Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	i_ACHILLES_Top_Genes	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	t_alt_count	t_ref_count	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	i_t_ALT_F1R2	i_t_ALT_F2R1	i_t_REF_F1R2	i_t_REF_F2R1	i_t_Foxog	dataset	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	newbase	is_coding	is_flank	is_indel	is_ins	is_del	is_missense	is_nonsense	is_splice	is_silent	context_orig	context65	categ	categ_ignoring_null_categ	gene_idx	pat_idx
VPS13D	55187	broad.mit.edu	37	1	12418559	12418559	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr1:12418559C>T	uc001atv.2	+	50	10184	c.10043C>T	c.(10042-10044)CCG>CTG	p.P3348L	VPS13D_uc001atw.2_Missense_Mutation_p.P3323L|VPS13D_uc001atx.2_Missense_Mutation_p.P2535L	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1	3347					protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		GAAGGCATGCCGGGCTGGTGT	0.512																0.151079	37.927292	54.103281	21	118	KEEP	---	---	---	---	11	13	72	64	-1	capture	Missense_Mutation	SNP	12418559	12418559	VPS13D	1	C	T	T	T	1	0	0	0	0	1	0	0	0	299	23	1	1	17074	3
RPL11	6135	broad.mit.edu	37	1	24018320	24018320	+	Splice_Site	SNP	G	C	C			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr1:24018320G>C	uc001bhk.2	+	1	26	c.6_splice	c.e1+1	p.A2_splice	RPL11_uc001bhl.2_Splice_Site_p.A2_splice|RPL11_uc001bhm.2_5'Flank|RPL11_uc001bhn.1_5'Flank	NM_000975	NP_000966	P62913	RL11_HUMAN	ribosomal protein L11						endocrine pancreas development|protein localization to nucleus|protein targeting|ribosomal large subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleolus	protein binding|rRNA binding|structural constituent of ribosome			central_nervous_system(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.13e-24)|Colorectal(126;5.06e-08)|COAD - Colon adenocarcinoma(152;2.92e-06)|GBM - Glioblastoma multiforme(114;4.4e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|KIRC - Kidney renal clear cell carcinoma(1967;0.00322)|STAD - Stomach adenocarcinoma(196;0.0124)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0837)|LUSC - Lung squamous cell carcinoma(448;0.185)		CATCATGGCGGTGAGTAGCTG	0.607														OREG0013231	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.029851	-22.806811	9.700205	4	130	KEEP	---	---	---	---	2	4	78	74	-1	capture	Splice_Site	SNP	24018320	24018320	RPL11	1	G	C	C	C	1	0	0	0	0	0	0	1	0	572	44	5	4	13449	3
LEPR	3953	broad.mit.edu	37	1	66083830	66083830	+	Splice_Site	SNP	G	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr1:66083830G>T	uc001dci.2	+	16	2597	c.2395_splice	c.e16+1	p.D799_splice	LEPR_uc001dcg.2_Splice_Site_p.D799_splice|LEPR_uc001dch.2_Splice_Site_p.D799_splice|LEPR_uc009waq.2_Intron|LEPR_uc001dcj.2_Splice_Site_p.D799_splice|LEPR_uc001dck.2_Splice_Site_p.D799_splice	NM_002303	NP_002294	P48357	LEPR_HUMAN	leptin receptor isoform 1						energy reserve metabolic process|multicellular organismal development	extracellular region|integral to membrane|plasma membrane	cytokine receptor activity			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		TATATCCATGGTAAGTTTACT	0.259																0.04878	-12.65972	13.955078	6	117	KEEP	---	---	---	---	2	4	65	58	0.333333333333	capture	Splice_Site	SNP	66083830	66083830	LEPR	1	G	T	T	T	1	0	0	0	0	0	0	1	0	572	44	5	4	8648	3
RPL5	6125	broad.mit.edu	37	1	93299218	93299218	+	Splice_Site	SNP	G	C	C			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr1:93299218G>C	uc001doz.2	+	3	267	c.189_splice	c.e3+1	p.Q63_splice	FAM69A_uc001dpc.2_Intron|RPL5_uc001dpa.2_Splice_Site|RPL5_uc001dpb.2_Splice_Site_p.Q13_splice|RPL5_uc001dpd.2_5'Flank	NM_000969	NP_000960	P46777	RL5_HUMAN	ribosomal protein L5						endocrine pancreas development|ribosomal large subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleolus	5S rRNA binding|protein binding|structural constituent of ribosome				0		all_lung(203;0.00265)|Lung NSC(277;0.0056)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000305)|all cancers(265;0.000343)|Epithelial(280;0.0927)		CATTTGTCAGGTAAGTTGTAT	0.393																0.038462	-11.143564	6.811402	3	75	KEEP	---	---	---	---	1	2	48	33	-1	capture	Splice_Site	SNP	93299218	93299218	RPL5	1	G	C	C	C	1	0	0	0	0	0	0	1	0	572	44	5	4	13489	3
CD101	9398	broad.mit.edu	37	1	117552817	117552817	+	Missense_Mutation	SNP	A	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr1:117552817A>T	uc010oxb.1	+	2	447	c.389A>T	c.(388-390)TAC>TTC	p.Y130F	CD101_uc009whd.2_Missense_Mutation_p.Y130F|CD101_uc010oxc.1_Missense_Mutation_p.Y130F|CD101_uc010oxd.1_Missense_Mutation_p.Y130F	NM_004258	NP_004249	Q93033	IGSF2_HUMAN	immunoglobulin superfamily, member 2 precursor	130	Extracellular (Potential).|Ig-like C2-type 1.				cell surface receptor linked signaling pathway	integral to membrane|plasma membrane	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4						GATGAGAAATACTATGGAAGT	0.463																0.234568	47.088876	52.306088	19	62	KEEP	---	---	---	---	12	11	38	31	-1	capture	Missense_Mutation	SNP	117552817	117552817	CD101	1	A	T	T	T	1	0	0	0	0	1	0	0	0	182	14	4	4	2933	3
NBPF9	400818	broad.mit.edu	37	1	144816536	144816536	+	Silent	SNP	T	G	G			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr1:144816536T>G	uc009wig.1	+	13	1519	c.1443T>G	c.(1441-1443)ACT>ACG	p.T481T	NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Silent_p.T481T|NBPF9_uc010oxr.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc001eli.3_RNA|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF9_uc009wii.1_Silent_p.T210T|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|NBPF9_uc001elp.2_Silent_p.T141T	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818	481	NBPF 2.					cytoplasm					0						GTGCCATCACTTATTCAAATA	0.463					20											0.101338	40.153437	123.152209	53	470	KEEP	---	---	---	---	51	51	397	451	-1	capture	Silent	SNP	144816536	144816536	NBPF9	1	T	G	G	G	1	0	0	0	0	0	0	0	1	717	56	4	4	10106	3
NBPF10	100132406	broad.mit.edu	37	1	145360624	145360624	+	Silent	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr1:145360624G>A	uc001end.3	+	76	9509	c.9474G>A	c.(9472-9474)TCG>TCA	p.S3158S	NBPF9_uc010oye.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_Intron|NBPF10_uc010oyk.1_Intron|NBPF10_uc010oyl.1_Intron|NBPF10_uc001enc.2_Intron|NBPF10_uc010oyq.1_Intron|NBPF10_uc010oyr.1_Silent_p.S456S	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	3083											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GATGTTATTCGACTCCTTCAG	0.478																0.444444	22.896353	22.944925	8	10	KEEP	---	---	---	---	4	7	3	10	-1	capture	Silent	SNP	145360624	145360624	NBPF10	1	G	A	A	A	1	0	0	0	0	0	0	0	1	470	37	1	1	10100	3
PTPRC	5788	broad.mit.edu	37	1	198721383	198721383	+	Silent	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr1:198721383C>T	uc001gur.1	+	30	3387	c.3207C>T	c.(3205-3207)ATC>ATT	p.I1069I	PTPRC_uc001gus.1_Silent_p.I1021I|PTPRC_uc001gut.1_Silent_p.I908I	NM_002838	NP_002829	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	1069	Tyrosine-protein phosphatase 2.|Cytoplasmic (Potential).				axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway	focal adhesion|integral to plasma membrane|membrane raft	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			breast(4)|skin(3)|ovary(2)|lung(1)|kidney(1)|pancreas(1)	12						TCTAGGAAATCTGTGCTCAGT	0.388					815											0.208955	66.720253	77.232766	28	106	KEEP	---	---	---	---	14	18	54	62	-1	capture	Silent	SNP	198721383	198721383	PTPRC	1	C	T	T	T	1	0	0	0	0	0	0	0	1	408	32	2	2	12692	3
NAV1	89796	broad.mit.edu	37	1	201750337	201750337	+	Silent	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr1:201750337C>T	uc001gwu.2	+	5	1910	c.1563C>T	c.(1561-1563)ATC>ATT	p.I521I	NAV1_uc001gwv.1_Silent_p.I29I|NAV1_uc001gww.1_Silent_p.I130I|NAV1_uc001gwx.2_Silent_p.I130I|NAV1_uc001gwy.1_5'Flank	NM_020443	NP_065176	Q8NEY1	NAV1_HUMAN	neuron navigator 1	521					cell differentiation|nervous system development	cytoplasm|microtubule	nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(3)|ovary(1)	4						AAAAGCCCATCAGCCTGGGCC	0.577																0.0625	-6.396265	9.571081	5	75	KEEP	---	---	---	---	3	2	37	38	-1	capture	Silent	SNP	201750337	201750337	NAV1	1	C	T	T	T	1	0	0	0	0	0	0	0	1	369	29	2	2	10090	3
PCNXL2	80003	broad.mit.edu	37	1	233395011	233395011	+	Silent	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr1:233395011C>T	uc001hvl.2	-	5	832	c.597G>A	c.(595-597)GCG>GCA	p.A199A	PCNXL2_uc009xfu.2_RNA|PCNXL2_uc009xfv.1_RNA	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2	199						integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)				GTGCTTGAGACGCAGGTAAGC	0.448																0.389262	168.518286	170.118125	58	91	KEEP	---	---	---	---	31	28	45	48	-1	capture	Silent	SNP	233395011	233395011	PCNXL2	1	C	T	T	T	1	0	0	0	0	0	0	0	1	236	19	1	1	11495	3
RYR2	6262	broad.mit.edu	37	1	237794836	237794836	+	Missense_Mutation	SNP	T	C	C			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr1:237794836T>C	uc001hyl.1	+	42	6670	c.6550T>C	c.(6550-6552)TCC>CCC	p.S2184P		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	2184	Cytoplasmic (By similarity).|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AGGTGGAGAGTCCAAGGTAAC	0.393																0.2	25.622722	29.807983	10	40	KEEP	---	---	---	---	6	6	19	23	-1	capture	Missense_Mutation	SNP	237794836	237794836	RYR2	1	T	C	C	C	1	0	0	0	0	1	0	0	0	754	58	3	3	13661	3
GPR158	57512	broad.mit.edu	37	10	25886887	25886887	+	Missense_Mutation	SNP	G	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr10:25886887G>T	uc001isj.2	+	11	2392	c.2332G>T	c.(2332-2334)GAC>TAC	p.D778Y	GPR158_uc001isk.2_Missense_Mutation_p.D153Y	NM_020752	NP_065803	Q5T848	GP158_HUMAN	G protein-coupled receptor 158 precursor	778	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)|large_intestine(2)|pancreas(1)|skin(1)	8						GGAGGGCGCCGACCATGGCAC	0.567																0.074236	-6.778411	35.83402	17	212	KEEP	---	---	---	---	6	11	81	134	0.352941176471	capture	Missense_Mutation	SNP	25886887	25886887	GPR158	10	G	T	T	T	1	0	0	0	0	1	0	0	0	481	37	4	4	6597	3
GPR158	57512	broad.mit.edu	37	10	25886905	25886905	+	Missense_Mutation	SNP	G	C	C			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr10:25886905G>C	uc001isj.2	+	11	2410	c.2350G>C	c.(2350-2352)GGC>CGC	p.G784R	GPR158_uc001isk.2_Missense_Mutation_p.G159R	NM_020752	NP_065803	Q5T848	GP158_HUMAN	G protein-coupled receptor 158 precursor	784	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)|large_intestine(2)|pancreas(1)|skin(1)	8						CACAGCCAAAGGCACTGCCCT	0.547																0.086777	8.684807	50.526197	21	221	KEEP	---	---	---	---	8	14	96	139	-1	capture	Missense_Mutation	SNP	25886905	25886905	GPR158	10	G	C	C	C	1	0	0	0	0	1	0	0	0	455	35	4	4	6597	3
MYO3A	53904	broad.mit.edu	37	10	26446423	26446423	+	Missense_Mutation	SNP	T	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr10:26446423T>A	uc001isn.2	+	26	3338	c.2978T>A	c.(2977-2979)CTT>CAT	p.L993H	MYO3A_uc009xko.1_Missense_Mutation_p.L993H|MYO3A_uc009xkp.1_RNA|MYO3A_uc009xkq.1_Intron	NM_017433	NP_059129	Q8NEV4	MYO3A_HUMAN	myosin IIIA	993	Myosin head-like.				protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception	cytoplasm|filamentous actin|filopodium|myosin complex	actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity			ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	18						CATCGGATACTTTTTGCTAAC	0.333					781											0.165563	40.577521	56.617842	25	126	KEEP	---	---	---	---	13	15	76	70	-1	capture	Missense_Mutation	SNP	26446423	26446423	MYO3A	10	T	A	A	A	1	0	0	0	0	1	0	0	0	728	56	4	4	9986	3
CXCL12	6387	broad.mit.edu	37	10	44876321	44876321	+	Silent	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr10:44876321G>A	uc001jbf.2	-	2	158	c.69C>T	c.(67-69)CCC>CCT	p.P23P	CXCL12_uc001jbh.2_Silent_p.P23P|CXCL12_uc001jbi.2_Silent_p.P23P	NM_000609	NP_000600	P48061	SDF1_HUMAN	chemokine (C-X-C motif) ligand 12 (stromal	23					blood circulation|cell adhesion|cellular calcium ion homeostasis|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|negative regulation of leukocyte apoptosis|positive regulation of monocyte chemotaxis|regulation of actin polymerization or depolymerization|response to virus	extracellular space	chemokine activity|growth factor activity|signal transducer activity				0					Dexamethasone(DB01234)	TCAGGCTGACGGGCTTCCCTA	0.507				p.P23P(KYSE520-Tumor)	379											0.017391	-81.616576	9.054688	6	339	KEEP	---	---	---	---	3	4	183	177	-1	capture	Silent	SNP	44876321	44876321	CXCL12	10	G	A	A	A	1	0	0	0	0	0	0	0	1	496	39	1	1	4040	3
OR52I2	143502	broad.mit.edu	37	11	4609074	4609074	+	Missense_Mutation	SNP	C	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr11:4609074C>A	uc010qyh.1	+	1	1032	c.1032C>A	c.(1030-1032)GAC>GAA	p.D344E		NM_001005170	NP_001005170	Q8NH67	O52I2_HUMAN	olfactory receptor, family 52, subfamily I,	344	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCCTCTTTGACCATTCCAACC	0.453																0.070352	-9.198219	28.701814	14	185	KEEP	---	---	---	---	6	8	98	105	0.571428571429	capture	Missense_Mutation	SNP	4609074	4609074	OR52I2	11	C	A	A	A	1	0	0	0	0	1	0	0	0	233	18	4	4	11025	3
TEAD1	7003	broad.mit.edu	37	11	12946585	12946585	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr11:12946585G>A	uc001mkj.3	+	11	1620	c.955G>A	c.(955-957)GTA>ATA	p.V319I	TEAD1_uc001mkk.3_Missense_Mutation_p.V238I|TEAD1_uc009ygl.2_Missense_Mutation_p.V155I	NM_021961	NP_068780	P28347	TEAD1_HUMAN	TEA domain family member 1	334	Transcriptional activation (Potential).				hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)		GAAGCAAGTAGTAGAAAAAGT	0.438																0.058252	-7.435847	13.631409	6	97	KEEP	---	---	---	---	5	3	54	49	-1	capture	Missense_Mutation	SNP	12946585	12946585	TEAD1	11	G	A	A	A	1	0	0	0	0	1	0	0	0	468	36	2	2	15623	3
OR5M3	219482	broad.mit.edu	37	11	56237516	56237516	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr11:56237516G>A	uc010rjk.1	-	1	458	c.458C>T	c.(457-459)ACG>ATG	p.T153M		NM_001004742	NP_001004742	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M,	153	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00448)					TGCCAGACTCGTCAGAAAACC	0.413																0.395	230.182388	232.112068	79	121	KEEP	---	---	---	---	54	49	87	72	-1	capture	Missense_Mutation	SNP	56237516	56237516	OR5M3	11	G	A	A	A	1	0	0	0	0	1	0	0	0	520	40	1	1	11079	3
SCYL1	57410	broad.mit.edu	37	11	65303487	65303487	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr11:65303487C>T	uc001oea.1	+	11	1527	c.1450C>T	c.(1450-1452)CGG>TGG	p.R484W	SCYL1_uc009yqk.2_Missense_Mutation_p.R484W|SCYL1_uc001oeb.1_Missense_Mutation_p.R484W|SCYL1_uc001oec.1_Missense_Mutation_p.R484W|SCYL1_uc001oed.1_Missense_Mutation_p.R341W|SCYL1_uc001oee.1_Missense_Mutation_p.R128W	NM_020680	NP_065731	Q96KG9	NTKL_HUMAN	SCY1-like 1 isoform A	484					regulation of transcription, DNA-dependent|retrograde vesicle-mediated transport, Golgi to ER|transcription, DNA-dependent	cis-Golgi network|COPI vesicle coat|ER-Golgi intermediate compartment|microtubule organizing center|nucleus	ATP binding|DNA binding|protein tyrosine kinase activity			skin(1)	1						TGCACCGTCCCGGGTTGCGGG	0.597					387											0.402597	189.989444	191.244507	62	92	KEEP	---	---	---	---	50	33	60	72	-1	capture	Missense_Mutation	SNP	65303487	65303487	SCYL1	11	C	T	T	T	1	0	0	0	0	1	0	0	0	295	23	1	1	13840	3
FAT3	120114	broad.mit.edu	37	11	92568240	92568240	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr11:92568240C>T	uc001pdj.3	+	14	10093	c.10076C>T	c.(10075-10077)TCT>TTT	p.S3359F		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	3359	Extracellular (Potential).|Cadherin 31.				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GTGGGAGACTCTGTCATTTTG	0.468													TCGA Ovarian(4;0.039)			0.08	0.658174	9.65711	4	46	KEEP	---	---	---	---	1	6	31	21	-1	capture	Missense_Mutation	SNP	92568240	92568240	FAT3	11	C	T	T	T	1	0	0	0	0	1	0	0	0	416	32	2	2	5637	3
EXPH5	23086	broad.mit.edu	37	11	108380635	108380635	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr11:108380635G>A	uc001pkk.2	-	6	5710	c.5599C>T	c.(5599-5601)CGC>TGC	p.R1867C	EXPH5_uc010rvy.1_Missense_Mutation_p.R1679C|EXPH5_uc010rvz.1_Missense_Mutation_p.R1711C|EXPH5_uc010rwa.1_Missense_Mutation_p.R1791C	NM_015065	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5 isoform a	1867					intracellular protein transport		Rab GTPase binding			skin(3)|ovary(2)	5		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)		GTCCCGCTGCGATAAGCCCAA	0.428																0.070922	-6.167803	20.606747	10	131	KEEP	---	---	---	---	6	4	64	73	-1	capture	Missense_Mutation	SNP	108380635	108380635	EXPH5	11	G	A	A	A	1	0	0	0	0	1	0	0	0	481	37	1	1	5277	3
DDX6	1656	broad.mit.edu	37	11	118626197	118626197	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr11:118626197C>T	uc001pub.2	-	12	1551	c.1190G>A	c.(1189-1191)GGT>GAT	p.G397D	DDX6_uc001pua.2_Missense_Mutation_p.G97D|DDX6_uc001puc.2_Missense_Mutation_p.G397D	NM_004397	NP_004388	P26196	DDX6_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	397	Helicase C-terminal.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol|RNA-induced silencing complex|stress granule	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding|RNA helicase activity			ovary(1)	1	all_hematologic(175;0.0839)	Renal(330;0.0183)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)|Hepatocellular(160;0.0893)|Breast(348;0.0979)|all_hematologic(192;0.103)		OV - Ovarian serous cystadenocarcinoma(223;3.39e-06)|BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Colorectal(284;0.0377)		TATATCAATACCTCGGGTAAA	0.323					317	T	IGH@	B-NHL								0.312	103.204584	107.125677	39	86	KEEP	---	---	---	---	18	22	42	49	-1	capture	Missense_Mutation	SNP	118626197	118626197	DDX6	11	C	T	T	T	1	0	0	0	0	1	0	0	0	234	18	2	2	4335	3
B4GALNT3	283358	broad.mit.edu	37	12	662979	662979	+	Silent	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr12:662979G>A	uc001qii.1	+	14	1890	c.1890G>A	c.(1888-1890)CCG>CCA	p.P630P	B4GALNT3_uc001qij.1_Silent_p.P533P|B4GALNT3_uc001qik.1_Silent_p.P179P	NM_173593	NP_775864	Q6L9W6	B4GN3_HUMAN	beta	630	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			ovary(1)|skin(1)	2	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			TGTTTGACCCGGTAGTAAACT	0.423																0.345528	249.210995	254.389306	85	161	KEEP	---	---	---	---	46	51	75	108	-1	capture	Silent	SNP	662979	662979	B4GALNT3	12	G	A	A	A	1	0	0	0	0	0	0	0	1	496	39	1	1	1257	3
CLSTN3	9746	broad.mit.edu	37	12	7294683	7294683	+	Silent	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr12:7294683G>A	uc001qsr.2	+	10	1766	c.1488G>A	c.(1486-1488)GAG>GAA	p.E496E	CLSTN3_uc001qss.2_Silent_p.E508E	NM_014718	NP_055533	Q9BQT9	CSTN3_HUMAN	calsyntenin 3 precursor	496	Extracellular (Potential).				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			large_intestine(1)	1						TATCCCCAGAGGAGAAGAACA	0.453														OREG0021650	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.466667	44.04492	44.074096	14	16	KEEP	---	---	---	---	7	9	9	9	-1	capture	Silent	SNP	7294683	7294683	CLSTN3	12	G	A	A	A	1	0	0	0	0	0	0	0	1	451	35	2	2	3528	3
BCL2L14	79370	broad.mit.edu	37	12	12247837	12247837	+	Silent	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr12:12247837G>A	uc001rac.2	+	5	1119	c.918G>A	c.(916-918)TCG>TCA	p.S306S	ETV6_uc001raa.1_Intron|BCL2L14_uc001raf.1_Intron|BCL2L14_uc001rad.2_Silent_p.S306S|BCL2L14_uc001rae.2_3'UTR	NM_138723	NP_620049	Q9BZR8	B2L14_HUMAN	BCL2-like 14 isoform 1	306					apoptosis|regulation of apoptosis	cytosol|endomembrane system|intracellular organelle|membrane	protein binding			skin(1)	1		Prostate(47;0.0872)		BRCA - Breast invasive adenocarcinoma(232;0.154)		AGAACTTCTCGCCATGGATCC	0.448					10											0.036496	-24.226439	7.69008	5	132	KEEP	---	---	---	---	2	3	72	76	-1	capture	Silent	SNP	12247837	12247837	BCL2L14	12	G	A	A	A	1	0	0	0	0	0	0	0	1	483	38	1	1	1361	3
LRP6	4040	broad.mit.edu	37	12	12274335	12274335	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr12:12274335G>A	uc001rah.3	-	23	4709	c.4567C>T	c.(4567-4569)CGG>TGG	p.R1523W	BCL2L14_uc001raf.1_Intron|LRP6_uc010shl.1_Missense_Mutation_p.R1478W	NM_002336	NP_002327	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein	1523	Cytoplasmic (Potential).				cellular response to cholesterol|negative regulation of protein phosphorylation|negative regulation of protein serine/threonine kinase activity|negative regulation of smooth muscle cell apoptosis|neural crest formation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell cycle|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	cell surface|cytoplasmic vesicle|endoplasmic reticulum|integral to membrane|plasma membrane	coreceptor activity|frizzled binding|kinase inhibitor activity|low-density lipoprotein receptor activity|protein homodimerization activity|toxin transporter activity|Wnt-protein binding			lung(4)|skin(4)|ovary(2)|kidney(1)|central_nervous_system(1)	12		Prostate(47;0.0865)				GCAAAGTGCCGGTAGCTATAT	0.458					618											0.038462	-43.544265	22.22009	11	275	KEEP	---	---	---	---	9	5	155	162	-1	capture	Missense_Mutation	SNP	12274335	12274335	LRP6	12	G	A	A	A	1	0	0	0	0	1	0	0	0	506	39	1	1	8878	3
TPTE2	93492	broad.mit.edu	37	13	20041405	20041405	+	Missense_Mutation	SNP	A	C	C			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr13:20041405A>C	uc001umd.2	-	8	683	c.472T>G	c.(472-474)TAC>GAC	p.Y158D	TPTE2_uc009zzk.2_Intron|TPTE2_uc009zzl.2_Intron|TPTE2_uc001ume.2_Intron|TPTE2_uc009zzm.2_Intron|TPTE2_uc010tcm.1_RNA	NM_199254	NP_954863	Q6XPS3	TPTE2_HUMAN	TPTE and PTEN homologous inositol lipid	158	Helical; (Potential).					endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		AAAAAAATGTAAATGACATCA	0.294																0.347826	112.177983	114.055831	32	60	KEEP	---	---	---	---	14	22	29	44	-1	capture	Missense_Mutation	SNP	20041405	20041405	TPTE2	13	A	C	C	C	1	0	0	0	0	1	0	0	0	169	13	4	4	16314	3
PABPC3	5042	broad.mit.edu	37	13	25671552	25671552	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr13:25671552G>A	uc001upy.2	+	1	1277	c.1216G>A	c.(1216-1218)GCT>ACT	p.A406T		NM_030979	NP_112241	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	406					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)		CTTCATGACAGCTGTCCCACA	0.532																0.395918	287.546302	289.860554	97	148	KEEP	---	---	---	---	49	55	66	94	-1	capture	Missense_Mutation	SNP	25671552	25671552	PABPC3	13	G	A	A	A	1	0	0	0	0	1	0	0	0	442	34	2	2	11269	3
C13orf23	80209	broad.mit.edu	37	13	39586362	39586362	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr13:39586362G>A	uc001uwy.2	-	12	3443	c.2570C>T	c.(2569-2571)TCT>TTT	p.S857F	C13orf23_uc001uwz.2_Missense_Mutation_p.S835F	NM_025138	NP_079414	Q86XN7	CM023_HUMAN	hypothetical protein LOC80209 isoform 1	857										ovary(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)	5		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;3.7e-08)|Epithelial(112;4.28e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00114)|BRCA - Breast invasive adenocarcinoma(63;0.00366)|GBM - Glioblastoma multiforme(144;0.0146)		TTGAAGTCCAGATGATAAACT	0.383																0.051136	-38.860437	36.256181	18	334	KEEP	---	---	---	---	7	12	147	206	-1	capture	Missense_Mutation	SNP	39586362	39586362	C13orf23	13	G	A	A	A	1	0	0	0	0	1	0	0	0	429	33	2	2	1707	3
DIS3	22894	broad.mit.edu	37	13	73336102	73336102	+	Missense_Mutation	SNP	T	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr13:73336102T>A	uc001vix.3	-	17	2675	c.2301A>T	c.(2299-2301)TTA>TTT	p.L767F	DIS3_uc001viy.3_Missense_Mutation_p.L737F|DIS3_uc001viz.2_RNA	NM_014953	NP_055768	Q9Y2L1	RRP44_HUMAN	DIS3 mitotic control isoform a	767					CUT catabolic process|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA catabolic process|rRNA processing	cytosol|exosome (RNase complex)|nucleolus|nucleoplasm	3'-5'-exoribonuclease activity|endonuclease activity|guanyl-nucleotide exchange factor activity|protein binding|RNA binding			central_nervous_system(1)	1		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)		TTGGAGACGCTAAGCCATAGT	0.328													Multiple Myeloma(4;0.011)			0.411765	168.176041	169.100531	56	80	KEEP	---	---	---	---	28	36	37	53	-1	capture	Missense_Mutation	SNP	73336102	73336102	DIS3	13	T	A	A	A	1	0	0	0	0	1	0	0	0	686	53	4	4	4493	3
GPR132	29933	broad.mit.edu	37	14	105518226	105518226	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr14:105518226C>T	uc001yqd.2	-	4	1147	c.248G>A	c.(247-249)TGC>TAC	p.C83Y	GPR132_uc001yqc.2_5'UTR|GPR132_uc001yqe.2_Missense_Mutation_p.C74Y	NM_013345	NP_037477	Q9UNW8	GP132_HUMAN	G protein-coupled receptor 132	83	Helical; Name=2; (Potential).				response to stress	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(2)|central_nervous_system(1)	3		all_cancers(154;0.0953)|Melanoma(154;0.155)|all_epithelial(191;0.219)	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.02)|all cancers(159;0.0419)|OV - Ovarian serous cystadenocarcinoma(161;0.0521)		GAGTGCCAGGCAGAGCAGGTA	0.662																0.320261	115.588345	119.998068	49	104	KEEP	---	---	---	---	25	25	51	61	-1	capture	Missense_Mutation	SNP	105518226	105518226	GPR132	14	C	T	T	T	1	0	0	0	0	1	0	0	0	325	25	2	2	6576	3
RYR3	6263	broad.mit.edu	37	15	34047281	34047281	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr15:34047281G>A	uc001zhi.2	+	58	8485	c.8415G>A	c.(8413-8415)ATG>ATA	p.M2805I	RYR3_uc010bar.2_Missense_Mutation_p.M2805I	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	2805	4.|Cytoplasmic (By similarity).|4 X approximate repeats.				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TGAAGGATATGGAGCTGGATG	0.458																0.324324	34.385771	35.399957	12	25	KEEP	---	---	---	---	5	7	9	20	-1	capture	Missense_Mutation	SNP	34047281	34047281	RYR3	15	G	A	A	A	1	0	0	0	0	1	0	0	0	611	47	2	2	13662	3
BUB1B	701	broad.mit.edu	37	15	40512942	40512942	+	Silent	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr15:40512942G>A	uc001zkx.3	+	23	3347	c.3135G>A	c.(3133-3135)GGG>GGA	p.G1045G	PAK6_uc010bbl.2_Intron|PAK6_uc010bbm.2_Intron	NM_001211	NP_001202	O60566	BUB1B_HUMAN	budding uninhibited by benzimidazoles 1 beta	1045	Protein kinase.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell division|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|phosphatidylinositol-mediated signaling|protein localization to kinetochore|spindle organization	anaphase-promoting complex|condensed chromosome outer kinetochore|cytosol|microtubule organizing center|perinuclear region of cytoplasm|spindle midzone	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)|kidney(1)	4		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)		CTAGTCCTGGGGCTTTGCTCT	0.443					298	Mis|N|F|S			rhabdomyosarcoma			Mosaic_Variegated_Aneuploidy_Syndrome				0.361842	167.281498	169.835808	55	97	KEEP	---	---	---	---	32	26	47	57	-1	capture	Silent	SNP	40512942	40512942	BUB1B	15	G	A	A	A	1	0	0	0	0	0	0	0	1	548	43	2	2	1559	3
ADAMTS7	11173	broad.mit.edu	37	15	79059831	79059831	+	Missense_Mutation	SNP	T	G	G			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr15:79059831T>G	uc002bej.3	-	18	2960	c.2749A>C	c.(2749-2751)AGC>CGC	p.S917R	ADAMTS7_uc010und.1_Intron	NM_014272	NP_055087	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1	917	TSP type-1 3.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0						TCCAGGGCGCTCTGCTCATCC	0.701																0.4375	47.247512	47.356107	14	18	KEEP	---	---	---	---	7	8	7	11	-1	capture	Missense_Mutation	SNP	79059831	79059831	ADAMTS7	15	T	G	G	G	1	0	0	0	0	1	0	0	0	702	54	4	4	271	3
C16orf91	283951	broad.mit.edu	37	16	1478504	1478504	+	Silent	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr16:1478504C>T	uc010uvd.1	-	2	147	c.147G>A	c.(145-147)GCG>GCA	p.A49A		NM_001010878	NP_001010878	Q4G0I0	CSMT1_HUMAN	hypothetical protein LOC283951	Error:Variant_position_missing_in_Q4G0I0_after_alignment						integral to membrane					0						CTGCCGCCCGCGCCTTTCAGG	0.677																0.409091	25.971565	26.130129	9	13	KEEP	---	---	---	---	6	6	11	7	-1	capture	Silent	SNP	1478504	1478504	C16orf91	16	C	T	T	T	1	0	0	0	0	0	0	0	1	340	27	1	1	1829	3
ABR	29	broad.mit.edu	37	17	953842	953842	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr17:953842C>T	uc002fsd.2	-	15	1704	c.1594G>A	c.(1594-1596)GGC>AGC	p.G532S	ABR_uc002fse.2_Missense_Mutation_p.G486S|ABR_uc010vqg.1_Missense_Mutation_p.G314S|ABR_uc002fsg.2_Missense_Mutation_p.G495S|ABR_uc002fsh.1_Intron	NM_021962	NP_068781	Q12979	ABR_HUMAN	active breakpoint cluster region-related	532	C2.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		ACAAAATAGCCGAAGGAATCC	0.617	Esophageal Squamous(197;2016 2115 4129 29033 46447)															0.280702	85.458672	90.38245	32	82	KEEP	---	---	---	---	18	18	49	42	-1	capture	Missense_Mutation	SNP	953842	953842	ABR	17	C	T	T	T	1	0	0	0	0	1	0	0	0	299	23	1	1	99	3
AMAC1	146861	broad.mit.edu	37	17	33521251	33521251	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr17:33521251G>A	uc002hjd.2	-	1	162	c.76C>T	c.(76-78)CGC>TGC	p.R26C		NM_152462	NP_689675	Q8N808	AMAC1_HUMAN	acyl-malonyl condensing enzyme 1	26						integral to membrane					0				BRCA - Breast invasive adenocarcinoma(366;0.0917)		TGGTACCAGCGGAGGCTGGGT	0.657																0.41	127.450181	128.158863	41	59	KEEP	---	---	---	---	28	28	41	39	-1	capture	Missense_Mutation	SNP	33521251	33521251	AMAC1	17	G	A	A	A	1	0	0	0	0	1	0	0	0	507	39	1	1	559	3
GSDMA	284110	broad.mit.edu	37	17	38122551	38122551	+	Silent	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr17:38122551C>T	uc002htl.1	+	3	371	c.253C>T	c.(253-255)CTG>TTG	p.L85L	GSDMA_uc002htm.1_Silent_p.L85L	NM_178171	NP_835465	Q96QA5	GSDMA_HUMAN	gasdermin 1	85					apoptosis|induction of apoptosis	perinuclear region of cytoplasm					0						TAAGAATATGCTGGACACCCG	0.463																0.311475	105.101694	108.964915	38	84	KEEP	---	---	---	---	20	26	39	63	-1	capture	Silent	SNP	38122551	38122551	GSDMA	17	C	T	T	T	1	0	0	0	0	0	0	0	1	363	28	2	2	6748	3
KRT15	3866	broad.mit.edu	37	17	39673185	39673185	+	Missense_Mutation	SNP	C	T	T	rs138271368		TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr17:39673185C>T	uc002hwy.2	-	3	804	c.613G>A	c.(613-615)GTT>ATT	p.V205I	KRT15_uc002hwz.2_Missense_Mutation_p.V107I|KRT15_uc002hxa.2_Missense_Mutation_p.V40I|KRT15_uc002hxb.1_Missense_Mutation_p.V40I	NM_002275	NP_002266	P19012	K1C15_HUMAN	keratin 15	205	Rod.|Coil 1B.				epidermis development	intermediate filament	protein binding|structural constituent of cytoskeleton				0		Breast(137;0.000286)				TCAGCCTCAACGCCCTGGCGC	0.612																0.381679	141.316213	142.925408	50	81	KEEP	---	---	---	---	30	34	54	70	-1	capture	Missense_Mutation	SNP	39673185	39673185	KRT15	17	C	T	T	T	1	0	0	0	0	1	0	0	0	247	19	1	1	8372	3
ARSG	22901	broad.mit.edu	37	17	66391258	66391258	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr17:66391258G>A	uc002jhc.2	+	10	1932	c.1136G>A	c.(1135-1137)AGC>AAC	p.S379N	ARSG_uc002jhb.1_Missense_Mutation_p.S215N	NM_014960	NP_055775	Q96EG1	ARSG_HUMAN	Arylsulfatase G precursor	379					sulfur compound metabolic process	endoplasmic reticulum|extracellular space|lysosome	arylsulfatase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			GCCCAGGCCAGCTTACCTCAA	0.587																0.262295	129.107756	138.468555	48	135	KEEP	---	---	---	---	22	27	78	65	-1	capture	Missense_Mutation	SNP	66391258	66391258	ARSG	17	G	A	A	A	1	0	0	0	0	1	0	0	0	442	34	2	2	985	3
NEDD4L	23327	broad.mit.edu	37	18	56010160	56010160	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr18:56010160G>A	uc002lgy.2	+	16	1674	c.1400G>A	c.(1399-1401)CGT>CAT	p.R467H	NEDD4L_uc002lgz.2_Missense_Mutation_p.R403H|NEDD4L_uc002lgx.2_Missense_Mutation_p.R447H|NEDD4L_uc010xee.1_Missense_Mutation_p.R346H|NEDD4L_uc002lhc.2_Missense_Mutation_p.R459H|NEDD4L_uc002lhd.2_Missense_Mutation_p.R346H|NEDD4L_uc002lhb.2_Missense_Mutation_p.R326H|NEDD4L_uc002lhe.2_Missense_Mutation_p.R439H|NEDD4L_uc002lhf.2_Missense_Mutation_p.R326H|NEDD4L_uc002lhg.2_Missense_Mutation_p.R346H|NEDD4L_uc002lhh.2_Missense_Mutation_p.R242H|NEDD4L_uc010dpm.1_Intron	NM_001144967	NP_001138439	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally	467					cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4						TCACCCGTACGTCGGGCTGTG	0.488																0.050633	-8.762397	8.139293	4	75	KEEP	---	---	---	---	4	0	33	50	-1	capture	Missense_Mutation	SNP	56010160	56010160	NEDD4L	18	G	A	A	A	1	0	0	0	0	1	0	0	0	520	40	1	1	10218	3
HMG20B	10362	broad.mit.edu	37	19	3578077	3578077	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr19:3578077G>A	uc002lya.2	+	9	975	c.907G>A	c.(907-909)GTC>ATC	p.V303I	HMG20B_uc002lyb.2_Missense_Mutation_p.V201I	NM_006339	NP_006330	Q9P0W2	HM20B_HUMAN	high-mobility group 20B	303					blood coagulation|cell cycle|chromatin modification	chromosome|nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0025)|STAD - Stomach adenocarcinoma(1328;0.18)		GAAGCTCATCGTCCGCATCAA	0.701																0.152174	11.941225	17.231071	7	39	KEEP	---	---	---	---	5	5	22	30	-1	capture	Missense_Mutation	SNP	3578077	3578077	HMG20B	19	G	A	A	A	1	0	0	0	0	1	0	0	0	520	40	1	1	7147	3
SAFB	6294	broad.mit.edu	37	19	5668177	5668177	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr19:5668177G>A	uc002mcf.2	+	21	2676	c.2623G>A	c.(2623-2625)GGC>AGC	p.G875S	SAFB_uc002mcg.2_Missense_Mutation_p.G877S|SAFB_uc002mce.3_Missense_Mutation_p.G876S|SAFB_uc010xir.1_Missense_Mutation_p.G874S|SAFB_uc010xis.1_Missense_Mutation_p.G808S|SAFB_uc010xit.1_Missense_Mutation_p.G719S|SAFB_uc010xiu.1_Missense_Mutation_p.G676S	NM_002967	NP_002958	Q15424	SAFB1_HUMAN	scaffold attachment factor B	875	Interaction with SAFB2.|Gly-rich.				chromatin organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	double-stranded DNA binding|nucleotide binding|protein binding|RNA binding			ovary(1)|liver(1)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)		TCCTAGGCGCGGCAGCTTTGC	0.677	Colon(88;338 1345 6184 8214 20897)															0.038217	-24.0555	12.11309	6	151	KEEP	---	---	---	---	4	3	97	91	-1	capture	Missense_Mutation	SNP	5668177	5668177	SAFB	19	G	A	A	A	1	0	0	0	0	1	0	0	0	507	39	1	1	13698	3
ZNF814	730051	broad.mit.edu	37	19	58385546	58385546	+	Missense_Mutation	SNP	G	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr19:58385546G>T	uc002qqo.2	-	3	1484	c.1212C>A	c.(1210-1212)GAC>GAA	p.D404E	ZNF814_uc002qqk.2_Intron|ZNF814_uc010yhl.1_Intron	NM_001144989	NP_001138461	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	404					regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0						AATGTTTTTTGTCAGTGTGAA	0.393																0.114286	4.377584	9.508864	4	31	KEEP	---	---	---	---	2	2	11	20	0.5	capture	Missense_Mutation	SNP	58385546	58385546	ZNF814	19	G	T	T	T	1	0	0	0	0	1	0	0	0	620	48	4	4	18052	3
SPTBN1	6711	broad.mit.edu	37	2	54852086	54852086	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr2:54852086G>A	uc002rxu.2	+	11	1577	c.1328G>A	c.(1327-1329)CGT>CAT	p.R443H	SPTBN1_uc002rxv.1_Missense_Mutation_p.R443H|SPTBN1_uc002rxx.2_Missense_Mutation_p.R430H	NM_003128	NP_003119	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1 isoform 1	443	Spectrin 2.				actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(3)|breast(2)|central_nervous_system(2)|skin(1)	8			Lung(47;0.24)			GAAAACCAGCGTCTGGTGTCT	0.507																0.266667	58.75836	63.185534	24	66	KEEP	---	---	---	---	14	13	32	45	-1	capture	Missense_Mutation	SNP	54852086	54852086	SPTBN1	2	G	A	A	A	1	0	0	0	0	1	0	0	0	520	40	1	1	15011	3
BCL11A	53335	broad.mit.edu	37	2	60688379	60688379	+	Missense_Mutation	SNP	C	G	G			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr2:60688379C>G	uc002sae.1	-	4	1896	c.1668G>C	c.(1666-1668)CAG>CAC	p.Q556H	BCL11A_uc002sab.2_Missense_Mutation_p.Q556H|BCL11A_uc002sac.2_Intron|BCL11A_uc010ypi.1_Missense_Mutation_p.Q225H|BCL11A_uc010ypj.1_Missense_Mutation_p.Q522H|BCL11A_uc002sad.1_Missense_Mutation_p.Q404H|BCL11A_uc002saf.1_Missense_Mutation_p.Q522H	NM_022893	NP_075044	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A isoform 1	556					negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|cytoplasm|nucleus|nucleus	nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding			central_nervous_system(6)|breast(3)|ovary(2)|skin(2)	13			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			CGCTGAAGTGCTGCATGGAGC	0.697					131	T	IGH@	B-CLL								0.101449	7.887746	18.807155	7	62	KEEP	---	---	---	---	2	5	42	34	-1	capture	Missense_Mutation	SNP	60688379	60688379	BCL11A	2	C	G	G	G	1	0	0	0	0	1	0	0	0	363	28	4	4	1352	3
SLC9A4	389015	broad.mit.edu	37	2	103095487	103095487	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr2:103095487G>A	uc002tbz.3	+	2	903	c.446G>A	c.(445-447)CGG>CAG	p.R149Q		NM_001011552	NP_001011552	Q6AI14	SL9A4_HUMAN	solute carrier family 9 (sodium/hydrogen	149	Cytoplasmic (Potential).				regulation of pH	apical plasma membrane|basolateral plasma membrane|integral to membrane	sodium:hydrogen antiporter activity			skin(2)|central_nervous_system(1)	3						ATGCCCACCCGGCCCTTCTTT	0.597																0.344538	117.516504	120.020346	41	78	KEEP	---	---	---	---	22	24	49	43	-1	capture	Missense_Mutation	SNP	103095487	103095487	SLC9A4	2	G	A	A	A	1	0	0	0	0	1	0	0	0	507	39	1	1	14608	3
IL1B	3553	broad.mit.edu	37	2	113588108	113588108	+	Nonsense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr2:113588108G>A	uc002tii.1	-	7	727	c.640C>T	c.(640-642)CGA>TGA	p.R214*	IL1B_uc002tih.1_Nonsense_Mutation_p.R183*	NM_000576	NP_000567	P01584	IL1B_HUMAN	interleukin 1, beta proprotein	214					activation of MAPK activity|anti-apoptosis|apoptosis|cell-cell signaling|cellular response to drug|cellular response to mechanical stimulus|cytokine-mediated signaling pathway|embryo implantation|fever generation|negative regulation of adiponectin secretion|negative regulation of cell proliferation|negative regulation of glucose transport|negative regulation of insulin receptor signaling pathway|negative regulation of lipid catabolic process|negative regulation of MAP kinase activity|positive regulation of angiogenesis|positive regulation of calcidiol 1-monooxygenase activity|positive regulation of cell adhesion molecule production|positive regulation of cell division|positive regulation of fever generation|positive regulation of granulocyte macrophage colony-stimulating factor production|positive regulation of heterotypic cell-cell adhesion|positive regulation of histone acetylation|positive regulation of histone phosphorylation|positive regulation of interferon-gamma production|positive regulation of interleukin-2 biosynthetic process|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of lipid catabolic process|positive regulation of membrane protein ectodomain proteolysis|positive regulation of mitosis|positive regulation of monocyte chemotactic protein-1 production|positive regulation of myosin light chain kinase activity|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric oxide biosynthetic process|positive regulation of prostaglandin secretion|positive regulation of protein export from nucleus|positive regulation of T cell proliferation|positive regulation vascular endothelial growth factor production|regulation of insulin secretion|sequestering of triglyceride|smooth muscle adaptation	cytosol|extracellular space	cytokine activity|growth factor activity|interleukin-1 receptor binding|protein domain specific binding			lung(3)|breast(1)	4					Anakinra(DB00026)|Minocycline(DB01017)|Procaterol(DB01366)	AAGACAAATCGCTTTTCCATC	0.423					108											0.078853	-5.778744	44.786754	22	257	KEEP	---	---	---	---	15	9	135	158	-1	capture	Nonsense_Mutation	SNP	113588108	113588108	IL1B	2	G	A	A	A	1	0	0	0	0	0	1	0	0	493	38	5	1	7574	3
TUBA4A	7277	broad.mit.edu	37	2	220116339	220116339	+	Missense_Mutation	SNP	T	C	C			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr2:220116339T>C	uc002vkt.1	-	3	381	c.323A>G	c.(322-324)TAT>TGT	p.Y108C	TUBA4A_uc010zkz.1_Missense_Mutation_p.Y93C|TUBA4B_uc002vku.2_5'Flank|TUBA4B_uc002vkv.1_5'Flank	NM_006000	NP_005991	P68366	TBA4A_HUMAN	tubulin, alpha 4a	108					'de novo' posttranslational protein folding|G2/M transition of mitotic cell cycle|microtubule-based movement|platelet activation|platelet degranulation|protein polymerization	cytosol|extracellular region|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity			ovary(3)	3		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCCAATGGTATAGTGACCACG	0.532																0.094017	9.8473	29.214922	11	106	KEEP	---	---	---	---	6	5	55	64	-1	capture	Missense_Mutation	SNP	220116339	220116339	TUBA4A	2	T	C	C	C	1	0	0	0	0	1	0	0	0	637	49	3	3	16631	3
DES	1674	broad.mit.edu	37	2	220286104	220286104	+	Missense_Mutation	SNP	T	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr2:220286104T>A	uc002vll.2	+	6	1152	c.1066T>A	c.(1066-1068)TTT>ATT	p.F356I		NM_001927	NP_001918	P17661	DESM_HUMAN	desmin	356	Rod.|Coil 2B.				cytoskeleton organization|muscle filament sliding|regulation of heart contraction	cytosol|Z disc	protein binding|structural constituent of cytoskeleton	p.F356I(1)		central_nervous_system(2)	2		Renal(207;0.0183)		Epithelial(149;5.25e-07)|all cancers(144;0.000103)|Lung(261;0.00533)|LUSC - Lung squamous cell carcinoma(224;0.008)		GGAGGACCGATTTGCCAGTGA	0.587																0.32	61.97741	64.134604	24	51	KEEP	---	---	---	---	19	12	43	25	-1	capture	Missense_Mutation	SNP	220286104	220286104	DES	2	T	A	A	A	1	0	0	0	0	1	0	0	0	676	52	4	4	4407	3
COL4A4	1286	broad.mit.edu	37	2	227886828	227886828	+	Silent	SNP	C	T	T	rs75398993	by1000genomes	TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr2:227886828C>T	uc010zlt.1	-	43	4806	c.4152G>A	c.(4150-4152)GCG>GCA	p.A1384A		NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor	1384	Triple-helical region.				axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|pancreas(1)|breast(1)|skin(1)	11		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		TCATGCCTGGCGCCCCAGGAA	0.567																0.025424	-99.983193	17.71212	12	460	KEEP	---	---	---	---	7	5	255	247	-1	capture	Silent	SNP	227886828	227886828	COL4A4	2	C	T	T	T	1	0	0	0	0	0	0	0	1	340	27	1	1	3658	3
BTBD3	22903	broad.mit.edu	37	20	11899075	11899075	+	Missense_Mutation	SNP	A	G	G			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr20:11899075A>G	uc002wnz.2	+	1	511	c.152A>G	c.(151-153)GAA>GGA	p.E51G	BTBD3_uc002wny.2_5'UTR|BTBD3_uc002woa.2_5'UTR|BTBD3_uc010zrf.1_5'UTR|BTBD3_uc010zrg.1_5'Flank|BTBD3_uc010zrh.1_5'Flank	NM_014962	NP_055777	Q9Y2F9	BTBD3_HUMAN	BTB/POZ domain containing protein 3 isoform a	51										ovary(2)|central_nervous_system(1)	3						GTTTGTTATGAAATAATTACC	0.383																0.391061	462.604298	466.329375	140	218	KEEP	---	---	---	---	51	111	107	142	-1	capture	Missense_Mutation	SNP	11899075	11899075	BTBD3	20	A	G	G	G	1	0	0	0	0	1	0	0	0	117	9	3	3	1532	3
RPRD1B	58490	broad.mit.edu	37	20	36676850	36676850	+	Missense_Mutation	SNP	T	C	C			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr20:36676850T>C	uc002xho.3	+	3	784	c.382T>C	c.(382-384)TCT>CCT	p.S128P		NM_021215	NP_067038	Q9NQG5	RPR1B_HUMAN	Regulation of nuclear pre-mRNA domain containing	128	CID.									pancreas(1)	1						GCTGAAGCTGTCTATGGAGGA	0.453																0.231579	55.3984	61.672431	22	73	KEEP	---	---	---	---	16	8	37	47	-1	capture	Missense_Mutation	SNP	36676850	36676850	RPRD1B	20	T	C	C	C	1	0	0	0	0	1	0	0	0	754	58	3	3	13508	3
DNAJC28	54943	broad.mit.edu	37	21	34860697	34860697	+	Missense_Mutation	SNP	A	G	G			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr21:34860697A>G	uc002yrv.2	-	2	1453	c.1004T>C	c.(1003-1005)GTC>GCC	p.V335A	DNAJC28_uc002yrw.2_Missense_Mutation_p.V335A	NM_017833	NP_060303	Q9NX36	DJC28_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 28	335	Potential.			LIVPILTRQKVHFDAQKEIVRAQKIYETLIKTKEVTDRNPN NLDQGEGEKTPEIKKGFLNWMNLWKFIKIRSF -> CSHPD QAKSPF (in Ref. 2; BAA91185).			heat shock protein binding				0						CTGGGCTCTGACAATTTCTTT	0.343																0.135747	60.603364	89.000846	30	191	KEEP	---	---	---	---	16	17	118	94	-1	capture	Missense_Mutation	SNP	34860697	34860697	DNAJC28	21	A	G	G	G	1	0	0	0	0	1	0	0	0	130	10	3	3	4602	3
SOX10	6663	broad.mit.edu	37	22	38369502	38369502	+	Nonstop_Mutation	SNP	T	G	G			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr22:38369502T>G	uc003aun.1	-	4	1679	c.1401A>C	c.(1399-1401)TAA>TAC	p.*467Y	POLR2F_uc003aum.2_Intron|SOX10_uc003auo.1_Nonstop_Mutation_p.*467Y	NM_006941	NP_008872	P56693	SOX10_HUMAN	SRY (sex determining region Y)-box 10	467						cytoplasm|nucleus	DNA binding|identical protein binding|transcription coactivator activity				0	Melanoma(58;0.045)					AGGGCCCCCTTTAGGGCCGGG	0.692	Melanoma(39;342 1098 6220 32775 40068)|GBM(21;140 497 5227 16059 19275)				67											0.454545	16.873933	16.893685	5	6	KEEP	---	---	---	---	5	1	7	6	-1	capture	Nonstop_Mutation	SNP	38369502	38369502	SOX10	22	T	G	G	G	1	0	0	0	0	0	0	0	0	829	64	5	4	14833	3
CELSR1	9620	broad.mit.edu	37	22	46807508	46807508	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr22:46807508C>T	uc003bhw.1	-	6	4760	c.4760G>A	c.(4759-4761)GGC>GAC	p.G1587D	CELSR1_uc011arc.1_5'Flank	NM_014246	NP_055061	Q9NYQ6	CELR1_HUMAN	cadherin EGF LAG seven-pass G-type receptor 1	1587	Extracellular (Potential).|Laminin G-like 1.				central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			lung(4)|breast(4)|pancreas(2)|skin(1)	11		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		CTTCTTGGAGCCGGTCTGAGT	0.632																0.320388	84.639525	87.591251	33	70	KEEP	---	---	---	---	19	16	35	43	-1	capture	Missense_Mutation	SNP	46807508	46807508	CELSR1	22	C	T	T	T	1	0	0	0	0	1	0	0	0	338	26	2	2	3189	3
PLXNB2	23654	broad.mit.edu	37	22	50719359	50719359	+	Silent	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr22:50719359C>T	uc003bkv.3	-	24	3913	c.3807G>A	c.(3805-3807)GAG>GAA	p.E1269E	PLXNB2_uc003bkt.1_Silent_p.E61E|PLXNB2_uc003bku.1_Silent_p.E254E	NM_012401	NP_036533	O15031	PLXB2_HUMAN	plexin B2 precursor	1269	Cytoplasmic (Potential).				regulation of small GTPase mediated signal transduction	integral to membrane|intracellular	GTPase activator activity|protein binding|receptor activity			ovary(4)|central_nervous_system(1)|skin(1)	6		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GGATGCCGGCCTCGTGCACGT	0.652																0.263158	52.963405	56.820636	20	56	KEEP	---	---	---	---	10	12	29	37	-1	capture	Silent	SNP	50719359	50719359	PLXNB2	22	C	T	T	T	1	0	0	0	0	0	0	0	1	311	24	2	2	12027	3
ZNF385D	79750	broad.mit.edu	37	3	21462765	21462765	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr3:21462765G>A	uc003cce.2	-	8	1537	c.1129C>T	c.(1129-1131)CGG>TGG	p.R377W		NM_024697	NP_078973	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	377						nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|skin(2)|ovary(1)	5						GGAGCTGGCCGCAGGAGTGCC	0.453																0.090909	2.398597	13.534966	6	60	KEEP	---	---	---	---	2	8	35	31	-1	capture	Missense_Mutation	SNP	21462765	21462765	ZNF385D	3	G	A	A	A	1	0	0	0	0	1	0	0	0	493	38	1	1	17758	3
PIK3CA	5290	broad.mit.edu	37	3	178921553	178921553	+	Missense_Mutation	SNP	T	A	A	rs121913284		TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr3:178921553T>A	uc003fjk.2	+	5	1192	c.1035T>A	c.(1033-1035)AAT>AAA	p.N345K		NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha	345					epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity	p.N345K(29)|p.N345I(2)|p.N345S(1)		breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)			CCTACGTGAATGTAAATATTC	0.308	Colon(199;1504 1750 3362 26421 31210 32040)		57		621	Mis		colorectal|gastric|gliobastoma|breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			0.333333	166.703561	170.685081	54	108	KEEP	---	---	---	---	25	35	58	57	-1	capture	Missense_Mutation	SNP	178921553	178921553	PIK3CA	3	T	A	A	A	1	0	0	0	0	1	0	0	0	660	51	4	4	11816	3
EPHA5	2044	broad.mit.edu	37	4	66467624	66467624	+	Missense_Mutation	SNP	T	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr4:66467624T>A	uc003hcy.2	-	3	838	c.645A>T	c.(643-645)CAA>CAT	p.Q215H	EPHA5_uc003hcx.2_Missense_Mutation_p.Q146H|EPHA5_uc003hcz.2_Missense_Mutation_p.Q215H|EPHA5_uc011cah.1_Missense_Mutation_p.Q215H|EPHA5_uc011cai.1_Missense_Mutation_p.Q215H|EPHA5_uc003hda.2_Missense_Mutation_p.Q215H	NM_004439	NP_004430	P54756	EPHA5_HUMAN	ephrin receptor EphA5 isoform a precursor	215	Extracellular (Potential).				cAMP-mediated signaling|neuron development	dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum	ATP binding|transmembrane-ephrin receptor activity			lung(19)|stomach(2)|ovary(2)|central_nervous_system(1)	24						CACCAACATCTTGAAAAGCAA	0.428					537								TSP Lung(17;0.13)			0.05618	-16.805334	20.061713	10	168	KEEP	---	---	---	---	5	5	74	105	-1	capture	Missense_Mutation	SNP	66467624	66467624	EPHA5	4	T	A	A	A	1	0	0	0	0	1	0	0	0	725	56	4	4	5125	3
FGA	2243	broad.mit.edu	37	4	155507575	155507575	+	Missense_Mutation	SNP	A	G	G			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr4:155507575A>G	uc003iod.1	-	5	1064	c.1006T>C	c.(1006-1008)TCT>CCT	p.S336P	FGA_uc003ioe.1_Missense_Mutation_p.S336P|FGA_uc003iof.1_Intron	NM_000508	NP_000499	P02671	FIBA_HUMAN	fibrinogen, alpha polypeptide isoform alpha-E	336	By similarity.				platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen	eukaryotic cell surface binding|protein binding, bridging|receptor binding			ovary(2)|breast(1)	3	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	GAGCTCCCAGAGTTCCAGCTT	0.567	NSCLC(143;340 1922 20892 22370 48145)															0.064407	-16.032553	42.283235	19	276	KEEP	---	---	---	---	13	9	153	148	-1	capture	Missense_Mutation	SNP	155507575	155507575	FGA	4	A	G	G	G	1	0	0	0	0	1	0	0	0	143	11	3	3	5776	3
FBXO8	26269	broad.mit.edu	37	4	175180976	175180976	+	Silent	SNP	C	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr4:175180976C>A	uc003itp.2	-	3	1180	c.330G>T	c.(328-330)GGG>GGT	p.G110G	FBXO8_uc003itq.2_Silent_p.G69G	NM_012180	NP_036312	Q9NRD0	FBX8_HUMAN	F-box only protein 8	110	F-box.				regulation of ARF protein signal transduction|ubiquitin-dependent protein catabolic process	cytoplasm|ubiquitin ligase complex	ARF guanyl-nucleotide exchange factor activity			breast(2)	2		Prostate(90;0.00201)|Melanoma(52;0.012)|Renal(120;0.0183)|all_neural(102;0.0887)|all_hematologic(60;0.107)		all cancers(43;7.29e-18)|Epithelial(43;1.85e-15)|OV - Ovarian serous cystadenocarcinoma(60;5.62e-09)|GBM - Glioblastoma multiforme(59;0.00115)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.1)		ATTTGCACAACCTATAAAATC	0.318																0.211679	68.794974	79.327998	29	108	KEEP	---	---	---	---	14	20	54	72	0.588235294118	capture	Silent	SNP	175180976	175180976	FBXO8	4	C	A	A	A	1	0	0	0	0	0	0	0	1	223	18	4	4	5707	3
WWC2	80014	broad.mit.edu	37	4	184201980	184201980	+	Missense_Mutation	SNP	G	C	C			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr4:184201980G>C	uc010irx.2	+	17	2796	c.2614G>C	c.(2614-2616)GAA>CAA	p.E872Q	WWC2_uc003ivk.3_Missense_Mutation_p.E667Q|WWC2_uc003ivl.3_RNA|WWC2_uc010iry.2_Missense_Mutation_p.E554Q|WWC2_uc003ivn.3_Missense_Mutation_p.E387Q|WWC2_uc010irz.2_Missense_Mutation_p.E189Q|WWC2_uc003ivo.3_5'Flank	NM_024949	NP_079225	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	872	Potential.									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)		GTTAGCTGTGgaacaagaatt	0.318																0.25	9.219425	9.900922	3	9	KEEP	---	---	---	---	2	2	5	4	-1	capture	Missense_Mutation	SNP	184201980	184201980	WWC2	4	G	C	C	C	1	0	0	0	0	1	0	0	0	533	41	4	4	17293	3
GFM2	84340	broad.mit.edu	37	5	74028894	74028894	+	Missense_Mutation	SNP	G	A	A	rs139234343		TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr5:74028894G>A	uc003kdh.1	-	16	1844	c.1540C>T	c.(1540-1542)CGT>TGT	p.R514C	GFM2_uc003kdi.1_Missense_Mutation_p.R467C|GFM2_uc010izj.1_Missense_Mutation_p.R546C|GFM2_uc010izk.1_RNA	NM_032380	NP_115756	Q969S9	RRF2M_HUMAN	mitochondrial elongation factor G2 isoform 1	514					mitochondrial translation|ribosome disassembly	mitochondrion	GTP binding|GTPase activity				0		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		GGATCTTCACGCTGAAGACAT	0.289																0.23913	77.20098	85.780375	33	105	KEEP	---	---	---	---	27	14	56	76	-1	capture	Missense_Mutation	SNP	74028894	74028894	GFM2	5	G	A	A	A	1	0	0	0	0	1	0	0	0	494	38	1	1	6282	3
GFM2	84340	broad.mit.edu	37	5	74041590	74041590	+	Silent	SNP	T	C	C			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr5:74041590T>C	uc003kdh.1	-	10	1066	c.762A>G	c.(760-762)AAA>AAG	p.K254K	GFM2_uc003kdi.1_Silent_p.K254K|GFM2_uc010izj.1_Silent_p.K286K|GFM2_uc010izk.1_RNA|GFM2_uc003kdj.1_Silent_p.K254K|GFM2_uc010izl.1_Silent_p.K212K	NM_032380	NP_115756	Q969S9	RRF2M_HUMAN	mitochondrial elongation factor G2 isoform 1	254					mitochondrial translation|ribosome disassembly	mitochondrion	GTP binding|GTPase activity				0		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		TCTCAAAGTCTTTTCCATCAT	0.358																0.330827	145.857927	149.229498	44	89	KEEP	---	---	---	---	28	24	41	53	-1	capture	Silent	SNP	74041590	74041590	GFM2	5	T	C	C	C	1	0	0	0	0	0	0	0	1	725	56	3	3	6282	3
PCDHGA8	9708	broad.mit.edu	37	5	140774103	140774103	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr5:140774103G>A	uc003lkd.1	+	1	2621	c.1723G>A	c.(1723-1725)GTG>ATG	p.V575M	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkb.3_Missense_Mutation_p.V575M	NM_032088	NP_114477	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8 isoform 1	575	Extracellular (Potential).|Cadherin 6.				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)			TTCCACTGGCGTGGAGCTGGC	0.657																0.261981	199.0014	215.051397	82	231	KEEP	---	---	---	---	36	55	135	145	-1	capture	Missense_Mutation	SNP	140774103	140774103	PCDHGA8	5	G	A	A	A	1	0	0	0	0	1	0	0	0	520	40	1	1	11463	3
ADAMTS2	9509	broad.mit.edu	37	5	178556976	178556976	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr5:178556976G>A	uc003mjw.2	-	16	2414	c.2414C>T	c.(2413-2415)ACG>ATG	p.T805M		NM_014244	NP_055059	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1	805	Spacer.				collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		GGTCTGCAGCGTCTCCCGGCC	0.607					1974											0.412371	111.780229	112.430799	40	57	KEEP	---	---	---	---	22	22	40	36	-1	capture	Missense_Mutation	SNP	178556976	178556976	ADAMTS2	5	G	A	A	A	1	0	0	0	0	1	0	0	0	520	40	1	1	265	3
ADAMTS2	9509	broad.mit.edu	37	5	178585775	178585775	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr5:178585775C>T	uc003mjw.2	-	6	1081	c.1081G>A	c.(1081-1083)GAT>AAT	p.D361N	ADAMTS2_uc011dgm.1_Missense_Mutation_p.D361N	NM_014244	NP_055059	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1	361	Peptidase M12B.				collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		ATGGCGTGATCGTGGTATTCA	0.607					1974											0.254144	115.176356	125.097531	46	135	KEEP	---	---	---	---	30	23	79	79	-1	capture	Missense_Mutation	SNP	178585775	178585775	ADAMTS2	5	C	T	T	T	1	0	0	0	0	1	0	0	0	403	31	1	1	265	3
TREML2	79865	broad.mit.edu	37	6	41162491	41162491	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr6:41162491G>A	uc010jxm.1	-	3	636	c.457C>T	c.(457-459)CCT>TCT	p.P153S		NM_024807	NP_079083	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid	153	Extracellular (Potential).				T cell activation	cell surface|integral to membrane|plasma membrane	protein binding|receptor activity			ovary(1)|central_nervous_system(1)	2	Ovarian(28;0.0418)|Colorectal(47;0.196)					CCTGAGGTAGGGGCTTGGCCA	0.542																0.289855	54.769509	57.501954	20	49	KEEP	---	---	---	---	15	18	32	28	-1	capture	Missense_Mutation	SNP	41162491	41162491	TREML2	6	G	A	A	A	1	0	0	0	0	1	0	0	0	559	43	2	2	16356	3
DEFB110	245913	broad.mit.edu	37	6	49976918	49976918	+	Missense_Mutation	SNP	G	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr6:49976918G>T	uc011dwr.1	-	2	168	c.122C>A	c.(121-123)ACG>AAG	p.T41K		NM_001037728	NP_001032817	Q30KQ9	DB110_HUMAN	beta-defensin 110 isoform b	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					defense response to bacterium	extracellular region				ovary(1)	1	Lung NSC(77;0.042)					ATCACAAAACGTTTTACATAT	0.333																0.083916	5.189518	30.330367	12	131	KEEP	---	---	---	---	12	5	89	67	0.705882352941	capture	Missense_Mutation	SNP	49976918	49976918	DEFB110	6	G	T	T	T	1	0	0	0	0	1	0	0	0	520	40	4	4	4358	3
FAM83B	222584	broad.mit.edu	37	6	54791195	54791195	+	Silent	SNP	T	C	C			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr6:54791195T>C	uc003pck.2	+	3	587	c.471T>C	c.(469-471)TTT>TTC	p.F157F		NM_001010872	NP_001010872	Q5T0W9	FA83B_HUMAN	hypothetical protein LOC222584	157										ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)					TGGATATATTTACAGATGTGG	0.299																0.078431	5.181624	32.961506	12	141	KEEP	---	---	---	---	8	6	89	69	-1	capture	Silent	SNP	54791195	54791195	FAM83B	6	T	C	C	C	1	0	0	0	0	0	0	0	1	790	61	3	3	5580	3
LAMA2	3908	broad.mit.edu	37	6	129371087	129371087	+	Missense_Mutation	SNP	T	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr6:129371087T>A	uc003qbn.2	+	2	242	c.137T>A	c.(136-138)CTT>CAT	p.L46H	LAMA2_uc003qbo.2_Missense_Mutation_p.L46H	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	46	Laminin N-terminal.				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GTCCTGAATCTTGCTTCTAAT	0.403																0.340136	141.200988	144.523757	50	97	KEEP	---	---	---	---	30	26	65	45	-1	capture	Missense_Mutation	SNP	129371087	129371087	LAMA2	6	T	A	A	A	1	0	0	0	0	1	0	0	0	728	56	4	4	8526	3
SASH1	23328	broad.mit.edu	37	6	148865365	148865365	+	Missense_Mutation	SNP	G	A	A	rs145411864		TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr6:148865365G>A	uc003qme.1	+	18	3234	c.2759G>A	c.(2758-2760)CGC>CAC	p.R920H	SASH1_uc011eeb.1_Missense_Mutation_p.R681H|SASH1_uc003qmf.1_Missense_Mutation_p.R330H	NM_015278	NP_056093	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	920							protein binding			central_nervous_system(1)	1		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		GCCTCTGGTCGCGGCCTGTCA	0.517																0.172589	59.075548	78.993503	34	163	KEEP	---	---	---	---	19	18	97	95	-1	capture	Missense_Mutation	SNP	148865365	148865365	SASH1	6	G	A	A	A	1	0	0	0	0	1	0	0	0	494	38	1	1	13740	3
PLEKHG1	57480	broad.mit.edu	37	6	151152163	151152163	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr6:151152163G>A	uc003qny.1	+	16	2228	c.1916G>A	c.(1915-1917)GGG>GAG	p.G639E	PLEKHG1_uc011eel.1_Missense_Mutation_p.G679E|PLEKHG1_uc011eem.1_Missense_Mutation_p.G698E|PLEKHG1_uc003qnz.2_Missense_Mutation_p.G639E	NM_001029884	NP_001025055	Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G	639					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		AAAACAGAAGGGCAGGAGGAG	0.478																0.230769	59.846192	66.754413	24	80	KEEP	---	---	---	---	9	15	47	37	-1	capture	Missense_Mutation	SNP	151152163	151152163	PLEKHG1	6	G	A	A	A	1	0	0	0	0	1	0	0	0	559	43	2	2	11971	3
PLG	5340	broad.mit.edu	37	6	161173177	161173177	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr6:161173177C>T	uc003qtm.3	+	18	2219	c.2156C>T	c.(2155-2157)GCC>GTC	p.A719V		NM_000301	NP_000292	P00747	PLMN_HUMAN	plasminogen	719	Peptidase S1.				extracellular matrix disassembly|fibrinolysis|negative regulation of cell proliferation|negative regulation of cell-substrate adhesion|negative regulation of fibrinolysis|platelet activation|platelet degranulation|positive regulation of fibrinolysis|proteolysis|tissue remodeling	extracellular space|extrinsic to external side of plasma membrane|platelet alpha granule lumen	apolipoprotein binding|cell surface binding|serine-type endopeptidase activity			skin(3)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Aminocaproic Acid(DB00513)|Streptokinase(DB00086)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	CTCAAGGAAGCCCAGCTCCCT	0.468																0.277778	75.11359	79.907163	30	78	KEEP	---	---	---	---	15	18	39	41	-1	capture	Missense_Mutation	SNP	161173177	161173177	PLG	6	C	T	T	T	1	0	0	0	0	1	0	0	0	338	26	2	2	11989	3
GAL3ST4	79690	broad.mit.edu	37	7	99758263	99758263	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr7:99758263C>T	uc003utt.2	-	3	1766	c.749G>A	c.(748-750)CGA>CAA	p.R250Q	C7orf43_uc011kjj.1_5'Flank|C7orf43_uc003utr.2_5'Flank|C7orf43_uc003uts.2_5'Flank|GAL3ST4_uc003utu.2_Missense_Mutation_p.R250Q|GAL3ST4_uc010lgq.2_Missense_Mutation_p.R188Q	NM_024637	NP_078913	Q96RP7	G3ST4_HUMAN	galactose-3-O-sulfotransferase 4	250	Lumenal (Potential).				cell-cell signaling|oligosaccharide metabolic process|proteoglycan biosynthetic process|sulfur compound metabolic process	Golgi cisterna membrane|integral to membrane|membrane fraction	3'-phosphoadenosine 5'-phosphosulfate binding|galactosylceramide sulfotransferase activity|proteoglycan sulfotransferase activity			ovary(3)	3	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GGTTTGGGCTCGAGGGCCAGC	0.567																0.325641	337.002915	347.518792	127	263	KEEP	---	---	---	---	72	70	162	138	-1	capture	Missense_Mutation	SNP	99758263	99758263	GAL3ST4	7	C	T	T	T	1	0	0	0	0	1	0	0	0	403	31	1	1	6140	3
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr7:140453136A>T	uc003vwc.3	-	15	1860	c.1799T>A	c.(1798-1800)GTG>GAG	p.V600E		NM_004333	NP_004324	P15056	BRAF_HUMAN	B-Raf	600	Protein kinase.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).		activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	p.V600E(16892)|p.V600?(325)|p.V600K(176)|p.V600R(36)|p.V600M(25)|p.V600A(23)|p.V600D(21)|p.V600G(11)|p.V600_K601>E(8)|p.T599_V600insTT(3)|p.T599_R603>I(2)|p.T599_V600>IAL(2)|p.V600L(2)|p.T599_V600insT(2)|p.V600_W604del(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insV(1)|p.T599_V600insDFGLAT(1)	KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)	TCGAGATTTCACTGTAGCTAG	0.368	Colon(40;35 892 2973 5743 27438)	V600E(UACC257_SKIN)|V600D(K029AX_SKIN)|V600E(HS695T_SKIN)|V600E(COLO679_SKIN)|V600E(BT474_BREAST)|V600E(IGR39_SKIN)|V600E(A101D_SKIN)|V600E(COLO783_SKIN)|V600E(IGR37_SKIN)|V600E(A375_SKIN)|V600E(WM793_SKIN)|V600E(COLO818_SKIN)|V600E(HS294T_SKIN)|V600E(SKMEL28_SKIN)|V600E(DU4475_BREAST)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(IGR1_SKIN)|V600E(SKHEP1_LIVER)|V600E(WM983B_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(RVH421_SKIN)|V600D(WM2664_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(SKMEL24_SKIN)|V600D(WM115_SKIN)|V600E(MALME3M_SKIN)|V600E(A673_BONE)|V600E(C32_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(COLO800_SKIN)|V600E(COLO741_SKIN)|V600E(HS939T_SKIN)|V600E(COLO205_LARGE_INTESTINE)|V600E(K029AX_SKIN)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(SH4_SKIN)|V600E(WM88_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(COLO849_SKIN)|V600E(MELHO_SKIN)|V600E(BHT101_THYROID)|V600E(G361_SKIN)|V600E(UACC62_SKIN)|V600E(BCPAP_THYROID)|V600E(8505C_THYROID)|V600E(SW1417_LARGE_INTESTINE)|V600E(COLO829_SKIN)|V600E(RKO_LARGE_INTESTINE)|V600E(A2058_SKIN)|V600E(RPMI7951_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(SKMEL5_SKIN)|V600E(ES2_OVARY)|V600E(LOXIMVI_SKIN)	61	p.V600E(G361-Tumor)|p.V600E(HT144-Tumor)|p.V600E(MDAMB361-Tumor)|p.V600E(COLO783-Tumor)|p.V600E(COLO201-Tumor)|p.V600E(8505C-Tumor)|p.V600E(COLO205-Tumor)|p.V600E(A673-Tumor)|p.V600E(WM88-Tumor)|p.V600E(LOXIMVI-Tumor)|p.V600D(WM2664-Tumor)|p.V600K(MDST8-Tumor)|p.V600E(HT29-Tumor)|p.V600E(CL34-Tumor)|p.V600E(COLO818-Tumor)|p.V600E(COLO741-Tumor)|p.V600E(LS411N-Tumor)|p.V600E(SKMEL28-Tumor)|p.V600E(NMCG1-Tumor)|p.V600E(MELHO-Tumor)|p.V600E(WM983B-Tumor)|p.V600E(OUMS23-Tumor)|p.V600E(NCIH854-Tumor)|p.V600E(IGR39-Tumor)|p.V600E(SKHEP1-Tumor)|p.V600E(COLO679-Tumor)|p.V600E(SKMEL5-Tumor)|p.V600E(UACC257-Tumor)|p.V600E(HS695T-Tumor)|p.V600E(A375-Tumor)|p.V600E(MALME3M-Tumor)|p.V600E(AM38-Tumor)|p.V600E(SIGM5-Tumor)|p.V600E(DBTRG05MG-Tumor)|p.V600E(8305C-Tumor)|p.V600E(SKMEL24-Tumor)|p.V600E(WM793-Tumor)|p.V600E(BCPAP-Tumor)|p.V600D(WM115-Tumor)|p.V600E(SNUC5-Tumor)|p.V600E(GCT-Tumor)|p.V600E(ES2-Tumor)|p.V600E(SW1417-Tumor)|p.V600E(MDAMB435S-Tumor)|p.V600E(HS294T-Tumor)|p.V600E(DU4475-Tumor)|p.V600E(C32-Tumor)|p.V600E(A101D-Tumor)|p.V600E(COLO829-Tumor)|p.V600E(SKMEL3-Tumor)|p.V600E(SKMEL1-Tumor)|p.V600E(WM1799-Tumor)|p.V600E(RKO-Tumor)|p.V600E(IGR37-Tumor)|p.V600E(K029AX-Tumor)|p.V600E(JHOM2B-Tumor)|p.V600E(SH4-Tumor)	451	Mis|T|O	AKAP9|KIAA1549	melanoma|colorectal|papillary thyroid|borderline ov|Non small-cell lung cancer (NSCLC)|cholangiocarcinoma|pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous_syndrome				0.041096	-19.574769	13.499518	6	140	KEEP	---	---	---	---	3	3	74	79	-1	capture	Missense_Mutation	SNP	140453136	140453136	BRAF	7	A	T	T	T	1	0	0	0	0	1	0	0	0	78	6	4	4	1484	3
FAM86B2	653333	broad.mit.edu	37	8	12286307	12286307	+	Missense_Mutation	SNP	T	C	C	rs148161726		TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr8:12286307T>C	uc003wvt.3	-	6	577	c.577A>G	c.(577-579)ATC>GTC	p.I193V	FAM66D_uc011kxp.1_Intron|uc003wvm.1_Intron|FAM86B2_uc003wvq.3_Intron|FAM86B2_uc003wvr.3_Missense_Mutation_p.I16V|FAM86B2_uc003wvs.3_Missense_Mutation_p.I93V|FAM86B2_uc010lsn.2_Intron|FAM86B2_uc003wvu.3_Intron|FAM86B2_uc010lso.2_Intron|FAM86B2_uc011kxt.1_Intron|FAM86B2_uc011kxu.1_Intron|FAM86B2_uc010lsl.2_Intron	NM_001137610	NP_001131082	P0C5J1	F86B2_HUMAN	hypothetical protein LOC653333	193											0						TGCTCGAGGATCCGGCTGTGA	0.602																0.078947	1.397873	8.27451	3	35	KEEP	---	---	---	---	2	2	17	21	-1	capture	Missense_Mutation	SNP	12286307	12286307	FAM86B2	8	T	C	C	C	1	0	0	0	0	1	0	0	0	650	50	3	3	5591	3
ASAH1	427	broad.mit.edu	37	8	17916969	17916969	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr8:17916969C>T	uc003wyl.2	-	12	1234	c.922G>A	c.(922-924)GAT>AAT	p.D308N	ASAH1_uc010ltb.1_RNA|ASAH1_uc003wym.2_Missense_Mutation_p.D283N|ASAH1_uc003wyn.2_Missense_Mutation_p.D324N|ASAH1_uc003wyo.2_Missense_Mutation_p.D302N	NM_177924	NP_808592	Q13510	ASAH1_HUMAN	N-acylsphingosine amidohydrolase 1 isoform a	308					ceramide metabolic process	lysosome	ceramidase activity				0				Colorectal(111;0.0646)|COAD - Colon adenocarcinoma(73;0.228)		TGCTTAGCATCGAGTCTAGAT	0.398																0.166667	67.589227	89.717349	35	175	KEEP	---	---	---	---	16	22	106	87	-1	capture	Missense_Mutation	SNP	17916969	17916969	ASAH1	8	C	T	T	T	1	0	0	0	0	1	0	0	0	403	31	1	1	998	3
DNAJC5B	85479	broad.mit.edu	37	8	66963845	66963845	+	Silent	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr8:66963845C>T	uc003xvs.1	+	3	354	c.63C>T	c.(61-63)TAC>TAT	p.Y21Y	DNAJC5B_uc003xvt.1_RNA	NM_033105	NP_149096	Q9UF47	DNJ5B_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 5	21	J.				protein folding	membrane	heat shock protein binding|unfolded protein binding				0		Lung NSC(129;0.114)|all_lung(136;0.188)	Epithelial(68;0.0213)|all cancers(69;0.0839)|BRCA - Breast invasive adenocarcinoma(89;0.0886)|OV - Ovarian serous cystadenocarcinoma(28;0.112)			AAGCTCTATACGAAATTCTTG	0.398																0.340206	182.686645	187.067222	66	128	KEEP	---	---	---	---	35	34	67	69	-1	capture	Silent	SNP	66963845	66963845	DNAJC5B	8	C	T	T	T	1	0	0	0	0	0	0	0	1	246	19	1	1	4607	3
RNF19A	25897	broad.mit.edu	37	8	101273881	101273881	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr8:101273881C>T	uc003yjj.1	-	9	1888	c.1571G>A	c.(1570-1572)CGA>CAA	p.R524Q	RNF19A_uc003yjk.1_Missense_Mutation_p.R524Q	NM_015435	NP_056250	Q9NV58	RN19A_HUMAN	ring finger protein 19	524					microtubule cytoskeleton organization|protein modification process	centrosome|integral to membrane	ligase activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(1)|skin(1)	4	all_cancers(14;3.5e-05)|all_epithelial(15;8.91e-08)|Lung NSC(17;0.000615)|all_lung(17;0.00166)		Epithelial(11;3.06e-11)|all cancers(13;5.78e-09)|OV - Ovarian serous cystadenocarcinoma(57;2.24e-05)|STAD - Stomach adenocarcinoma(118;0.0525)			GGCTCCTATTCGATCCATGTG	0.532																0.064935	-5.253	9.858471	5	72	KEEP	---	---	---	---	4	1	50	58	-1	capture	Missense_Mutation	SNP	101273881	101273881	RNF19A	8	C	T	T	T	1	0	0	0	0	1	0	0	0	403	31	1	1	13362	3
USP9X	8239	broad.mit.edu	37	X	41075440	41075440	+	Nonsense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chrX:41075440C>T	uc004dfb.2	+	35	6253	c.5620C>T	c.(5620-5622)CAA>TAA	p.Q1874*	USP9X_uc004dfc.2_Nonsense_Mutation_p.Q1874*	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform	1874					BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6						ACACAGTGGTCAAGCGAGTGG	0.443	Ovarian(172;1807 2695 35459 49286)															0.642857	137.485457	138.741383	45	25	KEEP	---	---	---	---	27	21	12	14	-1	capture	Nonsense_Mutation	SNP	41075440	41075440	USP9X	23	C	T	T	T	1	0	0	0	0	0	1	0	0	377	29	5	2	16972	3
KDM5A	5927	broad.mit.edu	37	12	416952	416953	+	Frame_Shift_Ins	INS	-	T	T			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr12:416952_416953insT	uc001qif.1	-	23	3960_3961	c.3597_3598insA	c.(3595-3600)AAAGGAfs	p.K1199fs	KDM5A_uc001qie.1_Frame_Shift_Ins_p.K1199fs	NM_001042603	NP_001036068	P29375	KDM5A_HUMAN	retinoblastoma binding protein 2 isoform 1	1199_1200	PHD-type 2.				chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3						CAGCTGGATCCTTTTTTTTGGG	0.475					958	T 	NUP98	AML								0.03			7	217		---	---	---	---						capture_indel	Frame_Shift_Ins	INS	416952	416953	KDM5A	12	-	T	T	T	1	0	1	1	0	0	0	0	0	312	24	5	5	8055	3
RIMKLB	57494	broad.mit.edu	37	12	8926145	8926162	+	In_Frame_Del	DEL	CTGGCCGGCTCACCCGGC	-	-	rs34259191		TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr12:8926145_8926162delCTGGCCGGCTCACCCGGC	uc001quu.2	+	6	1177_1194	c.926_943delCTGGCCGGCTCACCCGGC	c.(925-945)TCTGGCCGGCTCACCCGGCGT>TGT	p.309_315SGRLTRR>C	RIMKLB_uc009zgf.1_Intron|RIMKLB_uc001qux.2_In_Frame_Del_p.309_315SGRLTRR>C|RIMKLB_uc010sgl.1_In_Frame_Del_p.309_315SGRLTRR>C|RIMKLB_uc001quw.2_Intron	NM_020734	NP_065785	Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family	309_315					protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0						CTTCTACCCTCTGGCCGGCTCACCCGGCGTATGTCCCT	0.550																0.23			32	109		---	---	---	---						capture_indel	In_Frame_Del	DEL	8926145	8926162	RIMKLB	12	CTGGCCGGCTCACCCGGC	-	-	-	1	0	1	0	1	0	0	0	0	416	32	5	5	13258	3
ZNF280D	54816	broad.mit.edu	37	15	56993158	56993158	+	Frame_Shift_Del	DEL	A	-	-			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr15:56993158delA	uc002adu.2	-	6	571	c.354delT	c.(352-354)TCTfs	p.S118fs	ZNF280D_uc002adv.2_Frame_Shift_Del_p.S105fs|ZNF280D_uc010bfq.2_Frame_Shift_Del_p.S118fs|ZNF280D_uc002adw.1_Frame_Shift_Del_p.S146fs|ZNF280D_uc010bfr.1_RNA|ZNF280D_uc002ady.2_Frame_Shift_Del_p.S118fs|ZNF280D_uc002adx.2_Frame_Shift_Del_p.S118fs	NM_017661	NP_060131	Q6N043	Z280D_HUMAN	suppressor of hairy wing homolog 4 isoform 1	118					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)		GAACAATAACAGAACTATCTG	0.393																0.17			22	106		---	---	---	---						capture_indel	Frame_Shift_Del	DEL	56993158	56993158	ZNF280D	15	A	-	-	-	1	0	1	0	1	0	0	0	0	80	7	5	5	17697	3
CREBBP	1387	broad.mit.edu	37	16	3843446	3843446	+	Frame_Shift_Del	DEL	C	-	-			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr16:3843446delC	uc002cvv.2	-	4	1361	c.1157delG	c.(1156-1158)CGAfs	p.R386fs	CREBBP_uc002cvw.2_Frame_Shift_Del_p.R386fs	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a	386	TAZ-type 1.|Interaction with SRCAP.				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	p.R386*(1)		haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1)	127		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		TTTCATGGTTCGACAATGCGG	0.507					748	T|N|F|Mis|O	MLL|MORF|RUNXBP2	ALL|AML|DLBCL|B-NHL 		Rubinstein-Taybi syndrome		Rubinstein-Taybi_syndrome				0.06			18	287		---	---	---	---						capture_indel	Frame_Shift_Del	DEL	3843446	3843446	CREBBP	16	C	-	-	-	1	0	1	0	1	0	0	0	0	403	31	5	5	3826	3
SPACA3	124912	broad.mit.edu	37	17	31322643	31322643	+	Frame_Shift_Del	DEL	C	-	-			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr17:31322643delC	uc002hhs.1	+	2	326	c.251delC	c.(250-252)TCCfs	p.S84fs	SPACA3_uc010cte.1_RNA	NM_173847	NP_776246	Q8IXA5	SACA3_HUMAN	sperm acrosome associated 3	84	Helical; Signal-anchor for type II membrane protein; (Potential).				cell wall macromolecule catabolic process|defense response to Gram-positive bacterium|monocyte activation|peptidoglycan catabolic process|positive regulation of macrophage activation|positive regulation of phagocytosis|response to virus	acrosomal membrane|extracellular region|integral to membrane|lysosome	bacterial cell surface binding|lysozyme activity|protein binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.193)			CTGCTACCCTCCAGTGAGGCC	0.607																0.38			53	88		---	---	---	---						capture_indel	Frame_Shift_Del	DEL	31322643	31322643	SPACA3	17	C	-	-	-	1	0	1	0	1	0	0	0	0	390	30	5	5	14865	3
PDGFRA	5156	broad.mit.edu	37	4	55152112	55152113	+	In_Frame_Ins	INS	-	TTT	TTT			TCGA-02-0047-01	TCGA-02-0047-01									Unknown	Unspecified	Unspecified				Unspecified	g.chr4:55152112_55152113insTTT	uc003han.3	+	18	2875_2876	c.2544_2545insTTT	c.(2542-2547)insTTT	p.848_849insF	PDGFRA_uc003haa.2_In_Frame_Ins_p.608_609insF	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	848_849	Protein kinase.|Cytoplasmic (Potential).				cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity	p.H845_N848>P(3)|p.N848K(1)|p.H845_N848del(1)		soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	ATGATTCGAACTATGTGTCGAA	0.495	Pancreas(151;208 1913 7310 23853 37092)				1045	Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			0.04			12	286		---	---	---	---						capture_indel	In_Frame_Ins	INS	55152112	55152113	PDGFRA	4	-	TTT	TTT	TTT	1	0	1	1	0	0	0	0	0	259	20	5	5	11564	3
