw.2	-	7	787	c.756C>A	c.(754-756)GTC>GTA	p.V252V		NM_002772	NP_002763	P98073	ENTK_HUMAN	enterokinase precursor	252	Extracellular (Potential).|CUB 1.				proteolysis	brush border|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(5)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	8						TCCACTGGCAGACAACACTTG	0.368													135	186	---	---	---	---	PASS
MRAP	56246	broad.mit.edu	37	21	33678949	33678949	+	Splice_Site	SNP	A	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33678949A>G	uc002ypj.2	+	4	294	c.107_splice	c.e4-2	p.H36_splice	MRAP_uc002ypk.2_Splice_Site_p.H36_splice|MRAP_uc011ado.1_Splice_Site|MRAP_uc002ypl.2_Splice_Site_p.H36_splice|uc002ypm.2_RNA	NM_178817	NP_848932	Q8TCY5	MRAP_HUMAN	melanocortin 2 receptor accessory protein						positive regulation of cAMP biosynthetic process|protein localization at cell surface	endoplasmic reticulum|integral to membrane|perinuclear region of cytoplasm|plasma membrane	corticotropin hormone receptor binding|type 1 melanocortin receptor binding|type 3 melanocortin receptor binding|type 4 melanocortin receptor binding|type 5 melanocortin receptor binding				0						CTCCTCCCGCAGATTCCATCG	0.567													83	60	---	---	---	---	PASS
SIM2	6493	broad.mit.edu	37	21	38115753	38115753	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38115753C>T	uc002yvr.2	+	9	1120	c.1064C>T	c.(1063-1065)TCC>TTC	p.S355F	SIM2_uc002yvq.2_Missense_Mutation_p.S355F	NM_005069	NP_005060	Q14190	SIM2_HUMAN	single-minded homolog 2 long isoform	355	Single-minded C-terminal.				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(1)	1						TCCCAGGACTCCTGGAGGACC	0.512													128	23	---	---	---	---	PASS
KCNJ15	3772	broad.mit.edu	37	21	39671448	39671448	+	Missense_Mutation	SNP	G	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39671448G>A	uc002ywv.2	+	4	567	c.265G>A	c.(265-267)GCG>ACG	p.A89T	KCNJ15_uc002yww.2_Missense_Mutation_p.A89T|KCNJ15_uc002ywx.2_Missense_Mutation_p.A89T	NM_002243	NP_002234	Q99712	IRK15_HUMAN	potassium inwardly-rectifying channel J15	89	Extracellular (By similarity).				synaptic transmission	integral to plasma membrane	inward rectifier potassium channel activity			ovary(2)|skin(2)|breast(1)|central_nervous_system(1)	6						CTATGCCATCGCGTTTATTCA	0.478													11	138	---	---	---	---	PASS
PCNT	5116	broad.mit.edu	37	21	47754463	47754463	+	Silent	SNP	A	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47754463A>G	uc002zji.3	+	3	527	c.420A>G	c.(418-420)CCA>CCG	p.P140P	PCNT_uc002zjj.2_Silent_p.P22P|PCNT_uc010gqk.1_RNA	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin	140					cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)					ACCACCCACCAGAACAGCGTG	0.542													4	65	---	---	---	---	PASS
KREMEN1	83999	broad.mit.edu	37	22	29538035	29538035	+	Missense_Mutation	SNP	A	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29538035A>G	uc011akm.1	+	9	1376	c.1363A>G	c.(1363-1365)ATC>GTC	p.I455V	KREMEN1_uc003ael.2_Missense_Mutation_p.I438V|KREMEN1_uc011akn.1_Missense_Mutation_p.I338V	NM_032045	NP_114434	Q96MU8	KREM1_HUMAN	kringle-containing transmembrane protein 1	453	Cytoplasmic (Potential).				cell communication|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane|membrane fraction	protein binding			ovary(3)|lung(2)	5						TTCAATTTCCATCTTTAAGAA	0.478													76	145	---	---	---	---	PASS
MKL1	57591	broad.mit.edu	37	22	40825653	40825653	+	Silent	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40825653C>T	uc003ayv.1	-	4	465	c.258G>A	c.(256-258)AAG>AAA	p.K86K	MKL1_uc003ayw.1_Silent_p.K86K|MKL1_uc010gye.1_Silent_p.K86K|MKL1_uc010gyf.1_Silent_p.K86K	NM_020831	NP_065882	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia 1 protein	86	RPEL 2.|Mediates interaction with SCAI and ACTB (By similarity).				positive regulation of transcription from RNA polymerase II promoter|smooth muscle cell differentiation|transcription, DNA-dependent	cytoplasm|nucleus	actin monomer binding|leucine zipper domain binding|nucleic acid binding|transcription coactivator activity			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5						GAAGGATGTTCTTCTCCACCA	0.582			T	RBM15	acute megakaryocytic leukemia								45	120	---	---	---	---	PASS
EP300	2033	broad.mit.edu	37	22	41565527	41565527	+	Missense_Mutation	SNP	T	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41565527T>C	uc003azl.3	+	26	4588	c.4193T>C	c.(4192-4194)CTC>CCC	p.L1398P		NM_001429	NP_001420	Q09472	EP300_HUMAN	E1A binding protein p300	1398					apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia	centrosome|histone acetyltransferase complex	androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1)	64						ATATCTTACCTCGATAGTGTT	0.343			T| N|F|Mis|O	MLL|RUNXBP2	colorectal|breast|pancreatic|AML|ALL|DLBCL				Rubinstein-Taybi_syndrome				138	202	---	---	---	---	PASS
SHANK3	85358	broad.mit.edu	37	22	51160645	51160645	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51160645C>A	uc003bne.1	+	22	4432	c.4432C>A	c.(4432-4434)CGC>AGC	p.R1478S	SHANK3_uc003bnf.1_Missense_Mutation_p.R925S|SHANK3_uc010hbg.1_Missense_Mutation_p.R660S	NM_001080420	NP_001073889	F2Z3L0	F2Z3L0_HUMAN	SH3 and multiple ankyrin repeat domains 3	1478										central_nervous_system(1)	1		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		CGGGCCTGCCCGCCCTCGCTA	0.682													17	27	---	---	---	---	PASS
CRLF2	64109	broad.mit.edu	37	X	1325342	1325342	+	RNA	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1325342G>T	uc004cpm.1	-	3		c.333C>A						Q9HC73	CRLF2_HUMAN	Homo sapiens mRNA for IL-XR, complete cds.							extracellular region|integral to membrane|plasma membrane	receptor activity			haematopoietic_and_lymphoid_tissue(7)	7		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				AAACCATCCAGCGACTTGCGG	0.488			Mis|T	P2RY8|IGH@	B-ALL|Downs associated ALL								78	133	---	---	---	---	PASS
NHS	4810	broad.mit.edu	37	X	17745612	17745612	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17745612C>T	uc004cxx.2	+	6	3661	c.3323C>T	c.(3322-3324)CCG>CTG	p.P1108L	NHS_uc011mix.1_Missense_Mutation_p.P1129L|NHS_uc004cxy.2_Missense_Mutation_p.P952L|NHS_uc004cxz.2_Missense_Mutation_p.P931L|NHS_uc004cya.2_Missense_Mutation_p.P831L	NM_198270	NP_938011	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome protein isoform 1	1108						nucleus				skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	Hepatocellular(33;0.183)					AATCCTCCACCGTCCCTTGCA	0.408													123	18	---	---	---	---	PASS
CYBB	1536	broad.mit.edu	37	X	37642781	37642781	+	Silent	SNP	G	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37642781G>C	uc004ddr.2	+	3	241	c.180G>C	c.(178-180)CTG>CTC	p.L60L	CYBB_uc011mke.1_RNA|CYBB_uc011mkf.1_Silent_p.L28L|CYBB_uc011mkg.1_5'UTR	NM_000397	NP_000388	P04839	CY24B_HUMAN	cytochrome b-245 beta polypeptide	60	Helical; (Potential).|Ferric oxidoreductase.				electron transport chain|inflammatory response|innate immune response|respiratory burst|superoxide anion generation	NADPH oxidase complex	electron carrier activity|flavin adenine dinucleotide binding|heme binding|protein heterodimerization activity|superoxide-generating NADPH oxidase activity|voltage-gated ion channel activity			central_nervous_system(1)|skin(1)	2						CAGCCTGCCTGAATTTCAACT	0.517													57	12	---	---	---	---	PASS
DUSP21	63904	broad.mit.edu	37	X	44703624	44703624	+	Silent	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44703624C>T	uc004dgd.2	+	1	376	c.246C>T	c.(244-246)TAC>TAT	p.Y82Y		NM_022076	NP_071359	Q9H596	DUS21_HUMAN	dual specificity phosphatase 21	82	Tyrosine-protein phosphatase.|Sufficient for mitochondrial localization (By similarity).					cytoplasm|nucleus	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity			large_intestine(1)|lung(1)	2						CGCGTCTCTACGACTTTTTTG	0.542													72	11	---	---	---	---	PASS
ITIH5L	347365	broad.mit.edu	37	X	54784798	54784798	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54784798C>T	uc004dtj.2	-	8	1739	c.1709G>A	c.(1708-1710)GGA>GAA	p.G570E		NM_198510	NP_940912	Q6UXX5	ITH5L_HUMAN	inter-alpha (globulin) inhibitor H5-like	570					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			lung(2)|skin(2)|ovary(1)|breast(1)	6						CAGCAGTTCTCCAATGGTGAC	0.587													35	3	---	---	---	---	PASS
STARD8	9754	broad.mit.edu	37	X	67938352	67938352	+	Missense_Mutation	SNP	C	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67938352C>A	uc004dxa.2	+	5	1728	c.1356C>A	c.(1354-1356)GAC>GAA	p.D452E	STARD8_uc004dxb.2_Missense_Mutation_p.D532E|STARD8_uc004dxc.3_Missense_Mutation_p.D452E	NM_014725	NP_055540	Q92502	STAR8_HUMAN	StAR-related lipid transfer (START) domain	452					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion	GTPase activator activity			breast(3)|ovary(2)|pancreas(1)	6						GCGAACTTGACAGTAGTGGGA	0.597													43	0	---	---	---	---	PASS
PCDH11X	27328	broad.mit.edu	37	X	91873458	91873458	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:91873458G>T	uc004efk.1	+	7	4408	c.3563G>T	c.(3562-3564)CGA>CTA	p.R1188L	PCDH11X_uc004efl.1_Missense_Mutation_p.R1178L|PCDH11X_uc004efo.1_Missense_Mutation_p.R1151L|PCDH11X_uc010nmv.1_3'UTR|PCDH11X_uc004efm.1_Missense_Mutation_p.R1180L|PCDH11X_uc004efn.1_Missense_Mutation_p.R1170L	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	1188	Cytoplasmic (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						CACAGCCCACGAGTGACACAG	0.592													116	21	---	---	---	---	PASS
TEX13B	56156	broad.mit.edu	37	X	107225170	107225170	+	Missense_Mutation	SNP	A	G	G			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107225170A>G	uc004enn.1	-	2	281	c.188T>C	c.(187-189)GTC>GCC	p.V63A		NM_031273	NP_112563	Q9BXU2	TX13B_HUMAN	testis expressed 13B	63										ovary(1)	1						GGCCTCTTTGACCTCGCTGGG	0.597													120	11	---	---	---	---	PASS
C1GALT1C1	29071	broad.mit.edu	37	X	119760819	119760819	+	Missense_Mutation	SNP	C	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119760819C>T	uc004esy.2	-	3	550	c.203G>A	c.(202-204)CGA>CAA	p.R68Q	C1GALT1C1_uc004esz.2_Missense_Mutation_p.R68Q	NM_152692	NP_689905	Q96EU7	C1GLC_HUMAN	C1GALT1-specific chaperone 1	68	Lumenal (Potential).					integral to membrane					0						ACAGTATACTCGAAAGCTCTT	0.423													91	11	---	---	---	---	PASS
SLITRK2	84631	broad.mit.edu	37	X	144905786	144905786	+	Missense_Mutation	SNP	G	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:144905786G>C	uc004fcd.2	+	5	2833	c.1843G>C	c.(1843-1845)GAA>CAA	p.E615Q	SLITRK2_uc010nsp.2_Missense_Mutation_p.E615Q|SLITRK2_uc010nso.2_Missense_Mutation_p.E615Q|SLITRK2_uc011mwq.1_Missense_Mutation_p.E615Q|SLITRK2_uc011mwr.1_Missense_Mutation_p.E615Q|SLITRK2_uc011mws.1_Missense_Mutation_p.E615Q|SLITRK2_uc004fcg.2_Missense_Mutation_p.E615Q|SLITRK2_uc011mwt.1_Missense_Mutation_p.E615Q	NM_032539	NP_115928	Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2 precursor	615	Extracellular (Potential).					integral to membrane				ovary(5)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(192;6.56e-05)					ACTACACACTGAAGTTCCACT	0.433													99	6	---	---	---	---	PASS
SPRY3	10251	broad.mit.edu	37	X	155003826	155003826	+	Missense_Mutation	SNP	G	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155003826G>T	uc004fnq.1	+	2	747	c.293G>T	c.(292-294)AGG>ATG	p.R98M	SPRY3_uc010nvl.1_Intron	NM_005840	NP_005831	O43610	SPY3_HUMAN	sprouty homolog 3	98					multicellular organismal development|regulation of signal transduction	cytoplasm|membrane					0	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					TCTGATCAAAGGCTCTTGGCC	0.557													76	119	---	---	---	---	PASS
USP24	23358	broad.mit.edu	37	1	55607343	55607344	+	Frame_Shift_Ins	INS	-	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55607343_55607344insT	uc001cyg.3	-	21	2215_2216	c.2215_2216insA	c.(2215-2217)ATGfs	p.M739fs		NM_015306	NP_056121	Q9UPU5	UBP24_HUMAN	ubiquitin specific protease 24	899					ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(6)|kidney(6)|breast(1)	13						TGCTGTAAGCATTTTTGTTGCT	0.401													15	9	---	---	---	---	
MCOLN2	255231	broad.mit.edu	37	1	85412990	85412991	+	Intron	DEL	CA	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85412990_85412991delCA	uc001dkm.2	-						MCOLN2_uc001dkn.2_Intron	NM_153259	NP_694991	Q8IZK6	MCLN2_HUMAN	mucolipin 2							integral to membrane	ion channel activity			ovary(3)|upper_aerodigestive_tract(1)	4				all cancers(265;0.0111)|Epithelial(280;0.0263)|OV - Ovarian serous cystadenocarcinoma(397;0.217)		caccccccaccacacacacaca	0.069													5	3	---	---	---	---	
C1orf77	26097	broad.mit.edu	37	1	153608885	153608886	+	Intron	INS	-	A	A	rs80290962		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153608885_153608886insA	uc001fcm.1	+						C1orf77_uc001fcn.1_Intron|C1orf77_uc001fco.1_5'Flank|S100A13_uc001fcj.2_5'Flank|C1orf77_uc009woi.1_Intron|C1orf77_uc009woj.1_Intron	NM_015607	NP_056422	Q9Y3Y2	CHTOP_HUMAN	small protein rich in arginine and glycine						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	protein binding|RNA binding				0	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			gaccctgtctcaaaaaaaaaaa	0.158													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	204363979	204363980	+	IGR	INS	-	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204363979_204363980insA								LOC127841 (25132 upstream) : PPP1R15B (8514 downstream)																							atttgtttttcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	236261699	236261702	+	IGR	DEL	GGAA	-	-	rs113120632	by1000genomes	TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236261699_236261702delGGAA								NID1 (33218 upstream) : GPR137B (44130 downstream)																							ggaaaggaagggaaggaaggaagg	0.000													5	3	---	---	---	---	
HEATR1	55127	broad.mit.edu	37	1	236749420	236749420	+	Intron	DEL	G	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236749420delG	uc001hyd.1	-						HEATR1_uc009xgh.1_5'Flank	NM_018072	NP_060542	Q9H583	HEAT1_HUMAN	protein BAP28						rRNA processing	nucleolus|ribonucleoprotein complex	protein binding			ovary(2)|skin(1)	3	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			TTTTTATCTTGGCAAAAATTT	0.279													4	2	---	---	---	---	
APLF	200558	broad.mit.edu	37	2	68696121	68696122	+	Intron	INS	-	GT	GT	rs34695552		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68696121_68696122insGT	uc002sep.2	+						FBXO48_uc002seo.2_5'Flank|APLF_uc010fdf.2_Intron	NM_173545	NP_775816	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor						double-strand break repair|single strand break repair	cytosol|nucleus	3'-5' exonuclease activity|DNA-(apurinic or apyrimidinic site) lyase activity|endodeoxyribonuclease activity|metal ion binding|nucleotide binding|protein binding			ovary(2)	2						GTCCTAAAGGGgtgtgtgtgtg	0.317													4	2	---	---	---	---	
PDK1	5163	broad.mit.edu	37	2	173451225	173451227	+	Intron	DEL	AAG	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173451225_173451227delAAG	uc002uhr.2	+						PDK1_uc010zdz.1_Intron|PDK1_uc010zea.1_Intron|PDK1_uc002uhq.1_Intron|PDK1_uc002uhs.2_Intron|PDK1_uc010zeb.1_Intron	NM_002610	NP_002601	Q15118	PDK1_HUMAN	pyruvate dehydrogenase kinase 1 precursor						glucose metabolic process|peptidyl-histidine phosphorylation|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate|small GTPase mediated signal transduction	mitochondrial matrix	ATP binding|pyruvate dehydrogenase (acetyl-transferring) kinase activity|two-component sensor activity			lung(3)|central_nervous_system(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.12)			ACAAGGAAGAAAGAAGCTCTTAG	0.384									Autosomal_Dominant_Polycystic_Kidney_Disease				7	6	---	---	---	---	
STK17B	9262	broad.mit.edu	37	2	197008112	197008113	+	Intron	INS	-	CAATA	CAATA	rs142415504	by1000genomes	TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197008112_197008113insCAATA	uc002utk.2	-						STK17B_uc010fsh.2_Intron	NM_004226	NP_004217	O94768	ST17B_HUMAN	serine/threonine kinase 17B						apoptosis|induction of apoptosis|intracellular protein kinase cascade	nucleus	ATP binding|protein serine/threonine kinase activity			lung(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.141)			ATACTTTTATTCATTTCATTTA	0.282													3	3	---	---	---	---	
TRIP12	9320	broad.mit.edu	37	2	230679965	230679966	+	Intron	INS	-	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230679965_230679966insA	uc002vpw.1	-						TRIP12_uc002vpx.1_Intron|TRIP12_uc002vpy.1_Intron|TRIP12_uc010zlz.1_Intron|TRIP12_uc010fxh.1_Intron	NM_004238	NP_004229	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	proteasome complex	thyroid hormone receptor binding|ubiquitin-protein ligase activity			ovary(4)|lung(2)|breast(1)|central_nervous_system(1)|skin(1)	9		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		TATACACCATTAAAAAAATACA	0.287													24	15	---	---	---	---	
CLASP2	23122	broad.mit.edu	37	3	33626408	33626418	+	Splice_Site	DEL	ACCAGCTGAAC	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33626408_33626418delACCAGCTGAAC	uc003cfu.2	-	22	2423	c.2069_splice	c.e22-1	p.P690_splice	CLASP2_uc003cft.2_Splice_Site|CLASP2_uc010hgb.2_Splice_Site|CLASP2_uc011axt.1_Splice_Site_p.A283_splice	NM_015097	NP_055912	B2RTR1	B2RTR1_HUMAN	CLIP-associating protein 2											ovary(3)|central_nervous_system(1)	4						CAGACCGGCTACCAGCTGAACACCAAACACA	0.422													23	25	---	---	---	---	
FOXL2	668	broad.mit.edu	37	3	138665365	138665378	+	Frame_Shift_Del	DEL	ATCGCCATGGCGAT	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138665365_138665378delATCGCCATGGCGAT	uc003esw.2	-	1	605_618	c.187_200delATCGCCATGGCGAT	c.(187-201)ATCGCCATGGCGATCfs	p.I63fs	uc003esv.1_5'Flank|C3orf72_uc003esx.1_5'Flank|C3orf72_uc011bmr.1_5'Flank	NM_023067	NP_075555	P58012	FOXL2_HUMAN	forkhead box L2	63_67	Fork-head.				convergent extension|DNA fragmentation involved in apoptotic nuclear change|embryonic eye morphogenesis|extraocular skeletal muscle development|female somatic sex determination|induction of apoptosis|menstruation|negative regulation of transcription, DNA-dependent|ovarian follicle development|pattern specification process|positive regulation of caspase activity|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity	transcription factor complex	caspase regulator activity|DNA bending activity|double-stranded DNA binding|estrogen receptor binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin conjugating enzyme binding			ovary(266)|large_intestine(1)|skin(1)	268						GCTCTCGCGGATCGCCATGGCGATGAGCGCCACG	0.659			Mis		granulosa-cell tumour of the ovary		Blepharophimosis|ptosis and epicanthus inversus Types I|II; Premature ovarian failure type III						18	43	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	165862456	165862457	+	IGR	DEL	TG	-	-	rs67711845		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165862456_165862457delTG								BCHE (307203 upstream) : None (None downstream)																							tgtgtgtgtatgtgtgtgtgtg	0.307													7	4	---	---	---	---	
YEATS2	55689	broad.mit.edu	37	3	183528489	183528496	+	3'UTR	DEL	AACCTTTG	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183528489_183528496delAACCTTTG	uc003fly.2	+	31						NM_018023	NP_060493	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2						histone H3 acetylation|negative regulation of transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex	TBP-class protein binding			ovary(3)|large_intestine(1)	4	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			ATGGCTACCCAACCTTTGCCGCTGCCTG	0.567													6	12	---	---	---	---	
CHRD	8646	broad.mit.edu	37	3	184100392	184100393	+	Intron	INS	-	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184100392_184100393insA	uc003fov.2	+						CHRD_uc003fow.2_Intron|CHRD_uc003fox.2_Intron|CHRD_uc003foy.2_Intron|CHRD_uc010hyc.2_Intron|CHRD_uc011brr.1_Intron	NM_003741	NP_003732	Q9H2X0	CHRD_HUMAN	chordin precursor						BMP signaling pathway involved in spinal cord dorsal/ventral patterning|floor plate development|negative regulation of BMP signaling pathway|negative regulation of cell migration|positive regulation of cell adhesion|skeletal system development	extracellular space	cytokine binding			skin(2)|ovary(1)	3	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GAGGGTTTCTGACGGGCTCTCA	0.624													312	859	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	4078640	4078640	+	IGR	DEL	C	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4078640delC								LOC348926 (121492 upstream) : OTOP1 (111890 downstream)																							TATATCTTTTCCAATGTTGTC	0.388													3	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	25497613	25497614	+	IGR	INS	-	TCTTTCTTTCTTTC	TCTTTCTTTCTTTC	rs71190814		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25497613_25497614insTCTTTCTTTCTTTC								ANAPC4 (77494 upstream) : SLC34A2 (159821 downstream)																							ccttccttccttccttccttcc	0.030													3	3	---	---	---	---	
COX7B2	170712	broad.mit.edu	37	4	46736926	46736926	+	3'UTR	DEL	T	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46736926delT	uc003gxf.2	-	3					COX7B2_uc010ige.2_RNA	NM_130902	NP_570972	Q8TF08	CX7B2_HUMAN	cytochrome c oxidase subunit VIIb2 precursor							integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity				0						GACAAGTTGGTTTTTTAAACA	0.333													46	43	---	---	---	---	
C4orf3	401152	broad.mit.edu	37	4	120221760	120221761	+	5'UTR	DEL	CG	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120221760_120221761delCG	uc003icv.3	-	1						NM_001001701	NP_001001701	Q8WVX3	CD003_HUMAN	hypothetical protein LOC401152							integral to membrane					0						TGGTGTTCGCCGCACCGGAAAC	0.629													19	10	---	---	---	---	
GPM6A	2823	broad.mit.edu	37	4	176622884	176622885	+	Frame_Shift_Ins	INS	-	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176622884_176622885insC	uc003iuf.2	-	2	875_876	c.71_72insG	c.(70-72)GGCfs	p.G24fs	GPM6A_uc011ckj.1_Frame_Shift_Ins_p.G17fs|GPM6A_uc003iug.2_Frame_Shift_Ins_p.G24fs|GPM6A_uc003iuh.2_Frame_Shift_Ins_p.G13fs	NM_201591	NP_963885	P51674	GPM6A_HUMAN	glycoprotein M6A isoform 2	24	Helical; (Potential).					cell surface|integral to membrane					0		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)		CATAGGGAATGCCCCCCAGGCA	0.431													44	45	---	---	---	---	
MARCH11	441061	broad.mit.edu	37	5	16090981	16090983	+	Intron	DEL	GAA	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16090981_16090983delGAA	uc003jfo.2	-						MARCH11_uc010itw.1_Intron	NM_001102562	NP_001096032	A6NNE9	MARHB_HUMAN	membrane-associated ring finger (C3HC4) 11							cytoplasmic vesicle membrane|integral to membrane	ligase activity|zinc ion binding				0						TGTTAACGTTGAAGGTCATGGTC	0.419													39	40	---	---	---	---	
AGGF1	55109	broad.mit.edu	37	5	76355778	76355778	+	Intron	DEL	T	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76355778delT	uc003ket.2	+							NM_018046	NP_060516	Q8N302	AGGF1_HUMAN	angiogenic factor VG5Q						angiogenesis|cell adhesion|positive regulation of angiogenesis|positive regulation of endothelial cell proliferation|RNA processing|vasculogenesis	extracellular region|perinuclear region of cytoplasm	eukaryotic cell surface binding|nucleic acid binding|protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)		gcgattctcctgcctcagcct	0.000													4	2	---	---	---	---	
PAM	5066	broad.mit.edu	37	5	102342897	102342898	+	Intron	DEL	AC	-	-	rs34471961		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102342897_102342898delAC	uc003knw.2	+						PAM_uc003kns.2_Intron|PAM_uc003knt.2_Intron|PAM_uc003knu.2_Intron|PAM_uc003knv.2_Intron|PAM_uc011cuz.1_Intron|PAM_uc003knz.2_5'Flank	NM_000919	NP_000910	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase						peptide metabolic process|protein modification process	extracellular region|integral to membrane|stored secretory granule	L-ascorbic acid binding|peptidylamidoglycolate lyase activity|peptidylglycine monooxygenase activity|protein binding				0		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	acatatacatacacacacacac	0.277													2	4	---	---	---	---	
NOL7	51406	broad.mit.edu	37	6	13616628	13616628	+	Intron	DEL	C	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13616628delC	uc003naz.2	+							NM_016167	NP_057251	Q9UMY1	NOL7_HUMAN	nucleolar protein 7, 27kDa							mitochondrion|nucleolus					0	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.135)	Epithelial(50;0.176)			GCGGTAACTTCAGAAGCAACT	0.398													19	29	---	---	---	---	
GRM4	2914	broad.mit.edu	37	6	34035370	34035389	+	Intron	DEL	CCTTTCTTCCTCCCTTCATG	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34035370_34035389delCCTTTCTTCCTCCCTTCATG	uc003oir.3	-						GRM4_uc011dsn.1_Intron|GRM4_uc010jvh.2_Intron|GRM4_uc010jvi.2_Intron|GRM4_uc011dsl.1_Intron|GRM4_uc003oiq.2_Intron|GRM4_uc011dsm.1_Intron	NM_000841	NP_000832	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4 precursor						activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6					L-Glutamic Acid(DB00142)	ttcctccctccctttcttcctcccttcatgccttcctccc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	79424144	79424144	+	IGR	DEL	A	-	-	rs111390657		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79424144delA								None (None upstream) : IRAK1BP1 (153045 downstream)																							AAACACTGACAAAAAAAAAAA	0.393													4	2	---	---	---	---	
MDN1	23195	broad.mit.edu	37	6	90491503	90491504	+	Intron	INS	-	G	G	rs142798395	by1000genomes	TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90491503_90491504insG	uc003pnn.1	-						MDN1_uc003pno.1_Intron|MDN1_uc003pnp.1_Intron	NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		tgaattcaggatttgagatcaa	0.040													3	3	---	---	---	---	
TRDN	10345	broad.mit.edu	37	6	123714729	123714730	+	Intron	INS	-	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123714729_123714730insA	uc003pzj.1	-						TRDN_uc003pzk.1_Intron|TRDN_uc003pzl.1_Intron|TRDN_uc010kem.1_Intron	NM_006073	NP_006064	Q13061	TRDN_HUMAN	triadin						muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)		TATAGATGTTTAAAAAAAGGCA	0.337													12	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	133513219	133513220	+	IGR	DEL	GT	-	-	rs111509666		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133513219_133513220delGT								LOC285735 (85509 upstream) : EYA4 (48516 downstream)																							GTTATTCTGAgtgtgtgtgtgt	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65268568	65268570	+	IGR	DEL	CTT	-	-	rs75342027		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65268568_65268570delCTT								CCT6P1 (39907 upstream) : VKORC1L1 (69687 downstream)																							CCTCTTTTTCCTTCttttttaaa	0.365													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67206114	67206117	+	IGR	DEL	TTCT	-	-	rs56895053		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67206114_67206117delTTCT								STAG3L4 (419602 upstream) : None (None downstream)																							ccttccttccttctttccttcctt	0.113													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	134727424	134727427	+	IGR	DEL	CCTC	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134727424_134727427delCCTC								ST3GAL1 (143241 upstream) : ZFAT (762606 downstream)																							ctgtctccttcctccctccctccc	0.000													4	2	---	---	---	---	
COL22A1	169044	broad.mit.edu	37	8	139807772	139807775	+	Intron	DEL	ACAC	-	-	rs34313710		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139807772_139807775delACAC	uc003yvd.2	-							NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			tctctttcagacacacacacacac	0.000										HNSCC(7;0.00092)			3	3	---	---	---	---	
RNF20	56254	broad.mit.edu	37	9	104297516	104297516	+	Intron	DEL	T	-	-	rs76960510		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104297516delT	uc004bbn.2	+							NM_019592	NP_062538	Q5VTR2	BRE1A_HUMAN	ring finger protein 20						histone H2B ubiquitination|histone monoubiquitination|negative regulation of cell migration|positive regulation of transcription, DNA-dependent|protein polyubiquitination|ubiquitin-dependent protein catabolic process	nucleolus|ubiquitin ligase complex	histone binding|p53 binding|transcription coactivator activity|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(1)|breast(1)|kidney(1)|skin(1)	8		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)		TACaatttaattttttttttt	0.209													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	13199671	13199672	+	IGR	INS	-	G	G	rs113702003		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13199671_13199672insG								OPTN (19395 upstream) : MCM10 (3909 downstream)																							tttttttttttttttttttttg	0.183													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	19414308	19414311	+	IGR	DEL	TTCC	-	-	rs10450313	by1000genomes	TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19414308_19414311delTTCC								ARL5B (447368 upstream) : PLXDC2 (691061 downstream)																							ctttctttctttccttccttcctt	0.069													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42381642	42381646	+	IGR	DEL	TATAA	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42381642_42381646delTATAA								None (None upstream) : LOC441666 (445669 downstream)																							tccattccattataatccattccat	0.000													14	7	---	---	---	---	
PANK1	53354	broad.mit.edu	37	10	91353283	91353284	+	Intron	INS	-	G	G	rs113042864		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91353283_91353284insG	uc001kgp.1	-						PANK1_uc001kgn.1_Intron|PANK1_uc001kgo.1_Intron|PANK1_uc009xtu.1_Intron|uc001kgq.1_5'Flank|MIR107_hsa-mir-107|MI0000114_5'Flank	NM_148977	NP_683878	Q8TE04	PANK1_HUMAN	pantothenate kinase 1 isoform alpha						coenzyme A biosynthetic process|pantothenate metabolic process	cytosol|nucleus	ATP binding|pantothenate kinase activity				0					Bezafibrate(DB01393)	TGTCCATTAATGGGGGGGGAAA	0.381													2	4	---	---	---	---	
TLL2	7093	broad.mit.edu	37	10	98155808	98155808	+	Intron	DEL	G	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98155808delG	uc001kml.1	-						TLL2_uc009xvf.1_Intron	NM_012465	NP_036597	Q9Y6L7	TLL2_HUMAN	tolloid-like 2 precursor						cell differentiation|multicellular organismal development|proteolysis	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		AGAGGAAGACGGGGGCCCTGG	0.542											OREG0020398	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	20	30	---	---	---	---	
NOLC1	9221	broad.mit.edu	37	10	103920995	103920996	+	Intron	INS	-	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103920995_103920996insT	uc001kuo.2	+						NOLC1_uc001kup.2_Intron|NOLC1_uc001kuq.2_Intron|NOLC1_uc009xxb.1_Intron|NOLC1_uc001kur.2_Intron	NM_004741	NP_004732	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1						mitosis|rRNA processing	cytoplasm|nucleolus	ATP binding|GTP binding|protein binding			ovary(1)	1		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)		AACTGGTTACCttttttttttt	0.257													3	3	---	---	---	---	
PLEKHA1	59338	broad.mit.edu	37	10	124189011	124189016	+	Intron	DEL	TGTGTG	-	-	rs140551676		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124189011_124189016delTGTGTG	uc001lge.1	+						PLEKHA1_uc001lgf.1_Intron|PLEKHA1_uc001lgg.1_Intron	NM_001001974	NP_001001974	Q9HB21	PKHA1_HUMAN	pleckstrin homology domain containing, family A						B cell receptor signaling pathway|cellular response to hydrogen peroxide|establishment of protein localization|negative regulation of protein kinase B signaling cascade|phosphatidylinositol 3-kinase cascade|ruffle organization	cytoplasm|nucleus|ruffle membrane	PDZ domain binding|phosphatidylinositol-3,4-bisphosphate binding			kidney(1)	1		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CTGCTGCCTTtgtgtgtgtgtgtgtg	0.335													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	15302850	15302853	+	IGR	DEL	TGTG	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15302850_15302853delTGTG								INSC (34098 upstream) : SOX6 (685143 downstream)																							GTGTAGTTTAtgtgtgtgtgtgtg	0.294													9	5	---	---	---	---	
SOX6	55553	broad.mit.edu	37	11	16043877	16043878	+	Intron	INS	-	TTCC	TTCC			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16043877_16043878insTTCC	uc001mme.2	-						SOX6_uc001mmd.2_Intron|SOX6_uc001mmf.2_Intron|SOX6_uc001mmg.2_Intron	NM_001145819	NP_001139291	P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6 isoform 4						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3						tccttccttctttccttccttc	0.129													10	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	49104713	49104713	+	IGR	DEL	C	-	-	rs149147831		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49104713delC								OR4A47 (593441 upstream) : FOLH1 (63475 downstream)																							tttcttCCTTCCCCCCGCAAA	0.428													4	2	---	---	---	---	
REXO2	25996	broad.mit.edu	37	11	114315094	114315095	+	Intron	INS	-	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114315094_114315095insA	uc001poy.2	+						REXO2_uc001poz.2_Intron	NM_015523	NP_056338	Q9Y3B8	ORN_HUMAN	small fragment nuclease precursor						nucleotide metabolic process	mitochondrion|nucleus	3'-5' exonuclease activity|nucleic acid binding				0		all_cancers(61;5.06e-12)|all_epithelial(67;5.3e-06)|all_hematologic(158;7.68e-05)|Acute lymphoblastic leukemia(157;0.000966)|Melanoma(852;0.00153)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Breast(348;0.0818)|Prostate(24;0.104)		BRCA - Breast invasive adenocarcinoma(274;2.65e-06)|Epithelial(105;6.09e-05)|all cancers(92;0.000494)		GATTCTTGAAGAAAAAAAAATG	0.351													4	2	---	---	---	---	
ADIPOR2	79602	broad.mit.edu	37	12	1805564	1805565	+	Intron	INS	-	T	T			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1805564_1805565insT	uc001qjm.2	+						ADIPOR2_uc001qjn.2_Intron	NM_024551	NP_078827	Q86V24	ADR2_HUMAN	adiponectin receptor 2						fatty acid oxidation|hormone-mediated signaling pathway	integral to membrane	hormone binding|receptor activity				0	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000382)			ttttttccttcttttttttttt	0.203													3	3	---	---	---	---	
VWF	7450	broad.mit.edu	37	12	6138253	6138254	+	Intron	INS	-	A	A	rs71445694		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6138253_6138254insA	uc001qnn.1	-						VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein						blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)	aaatggaaggcaaaaaaaaaaa	0.000													6	5	---	---	---	---	
CD27	939	broad.mit.edu	37	12	6560392	6560393	+	Intron	INS	-	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6560392_6560393insC	uc001qod.2	+						LOC678655_uc001qob.2_Intron|LOC678655_uc001qoc.2_Intron|LOC678655_uc009zel.1_RNA|CD27_uc001qoe.2_Intron|LOC678655_uc009zem.1_Intron|LOC678655_uc001qof.2_Intron|TAPBPL_uc001qog.3_5'Flank|TAPBPL_uc001qoh.3_5'Flank|TAPBPL_uc001qoi.1_5'Flank	NM_001242	NP_001233	P26842	CD27_HUMAN	tumor necrosis factor receptor superfamily,						anti-apoptosis|apoptosis|cell surface receptor linked signaling pathway|immunoglobulin mediated immune response|induction of apoptosis|positive regulation of B cell differentiation|positive regulation of JNK cascade|release of cytoplasmic sequestered NF-kappaB	extracellular region|integral to plasma membrane	caspase inhibitor activity|protein binding|transmembrane receptor activity				0						GTCTCCCCCTGCCCCCACTGCT	0.624													55	39	---	---	---	---	
LIMA1	51474	broad.mit.edu	37	12	50634082	50634082	+	Intron	DEL	G	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50634082delG	uc001rwj.3	-						LIMA1_uc001rwk.3_Intron|LIMA1_uc010smr.1_Intron|LIMA1_uc010sms.1_Intron	NM_016357	NP_057441	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1 isoform b						actin filament bundle assembly|negative regulation of actin filament depolymerization|ruffle organization	cytoplasm|focal adhesion|stress fiber	actin filament binding|actin monomer binding|zinc ion binding			ovary(1)	1						tgaggcgggaggcagggatgg	0.000													4	2	---	---	---	---	
GTSF1	121355	broad.mit.edu	37	12	54859084	54859084	+	Intron	DEL	A	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54859084delA	uc001sgb.2	-							NM_144594	NP_653195	Q8WW33	GTSF1_HUMAN	gametocyte specific factor 1								metal ion binding				0		Myeloproliferative disorder(1001;0.00452)				AACTTGGATTAAAAAAAAAGG	0.333													4	3	---	---	---	---	
LRP1	4035	broad.mit.edu	37	12	57586763	57586764	+	Intron	INS	-	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57586763_57586764insC	uc001snd.2	+						MIR1228_hsa-mir-1228|MI0006318_5'Flank	NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1						aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2)	22				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GGTGAGAGAGGCGGGGGGGAGG	0.639													20	51	---	---	---	---	
RAD9B	144715	broad.mit.edu	37	12	110950776	110950776	+	Intron	DEL	T	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110950776delT	uc001trf.3	+						RAD9B_uc001trg.3_Intron|RAD9B_uc010sya.1_Intron|RAD9B_uc001tre.3_Intron|RAD9B_uc001trd.3_Intron	NM_152442	NP_689655	Q6WBX8	RAD9B_HUMAN	RAD9 homolog B						cell cycle checkpoint|DNA repair|DNA replication	nucleoplasm	protein binding			pancreas(1)|skin(1)	2						AGTCGGCACAttttttttttt	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	19537994	19537994	+	IGR	DEL	C	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19537994delC								LOC284232 (91885 upstream) : LOC348021 (44405 downstream)																							TGCAGACAGACCCCGTGGTGG	0.647													2	7	---	---	---	---	
C14orf37	145407	broad.mit.edu	37	14	58724850	58724851	+	Intron	DEL	AC	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58724850_58724851delAC	uc010tro.1	-						PSMA3_uc001xdj.1_Intron|PSMA3_uc001xdk.1_Intron	NM_001001872	NP_001001872	Q86TY3	CN037_HUMAN	hypothetical protein LOC145407 precursor							integral to membrane	binding				0						ATTAAATAAAACAGTGTACATA	0.183													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	45755213	45755213	+	Intron	DEL	C	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45755213delC	uc001zvi.1	+											Homo sapiens cDNA FLJ32124 fis, clone PEBLM1000180.																		accatcaccaccaccaccacc	0.000													4	2	---	---	---	---	
RPH3AL	9501	broad.mit.edu	37	17	165596	165597	+	Intron	INS	-	C	C			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:165596_165597insC	uc002frd.1	-						RPH3AL_uc010vpy.1_Intron|RPH3AL_uc002fre.1_Intron|RPH3AL_uc002frf.1_Intron|RPH3AL_uc010cjl.1_Intron	NM_006987	NP_008918	Q9UNE2	RPH3L_HUMAN	rabphilin 3A-like (without C2 domains)						exocytosis|intracellular protein transport	transport vesicle membrane	cytoskeletal protein binding|Rab GTPase binding|zinc ion binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)		TAGTCCCTGTGCCCCACCTCCA	0.569													4	3	---	---	---	---	
KRT25	147183	broad.mit.edu	37	17	38910970	38910971	+	Intron	INS	-	AA	AA	rs33924883		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38910970_38910971insAA	uc002hve.2	-							NM_181534	NP_853512	Q7Z3Z0	K1C25_HUMAN	keratin 25							cytoplasm|intermediate filament	structural molecule activity			ovary(2)	2		Breast(137;0.00526)				aactccttctcaaaaaaaaaaa	0.084													4	2	---	---	---	---	
KRTAP3-1	83896	broad.mit.edu	37	17	39165499	39165502	+	5'Flank	DEL	TAAG	-	-	rs3841252		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39165499_39165502delTAAG	uc002hvt.1	-							NM_031958	NP_114164	Q9BYR8	KRA31_HUMAN	keratin associated protein 3.1							keratin filament	structural molecule activity				0		Breast(137;0.00043)				CCTAATTACTTAAGTGTTTATTAC	0.377													4	7	---	---	---	---	
TAC4	255061	broad.mit.edu	37	17	47925055	47925058	+	Intron	DEL	ACAC	-	-	rs113382605		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47925055_47925058delACAC	uc002ipo.1	-						TAC4_uc002ipp.1_Intron|TAC4_uc002ipq.1_Intron|TAC4_uc002ipr.1_Intron|TAC4_uc002ips.1_Intron|TAC4_uc002ipt.2_Intron|TAC4_uc002ipu.2_Intron	NM_170685	NP_733786	Q86UU9	TKN4_HUMAN	tachykinin 4 isoform alpha						regulation of blood pressure	extracellular region				breast(1)	1						acacacacagacacacacacacac	0.191													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	78016235	78016235	+	IGR	DEL	A	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:78016235delA								PARD6G (10838 upstream) : None (None downstream)																							ggttagggttagggtgagggt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	21838604	21838604	+	IGR	DEL	C	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21838604delC								ZNF429 (99536 upstream) : ZNF100 (68240 downstream)																							TGTGGCAAAGCTTTTCACCAA	0.423													28	16	---	---	---	---	
MED25	81857	broad.mit.edu	37	19	50331564	50331565	+	Intron	INS	-	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50331564_50331565insA	uc002ppw.1	+						MED25_uc010ybe.1_Intron	NM_030973	NP_112235	Q71SY5	MED25_HUMAN	mediator complex subunit 25						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm				ovary(1)	1		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00822)|GBM - Glioblastoma multiforme(134;0.0122)		AGGGATTGGGTAGGGAACTCAG	0.490													26	19	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	52895996	52895997	+	IGR	INS	-	A	A			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52895996_52895997insA								ZNF880 (6952 upstream) : ZNF528 (5124 downstream)																							GGGAAAATAGCAAAAAAATCCA	0.396													9	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	23961024	23961025	+	IGR	INS	-	AC	AC	rs146633246	by1000genomes	TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23961024_23961025insAC								CST5 (100644 upstream) : GGTLC1 (4666 downstream)																							cactcacacatacacacacaaa	0.000													7	5	---	---	---	---	
C20orf117	140710	broad.mit.edu	37	20	35445688	35445688	+	Intron	DEL	G	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35445688delG	uc002xgd.1	-						C20orf117_uc002xge.1_5'Flank	NM_199181	NP_954650	O94964	K0889_HUMAN	hypothetical protein LOC140710 isoform 2												0		Myeloproliferative disorder(115;0.00874)				aaaaaaaaaagaaaagaaaaa	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	36231849	36231860	+	IGR	DEL	CTTCCTTCCTTC	-	-	rs58334626		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36231849_36231860delCTTCCTTCCTTC								BLCAP (75546 upstream) : CTNNBL1 (90574 downstream)																							ttctttgtttcttccttccttccttccttcct	0.000													2	6	---	---	---	---	
USP16	10600	broad.mit.edu	37	21	30400444	30400445	+	Intron	INS	-	T	T	rs72433476		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30400444_30400445insT	uc002ymy.2	+						USP16_uc002ymx.2_Intron|USP16_uc002ymw.2_Intron|USP16_uc011acm.1_Intron|USP16_uc011acn.1_Intron	NM_006447	NP_006438	Q9Y5T5	UBP16_HUMAN	ubiquitin specific protease 16 isoform a						cell division|histone deubiquitination|mitosis|positive regulation of transcription, DNA-dependent|protein homotetramerization|transcription, DNA-dependent|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	cysteine-type endopeptidase activity|histone binding|transcription coactivator activity|ubiquitin binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(2)|breast(1)|pancreas(1)	4						TAGTCTTCTACttttttttttt	0.104													2	5	---	---	---	---	
GCFC1	94104	broad.mit.edu	37	21	34133202	34133205	+	Intron	DEL	GTGC	-	-			TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34133202_34133205delGTGC	uc002yqn.2	-						GCFC1_uc002yqo.2_Intron|GCFC1_uc002yqp.2_Intron|GCFC1_uc002yqr.2_Intron	NM_016631	NP_057715	Q9Y5B6	GCFC1_HUMAN	GC-rich sequence DNA-binding factor candidate							cytosol|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2						GTGTCTCtgtgtgcgtgcgtgcgt	0.270													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	35024822	35024823	+	IGR	INS	-	TGCCCCTGCCCT	TGCCCCTGCCCT	rs146162499	by1000genomes	TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35024822_35024823insTGCCCCTGCCCT								LARGE (706238 upstream) : ISX (437306 downstream)																							acagcagttcctgcccctgccc	0.005													3	3	---	---	---	---	
PIR	8544	broad.mit.edu	37	X	15478038	15478038	+	Intron	DEL	A	-	-	rs146737236		TCGA-56-1622-01A-01D-1521-08	TCGA-56-1622-11A-01D-1521-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15478038delA	uc004cwu.2	-						PIR_uc004cwv.2_Intron	NM_003662	NP_003653	O00625	PIR_HUMAN	pirin						transcription from RNA polymerase II promoter	cytoplasm|nucleus	metal ion binding|protein binding|quercetin 2,3-dioxygenase activity|transcription cofactor activity			ovary(1)	1	Hepatocellular(33;0.183)					ccttttcattAAAAAAAAAAa	0.000													3	3	---	---	---	---	
