Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
RELN	5649	broad.mit.edu	37	7	103202062	103202062	+	Missense_Mutation	SNP	G	G	T			TCGA-MK-A4N7-01A-11D-A257-08	TCGA-MK-A4N7-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c1565fa2-c035-429d-859e-9b4746a7322e	0fc0bdda-7d6c-43d0-8ff0-ba8450a96c27	g.chr7:103202062G>T	uc022ajr.1	-	35	5606	c.5446C>A	c.(5446-5448)Ctt>Att	p.L1816I	RELN_uc022ajq.1_Missense_Mutation_p.L1816I|RELN_uc010liz.3_Missense_Mutation_p.L1816I	NM_005045	NP_005036	P78509	RELN_HUMAN	Homo sapiens reelin (RELN), transcript variant 1, mRNA.	1816					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		TCAGGCCAAAGGTCAGGATGT	0.443000													12	32					0	0	1	0	0
GABRQ	55879	broad.mit.edu	37	X	151806720	151806720	+	Missense_Mutation	SNP	G	G	A			TCGA-MK-A4N7-01A-11D-A257-08	TCGA-MK-A4N7-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c1565fa2-c035-429d-859e-9b4746a7322e	0fc0bdda-7d6c-43d0-8ff0-ba8450a96c27	g.chrX:151806720G>A	uc004ffp.1	+	0	84	c.64G>A	c.(64-66)Gag>Aag	p.E22K		NM_018558	NP_061028	Q9UN88	GBRT_HUMAN	Homo sapiens gamma-aminobutyric acid (GABA) receptor, theta (GABRQ), mRNA.	22						cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	GABA-A receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|neurotransmitter transporter activity	p.A21V(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)					CTGGCTCGCGGAGGGCAACTA	0.647000													7	85					0	0	1	0	0
ACOT7	11332	broad.mit.edu	37	1	6341211	6341211	+	Missense_Mutation	SNP	T	T	A			TCGA-MK-A4N7-01A-11D-A257-08	TCGA-MK-A4N7-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c1565fa2-c035-429d-859e-9b4746a7322e	0fc0bdda-7d6c-43d0-8ff0-ba8450a96c27	g.chr1:6341211T>A	uc001ams.3	-	7	1152	c.995A>T	c.(994-996)tAc>tTc	p.Y332F	ACOT7_uc001amt.3_Missense_Mutation_p.Y322F|ACOT7_uc001amu.3_Non-coding_Transcript|ACOT7_uc001amq.3_Missense_Mutation_p.Y281F|ACOT7_uc001amr.3_Missense_Mutation_p.Y302F	NM_181864	NP_863654	O00154	BACH_HUMAN	Homo sapiens acyl-CoA thioesterase 7 (ACOT7), transcript variant hBACHb, mRNA.	332						mitochondrion|nucleus	carboxylesterase activity|fatty-acyl-CoA binding|palmitoyl-CoA hydrolase activity			kidney(1)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1)	16	Ovarian(185;0.0634)|all_lung(157;0.175)	all_cancers(23;1.42e-38)|all_epithelial(116;3.96e-23)|all_lung(118;3.69e-08)|Lung NSC(185;8.52e-07)|all_hematologic(16;6.92e-06)|Colorectal(325;4.53e-05)|Acute lymphoblastic leukemia(12;5e-05)|all_neural(13;0.000164)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;9.16e-37)|GBM - Glioblastoma multiforme(13;5.89e-29)|OV - Ovarian serous cystadenocarcinoma(86;7.63e-19)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;2.06e-05)|Kidney(185;7.74e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00129)|BRCA - Breast invasive adenocarcinoma(365;0.00132)|STAD - Stomach adenocarcinoma(132;0.00195)|READ - Rectum adenocarcinoma(331;0.0481)		CAGCGACACGTAGGTGAAGAA	0.642000											OREG0013034	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	19	34					0	0	1	0	0
VPS11	55823	broad.mit.edu	37	11	118951865	118951865	+	Silent	SNP	C	C	G			TCGA-MK-A4N7-01A-11D-A257-08	TCGA-MK-A4N7-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c1565fa2-c035-429d-859e-9b4746a7322e	0fc0bdda-7d6c-43d0-8ff0-ba8450a96c27	g.chr11:118951865C>G	uc010ryx.2	+	15	2538	c.2496C>G	c.(2494-2496)gtC>gtG	p.V832V	VPS11_uc010ryy.2_Silent_p.V680V	NM_021729	NP_068375	Q9H270	VPS11_HUMAN	Homo sapiens vacuolar protein sorting 11 homolog (S. cerevisiae) (VPS11), mRNA.	834					protein transport	HOPS complex|endocytic vesicle|late endosome membrane|lysosomal membrane	nucleotide binding|protein binding|zinc ion binding			autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	29	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.88e-05)		TGCCCTCAGTCCACTTCCTGT	0.507000													12	174					0	0	1	0	0
AKAP12	9590	broad.mit.edu	37	6	151671522	151671522	+	Missense_Mutation	SNP	C	C	A			TCGA-MK-A4N7-01A-11D-A257-08	TCGA-MK-A4N7-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c1565fa2-c035-429d-859e-9b4746a7322e	0fc0bdda-7d6c-43d0-8ff0-ba8450a96c27	g.chr6:151671522C>A	uc011eep.2	+	3	2236	c.1996C>A	c.(1996-1998)Ccg>Acg	p.P666T	AKAP12_uc003qoe.3_Missense_Mutation_p.P666T|AKAP12_uc003qof.3_Missense_Mutation_p.P568T|AKAP12_uc010kim.3_Intron|AKAP12_uc003qog.3_Missense_Mutation_p.P561T	NM_005100	NP_005091	Q02952	AKA12_HUMAN	Homo sapiens A kinase (PRKA) anchor protein 12 (AKAP12), transcript variant 1, mRNA.	666					G-protein coupled receptor protein signaling pathway|positive regulation of cAMP biosynthetic process|positive regulation of protein kinase A signaling cascade|protein targeting	cell cortex|cytoskeleton|plasma membrane	adenylate cyclase binding|protein kinase A binding			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		AGAGCCAAAGCCGGAAGAACC	0.493000													17	40					0	0	1	0	0
FBXL5	26234	broad.mit.edu	37	4	15629584	15629584	+	Missense_Mutation	SNP	T	T	C			TCGA-MK-A4N7-01A-11D-A257-08	TCGA-MK-A4N7-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c1565fa2-c035-429d-859e-9b4746a7322e	0fc0bdda-7d6c-43d0-8ff0-ba8450a96c27	g.chr4:15629584T>C	uc003goc.2	-	6	1090	c.965A>G	c.(964-966)cAt>cGt	p.H322R	FBXL5_uc010idw.2_Missense_Mutation_p.H235R|FBXL5_uc003gob.2_Missense_Mutation_p.H184R|FBXL5_uc010idx.2_Missense_Mutation_p.H321R|FBXL5_uc003god.2_Missense_Mutation_p.H305R|FBXL5_uc010idy.2_Missense_Mutation_p.H322R	NM_012161	NP_036293	Q9UKA1	FBXL5_HUMAN	Homo sapiens F-box and leucine-rich repeat protein 5 (FBXL5), transcript variant 1, mRNA.	322					SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|iron ion homeostasis	SCF ubiquitin ligase complex|perinuclear region of cytoplasm	iron ion binding|protein binding|ubiquitin-protein ligase activity			endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	13						TAGAACGTTATGAATTAAGCC	0.348000													9	10					0	0	1	0	0
FGFR2	2263	broad.mit.edu	37	10	123279544	123279544	+	Missense_Mutation	SNP	C	C	G			TCGA-MK-A4N7-01A-11D-A257-08	TCGA-MK-A4N7-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c1565fa2-c035-429d-859e-9b4746a7322e	0fc0bdda-7d6c-43d0-8ff0-ba8450a96c27	g.chr10:123279544C>G	uc021pzy.1	-	6	1535	c.888G>C	c.(886-888)aaG>aaC	p.K296N	FGFR2_uc021pzv.1_Intron|FGFR2_uc021pzw.1_Missense_Mutation_p.K181N|FGFR2_uc021pzx.1_Missense_Mutation_p.K207N|FGFR2_uc021pzz.1_Missense_Mutation_p.K296N|FGFR2_uc010qtl.2_Missense_Mutation_p.K296N|FGFR2_uc010qtm.2_Missense_Mutation_p.K181N|FGFR2_uc021qaa.1_Missense_Mutation_p.K296N|FGFR2_uc021qab.1_Missense_Mutation_p.K207N|FGFR2_uc021qac.1_Missense_Mutation_p.K226N|FGFR2_uc001lfn.4_Non-coding_Transcript|FGFR2_uc010qtn.2_Missense_Mutation_p.K315N|FGFR2_uc010qto.2_Missense_Mutation_p.K200N|FGFR2_uc001lfo.1_Missense_Mutation_p.K315N|FGFR2_uc010qtp.2_Missense_Mutation_p.K315N|FGFR2_uc001lfg.4_5'Flank	NM_022970	NP_075259	P21802	FGFR2_HUMAN	Homo sapiens fibroblast growth factor receptor 2 (FGFR2), transcript variant 2, mRNA.	296	Ig-like C2-type 3.				angiogenesis|axonogenesis|bone mineralization|bone morphogenesis|branch elongation involved in salivary gland morphogenesis|branching involved in embryonic placenta morphogenesis|branching morphogenesis of a nerve|bud elongation involved in lung branching|cell fate commitment|cell growth|cell-cell signaling|cellular response to protein stimulus|embryonic digestive tract morphogenesis|embryonic pattern specification|epithelial cell proliferation involved in salivary gland morphogenesis|fibroblast growth factor receptor signaling pathway involved in hemopoiesis|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptosis in bone marrow|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow|hair follicle morphogenesis|insulin receptor signaling pathway|lacrimal gland development|lateral sprouting from an epithelium|limb bud formation|lung alveolus development|lung lobe morphogenesis|lung-associated mesenchyme development|mammary gland bud formation|membranous septum morphogenesis|mesenchymal cell differentiation involved in lung development|mesenchymal cell proliferation involved in lung development|midbrain development|multicellular organism growth|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|organ growth|otic vesicle formation|outflow tract septum morphogenesis|positive regulation of ERK1 and ERK2 cascade|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell cycle|positive regulation of cell division|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis|prostate epithelial cord elongation|pyramidal neuron development|regulation of branching involved in prostate gland morphogenesis|regulation of cell fate commitment|regulation of fibroblast growth factor receptor signaling pathway|regulation of multicellular organism growth|regulation of smooth muscle cell differentiation|regulation of smoothened signaling pathway|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development|ureteric bud development|ventricular cardiac muscle tissue morphogenesis|ventricular zone neuroblast division	cell cortex|cell surface|excitatory synapse|extracellular region|integral to membrane|nucleus|plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|heparin binding|protein binding			breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)	TACTGCCGTTCTTTTCCACGT	0.537000		5	Mis		"""gastric. NSCLC, endometrial"""		"""Crouzon, Pfeiffer, and Apert syndromes"""		Saethre-Chotzen syndrome;Apert syndrome				8	72					0	0	1	0	0
MAP2	4133	broad.mit.edu	37	2	210559316	210559316	+	Nonsense_Mutation	SNP	G	G	T			TCGA-MK-A4N7-01A-11D-A257-08	TCGA-MK-A4N7-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c1565fa2-c035-429d-859e-9b4746a7322e	0fc0bdda-7d6c-43d0-8ff0-ba8450a96c27	g.chr2:210559316G>T	uc002vde.1	+	6	2670	c.2422G>T	c.(2422-2424)Gaa>Taa	p.E808*	MAP2_uc002vdc.1_Nonsense_Mutation_p.E808*|MAP2_uc002vdd.1_Intron|MAP2_uc002vdf.1_Intron|MAP2_uc002vdg.1_Intron|MAP2_uc002vdh.1_Intron|MAP2_uc002vdi.1_Nonsense_Mutation_p.E804*	NM_002374	NP_002365	P11137	MAP2_HUMAN	Homo sapiens microtubule-associated protein 2 (MAP2), transcript variant 1, mRNA.	808					central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)	TGACCTTCCTGAAATGCTAGA	0.463000													11	100					0	0	1	0	0
SVEP1	79987	broad.mit.edu	37	9	113234582	113234582	+	Missense_Mutation	SNP	G	G	A			TCGA-MK-A4N7-01A-11D-A257-08	TCGA-MK-A4N7-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c1565fa2-c035-429d-859e-9b4746a7322e	0fc0bdda-7d6c-43d0-8ff0-ba8450a96c27	g.chr9:113234582G>A	uc010mtz.3	-	14	2958	c.2621C>T	c.(2620-2622)gCt>gTt	p.A874V	SVEP1_uc010mua.1_Missense_Mutation_p.A874V	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	Homo sapiens sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1 (SVEP1), mRNA.	874					cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						CAGCCTATTAGCTGCACCCCA	0.493000													7	59					0	0	1	0	0
SOWAHD	347454	broad.mit.edu	37	X	118893168	118893168	+	Missense_Mutation	SNP	G	G	A			TCGA-MK-A4N7-01A-11D-A257-08	TCGA-MK-A4N7-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c1565fa2-c035-429d-859e-9b4746a7322e	0fc0bdda-7d6c-43d0-8ff0-ba8450a96c27	g.chrX:118893168G>A	uc010nql.3	+	0	593	c.538G>A	c.(538-540)Gtg>Atg	p.V180M		NM_001105576	NP_001099046	A6NJG2	ANR58_HUMAN	Homo sapiens sosondowah ankyrin repeat domain family member D (SOWAHD), mRNA.	180																	GAGGCTCGACGTGAGCGCCCC	0.692000													6	4					0	0	1	0	0
ZNRF3	84133	broad.mit.edu	37	22	29446145	29446145	+	Missense_Mutation	SNP	C	C	G			TCGA-MK-A4N7-01A-11D-A257-08	TCGA-MK-A4N7-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c1565fa2-c035-429d-859e-9b4746a7322e	0fc0bdda-7d6c-43d0-8ff0-ba8450a96c27	g.chr22:29446145C>G	uc003aeg.3	+	7	1976	c.1976C>G	c.(1975-1977)tCc>tGc	p.S659C	ZNRF3_uc021wnq.1_Missense_Mutation_p.S559C	NM_001206998	NP_001193927	Q9ULT6	ZNRF3_HUMAN	Homo sapiens zinc and ring finger 3 (ZNRF3), transcript variant 1, mRNA.	659						integral to membrane	zinc ion binding			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(4)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	28						GATCAGGTGTCCACCTGCAGC	0.682000													9	91					0	0	1	0	0
LOXL2	4017	broad.mit.edu	37	8	23167321	23167321	+	Silent	SNP	G	G	A			TCGA-MK-A4N7-01A-11D-A257-08	TCGA-MK-A4N7-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c1565fa2-c035-429d-859e-9b4746a7322e	0fc0bdda-7d6c-43d0-8ff0-ba8450a96c27	g.chr8:23167321G>A	uc003xdh.1	-	9	2079	c.1740C>T	c.(1738-1740)ctC>ctT	p.L580L	LOXL2_uc010lty.1_Silent_p.L119L	NM_002318	NP_002309	Q9Y4K0	LOXL2_HUMAN	Homo sapiens lysyl oxidase-like 2 (LOXL2), mRNA.	580	Lysyl-oxidase like.				aging|cell adhesion|protein modification process	extracellular space|membrane	copper ion binding|electron carrier activity|oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor|scavenger receptor activity			breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(5)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(55;0.0453)|Breast(100;0.143)		Colorectal(74;0.0288)|COAD - Colon adenocarcinoma(73;0.096)		CTGAGGCCGAGAGGCAGTTCT	0.652000													4	41					0	0	1	0	0
PPAPDC2	403313	broad.mit.edu	37	9	4662753	4662753	+	Silent	SNP	G	G	C			TCGA-MK-A4N7-01A-11D-A257-08	TCGA-MK-A4N7-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c1565fa2-c035-429d-859e-9b4746a7322e	0fc0bdda-7d6c-43d0-8ff0-ba8450a96c27	g.chr9:4662753G>C	uc003zin.3	+	0	456	c.378G>C	c.(376-378)tcG>tcC	p.S126S	SPATA6L_uc003zik.3_Intron|SPATA6L_uc003zil.3_Intron|SPATA6L_uc011lly.2_Intron|SPATA6L_uc011llz.2_Intron|SPATA6L_uc003zim.3_Intron	NM_203453	NP_982278	Q8IY26	PPAC2_HUMAN	Homo sapiens phosphatidic acid phosphatase type 2 domain containing 2 (PPAPDC2), mRNA.	126						integral to membrane	hydrolase activity			endometrium(1)|large_intestine(2)|lung(1)	4	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.026)		AGAGCTCGTCGTGGGGCAGCG	0.657000											OREG0019084	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	37					0	0	1	0	0
ZFR2	23217	broad.mit.edu	37	19	3821446	3821446	+	Missense_Mutation	SNP	G	G	A			TCGA-MK-A4N7-01A-11D-A257-08	TCGA-MK-A4N7-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c1565fa2-c035-429d-859e-9b4746a7322e	0fc0bdda-7d6c-43d0-8ff0-ba8450a96c27	g.chr19:3821446G>A	uc002lyw.2	-	9	1535	c.1523C>T	c.(1522-1524)aCg>aTg	p.T508M	ZFR2_uc010xhx.1_Non-coding_Transcript	NM_015174	NP_055989	Q9UPR6	ZFR2_HUMAN	Homo sapiens zinc finger RNA binding protein 2 (ZFR2), transcript variant 1, mRNA.	508						intracellular	nucleic acid binding|zinc ion binding			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)		GCTGGGCTCCGTGGCAATGGG	0.642000													18	25					0	0	1	0	0
MYT1L	23040	broad.mit.edu	37	2	1915828	1915828	+	Missense_Mutation	SNP	C	C	T			TCGA-MK-A4N7-01A-11D-A257-08	TCGA-MK-A4N7-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c1565fa2-c035-429d-859e-9b4746a7322e	0fc0bdda-7d6c-43d0-8ff0-ba8450a96c27	g.chr2:1915828C>T	uc002qxe.3	-	11	2500	c.1673G>A	c.(1672-1674)cGc>cAc	p.R558H	MYT1L_uc002qxd.3_Missense_Mutation_p.R556H|MYT1L_uc010ewl.2_Non-coding_Transcript	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	Homo sapiens myelin transcription factor 1-like (MYT1L), mRNA.	558					cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		GACATGCCCGCGCCCCGTGCA	0.597000													10	9					0	0	1	0	0
HUWE1	10075	broad.mit.edu	37	X	53575049	53575049	+	Silent	SNP	G	G	A			TCGA-MK-A4N7-01A-11D-A257-08	TCGA-MK-A4N7-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c1565fa2-c035-429d-859e-9b4746a7322e	0fc0bdda-7d6c-43d0-8ff0-ba8450a96c27	g.chrX:53575049G>A	uc004dsp.3	-	67	10623	c.10221C>T	c.(10219-10221)tcC>tcT	p.S3407S	HUWE1_uc004dsn.3_Silent_p.S2215S	NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	Homo sapiens HECT, UBA and WWE domain containing 1 (HUWE1), mRNA.	3407					base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity	p.A3406S(1)		NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						CTGACTTCACGGAGTTCTTGC	0.547000													16	37					0	0	1	0	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377		TCGA-MK-A4N7-01A-11D-A257-08	TCGA-MK-A4N7-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c1565fa2-c035-429d-859e-9b4746a7322e	0fc0bdda-7d6c-43d0-8ff0-ba8450a96c27	g.chr7:140453136A>T	uc003vwc.4	-	14	1860	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333	NP_004324	P15056	BRAF_HUMAN	Homo sapiens v-raf murine sarcoma viral oncogene homolog B1 (BRAF), mRNA.	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(41204)|p.V600K(615)|p.V600?(377)|p.V600R(99)|p.V600D(40)|p.V600_K601>E(30)|p.V600L(28)|p.V600A(24)|p.V600G(22)|p.V600M(22)|p.A598_T599insV(7)|p.T599_V600insT(7)|p.T599I(5)|p.V600Q(4)|p.T599_R603>I(4)|p.T599_V600insTT(3)|p.T599_V600insDFGLAT(2)|p.T599_V600>IAL(2)|p.V600_S605>EK(2)|p.T599T(2)|p.V600_S605>DV(2)|p.V600_S605>D(2)|p.V600_W604del(1)|p.V600V(1)|p.T599_V600insV(1)|p.V600>DLAT(1)|p.D594_T599del(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Sorafenib(DB00398)	TCGAGATTTCACTGTAGCTAG	0.368000	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""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				12	20					0	0	1	0	0
SIKE1	80143	broad.mit.edu	37	1	115321764	115321764	+	Splice_Site	SNP	G	G	A			TCGA-MK-A4N7-01A-11D-A257-08	TCGA-MK-A4N7-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c1565fa2-c035-429d-859e-9b4746a7322e	0fc0bdda-7d6c-43d0-8ff0-ba8450a96c27	g.chr1:115321764G>A	uc001efp.4	-	3	500	c.420_splice	c.e3+1	p.A140_splice	SIKE1_uc001efo.4_Splice_Site_p.A136_splice	NM_001102396	NP_001095866	Q9BRV8	SIKE1_HUMAN	Homo sapiens suppressor of IKBKE 1 (SIKE1), transcript variant 1, mRNA.	136						cytosol	protein binding			endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	6						GTTTCTTACTGCAGAGTGAGA	0.378000													18	32					0	0	1	0	0
MCM8	84515	broad.mit.edu	37	20	5965510	5965510	+	Missense_Mutation	SNP	C	C	G			TCGA-MK-A4N7-01A-11D-A257-08	TCGA-MK-A4N7-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c1565fa2-c035-429d-859e-9b4746a7322e	0fc0bdda-7d6c-43d0-8ff0-ba8450a96c27	g.chr20:5965510C>G	uc002wmk.3	+	14	2314	c.1937C>G	c.(1936-1938)tCt>tGt	p.S646C	MCM8_uc002wmi.3_Missense_Mutation_p.S606C|MCM8_uc002wmj.3_Missense_Mutation_p.S590C|MCM8_uc002wml.3_Missense_Mutation_p.S606C|MCM8_uc010gbp.3_Missense_Mutation_p.S559C|MCM8_uc002wmm.3_Missense_Mutation_p.S144C	NM_032485	NP_115874	Q9UJA3	MCM8_HUMAN	Homo sapiens minichromosome maintenance complex component 8 (MCM8), transcript variant 1, mRNA.	606					DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|cell cycle checkpoint|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|nucleoside-triphosphatase activity	p.P646L(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						CACTTACTCTCTGAACATGTG	0.393000													4	29					0	0	1	0	0
DNAJC7	7266	broad.mit.edu	37	17	40135606	40135606	+	Frame_Shift_Del	DEL	T	T	-			TCGA-MK-A4N7-01A-11D-A257-08	TCGA-MK-A4N7-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c1565fa2-c035-429d-859e-9b4746a7322e	0fc0bdda-7d6c-43d0-8ff0-ba8450a96c27	g.chr17:40135606delT	uc002hyo.3	-	9	1340	c.1059delA	c.(1057-1059)aaafs	p.K353fs	DNAJC7_uc010wgb.2_Frame_Shift_Del_p.K297fs|DNAJC7_uc002hyp.3_Frame_Shift_Del_p.K297fs|DNAJC7_uc010wgc.2_Frame_Shift_Del_p.K211fs	NM_003315	NP_001138238	Q99615	DNJC7_HUMAN	Homo sapiens DnaJ (Hsp40) homolog, subfamily C, member 7 (DNAJC7), transcript variant 1, mRNA.	353					chaperone cofactor-dependent protein refolding	cytoplasm|cytoskeleton|nucleus	heat shock protein binding|unfolded protein binding			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)	9		all_cancers(22;0.00273)|Breast(137;0.00104)|all_epithelial(22;0.0305)				TCTGGTATACTTTTTCATAGT	0.368													2	4	---	---	---	---					
