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	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	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	Oncotatorv0393GAF20hg19Feb2011dbSNPbuild132UniProtRelease2011_6	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	newbase	context_orig	context65	gene_name	categ	categ_ignoring_null_categ
LYZL1	84569	broad.mit.edu	37	10	29580783	29580783	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:29580783G>A	uc001iul.2	+	c.125G>A	c.(124-126)CGG>CAG	p.R42Q		NM_032517	NP_115906	Q6UWQ5	LYZL1_HUMAN	lysozyme-like 1	Error:Variant_position_missing_in_Q6UWQ5_after_alignment					cell wall macromolecule catabolic process	extracellular region	lysozyme activity				0		Breast(68;0.203)												0.44	33.125939	33.203226	11	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29580783	29580783	9508	10	G	A	A	A	507	39	LYZL1	1	1
HK1	3098	broad.mit.edu	37	10	71142474	71142474	+	Silent	SNP	G	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:71142474G>T	uc001jpj.3	+	c.1602G>T	c.(1600-1602)CTG>CTT	p.L534L	HK1_uc001jpg.3_Silent_p.L487L|HK1_uc001jph.3_Silent_p.L503L|HK1_uc001jpi.3_Silent_p.L503L|HK1_uc001jpk.3_Silent_p.L498L|HK1_uc009xqd.2_Silent_p.L377L|HK1_uc001jpl.3_Silent_p.L499L	NM_033500	NP_277035	P19367	HXK1_HUMAN	hexokinase 1 isoform HKI-td	499	Catalytic.				glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane|nucleus	ATP binding|glucokinase activity			ovary(1)	1														0.15	4.009371	6.362817	3	17	KEEP	---	---	---	---	capture		Silent	SNP	71142474	71142474	7481	10	G	T	T	T	574	45	HK1	2	2
KCNMA1	3778	broad.mit.edu	37	10	78729751	78729751	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:78729751T>A	uc001jxn.2	-	c.2341A>T	c.(2341-2343)ACC>TCC	p.T781S	KCNMA1_uc001jxj.2_Missense_Mutation_p.T727S|KCNMA1_uc001jxk.1_Missense_Mutation_p.T399S|KCNMA1_uc009xrt.1_Missense_Mutation_p.T572S|KCNMA1_uc001jxl.1_Missense_Mutation_p.T406S|KCNMA1_uc001jxo.2_Missense_Mutation_p.T723S|KCNMA1_uc001jxm.2_Missense_Mutation_p.T723S|KCNMA1_uc001jxq.2_Missense_Mutation_p.T726S	NM_001161352	NP_001154824	Q12791	KCMA1_HUMAN	large conductance calcium-activated potassium	781	Cytoplasmic (Potential).				cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|catalytic activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)									0.064815	-6.044498	15.190853	7	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78729751	78729751	8378	10	T	A	A	A	767	59	KCNMA1	3	3
CNTN5	53942	broad.mit.edu	37	11	100211244	100211244	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:100211244A>G	uc001pga.2	+	c.2780A>G	c.(2779-2781)AAA>AGA	p.K927R	CNTN5_uc001pgb.2_Missense_Mutation_p.K853R|CNTN5_uc010ruk.1_Missense_Mutation_p.K198R	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long	927	Fibronectin type-III 3.				cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)						1117				0.116667	20.764502	38.110569	14	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100211244	100211244	3782	11	A	G	G	G	13	1	CNTN5	4	4
ACAD8	27034	broad.mit.edu	37	11	134129553	134129553	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:134129553A>G	uc001qhk.2	+	c.619A>G	c.(619-621)ACA>GCA	p.T207A	ACAD8_uc009zdc.2_3'UTR|ACAD8_uc010sco.1_Missense_Mutation_p.T109A|ACAD8_uc010scp.1_Non-coding_Transcript|ACAD8_uc010scq.1_Missense_Mutation_p.T130A|ACAD8_uc001qhl.2_Missense_Mutation_p.T80A|ACAD8_uc010scr.1_Missense_Mutation_p.T169A|ACAD8_uc009zde.1_Missense_Mutation_p.T80A	NM_014384	NP_055199	Q9UKU7	ACAD8_HUMAN	acyl-Coenzyme A dehydrogenase family, member 8	207					branched chain family amino acid catabolic process|lipid metabolic process|oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrial matrix	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding				0	all_hematologic(175;0.127)	all_cancers(12;8e-23)|all_epithelial(12;2.59e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|all_neural(223;0.0189)|Medulloblastoma(222;0.0245)|Esophageal squamous(93;0.0559)		Epithelial(10;1.92e-10)|all cancers(11;2.26e-09)|BRCA - Breast invasive adenocarcinoma(10;8.73e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00154)|Lung(977;0.21)		GBM(65;238 1125 33403 41853 48889)								0.095238	6.20457	16.559931	6	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	134129553	134129553	111	11	A	G	G	G	26	2	ACAD8	4	4
NELL1	4745	broad.mit.edu	37	11	20959354	20959354	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:20959354A>T	uc009yid.2	+	c.1104A>T	c.(1102-1104)AAA>AAT	p.K368N	NELL1_uc001mqe.2_Missense_Mutation_p.K340N|NELL1_uc001mqf.2_Missense_Mutation_p.K340N|NELL1_uc010rdo.1_Missense_Mutation_p.K283N|NELL1_uc010rdp.1_Missense_Mutation_p.K100N	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor	340	VWFC 2.				cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3														0.045685	-25.855509	17.531737	9	188	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20959354	20959354	10732	11	A	T	T	T	37	3	NELL1	3	3
CHRM4	1132	broad.mit.edu	37	11	46408021	46408021	+	Silent	SNP	C	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:46408021C>T	uc001nct.1	-	c.87G>A	c.(85-87)ACG>ACA	p.T29T		NM_000741	NP_000732	P08173	ACM4_HUMAN	cholinergic receptor, muscarinic 4	29	Extracellular (By similarity).				cell proliferation	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity				0				GBM - Glioblastoma multiforme(35;0.0254)|Lung(87;0.14)	Atropine(DB00572)|Benzquinamide(DB00767)|Cryptenamine(DB00785)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Thiethylperazine(DB00372)|Tropicamide(DB00809)	Esophageal Squamous(171;1020 1936 4566 30205 42542)								0.12	4.607924	8.148396	3	22	KEEP	---	---	---	---	capture		Silent	SNP	46408021	46408021	3513	11	C	T	T	T	288	23	CHRM4	1	1
NEU3	10825	broad.mit.edu	37	11	74716632	74716632	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:74716632T>G	uc001ovw.2	+	c.481T>G	c.(481-483)TTC>GTC	p.F161V	NEU3_uc001ovv.2_Missense_Mutation_p.F151V|NEU3_uc010rrl.1_Missense_Mutation_p.F52V	NM_006656	NP_006647	A8K327	A8K327_HUMAN	sialidase 3	161										ovary(2)	2														0.144444	21.612942	32.567308	13	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74716632	74716632	10742	11	T	G	G	G	728	56	NEU3	4	4
GAB2	9846	broad.mit.edu	37	11	77937572	77937572	+	Silent	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:77937572G>A	uc001ozh.2	-	c.1146C>T	c.(1144-1146)GTC>GTT	p.V382V	GAB2_uc001ozg.2_Silent_p.V344V	NM_080491	NP_536739	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2 isoform a	382					osteoclast differentiation|phosphatidylinositol-mediated signaling|positive regulation of cell proliferation|positive regulation of mast cell degranulation	cytosol|plasma membrane	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|transmembrane receptor protein tyrosine kinase adaptor activity			ovary(5)|lung(1)	6	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)											0.055556	-6.256922	8.703368	4	68	KEEP	---	---	---	---	capture		Silent	SNP	77937572	77937572	6400	11	G	A	A	A	470	37	GAB2	1	1
C12orf51	283450	broad.mit.edu	37	12	112686139	112686139	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:112686139C>T	uc009zwc.2	-	c.2862G>A	c.(2860-2862)ATG>ATA	p.M954I		NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)	1														0.166667	6.013686	7.909928	3	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112686139	112686139	1740	12	C	T	T	T	273	21	C12orf51	2	2
PDE3A	5139	broad.mit.edu	37	12	20769252	20769252	+	Nonsense_Mutation	SNP	T	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:20769252T>A	uc001reh.1	+	c.1358T>A	c.(1357-1359)TTG>TAG	p.L453*		NM_000921	NP_000912	Q14432	PDE3A_HUMAN	phosphodiesterase 3A	453					lipid metabolic process|platelet activation|signal transduction	cytosol|integral to membrane	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(3)	3	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Cilostazol(DB01166)|Enoximone(DB04880)|Milrinone(DB00235)|Theophylline(DB00277)									0.098592	1.240938	12.803701	7	64	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	20769252	20769252	12058	12	T	A	A	A	819	63	PDE3A	5	3
ABCC9	10060	broad.mit.edu	37	12	22012522	22012522	+	Silent	SNP	A	G	G			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:22012522A>G	uc001rfh.2	-	c.2503T>C	c.(2503-2505)TTG>CTG	p.L835L	ABCC9_uc001rfi.1_Silent_p.L835L|ABCC9_uc001rfj.1_Silent_p.L799L	NM_020297	NP_064693	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	835	Cytoplasmic (Potential).|ABC transporter 1.				defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)	4					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)									0.028807	-43.970789	15.368768	7	236	KEEP	---	---	---	---	capture		Silent	SNP	22012522	22012522	60	12	A	G	G	G	11	1	ABCC9	4	4
MON2	23041	broad.mit.edu	37	12	62936948	62936948	+	Silent	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:62936948G>A	uc001sre.2	+	c.2436G>A	c.(2434-2436)CTG>CTA	p.L812L	MON2_uc009zqj.2_Silent_p.L812L|MON2_uc010ssl.1_Silent_p.L740L|MON2_uc010ssm.1_Silent_p.L789L|MON2_uc010ssn.1_Silent_p.L812L|MON2_uc001srf.2_Silent_p.L575L	NM_015026	NP_055841	Q7Z3U7	MON2_HUMAN	MON2 homolog	812					Golgi to endosome transport|protein transport	cytoplasm	ARF guanyl-nucleotide exchange factor activity|binding			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)										0.297297	29.308882	30.669173	11	26	KEEP	---	---	---	---	capture		Silent	SNP	62936948	62936948	10091	12	G	A	A	A	613	48	MON2	2	2
IRAK3	11213	broad.mit.edu	37	12	66641740	66641740	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:66641740G>T	uc001sth.2	+	c.1580G>T	c.(1579-1581)AGA>ATA	p.R527I	IRAK3_uc010ssy.1_Missense_Mutation_p.R466I	NM_007199	NP_009130	Q9Y616	IRAK3_HUMAN	interleukin-1 receptor-associated kinase 3	527					interleukin-1-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|negative regulation of cytokine-mediated signaling pathway|negative regulation of innate immune response|negative regulation of interleukin-12 production|negative regulation of interleukin-6 production|negative regulation of macrophage cytokine production|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein catabolic process|negative regulation of protein complex disassembly|negative regulation of toll-like receptor signaling pathway|negative regulation of tumor necrosis factor production|positive regulation of macrophage tolerance induction|positive regulation of NF-kappaB transcription factor activity|response to exogenous dsRNA|response to lipopolysaccharide|response to peptidoglycan|response to virus	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein heterodimerization activity|protein homodimerization activity|protein serine/threonine kinase activity			ovary(2)|lung(1)|central_nervous_system(1)	4				GBM - Glioblastoma multiforme(28;0.0203)						206				0.068627	-10.8232	28.443045	14	190	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66641740	66641740	8127	12	G	T	T	T	429	33	IRAK3	2	2
C12orf26	84190	broad.mit.edu	37	12	82792957	82792957	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:82792957T>G	uc001szq.2	+	c.915T>G	c.(913-915)AAT>AAG	p.N305K		NM_032230	NP_115606	Q8N6Q8	CL026_HUMAN	hypothetical protein LOC84190	305											0														0.25	59.636828	64.407068	21	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82792957	82792957	1723	12	T	G	G	G	673	52	C12orf26	4	4
SLC6A15	55117	broad.mit.edu	37	12	85255686	85255686	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:85255686G>A	uc001szv.2	-	c.1918C>T	c.(1918-1920)CGT>TGT	p.R640C	SLC6A15_uc010sul.1_Missense_Mutation_p.R533C|SLC6A15_uc001szw.1_Intron	NM_182767	NP_877499	Q9H2J7	S6A15_HUMAN	solute carrier family 6, member 15 isoform 1	640	Helical; Name=12; (Potential).				cellular nitrogen compound metabolic process|leucine transport|proline transport	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity			pancreas(2)|ovary(1)	3														0.252137	150.789614	163.874327	59	175	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85255686	85255686	15175	12	G	A	A	A	481	37	SLC6A15	1	1
USP44	84101	broad.mit.edu	37	12	95927783	95927783	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:95927783C>A	uc001teg.2	-	c.250G>T	c.(250-252)GAT>TAT	p.D84Y	USP44_uc001teh.2_Missense_Mutation_p.D84Y|USP44_uc009zte.2_Missense_Mutation_p.D81Y	NM_001042403	NP_001035862	Q9H0E7	UBP44_HUMAN	ubiquitin thiolesterase 44	84	UBP-type.				anaphase|cell division|mitosis|negative regulation of mitotic anaphase-promoting complex activity|protein deubiquitination|regulation of spindle checkpoint|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)	1												OREG0022039	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.111111	4.839984	11.570806	5	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95927783	95927783	17639	12	C	A	A	A	377	29	USP44	2	2
SACS	26278	broad.mit.edu	37	13	23912692	23912692	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:23912692C>A	uc001uon.2	-	c.5323G>T	c.(5323-5325)GCT>TCT	p.A1775S	SACS_uc001uoo.2_Missense_Mutation_p.A1628S|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	1775					cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)|skin(1)	11		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)						738				0.096774	6.748944	21.862101	9	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23912692	23912692	14284	13	C	A	A	A	325	25	SACS	2	2
ATP8A2	51761	broad.mit.edu	37	13	26411405	26411405	+	Silent	SNP	C	G	G			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:26411405C>G	uc001uqk.2	+	c.2859C>G	c.(2857-2859)GGC>GGG	p.G953G	ATP8A2_uc010tdi.1_Silent_p.G888G|ATP8A2_uc010tdj.1_Non-coding_Transcript|ATP8A2_uc010aaj.1_Silent_p.G503G	NM_016529	NP_057613	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter-like,	913	Cytoplasmic (Potential).				ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)	3		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)										0.150794	37.064601	51.788555	19	107	KEEP	---	---	---	---	capture		Silent	SNP	26411405	26411405	1212	13	C	G	G	G	340	27	ATP8A2	3	3
FLT3	2322	broad.mit.edu	37	13	28578244	28578244	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:28578244C>A	uc001urw.2	-	c.2927G>T	c.(2926-2928)AGC>ATC	p.S976I	FLT3_uc010aao.2_Non-coding_Transcript|FLT3_uc010tdn.1_Missense_Mutation_p.S935I	NM_004119	NP_004110	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3 precursor	976	Cytoplasmic (Potential).				positive regulation of cell proliferation	integral to plasma membrane	ATP binding|vascular endothelial growth factor receptor activity			haematopoietic_and_lymphoid_tissue(8072)|ovary(2)|lung(1)|central_nervous_system(1)	8076	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Sorafenib(DB00398)|Sunitinib(DB01268)					630				0.07	-5.258855	13.83557	7	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28578244	28578244	6184	13	C	A	A	A	364	28	FLT3	2	2
NBEA	26960	broad.mit.edu	37	13	35672502	35672502	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:35672502G>T	uc001uvb.2	+	c.1640G>T	c.(1639-1641)GGT>GTT	p.G547V		NM_015678	NP_056493	Q8NFP9	NBEA_HUMAN	neurobeachin	547						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)										0.071429	-1.646326	8.953663	4	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35672502	35672502	10583	13	G	T	T	T	572	44	NBEA	2	2
RAB2B	84932	broad.mit.edu	37	14	21944687	21944687	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:21944687C>T	uc010tlt.1	-	c.118G>A	c.(118-120)GGT>AGT	p.G40S	RAB2B_uc010tls.1_5'UTR|RAB2B_uc001wax.2_5'UTR|RAB2B_uc010ain.2_5'UTR|TOX4_uc001way.2_5'Flank|TOX4_uc001waz.2_5'Flank|TOX4_uc001wba.2_5'Flank|TOX4_uc010tlu.1_5'Flank	NM_032846	NP_116235	Q8WUD1	RAB2B_HUMAN	RAB2B protein isoform 1	40	Effector region (By similarity).				protein transport|small GTPase mediated signal transduction|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane|plasma membrane	GTP binding			ovary(1)	1	all_cancers(95;0.000858)		Epithelial(56;1.53e-06)|all cancers(55;1.44e-05)	GBM - Glioblastoma multiforme(265;0.00391)		Melanoma(131;1007 1750 28652 34486 42672)								0.411765	45.243833	45.475059	14	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21944687	21944687	13377	14	C	T	T	T	312	24	RAB2B	2	2
MYO9A	4649	broad.mit.edu	37	15	72141239	72141239	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:72141239C>G	uc002atl.3	-	c.6784G>C	c.(6784-6786)GAA>CAA	p.E2262Q	MYO9A_uc002atj.2_Missense_Mutation_p.E175Q|MYO9A_uc002atk.2_Missense_Mutation_p.E1057Q	NM_006901	NP_008832	B2RTY4	MYO9A_HUMAN	myosin IXA	2262	Tail.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|visual perception	cytosol|integral to membrane|unconventional myosin complex	actin binding|ATP binding|GTPase activator activity|metal ion binding|motor activity			ovary(1)|pancreas(1)|skin(1)	3														0.190476	20.275284	24.036473	8	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72141239	72141239	10479	15	C	G	G	G	390	30	MYO9A	3	3
MYH4	4622	broad.mit.edu	37	17	10358095	10358095	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10358095C>T	uc002gmn.2	-	c.2468G>A	c.(2467-2469)CGT>CAT	p.R823H		NM_017533	NP_060003	Q9Y623	MYH4_HUMAN	myosin, heavy polypeptide 4, skeletal muscle	823					muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(10)|central_nervous_system(1)	11														0.153846	13.365748	19.331382	8	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10358095	10358095	10432	17	C	T	T	T	247	19	MYH4	1	1
MYH2	4620	broad.mit.edu	37	17	10432234	10432234	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10432234G>A	uc010coi.2	-	c.3517C>T	c.(3517-3519)CGG>TGG	p.R1173W	MYH2_uc002gmp.3_Missense_Mutation_p.R1173W|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	1173	Potential.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|lung(1)|kidney(1)	11														0.263158	48.364394	52.222399	20	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10432234	10432234	10430	17	G	A	A	A	493	38	MYH2	1	1
CWC25	54883	broad.mit.edu	37	17	36958457	36958457	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:36958457C>T	uc002hqu.2	-	c.1166G>A	c.(1165-1167)CGC>CAC	p.R389H	CWC25_uc010wdv.1_Missense_Mutation_p.R326H|PIP4K2B_uc002hqs.2_5'Flank|PIP4K2B_uc010wdt.1_5'Flank	NM_017748	NP_060218	Q9NXE8	CWC25_HUMAN	coiled-coil domain containing 49	389											0														0.321429	24.966035	25.758596	9	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36958457	36958457	4229	17	C	T	T	T	351	27	CWC25	1	1
FAM134C	162427	broad.mit.edu	37	17	40761280	40761280	+	Silent	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:40761280G>A	uc002ial.2	-	c.63C>T	c.(61-63)GGC>GGT	p.G21G	TUBG1_uc002ian.2_5'Flank|FAM134C_uc010wgq.1_5'UTR|FAM134C_uc002iam.1_5'UTR|FAM134C_uc010cyk.1_Intron	NM_178126	NP_835227	Q86VR2	F134C_HUMAN	hypothetical protein LOC162427	21						integral to membrane				ovary(1)	1		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.134)										0.266667	9.892802	10.630811	4	11	KEEP	---	---	---	---	capture		Silent	SNP	40761280	40761280	5644	17	G	A	A	A	535	42	FAM134C	2	2
C17orf57	124989	broad.mit.edu	37	17	45451930	45451930	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:45451930A>T	uc002iln.2	+	c.970A>T	c.(970-972)AGT>TGT	p.S324C	C17orf57_uc002ilm.2_Missense_Mutation_p.S228C|C17orf57_uc002ill.1_Missense_Mutation_p.S80C|C17orf57_uc010daz.1_Missense_Mutation_p.S276C	NM_152347	NP_689560	Q8IY85	CQ057_HUMAN	hypothetical protein LOC124989	324							calcium ion binding			breast(1)|central_nervous_system(1)	2														0.192308	22.732209	27.320203	10	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45451930	45451930	1922	17	A	T	T	T	195	15	C17orf57	3	3
NACA2	342538	broad.mit.edu	37	17	59667970	59667970	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:59667970G>A	uc002izj.2	-	c.572C>T	c.(571-573)TCG>TTG	p.S191L		NM_199290	NP_954984	Q9H009	NACA2_HUMAN	nascent-polypeptide-associated complex alpha	191	UBA.				protein transport	cytoplasm|nucleus				ovary(1)	1	all_epithelial(1;3.12e-14)													0.07907	-0.457646	38.411802	17	198	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	59667970	59667970	10529	17	G	A	A	A	481	37	NACA2	1	1
TP53	7157	broad.mit.edu	37	17	7577536	7577536	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7577536T>C	uc002gim.2	-	c.745A>G	c.(745-747)AGG>GGG	p.R249G	TP53_uc002gig.1_Missense_Mutation_p.R249G|TP53_uc002gih.2_Missense_Mutation_p.R249G|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R117G|TP53_uc010cng.1_Missense_Mutation_p.R117G|TP53_uc002gii.1_Missense_Mutation_p.R117G|TP53_uc010cnh.1_Missense_Mutation_p.R249G|TP53_uc010cni.1_Missense_Mutation_p.R249G|TP53_uc002gij.2_Missense_Mutation_p.R249G|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.R156G|TP53_uc002gio.2_Missense_Mutation_p.R117G	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	249	|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> W (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|RP -> SS (in sporadic cancers; somatic mutation).|R -> T (in sporadic cancers; somatic mutation).|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> I (in a sporadic cancer; somatic mutation).|R -> M (in sporadic cancers; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> K (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 gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|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|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	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|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|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.R249G(24)|p.R249W(23)|p.0?(6)|p.M246_P250delMNRRP(2)|p.R249R(1)|p.R248_P250delRRP(1)|p.R249_P250delRP(1)|p.N247_R248delNR(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*96(1)|p.G245fs*14(1)|p.R249fs*15(1)|p.R249fs*14(1)|p.R249_T256delRPILTIIT(1)|p.R249fs*19(1)|p.R249_I251delRPI(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|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)	21904		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)		Pancreas(47;798 1329 9957 10801)		111	p.R249G(A4FUK-Tumor)|p.R249W(SF126-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.313725	46.982299	48.556813	16	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7577536	7577536	16923	17	T	C	C	C	700	54	TP53	4	4
GLP2R	9340	broad.mit.edu	37	17	9739737	9739737	+	Silent	SNP	T	G	G			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:9739737T>G	uc002gmd.1	+	c.327T>G	c.(325-327)TCT>TCG	p.S109S	GLP2R_uc010cog.1_Non-coding_Transcript	NM_004246	NP_004237	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor precursor	109	Extracellular (Potential).				G-protein signaling, coupled to cAMP nucleotide second messenger|positive regulation of cell proliferation	integral to membrane|plasma membrane				ovary(1)	1					Glucagon recombinant(DB00040)									0.088235	1.187165	24.517396	12	124	KEEP	---	---	---	---	capture		Silent	SNP	9739737	9739737	6721	17	T	G	G	G	717	56	GLP2R	4	4
CCDC105	126402	broad.mit.edu	37	19	15132685	15132685	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:15132685A>G	uc002nae.2	+	c.1205A>G	c.(1204-1206)CAG>CGG	p.Q402R		NM_173482	NP_775753	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	402					microtubule cytoskeleton organization	microtubule				ovary(1)	1														0.125	13.794658	24.786303	10	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15132685	15132685	2860	19	A	G	G	G	91	7	CCDC105	4	4
KCNK6	9424	broad.mit.edu	37	19	38817875	38817875	+	Silent	SNP	C	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:38817875C>T	uc002oic.2	+	c.774C>T	c.(772-774)CAC>CAT	p.H258H	KCNK6_uc002oid.2_Silent_p.H124H	NM_004823	NP_004814	Q9Y257	KCNK6_HUMAN	potassium channel, subfamily K, member 6	258	Cytoplasmic (Potential).					voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(1)	1	all_cancers(60;5.83e-07)		Lung(45;0.00047)|LUSC - Lung squamous cell carcinoma(53;0.000613)		Ibutilide(DB00308)|Quinidine(DB00908)									0.272727	6.118323	6.63236	3	8	KEEP	---	---	---	---	capture		Silent	SNP	38817875	38817875	8375	19	C	T	T	T	246	19	KCNK6	1	1
GJA8	2703	broad.mit.edu	37	1	147380379	147380379	+	Silent	SNP	C	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:147380379C>T	uc001epu.1	+	c.297C>T	c.(295-297)TAC>TAT	p.Y99Y		NM_005267	NP_005258	P48165	CXA8_HUMAN	connexin 50	99	Helical; (Potential).				cell communication|visual perception	connexon complex|integral to plasma membrane	channel activity			ovary(2)|large_intestine(2)|breast(1)	5	all_hematologic(923;0.0276)					Melanoma(76;1255 1795 8195 52096)								0.267606	47.399457	50.858233	19	52	KEEP	---	---	---	---	capture		Silent	SNP	147380379	147380379	6673	1	C	T	T	T	246	19	GJA8	1	1
FLG	2312	broad.mit.edu	37	1	152275390	152275390	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152275390A>T	uc001ezu.1	-	c.11972T>A	c.(11971-11973)TTT>TAT	p.F3991Y		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	3991					keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.067416	-4.714764	12.526822	6	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152275390	152275390	6160	1	A	T	T	T	13	1	FLG	3	3
IQGAP3	128239	broad.mit.edu	37	1	156524106	156524106	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:156524106G>A	uc001fpf.2	-	c.1369C>T	c.(1369-1371)CGG>TGG	p.R457W	IQGAP3_uc009wsb.1_Missense_Mutation_p.R414W	NM_178229	NP_839943	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	457					small GTPase mediated signal transduction	intracellular	calmodulin binding|Ras GTPase activator activity			ovary(5)	5	all_hematologic(923;0.088)|Hepatocellular(266;0.158)													0.347826	22.598185	23.065871	8	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	156524106	156524106	8119	1	G	A	A	A	506	39	IQGAP3	1	1
ETNK2	55224	broad.mit.edu	37	1	204115885	204115885	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:204115885C>T	uc001hao.3	-	c.526G>A	c.(526-528)GCC>ACC	p.A176T	ETNK2_uc010pqr.1_5'UTR|ETNK2_uc001han.3_Missense_Mutation_p.A176T|ETNK2_uc010pqs.1_Intron|ETNK2_uc010pqt.1_5'UTR	NM_018208	NP_060678	Q9NVF9	EKI2_HUMAN	ethanolamine kinase 2	176							ATP binding|choline kinase activity|ethanolamine kinase activity			ovary(1)|central_nervous_system(1)	2	all_cancers(21;0.032)|Breast(84;0.116)|all_epithelial(62;0.196)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)											0.216216	18.984916	21.730195	8	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	204115885	204115885	5467	1	C	T	T	T	351	27	ETNK2	1	1
TARBP1	6894	broad.mit.edu	37	1	234529569	234529569	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:234529569C>T	uc001hwd.2	-	c.4258G>A	c.(4258-4260)GAA>AAA	p.E1420K		NM_005646	NP_005637	Q13395	TARB1_HUMAN	TAR RNA binding protein 1	1420					regulation of transcription from RNA polymerase II promoter|RNA processing	nucleus	RNA binding|RNA methyltransferase activity			ovary(2)	2	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)											0.102564	3.774814	9.909726	4	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	234529569	234529569	16076	1	C	T	T	T	403	31	TARBP1	1	1
PGBD2	267002	broad.mit.edu	37	1	249211872	249211872	+	Silent	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:249211872G>A	uc001ifh.2	+	c.1089G>A	c.(1087-1089)TTG>TTA	p.L363L	PGBD2_uc001ifg.2_Silent_p.L112L|PGBD2_uc009xhd.2_Silent_p.L360L	NM_170725	NP_733843	Q6P3X8	PGBD2_HUMAN	hypothetical protein LOC267002 isoform a	363										ovary(1)	1	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.012)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)											0.227273	69.875976	78.892496	30	102	KEEP	---	---	---	---	capture		Silent	SNP	249211872	249211872	12204	1	G	A	A	A	581	45	PGBD2	2	2
SLC9A1	6548	broad.mit.edu	37	1	27436121	27436121	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:27436121G>A	uc001bnm.2	-	c.961C>T	c.(961-963)CGA>TGA	p.R321*	SLC9A1_uc010ofk.1_5'UTR|SLC9A1_uc001bnn.2_Nonsense_Mutation_p.R321*	NM_003047	NP_003038	P19634	SL9A1_HUMAN	solute carrier family 9, isoform A1	321	Cytoplasmic (Potential).				regulation of pH	integral to membrane	sodium:hydrogen antiporter activity			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;2.19e-50)|OV - Ovarian serous cystadenocarcinoma(117;1.8e-29)|Colorectal(126;7.61e-09)|COAD - Colon adenocarcinoma(152;9.32e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000521)|KIRC - Kidney renal clear cell carcinoma(1967;0.00079)|STAD - Stomach adenocarcinoma(196;0.00125)|READ - Rectum adenocarcinoma(331;0.046)	Amiloride(DB00594)									0.266667	10.893953	11.631137	4	11	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	27436121	27436121	15206	1	G	A	A	A	506	39	SLC9A1	5	1
PRDM16	63976	broad.mit.edu	37	1	3327964	3327964	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:3327964G>C	uc001akf.2	+	c.1203G>C	c.(1201-1203)AAG>AAC	p.K401N	PRDM16_uc001akc.2_Missense_Mutation_p.K401N|PRDM16_uc001akd.2_Missense_Mutation_p.K401N|PRDM16_uc001ake.2_Missense_Mutation_p.K401N|PRDM16_uc009vlh.2_Missense_Mutation_p.K102N	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1	401	C2H2-type 6.				brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription activator activity|transcription coactivator activity|transcription repressor activity|zinc ion binding			ovary(1)|lung(1)|central_nervous_system(1)	3	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)						1161				0.26087	16.839646	18.029911	6	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3327964	3327964	12899	1	G	C	C	C	464	36	PRDM16	3	3
LEPRE1	64175	broad.mit.edu	37	1	43213468	43213468	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:43213468C>T	uc001chx.3	-	c.1840G>A	c.(1840-1842)GCC>ACC	p.A614T	LEPRE1_uc001chv.2_Missense_Mutation_p.A614T|LEPRE1_uc001chw.2_Missense_Mutation_p.A614T	NM_001146289	NP_001139761	Q32P28	P3H1_HUMAN	leprecan 1 isoform 2	614	Fe2OG dioxygenase.				negative regulation of cell proliferation|oxidation-reduction process	endoplasmic reticulum|proteinaceous extracellular matrix	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 3-dioxygenase activity			ovary(3)|lung(1)	4	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)									0.25	31.182882	33.905813	12	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43213468	43213468	9053	1	C	T	T	T	351	27	LEPRE1	1	1
DPYD	1806	broad.mit.edu	37	1	98187108	98187108	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:98187108C>A	uc001drv.2	-	c.441G>T	c.(439-441)GAG>GAT	p.E147D	DPYD_uc010oub.1_Non-coding_Transcript|DPYD_uc001drw.2_Missense_Mutation_p.E147D	NM_000110	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase isoform 1	147					'de novo' pyrimidine base biosynthetic process|oxidation-reduction 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)|breast(2)	5		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)					533				0.194805	30.782219	37.470778	15	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	98187108	98187108	4929	1	C	A	A	A	311	24	DPYD	2	2
MOCS3	27304	broad.mit.edu	37	20	49575564	49575564	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:49575564G>A	uc002xvy.1	+	c.185G>A	c.(184-186)CGC>CAC	p.R62H	DPM1_uc002xvw.1_5'Flank|DPM1_uc002xvx.1_5'Flank	NM_014484	NP_055299	O95396	MOCS3_HUMAN	molybdenum cofactor synthesis 3	62					enzyme active site formation via L-cysteine persulfide|Mo-molybdopterin cofactor biosynthetic process|tRNA thio-modification|tRNA wobble uridine modification|water-soluble vitamin metabolic process	cytosol	ATP binding|metal ion binding|nucleotidyltransferase activity|protein binding|thiosulfate sulfurtransferase activity|URM1 activating enzyme activity			ovary(1)|skin(1)	2														0.333333	32.193982	33.07662	12	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49575564	49575564	10083	20	G	A	A	A	494	38	MOCS3	1	1
DSCAM	1826	broad.mit.edu	37	21	41710046	41710046	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:41710046C>T	uc002yyq.1	-	c.1765G>A	c.(1765-1767)GTC>ATC	p.V589I	DSCAM_uc002yyr.1_Non-coding_Transcript	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform	589	Extracellular (Potential).|Ig-like C2-type 6.				cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)	6		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				Melanoma(134;970 1778 1785 21664 32388)								0.27	70.991471	75.75805	27	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41710046	41710046	4952	21	C	T	T	T	247	19	DSCAM	1	1
C21orf29	54084	broad.mit.edu	37	21	45941910	45941910	+	Silent	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:45941910G>A	uc002zfe.1	-	c.1422C>T	c.(1420-1422)TCC>TCT	p.S474S	C21orf29_uc010gpv.1_Silent_p.S406S	NM_144991	NP_659428	Q8WU66	TSEAR_HUMAN	chromosome 21 open reading frame 29 precursor	474	EAR 4.				cell adhesion	extracellular region	structural molecule activity				0														0.194444	16.609111	19.740348	7	29	KEEP	---	---	---	---	capture		Silent	SNP	45941910	45941910	2204	21	G	A	A	A	496	39	C21orf29	1	1
PNPLA5	150379	broad.mit.edu	37	22	44282341	44282341	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:44282341G>A	uc003beg.2	-	c.791C>T	c.(790-792)ACG>ATG	p.T264M	PNPLA5_uc011aqc.1_Missense_Mutation_p.T124M|PNPLA5_uc003beh.2_Missense_Mutation_p.T150M	NM_138814	NP_620169	Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	264					lipid catabolic process		hydrolase activity				0		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)												0.176471	5.914769	7.591739	3	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44282341	44282341	12595	22	G	A	A	A	520	40	PNPLA5	1	1
FMNL2	114793	broad.mit.edu	37	2	153476138	153476138	+	Silent	SNP	T	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:153476138T>A	uc002tye.2	+	c.1743T>A	c.(1741-1743)ACT>ACA	p.T581T	FMNL2_uc010fob.2_Silent_p.T30T|FMNL2_uc002tyf.2_Silent_p.T30T	NM_052905	NP_443137	Q96PY5	FMNL2_HUMAN	formin-like 2	581	Pro-rich.				actin cytoskeleton organization	cytoplasm	actin binding|Rho GTPase binding			central_nervous_system(2)|ovary(1)	3														0.09375	1.901175	7.209048	3	29	KEEP	---	---	---	---	capture		Silent	SNP	153476138	153476138	6194	2	T	A	A	A	704	55	FMNL2	3	3
TTN	7273	broad.mit.edu	37	2	179593263	179593263	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179593263C>A	uc010zfg.1	-	c.15658G>T	c.(15658-15660)GGA>TGA	p.G5220*	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Nonsense_Mutation_p.G1881*	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	2251										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)							8722				0.122449	9.416784	16.253083	6	43	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	179593263	179593263	17290	2	C	A	A	A	299	23	TTN	5	1
EEF1B2	1933	broad.mit.edu	37	2	207025358	207025358	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:207025358A>G	uc002vbf.1	+	c.127A>G	c.(127-129)AGC>GGC	p.S43G	NDUFS1_uc010ziq.1_5'Flank|NDUFS1_uc002vbe.2_5'Flank|NDUFS1_uc010zir.1_5'Flank|NDUFS1_uc010zis.1_5'Flank|NDUFS1_uc010zit.1_5'Flank|NDUFS1_uc010ziu.1_5'Flank|EEF1B2_uc002vbg.1_Missense_Mutation_p.S43G|EEF1B2_uc002vbh.1_Missense_Mutation_p.S43G|SNORD51_uc002vbi.1_5'Flank|SNORA41_uc002vbj.2_5'Flank	NM_001037663	NP_001032752	P24534	EF1B_HUMAN	eukaryotic translation elongation factor 1 beta	43	GST C-terminal.					cytosol|eukaryotic translation elongation factor 1 complex	protein binding|translation elongation factor activity				0														0.190476	7.288013	9.169638	4	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	207025358	207025358	5112	2	A	G	G	G	91	7	EEF1B2	4	4
SCG2	7857	broad.mit.edu	37	2	224463855	224463855	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:224463855T>G	uc002vnm.2	-	c.146A>C	c.(145-147)AAG>ACG	p.K49T		NM_003469	NP_003460	P13521	SCG2_HUMAN	secretogranin II precursor	49					angiogenesis|endothelial cell migration|eosinophil chemotaxis|induction of positive chemotaxis|inflammatory response|MAPKKK cascade|negative regulation of apoptosis|negative regulation of endothelial cell proliferation|positive regulation of endothelial cell proliferation|protein secretion	extracellular space	chemoattractant activity|cytokine activity			ovary(1)	1		Renal(207;0.0112)|Lung NSC(271;0.0185)|all_lung(227;0.0271)		Epithelial(121;8.16e-11)|all cancers(144;4.66e-08)|Lung(261;0.00714)|LUSC - Lung squamous cell carcinoma(224;0.008)										0.098901	13.62715	42.897047	18	164	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	224463855	224463855	14372	2	T	G	G	G	728	56	SCG2	4	4
PSMD1	5707	broad.mit.edu	37	2	231926010	231926010	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:231926010G>T	uc002vrn.1	+	c.46G>T	c.(46-48)GAA>TAA	p.E16*	PSMD1_uc002vrm.1_Nonsense_Mutation_p.E16*|PSMD1_uc010fxu.1_5'UTR	NM_002807	NP_002798	Q99460	PSMD1_HUMAN	proteasome 26S non-ATPase subunit 1	16					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of protein catabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	enzyme regulator activity|protein binding			ovary(1)	1		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)									0.078947	-0.506832	6.376215	3	35	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	231926010	231926010	13145	2	G	T	T	T	585	45	PSMD1	5	2
LTBP1	4052	broad.mit.edu	37	2	33500077	33500077	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:33500077G>A	uc002ros.2	+	c.2792G>A	c.(2791-2793)CGC>CAC	p.R931H	LTBP1_uc002rot.2_Missense_Mutation_p.R605H|LTBP1_uc002rou.2_Missense_Mutation_p.R604H|LTBP1_uc002rov.2_Missense_Mutation_p.R551H|LTBP1_uc010ymz.1_Missense_Mutation_p.R604H|LTBP1_uc010yna.1_Missense_Mutation_p.R551H	NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding	930	EGF-like 5; calcium-binding (Potential).				negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|lung(1)|central_nervous_system(1)	7	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)												0.428571	88.441819	88.752486	30	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33500077	33500077	9449	2	G	A	A	A	494	38	LTBP1	1	1
POLQ	10721	broad.mit.edu	37	3	121248522	121248522	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:121248522C>G	uc003eee.3	-	c.1078G>C	c.(1078-1080)GAG>CAG	p.E360Q		NM_199420	NP_955452	O75417	DPOLQ_HUMAN	DNA polymerase theta	360	Helicase C-terminal.				DNA repair|DNA replication	nucleoplasm	ATP binding|ATP-dependent helicase activity|damaged DNA binding|DNA-directed DNA polymerase activity			ovary(4)|skin(1)	5				GBM - Glioblastoma multiforme(114;0.0915)		Pancreas(152;907 1925 26081 31236 36904)								0.151899	23.945225	33.113401	12	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	121248522	121248522	12636	3	C	G	G	G	416	32	POLQ	3	3
DNAJC13	23317	broad.mit.edu	37	3	132172941	132172941	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:132172941C>A	uc003eor.2	+	c.872C>A	c.(871-873)CCA>CAA	p.P291Q	DNAJC13_uc010htq.1_Missense_Mutation_p.P291Q|DNAJC13_uc003eos.1_5'Flank	NM_015268	NP_056083	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	291							heat shock protein binding			breast(1)	1														0.075472	-0.643379	9.15242	4	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	132172941	132172941	4815	3	C	A	A	A	273	21	DNAJC13	2	2
TRIM42	287015	broad.mit.edu	37	3	140407231	140407231	+	Silent	SNP	C	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:140407231C>T	uc003eto.1	+	c.1707C>T	c.(1705-1707)GAC>GAT	p.D569D		NM_152616	NP_689829	Q8IWZ5	TRI42_HUMAN	tripartite motif-containing 42	569						intracellular	zinc ion binding			lung(2)|upper_aerodigestive_tract(1)|breast(1)|central_nervous_system(1)|skin(1)	6										261				0.201754	45.046433	54.492296	23	91	KEEP	---	---	---	---	capture		Silent	SNP	140407231	140407231	17061	3	C	T	T	T	246	19	TRIM42	1	1
DCLK3	85443	broad.mit.edu	37	3	36756835	36756835	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:36756835A>T	uc003cgi.2	-	c.1931T>A	c.(1930-1932)GTG>GAG	p.V644E		NM_033403	NP_208382	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3	644					protein phosphorylation	cytoplasm|nucleus	ATP binding|protein serine/threonine kinase activity			lung(3)|large_intestine(2)|ovary(1)|breast(1)|kidney(1)	8										128				0.115942	10.875077	20.872308	8	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36756835	36756835	4464	3	A	T	T	T	78	6	DCLK3	3	3
KBTBD5	131377	broad.mit.edu	37	3	42733406	42733406	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:42733406T>C	uc003clv.1	+	c.1787T>C	c.(1786-1788)GTC>GCC	p.V596A		NM_152393	NP_689606	Q2TBA0	KBTB5_HUMAN	kelch repeat and BTB (POZ) domain containing 5	596	Kelch 5.									ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.214)										0.084746	4.296807	35.270084	15	162	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42733406	42733406	8301	3	T	C	C	C	754	58	KBTBD5	4	4
ROBO1	6091	broad.mit.edu	37	3	78795962	78795962	+	Silent	SNP	G	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:78795962G>T	uc003dqe.2	-	c.588C>A	c.(586-588)GGC>GGA	p.G196G	ROBO1_uc003dqb.2_Silent_p.G157G|ROBO1_uc003dqc.2_Silent_p.G157G|ROBO1_uc003dqd.2_Silent_p.G157G	NM_002941	NP_002932	Q9Y6N7	ROBO1_HUMAN	roundabout 1 isoform a	196	Extracellular (Potential).|Ig-like C2-type 2.				activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)						693				0.195402	32.670994	40.176139	17	70	KEEP	---	---	---	---	capture		Silent	SNP	78795962	78795962	13992	3	G	T	T	T	535	42	ROBO1	2	2
PPEF2	5470	broad.mit.edu	37	4	76793210	76793210	+	Silent	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:76793210G>A	uc003hix.2	-	c.1617C>T	c.(1615-1617)AAC>AAT	p.N539N	PPEF2_uc003hiy.2_Non-coding_Transcript|PPEF2_uc003hiz.1_Silent_p.N539N	NM_006239	NP_006230	O14830	PPE2_HUMAN	serine/threonine protein phosphatase with	539	Catalytic.				detection of stimulus involved in sensory perception|protein dephosphorylation|visual perception	cytoplasm|photoreceptor inner segment|photoreceptor outer segment	calcium ion binding|iron ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity			ovary(2)|lung(1)|central_nervous_system(1)	4			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			NSCLC(105;1359 1603 15961 44567 47947)								0.142857	9.835849	16.778746	8	48	KEEP	---	---	---	---	capture		Silent	SNP	76793210	76793210	12738	4	G	A	A	A	620	48	PPEF2	2	2
SPOCK1	6695	broad.mit.edu	37	5	136324155	136324155	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:136324155T>C	uc003lbo.2	-	c.884A>G	c.(883-885)AAG>AGG	p.K295R	SPOCK1_uc003lbp.2_Missense_Mutation_p.K295R	NM_004598	NP_004589	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains	295					cell adhesion|cell proliferation|cellular component movement|nervous system development|signal transduction	proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)											0.110345	18.604677	40.37764	16	129	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	136324155	136324155	15592	5	T	C	C	C	728	56	SPOCK1	4	4
PCDHA3	56145	broad.mit.edu	37	5	140182819	140182819	+	Silent	SNP	G	A	A	rs34395025		TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140182819G>A	uc003lhf.2	+	c.2037G>A	c.(2035-2037)TCG>TCA	p.S679S	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA2_uc011czy.1_Intron|PCDHA3_uc011czz.1_Silent_p.S679S	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3 isoform 1 precursor	679	Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(5)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.333333	33.720576	34.76207	14	28	KEEP	---	---	---	---	capture		Silent	SNP	140182819	140182819	11945	5	G	A	A	A	509	40	PCDHA3	1	1
PCDHA11	56138	broad.mit.edu	37	5	140250075	140250075	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140250075G>A	uc003lia.2	+	c.1387G>A	c.(1387-1389)GTG>ATG	p.V463M	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc011dae.1_Missense_Mutation_p.V463M	NM_018902	NP_061725	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11 isoform 1 precursor	463	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.256098	50.551529	54.966051	21	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140250075	140250075	11941	5	G	A	A	A	520	40	PCDHA11	1	1
PCDHB1	29930	broad.mit.edu	37	5	140432692	140432692	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140432692T>G	uc003lik.1	+	c.1637T>G	c.(1636-1638)GTT>GGT	p.V546G		NM_013340	NP_037472	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1 precursor	546	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.162162	11.726394	15.742232	6	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140432692	140432692	11954	5	T	G	G	G	780	60	PCDHB1	4	4
VCAN	1462	broad.mit.edu	37	5	82849190	82849190	+	Silent	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:82849190G>A	uc003kii.3	+	c.9501G>A	c.(9499-9501)GAG>GAA	p.E3167E	VCAN_uc003kij.3_Silent_p.E2180E|VCAN_uc010jau.2_Silent_p.E1413E|VCAN_uc003kik.3_Silent_p.E426E|VCAN_uc003kil.3_Silent_p.E1831E	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	3167					cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(3)|lung(2)|central_nervous_system(1)	13		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)										0.22619	47.572446	53.365024	19	65	KEEP	---	---	---	---	capture		Silent	SNP	82849190	82849190	17703	5	G	A	A	A	425	33	VCAN	2	2
TPMT	7172	broad.mit.edu	37	6	18130960	18130960	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:18130960C>T	uc003ncm.2	-	c.677G>A	c.(676-678)CGA>CAA	p.R226Q		NM_000367	NP_000358	P51580	TPMT_HUMAN	thiopurine S-methyltransferase	226					xenobiotic metabolic process	cytosol	thiopurine S-methyltransferase activity				0	Ovarian(93;0.016)|Breast(50;0.0245)	all_hematologic(90;0.146)	all cancers(50;0.06)|Epithelial(50;0.0654)		Mercaptopurine(DB01033)	Colon(190;1381 2791 16728 32493)								0.083333	0.696636	7.048547	3	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18130960	18130960	16953	6	C	T	T	T	403	31	TPMT	1	1
COL11A2	1302	broad.mit.edu	37	6	33139548	33139548	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:33139548G>A	uc003ocx.1	-	c.3092C>T	c.(3091-3093)CCG>CTG	p.P1031L	COL11A2_uc010jul.1_Intron|COL11A2_uc003ocy.1_Missense_Mutation_p.P945L|COL11A2_uc003ocz.1_Missense_Mutation_p.P924L	NM_080680	NP_542411	P13942	COBA2_HUMAN	collagen, type XI, alpha 2 isoform 1	1031	Triple-helical region.			PP -> RQ (in Ref. 1; AAC50213/AAC50214/ AAC50215 and 6; AAA52034).	cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging			ovary(3)|skin(1)	4						Melanoma(1;90 116 3946 5341 17093)								0.375	17.046641	17.265857	6	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33139548	33139548	3806	6	G	A	A	A	507	39	COL11A2	1	1
FILIP1	27145	broad.mit.edu	37	6	76022197	76022197	+	Silent	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:76022197G>A	uc010kbe.2	-	c.3360C>T	c.(3358-3360)TCC>TCT	p.S1120S	FILIP1_uc003phy.1_Silent_p.S1117S|FILIP1_uc003phz.2_Silent_p.S1018S|FILIP1_uc003pia.2_Silent_p.S1117S|FILIP1_uc003pib.1_Silent_p.S869S	NM_015687	NP_056502	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	1117											0														0.058824	-10.252784	20.93604	9	144	KEEP	---	---	---	---	capture		Silent	SNP	76022197	76022197	6132	6	G	A	A	A	444	35	FILIP1	2	2
FILIP1	27145	broad.mit.edu	37	6	76022205	76022205	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:76022205G>C	uc010kbe.2	-	c.3352C>G	c.(3352-3354)CAC>GAC	p.H1118D	FILIP1_uc003phy.1_Missense_Mutation_p.H1115D|FILIP1_uc003phz.2_Missense_Mutation_p.H1016D|FILIP1_uc003pia.2_Missense_Mutation_p.H1115D|FILIP1_uc003pib.1_Missense_Mutation_p.H867D	NM_015687	NP_056502	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	1115											0														0.059603	-7.549478	23.085743	9	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76022205	76022205	6132	6	G	C	C	C	585	45	FILIP1	3	3
CYCS	54205	broad.mit.edu	37	7	25163649	25163649	+	Silent	SNP	C	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:25163649C>T	uc003sxl.2	-	c.90G>A	c.(88-90)GGG>GGA	p.G30G		NM_018947	NP_061820	P99999	CYC_HUMAN	cytochrome c	30					activation of caspase activity by cytochrome c|DNA fragmentation involved in apoptotic nuclear change|induction of apoptosis by intracellular signals|respiratory electron transport chain|transport	cytosol|mitochondrial inner membrane|mitochondrial intermembrane space|mitochondrial matrix|nucleus|protein phosphatase type 2A complex|respiratory chain	electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity|heme binding|protein binding			ovary(1)|lung(1)	2					Melatonin(DB01065)|Minocycline(DB01017)					46				0.081081	0.304952	6.912371	3	34	KEEP	---	---	---	---	capture		Silent	SNP	25163649	25163649	4301	7	C	T	T	T	327	26	CYCS	2	2
OGDH	4967	broad.mit.edu	37	7	44747321	44747321	+	Silent	SNP	C	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:44747321C>T	uc003tlp.2	+	c.2970C>T	c.(2968-2970)CGC>CGT	p.R990R	OGDH_uc003tln.2_Silent_p.R979R|OGDH_uc011kbx.1_Silent_p.R975R|OGDH_uc011kby.1_Silent_p.R829R|OGDH_uc011kbz.1_Silent_p.R774R	NM_002541	NP_002532	Q02218	ODO1_HUMAN	oxoglutarate dehydrogenase isoform 1 precursor	979					glycolysis|lysine catabolic process|tricarboxylic acid cycle	mitochondrial matrix|mitochondrial membrane	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			ovary(1)	1					NADH(DB00157)									0.125	7.884685	14.4214	6	42	KEEP	---	---	---	---	capture		Silent	SNP	44747321	44747321	11244	7	C	T	T	T	340	27	OGDH	1	1
ABCA13	154664	broad.mit.edu	37	7	48450174	48450174	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:48450174G>A	uc003toq.2	+	c.12128G>A	c.(12127-12129)CGC>CAC	p.R4043H	ABCA13_uc010kys.1_Missense_Mutation_p.R1117H|ABCA13_uc010kyt.1_Non-coding_Transcript	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	4043	ABC transporter 1.				transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10														0.122677	39.089525	76.495991	33	236	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48450174	48450174	32	7	G	A	A	A	494	38	ABCA13	1	1
HGF	3082	broad.mit.edu	37	7	81372779	81372779	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:81372779T>G	uc003uhl.2	-	c.755A>C	c.(754-756)GAC>GCC	p.D252A	HGF_uc003uhm.2_Missense_Mutation_p.D247A|HGF_uc003uhn.1_Missense_Mutation_p.D252A|HGF_uc003uho.1_Missense_Mutation_p.D247A	NM_000601	NP_000592	P14210	HGF_HUMAN	hepatocyte growth factor isoform 1	252	Kringle 2.				epithelial to mesenchymal transition|mitosis|platelet activation|platelet degranulation|proteolysis|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling	platelet alpha granule lumen	growth factor activity|serine-type endopeptidase activity			ovary(2)|central_nervous_system(2)	4										800				0.049383	-8.958122	8.495232	4	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	81372779	81372779	7369	7	T	G	G	G	754	58	HGF	4	4
PCLO	27445	broad.mit.edu	37	7	82586125	82586125	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:82586125G>A	uc003uhx.2	-	c.4144C>T	c.(4144-4146)CCA>TCA	p.P1382S	PCLO_uc003uhv.2_Missense_Mutation_p.P1382S	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	1313					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity|zinc ion binding			ovary(7)	7														0.206186	46.247432	54.009497	20	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82586125	82586125	12003	7	G	A	A	A	533	41	PCLO	2	2
HEPACAM2	253012	broad.mit.edu	37	7	92844778	92844778	+	Nonsense_Mutation	SNP	G	C	C			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:92844778G>C	uc011khy.1	-	c.720C>G	c.(718-720)TAC>TAG	p.Y240*	HEPACAM2_uc003uml.2_Nonsense_Mutation_p.Y205*|HEPACAM2_uc010lff.2_Nonsense_Mutation_p.Y205*|HEPACAM2_uc003umm.2_Nonsense_Mutation_p.Y217*	NM_198151	NP_937794	A8MVW5	HECA2_HUMAN	HEPACAM family member 2 isoform 2	217	Ig-like C2-type 1.|Extracellular (Potential).					integral to membrane				ovary(3)|breast(1)|kidney(1)	5														0.067568	-2.584723	11.74367	5	69	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	92844778	92844778	7336	7	G	C	C	C	620	48	HEPACAM2	5	3
PKHD1L1	93035	broad.mit.edu	37	8	110441625	110441625	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:110441625G>C	uc003yne.2	+	c.3057G>C	c.(3055-3057)AAG>AAC	p.K1019N		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	1019	Extracellular (Potential).				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)											0.185185	12.258257	14.767387	5	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110441625	110441625	12397	8	G	C	C	C	451	35	PKHD1L1	3	3
HSPA5	3309	broad.mit.edu	37	9	128001021	128001021	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:128001021A>T	uc004bpn.2	-	c.1082T>A	c.(1081-1083)CTT>CAT	p.L361H		NM_005347	NP_005338	P11021	GRP78_HUMAN	heat shock 70kDa protein 5	361					anti-apoptosis|cellular response to glucose starvation|ER-associated protein catabolic process|negative regulation of caspase activity|platelet activation|platelet degranulation|regulation of protein folding in endoplasmic reticulum	cell surface|endoplasmic reticulum chaperone complex|endoplasmic reticulum lumen|ER-Golgi intermediate compartment|integral to endoplasmic reticulum membrane|melanosome|midbody|nucleus|perinuclear region of cytoplasm	ATP binding|ATPase activity|calcium ion binding|caspase inhibitor activity|chaperone binding|misfolded protein binding|protein binding, bridging|protein domain specific binding|ubiquitin protein ligase binding|unfolded protein binding			ovary(3)	3					Antihemophilic Factor(DB00025)						Prostate(1;0.17)			0.125	5.783668	10.174587	4	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128001021	128001021	7713	9	A	T	T	T	39	3	HSPA5	3	3
BAT2L1	84726	broad.mit.edu	37	9	134351251	134351251	+	Silent	SNP	C	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:134351251C>T	uc004can.3	+	c.3735C>T	c.(3733-3735)TGC>TGT	p.C1245C	BAT2L1_uc010mzj.1_Silent_p.C828C|BAT2L1_uc004cao.3_Silent_p.C603C	NM_013318	NP_037450	Q5JSZ5	PRC2B_HUMAN	HLA-B associated transcript 2-like	1245							protein binding				0												OREG0019561	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.227273	11.872585	13.368254	5	17	KEEP	---	---	---	---	capture		Silent	SNP	134351251	134351251	1341	9	C	T	T	T	350	27	BAT2L1	1	1
TLN1	7094	broad.mit.edu	37	9	35714249	35714249	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:35714249G>A	uc003zxt.2	-	c.3107C>T	c.(3106-3108)ACG>ATG	p.T1036M		NM_006289	NP_006280	Q9Y490	TLN1_HUMAN	talin 1	1036					axon guidance|cell adhesion|cell-cell junction assembly|cellular component movement|cytoskeletal anchoring at plasma membrane|muscle contraction|platelet activation|platelet degranulation	actin cytoskeleton|cell-cell junction|centrosome|cytosol|extracellular region|focal adhesion|intracellular membrane-bounded organelle|ruffle membrane	actin binding|insulin receptor binding|LIM domain binding|structural constituent of cytoskeleton|vinculin binding			breast(2)|ovary(1)|central_nervous_system(1)	4	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)							587				0.254237	37.602042	40.833299	15	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35714249	35714249	16477	9	G	A	A	A	520	40	TLN1	1	1
AGTR2	186	broad.mit.edu	37	X	115304268	115304268	+	Silent	SNP	G	T	T			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:115304268G>T	uc004eqh.3	+	c.735G>T	c.(733-735)GGG>GGT	p.G245G		NM_000686	NP_000677	P50052	AGTR2_HUMAN	angiotensin II receptor, type 2	245	Cytoplasmic (Potential).				behavior|blood vessel remodeling|brain development|G-protein signaling, coupled to cGMP nucleotide second messenger|intracellular protein kinase cascade|negative regulation of blood vessel endothelial cell migration|negative regulation of cell growth|negative regulation of heart rate|negative regulation of nerve growth factor receptor signaling pathway|nitric oxide mediated signal transduction|positive regulation of apoptosis|positive regulation of nitric oxide biosynthetic process|positive regulation of nitric-oxide synthase activity|positive regulation of phosphoprotein phosphatase activity|positive regulation of vasodilation|regulation of systemic arterial blood pressure by circulatory renin-angiotensin	integral to plasma membrane	angiotensin type II receptor activity|receptor antagonist activity			ovary(2)|lung(1)	3														0.047619	-21.470011	15.067662	8	160	KEEP	---	---	---	---	capture		Silent	SNP	115304268	115304268	405	23	G	T	T	T	522	41	AGTR2	2	2
GLUD2	2747	broad.mit.edu	37	X	120181912	120181912	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:120181912A>G	uc004eto.2	+	c.374A>G	c.(373-375)GAC>GGC	p.D125G		NM_012084	NP_036216	P49448	DHE4_HUMAN	glutamate dehydrogenase 2 precursor	125					glutamate biosynthetic process|glutamate catabolic process|oxidation-reduction process	mitochondrial matrix	ADP binding|glutamate dehydrogenase|glutamate dehydrogenase activity|GTP binding|leucine binding			pancreas(1)	1					L-Glutamic Acid(DB00142)|NADH(DB00157)									0.137931	6.382756	10.057639	4	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	120181912	120181912	6745	23	A	G	G	G	130	10	GLUD2	4	4
DCAF12L1	139170	broad.mit.edu	37	X	125686548	125686548	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:125686548G>A	uc004eul.2	-	c.44C>T	c.(43-45)GCG>GTG	p.A15V		NM_178470	NP_848565	Q5VU92	DC121_HUMAN	DDB1 and CUL4 associated factor 12-like 1	15										skin(3)	3														0.315789	16.242977	16.81655	6	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125686548	125686548	4435	23	G	A	A	A	494	38	DCAF12L1	1	1
DMD	1756	broad.mit.edu	37	X	32509548	32509548	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:32509548A>C	uc004dda.1	-	c.2468T>G	c.(2467-2469)CTT>CGT	p.L823R	DMD_uc004dcz.2_Missense_Mutation_p.L700R|DMD_uc004dcy.1_Missense_Mutation_p.L819R|DMD_uc004ddb.1_Missense_Mutation_p.L815R|DMD_uc010ngo.1_Intron	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform	823	Spectrin 4.				muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)												0.129032	5.179218	9.33355	4	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32509548	32509548	4760	23	A	C	C	C	39	3	DMD	4	4
LLGL2	3993	broad.mit.edu	37	17	73569700	73569701	+	Frame_Shift_Ins	INS	-	G	G	rs112393371		TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:73569700_73569701insG	uc002joh.2	+	c.2864_2865insG	c.(2863-2865)CCGfs	p.P955fs	LLGL2_uc002joi.2_Frame_Shift_Ins_p.P955fs|LLGL2_uc010dgg.1_Frame_Shift_Ins_p.P955fs|LLGL2_uc002joj.2_Frame_Shift_Ins_p.P944fs|LLGL2_uc010wsd.1_Frame_Shift_Ins_p.P582fs	NM_001031803	NP_001026973	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 isoform c	955					cell cycle|cell division|exocytosis|regulation of establishment or maintenance of cell polarity	cytoplasm|intracellular membrane-bounded organelle	PDZ domain binding			ovary(2)	2	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)											0.75			6	2		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	73569700	73569701	9163	17	-	G	G	G	299	23	LLGL2	5	5
BBC3	27113	broad.mit.edu	37	19	47724978	47724978	+	Frame_Shift_Del	DEL	C	-	-			TCGA-17-Z007-01	TCGA-17-Z007-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:47724978_47724978delC	uc010xyl.1	-	c.766_766delG	c.(766-768)GACfs	p.D256fs	BBC3_uc002pgf.3_3'UTR|BBC3_uc010eky.2_3'UTR|BBC3_uc010ekz.2_Frame_Shift_Del_p.D96fs	NM_001127240	NP_001120712	Q9BXH1	BBC3_HUMAN	BCL2 binding component 3 isoform 1	Error:Variant_position_missing_in_Q9BXH1_after_alignment					activation of caspase activity|activation of pro-apoptotic gene products|cellular response to hypoxia|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|negative regulation of growth|positive regulation of protein homooligomerization|positive regulation of release of cytochrome c from mitochondria|positive regulation of thymocyte apoptosis|protein insertion into mitochondrial membrane involved in induction of apoptosis|reduction of endoplasmic reticulum calcium ion concentration|release of cytochrome c from mitochondria|release of sequestered calcium ion into cytosol	cytosol|mitochondrial outer membrane	protein binding|protein binding				0		all_cancers(25;1.13e-05)|all_lung(116;0.000192)|all_epithelial(76;0.000274)|Lung NSC(112;0.000446)|all_neural(266;0.0652)|Ovarian(192;0.15)		all cancers(93;0.000179)|OV - Ovarian serous cystadenocarcinoma(262;0.00029)|Epithelial(262;0.0103)|GBM - Glioblastoma multiforme(486;0.0234)										0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	47724978	47724978	1354	19	C	-	-	-	390	30	BBC3	5	5
