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	validation_method	t_ref_count	validation_status	validation_tumor_sample	t_alt_count	validation_alt_allele	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
CROCCP2	84809	broad.mit.edu	37	1	16946434	16946434	+	RNA	SNP	C	T	T	rs367060		TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr1:16946434C>T	uc010ocf.2	-	2		c.464G>A			CROCCP2_uc009vov.2_Non-coding_Transcript|CROCCP2_uc001aze.3_Non-coding_Transcript|CROCCP2_uc001azf.3_Non-coding_Transcript					Homo sapiens ciliary rootlet coiled-coil, rootletin pseudogene 2 (CROCCP2), non-coding RNA.																		CTCAGCCTTCCGCCGGGCCAG	0.672000														9			3		0	0	0.00024832	0	0
UBE3A	7337	broad.mit.edu	37	15	25616649	25616649	+	Missense_Mutation	SNP	T	A	A			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr15:25616649T>A	uc001zaq.3	-	6	1441	c.681A>T	c.(679-681)ttA>ttT	p.L227F	SNRPN_uc001zae.3_Intron|UBE3A_uc001zar.3_Missense_Mutation_p.L204F|UBE3A_uc001zas.3_Missense_Mutation_p.L224F|UBE3A_uc001zat.3_Missense_Mutation_p.L204F	NM_000462	NP_570853	Q05086	UBE3A_HUMAN	Homo sapiens ubiquitin protein ligase E3A (UBE3A), transcript variant 2, mRNA.	227					brain development|interspecies interaction between organisms|protein K48-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			breast(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	38		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		CATCAGGGCCTAATTTTTGCA	0.418000														130			63		0	0	0.00361006	0	0
GP1BA	2811	broad.mit.edu	37	17	4837738	4837738	+	RNA	SNP	A	G	G			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr17:4837738A>G	uc021toc.1	-	0		c.119T>C			GP1BA_uc021tnz.1_Silent_p.V613V|GP1BA_uc021toa.1_5'Flank|GP1BA_uc021tob.1_Silent_p.V613V			E7ES66	E7ES66_HUMAN	Synthetic construct clone IMAGE:100003573; FLH167768.01X; RZPDo839F0190D glycoprotein Ib (platelet), alpha polypeptide (GP1BA) gene, encodes complete protein.											central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(5)|stomach(1)|urinary_tract(1)	20						TCCTGTGGGTACGGCCTAATG	0.627000											OREG0024109	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		82			60		0	0	0.00361006	0	0
abParts	0	broad.mit.edu	37	14	107062402	107062402	+	RNA	SNP	G	C	C			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr14:107062402G>C	uc021ser.1	-	150		c.6584C>G								Parts of antibodies, mostly variable regions.																		TCCTGGGCCCGACTCCTGCAG	0.597000														69			5		0	0	0.00307968	0	0
AK128361	0	broad.mit.edu	37	19	52496292	52496292	+	Missense_Mutation	SNP	C	A	A	rs146634089		TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr19:52496292C>A	uc021uys.1	-	0	159	c.158G>T	c.(157-159)cGt>cTt	p.R53L	ZNF615_uc002pyf.2_Silent_p.P690P|ZNF615_uc002pye.2_Silent_p.P679P|ZNF615_uc002pyh.2_Silent_p.P690P|ZNF615_uc010epi.2_Silent_p.P686P|ZNF615_uc002pyg.2_Silent_p.P571P|ZNF615_uc010ydg.2_Silent_p.P684P					Homo sapiens cDNA FLJ33710 fis, clone BRAWH2008058.									p.P679P(1)|p.P690P(1)									TGCATTTGTACGGTTTCTCTC	0.408000														103			73		2.94884e-30	2.66152e-29	0.00361006	1	0
ZNF700	90592	broad.mit.edu	37	19	12060395	12060395	+	Missense_Mutation	SNP	C	G	G			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr19:12060395C>G	uc010xme.2	+	4	1801	c.1610C>G	c.(1609-1611)tCt>tGt	p.S537C	ZNF700_uc002msu.3_Missense_Mutation_p.S519C|ZNF700_uc010xmf.2_Intron			Q9H0M5	ZN700_HUMAN	Homo sapiens zinc finger protein 700 (ZNF700), mRNA.	519					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding		ZNF700/MAST1_ENST00000251472(2)	breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	33						GGCTTTTATTCTGCCAAGTCA	0.383000														29			28		0	0	0.000878237	0	0
CHD4	1108	broad.mit.edu	37	12	6711561	6711561	+	Missense_Mutation	SNP	C	G	G			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr12:6711561C>G	uc001qpo.3	-	2	367	c.203G>C	c.(202-204)aGc>aCc	p.S68T	CHD4_uc001qpn.3_Missense_Mutation_p.S68T|CHD4_uc001qpp.3_Missense_Mutation_p.S65T	NM_001273	NP_001264	Q14839	CHD4_HUMAN	Homo sapiens chromodomain helicase DNA binding protein 4 (CHD4), mRNA.	68					chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	NuRD complex|microtubule organizing center	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding			central_nervous_system(2)	2						TTGGCGCTTGCTCTTAGGGAT	0.478000														222			103		0	0	0.00361006	0	0
GPC4	2239	broad.mit.edu	37	X	132458560	132458560	+	Silent	SNP	G	A	A			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chrX:132458560G>A	uc004exc.1	-	2	536	c.324C>T	c.(322-324)ttC>ttT	p.F108F	GPC4_uc011mvg.1_Silent_p.F38F	NM_001448	NP_001439	O75487	GPC4_HUMAN	Homo sapiens glypican 4 (GPC4), mRNA.	108					anatomical structure morphogenesis|cell proliferation	anchored to membrane|external side of plasma membrane|extracellular space|insoluble fraction|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	28	Acute lymphoblastic leukemia(192;0.000127)					GTTCTTTGAAGAATTCTGAAA	0.294000														106			10		0	0	0.000978159	0	0
abParts	0	broad.mit.edu	37	14	107062535	107062535	+	RNA	SNP	C	G	G			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr14:107062535C>G	uc021ser.1	-	149		c.6534G>C								Parts of antibodies, mostly variable regions.																		CTGCCACCAGCAGGAGGAAGA	0.512000														44			3		0	0	0.00024832	0	0
HELQ	113510	broad.mit.edu	37	4	84342848	84342848	+	Silent	SNP	A	G	G			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr4:84342848A>G	uc003hom.3	-	14	2996	c.2817T>C	c.(2815-2817)ttT>ttC	p.F939F	HELQ_uc010ikb.3_Silent_p.F872F|HELQ_uc003hol.4_Non-coding_Transcript|HELQ_uc010ikc.3_Non-coding_Transcript	NM_133636	NP_598375	Q8TDG4	HELQ_HUMAN	Homo sapiens helicase, POLQ-like (HELQ), mRNA.	939							ATP binding|ATP-dependent helicase activity|nucleic acid binding	p.F939V(1)		breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						TATAAAGAACAAAAGACAGAT	0.343000								Other identified genes with known or suspected DNA repair function						23			22		0	0	0.00229938	0	0
MCOLN3	55283	broad.mit.edu	37	1	85491894	85491894	+	Silent	SNP	G	C	C			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr1:85491894G>C	uc001dkp.3	-	7	1053	c.906C>G	c.(904-906)ctC>ctG	p.L302L	MCOLN3_uc001dko.3_5'Flank|MCOLN3_uc001dkq.3_Silent_p.L246L|MCOLN3_uc001dkr.3_Silent_p.L302L|MCOLN3_uc001dks.4_Silent_p.L147L	NM_018298	NP_060768	Q8TDD5	MCLN3_HUMAN	Homo sapiens mucolipin 3 (MCOLN3), transcript variant 1, mRNA.	302						integral to membrane	ion channel activity			endometrium(6)|kidney(3)|large_intestine(9)|lung(12)|prostate(3)|skin(1)	34				all cancers(265;0.00957)|Epithelial(280;0.0254)		ATCTAATGCAGAGGATTAATG	0.398000														59			36		0	0	0.00148497	0	0
LCE3D	84648	broad.mit.edu	37	1	152552161	152552161	+	Silent	SNP	G	A	A			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr1:152552161G>A	uc021oza.1	-	0	252	c.252C>T	c.(250-252)tgC>tgT	p.C84C	LCE3D_uc001fab.3_Silent_p.C84C	NM_032563	NP_115952	Q9BYE3	LCE3D_HUMAN	Homo sapiens late cornified envelope 3D (LCE3D), mRNA.	84					keratinization					breast(1)|endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)|stomach(2)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)|KIRC - Kidney renal clear cell carcinoma(4;0.0323)|Kidney(5;0.0378)		AGCCATGGCCGCAGCCAGAGC	0.622000														132			65		0	0	0.00361006	0	0
CCDC78	124093	broad.mit.edu	37	16	775528	775528	+	Missense_Mutation	SNP	G	T	T			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr16:775528G>T	uc002cjg.3	-	3	426	c.320C>A	c.(319-321)aCc>aAc	p.T107N	CCDC78_uc002cjh.3_5'UTR|CCDC78_uc002cji.3_Missense_Mutation_p.T181N|CCDC78_uc002cjj.3_Intron|CCDC78_uc010uuo.1_Missense_Mutation_p.T107N|CCDC78_uc002cjk.2_Missense_Mutation_p.T107N|HAGHL_uc002cjl.1_5'Flank|HAGHL_uc002cjn.1_5'Flank|HAGHL_uc002cjo.1_5'Flank|HAGHL_uc010uup.1_5'Flank	NM_001031737	NP_001026907	A2IDD5	CCD78_HUMAN	Homo sapiens coiled-coil domain containing 78 (CCDC78), mRNA.	107										central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|lung(2)|skin(3)	9		Hepatocellular(780;0.0218)				GCCCTGGCTGGTGCCATCTCC	0.652000														36			18		6.49762e-13	5.57844e-12	0.00074312	1	0
ACTG2	72	broad.mit.edu	37	2	74128513	74128513	+	Silent	SNP	T	C	C			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr2:74128513T>C	uc002sjw.3	+	1	197	c.75T>C	c.(73-75)gaT>gaC	p.D25D	ACTG2_uc010fex.1_Silent_p.D25D|ACTG2_uc010yrn.2_Silent_p.D25D|ACTG2_uc010fey.3_Silent_p.D25D	NM_001615	NP_001606	P63267	ACTH_HUMAN	Homo sapiens actin, gamma 2, smooth muscle, enteric (ACTG2), transcript variant 1, mRNA.	25					muscle contraction	cytoskeleton|cytosol	ATP binding			large_intestine(3)|lung(14)|skin(1)	18						TCGCAGGAGATGATGCCCCCC	0.622000														54			28		0	0	0.001512	0	0
FGFR4	2264	broad.mit.edu	37	5	176522539	176522539	+	Silent	SNP	C	T	T			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr5:176522539C>T	uc003mfl.3	+	12	1803	c.1636C>T	c.(1636-1638)Ctg>Ttg	p.L546L	FGFR4_uc003mfm.3_Silent_p.L546L|FGFR4_uc011dfu.2_Silent_p.L478L|FGFR4_uc003mfo.3_Silent_p.L506L	NM_002011	NP_998812	P22455	FGFR4_HUMAN	Homo sapiens fibroblast growth factor receptor 4 (FGFR4), transcript variant 1, mRNA.	546	Protein kinase.				insulin receptor signaling pathway|positive regulation of cell proliferation	integral to plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor receptor activity			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)	TGCAGGGCCCCTGTACGTGAT	0.716000										TSP Lung(9;0.080)				9			3		0	0	6.4e-05	0	0
LNX2	222484	broad.mit.edu	37	13	28143269	28143269	+	Silent	SNP	G	A	A			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr13:28143269G>A	uc001url.4	-	2	861	c.552C>T	c.(550-552)ggC>ggT	p.G184G	LNX2_uc001urm.1_Silent_p.G184G	NM_153371	NP_699202	Q8N448	LNX2_HUMAN	Homo sapiens ligand of numb-protein X 2 (LNX2), mRNA.	184							zinc ion binding	p.G184C(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	31		Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.113)|all cancers(112;0.127)|Epithelial(112;0.248)		CAGGCACTGCGCCTGTCCCCA	0.532000														184			91		0	0	0.00361006	0	0
REV3L	5980	broad.mit.edu	37	6	111632330	111632330	+	Missense_Mutation	SNP	A	T	T			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr6:111632330A>T	uc003puy.4	-	28	9078	c.8737T>A	c.(8737-8739)Tac>Aac	p.Y2913N	REV3L_uc003pux.4_Missense_Mutation_p.Y2835N|REV3L_uc003puz.4_Missense_Mutation_p.Y2835N|REV3L_uc003pva.1_Non-coding_Transcript|REV3L_uc003puw.4_5'Flank	NM_002912	NP_002903	O60673	DPOLZ_HUMAN	Homo sapiens REV3-like, catalytic subunit of DNA polymerase zeta (yeast) (REV3L), mRNA.	2913					DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		CTTCCTCTGTATTCCTTGGCA	0.408000								DNA polymerases (catalytic subunits)						154			78		0	0	0.00361006	0	0
CDK5R1	8851	broad.mit.edu	37	17	30815101	30815101	+	Silent	SNP	C	T	T			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr17:30815101C>T	uc002hhn.3	+	1	684	c.463C>T	c.(463-465)Ctg>Ttg	p.L155L	CDK5R1_uc010wca.1_Silent_p.L155L|CDK5R1_uc021tux.1_Silent_p.L155L|CDK5R1_uc010ctc.3_5'UTR	NM_003885	NP_003876	Q15078	CD5R1_HUMAN	Homo sapiens cyclin-dependent kinase 5, regulatory subunit 1 (p35) (CDK5R1), mRNA.	155					axon guidance|axonal fasciculation|brain development|cell proliferation|embryo development|ionotropic glutamate receptor signaling pathway|muscarinic acetylcholine receptor signaling pathway|negative regulation of transcription, DNA-dependent|neuron cell-cell adhesion|neuron migration|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of neuron apoptosis|regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation	axon|contractile fiber|cyclin-dependent protein kinase 5 holoenzyme complex|cytosol|dendritic spine|growth cone|neuromuscular junction|neuronal cell body|perinuclear region of cytoplasm|plasma membrane	cadherin binding|calcium ion binding|protein kinase binding			cervix(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)	8		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.0938)			GCTTCGCTGCCTGGGTGAGTT	0.667000														37			23		0	0	0.00278032	0	0
PKDREJ	10343	broad.mit.edu	37	22	46654232	46654232	+	Missense_Mutation	SNP	A	T	T			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr22:46654232A>T	uc003bhh.3	-	0	4988	c.4988T>A	c.(4987-4989)aTg>aAg	p.M1663K		NM_006071	NP_006062	Q9NTG1	PKDRE_HUMAN	Homo sapiens polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin) (PKDREJ), mRNA.	1663					acrosome reaction|neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		ATGCATACGCATTCCATCCAA	0.418000														55			38		0	0	0.00111076	0	0
IL4I1	259307	broad.mit.edu	37	19	50393785	50393785	+	Silent	SNP	C	T	T			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr19:50393785C>T	uc002pqv.2	-	10	1702	c.873G>A	c.(871-873)ctG>ctA	p.L291L	IL4I1_uc002pqt.1_Silent_p.L282L|IL4I1_uc021uxy.1_Silent_p.L304L|IL4I1_uc002pqu.2_Silent_p.L304L|IL4I1_uc010eno.2_Silent_p.L290L	NM_152899	NP_690863	Q96RQ9	OXLA_HUMAN	Homo sapiens interleukin 4 induced 1 (IL4I1), transcript variant 1, mRNA.	282						lysosome	L-amino-acid oxidase activity			endometrium(3)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)		GCGCGTTCAACAGCACAAGCC	0.711000											OREG0025629	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		21			16		0	0	0.000958276	0	0
ODF4	146852	broad.mit.edu	37	17	8243446	8243446	+	Missense_Mutation	SNP	A	G	G			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr17:8243446A>G	uc002gle.1	+	0	259	c.77A>G	c.(76-78)gAa>gGa	p.E26G		NM_153007	NP_694552	Q2M2E3	ODFP4_HUMAN	Homo sapiens outer dense fiber of sperm tails 4 (ODF4), mRNA.	26					cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|stomach(1)	8						CCTGGAAAGGAAAGGAAGAGT	0.552000														57			3		0	0	0.00024832	0	0
LOC650368	650368	broad.mit.edu	37	11	3427845	3427845	+	RNA	SNP	C	T	T			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr11:3427845C>T	uc010qxs.1	+	8		c.838C>T			LOC650368_uc001lxy.2_Non-coding_Transcript					Homo sapiens asparagine-linked glycosylation 1-like pseudogene (LOC650368), non-coding RNA.																		CTTCAAGTGGCAGGAGCAGAA	0.587000														53			5		0	0	0.000602214	0	0
FAM83G	644815	broad.mit.edu	37	17	18881233	18881233	+	Missense_Mutation	SNP	T	A	A			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr17:18881233T>A	uc002guw.3	-	4	1913	c.1746A>T	c.(1744-1746)gaA>gaT	p.E582D	SLC5A10_uc002gur.1_Intron|SLC5A10_uc002guu.1_Intron|SLC5A10_uc002gut.1_Intron|SLC5A10_uc002guv.1_Intron|SLC5A10_uc010vyl.1_Intron	NM_001039999	NP_001035088	A6ND36	FA83G_HUMAN	Homo sapiens family with sequence similarity 83, member G (FAM83G), mRNA.	582										central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(3)|stomach(1)	22						CGTCATCATCTTCTTCTTCCA	0.657000														73			37		0	0	0.00111076	0	0
SNX29	92017	broad.mit.edu	37	16	12618621	12618621	+	Silent	SNP	C	T	T			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr16:12618621C>T	uc002dby.4	+	19	2303	c.1086C>T	c.(1084-1086)aaC>aaT	p.N362N		NM_032167	NP_115543	Q8TEQ0	SNX29_HUMAN	Homo sapiens sorting nexin 29 (SNX29), mRNA.	362	PX.				cell communication		phosphatidylinositol binding			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						GCGTCATGAACAAAGTCATCC	0.522000														57			37		0	0	0.00375469	0	0
TRIM28	10155	broad.mit.edu	37	19	59057198	59057198	+	Missense_Mutation	SNP	G	A	A			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr19:59057198G>A	uc002qtg.1	+	2	810	c.521G>A	c.(520-522)tGt>tAt	p.C174Y	TRIM28_uc010eut.1_Intron|TRIM28_uc002qth.1_5'Flank	NM_005762	NP_005753	Q13263	TIF1B_HUMAN	Homo sapiens tripartite motif containing 28 (TRIM28), mRNA.	174	RBCC domain.				epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent	nucleoplasm	chromo shadow domain binding|ligase activity|transcription corepressor activity|zinc ion binding			biliary_tract(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		GAGCCTCTGTGTGAGACCTGT	0.577000														49			31		0	0	0.0024448	0	0
SPTAN1	6709	broad.mit.edu	37	9	131361264	131361264	+	Splice_Site	SNP	G	T	T			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr9:131361264G>T	uc004bvl.4	+	26	3685	c.3543_splice	c.e26+1	p.R1181_splice	SPTAN1_uc011mbg.2_Missense_Mutation_p.R1161M|SPTAN1_uc011mbh.2_Splice_Site_p.R1193_splice|SPTAN1_uc004bvm.4_Splice_Site_p.R1181_splice|SPTAN1_uc004bvn.4_Splice_Site_p.R1161_splice	NM_003127	NP_003118	Q13813	SPTA2_HUMAN	Homo sapiens spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) (SPTAN1), transcript variant 2, mRNA.	1181					actin filament capping|axon guidance|cellular component disassembly involved in apoptosis	cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin	actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						ATGATGCCCAGGGTAAGTTTC	0.398000														51			45		2.0833e-19	1.8333e-18	0.00361006	1	0
ACTB	60	broad.mit.edu	37	7	5567465	5567465	+	Missense_Mutation	SNP	A	G	G			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr7:5567465A>G	uc003sot.4	-	5	1126	c.1042T>C	c.(1042-1044)Tcg>Ccg	p.S348P	ACTB_uc003sor.4_Missense_Mutation_p.S226P|ACTB_uc003soq.4_Missense_Mutation_p.S226P	NM_001101	NP_001092	P60709	ACTB_HUMAN	Homo sapiens actin, beta (ACTB), mRNA.	348					'de novo' posttranslational protein folding|adherens junction organization|axon guidance|blood coagulation|cell junction assembly|cellular component movement	MLL5-L complex|NuA4 histone acetyltransferase complex|cytoskeleton|cytosol|ribonucleoprotein complex	ATP binding|kinesin binding|nitric-oxide synthase binding|structural constituent of cytoskeleton			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(2)	8		Ovarian(82;0.0606)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)|OV - Ovarian serous cystadenocarcinoma(56;4.24e-37)		GTGGACAGCGAGGCCAGGATG	0.592000														72			50		0	0	0.00361006	0	0
TOPORS	10210	broad.mit.edu	37	9	32543270	32543270	+	Missense_Mutation	SNP	T	C	C			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr9:32543270T>C	uc003zrb.3	-	2	1445	c.1253A>G	c.(1252-1254)gAt>gGt	p.D418G	TOPORS_uc003zrc.3_Missense_Mutation_p.D353G	NM_005802	NP_001182551	Q9NS56	TOPRS_HUMAN	Homo sapiens topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase (TOPORS), transcript variant 1, mRNA.	418					DNA damage response, signal transduction resulting in induction of apoptosis|maintenance of protein location in nucleus|proteasomal ubiquitin-dependent protein catabolic process|protein sumoylation|transcription, DNA-dependent	PML body|nuclear speck	DNA binding|DNA topoisomerase I binding|SUMO ligase activity|antigen binding|ubiquitin-protein ligase activity|zinc ion binding			large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		TGGAGTTTCATCATCCCATGG	0.423000														69			52		0	0	0.00361006	0	0
MET	4233	broad.mit.edu	37	7	116423474	116423474	+	Missense_Mutation	SNP	T	C	C	rs121913245		TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr7:116423474T>C	uc003vij.3	+	18	3936	c.3749T>C	c.(3748-3750)aTg>aCg	p.M1250T	MET_uc010lkh.3_Missense_Mutation_p.M1268T|MET_uc011knj.2_Missense_Mutation_p.M820T	NM_000245	NP_000236	P08581	MET_HUMAN	Homo sapiens met proto-oncogene (hepatocyte growth factor receptor) (MET), transcript variant 2, mRNA.	1250	Interaction with RANBP9.|Protein kinase.		M -> I (in HCC).|M -> T (in RCCP; somatic mutation).		axon guidance|cell proliferation	basal plasma membrane|integral to plasma membrane	ATP binding|hepatocyte growth factor receptor activity|protein binding	p.M1268T(4)		NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GTGAAGTGGATGGCTTTGGAA	0.393000			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)					28			23		0	0	0.00229938	0	0
KLHL1	57626	broad.mit.edu	37	13	70549759	70549759	+	Missense_Mutation	SNP	C	G	G			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr13:70549759C>G	uc001vip.3	-	1	1467	c.673G>C	c.(673-675)Gca>Cca	p.A225P	KLHL1_uc010thm.2_Intron	NM_020866	NP_065917	Q9NR64	KLHL1_HUMAN	Homo sapiens kelch-like 1 (Drosophila) (KLHL1), mRNA.	225	BTB.				actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(56)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	84		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)		TACCTATGTGCAGGTATCTTT	0.403000														87			40		0	0	0.00285205	0	0
PGGT1B	5229	broad.mit.edu	37	5	114573574	114573574	+	Missense_Mutation	SNP	G	A	A			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr5:114573574G>A	uc003kqw.4	-	3	481	c.460C>T	c.(460-462)Ctt>Ttt	p.L154F	PGGT1B_uc010jch.3_Missense_Mutation_p.L154F	NM_005023	NP_005014	P53609	PGTB1_HUMAN	Homo sapiens protein geranylgeranyltransferase type I, beta subunit (PGGT1B), mRNA.	154					protein geranylgeranylation	CAAX-protein geranylgeranyltransferase complex	CAAX-protein geranylgeranyltransferase activity			breast(2)|endometrium(1)|large_intestine(2)|lung(1)	6		all_cancers(142;0.000523)|all_epithelial(76;6.45e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		Epithelial(69;2.95e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.98e-08)|all cancers(49;3.1e-06)	Pravastatin(DB00175)	TCCAGCTGAAGGGCTCTCAAG	0.383000														83			55		0	0	0.00361006	0	0
VPS11	55823	broad.mit.edu	37	11	118949934	118949934	+	Missense_Mutation	SNP	C	A	A			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr11:118949934C>A	uc010ryx.2	+	14	2398	c.2356C>A	c.(2356-2358)Cag>Aag	p.Q786K	VPS11_uc010ryy.2_Missense_Mutation_p.Q634K	NM_021729	NP_068375	Q9H270	VPS11_HUMAN	Homo sapiens vacuolar protein sorting 11 homolog (S. cerevisiae) (VPS11), mRNA.	788					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)		GCAGATTGCACAGGATGAGCT	0.592000														19			10		0.000978159	0.00800725	0.000978159	1	0
BCAN	63827	broad.mit.edu	37	1	156615922	156615922	+	Missense_Mutation	SNP	G	C	C			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr1:156615922G>C	uc001fpp.3	+	1	412	c.76G>C	c.(76-78)Gaa>Caa	p.E26Q	BC005081_uc021pbg.1_5'Flank|BCAN_uc001fpo.3_Missense_Mutation_p.E26Q	NM_021948	NP_068767	Q96GW7	PGCB_HUMAN	Homo sapiens brevican (BCAN), transcript variant 1, mRNA.	26					cell adhesion	anchored to membrane|proteinaceous extracellular matrix	hyaluronic acid binding|sugar binding			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					AGATGTTCTGGAAGGAGACAG	0.602000														53			3		0	0	6.4e-05	0	0
WDR55	54853	broad.mit.edu	37	5	140049032	140049032	+	Silent	SNP	T	C	C			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr5:140049032T>C	uc003lgr.4	+	6	1059	c.945T>C	c.(943-945)caT>caC	p.H315H	WDR55_uc011czl.1_Intron	NM_017706	NP_060176	Q9H6Y2	WDR55_HUMAN	Homo sapiens WD repeat domain 55 (WDR55), mRNA.	315					rRNA processing	cytoplasm|nucleolus				NS(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTAGTGGCCATGACCAGCGCC	0.632000														24			16		0	0	0.00400662	0	0
BHMT	635	broad.mit.edu	37	5	78415091	78415091	+	Missense_Mutation	SNP	T	C	C			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr5:78415091T>C	uc003kfu.4	+	2	281	c.176T>C	c.(175-177)cTt>cCt	p.L59P	BHMT_uc011cti.2_Intron	NM_001713	NP_001704	Q93088	BHMT1_HUMAN	Homo sapiens betaine--homocysteine S-methyltransferase (BHMT), mRNA.	59	Hcy-binding.				protein methylation|regulation of homocysteine metabolic process	cytoplasm	betaine-homocysteine S-methyltransferase activity|homocysteine S-methyltransferase activity|zinc ion binding			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)	29		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.88e-45)|Epithelial(54;8.07e-41)|all cancers(79;3.51e-36)	L-Methionine(DB00134)	GTTCGCCAGCTTCATCGAGAG	0.438000														57			33		0	0	0.00111076	0	0
SSR3	6747	broad.mit.edu	37	3	156266708	156266708	+	Missense_Mutation	SNP	C	A	A			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr3:156266708C>A	uc011bop.2	-	2	440	c.345G>T	c.(343-345)aaG>aaT	p.K115N	SSR3_uc003fau.3_Missense_Mutation_p.K115N	NM_007107	NP_009038	Q9UNL2	SSRG_HUMAN	Homo sapiens signal sequence receptor, gamma (translocon-associated protein gamma) (SSR3), mRNA.	115					cotranslational protein targeting to membrane	Sec61 translocon complex|integral to endoplasmic reticulum membrane|microsome	protein binding|signal sequence binding	p.R114W(1)		endometrium(1)|prostate(2)	3			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			CATCTTTCTCCTTCCGAGACA	0.363000														73			24		6.44725e-10	5.40341e-09	0.00229938	1	0
SULT1C4	27233	broad.mit.edu	37	2	108994906	108994906	+	Missense_Mutation	SNP	T	C	C			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr2:108994906T>C	uc002tea.1	+	0	486	c.113T>C	c.(112-114)aTc>aCc	p.I38T	SULT1C4_uc010ywr.1_Non-coding_Transcript|SULT1C4_uc002teb.1_Missense_Mutation_p.I38T	NM_006588	NP_006579	O75897	ST1C4_HUMAN	Homo sapiens sulfotransferase family, cytosolic, 1C, member 4 (SULT1C4), mRNA.	38					3'-phosphoadenosine 5'-phosphosulfate metabolic process|sulfation|xenobiotic metabolic process	cytosol	sulfotransferase activity			endometrium(1)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	12						TGGGATAAGATCTGGAACTTC	0.473000														143			111		0	0	0.00361006	0	0
BC063132	0	broad.mit.edu	37	GL000241.1	36864	36864	+	RNA	SNP	T	A	A			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chrGL000241.1:36864T>A	uc011mgv.2	-	0		c.12A>T								Homo sapiens cDNA clone IMAGE:4673444, containing frame-shift errors.																		GCGGGGAGGATCAGAAGTGGA	0.582000														4			5		0	0	0.000602214	0	0
UBE3A	7337	broad.mit.edu	37	15	25616649	25616649	+	Missense_Mutation	SNP	T	A	A			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr15:25616649T>A	uc001zaq.3	-	6	1441	c.681A>T	c.(679-681)ttA>ttT	p.L227F	SNRPN_uc001zae.3_Intron|UBE3A_uc001zar.3_Missense_Mutation_p.L204F|UBE3A_uc001zas.3_Missense_Mutation_p.L224F|UBE3A_uc001zat.3_Missense_Mutation_p.L204F	NM_000462	NP_570853	Q05086	UBE3A_HUMAN	Homo sapiens ubiquitin protein ligase E3A (UBE3A), transcript variant 2, mRNA.	227					brain development|interspecies interaction between organisms|protein K48-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			breast(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	38		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		CATCAGGGCCTAATTTTTGCA	0.418000														130			63		0	0	0.00361006	0	0
GP1BA	2811	broad.mit.edu	37	17	4837738	4837738	+	RNA	SNP	A	G	G			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr17:4837738A>G	uc021toc.1	-	0		c.119T>C			GP1BA_uc021tnz.1_Silent_p.V613V|GP1BA_uc021toa.1_5'Flank|GP1BA_uc021tob.1_Silent_p.V613V			E7ES66	E7ES66_HUMAN	Synthetic construct clone IMAGE:100003573; FLH167768.01X; RZPDo839F0190D glycoprotein Ib (platelet), alpha polypeptide (GP1BA) gene, encodes complete protein.											central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(5)|stomach(1)|urinary_tract(1)	20						TCCTGTGGGTACGGCCTAATG	0.627000											OREG0024109	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		82			60		0	0	0.00361006	0	0
AK128361	0	broad.mit.edu	37	19	52496292	52496292	+	Missense_Mutation	SNP	C	A	A	rs146634089		TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr19:52496292C>A	uc021uys.1	-	0	159	c.158G>T	c.(157-159)cGt>cTt	p.R53L	ZNF615_uc002pyf.2_Silent_p.P690P|ZNF615_uc002pye.2_Silent_p.P679P|ZNF615_uc002pyh.2_Silent_p.P690P|ZNF615_uc010epi.2_Silent_p.P686P|ZNF615_uc002pyg.2_Silent_p.P571P|ZNF615_uc010ydg.2_Silent_p.P684P					Homo sapiens cDNA FLJ33710 fis, clone BRAWH2008058.									p.P679P(1)|p.P690P(1)									TGCATTTGTACGGTTTCTCTC	0.408000														103			73		2.94884e-30	2.74708e-29	0.00361006	1	0
ZNF700	90592	broad.mit.edu	37	19	12060395	12060395	+	Missense_Mutation	SNP	C	G	G			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr19:12060395C>G	uc010xme.2	+	4	1801	c.1610C>G	c.(1609-1611)tCt>tGt	p.S537C	ZNF700_uc002msu.3_Missense_Mutation_p.S519C|ZNF700_uc010xmf.2_Intron			Q9H0M5	ZN700_HUMAN	Homo sapiens zinc finger protein 700 (ZNF700), mRNA.	519					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding		ZNF700/MAST1_ENST00000251472(2)	breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	33						GGCTTTTATTCTGCCAAGTCA	0.383000														29			28		0	0	0.000878237	0	0
CHD4	1108	broad.mit.edu	37	12	6711561	6711561	+	Missense_Mutation	SNP	C	G	G			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr12:6711561C>G	uc001qpo.3	-	2	367	c.203G>C	c.(202-204)aGc>aCc	p.S68T	CHD4_uc001qpn.3_Missense_Mutation_p.S68T|CHD4_uc001qpp.3_Missense_Mutation_p.S65T	NM_001273	NP_001264	Q14839	CHD4_HUMAN	Homo sapiens chromodomain helicase DNA binding protein 4 (CHD4), mRNA.	68					chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	NuRD complex|microtubule organizing center	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding			central_nervous_system(2)	2						TTGGCGCTTGCTCTTAGGGAT	0.478000														222			103		0	0	0.00361006	0	0
GPC4	2239	broad.mit.edu	37	X	132458560	132458560	+	Silent	SNP	G	A	A			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chrX:132458560G>A	uc004exc.1	-	2	536	c.324C>T	c.(322-324)ttC>ttT	p.F108F	GPC4_uc011mvg.1_Silent_p.F38F	NM_001448	NP_001439	O75487	GPC4_HUMAN	Homo sapiens glypican 4 (GPC4), mRNA.	108					anatomical structure morphogenesis|cell proliferation	anchored to membrane|external side of plasma membrane|extracellular space|insoluble fraction|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	28	Acute lymphoblastic leukemia(192;0.000127)					GTTCTTTGAAGAATTCTGAAA	0.294000														106			10		0	0	0.000978159	0	0
HELQ	113510	broad.mit.edu	37	4	84342848	84342848	+	Silent	SNP	A	G	G			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr4:84342848A>G	uc003hom.3	-	14	2996	c.2817T>C	c.(2815-2817)ttT>ttC	p.F939F	HELQ_uc010ikb.3_Silent_p.F872F|HELQ_uc003hol.4_Non-coding_Transcript|HELQ_uc010ikc.3_Non-coding_Transcript	NM_133636	NP_598375	Q8TDG4	HELQ_HUMAN	Homo sapiens helicase, POLQ-like (HELQ), mRNA.	939							ATP binding|ATP-dependent helicase activity|nucleic acid binding	p.F939V(1)		breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						TATAAAGAACAAAAGACAGAT	0.343000								Other identified genes with known or suspected DNA repair function						23			22		0	0	0.00229938	0	0
MCOLN3	55283	broad.mit.edu	37	1	85491894	85491894	+	Silent	SNP	G	C	C			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr1:85491894G>C	uc001dkp.3	-	7	1053	c.906C>G	c.(904-906)ctC>ctG	p.L302L	MCOLN3_uc001dko.3_5'Flank|MCOLN3_uc001dkq.3_Silent_p.L246L|MCOLN3_uc001dkr.3_Silent_p.L302L|MCOLN3_uc001dks.4_Silent_p.L147L	NM_018298	NP_060768	Q8TDD5	MCLN3_HUMAN	Homo sapiens mucolipin 3 (MCOLN3), transcript variant 1, mRNA.	302						integral to membrane	ion channel activity			endometrium(6)|kidney(3)|large_intestine(9)|lung(12)|prostate(3)|skin(1)	34				all cancers(265;0.00957)|Epithelial(280;0.0254)		ATCTAATGCAGAGGATTAATG	0.398000														59			36		0	0	0.00148497	0	0
LCE3D	84648	broad.mit.edu	37	1	152552161	152552161	+	Silent	SNP	G	A	A			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr1:152552161G>A	uc021oza.1	-	0	252	c.252C>T	c.(250-252)tgC>tgT	p.C84C	LCE3D_uc001fab.3_Silent_p.C84C	NM_032563	NP_115952	Q9BYE3	LCE3D_HUMAN	Homo sapiens late cornified envelope 3D (LCE3D), mRNA.	84					keratinization					breast(1)|endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)|stomach(2)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)|KIRC - Kidney renal clear cell carcinoma(4;0.0323)|Kidney(5;0.0378)		AGCCATGGCCGCAGCCAGAGC	0.622000														132			65		0	0	0.00361006	0	0
CCDC78	124093	broad.mit.edu	37	16	775528	775528	+	Missense_Mutation	SNP	G	T	T			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr16:775528G>T	uc002cjg.3	-	3	426	c.320C>A	c.(319-321)aCc>aAc	p.T107N	CCDC78_uc002cjh.3_5'UTR|CCDC78_uc002cji.3_Missense_Mutation_p.T181N|CCDC78_uc002cjj.3_Intron|CCDC78_uc010uuo.1_Missense_Mutation_p.T107N|CCDC78_uc002cjk.2_Missense_Mutation_p.T107N|HAGHL_uc002cjl.1_5'Flank|HAGHL_uc002cjn.1_5'Flank|HAGHL_uc002cjo.1_5'Flank|HAGHL_uc010uup.1_5'Flank	NM_001031737	NP_001026907	A2IDD5	CCD78_HUMAN	Homo sapiens coiled-coil domain containing 78 (CCDC78), mRNA.	107										central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|lung(2)|skin(3)	9		Hepatocellular(780;0.0218)				GCCCTGGCTGGTGCCATCTCC	0.652000														36			18		6.49762e-13	5.75039e-12	0.00074312	1	0
ACTG2	72	broad.mit.edu	37	2	74128513	74128513	+	Silent	SNP	T	C	C			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr2:74128513T>C	uc002sjw.3	+	1	197	c.75T>C	c.(73-75)gaT>gaC	p.D25D	ACTG2_uc010fex.1_Silent_p.D25D|ACTG2_uc010yrn.2_Silent_p.D25D|ACTG2_uc010fey.3_Silent_p.D25D	NM_001615	NP_001606	P63267	ACTH_HUMAN	Homo sapiens actin, gamma 2, smooth muscle, enteric (ACTG2), transcript variant 1, mRNA.	25					muscle contraction	cytoskeleton|cytosol	ATP binding			large_intestine(3)|lung(14)|skin(1)	18						TCGCAGGAGATGATGCCCCCC	0.622000														54			28		0	0	0.001512	0	0
FGFR4	2264	broad.mit.edu	37	5	176522539	176522539	+	Silent	SNP	C	T	T			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr5:176522539C>T	uc003mfl.3	+	12	1803	c.1636C>T	c.(1636-1638)Ctg>Ttg	p.L546L	FGFR4_uc003mfm.3_Silent_p.L546L|FGFR4_uc011dfu.2_Silent_p.L478L|FGFR4_uc003mfo.3_Silent_p.L506L	NM_002011	NP_998812	P22455	FGFR4_HUMAN	Homo sapiens fibroblast growth factor receptor 4 (FGFR4), transcript variant 1, mRNA.	546	Protein kinase.				insulin receptor signaling pathway|positive regulation of cell proliferation	integral to plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor receptor activity			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)	TGCAGGGCCCCTGTACGTGAT	0.716000										TSP Lung(9;0.080)				9			3		0	0	6.4e-05	0	0
LNX2	222484	broad.mit.edu	37	13	28143269	28143269	+	Silent	SNP	G	A	A			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr13:28143269G>A	uc001url.4	-	2	861	c.552C>T	c.(550-552)ggC>ggT	p.G184G	LNX2_uc001urm.1_Silent_p.G184G	NM_153371	NP_699202	Q8N448	LNX2_HUMAN	Homo sapiens ligand of numb-protein X 2 (LNX2), mRNA.	184							zinc ion binding	p.G184C(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	31		Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.113)|all cancers(112;0.127)|Epithelial(112;0.248)		CAGGCACTGCGCCTGTCCCCA	0.532000														184			91		0	0	0.00361006	0	0
REV3L	5980	broad.mit.edu	37	6	111632330	111632330	+	Missense_Mutation	SNP	A	T	T			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr6:111632330A>T	uc003puy.4	-	28	9078	c.8737T>A	c.(8737-8739)Tac>Aac	p.Y2913N	REV3L_uc003pux.4_Missense_Mutation_p.Y2835N|REV3L_uc003puz.4_Missense_Mutation_p.Y2835N|REV3L_uc003pva.1_Non-coding_Transcript|REV3L_uc003puw.4_5'Flank	NM_002912	NP_002903	O60673	DPOLZ_HUMAN	Homo sapiens REV3-like, catalytic subunit of DNA polymerase zeta (yeast) (REV3L), mRNA.	2913					DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		CTTCCTCTGTATTCCTTGGCA	0.408000								DNA polymerases (catalytic subunits)						154			78		0	0	0.00361006	0	0
CDK5R1	8851	broad.mit.edu	37	17	30815101	30815101	+	Silent	SNP	C	T	T			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr17:30815101C>T	uc002hhn.3	+	1	684	c.463C>T	c.(463-465)Ctg>Ttg	p.L155L	CDK5R1_uc010wca.1_Silent_p.L155L|CDK5R1_uc021tux.1_Silent_p.L155L|CDK5R1_uc010ctc.3_5'UTR	NM_003885	NP_003876	Q15078	CD5R1_HUMAN	Homo sapiens cyclin-dependent kinase 5, regulatory subunit 1 (p35) (CDK5R1), mRNA.	155					axon guidance|axonal fasciculation|brain development|cell proliferation|embryo development|ionotropic glutamate receptor signaling pathway|muscarinic acetylcholine receptor signaling pathway|negative regulation of transcription, DNA-dependent|neuron cell-cell adhesion|neuron migration|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of neuron apoptosis|regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation	axon|contractile fiber|cyclin-dependent protein kinase 5 holoenzyme complex|cytosol|dendritic spine|growth cone|neuromuscular junction|neuronal cell body|perinuclear region of cytoplasm|plasma membrane	cadherin binding|calcium ion binding|protein kinase binding			cervix(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)	8		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.0938)			GCTTCGCTGCCTGGGTGAGTT	0.667000														37			23		0	0	0.00278032	0	0
PKDREJ	10343	broad.mit.edu	37	22	46654232	46654232	+	Missense_Mutation	SNP	A	T	T			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr22:46654232A>T	uc003bhh.3	-	0	4988	c.4988T>A	c.(4987-4989)aTg>aAg	p.M1663K		NM_006071	NP_006062	Q9NTG1	PKDRE_HUMAN	Homo sapiens polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin) (PKDREJ), mRNA.	1663					acrosome reaction|neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		ATGCATACGCATTCCATCCAA	0.418000														55			38		0	0	0.00111076	0	0
IL4I1	259307	broad.mit.edu	37	19	50393785	50393785	+	Silent	SNP	C	T	T			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr19:50393785C>T	uc002pqv.2	-	10	1702	c.873G>A	c.(871-873)ctG>ctA	p.L291L	IL4I1_uc002pqt.1_Silent_p.L282L|IL4I1_uc021uxy.1_Silent_p.L304L|IL4I1_uc002pqu.2_Silent_p.L304L|IL4I1_uc010eno.2_Silent_p.L290L	NM_152899	NP_690863	Q96RQ9	OXLA_HUMAN	Homo sapiens interleukin 4 induced 1 (IL4I1), transcript variant 1, mRNA.	282						lysosome	L-amino-acid oxidase activity			endometrium(3)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)		GCGCGTTCAACAGCACAAGCC	0.711000											OREG0025629	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		21			16		0	0	0.000958276	0	0
ODF4	146852	broad.mit.edu	37	17	8243446	8243446	+	Missense_Mutation	SNP	A	G	G			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr17:8243446A>G	uc002gle.1	+	0	259	c.77A>G	c.(76-78)gAa>gGa	p.E26G		NM_153007	NP_694552	Q2M2E3	ODFP4_HUMAN	Homo sapiens outer dense fiber of sperm tails 4 (ODF4), mRNA.	26					cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|stomach(1)	8						CCTGGAAAGGAAAGGAAGAGT	0.552000														57			3		0	0	0.00024832	0	0
FAM83G	644815	broad.mit.edu	37	17	18881233	18881233	+	Missense_Mutation	SNP	T	A	A			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr17:18881233T>A	uc002guw.3	-	4	1913	c.1746A>T	c.(1744-1746)gaA>gaT	p.E582D	SLC5A10_uc002gur.1_Intron|SLC5A10_uc002guu.1_Intron|SLC5A10_uc002gut.1_Intron|SLC5A10_uc002guv.1_Intron|SLC5A10_uc010vyl.1_Intron	NM_001039999	NP_001035088	A6ND36	FA83G_HUMAN	Homo sapiens family with sequence similarity 83, member G (FAM83G), mRNA.	582										central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(3)|stomach(1)	22						CGTCATCATCTTCTTCTTCCA	0.657000														73			37		0	0	0.00111076	0	0
SNX29	92017	broad.mit.edu	37	16	12618621	12618621	+	Silent	SNP	C	T	T			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr16:12618621C>T	uc002dby.4	+	19	2303	c.1086C>T	c.(1084-1086)aaC>aaT	p.N362N		NM_032167	NP_115543	Q8TEQ0	SNX29_HUMAN	Homo sapiens sorting nexin 29 (SNX29), mRNA.	362	PX.				cell communication		phosphatidylinositol binding			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						GCGTCATGAACAAAGTCATCC	0.522000														57			37		0	0	0.00375469	0	0
TRIM28	10155	broad.mit.edu	37	19	59057198	59057198	+	Missense_Mutation	SNP	G	A	A			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr19:59057198G>A	uc002qtg.1	+	2	810	c.521G>A	c.(520-522)tGt>tAt	p.C174Y	TRIM28_uc010eut.1_Intron|TRIM28_uc002qth.1_5'Flank	NM_005762	NP_005753	Q13263	TIF1B_HUMAN	Homo sapiens tripartite motif containing 28 (TRIM28), mRNA.	174	RBCC domain.				epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent	nucleoplasm	chromo shadow domain binding|ligase activity|transcription corepressor activity|zinc ion binding			biliary_tract(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		GAGCCTCTGTGTGAGACCTGT	0.577000														49			31		0	0	0.0024448	0	0
SPTAN1	6709	broad.mit.edu	37	9	131361264	131361264	+	Splice_Site	SNP	G	T	T			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr9:131361264G>T	uc004bvl.4	+	26	3685	c.3543_splice	c.e26+1	p.R1181_splice	SPTAN1_uc011mbg.2_Missense_Mutation_p.R1161M|SPTAN1_uc011mbh.2_Splice_Site_p.R1193_splice|SPTAN1_uc004bvm.4_Splice_Site_p.R1181_splice|SPTAN1_uc004bvn.4_Splice_Site_p.R1161_splice	NM_003127	NP_003118	Q13813	SPTA2_HUMAN	Homo sapiens spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) (SPTAN1), transcript variant 2, mRNA.	1181					actin filament capping|axon guidance|cellular component disassembly involved in apoptosis	cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin	actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						ATGATGCCCAGGGTAAGTTTC	0.398000														51			45		2.0833e-19	1.891e-18	0.00361006	1	0
ACTB	60	broad.mit.edu	37	7	5567465	5567465	+	Missense_Mutation	SNP	A	G	G			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr7:5567465A>G	uc003sot.4	-	5	1126	c.1042T>C	c.(1042-1044)Tcg>Ccg	p.S348P	ACTB_uc003sor.4_Missense_Mutation_p.S226P|ACTB_uc003soq.4_Missense_Mutation_p.S226P	NM_001101	NP_001092	P60709	ACTB_HUMAN	Homo sapiens actin, beta (ACTB), mRNA.	348					'de novo' posttranslational protein folding|adherens junction organization|axon guidance|blood coagulation|cell junction assembly|cellular component movement	MLL5-L complex|NuA4 histone acetyltransferase complex|cytoskeleton|cytosol|ribonucleoprotein complex	ATP binding|kinesin binding|nitric-oxide synthase binding|structural constituent of cytoskeleton			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(2)	8		Ovarian(82;0.0606)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)|OV - Ovarian serous cystadenocarcinoma(56;4.24e-37)		GTGGACAGCGAGGCCAGGATG	0.592000														72			50		0	0	0.00361006	0	0
MET	4233	broad.mit.edu	37	7	116423474	116423474	+	Missense_Mutation	SNP	T	C	C	rs121913245		TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr7:116423474T>C	uc003vij.3	+	18	3936	c.3749T>C	c.(3748-3750)aTg>aCg	p.M1250T	MET_uc010lkh.3_Missense_Mutation_p.M1268T|MET_uc011knj.2_Missense_Mutation_p.M820T	NM_000245	NP_000236	P08581	MET_HUMAN	Homo sapiens met proto-oncogene (hepatocyte growth factor receptor) (MET), transcript variant 2, mRNA.	1250	Interaction with RANBP9.|Protein kinase.		M -> I (in HCC).|M -> T (in RCCP; somatic mutation).		axon guidance|cell proliferation	basal plasma membrane|integral to plasma membrane	ATP binding|hepatocyte growth factor receptor activity|protein binding	p.M1268T(4)		NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GTGAAGTGGATGGCTTTGGAA	0.393000			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)					28			23		0	0	0.00229938	0	0
KLHL1	57626	broad.mit.edu	37	13	70549759	70549759	+	Missense_Mutation	SNP	C	G	G			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr13:70549759C>G	uc001vip.3	-	1	1467	c.673G>C	c.(673-675)Gca>Cca	p.A225P	KLHL1_uc010thm.2_Intron	NM_020866	NP_065917	Q9NR64	KLHL1_HUMAN	Homo sapiens kelch-like 1 (Drosophila) (KLHL1), mRNA.	225	BTB.				actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(56)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	84		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)		TACCTATGTGCAGGTATCTTT	0.403000														87			40		0	0	0.00285205	0	0
PGGT1B	5229	broad.mit.edu	37	5	114573574	114573574	+	Missense_Mutation	SNP	G	A	A			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr5:114573574G>A	uc003kqw.4	-	3	481	c.460C>T	c.(460-462)Ctt>Ttt	p.L154F	PGGT1B_uc010jch.3_Missense_Mutation_p.L154F	NM_005023	NP_005014	P53609	PGTB1_HUMAN	Homo sapiens protein geranylgeranyltransferase type I, beta subunit (PGGT1B), mRNA.	154					protein geranylgeranylation	CAAX-protein geranylgeranyltransferase complex	CAAX-protein geranylgeranyltransferase activity			breast(2)|endometrium(1)|large_intestine(2)|lung(1)	6		all_cancers(142;0.000523)|all_epithelial(76;6.45e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		Epithelial(69;2.95e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.98e-08)|all cancers(49;3.1e-06)	Pravastatin(DB00175)	TCCAGCTGAAGGGCTCTCAAG	0.383000														83			55		0	0	0.00361006	0	0
VPS11	55823	broad.mit.edu	37	11	118949934	118949934	+	Missense_Mutation	SNP	C	A	A			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr11:118949934C>A	uc010ryx.2	+	14	2398	c.2356C>A	c.(2356-2358)Cag>Aag	p.Q786K	VPS11_uc010ryy.2_Missense_Mutation_p.Q634K	NM_021729	NP_068375	Q9H270	VPS11_HUMAN	Homo sapiens vacuolar protein sorting 11 homolog (S. cerevisiae) (VPS11), mRNA.	788					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)		GCAGATTGCACAGGATGAGCT	0.592000														19			10		0.000978159	0.00824448	0.000978159	1	0
MGC70870	403340	broad.mit.edu	37	GL000205.1	118680	118680	+	RNA	SNP	T	C	C			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chrGL000205.1:118680T>C	uc002kgk.4	+	0		c.2058T>C								Homo sapiens C-terminal binding protein 2 pseudogene (MGC70870), non-coding RNA.																		GTGTGATTTATTAACGCCCAA	0.378000														2			3		0	0	6.4e-05	0	0
BCAN	63827	broad.mit.edu	37	1	156615922	156615922	+	Missense_Mutation	SNP	G	C	C			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr1:156615922G>C	uc001fpp.3	+	1	412	c.76G>C	c.(76-78)Gaa>Caa	p.E26Q	BC005081_uc021pbg.1_5'Flank|BCAN_uc001fpo.3_Missense_Mutation_p.E26Q	NM_021948	NP_068767	Q96GW7	PGCB_HUMAN	Homo sapiens brevican (BCAN), transcript variant 1, mRNA.	26					cell adhesion	anchored to membrane|proteinaceous extracellular matrix	hyaluronic acid binding|sugar binding			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					AGATGTTCTGGAAGGAGACAG	0.602000														53			3		0	0	6.4e-05	0	0
TOPORS	10210	broad.mit.edu	37	9	32543270	32543270	+	Missense_Mutation	SNP	T	C	C			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr9:32543270T>C	uc003zrb.3	-	2	1445	c.1253A>G	c.(1252-1254)gAt>gGt	p.D418G	TOPORS_uc003zrc.3_Missense_Mutation_p.D353G	NM_005802	NP_001182551	Q9NS56	TOPRS_HUMAN	Homo sapiens topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase (TOPORS), transcript variant 1, mRNA.	418					DNA damage response, signal transduction resulting in induction of apoptosis|maintenance of protein location in nucleus|proteasomal ubiquitin-dependent protein catabolic process|protein sumoylation|transcription, DNA-dependent	PML body|nuclear speck	DNA binding|DNA topoisomerase I binding|SUMO ligase activity|antigen binding|ubiquitin-protein ligase activity|zinc ion binding			large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		TGGAGTTTCATCATCCCATGG	0.423000														69			52		0	0	0.00361006	0	0
KRTAP26-1	388818	broad.mit.edu	37	21	31692296	31692296	+	Missense_Mutation	SNP	G	A	A			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr21:31692296G>A	uc002ynw.3	-	0	312	c.58C>T	c.(58-60)Cgc>Tgc	p.R20C		NM_203405	NP_981950	Q6PEX3	KR261_HUMAN	Homo sapiens keratin associated protein 26-1 (KRTAP26-1), mRNA.	20						intermediate filament				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16						GGAATATGGCGGGAGGTTCTG	0.532000														57			5		0	0	0.000602214	0	0
WDR55	54853	broad.mit.edu	37	5	140049032	140049032	+	Silent	SNP	T	C	C			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr5:140049032T>C	uc003lgr.4	+	6	1059	c.945T>C	c.(943-945)caT>caC	p.H315H	WDR55_uc011czl.1_Intron	NM_017706	NP_060176	Q9H6Y2	WDR55_HUMAN	Homo sapiens WD repeat domain 55 (WDR55), mRNA.	315					rRNA processing	cytoplasm|nucleolus				NS(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTAGTGGCCATGACCAGCGCC	0.632000														24			16		0	0	0.00400662	0	0
BHMT	635	broad.mit.edu	37	5	78415091	78415091	+	Missense_Mutation	SNP	T	C	C			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr5:78415091T>C	uc003kfu.4	+	2	281	c.176T>C	c.(175-177)cTt>cCt	p.L59P	BHMT_uc011cti.2_Intron	NM_001713	NP_001704	Q93088	BHMT1_HUMAN	Homo sapiens betaine--homocysteine S-methyltransferase (BHMT), mRNA.	59	Hcy-binding.				protein methylation|regulation of homocysteine metabolic process	cytoplasm	betaine-homocysteine S-methyltransferase activity|homocysteine S-methyltransferase activity|zinc ion binding			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)	29		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.88e-45)|Epithelial(54;8.07e-41)|all cancers(79;3.51e-36)	L-Methionine(DB00134)	GTTCGCCAGCTTCATCGAGAG	0.438000														57			33		0	0	0.00111076	0	0
SSR3	6747	broad.mit.edu	37	3	156266708	156266708	+	Missense_Mutation	SNP	C	A	A			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr3:156266708C>A	uc011bop.2	-	2	440	c.345G>T	c.(343-345)aaG>aaT	p.K115N	SSR3_uc003fau.3_Missense_Mutation_p.K115N	NM_007107	NP_009038	Q9UNL2	SSRG_HUMAN	Homo sapiens signal sequence receptor, gamma (translocon-associated protein gamma) (SSR3), mRNA.	115					cotranslational protein targeting to membrane	Sec61 translocon complex|integral to endoplasmic reticulum membrane|microsome	protein binding|signal sequence binding	p.R114W(1)		endometrium(1)|prostate(2)	3			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			CATCTTTCTCCTTCCGAGACA	0.363000														73			24		6.44725e-10	5.56665e-09	0.00229938	1	0
SULT1C4	27233	broad.mit.edu	37	2	108994906	108994906	+	Missense_Mutation	SNP	T	C	C			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr2:108994906T>C	uc002tea.1	+	0	486	c.113T>C	c.(112-114)aTc>aCc	p.I38T	SULT1C4_uc010ywr.1_Non-coding_Transcript|SULT1C4_uc002teb.1_Missense_Mutation_p.I38T	NM_006588	NP_006579	O75897	ST1C4_HUMAN	Homo sapiens sulfotransferase family, cytosolic, 1C, member 4 (SULT1C4), mRNA.	38					3'-phosphoadenosine 5'-phosphosulfate metabolic process|sulfation|xenobiotic metabolic process	cytosol	sulfotransferase activity			endometrium(1)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	12						TGGGATAAGATCTGGAACTTC	0.473000														143			111		0	0	0.00361006	0	0
SPRED2	200734	broad.mit.edu	37	2	65561771	65561771	+	Frame_Shift_Del	DEL	C	-	-			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr2:65561771delC	uc002sdr.4	-	2	876	c.341delG	c.(340-342)ggafs	p.G114fs	SPRED2_uc010fcw.3_Frame_Shift_Del_p.G111fs|SPRED2_uc010fcx.1_Intron	NM_181784	NP_861449	Q7Z698	SPRE2_HUMAN	Homo sapiens sprouty-related, EVH1 domain containing 2 (SPRED2), transcript variant 1, mRNA.	114	WH1.				inactivation of MAPK activity|multicellular organismal development	transport vesicle membrane	stem cell factor receptor binding			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(7)|ovary(2)|upper_aerodigestive_tract(3)	34						TTTCCTTACTCCCCTGTCAAA	0.413													---	124	---	---	68	---					
LRP2	4036	broad.mit.edu	37	2	170145584	170145584	+	Frame_Shift_Del	DEL	A	-	-			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr2:170145584delA	uc002ues.3	-	8	1207	c.994delT	c.(994-996)tgtfs	p.C332fs	LRP2_uc010zdf.1_Frame_Shift_Del_p.C332fs	NM_004525	NP_004516	P98164	LRP2_HUMAN	Homo sapiens low density lipoprotein receptor-related protein 2 (LRP2), mRNA.	332	EGF-like 1.				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	SH3 domain binding|calcium ion binding|receptor activity			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	CCTGGGGGACAAAAACACGCT	0.483													---	102	---	---	41	---					
NFE2L3	9603	broad.mit.edu	37	7	26223344	26223347	+	Frame_Shift_Del	DEL	TTCT	-	-			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr7:26223344_26223347delTTCT	uc003sxq.3	+	2	1046_1049	c.774_777delTTCT	c.(772-777)acttctfs	p.T258fs		NM_004289	NP_004280	Q9Y4A8	NF2L3_HUMAN	Homo sapiens nuclear factor (erythroid-derived 2)-like 3 (NFE2L3), mRNA.	258					transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(5)|urinary_tract(7)	29						GGACAGATACTTCTTTCTCTCTGG	0.402													---	92	---	---	39	---					
TRBV5-5	28610	broad.mit.edu	37	7	142149130	142149130	+	Frame_Shift_Del	DEL	C	-	-			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr7:142149130delC	uc010lnw.1	-	1	223	c.141delG	c.(139-141)gggfs	p.G47fs	TRBV2_uc011kro.1_Intron|TRBV5-1_uc011krr.1_Intron|TRBV5-5_uc022anh.1_5'Flank					SubName: Full=V_segment translation product; Flags: Fragment;																		CACTCTTGTGCCCAGAGATAG	0.522													---	73	---	---	53	---					
SPRED2	200734	broad.mit.edu	37	2	65561771	65561771	+	Frame_Shift_Del	DEL	C	-	-			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr2:65561771delC	uc002sdr.4	-	2	876	c.341delG	c.(340-342)ggafs	p.G114fs	SPRED2_uc010fcw.3_Frame_Shift_Del_p.G111fs|SPRED2_uc010fcx.1_Intron	NM_181784	NP_861449	Q7Z698	SPRE2_HUMAN	Homo sapiens sprouty-related, EVH1 domain containing 2 (SPRED2), transcript variant 1, mRNA.	114	WH1.				inactivation of MAPK activity|multicellular organismal development	transport vesicle membrane	stem cell factor receptor binding			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(7)|ovary(2)|upper_aerodigestive_tract(3)	34						TTTCCTTACTCCCCTGTCAAA	0.413													---	124	---	---	68	---					
LRP2	4036	broad.mit.edu	37	2	170145584	170145584	+	Frame_Shift_Del	DEL	A	-	-			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr2:170145584delA	uc002ues.3	-	8	1207	c.994delT	c.(994-996)tgtfs	p.C332fs	LRP2_uc010zdf.1_Frame_Shift_Del_p.C332fs	NM_004525	NP_004516	P98164	LRP2_HUMAN	Homo sapiens low density lipoprotein receptor-related protein 2 (LRP2), mRNA.	332	EGF-like 1.				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	SH3 domain binding|calcium ion binding|receptor activity			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	CCTGGGGGACAAAAACACGCT	0.483													---	102	---	---	41	---					
GUSBP2	387036	broad.mit.edu	37	6	26856964	26856964	+	RNA	DEL	T	-	-			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr6:26856964delT	uc003nim.2	-	3		c.409delA								Homo sapiens glucuronidase, beta pseudogene 2 (GUSBP2), non-coding RNA.																		GGAGATCTGGTAATTCACCAG	0.542													---	4	---	---	2	---					
NFE2L3	9603	broad.mit.edu	37	7	26223344	26223347	+	Frame_Shift_Del	DEL	TTCT	-	-			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr7:26223344_26223347delTTCT	uc003sxq.3	+	2	1046_1049	c.774_777delTTCT	c.(772-777)acttctfs	p.T258fs		NM_004289	NP_004280	Q9Y4A8	NF2L3_HUMAN	Homo sapiens nuclear factor (erythroid-derived 2)-like 3 (NFE2L3), mRNA.	258					transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(5)|urinary_tract(7)	29						GGACAGATACTTCTTTCTCTCTGG	0.402													---	92	---	---	39	---					
TRBV5-5	28610	broad.mit.edu	37	7	142149130	142149130	+	Frame_Shift_Del	DEL	C	-	-			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr7:142149130delC	uc010lnw.1	-	1	223	c.141delG	c.(139-141)gggfs	p.G47fs	TRBV2_uc011kro.1_Intron|TRBV5-1_uc011krr.1_Intron|TRBV5-5_uc022anh.1_5'Flank					SubName: Full=V_segment translation product; Flags: Fragment;																		CACTCTTGTGCCCAGAGATAG	0.522													---	73	---	---	53	---					
abParts	0	broad.mit.edu	37	14	106405448	106405448	+	Splice_Site	DEL	C	-	-	rs77404616		TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	9f300007-0c7a-4c79-a2b9-55a9edf8333b	g.chr14:106405448delC	uc021ser.1	-	3035		c.50197_splice	c.e3035-1							Parts of antibodies, mostly variable regions.																		aaaaaaaaaacaacaaCAGTT	0.408													---	4	---	---	2	---					
