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	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	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	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
KIAA0467	23334	broad.mit.edu	37	1	43888908	43888908	+	Translation_Start_Site	SNP	G	A	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr1:43888908G>A	uc001cjk.1	+	1	112	c.-350G>A	c.(-352--348)CCGTG>CCATG		KIAA0467_uc009vws.1_Missense_Mutation_p.V726M	NM_015284	NP_056099	Q5T011	SZT2_HUMAN	hypothetical protein LOC23334							peroxisome					0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GTCACCCCCCGTGCTGGGGCC	0.617000													18	27					0	0	0.006122	0	0
USP24	23358	broad.mit.edu	37	1	55638164	55638164	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr1:55638164C>T	uc001cyg.3	-	3	252	c.252G>A	c.(250-252)TGG>TGA	p.W84*		NM_015306	NP_056121	Q9UPU5	UBP24_HUMAN	ubiquitin specific protease 24	196					ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(6)|kidney(6)|breast(1)	13						TTTCAGTACCCCACTTGTGAA	0.368000													18	70					0	0	0.014323	0	0
Unknown	0	broad.mit.edu	37	1	148882025	148882025	+	RNA	SNP	C	T	T	rs150449871	by1000genomes	TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr1:148882025C>T	uc009wkv.1	+	3		c.246C>T								Homo sapiens cDNA, FLJ17483.																		TGTTTTCTAGCAGTGACAAAT	0.343000													4	137					0	0	0.014758	0	0
CD1A	909	broad.mit.edu	37	1	158226760	158226760	+	Silent	SNP	C	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr1:158226760C>T	uc001frt.2	+	4	1322	c.789C>T	c.(787-789)CGC>CGT	p.R263R		NM_001763	NP_001754	P06126	CD1A_HUMAN	CD1A antigen precursor	263	Extracellular (Potential).|Ig-like.				antigen processing and presentation|immune response	endosome membrane|integral to plasma membrane|MHC class I protein complex				pancreas(2)|skin(1)	3	all_hematologic(112;0.0378)				Antithymocyte globulin(DB00098)	GGTATCTCCGCGCAACCCTGG	0.632000													66	95					0	0	0.014410	0	0
LY9	4063	broad.mit.edu	37	1	160783596	160783596	+	Missense_Mutation	SNP	G	A	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr1:160783596G>A	uc001fwu.2	+	3	675	c.625G>A	c.(625-627)GTC>ATC	p.V209I	LY9_uc010pjs.1_Missense_Mutation_p.V209I|LY9_uc001fwv.2_Missense_Mutation_p.V209I|LY9_uc001fww.2_Missense_Mutation_p.V209I|LY9_uc001fwx.2_Missense_Mutation_p.V209I|LY9_uc001fwy.1_Missense_Mutation_p.V111I|LY9_uc001fwz.2_5'Flank	NM_002348	NP_002339	Q9HBG7	LY9_HUMAN	lymphocyte antigen 9 isoform a	209	Extracellular (Potential).|Ig-like C2-type 1.				cell adhesion|immunoglobulin mediated immune response	integral to membrane				ovary(1)	1	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			CATTCTTACCGTCTCCCGAAC	0.562000													8	273					0	0	0.003080	0	0
DDR2	4921	broad.mit.edu	37	1	162741843	162741843	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr1:162741843C>T	uc001gcf.2	+	14	1999	c.1534C>T	c.(1534-1536)CCC>TCC	p.P512S	DDR2_uc001gcg.2_Missense_Mutation_p.P512S	NM_001014796	NP_001014796	Q16832	DDR2_HUMAN	discoidin domain receptor family, member 2	512	Cytoplasmic (Potential).				cell adhesion	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(2)|central_nervous_system(2)|ovary(1)|kidney(1)	6	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)			GCCAGTCCAGCCCAGTGGCCC	0.577000													11	16					0	0	0.013537	0	0
OBSCN	84033	broad.mit.edu	37	1	228431148	228431148	+	Missense_Mutation	SNP	T	C	C			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr1:228431148T>C	uc009xez.1	+	10	3238	c.3194T>C	c.(3193-3195)CTG>CCG	p.L1065P	OBSCN_uc001hsn.2_Missense_Mutation_p.L1065P	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	1065	Ig-like 10.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)				TCCTTCCGCCTGCACATCACA	0.547000													11	16					0	0	0.008291	0	0
Unknown	0	broad.mit.edu	37	10	48968566	48968566	+	RNA	SNP	A	G	G			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr10:48968566A>G	uc001jgc.1	+	3		c.1234A>G								full-length cDNA clone CS0DI009YC01 of Placenta Cot 25-normalized of Homo sapiens (human).																		ACAGGATAACAAACTGGAAAA	0.284000													11	16					0	0	0.013537	0	0
PTEN	5728	broad.mit.edu	37	10	89711899	89711899	+	Missense_Mutation	SNP	C	T	T	rs121913293		TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr10:89711899C>T	uc001kfb.2	+	7	1548	c.517C>T	c.(517-519)CGC>TGC	p.R173C		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	173	Phosphatase tensin-type.		R -> C (in endometrial hyperplasia; loss of phosphatase activity towards Ins(1,3,4,5)P4 and PtdIns(3,4,5)P3; retains ability to bind phospholipid membranes).|R -> P (loss of phosphatase activity towards Ins(1,3,4,5)P4).|R -> H (loss of phosphatase activity towards Ins(1,3,4,5)P4).		activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.R173C(32)|p.R173H(22)|p.R55fs*1(4)|p.V166fs*17(3)|p.?(3)|p.G165fs*9(3)|p.R173fs*10(2)|p.Y27fs*1(2)|p.Y27_N212>Y(2)|p.G165_K342del(1)|p.G165_*404del(1)|p.R173R(1)|p.R173P(1)|p.R172fs*5(1)		endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		CAGTCAGAGGCGCTATGTGTA	0.348000	R173C(REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	31	D|Mis|N|F|S		glioma| prostate|endometrial	harmartoma|glioma| prostate|endometrial			Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)			73	51					0	0	0.014410	0	0
C10orf46	143384	broad.mit.edu	37	10	120489879	120489879	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr10:120489879C>T	uc001lds.1	-	2	895	c.411G>A	c.(409-411)TGG>TGA	p.W137*	C10orf46_uc010qst.1_RNA	NM_153810	NP_722517	Q86Y37	CJ046_HUMAN	chromosome 10 open reading frame 46	137					ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex	ubiquitin protein ligase binding				0		Lung NSC(174;0.142)|all_lung(145;0.175)		all cancers(201;0.0131)		CCAATTTTGGCCAGTATGTGC	0.323000													3	63					0	0	0.004672	0	0
LOC650368	650368	broad.mit.edu	37	11	3427830	3427830	+	RNA	SNP	G	A	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr11:3427830G>A	uc010qxs.1	+	9		c.823G>A			LOC650368_uc001lxx.2_RNA|LOC650368_uc001lxy.2_RNA	NR_024248				Homo sapiens cDNA FLJ41654 fis, clone FEBRA2025463, weakly  similar to Homo sapiens HMT-1 mRNA for beta-1,4 mannosyltransferase.												0						TGTGTGTGCCGTGAACTTCAA	0.582000													4	78					0	0	0.009096	0	0
NUP160	23279	broad.mit.edu	37	11	47809761	47809761	+	Missense_Mutation	SNP	G	A	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr11:47809761G>A	uc001ngm.2	-	31	3804	c.3719C>T	c.(3718-3720)ACG>ATG	p.T1240M	NUP160_uc009ylw.2_RNA	NM_015231	NP_056046	Q12769	NU160_HUMAN	nucleoporin 160kDa	1240					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7						AAAGACTGGCGTTAAGGGAAG	0.398000													28	45					0	0	0.008361	0	0
VWF	7450	broad.mit.edu	37	12	6219737	6219737	+	Missense_Mutation	SNP	G	A	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr12:6219737G>A	uc001qnn.1	-	5	585	c.335C>T	c.(334-336)CCC>CTC	p.P112L	VWF_uc010set.1_Missense_Mutation_p.P112L|VWF_uc001qno.1_Missense_Mutation_p.P149L	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein	112	VWFD 1.				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)	GGAGGCATAGGGCATGGAGAC	0.537000													4	136					0	0	0.009096	0	0
PTPN11	5781	broad.mit.edu	37	12	112888199	112888199	+	Missense_Mutation	SNP	C	A	A	rs121918454		TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr12:112888199C>A	uc001ttx.2	+	3	595	c.215C>A	c.(214-216)GCC>GAC	p.A72D	PTPN11_uc001ttw.1_Missense_Mutation_p.A72D	NM_002834	NP_002825	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type	72	SH2 1.		A -> T (in JMML).|A -> V (in JMML).|A -> S (in NS1).|A -> G (in NS1).		axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol	non-membrane spanning protein tyrosine phosphatase activity|protein binding	p.A72V(34)|p.A72T(31)|p.A72D(3)		haematopoietic_and_lymphoid_tissue(375)|lung(6)|autonomic_ganglia(2)|soft_tissue(2)|central_nervous_system(2)|large_intestine(1)|skin(1)|ovary(1)|NS(1)|kidney(1)	392						GAGAAATTTGCCACTTTGGCT	0.418000			Mis		JMML|AML|MDS		Noonan Syndrome		Noonan_syndrome				74	120					5.32961e-40	6.12185e-40	0.014410	1	0
SUPT16H	11198	broad.mit.edu	37	14	21821703	21821703	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr14:21821703C>T	uc001wao.2	-	25	3281	c.2942G>A	c.(2941-2943)GGT>GAT	p.G981D	SUPT16H_uc001wan.2_Missense_Mutation_p.G125D	NM_007192	NP_009123	Q9Y5B9	SP16H_HUMAN	chromatin-specific transcription elongation	981	Glu-rich (acidic).				DNA repair|DNA replication|nucleosome disassembly|positive regulation of transcription elongation, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	chromosome|nucleoplasm	GTP binding				0	all_cancers(95;0.00115)		Epithelial(56;1.62e-06)|all cancers(55;1.49e-05)	GBM - Glioblastoma multiforme(265;0.0159)		TTCTTCACTACCCAATGACTC	0.373000													47	108					0	0	0.014410	0	0
C14orf182	283551	broad.mit.edu	37	14	50472373	50472373	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr14:50472373G>A	uc001wxi.1	-	1	1866	c.145C>T	c.(145-147)CGA>TGA	p.R49*		NM_001012706	NP_001012724	A1A4T8	CN182_HUMAN	hypothetical protein LOC283551	49											0						TGTCTGTGTCGTAGAACTGTG	0.527000													6	288					0	0	0.001168	0	0
SIPA1L1	26037	broad.mit.edu	37	14	72138006	72138006	+	Missense_Mutation	SNP	G	A	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr14:72138006G>A	uc001xms.2	+	8	2774	c.2426G>A	c.(2425-2427)CGC>CAC	p.R809H	SIPA1L1_uc001xmt.2_Missense_Mutation_p.R809H|SIPA1L1_uc001xmu.2_Missense_Mutation_p.R809H|SIPA1L1_uc001xmv.2_Missense_Mutation_p.R809H|SIPA1L1_uc010ttm.1_Missense_Mutation_p.R284H	NM_015556	NP_056371	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like	809	Rap-GAP.				actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		ACTCGGACCCGCCAGGAATAC	0.473000													29	49					0	0	0.010818	0	0
ADAM6	8755	broad.mit.edu	37	14	106173520	106173520	+	RNA	SNP	G	A	A	rs1130897	by1000genomes	TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr14:106173520G>A	uc010tyt.1	-	3633		c.60378C>T			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001ysc.2_5'Flank					Parts of antibodies, mostly variable regions.												0						AGCAGGTGCCGTCCACCTCCG	0.637000													6	15					0	0	0.001984	0	0
NF1P1	440225	broad.mit.edu	37	15	21134375	21134375	+	RNA	SNP	G	A	A	rs147626107		TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr15:21134375G>A	uc001ytv.1	-	2		c.131C>T								Human NF1-related locus DNA in A9 mouse DNA background.												0						CATAAATGTAGCTGTCTGGAG	0.398000													8	28					0	0	0.010729	0	0
C15orf2	23742	broad.mit.edu	37	15	24921561	24921561	+	Missense_Mutation	SNP	G	A	A	rs151186438	byFrequency	TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr15:24921561G>A	uc001ywo.2	+	1	1021	c.547G>A	c.(547-549)GGA>AGA	p.G183R		NM_018958	NP_061831	Q9NZP6	CO002_HUMAN	hypothetical protein LOC23742	183					cell differentiation|multicellular organismal development|spermatogenesis					ovary(2)|large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1)	8		all_cancers(20;2.14e-21)|all_epithelial(15;4.77e-19)|Lung NSC(15;1.43e-14)|all_lung(15;9.57e-14)|Breast(32;0.00086)		all cancers(64;3.19e-24)|Epithelial(43;2.67e-17)|GBM - Glioblastoma multiforme(186;7.36e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000273)|Lung(196;0.229)		CCTTAGCAGCGGAGAAGCATC	0.597000													20	27					0	0	0.008871	0	0
ATP8B4	79895	broad.mit.edu	37	15	50288937	50288937	+	Missense_Mutation	SNP	G	A	A	rs116334504	by1000genomes	TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr15:50288937G>A	uc001zxu.2	-	9	668	c.526C>T	c.(526-528)CGC>TGC	p.R176C	ATP8B4_uc010ber.2_Missense_Mutation_p.R49C|ATP8B4_uc010ufd.1_Missense_Mutation_p.R49C|ATP8B4_uc010ufe.1_RNA	NM_024837	NP_079113	Q8TF62	AT8B4_HUMAN	ATPase class I type 8B member 4	176	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			skin(3)|ovary(2)|breast(2)|large_intestine(1)	8		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		AGTGCATGGCGGACTTTTAGG	0.398000													22	44					0	0	0.016522	0	0
CSPG4	1464	broad.mit.edu	37	15	75981730	75981730	+	Missense_Mutation	SNP	T	C	C			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr15:75981730T>C	uc002baw.2	-	3	1769	c.1676A>G	c.(1675-1677)CAT>CGT	p.H559R		NM_001897	NP_001888	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4 precursor	559	Extracellular (Potential).|CSPG 2.|Globular or compact configuration stabilized by disulfide bonds.|Neurite growth inhibition (By similarity).				angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling	apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane	protein kinase binding|signal transducer activity			ovary(2)|pancreas(1)	3						GAGGCTGCCATGTGGGAAGAT	0.612000													3	56					0	0	0.009096	0	0
GOLGA6L5	374650	broad.mit.edu	37	15	85056044	85056044	+	RNA	SNP	G	A	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr15:85056044G>A	uc002bkm.2	-	6		c.516C>T				NR_003246				Homo sapiens cDNA FLJ33459 fis, clone BRAMY2000585.												0						CCTGCTGGGGGCTCTGGGGCC	0.532000													3	19					0	0	0.001168	0	0
TMEM170A	124491	broad.mit.edu	37	16	75481522	75481522	+	Silent	SNP	T	G	G			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr16:75481522T>G	uc002fee.1	-	3	455	c.369A>C	c.(367-369)ACA>ACC	p.T123T	TMEM170A_uc002feb.2_Silent_p.T85T|TMEM170A_uc002fec.2_Silent_p.T100T|TMEM170A_uc002fed.1_RNA	NM_145254	NP_660297	Q8WVE7	T170A_HUMAN	transmembrane protein 170A	123	Helical; (Potential).					integral to membrane					0						CAGTGCCCAGTGTGAGGGCTT	0.408000													65	113					0	0	0.014410	0	0
Unknown	0	broad.mit.edu	37	17	18333005	18333005	+	RNA	SNP	C	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr17:18333005C>T	uc010vxz.1	+	4		c.827C>T								Homo sapiens cDNA FLJ61294 complete cds, highly similar to Keratin, type I cytoskeletal 17.																		AGGAGATGAACGCCCCGCGAG	0.607000													8	3					0	0	0.010729	0	0
KRT28	162605	broad.mit.edu	37	17	38955859	38955859	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr17:38955859C>T	uc002hvh.1	-	1	353	c.287G>A	c.(286-288)CGC>CAC	p.R96H		NM_181535	NP_853513	Q7Z3Y7	K1C28_HUMAN	keratin 25D	96	Rod.|Coil 1A.					cytoplasm|intermediate filament	structural molecule activity			ovary(1)	1		Breast(137;0.000301)				GGATGCCAAGCGGTCATTAAG	0.478000													6	175					0	0	0.001168	0	0
CARD14	79092	broad.mit.edu	37	17	78171904	78171904	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr17:78171904C>T	uc002jxw.1	+	12	1796	c.1601C>T	c.(1600-1602)CCG>CTG	p.P534L	CARD14_uc002jxt.1_RNA|CARD14_uc002jxv.2_Missense_Mutation_p.P534L|CARD14_uc010wud.1_RNA|CARD14_uc002jxx.2_Missense_Mutation_p.P297L	NM_024110	NP_077015	Q9BXL6	CAR14_HUMAN	caspase recruitment domain protein 14 isoform 1	534					activation of NF-kappaB-inducing kinase activity|positive regulation of protein phosphorylation|regulation of apoptosis	aggresome|cytoplasm|plasma membrane	CARD domain binding			ovary(4)|skin(1)	5	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			CCAGACCTTCCGCAGCTGGAA	0.592000													27	104					0	0	0.007291	0	0
LAMA1	284217	broad.mit.edu	37	18	6961754	6961754	+	Missense_Mutation	SNP	A	G	G			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr18:6961754A>G	uc002knm.2	-	53	7551	c.7457T>C	c.(7456-7458)ATC>ACC	p.I2486T	LAMA1_uc002knl.2_Intron|LAMA1_uc010wzj.1_Missense_Mutation_p.I1962T	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	2486	Laminin G-like 3.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1)	21		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	AACACTCCGGATGGGCTGGAC	0.517000													14	27					0	0	0.020292	0	0
ZNF430	80264	broad.mit.edu	37	19	21240178	21240178	+	Missense_Mutation	SNP	A	G	G			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr19:21240178A>G	uc002npj.2	+	5	1174	c.1064A>G	c.(1063-1065)AAC>AGC	p.N355S	ZNF430_uc002npk.2_Missense_Mutation_p.N354S	NM_025189	NP_079465	Q9H8G1	ZN430_HUMAN	zinc finger protein 430	355	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)	2						AAAGCTTTTAACCAATCCTCA	0.388000													4	225					0	0	0.009096	0	0
ZNF229	7772	broad.mit.edu	37	19	44933647	44933647	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr19:44933647C>T	uc002oze.1	-	6	1743	c.1309G>A	c.(1309-1311)GAG>AAG	p.E437K	ZNF229_uc010ejk.1_Missense_Mutation_p.E91K|ZNF229_uc010ejl.1_Missense_Mutation_p.E431K	NM_014518	NP_055333	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	437	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)|pancreas(1)	4		Prostate(69;0.0352)				TTGCCACACTCGCTGCAGGTG	0.537000													31	59					0	0	0.007291	0	0
HIF3A	64344	broad.mit.edu	37	19	46800337	46800337	+	Missense_Mutation	SNP	G	A	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr19:46800337G>A	uc002peh.2	+	1	33	c.4G>A	c.(4-6)GCG>ACG	p.A2T	HIF3A_uc002pef.1_Missense_Mutation_p.A2T|HIF3A_uc002peg.3_Missense_Mutation_p.A2T|HIF3A_uc010xxx.1_5'Flank|HIF3A_uc002pei.3_5'Flank|HIF3A_uc002pej.1_5'Flank|HIF3A_uc002pek.2_5'Flank|HIF3A_uc010xxy.1_5'Flank	NM_152795	NP_690008	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	2					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)		GCGAGCCATGGCGCTGGGGCT	0.716000													12	19					0	0	0.020292	0	0
YSK4	80122	broad.mit.edu	37	2	135745373	135745373	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr2:135745373G>A	uc002tue.1	-	7	1100	c.1069C>T	c.(1069-1071)CGA>TGA	p.R357*	YSK4_uc002tuf.1_Intron|YSK4_uc010fnc.1_Intron|YSK4_uc010fnd.1_Nonsense_Mutation_p.R244*|YSK4_uc010zbg.1_Intron|YSK4_uc002tuh.3_Nonsense_Mutation_p.R85*|YSK4_uc002tui.3_Nonsense_Mutation_p.R374*	NM_025052	NP_079328	Q56UN5	YSK4_HUMAN	Yeast Sps1/Ste20-related kinase 4 isoform 1	357							ATP binding|protein serine/threonine kinase activity			stomach(2)|urinary_tract(1)|ovary(1)|breast(1)	5				BRCA - Breast invasive adenocarcinoma(221;0.112)		TCAGGTTTTCGCGTTTTACTA	0.378000													50	69					0	0	0.014410	0	0
COL6A3	1293	broad.mit.edu	37	2	238249727	238249727	+	Missense_Mutation	SNP	G	A	A	rs114806654	by1000genomes	TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr2:238249727G>A	uc002vwl.2	-	38	8117	c.7832C>T	c.(7831-7833)GCG>GTG	p.A2611V	COL6A3_uc002vwo.2_Missense_Mutation_p.A2405V|COL6A3_uc010znj.1_Missense_Mutation_p.A2004V|COL6A3_uc002vwj.2_5'UTR	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	2611	Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		GCTCCCTGCCGCTCTCCTGTC	0.512000													76	118					0	0	0.014410	0	0
ANKRD5	63926	broad.mit.edu	37	20	10030224	10030224	+	Missense_Mutation	SNP	G	A	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr20:10030224G>A	uc002wno.2	+	7	1400	c.1007G>A	c.(1006-1008)CGT>CAT	p.R336H	uc002wnn.1_Intron|ANKRD5_uc002wnp.2_Missense_Mutation_p.R336H|ANKRD5_uc010gbz.2_Missense_Mutation_p.R147H	NM_022096	NP_071379	Q9NU02	ANKR5_HUMAN	ankyrin repeat domain protein 5	336	EF-hand.						calcium ion binding			ovary(1)|breast(1)	2						TCCGTAGAACGTGAGGCTTTC	0.512000													44	99					0	0	0.011902	0	0
PCSK2	5126	broad.mit.edu	37	20	17410117	17410117	+	Missense_Mutation	SNP	G	A	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr20:17410117G>A	uc002wpm.2	+	7	978	c.658G>A	c.(658-660)GCC>ACC	p.A220T	PCSK2_uc002wpl.2_Missense_Mutation_p.A201T|PCSK2_uc010zrm.1_Missense_Mutation_p.A185T	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	220	Catalytic.				enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	TTCTGCTGCCGCCAACAACAA	0.473000													105	267					0	0	0.014410	0	0
LOC96610	96610	broad.mit.edu	37	22	22661478	22661478	+	RNA	SNP	T	G	G			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr22:22661478T>G	uc011aim.1	+	28		c.1702T>G			LOC96610_uc011aiq.1_RNA|LOC96610_uc011aip.1_RNA|LOC96610_uc010gto.2_RNA					Parts of antibodies, mostly variable regions.												0						CAGATGCGTCTGAAGAAACAT	0.488000													4	101					0	0	0.003080	0	0
ATP2B2	491	broad.mit.edu	37	3	10452378	10452378	+	Silent	SNP	C	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr3:10452378C>T	uc003bvt.2	-	3	760	c.321G>A	c.(319-321)ACG>ACA	p.T107T	ATP2B2_uc003bvv.2_Silent_p.T107T|ATP2B2_uc003bvw.2_Silent_p.T107T|ATP2B2_uc010hdp.2_Silent_p.T107T|ATP2B2_uc010hdo.2_5'UTR	NM_001001331	NP_001001331	Q01814	AT2B2_HUMAN	plasma membrane calcium ATPase 2 isoform 1	107	Helical; (Potential).				ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	cytosol|integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|skin(2)|central_nervous_system(1)	6						GGATGATGAGCGTCACGTCCT	0.552000													8	355					0	0	0.003080	0	0
SEMA3F	6405	broad.mit.edu	37	3	50225347	50225347	+	Silent	SNP	C	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr3:50225347C>T	uc003cyj.2	+	19	2355	c.2157C>T	c.(2155-2157)GGC>GGT	p.G719G	SEMA3F_uc003cyk.2_Silent_p.G688G	NM_004186	NP_004177	Q13275	SEM3F_HUMAN	semaphorin 3F precursor	719					axon guidance	extracellular space|membrane	chemorepellent activity|receptor activity			lung(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)		CACCCCCAGGCGCAGGCCCCC	0.667000													10	10					0	0	0.008291	0	0
PDE6B	5158	broad.mit.edu	37	4	647918	647918	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr4:647918C>T	uc003gap.2	+	5	955	c.902C>T	c.(901-903)TCG>TTG	p.S301L	PDE6B_uc003gao.3_Missense_Mutation_p.S301L|PDE6B_uc011buy.1_Missense_Mutation_p.S22L|PDE6B_uc010ibg.2_Missense_Mutation_p.S22L|uc003gaq.1_RNA	NM_000283	NP_000274	P35913	PDE6B_HUMAN	phosphodiesterase 6B isoform 1	301	GAF 2.				cytosolic calcium ion homeostasis|GMP metabolic process|phototransduction, visible light|platelet activation|visual perception	cytosol|membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding				0						CAGCCGTACTCGGGCCCACGC	0.647000													24	49					0	0	0.012213	0	0
PITX2	5308	broad.mit.edu	37	4	111539762	111539762	+	Missense_Mutation	SNP	G	A	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr4:111539762G>A	uc003iad.2	-	5	1055	c.473C>T	c.(472-474)CCG>CTG	p.P158L	PITX2_uc003iac.2_Missense_Mutation_p.P165L|PITX2_uc003iae.2_Missense_Mutation_p.P112L|PITX2_uc010iml.2_Missense_Mutation_p.P29L|PITX2_uc003iaf.2_Missense_Mutation_p.P158L	NM_153426	NP_700475	Q99697	PITX2_HUMAN	paired-like homeodomain transcription factor 2	158					determination of left/right symmetry|organ morphogenesis	transcription factor complex	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription factor binding				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00222)		ATTGAACTGCGGCCCGAAGCC	0.592000													4	102					0	0	0.009096	0	0
EDNRA	1909	broad.mit.edu	37	4	148407184	148407184	+	Silent	SNP	G	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr4:148407184G>T	uc003iky.2	+	2	1043	c.351G>T	c.(349-351)GCG>GCT	p.A117A	EDNRA_uc011cid.1_Intron|EDNRA_uc010ipe.1_Silent_p.A117A|EDNRA_uc010ipf.1_RNA|EDNRA_uc010ipg.1_Silent_p.A117A	NM_001957	NP_001948	P25101	EDNRA_HUMAN	endothelin receptor type A isoform a precursor	117	Helical; Name=2; (Potential).				activation of adenylate cyclase activity|artery smooth muscle contraction|cell proliferation|glucose transport|respiratory gaseous exchange	integral to plasma membrane	endothelin-A receptor activity|phosphatidylinositol phospholipase C activity			ovary(1)|breast(1)	2	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.154)	Bosentan(DB00559)	GCCCCAACGCGCTGATAGCCA	0.423000													70	91					2.08929e-35	2.36786e-35	0.014410	1	0
TRIP13	9319	broad.mit.edu	37	5	908507	908507	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr5:908507C>T	uc003jbr.2	+	9	907	c.797C>T	c.(796-798)GCG>GTG	p.A266V	TRIP13_uc010ite.1_Missense_Mutation_p.A266V	NM_004237	NP_004228	Q15645	PCH2_HUMAN	thyroid hormone receptor interactor 13	266					double-strand break repair|reciprocal meiotic recombination|synaptonemal complex assembly|transcription from RNA polymerase II promoter		ATP binding|identical protein binding|nucleoside-triphosphatase activity|transcription cofactor activity				0			Epithelial(17;0.00147)|OV - Ovarian serous cystadenocarcinoma(19;0.00271)|all cancers(22;0.00622)|Lung(60;0.165)			GCCTGCAGGGCGGGCACCGAG	0.562000													46	69					0	0	0.014410	0	0
CDH12	1010	broad.mit.edu	37	5	21817101	21817101	+	Missense_Mutation	SNP	T	G	G			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr5:21817101T>G	uc010iuc.2	-	6	1413	c.955A>C	c.(955-957)ATC>CTC	p.I319L	CDH12_uc011cno.1_Missense_Mutation_p.I279L|CDH12_uc003jgk.2_Missense_Mutation_p.I319L	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein	319	Extracellular (Potential).|Cadherin 3.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						TCTGTGACGATGTCAAACAAA	0.338000										HNSCC(59;0.17)			7	295					0	0	0.003080	0	0
TRPC7	57113	broad.mit.edu	37	5	135610458	135610458	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr5:135610458C>T	uc003lbn.1	-	3	1031	c.1028G>A	c.(1027-1029)CGT>CAT	p.R343H	TRPC7_uc010jef.1_Intron|TRPC7_uc010jeg.1_RNA|TRPC7_uc010jeh.1_Missense_Mutation_p.R274H|TRPC7_uc010jei.1_Intron|TRPC7_uc010jej.1_Intron	NM_020389	NP_065122	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel,	344	Cytoplasmic (Potential).				axon guidance|platelet activation	integral to membrane|plasma membrane	calcium channel activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGACTGTTGACGTAAGCCTGA	0.418000													9	20					0	0	0.004482	0	0
PCDHGA2	56113	broad.mit.edu	37	5	140719281	140719281	+	Missense_Mutation	SNP	G	A	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr5:140719281G>A	uc003ljk.1	+	1	928	c.743G>A	c.(742-744)CGC>CAC	p.R248H	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc011dao.1_Missense_Mutation_p.R248H	NM_018915	NP_061738	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2 isoform 1	248	Cadherin 3.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCCGAGTACCGCATAAGCATT	0.557000													4	152					0	0	0.009096	0	0
ATP10B	23120	broad.mit.edu	37	5	160025790	160025790	+	Missense_Mutation	SNP	C	A	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr5:160025790C>A	uc003lym.1	-	22	4398	c.3551G>T	c.(3550-3552)GGC>GTC	p.G1184V	ATP10B_uc010jit.1_Intron	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B	1184	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AGAGTTCTGGCCACTCTTGTA	0.502000													193	275					8.57144e-96	1.02616e-95	0.014410	1	0
PKHD1	5314	broad.mit.edu	37	6	51613287	51613287	+	Missense_Mutation	SNP	C	A	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr6:51613287C>A	uc003pah.1	-	58	9403	c.9127G>T	c.(9127-9129)GTG>TTG	p.V3043L	PKHD1_uc010jzn.1_Missense_Mutation_p.V1026L|PKHD1_uc003pai.2_Missense_Mutation_p.V3043L	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	3043	PbH1 8.|Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					GTGCCAAACACAATATTGTCA	0.493000													46	45					1.76056e-25	1.96904e-25	0.011902	1	0
PKHD1	5314	broad.mit.edu	37	6	51892973	51892973	+	Missense_Mutation	SNP	C	A	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr6:51892973C>A	uc003pah.1	-	30	3817	c.3541G>T	c.(3541-3543)GTC>TTC	p.V1181F	PKHD1_uc003pai.2_Missense_Mutation_p.V1181F	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	1181	Extracellular (Potential).|IPT/TIG 6; atypical.				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					TGAATGCTGACCCCATTGATA	0.498000													124	212					8.80896e-55	1.0257e-54	0.014410	1	0
PHF3	23469	broad.mit.edu	37	6	64422637	64422637	+	Missense_Mutation	SNP	T	C	C			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr6:64422637T>C	uc003pep.1	+	15	5179	c.5153T>C	c.(5152-5154)GTT>GCT	p.V1718A	PHF3_uc003pen.2_Missense_Mutation_p.V1630A|PHF3_uc011dxs.1_Missense_Mutation_p.V987A	NM_015153	NP_055968	Q92576	PHF3_HUMAN	PHD finger protein 3	1718					multicellular organismal development|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			AATTTAAAAGTTGCACAAAAC	0.368000													3	100					0	0	0.004672	0	0
COL19A1	1310	broad.mit.edu	37	6	70866054	70866054	+	Silent	SNP	G	A	A			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr6:70866054G>A	uc003pfc.1	+	32	2232	c.2115G>A	c.(2113-2115)GGG>GGA	p.G705G	COL19A1_uc010kam.1_Silent_p.G601G	NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor	705	Triple-helical region 4 (COL4).				cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4						GTGTCCCAGGGCTGAAAAGCA	0.473000													39	48					0	0	0.009718	0	0
CALN1	83698	broad.mit.edu	37	7	71252834	71252834	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr7:71252834C>T	uc003twa.3	-	6	1113	c.586G>A	c.(586-588)GCC>ACC	p.A196T	CALN1_uc003twb.3_Missense_Mutation_p.A238T|CALN1_uc003twc.3_Missense_Mutation_p.A196T	NM_001017440	NP_001017440	Q9BXU9	CABP8_HUMAN	calneuron 1 isoform 2	196	Helical; Anchor for type IV membrane protein; (Potential).					Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)				ATAGCAAAGGCGCATATGAGG	0.567000													27	80					0	0	0.004656	0	0
ADAM28	10863	broad.mit.edu	37	8	24200636	24200636	+	Missense_Mutation	SNP	T	C	C			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr8:24200636T>C	uc003xdy.2	+	17	1936	c.1853T>C	c.(1852-1854)GTG>GCG	p.V618A	ADAM28_uc011laa.1_RNA|ADAM28_uc010lua.2_Missense_Mutation_p.V305A	NM_014265	NP_055080	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28 isoform 1	618	Extracellular (Potential).|Cys-rich.				proteolysis|spermatogenesis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(3)|lung(1)|central_nervous_system(1)	5		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		GCAGAATGTGTGGATATTGAG	0.383000													3	90					0	0	0.009096	0	0
ADAM7	8756	broad.mit.edu	37	8	24346749	24346749	+	Missense_Mutation	SNP	T	G	G			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr8:24346749T>G	uc003xeb.2	+	12	1282	c.1169T>G	c.(1168-1170)ATG>AGG	p.M390R	ADAM7_uc003xec.2_Missense_Mutation_p.M162R	NM_003817	NP_003808	Q9H2U9	ADAM7_HUMAN	a disintegrin and metalloproteinase domain 7	390	Peptidase M12B.|Extracellular (Potential).				proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(1)|kidney(1)	5		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		CCAACATGCATGCTCAACATT	0.398000													44	72					0	0	0.014410	0	0
PTTG3P	26255	broad.mit.edu	37	8	67680233	67680233	+	Missense_Mutation	SNP	G	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr8:67680233G>T	uc011leu.1	-	1	8	c.8C>A	c.(7-9)ACT>AAT	p.T3N	SGK3_uc003xwp.2_Intron|SGK3_uc003xwr.2_Intron	NR_002734				RecName: Full=Securin-3; AltName: Full=Pituitary tumor transforming gene 3 protein;          Short=hPTTG3; AltName: Full=rcPTTG1;												0						ATAGATCAGAGTAGCCATTCT	0.308000													4	31					1.58986e-06	1.75504e-06	0.008291	1	0
FER1L6	654463	broad.mit.edu	37	8	125094698	125094698	+	Missense_Mutation	SNP	A	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr8:125094698A>T	uc003yqw.2	+	33	4596	c.4390A>T	c.(4390-4392)ATA>TTA	p.I1464L	uc003yqy.1_Intron	NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6	1464	Cytoplasmic (Potential).					integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			CCAGTATGAGATGTAAGTTCT	0.512000													62	103					0	0	0.014410	0	0
RFX3	5991	broad.mit.edu	37	9	3270522	3270522	+	Missense_Mutation	SNP	A	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr9:3270522A>T	uc003zhr.2	-	12	1518	c.1206T>A	c.(1204-1206)AAT>AAA	p.N402K	RFX3_uc010mhd.2_Missense_Mutation_p.N402K|RFX3_uc003zhs.1_Missense_Mutation_p.N402K	NM_134428	NP_602304	P48380	RFX3_HUMAN	regulatory factor X3 isoform b	402					cell maturation|ciliary cell motility|cilium assembly|cilium movement involved in determination of left/right asymmetry|endocrine pancreas development|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type B pancreatic cell development|regulation of insulin secretion	nuclear chromatin	protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)		TTTCACTCAGATTGCTGGTGT	0.348000													3	73					0	0	0.009096	0	0
TRPM6	140803	broad.mit.edu	37	9	77377508	77377508	+	Missense_Mutation	SNP	G	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr9:77377508G>T	uc004ajl.1	-	26	4317	c.4079C>A	c.(4078-4080)ACT>AAT	p.T1360N	TRPM6_uc004ajk.1_Missense_Mutation_p.T1355N|TRPM6_uc010mpb.1_RNA|TRPM6_uc010mpc.1_Intron|TRPM6_uc010mpd.1_Intron|TRPM6_uc010mpe.1_Intron|TRPM6_uc004ajj.1_Missense_Mutation_p.T316N	NM_017662	NP_060132	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel,	1360	Cytoplasmic (Potential).				response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	8						AGGCAAGACAGTTTCTGCTGA	0.507000													104	160					4.80225e-73	5.66932e-73	0.014410	1	0
OR13C5	138799	broad.mit.edu	37	9	107361264	107361264	+	Missense_Mutation	SNP	A	C	C			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr9:107361264A>C	uc011lvp.1	-	1	431	c.431T>G	c.(430-432)ATG>AGG	p.M144R		NM_001004482	NP_001004482	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C,	144	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	p.M144I(1)		ovary(2)|pancreas(1)|skin(1)	4						CCCAGCTGCCATGGGTACATA	0.473000													21	291					0	0	0.004656	0	0
OR13C2	392376	broad.mit.edu	37	9	107367478	107367478	+	Missense_Mutation	SNP	A	C	C			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr9:107367478A>C	uc011lvq.1	-	1	431	c.431T>G	c.(430-432)ATG>AGG	p.M144R		NM_001004481	NP_001004481	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C,	144	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1						CCCAGCTGCCATGGGTACATA	0.468000													32	99					0	0	0.009718	0	0
SVEP1	79987	broad.mit.edu	37	9	113217968	113217968	+	Missense_Mutation	SNP	G	C	C			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr9:113217968G>C	uc010mtz.2	-	22	4026	c.3689C>G	c.(3688-3690)ACA>AGA	p.T1230R	SVEP1_uc010mua.1_Missense_Mutation_p.T1230R	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom	1230					cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7						ATCGATGTCTGTTTCACACTT	0.418000													20	33					0	0	0.012319	0	0
RGN	9104	broad.mit.edu	37	X	46943843	46943843	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chrX:46943843C>T	uc004dgz.1	+	4	1159	c.190C>T	c.(190-192)CGC>TGC	p.R64C	RGN_uc004dha.1_Missense_Mutation_p.R64C|RGN_uc010nho.1_Missense_Mutation_p.R11C|RGN_uc010nhp.1_Missense_Mutation_p.R64C	NM_152869	NP_690608	Q15493	RGN_HUMAN	regucalcin	64					cellular calcium ion homeostasis|positive regulation of ATPase activity|regulation of calcium-mediated signaling	cytoplasm|nucleus	calcium ion binding|enzyme regulator activity|gluconolactonase activity|zinc ion binding				0						CGTGGCTCTTCGCCAGTCGGG	0.493000													16	4					0	0	0.006122	0	0
SSX8	280659	broad.mit.edu	37	X	52661935	52661935	+	RNA	SNP	T	C	C			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chrX:52661935T>C	uc011mob.1	+	7		c.846T>C				NR_027250				Homo sapiens cDNA FLJ56587 complete cds, highly similar to Protein SSX8.												0						AGGAAGATGATGAGTAACTCC	0.483000													7	168					0	0	0.020292	0	0
ODZ1	10178	broad.mit.edu	37	X	123654451	123654451	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chrX:123654451C>T	uc004euj.2	-	18	3281	c.3217G>A	c.(3217-3219)GCC>ACC	p.A1073T	ODZ1_uc011muj.1_Missense_Mutation_p.A1072T|ODZ1_uc010nqy.2_Missense_Mutation_p.A1073T	NM_014253	NP_055068	Q9UKZ4	TEN1_HUMAN	odz, odd Oz/ten-m homolog 1 isoform 3	1073	Extracellular (Potential).				immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23						TTAATTGCGGCGGGAAACCAC	0.473000													111	24					0	0	0.014410	0	0
FRMD4A	55691	broad.mit.edu	37	10	13699134	13699142	+	In_Frame_Del	DEL	CGCCCCCCG	-	-			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr10:13699134_13699142delCGCCCCCCG	uc001ims.2	-	22	2799_2807	c.2447_2455delCGGGGGGCG	c.(2446-2457)GCGGGGGGCGGT>GGT	p.AGG816del	FRMD4A_uc009xjf.1_In_Frame_Del_p.AGG816del	NM_018027	NP_060497	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A	816_818						cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3						AGGTACACAccgccccccgcgccccccgc	0.550													5	4	---	---	---	---					
TSKU	25987	broad.mit.edu	37	11	76506673	76506675	+	In_Frame_Del	DEL	CTG	-	-			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr11:76506673_76506675delCTG	uc001oxt.2	+	2	185_187	c.13_15delCTG	c.(13-15)CTGdel	p.L9del		NM_015516	NP_056331	Q8WUA8	TSK_HUMAN	tsukushin precursor	9						extracellular region					0	Ovarian(111;0.112)					GCCGTGGCCCCTGCTGCTGCTGC	0.616													7	98	---	---	---	---					
CDC27	996	broad.mit.edu	37	17	45219612	45219612	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr17:45219612delA	uc002ild.3	-	11	1488	c.1361delT	c.(1360-1362)CTAfs	p.L454fs	CDC27_uc002ile.3_Frame_Shift_Del_p.L460fs|CDC27_uc002ilf.3_Frame_Shift_Del_p.L454fs|CDC27_uc010wkp.1_Frame_Shift_Del_p.L393fs|CDC27_uc010wkq.1_Intron	NM_001256	NP_001247	P30260	CDC27_HUMAN	cell division cycle protein 27 isoform 2	454					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding			lung(2)|breast(2)|ovary(1)	5						TGCTTTTTGTAGATTAAAGGC	0.308													7	89	---	---	---	---					
SLC30A6	55676	broad.mit.edu	37	2	32422896	32422896	+	Splice_Site	DEL	G	-	-			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr2:32422896delG	uc002roe.1	+	10	702	c.665_splice	c.e10+1	p.N222_splice	SLC30A6_uc002rof.1_Splice_Site_p.N262_splice|SLC30A6_uc010ymw.1_Splice_Site_p.N193_splice|SLC30A6_uc010ezr.1_Splice_Site_p.N222_splice|SLC30A6_uc002rog.1_Splice_Site_p.N25_splice|SLC30A6_uc010ezs.1_Splice_Site_p.N148_splice|SLC30A6_uc002roh.1_Splice_Site_p.N25_splice	NM_017964	NP_060434	Q6NXT4	ZNT6_HUMAN	solute carrier family 30 (zinc transporter),							Golgi membrane|integral to membrane	zinc ion transmembrane transporter activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					TTGAAATTAAGTGAGTATTTT	0.254													47	92	---	---	---	---					
PLCG1	5335	broad.mit.edu	37	20	39802386	39802387	+	In_Frame_Ins	INS	-	GAAGAA	GAAGAA			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr20:39802386_39802387insGAAGAA	uc002xjp.1	+	29	3610_3611	c.3489_3490insGAAGAA	c.(3487-3492)insGAAGAA	p.1163_1164insEE	PLCG1_uc002xjo.1_In_Frame_Ins_p.1163_1164insEE|PLCG1_uc010zwe.1_In_Frame_Ins_p.828_829insEE	NM_182811	NP_877963	P19174	PLCG1_HUMAN	phospholipase C, gamma 1 isoform b	1163_1164	C2.				activation of phospholipase C activity|axon guidance|blood coagulation|cellular response to epidermal growth factor stimulus|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|interspecies interaction between organisms|intracellular signal transduction|leukocyte migration|nerve growth factor receptor signaling pathway|phospholipid catabolic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of epithelial cell migration|T cell receptor signaling pathway	cytosol|lamellipodium|plasma membrane|ruffle	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|receptor signaling protein activity			lung(3)|breast(3)|skin(2)	8		Myeloproliferative disorder(115;0.00878)				TGGTGTATGAGGAAGACATGTT	0.515											OREG0025953	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	47	234	---	---	---	---					
CLOCK	9575	broad.mit.edu	37	4	56336954	56336954	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr4:56336954delA	uc003haz.1	-	9	1294	c.368delT	c.(367-369)TTAfs	p.L123fs	CLOCK_uc003hba.1_Frame_Shift_Del_p.L123fs	NM_004898	NP_004889	O15516	CLOCK_HUMAN	clock	123	PAS 1.				circadian rhythm|photoperiodism|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|transcription factor complex	DNA binding|histone acetyltransferase activity|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(2)|ovary(1)	3	Lung NSC(11;0.00335)|Glioma(25;0.08)|all_epithelial(27;0.0992)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0107)			CATGATTGCTAAAAAAAAACC	0.289													7	255	---	---	---	---					
PRKDC	5591	broad.mit.edu	37	8	48866909	48866910	+	Frame_Shift_Ins	INS	-	T	T			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chr8:48866909_48866910insT	uc003xqi.2	-	5	553_554	c.496_497insA	c.(496-498)ATAfs	p.I166fs	PRKDC_uc003xqj.2_Frame_Shift_Ins_p.I166fs|PRKDC_uc011ldh.1_Frame_Shift_Ins_p.I166fs	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic	166					cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)				TGTATCTGGTATTTTTTTTTTC	0.267								NHEJ					2	4	---	---	---	---					
SLC25A5	292	broad.mit.edu	37	X	118603962	118603962	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CS-5395-01A-01D-1468-08	TCGA-CS-5395-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	3d477ac1-3bdf-4410-9594-1a3a1412c6ae	baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db	g.chrX:118603962delT	uc004erh.3	+	2	566	c.450delT	c.(448-450)GCTfs	p.A150fs	LOC100303728_uc004ere.1_5'Flank|LOC100303728_uc004erg.1_5'Flank	NM_001152	NP_001143	P05141	ADT2_HUMAN	adenine nucleotide translocator 2	150	Solcar 2.				chromosome segregation|energy reserve metabolic process|interspecies interaction between organisms|regulation of insulin secretion|viral reproduction	integral to plasma membrane|mitochondrial inner membrane|mitochondrial nucleoid|MMXD complex	adenine transmembrane transporter activity|protein binding			ovary(1)	1					Clodronate(DB00720)	AAGCTGGAGCTGAAAGGGAAT	0.537													9	124	---	---	---	---					
