Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
SHC1	6464	broad.mit.edu	37	1	154940985	154940985	+	Missense_Mutation	SNP	C	T	T			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr1:154940985C>T	uc001ffv.2	-	4	957	c.736G>A	c.(736-738)GCA>ACA	p.A246T	SHC1_uc001ffu.2_5'Flank|SHC1_uc001ffz.1_Missense_Mutation_p.A17T|SHC1_uc001ffw.2_Missense_Mutation_p.A246T|SHC1_uc001ffx.2_Missense_Mutation_p.A136T|SHC1_uc001ffy.2_Missense_Mutation_p.A136T	NM_183001	NP_892113	P29353	SHC1_HUMAN	SHC-transforming protein 1 isoform 1	246	PID.				activation of MAPK activity|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|positive regulation of DNA replication|Ras protein signal transduction|regulation of epidermal growth factor receptor activity|regulation of growth	cytosol|mitochondrial matrix|Shc-EGFR complex	epidermal growth factor receptor binding|insulin receptor binding|insulin-like growth factor receptor binding|phospholipid binding|protein binding|transmembrane receptor protein tyrosine kinase adaptor activity			lung(1)|skin(1)	2	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			TTGCAGTCTGCGGCCATGAGG	0.552000													5	469	---	---	---	---	0	0	0.021553	0	0
HSD17B7P2	158160	broad.mit.edu	37	10	38654432	38654432	+	Missense_Mutation	SNP	A	G	G	rs2257765		TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr10:38654432A>G	uc010qex.1	+	5	599	c.524A>G	c.(523-525)AAT>AGT	p.N175S	HSD17B7P2_uc001izq.2_RNA|HSD17B7P2_uc001izo.1_RNA|HSD17B7P2_uc001izp.1_Missense_Mutation_p.N173S					SubName: Full=cDNA FLJ60462, highly similar to 3-keto-steroid reductase (EC 1.1.1.270);												0						TCATCTCGCAATGCAAGGAAA	0.453000													3	64	---	---	---	---	0	0	0.115264	0	0
LOC642826	642826	broad.mit.edu	37	10	47207813	47207813	+	RNA	SNP	T	C	C			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr10:47207813T>C	uc001jei.2	-	12		c.1586A>G			uc009xnf.2_Missense_Mutation_p.H132R					Homo sapiens cDNA, FLJ99065.												0						TTTACTTACATGGTTTGTACA	0.294000													3	30	---	---	---	---	0	0	0.115264	0	0
NAP1L4	4676	broad.mit.edu	37	11	2981037	2981037	+	Missense_Mutation	SNP	A	G	G			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr11:2981037A>G	uc001lxc.2	-	9	850	c.709T>C	c.(709-711)TTT>CTT	p.F237L	NAP1L4_uc009ydt.2_RNA|NAP1L4_uc010qxm.1_Missense_Mutation_p.F237L|NAP1L4_uc010qxn.1_Missense_Mutation_p.F237L	NM_005969	NP_005960	Q99733	NP1L4_HUMAN	nucleosome assembly protein 1-like 4	237					nucleosome assembly	chromatin assembly complex|cytoplasm	unfolded protein binding			ovary(1)	1		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00301)|LUSC - Lung squamous cell carcinoma(625;0.211)		TCAAAGGAAAAGGGATCAGCC	0.373000													3	69	---	---	---	---	0	0	0.009096	0	0
C11orf65	160140	broad.mit.edu	37	11	108332225	108332225	+	Missense_Mutation	SNP	T	C	C			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr11:108332225T>C	uc001pkh.2	-	2	132	c.62A>G	c.(61-63)CAG>CGG	p.Q21R	C11orf65_uc010rvx.1_Missense_Mutation_p.Q21R|C11orf65_uc009yxu.1_RNA	NM_152587	NP_689800	Q8NCR3	CK065_HUMAN	hypothetical protein LOC160140	21										ovary(1)	1		all_cancers(61;1.38e-11)|all_epithelial(67;3.16e-07)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;8.21e-06)|BRCA - Breast invasive adenocarcinoma(274;1.01e-05)|all cancers(92;0.000189)|Colorectal(284;0.114)|OV - Ovarian serous cystadenocarcinoma(223;0.144)		TTTCCAGGCCTGCTGAATGAC	0.254000													3	79	---	---	---	---	0	0	0.115264	0	0
CSRNP2	81566	broad.mit.edu	37	12	51467752	51467752	+	Missense_Mutation	SNP	C	G	G			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr12:51467752C>G	uc001rxu.1	-	3	563	c.265G>C	c.(265-267)GGT>CGT	p.G89R		NM_030809	NP_110436	Q9H175	CSRN2_HUMAN	TGF-beta induced apoptosis protein 12	89					apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0						GAGCTACCACCCTGGCTGGGC	0.552000													9	118	---	---	---	---	0	0	0.058154	0	0
OR6S1	341799	broad.mit.edu	37	14	21109731	21109731	+	Missense_Mutation	SNP	A	T	T			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr14:21109731A>T	uc001vxv.1	-	1	120	c.120T>A	c.(118-120)AAT>AAA	p.N40K		NM_001001968	NP_001001968	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S,	40	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	all_cancers(95;0.00304)		Epithelial(56;1.23e-06)|all cancers(55;1.01e-05)	GBM - Glioblastoma multiforme(265;0.0135)		TGCCTGTCAGATTCAGGAGAT	0.473000													19	119	---	---	---	---	0	0	0.055883	0	0
ADAM6	8755	broad.mit.edu	37	14	106237582	106237582	+	RNA	SNP	C	T	T	rs2983776		TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr14:106237582C>T	uc010tyt.1	-	3611		c.57301G>A			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Intron|uc001ysf.2_Intron|uc001ysh.1_RNA|uc001ysi.1_RNA					Parts of antibodies, mostly variable regions.												0						GTAGGACAGCCGGGAAGGTGT	0.637000													3	50	---	---	---	---	0	0	0.115264	0	0
Unknown	0	broad.mit.edu	37	15	102294771	102294771	+	5'Flank	SNP	A	C	C			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr15:102294771A>C	uc002bxo.2	-						uc002bxq.2_5'Flank|uc002bxr.2_5'Flank|uc010usk.1_5'Flank|uc002bxs.2_5'Flank|uc002bxu.1_5'Flank|uc002bxv.1_5'Flank|uc002bxw.1_5'Flank|uc002bxy.1_5'Flank|uc002byb.1_5'Flank|uc002byd.2_RNA|uc002byc.2_5'Flank|uc002bye.2_5'Flank|uc002byf.1_5'Flank|uc002byg.2_5'Flank|uc002byi.2_5'Flank|uc002byk.2_5'Flank|uc002bym.2_5'Flank|uc002byn.2_5'Flank|uc010usm.1_5'Flank|uc002byr.2_5'Flank|uc002bys.2_5'Flank|uc002byv.2_5'Flank|uc002byx.3_5'Flank|uc002bza.2_5'Flank|uc002bzb.2_5'Flank|uc002bzc.1_5'Flank|uc002bzd.2_5'Flank|uc002bze.2_5'Flank|uc002bzg.2_5'Flank|uc002bzi.1_5'Flank|uc002bzj.2_5'Flank|uc002bzl.2_5'Flank|uc002bzm.2_5'Flank|uc002bzo.2_5'Flank|uc002bzp.2_5'Flank|uc002bzq.2_5'Flank|uc002bzr.2_5'Flank					DQ593630																		TGGGAACGAGAAGACACTCGT	0.577000													2	7	---	---	---	---	0	0	0.115264	0	0
NF1	4763	broad.mit.edu	37	17	29701105	29701105	+	Missense_Mutation	SNP	G	A	A			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr17:29701105G>A	uc002hgg.2	+	58	8785	c.8452G>A	c.(8452-8454)GCA>ACA	p.A2818T	NF1_uc002hgh.2_Missense_Mutation_p.A2797T|NF1_uc010cso.2_Missense_Mutation_p.A1024T|NF1_uc010wbu.1_RNA	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	2818					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity			soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		CCACGGATCCGCAAGCCAAGT	0.458000			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			4	63	---	---	---	---	0	0	0.009096	0	0
SFRS2	6427	broad.mit.edu	37	17	74732250	74732250	+	Missense_Mutation	SNP	G	C	C			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr17:74732250G>C	uc002jsv.2	-	2	829	c.659C>G	c.(658-660)TCC>TGC	p.S220C	SFRS2_uc002jsw.1_RNA|SFRS2_uc002jsx.1_RNA|SFRS2_uc002jsy.3_Missense_Mutation_p.S220C|SFRS2_uc010wtg.1_Missense_Mutation_p.S208C|MFSD11_uc002jsz.1_5'Flank|MFSD11_uc002jta.2_5'Flank|MFSD11_uc002jtb.2_5'Flank|MFSD11_uc010dha.2_5'Flank|MFSD11_uc002jtc.2_5'Flank|MFSD11_uc002jtd.3_5'Flank|MFSD11_uc010dhb.2_5'Flank|MFSD11_uc002jte.2_5'Flank	NM_003016	NP_003007	Q01130	SRSF2_HUMAN	splicing factor, arginine/serine-rich 2	220	Arg/Ser-rich (RS domain).				mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nuclear speck	nucleotide binding|protein binding|RNA binding|transcription corepressor activity				0						TTCTTAAGAGGACACCGCTCC	0.483000													3	146	---	---	---	---	0	0	0.115264	0	0
CASP14	23581	broad.mit.edu	37	19	15166255	15166255	+	Nonsense_Mutation	SNP	C	T	T			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr19:15166255C>T	uc010dzv.1	+	6	843	c.535C>T	c.(535-537)CGA>TGA	p.R179*	CASP14_uc002naf.2_Nonsense_Mutation_p.R179*	NM_012114	NP_036246	P31944	CASPE_HUMAN	caspase 14 precursor	179					apoptosis|cell differentiation|epidermis development|proteolysis	cytoplasm|nucleus	cysteine-type endopeptidase activity			skin(2)|ovary(1)|lung(1)	4						CATCGCCTACCGACATGATCA	0.537000													3	105	---	---	---	---	0	0	0.009096	0	0
PLA2R1	22925	broad.mit.edu	37	2	160869870	160869870	+	Missense_Mutation	SNP	C	A	A			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr2:160869870C>A	uc002ube.1	-	10	1775	c.1568G>T	c.(1567-1569)GGT>GTT	p.G523V	PLA2R1_uc010zcp.1_Missense_Mutation_p.G523V|PLA2R1_uc002ubf.2_Missense_Mutation_p.G523V	NM_007366	NP_031392	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1 isoform 1 precursor	523	Extracellular (Potential).|C-type lectin 3.			RHG -> ETC (in Ref. 1; AAA70110/ AAC50163).	endocytosis	extracellular space|integral to plasma membrane	receptor activity|sugar binding			skin(2)|ovary(1)	3						ACAGAATCCACCATGTCTCTC	0.378000													16	43	---	---	---	---	1.3612e-06	1.65712e-06	0.132662	1	0
TTN	7273	broad.mit.edu	37	2	179529585	179529585	+	Missense_Mutation	SNP	C	A	A			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr2:179529585C>A	uc010zfk.1	-	11	1098	c.550G>T	c.(550-552)GTT>TTT	p.V184F	TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron|TTN_uc010fre.1_Intron			Q8WZ42	TITIN_HUMAN	SubName: Full=Titin; Flags: Fragment;	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTACCTTTAACTGATGGGGGT	0.383000													5	15	---	---	---	---	0.00198382	0.00222188	0.029380	1	0
SAMSN1	64092	broad.mit.edu	37	21	15893509	15893509	+	Missense_Mutation	SNP	G	A	A			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr21:15893509G>A	uc002yju.1	-	2	173	c.91C>T	c.(91-93)CGG>TGG	p.R31W	SAMSN1_uc010gky.1_Intron|SAMSN1_uc002yjv.1_Missense_Mutation_p.R99W	NM_022136	NP_071419	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization	31					negative regulation of adaptive immune response|negative regulation of B cell activation|negative regulation of peptidyl-tyrosine phosphorylation	cytoplasm|nucleus|ruffle	phosphotyrosine binding			ovary(3)|pancreas(1)	4				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		GAATTATTCCGAAAACGATCG	0.299000													5	29	---	---	---	---	0	0	0.029380	0	0
LRPAP1	4043	broad.mit.edu	37	4	3534117	3534117	+	Missense_Mutation	SNP	G	A	A			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr4:3534117G>A	uc003ghi.2	-	1	108	c.23C>T	c.(22-24)TCG>TTG	p.S8L		NM_002337	NP_002328	P30533	AMRP_HUMAN	low density lipoprotein receptor-related protein	8					negative regulation of protein binding|negative regulation of very-low-density lipoprotein particle clearance|protein folding|vesicle-mediated transport	cell surface|integral to membrane|plasma membrane	asialoglycoprotein receptor activity|heparin binding|low-density lipoprotein particle receptor binding|receptor antagonist activity|unfolded protein binding|very-low-density lipoprotein particle receptor binding			ovary(1)|skin(1)	2				UCEC - Uterine corpus endometrioid carcinoma (64;0.165)		GCGCAGAAACGACCTGACCCT	0.711000													3	4	---	---	---	---	0	0	0.115264	0	0
RGMB	285704	broad.mit.edu	37	5	98115491	98115491	+	Missense_Mutation	SNP	T	A	A			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr5:98115491T>A	uc003knc.2	+	4	869	c.467T>A	c.(466-468)CTC>CAC	p.L156H	RGMB_uc003knb.2_Missense_Mutation_p.L156H	NM_001012761	NP_001012779	Q6NW40	RGMB_HUMAN	RGM domain family, member B	115					axon guidance|BMP signaling pathway|cell adhesion|positive regulation of transcription, DNA-dependent	anchored to plasma membrane|ER-Golgi intermediate compartment|membrane raft	identical protein binding				0		all_cancers(142;2.76e-08)|all_epithelial(76;2.98e-11)|all_lung(232;0.000485)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0587)		ATCAGTGACCTCATGAGCCAG	0.557000													3	65	---	---	---	---	0	0	0.115264	0	0
HS3ST5	222537	broad.mit.edu	37	6	114379018	114379018	+	Silent	SNP	A	G	G			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr6:114379018A>G	uc003pwg.3	-	2	476	c.444T>C	c.(442-444)CCT>CCC	p.P148P	uc003pwf.2_Intron|HS3ST5_uc003pwh.3_Silent_p.P148P	NM_153612	NP_705840	Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine)	148	Lumenal (Potential).				heparan sulfate proteoglycan biosynthetic process, enzymatic modification|negative regulation of coagulation|protein sulfation|regulation of virion penetration into host cell	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity|protein binding			ovary(1)|pancreas(1)	2		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)		TGATTTGCTGAGGGTAGGAAA	0.373000													67	133	---	---	---	---	0	0	0.139131	0	0
LAMA2	3908	broad.mit.edu	37	6	129588337	129588337	+	Silent	SNP	C	A	A			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr6:129588337C>A	uc003qbn.2	+	16	2400	c.2295C>A	c.(2293-2295)TCC>TCA	p.S765S	LAMA2_uc003qbo.2_Silent_p.S765S	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	765	Laminin EGF-like 6.				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)		ATGCGGAGTCCTGTGATGACG	0.488000													4	227	---	---	---	---	0.00024832	0.000289707	0.009096	1	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	T	T			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	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	0.368000	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	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				23	59	---	---	---	---	0	0	0.076483	0	0
MST1P2	11209	broad.mit.edu	37	1	16974141	16974141	+	RNA	DEL	G	-	-			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr1:16974141delG	uc009vow.2	+	5		c.951delG			CROCCL1_uc001azg.1_5'Flank|CROCCL1_uc001azi.1_5'Flank|MST1P2_uc010ocg.1_RNA|MST1P2_uc010och.1_Intron|MST1P2_uc010oci.1_RNA|MST1P2_uc001azk.2_Intron|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_Intron|MST1P2_uc001azm.3_Intron					Homo sapiens cDNA FLJ53774 complete cds, moderately similar to Hepatocyte growth factor-like protein precursor.												0						TGGCTTGGCCGGGGAGGTCAG	0.667													3	4	---	---	---	---					
OR2T29	343563	broad.mit.edu	37	1	248722467	248722470	+	Frame_Shift_Del	DEL	AGAT	-	-			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr1:248722467_248722470delAGAT	uc001ieo.1	-	1	305_308	c.305_308delATCT	c.(304-309)TATCTGfs	p.Y102fs		NM_001004694	NP_001004694	Q8NH02	O2T29_HUMAN	olfactory receptor, family 2, subfamily T,	108_109	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGCTAGTGTCAGATAGAGGAACAT	0.525													2	4	---	---	---	---					
NUP98	4928	broad.mit.edu	37	11	3720389	3720389	+	Frame_Shift_Del	DEL	T	-	-			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr11:3720389delT	uc001lyh.2	-	25	4223	c.3932delA	c.(3931-3933)AACfs	p.N1311fs	NUP98_uc001lyi.2_Frame_Shift_Del_p.N1311fs|NUP98_uc001lyg.2_Frame_Shift_Del_p.N276fs	NM_016320	NP_057404	P52948	NUP98_HUMAN	nucleoporin 98kD isoform 1	1328					carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex	protein binding|structural constituent of nuclear pore|transporter activity			breast(4)|skin(3)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1)	12		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		CACAGGGCTGTTTTTTTGGGT	0.512			T	HOXA9|NSD1|WHSC1L1|DDX10|TOP1|HOXD13|PMX1|HOXA13|HOXD11|HOXA11|RAP1GDS1|HOXC11	AML								7	343	---	---	---	---					
Unknown	0	broad.mit.edu	37	11	58861242	58861243	+	IGR	INS	-	AG	AG	rs143391260	by1000genomes	TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr11:58861242_58861243insAG								GLYATL1 (136726 upstream) : FAM111B (13415 downstream)																							tgaaattctcagagctgggaga	0.089													6	0	---	---	---	---					
EMG1	10436	broad.mit.edu	37	12	7080212	7080213	+	Splice_Site	INS	-	C	C	rs17857448		TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr12:7080212_7080213insC	uc001qsh.3	+	2	272	c.129_splice	c.e2+1	p.L43_splice	PHB2_uc001qsd.2_5'Flank|PHB2_uc010sft.1_5'Flank|PHB2_uc010sfu.1_5'Flank|EMG1_uc009zfo.2_RNA|EMG1_uc010sfv.1_RNA	NM_006331	NP_006322	Q92979	NEP1_HUMAN	ribosome biogenesis protein NEP1						ribosomal small subunit biogenesis	cytoplasm|nucleolus	rRNA (pseudouridine) methyltransferase activity|rRNA binding				0						GAGGCCGTAGTTTATTGTGGTG	0.569													9	15	---	---	---	---					
Unknown	0	broad.mit.edu	37	12	77054687	77054687	+	IGR	DEL	T	-	-	rs2369296	by1000genomes	TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr12:77054687delT								OSBPL8 (101098 upstream) : ZDHHC17 (103167 downstream)																							aaaaaaaaaataaataaaGGA	0.358													4	2	---	---	---	---					
KCNG2	26251	broad.mit.edu	37	18	77623624	77623634	+	5'Flank	DEL	GCAGGAGCCGG	-	-			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr18:77623624_77623634delGCAGGAGCCGG	uc010xfl.1	+							NM_012283	NP_036415	Q9UJ96	KCNG2_HUMAN	potassium voltage-gated channel, subfamily G,						energy reserve metabolic process|regulation of heart contraction|regulation of insulin secretion	voltage-gated potassium channel complex	delayed rectifier potassium channel activity				0		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;6.92e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0244)		CGTTCCTTTTGCAGGAGCCGGGCAGGAGCCC	0.611													2	4	---	---	---	---					
FRG1B	284802	broad.mit.edu	37	20	29623381	29623382	+	5'Flank	DEL	TT	-	-	rs71881437		TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr20:29623381_29623382delTT	uc010ztl.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						GACTCTTCCATTTTTTTTAATT	0.337													11	38	---	---	---	---					
SP8	221833	broad.mit.edu	37	7	20824941	20824943	+	In_Frame_Del	DEL	GCC	-	-			TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr7:20824941_20824943delGCC	uc003suy.2	-	3	680_682	c.439_441delGGC	c.(439-441)GGCdel	p.G147del	SP8_uc003suz.2_In_Frame_Del_p.G165del	NM_198956	NP_945194	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor isoform 2	147					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1						GCGCGGAGGAgccgccgccgccg	0.493													4	6	---	---	---	---					
Unknown	0	broad.mit.edu	37	9	98910245	98910246	+	IGR	INS	-	A	A	rs139074595		TCGA-IM-A3EB-01A-11D-A202-08	TCGA-IM-A3EB-10A-01D-A202-08									Somatic	Phase_I	Capture				Illumina GAIIx	9d2ce873-ca14-42b9-97c2-6d62990c8e29	ee7db9b2-b212-4456-8a4b-ef93d52aea0d	g.chr9:98910245_98910246insA								NCRNA00092 (126208 upstream) : HSD17B3 (87343 downstream)																							ACCATCTCCTGAAAAAAAAAAA	0.312													3	6	---	---	---	---					
