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
PFKP	5214	broad.mit.edu	37	10	3178698	3178698	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:3178698T>C	uc001igp.2	+	c.2282T>C	c.(2281-2283)CTG>CCG	p.L761P	PFKP_uc001igq.2_Missense_Mutation_p.L753P|PFKP_uc009xhr.2_Missense_Mutation_p.L723P|PFKP_uc009xht.2_Missense_Mutation_p.L499P|PFKP_uc009xhu.2_Missense_Mutation_p.L267P	NM_002627	NP_002618	Q01813	K6PP_HUMAN	phosphofructokinase, platelet	761					glycolysis	6-phosphofructokinase complex	6-phosphofructokinase activity|ATP binding|metal ion binding|protein binding			ovary(1)|lung(1)	2				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)										0.333333	38.162402	39.121625	13	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3178698	3178698	12188	10	T	C	C	C	715	55	PFKP	4	4
EXPH5	23086	broad.mit.edu	37	11	108384669	108384669	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:108384669C>T	uc001pkk.2	-	c.1565G>A	c.(1564-1566)GGC>GAC	p.G522D	EXPH5_uc010rvy.1_Missense_Mutation_p.G334D|EXPH5_uc010rvz.1_Missense_Mutation_p.G366D|EXPH5_uc010rwa.1_Missense_Mutation_p.G446D	NM_015065	NP_055880	Q149M6	Q149M6_HUMAN	exophilin 5 isoform a	522					intracellular protein transport		Rab GTPase binding			ovary(2)	2		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)										0.402062	108.206217	109.019212	39	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108384669	108384669	5516	11	C	T	T	T	338	26	EXPH5	2	2
OR4B1	119765	broad.mit.edu	37	11	48238768	48238768	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:48238768G>A	uc010rhs.1	+	c.407G>A	c.(406-408)CGT>CAT	p.R136H		NM_001005470	NP_001005470	Q8NGF8	OR4B1_HUMAN	olfactory receptor, family 4, subfamily B,	136	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2														0.327434	93.631681	96.618463	37	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48238768	48238768	11450	11	G	A	A	A	520	40	OR4B1	1	1
OR4A16	81327	broad.mit.edu	37	11	55110931	55110931	+	Silent	SNP	T	C	C			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55110931T>C	uc010rie.1	+	c.255T>C	c.(253-255)TGT>TGC	p.C85C		NM_001005274	NP_001005274	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A,	85	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(2)|pancreas(1)	3														0.061404	-15.899299	30.243647	14	214	KEEP	---	---	---	---	capture		Silent	SNP	55110931	55110931	11447	11	T	C	C	C	764	59	OR4A16	4	4
PCNXL3	399909	broad.mit.edu	37	11	65403699	65403699	+	Silent	SNP	A	G	G			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:65403699A>G	uc001oey.2	+	c.5514A>G	c.(5512-5514)TCA>TCG	p.S1838S	PCNXL3_uc001oez.2_Silent_p.S725S	NM_032223	NP_115599	Q9H6A9	PCX3_HUMAN	pecanex-like 3	1838	Gly-rich.					integral to membrane					0														0.166667	5.14267	6.406373	2	10	KEEP	---	---	---	---	capture		Silent	SNP	65403699	65403699	12013	11	A	G	G	G	80	7	PCNXL3	4	4
PABPC3	5042	broad.mit.edu	37	13	25671090	25671090	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:25671090A>G	uc001upy.2	+	c.754A>G	c.(754-756)AAT>GAT	p.N252D		NM_030979	NP_112241	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	252	RRM 3.				mRNA metabolic process	cytoplasm	nucleotide binding|poly(A) RNA binding			ovary(3)|skin(1)	4		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)										0.482759	204.510536	204.539531	56	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25671090	25671090	11780	13	A	G	G	G	117	9	PABPC3	4	4
PCDH17	27253	broad.mit.edu	37	13	58208287	58208287	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:58208287C>A	uc001vhq.1	+	c.1607C>A	c.(1606-1608)GCC>GAC	p.A536D	PCDH17_uc010aec.1_Missense_Mutation_p.A536D	NM_001040429	NP_001035519	O14917	PCD17_HUMAN	protocadherin 17 precursor	536	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			ovary(2)|pancreas(2)	4		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		Melanoma(72;952 1291 1619 12849 33676)								0.207547	45.49453	53.89331	22	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58208287	58208287	11932	13	C	A	A	A	338	26	PCDH17	2	2
VIPAR	63894	broad.mit.edu	37	14	77895357	77895357	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:77895357C>T	uc001xtt.1	-	c.1348G>A	c.(1348-1350)GTC>ATC	p.V450I	VIPAR_uc001xtu.1_Missense_Mutation_p.V450I|VIPAR_uc010tvj.1_Missense_Mutation_p.V401I|VIPAR_uc001xtv.1_Missense_Mutation_p.V450I	NM_022067	NP_071350	Q9H9C1	VIPAR_HUMAN	hypothetical protein LOC63894	450					endosome to lysosome transport|intracellular protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	early endosome|late endosome|recycling endosome	protein binding			central_nervous_system(1)	1														0.266055	68.61972	74.014211	29	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77895357	77895357	17735	14	C	T	T	T	247	19	VIPAR	1	1
UNC13C	440279	broad.mit.edu	37	15	54825193	54825193	+	Silent	SNP	A	T	T			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:54825193A>T	uc002ack.2	+	c.5625A>T	c.(5623-5625)ACA>ACT	p.T1875T		NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C	1875					exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)						2691				0.5	15.574211	15.574211	5	5	KEEP	---	---	---	---	capture		Silent	SNP	54825193	54825193	17544	15	A	T	T	T	93	8	UNC13C	3	3
CCPG1	9236	broad.mit.edu	37	15	55652008	55652008	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:55652008C>T	uc010bfk.1	-	c.1963G>A	c.(1963-1965)GAA>AAA	p.E655K	CCPG1_uc002acy.2_Missense_Mutation_p.E655K|CCPG1_uc002acu.1_Missense_Mutation_p.E511K|CCPG1_uc002acw.1_Missense_Mutation_p.E380K|CCPG1_uc002acv.1_Missense_Mutation_p.E655K|CCPG1_uc002acx.2_Intron|CCPG1_uc002acz.1_Missense_Mutation_p.E655K	NM_020739	NP_065790	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1 isoform 2	655	Lumenal (Potential).				cell cycle	integral to membrane				ovary(1)	1				all cancers(107;0.0354)										0.105263	4.304255	13.137113	6	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55652008	55652008	3065	15	C	T	T	T	377	29	CCPG1	2	2
CREBBP	1387	broad.mit.edu	37	16	3779782	3779782	+	Nonsense_Mutation	SNP	G	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:3779782G>A	uc002cvv.2	-	c.5266C>T	c.(5266-5268)CAG>TAG	p.Q1756*	CREBBP_uc002cvw.2_Nonsense_Mutation_p.Q1718*	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a	1756	Interaction with TRERF1.				cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			ovary(6)|skin(2)|pancreas(1)|lung(1)	10		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)						748				0.419355	34.263851	34.440943	13	18	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	3779782	3779782	4000	16	G	A	A	A	611	47	CREBBP	5	2
KIAA0182	23199	broad.mit.edu	37	16	85699584	85699584	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:85699584C>T	uc002fix.2	+	c.2761C>T	c.(2761-2763)CCA>TCA	p.P921S	KIAA0182_uc002fiw.2_Missense_Mutation_p.P817S|KIAA0182_uc002fiy.2_Missense_Mutation_p.P848S|KIAA0182_uc002fiz.2_Missense_Mutation_p.P63S|KIAA0182_uc010cho.2_Missense_Mutation_p.P101S	NM_014615	NP_055430	Q14687	GSE1_HUMAN	genetic suppressor element 1 isoform 1	921							protein binding			large_intestine(3)|ovary(1)|skin(1)	5														0.25	43.621381	47.918499	19	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85699584	85699584	8466	16	C	T	T	T	234	18	KIAA0182	2	2
USP7	7874	broad.mit.edu	37	16	9009171	9009171	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:9009171G>A	uc002czl.2	-	c.1018C>T	c.(1018-1020)CGG>TGG	p.R340W	USP7_uc010uyk.1_Missense_Mutation_p.R241W|USP7_uc010uyj.1_Missense_Mutation_p.R241W|USP7_uc002czk.2_Missense_Mutation_p.R324W|USP7_uc010uyl.1_Non-coding_Transcript	NM_003470	NP_003461	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7	340					interspecies interaction between organisms|multicellular organismal development|protein deubiquitination|regulation of sequence-specific DNA binding transcription factor activity|ubiquitin-dependent protein catabolic process	cytoplasm|PML body	cysteine-type endopeptidase activity|p53 binding|protein C-terminus binding|transcription factor binding|ubiquitin protein ligase binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)	3														0.324324	95.151398	98.197236	36	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9009171	9009171	17652	16	G	A	A	A	480	37	USP7	1	1
C17orf78	284099	broad.mit.edu	37	17	35734872	35734872	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:35734872C>A	uc002hns.2	+	c.114C>A	c.(112-114)GAC>GAA	p.D38E	ACACA_uc002hnn.2_Intron|ACACA_uc002hno.2_Intron|ACACA_uc002hnq.2_Intron|C17orf78_uc010cva.1_Missense_Mutation_p.D38E	NM_173625	NP_775896	Q8N4C9	CQ078_HUMAN	hypothetical protein LOC284099	38						integral to membrane					0		Breast(25;0.00295)|Ovarian(249;0.15)												0.048387	-6.628294	6.817068	3	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35734872	35734872	1941	17	C	A	A	A	246	19	C17orf78	1	1
KRTAP9-2	83899	broad.mit.edu	37	17	39383064	39383064	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:39383064G>A	uc002hwf.2	+	c.158G>A	c.(157-159)CGC>CAC	p.R53H		NM_031961	NP_114167	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9.2	53	6.|17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].					keratin filament	protein binding				0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)											0.176471	28.681779	38.756001	18	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39383064	39383064	8896	17	G	A	A	A	494	38	KRTAP9-2	1	1
ARRB2	409	broad.mit.edu	37	17	4621224	4621224	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:4621224C>T	uc010vsg.1	+	c.590C>T	c.(589-591)CCG>CTG	p.P197L	ARRB2_uc002fyj.2_Missense_Mutation_p.P176L|ARRB2_uc002fyk.2_Missense_Mutation_p.P161L|ARRB2_uc002fyl.2_Missense_Mutation_p.P176L|ARRB2_uc002fym.2_Missense_Mutation_p.P161L|ARRB2_uc002fyn.2_5'UTR|ARRB2_uc010ckq.2_5'UTR|ARRB2_uc002fyo.2_5'UTR	NM_004313	NP_004304	P32121	ARRB2_HUMAN	arrestin, beta 2 isoform 1	176					cell chemotaxis|desensitization of G-protein coupled receptor protein signaling pathway by arrestin|G-protein coupled receptor internalization|negative regulation of natural killer cell mediated cytotoxicity|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein ubiquitination|platelet activation|positive regulation of ERK1 and ERK2 cascade|proteasomal ubiquitin-dependent protein catabolic process|protein transport|protein ubiquitination|transcription from RNA polymerase II promoter|transforming growth factor beta receptor signaling pathway	coated pit|cytoplasmic membrane-bounded vesicle|cytosol|nucleus|plasma membrane	angiotensin receptor binding|ubiquitin protein ligase binding				0														0.52	38.792593	38.802739	13	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4621224	4621224	999	17	C	T	T	T	299	23	ARRB2	1	1
PITPNC1	26207	broad.mit.edu	37	17	65688807	65688807	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:65688807G>A	uc002jgc.2	+	c.802G>A	c.(802-804)GTC>ATC	p.V268I	PITPNC1_uc002jgb.2_3'UTR	NM_012417	NP_036549	Q9UKF7	PITC1_HUMAN	phosphatidylinositol transfer protein,	268					signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding			skin(1)	1	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)											0.323944	115.09324	119.004037	46	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65688807	65688807	12373	17	G	A	A	A	520	40	PITPNC1	1	1
TP53	7157	broad.mit.edu	37	17	7578466	7578466	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7578466G>A	uc002gim.2	-	c.464C>T	c.(463-465)ACC>ATC	p.T155I	TP53_uc002gig.1_Missense_Mutation_p.T155I|TP53_uc002gih.2_Missense_Mutation_p.T155I|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.T23I|TP53_uc010cng.1_Missense_Mutation_p.T23I|TP53_uc002gii.1_Missense_Mutation_p.T23I|TP53_uc010cnh.1_Missense_Mutation_p.T155I|TP53_uc010cni.1_Missense_Mutation_p.T155I|TP53_uc002gij.2_Missense_Mutation_p.T155I|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.T62I|TP53_uc002gio.2_Missense_Mutation_p.T23I|TP53_uc010vug.1_Missense_Mutation_p.T116I	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	155	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		T -> N (in LFS; germline mutation and in sporadic cancers; somatic mutation).|T -> S (in sporadic cancers; somatic mutation).|T -> P (in sporadic cancers; somatic mutation).|T -> A (in sporadic cancers; somatic mutation).|T -> I (in sporadic cancers; somatic mutation).|T -> M (in a sporadic cancer; 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.T155N(19)|p.T155I(10)|p.0?(6)|p.P152fs*14(3)|p.P153fs*22(2)|p.T155fs*23(2)|p.G154fs*14(2)|p.T155_A161delTRVRAMA(1)|p.G154fs*22(1)|p.R156fs*25(1)|p.T155_R156delTR(1)|p.P151_V173del23(1)|p.T155fs*25(1)|p.D148fs*23(1)|p.S149fs*72(1)|p.G154_R156delGTR(1)|p.T155S(1)|p.D148_T155delDSTPPPGT(1)|p.R156_A161del(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.P152fs(RH41-Tumor)|p.T155N(NCIH524-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.077922	-3.283672	10.72779	6	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7578466	7578466	16923	17	G	A	A	A	572	44	TP53	2	2
MFSD6L	162387	broad.mit.edu	37	17	8701497	8701497	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:8701497C>A	uc002glp.1	-	c.942G>T	c.(940-942)ATG>ATT	p.M314I		NM_152599	NP_689812	Q8IWD5	MFS6L_HUMAN	major facilitator superfamily domain containing	314						integral to membrane					0														0.517241	81.653229	81.668727	30	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8701497	8701497	9926	17	C	A	A	A	377	29	MFSD6L	2	2
USP14	9097	broad.mit.edu	37	18	197634	197634	+	Missense_Mutation	SNP	A	C	C			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:197634A>C	uc002kkf.1	+	c.613A>C	c.(613-615)ATA>CTA	p.I205L	USP14_uc002kkg.1_Missense_Mutation_p.I170L|USP14_uc010wyr.1_Missense_Mutation_p.I194L	NM_005151	NP_005142	P54578	UBP14_HUMAN	ubiquitin specific protease 14 isoform a	205					regulation of chemotaxis|regulation of proteasomal protein catabolic process|ubiquitin-dependent protein catabolic process	cell surface|cytoplasmic membrane-bounded vesicle|plasma membrane|proteasome complex	cysteine-type endopeptidase activity|endopeptidase inhibitor activity|proteasome binding|tRNA guanylyltransferase activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(1)	1		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)												0.166667	24.61596	30.932632	10	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	197634	197634	17607	18	A	C	C	C	156	12	USP14	4	4
CYP4F8	11283	broad.mit.edu	37	19	15730354	15730354	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:15730354G>T	uc002nbi.2	+	c.397G>T	c.(397-399)GGG>TGG	p.G133W	CYP4F8_uc010xoi.1_3'UTR|CYP4F8_uc010xoj.1_Intron	NM_007253	NP_009184	P98187	CP4F8_HUMAN	cytochrome P450, family 4, subfamily F,	133					oxidation-reduction process|prostaglandin metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	alkane 1-monooxygenase activity|aromatase activity|electron carrier activity|heme binding|oxygen binding|protein binding			large_intestine(1)	1														0.288136	40.448766	42.825153	17	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15730354	15730354	4356	19	G	T	T	T	559	43	CYP4F8	2	2
NTN5	126147	broad.mit.edu	37	19	49173881	49173881	+	Silent	SNP	C	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:49173881C>A	uc002pkb.2	-	c.363G>T	c.(361-363)GTG>GTT	p.V121V	SEC1_uc010xzv.1_Intron|SEC1_uc002pka.2_Intron|SEC1_uc010xzw.1_Intron|SEC1_uc010ema.2_Intron|NTN5_uc002pkc.2_Silent_p.V121V	NM_145807	NP_665806	Q8WTR8	NET5_HUMAN	netrin 5 precursor	121						extracellular region				large_intestine(1)|pancreas(1)	2														0.428571	7.823044	7.854342	3	4	KEEP	---	---	---	---	capture		Silent	SNP	49173881	49173881	11108	19	C	A	A	A	366	29	NTN5	2	2
ANKRD34A	284615	broad.mit.edu	37	1	145473962	145473962	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:145473962G>T	uc001enq.1	+	c.634G>T	c.(634-636)GAC>TAC	p.D212Y	NBPF10_uc001emp.3_Intron	NM_001039888	NP_001034977	Q69YU3	AN34A_HUMAN	ankyrin repeat domain 34	212											0	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)													0.313131	141.645355	147.818833	62	136	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	145473962	145473962	669	1	G	T	T	T	533	41	ANKRD34A	2	2
INSRR	3645	broad.mit.edu	37	1	156823801	156823801	+	Missense_Mutation	SNP	G	A	A	rs55757706		TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:156823801G>A	uc010pht.1	-	c.380C>T	c.(379-381)GCA>GTA	p.A127V	NTRK1_uc001fqf.1_Intron|NTRK1_uc009wsi.1_Intron|INSRR_uc009wsj.1_Missense_Mutation_p.A127V	NM_014215	NP_055030	P14616	INSRR_HUMAN	insulin receptor-related receptor precursor	127					protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|insulin receptor substrate binding|metal ion binding|phosphatidylinositol 3-kinase binding|transmembrane receptor protein tyrosine kinase activity			lung(7)|ovary(4)|kidney(1)|central_nervous_system(1)|skin(1)	14	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)								p.A127E(NCIH2227-Tumor)	299				0.317073	27.304305	28.557115	13	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	156823801	156823801	8075	1	G	A	A	A	598	46	INSRR	2	2
SPTA1	6708	broad.mit.edu	37	1	158627413	158627413	+	Nonsense_Mutation	SNP	G	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158627413G>A	uc001fst.1	-	c.2659C>T	c.(2659-2661)CGA>TGA	p.R887*		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	887	Spectrin 9.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.255952	101.852251	110.923868	43	125	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	158627413	158627413	15630	1	G	A	A	A	480	37	SPTA1	5	1
RXRG	6258	broad.mit.edu	37	1	165380300	165380300	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:165380300C>A	uc001gda.2	-	c.669G>T	c.(667-669)GAG>GAT	p.E223D		NM_006917	NP_008848	P48443	RXRG_HUMAN	retinoid X receptor, gamma isoform a	223	Hinge.				regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding				0	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tretinoin(DB00755)									0.384615	104.791401	105.998858	40	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	165380300	165380300	14245	1	C	A	A	A	311	24	RXRG	2	2
FMO3	2328	broad.mit.edu	37	1	171083304	171083304	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:171083304A>G	uc001ghi.2	+	c.985A>G	c.(985-987)ACA>GCA	p.T329A	FMO3_uc001ghh.2_Missense_Mutation_p.T329A|FMO3_uc010pmb.1_Missense_Mutation_p.T309A|FMO3_uc010pmc.1_Missense_Mutation_p.T266A	NM_001002294	NP_001002294	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	329					oxidation-reduction process|xenobiotic metabolic process	integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity				0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)													0.33	111.347515	113.90571	33	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	171083304	171083304	6198	1	A	G	G	G	26	2	FMO3	4	4
RALGAPA2	57186	broad.mit.edu	37	20	20582431	20582431	+	Silent	SNP	G	T	T			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:20582431G>T	uc002wrz.2	-	c.2098C>A	c.(2098-2100)CGG>AGG	p.R700R	RALGAPA2_uc010gcx.2_Silent_p.R404R|RALGAPA2_uc010zsg.1_Silent_p.R101R	NM_020343	NP_065076	Q2PPJ7	RGPA2_HUMAN	akt substrate AS250	700					activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1														0.076923	-0.506544	6.640452	3	36	KEEP	---	---	---	---	capture		Silent	SNP	20582431	20582431	13474	20	G	T	T	T	493	38	RALGAPA2	1	1
STK35	140901	broad.mit.edu	37	20	2097560	2097560	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:2097560G>T	uc010gak.2	+	c.1141G>T	c.(1141-1143)GAC>TAC	p.D381Y	STK35_uc010zpu.1_Intron|STK35_uc002wfw.3_Missense_Mutation_p.D248Y	NM_080836	NP_543026	Q8TDR2	STK35_HUMAN	serine/threonine kinase 35	381	Protein kinase.				protein phosphorylation	cytoplasm|nucleolus	ATP binding|protein serine/threonine kinase activity			ovary(1)	1										88				0.41791	78.786453	79.180656	28	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2097560	2097560	15821	20	G	T	T	T	481	37	STK35	1	1
CSE1L	1434	broad.mit.edu	37	20	47682732	47682732	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:47682732G>A	uc002xty.2	+	c.232G>A	c.(232-234)GAA>AAA	p.E78K	CSE1L_uc010zyg.1_Intron|CSE1L_uc010ghx.2_Missense_Mutation_p.E78K	NM_001316	NP_001307	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like protein	78	Importin N-terminal.				apoptosis|cell proliferation|intracellular protein transport	cytoplasm|nucleus	importin-alpha export receptor activity			large_intestine(1)	1			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)											0.371429	64.521335	65.541817	26	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47682732	47682732	4071	20	G	A	A	A	585	45	CSE1L	2	2
SLC2A4RG	56731	broad.mit.edu	37	20	62373320	62373320	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:62373320G>A	uc002ygq.2	+	c.490G>A	c.(490-492)GAC>AAC	p.D164N	SLC2A4RG_uc002ygr.2_Missense_Mutation_p.D59N|SLC2A4RG_uc011abj.1_Missense_Mutation_p.D59N|SLC2A4RG_uc002ygs.2_Intron|SLC2A4RG_uc002ygt.2_5'UTR	NM_020062	NP_064446	Q9NR83	S2A4R_HUMAN	SLC2A4 regulator	164					regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)													0.225	16.451212	19.234588	9	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62373320	62373320	15044	20	G	A	A	A	585	45	SLC2A4RG	2	2
GAL3ST1	9514	broad.mit.edu	37	22	30951309	30951309	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:30951309G>C	uc003aig.1	-	c.903C>G	c.(901-903)AAC>AAG	p.N301K	GAL3ST1_uc003aih.1_Missense_Mutation_p.N301K|GAL3ST1_uc003aii.1_Missense_Mutation_p.N301K|GAL3ST1_uc010gvz.1_Missense_Mutation_p.N301K	NM_004861	NP_004852	Q99999	G3ST1_HUMAN	galactose-3-O-sulfotransferase 1	301	Lumenal (Potential).				protein N-linked glycosylation	Golgi membrane|integral to plasma membrane|membrane fraction	galactosylceramide sulfotransferase activity				0														0.409091	29.970799	30.129717	9	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30951309	30951309	6461	22	G	C	C	C	620	48	GAL3ST1	3	3
POLDIP3	84271	broad.mit.edu	37	22	42988085	42988085	+	Silent	SNP	A	C	C			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:42988085A>C	uc011apq.1	-	c.948T>G	c.(946-948)CTT>CTG	p.L316L	POLDIP3_uc011app.1_Silent_p.L220L|POLDIP3_uc003bcu.2_Silent_p.L299L|POLDIP3_uc003bcv.2_Silent_p.L270L|POLDIP3_uc010gza.2_Non-coding_Transcript|POLDIP3_uc011apr.1_Non-coding_Transcript|POLDIP3_uc010gzb.1_Intron	NM_032311	NP_115687	Q9BY77	PDIP3_HUMAN	DNA polymerase delta interacting protein 3	299	RRM.				positive regulation of translation	cytoplasm|nuclear speck	nucleotide binding|protein binding|RNA binding				0						Ovarian(52;967 1128 5875 19997 42537)								0.232143	119.548859	130.578979	39	129	KEEP	---	---	---	---	capture		Silent	SNP	42988085	42988085	12623	22	A	C	C	C	2	1	POLDIP3	4	4
IL1RL2	8808	broad.mit.edu	37	2	102851496	102851496	+	Silent	SNP	C	T	T	rs35960329	by1000genomes	TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:102851496C>T	uc002tbs.2	+	c.1437C>T	c.(1435-1437)GAC>GAT	p.D479D	IL1RL2_uc002tbt.2_Silent_p.D361D	NM_003854	NP_003845	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2 precursor	479	TIR.|Cytoplasmic (Potential).				cellular defense response|innate immune response	integral to plasma membrane	interleukin-1, Type I, activating receptor activity			ovary(2)	2														0.341317	146.411322	150.133444	57	110	KEEP	---	---	---	---	capture		Silent	SNP	102851496	102851496	7965	2	C	T	T	T	246	19	IL1RL2	1	1
ATP6V1C2	245973	broad.mit.edu	37	2	10914974	10914974	+	Silent	SNP	T	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:10914974T>A	uc002ras.2	+	c.699T>A	c.(697-699)ATT>ATA	p.I233I	ATP6V1C2_uc002rat.2_Silent_p.I233I	NM_001039362	NP_001034451	Q8NEY4	VATC2_HUMAN	vacuolar H+ ATPase C2 isoform a	233					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|proton-transporting V-type ATPase, V1 domain				ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.15)|OV - Ovarian serous cystadenocarcinoma(76;0.152)		NSCLC(188;1042 2136 10807 16813 47705)								0.107438	27.482985	64.467992	26	216	KEEP	---	---	---	---	capture		Silent	SNP	10914974	10914974	1200	2	T	A	A	A	809	63	ATP6V1C2	3	3
MBD5	55777	broad.mit.edu	37	2	149228015	149228015	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:149228015A>G	uc002twm.3	+	c.2503A>G	c.(2503-2505)ACA>GCA	p.T835A	MBD5_uc010zbs.1_Non-coding_Transcript|MBD5_uc010fns.2_Missense_Mutation_p.T835A|MBD5_uc002twn.1_Missense_Mutation_p.T276A	NM_018328	NP_060798	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	835						chromosome|nucleus	chromatin binding|DNA binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.0569)										0.285714	63.077869	65.95789	20	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	149228015	149228015	9735	2	A	G	G	G	26	2	MBD5	4	4
USP40	55230	broad.mit.edu	37	2	234460051	234460051	+	Silent	SNP	G	T	T			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:234460051G>T	uc010zmr.1	-	c.844C>A	c.(844-846)CGG>AGG	p.R282R	USP40_uc010zmt.1_5'Flank|USP40_uc010zmu.1_Silent_p.R270R	NM_018218	NP_060688	Q9NVE5	UBP40_HUMAN	ubiquitin thioesterase 40	270					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)	1		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)										0.09375	1.599761	6.909295	3	29	KEEP	---	---	---	---	capture		Silent	SNP	234460051	234460051	17636	2	G	T	T	T	506	39	USP40	1	1
CAPN10	11132	broad.mit.edu	37	2	241534077	241534077	+	Silent	SNP	C	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:241534077C>A	uc002vzk.1	+	c.948C>A	c.(946-948)ACC>ACA	p.T316T	CAPN10_uc010zoh.1_Silent_p.T316T|CAPN10_uc002vzl.1_Silent_p.T316T|CAPN10_uc002vzm.1_Intron|CAPN10_uc002vzn.1_Silent_p.T188T|CAPN10_uc002vzo.1_Non-coding_Transcript|CAPN10_uc010fzg.1_Non-coding_Transcript|CAPN10_uc002vzp.1_Non-coding_Transcript|CAPN10_uc002vzq.1_Intron	NM_023083	NP_075571	Q9HC96	CAN10_HUMAN	calpain 10 isoform a	316	Calpain catalytic.				actin cytoskeleton reorganization|cellular response to insulin stimulus|positive regulation of apoptosis|positive regulation of glucose import|positive regulation of insulin secretion|positive regulation of intracellular transport|proteolysis	cytosol|plasma membrane	calcium-dependent cysteine-type endopeptidase activity|cytoskeletal protein binding|SNARE binding			ovary(3)|large_intestine(2)|lung(1)	6		all_epithelial(40;1.72e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|all_neural(83;0.0459)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.13e-31)|all cancers(36;3.24e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.82e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.1e-06)|Lung(119;0.00168)|Colorectal(34;0.00495)|LUSC - Lung squamous cell carcinoma(224;0.00813)|COAD - Colon adenocarcinoma(134;0.032)										0.037313	-21.309441	9.724963	5	129	KEEP	---	---	---	---	capture		Silent	SNP	241534077	241534077	2740	2	C	A	A	A	288	23	CAPN10	1	1
DCTN1	1639	broad.mit.edu	37	2	74597184	74597184	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:74597184G>C	uc002skx.2	-	c.1300C>G	c.(1300-1302)CTG>GTG	p.L434V	DCTN1_uc002skv.2_Missense_Mutation_p.L300V|DCTN1_uc002sku.2_Missense_Mutation_p.L300V|DCTN1_uc002skw.1_Missense_Mutation_p.L410V|DCTN1_uc010ffd.2_Missense_Mutation_p.L414V|DCTN1_uc002sky.2_Missense_Mutation_p.L397V	NM_004082	NP_004073	Q14203	DCTN1_HUMAN	dynactin 1 isoform 1	434	Potential.				cell death|G2/M transition of mitotic cell cycle|mitosis|nervous system development	cytosol|kinetochore|microtubule|spindle pole	motor activity|protein binding			ovary(3)	3														0.277487	166.874753	175.397966	53	138	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74597184	74597184	4477	2	G	C	C	C	425	33	DCTN1	3	3
LRRIQ4	344657	broad.mit.edu	37	3	169540678	169540678	+	Nonsense_Mutation	SNP	T	A	A	rs13062420		TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:169540678T>A	uc003fgb.2	+	c.969T>A	c.(967-969)TGT>TGA	p.C323*		NM_001080460	NP_001073929	A6NIV6	LRIQ4_HUMAN	leucine-rich repeats and IQ motif containing 4	323	LRR 13.										0														0.357143	30.544251	31.046684	10	18	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	169540678	169540678	9407	3	T	A	A	A	764	59	LRRIQ4	5	3
DHX30	22907	broad.mit.edu	37	3	47888987	47888987	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:47888987G>T	uc003cru.2	+	c.2071G>T	c.(2071-2073)GCC>TCC	p.A691S	DHX30_uc003crt.2_Missense_Mutation_p.A652S|MIR1226_hsa-mir-1226|MI0006313_5'Flank	NM_138615	NP_619520	Q7L2E3	DHX30_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 30	691	Helicase C-terminal.					mitochondrial nucleoid	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(2)|skin(2)	4				BRCA - Breast invasive adenocarcinoma(193;0.000696)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)										0.170732	3.565467	7.912949	7	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47888987	47888987	4683	3	G	T	T	T	546	42	DHX30	2	2
IFRD2	7866	broad.mit.edu	37	3	50330118	50330118	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:50330118C>A	uc003czb.2	-	c.187G>T	c.(187-189)GAC>TAC	p.D63Y	IFRD2_uc011bdp.1_5'Flank	NM_006764	NP_006755	Q12894	IFRD2_HUMAN	interferon-related developmental regulator 2	Error:Variant_position_missing_in_Q12894_after_alignment							binding			ovary(1)|lung(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)										0.44086	109.855519	110.139643	41	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50330118	50330118	7855	3	C	A	A	A	378	30	IFRD2	2	2
IL17RE	132014	broad.mit.edu	37	3	9950949	9950949	+	Nonsense_Mutation	SNP	C	T	T			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:9950949C>T	uc003btu.2	+	c.784C>T	c.(784-786)CAG>TAG	p.Q262*	CIDEC_uc003bto.2_Intron|IL17RE_uc003btv.2_Nonsense_Mutation_p.Q262*|IL17RE_uc011atn.1_Intron|IL17RE_uc003btw.2_Nonsense_Mutation_p.Q262*|IL17RE_uc003btx.2_Nonsense_Mutation_p.Q146*|IL17RE_uc010hcq.2_Nonsense_Mutation_p.Q262*|IL17RE_uc003bty.2_Non-coding_Transcript	NM_153483	NP_705616	Q8NFR9	I17RE_HUMAN	interleukin 17 receptor E isoform 1	262	Extracellular (Potential).					cytoplasm|extracellular region|integral to membrane	receptor activity			central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(96;5.34e-64)										0.290323	20.011272	21.269874	9	22	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	9950949	9950949	7944	3	C	T	T	T	273	21	IL17RE	5	2
CCNA2	890	broad.mit.edu	37	4	122741887	122741887	+	Nonsense_Mutation	SNP	T	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:122741887T>A	uc003iec.3	-	c.604A>T	c.(604-606)AAA>TAA	p.K202*		NM_001237	NP_001228	P20248	CCNA2_HUMAN	cyclin A	202					cell division|mitosis|mitotic cell cycle G2/M transition DNA damage checkpoint|Ras protein signal transduction	cytoplasm|nucleoplasm	protein binding			ovary(1)	1										93				0.392405	163.699955	165.305558	62	96	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	122741887	122741887	3037	4	T	A	A	A	806	62	CCNA2	5	3
WWC2	80014	broad.mit.edu	37	4	184182392	184182392	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:184182392C>A	uc010irx.2	+	c.1616C>A	c.(1615-1617)GCC>GAC	p.A539D	WWC2_uc003ivk.3_Missense_Mutation_p.A334D|WWC2_uc003ivl.3_Non-coding_Transcript|WWC2_uc010iry.2_Missense_Mutation_p.A221D|WWC2_uc003ivn.3_Missense_Mutation_p.A103D	NM_024949	NP_079225	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	539										ovary(2)|lung(1)	3		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)										0.238095	10.466964	11.781571	5	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	184182392	184182392	17986	4	C	A	A	A	338	26	WWC2	2	2
GPR125	166647	broad.mit.edu	37	4	22389442	22389442	+	Silent	SNP	G	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:22389442G>A	uc003gqm.1	-	c.3852C>T	c.(3850-3852)AAC>AAT	p.N1284N	GPR125_uc010ieo.1_Silent_p.N1140N|GPR125_uc003gql.1_Silent_p.N411N	NM_145290	NP_660333	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125 precursor	1284	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity				0		Breast(46;0.198)												0.197531	33.248692	40.154826	16	65	KEEP	---	---	---	---	capture		Silent	SNP	22389442	22389442	6913	4	G	A	A	A	464	36	GPR125	2	2
PCDHGA4	56111	broad.mit.edu	37	5	140734993	140734993	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140734993G>A	uc003ljq.1	+	c.226G>A	c.(226-228)GCC>ACC	p.A76T	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljp.1_Missense_Mutation_p.A76T	NM_018917	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4 isoform 1	76	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.237762	66.870551	75.869304	34	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140734993	140734993	11976	5	G	A	A	A	494	38	PCDHGA4	1	1
SH3TC2	79628	broad.mit.edu	37	5	148407707	148407707	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:148407707G>C	uc003lpu.2	-	c.1588C>G	c.(1588-1590)CTC>GTC	p.L530V	SH3TC2_uc003lpp.1_Non-coding_Transcript|SH3TC2_uc010jgw.2_Missense_Mutation_p.L174V|SH3TC2_uc003lps.2_Non-coding_Transcript|SH3TC2_uc003lpt.2_Missense_Mutation_p.L77V|SH3TC2_uc010jgx.2_Missense_Mutation_p.L523V|SH3TC2_uc003lpv.1_Missense_Mutation_p.L77V|SH3TC2_uc011dbz.1_Missense_Mutation_p.L415V	NM_024577	NP_078853	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	530	TPR 1.						binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.254386	158.125597	170.62412	58	170	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	148407707	148407707	14754	5	G	C	C	C	429	33	SH3TC2	3	3
FBXL7	23194	broad.mit.edu	37	5	15936591	15936591	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:15936591C>T	uc003jfn.1	+	c.772C>T	c.(772-774)CGG>TGG	p.R258W		NM_012304	NP_036436	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	258	LRR 4.				ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3														0.691489	206.192372	209.271167	65	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15936591	15936591	5961	5	C	T	T	T	295	23	FBXL7	1	1
FOXI1	2299	broad.mit.edu	37	5	169533097	169533097	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:169533097C>T	uc003mai.3	+	c.136C>T	c.(136-138)CGG>TGG	p.R46W	FOXI1_uc003maj.3_Missense_Mutation_p.R46W	NM_012188	NP_036320	Q12951	FOXI1_HUMAN	forkhead box I1 isoform a	46	Pro-rich.				epidermal cell fate specification|negative regulation of gene-specific transcription from RNA polymerase II promoter|otic placode formation|pattern specification process|positive regulation of gene-specific transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			breast(3)|central_nervous_system(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)											0.0625	-9.020589	10.136284	6	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	169533097	169533097	6254	5	C	T	T	T	347	27	FOXI1	1	1
TLX3	30012	broad.mit.edu	37	5	170736693	170736693	+	Silent	SNP	A	T	T			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:170736693A>T	uc003mbf.2	+	c.324A>T	c.(322-324)CTA>CTT	p.L108L		NM_021025	NP_066305	O43711	TLX3_HUMAN	T-cell leukemia homeobox 3	108					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			central_nervous_system(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			Esophageal Squamous(33;43 807 3116 3348 30094)				30				0.183333	18.596015	24.24205	11	49	KEEP	---	---	---	---	capture		Silent	SNP	170736693	170736693	16492	5	A	T	T	T	171	14	TLX3	3	3
TNPO1	3842	broad.mit.edu	37	5	72196889	72196889	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:72196889G>A	uc003kck.3	+	c.2503G>A	c.(2503-2505)GGC>AGC	p.G835S	TNPO1_uc011csj.1_Missense_Mutation_p.G785S|TNPO1_uc003kch.2_Missense_Mutation_p.G827S|TNPO1_uc003kci.3_Missense_Mutation_p.G827S|TNPO1_uc003kcg.3_Missense_Mutation_p.G827S	NM_002270	NP_002261	Q92973	TNPO1_HUMAN	transportin 1 isoform 1	835					interspecies interaction between organisms|mRNA metabolic process|protein import into nucleus, translocation	cytosol|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			skin(3)|urinary_tract(1)|ovary(1)|kidney(1)|central_nervous_system(1)	7		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)										0.341463	41.135773	42.047257	14	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72196889	72196889	16876	5	G	A	A	A	611	47	TNPO1	2	2
GRM1	2911	broad.mit.edu	37	6	146720225	146720225	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:146720225C>T	uc010khw.1	+	c.2050C>T	c.(2050-2052)CGC>TGC	p.R684C	GRM1_uc010khv.1_Missense_Mutation_p.R684C|GRM1_uc003qll.2_Missense_Mutation_p.R684C|GRM1_uc011edz.1_Missense_Mutation_p.R684C|GRM1_uc011eea.1_Missense_Mutation_p.R684C	NM_000838	NP_000829	Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1 isoform alpha	684	Cytoplasmic (Potential).				synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity	p.R684C(1)		ovary(4)|central_nervous_system(3)|large_intestine(2)	9		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)									0.504808	298.14824	298.152196	105	103	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	146720225	146720225	7075	6	C	T	T	T	247	19	GRM1	1	1
HIST1H3E	8353	broad.mit.edu	37	6	26225700	26225700	+	Silent	SNP	G	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:26225700G>A	uc003nhb.2	+	c.318G>A	c.(316-318)GAG>GAA	p.E106E	HIST1H3E_uc003nhc.3_Silent_p.E106E	NM_021018	NP_066298	P68431	H31_HUMAN	histone cluster 1, H3f	106					blood coagulation|nucleosome assembly|regulation of gene silencing|S phase	nucleoplasm|nucleosome	DNA binding|protein binding				0		all_hematologic(11;0.0223)|Acute lymphoblastic leukemia(11;0.0351)										OREG0017240	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.068376	-6.075015	16.462735	8	109	KEEP	---	---	---	---	capture		Silent	SNP	26225700	26225700	7444	6	G	A	A	A	451	35	HIST1H3E	2	2
CCDC129	223075	broad.mit.edu	37	7	31617968	31617968	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:31617968G>C	uc011kae.1	+	c.1168G>C	c.(1168-1170)GAG>CAG	p.E390Q	CCDC129_uc011kad.1_Missense_Mutation_p.E374Q|CCDC129_uc003tcj.1_Missense_Mutation_p.E364Q|CCDC129_uc003tci.1_Intron|CCDC129_uc003tck.1_Missense_Mutation_p.E272Q	NM_194300	NP_919276	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	364											0														0.25	48.268761	51.905036	16	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31617968	31617968	2884	7	G	C	C	C	533	41	CCDC129	3	3
ASL	435	broad.mit.edu	37	7	65554160	65554160	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:65554160C>T	uc003tuo.2	+	c.916C>T	c.(916-918)CGG>TGG	p.R306W	ASL_uc003tup.2_Missense_Mutation_p.R306W|ASL_uc003tur.2_Missense_Mutation_p.R280W|ASL_uc003tuq.2_Missense_Mutation_p.R306W	NM_000048	NP_000039	P04424	ARLY_HUMAN	argininosuccinate lyase isoform 1	306					arginine biosynthetic process via ornithine|arginine catabolic process|urea cycle	cytosol	argininosuccinate lyase activity			breast(2)	2					L-Arginine(DB00125)									0.2125	34.330961	40.444282	17	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65554160	65554160	1063	7	C	T	T	T	347	27	ASL	1	1
DENND3	22898	broad.mit.edu	37	8	142176386	142176386	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:142176386G>A	uc003yvy.2	+	c.1411G>A	c.(1411-1413)GTC>ATC	p.V471I	DENND3_uc010mep.2_Missense_Mutation_p.V432I|DENND3_uc003yvz.1_Missense_Mutation_p.V155I	NM_014957	NP_055772	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	471										ovary(1)	1	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)											0.322314	202.181221	208.957869	78	164	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	142176386	142176386	4611	8	G	A	A	A	572	44	DENND3	2	2
CDKN2A	1029	broad.mit.edu	37	9	21971209	21971209	+	Splice_Site_SNP	SNP	T	A	A			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:21971209T>A	uc003zpl.2	-	c.317_splice	c.e2-1	p.G106_splice	MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_Splice_Site_SNP|CDKN2A_uc003zpk.2_Splice_Site_SNP_p.V51_splice|CDKN2A_uc010miu.2_Splice_Site_SNP	NM_058195	NP_478102			cyclin-dependent kinase inhibitor 2A isoform 4						cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding	p.0?(425)|p.?(9)|p.V28_V51del(1)		haematopoietic_and_lymphoid_tissue(647)|skin(417)|upper_aerodigestive_tract(405)|central_nervous_system(380)|lung(319)|pancreas(237)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|ovary(76)|soft_tissue(73)|biliary_tract(71)|bone(70)|breast(46)|stomach(44)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|large_intestine(9)|salivary_gland(8)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1)	3636		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)				17		76	TSP Lung(5;3.83e-07)			0.666667	26.202643	26.49762	8	4	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	21971209	21971209	3290	9	T	A	A	A	715	55	CDKN2A	5	3
RBMX	27316	broad.mit.edu	37	X	135958803	135958803	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:135958803A>G	uc004fae.1	-	c.400T>C	c.(400-402)TAT>CAT	p.Y134H	RBMX_uc004fac.1_5'Flank|RBMX_uc011mwf.1_Intron|RBMX_uc004fad.1_Missense_Mutation_p.Y134H|RBMX_uc011mwg.1_Missense_Mutation_p.Y95H|RBMX_uc004faf.1_5'UTR|RBMX_uc010nsf.1_Missense_Mutation_p.Y95H|RBMX_uc004fag.1_Missense_Mutation_p.Y6H	NM_002139	NP_002130	P38159	HNRPG_HUMAN	RNA binding motif protein, X-linked isoform 1	134					nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)													0.078689	9.098094	64.363346	24	281	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135958803	135958803	13613	23	A	G	G	G	208	16	RBMX	4	4
NONO	4841	broad.mit.edu	37	X	70517741	70517741	+	Missense_Mutation	SNP	A	C	C			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:70517741A>C	uc004dzo.2	+	c.1084A>C	c.(1084-1086)ATG>CTG	p.M362L	BCYRN1_uc011mpt.1_Intron|NONO_uc004dzn.2_Missense_Mutation_p.M362L|NONO_uc004dzp.2_Missense_Mutation_p.M362L|NONO_uc011mpv.1_Missense_Mutation_p.M273L|NONO_uc004dzq.2_Missense_Mutation_p.M231L	NM_001145408	NP_001138880	Q15233	NONO_HUMAN	non-POU domain containing, octamer-binding	362	Potential.|DBHS.				DNA recombination|DNA repair|mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|transcription, DNA-dependent	nuclear matrix|paraspeckles	DNA binding|identical protein binding|nucleotide binding|RNA binding		NONO/TFE3(2)	ovary(2)|kidney(2)	4	Renal(35;0.156)									130				0.086207	5.233358	15.28947	5	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70517741	70517741	10937	23	A	C	C	C	52	4	NONO	4	4
TYSND1	219743	broad.mit.edu	37	10	71905929	71905931	+	In_Frame_Del	DEL	CAG	-	-			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:71905929_71905931delCAG	uc001jqr.2	-	c.412_414delCTG	c.(412-414)CTGdel	p.L138del	TYSND1_uc001jqq.2_Intron|TYSND1_uc001jqs.2_In_Frame_Del_p.L138del|TYSND1_uc001jqt.2_Intron	NM_173555	NP_775826	Q2T9J0	TYSD1_HUMAN	trypsin domain containing 1 isoform a	138					proteolysis	peroxisome	serine-type endopeptidase activity			large_intestine(1)	1														0.33			2	4		---	---	---	---	capture_indel		In_Frame_Del	DEL	71905929	71905931	17374	10	CAG	-	-	-	366	29	TYSND1	5	5
SERPINA4	5267	broad.mit.edu	37	14	95035754	95035754	+	Frame_Shift_Del	DEL	A	-	-			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:95035754_95035754delA	uc010avd.2	+	c.1217_1217delA	c.(1216-1218)GACfs	p.D406fs	SERPINA4_uc001ydk.2_Frame_Shift_Del_p.D369fs|SERPINA4_uc001ydl.2_Frame_Shift_Del_p.D369fs	NM_006215	NP_006206	P29622	KAIN_HUMAN	serine (or cysteine) proteinase inhibitor, clade	369					regulation of proteolysis	extracellular space	serine-type endopeptidase inhibitor activity			ovary(3)	3				COAD - Colon adenocarcinoma(157;0.211)										0.33			16	33		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	95035754	95035754	14579	14	A	-	-	-	130	10	SERPINA4	5	5
POLDIP2	26073	broad.mit.edu	37	17	26684390	26684391	+	Splice_Site_Ins	INS	-	C	C	rs67934205;rs68078752		TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:26684390_26684391insC	uc002haz.2	-	c.79_splice	c.e3+0	p.P27_splice	POLDIP2_uc010wag.1_Non-coding_Transcript|TMEM199_uc002hba.2_5'Flank|SARM1_uc010wah.1_5'Flank	NM_015584	NP_056399			DNA polymerase delta interacting protein 2							mitochondrial nucleoid|nucleus					0	all_lung(13;0.000354)|Lung NSC(42;0.00115)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)										0.33			3	6		---	---	---	---	capture_indel		Splice_Site_Ins	INS	26684390	26684391	12622	17	-	C	C	C	542	42	POLDIP2	5	5
FOXD2	2306	broad.mit.edu	37	1	47905079	47905090	+	In_Frame_Del	DEL	GGCAGCACCCCC	-	-			TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:47905079_47905090delGGCAGCACCCCC	uc001crm.2	+	c.1272_1283delGGCAGCACCCCC	c.(1270-1284)GGGGCAGCACCCCCG>GGG	p.AAPP425del		NM_004474	NP_004465	O60548	FOXD2_HUMAN	forkhead box D2	425_428	Gly-rich.|Ala-rich.				axon extension involved in axon guidance|cartilage development|dichotomous subdivision of terminal units involved in ureteric bud branching|embryo development|enteric nervous system development|iridophore differentiation|lateral line nerve glial cell development|melanocyte differentiation|negative regulation of gene-specific transcription from RNA polymerase II promoter|neural crest cell migration|pattern specification process|peripheral nervous system development|positive regulation of BMP signaling pathway|positive regulation of kidney development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|sympathetic nervous system development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0				READ - Rectum adenocarcinoma(2;0.0908)										0.33			2	4		---	---	---	---	capture_indel		In_Frame_Del	DEL	47905079	47905090	6239	1	GGCAGCACCCCC	-	-	-	548	43	FOXD2	5	5
KIF13A	63971	broad.mit.edu	37	6	17764530	17764531	+	Frame_Shift_Del	DEL	CT	-	-	rs9371018	byFrequency;by1000genomes	TCGA-05-4426-01	TCGA-05-4426-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:17764530_17764531delCT	uc003ncg.3	-	c.5228_5229delAG	c.(5227-5229)GAGfs	p.E1743fs	KIF13A_uc003ncf.2_Frame_Shift_Del_p.E1695fs|KIF13A_uc003nch.3_Frame_Shift_Del_p.E1708fs|KIF13A_uc003nci.3_Frame_Shift_Del_p.E1695fs|KIF13A_uc003nce.1_Frame_Shift_Del_p.E294fs	NM_022113	NP_071396	Q9H1H9	KI13A_HUMAN	kinesin family member 13A isoform a	1743					cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)											0.32			21	44		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	17764530	17764531	8585	6	CT	-	-	-	311	24	KIF13A	5	5
