Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
CROCCP2	84809	broad.mit.edu	37	1	16946368	16946368	+	RNA	SNP	A	A	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr1:16946368A>G	ENST00000412962.1	-	0	1151																											GGCCAGGAGGAGGCCCTCGTC	0.667													2	16	---	---	---	---
ZNF683	257101	broad.mit.edu	37	1	26691329	26691329	+	Silent	SNP	C	C	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr1:26691329C>A	ENST00000436292.1	-	4	828	c.708G>T	c.(706-708)ctG>ctT	p.L236L	ZNF683_ENST00000374204.1_Silent_p.L236L|ZNF683_ENST00000349618.3_Silent_p.L236L|ZNF683_ENST00000403843.1_Silent_p.L236L			Q8IZ20	ZN683_HUMAN	zinc finger protein 683	236					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	p.L236L(1)|p.L221L(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(1)	15		all_cancers(24;2.39e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.76e-26)|Colorectal(126;1.38e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00793)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.159)|LUSC - Lung squamous cell carcinoma(448;0.233)		CCATCATCAGCAGGCTAGGCA	0.632													13	119	---	---	---	---
CYR61	3491	broad.mit.edu	37	1	86048170	86048170	+	Missense_Mutation	SNP	T	T	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr1:86048170T>C	ENST00000451137.2	+	4	930	c.706T>C	c.(706-708)Tgg>Cgg	p.W236R		NM_001554.4	NP_001545.2	O00622	CYR61_HUMAN	cysteine-rich, angiogenic inducer, 61	236	TSP type-1.				cell proliferation|chemotaxis|positive regulation of BMP signaling pathway|positive regulation of cell migration|positive regulation of osteoblast differentiation|positive regulation of osteoblast proliferation|positive regulation of protein kinase activity|positive regulation of protein phosphorylation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell growth|regulation of ERK1 and ERK2 cascade|wound healing, spreading of cells	extracellular region	heparin binding|insulin-like growth factor binding	p.W236R(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|prostate(1)	5				all cancers(265;0.0216)|Epithelial(280;0.0441)		AACAACTTCATGGTCCCAGTG	0.458											OREG0013583	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	13	110	---	---	---	---
PDK1	5163	broad.mit.edu	37	2	173457705	173457705	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr2:173457705C>A	ENST00000282077.3	+	10	1281	c.1099C>A	c.(1099-1101)Caa>Aaa	p.Q367K	PDK1_ENST00000543905.1_Missense_Mutation_p.Q291K|PDK1_ENST00000392571.2_Missense_Mutation_p.Q387K|PDK1_ENST00000544863.1_Missense_Mutation_p.Q212K|PDK1_ENST00000410055.1_Missense_Mutation_p.Q367K			Q15118	PDK1_HUMAN	pyruvate dehydrogenase kinase, isozyme 1		Histidine kinase.				glucose metabolic process|peptidyl-histidine phosphorylation|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate|small GTPase mediated signal transduction	mitochondrial matrix	ATP binding|pyruvate dehydrogenase (acetyl-transferring) kinase activity|two-component sensor activity	p.Q367K(1)		central_nervous_system(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)	16			OV - Ovarian serous cystadenocarcinoma(117;0.12)			TCTTTACGCACAATACTTCCA	0.378									Autosomal Dominant Polycystic Kidney Disease				4	160	---	---	---	---
CHPF	79586	broad.mit.edu	37	2	220406592	220406592	+	Missense_Mutation	SNP	G	G	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr2:220406592G>T	ENST00000243776.6	-	2	882	c.634C>A	c.(634-636)Cta>Ata	p.L212I	CHPF_ENST00000373891.2_Missense_Mutation_p.L212I|CHPF_ENST00000535926.1_Missense_Mutation_p.L50I	NM_024536.5	NP_078812	Q8IZ52	CHSS2_HUMAN	chondroitin polymerizing factor	212						Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity|protein binding	p.L212I(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	21		Renal(207;0.0183)		Epithelial(149;3.02e-08)|all cancers(144;3.41e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		TGGCCAGTTAGGCGTGCCAGG	0.706											OREG0015229	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	30	---	---	---	---
JADE2	23338	broad.mit.edu	37	5	133914476	133914476	+	Silent	SNP	G	G	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr5:133914476G>A	ENST00000395003.1	+	11	2021	c.1842G>A	c.(1840-1842)ggG>ggA	p.G614G	PHF15_ENST00000402835.1_3'UTR|PHF15_ENST00000361895.2_Silent_p.G615G|PHF15_ENST00000282605.4_Silent_p.G658G	NM_015288.4	NP_056103.4	Q9NQC1	JADE2_HUMAN		614	Pro-rich.				histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding	p.G614G(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CGCAGGACGGGCCTGGTTCAC	0.672													5	48	---	---	---	---
DPYSL2	1808	broad.mit.edu	37	8	26484737	26484737	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr8:26484737G>A	ENST00000311151.5	+	6	959	c.547G>A	c.(547-549)Gaa>Aaa	p.E183K	DPYSL2_ENST00000521913.1_Missense_Mutation_p.E147K|DPYSL2_ENST00000523027.1_Missense_Mutation_p.E147K|DPYSL2_ENST00000521983.1_3'UTR	NM_001386.5	NP_001377.1	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2	183					axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	dihydropyrimidinase activity|protein binding	p.E183K(1)		breast(1)|endometrium(5)|large_intestine(8)|lung(3)|prostate(1)|skin(1)|stomach(1)	20		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)		TCAGATTTATGAAGTACTGAG	0.483													14	55	---	---	---	---
YME1L1	10730	broad.mit.edu	37	10	27436415	27436415	+	Silent	SNP	C	C	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr10:27436415C>T	ENST00000477432.1	-	3	1406	c.351G>A	c.(349-351)ggG>ggA	p.G117G	YME1L1_ENST00000326799.3_Intron|YME1L1_ENST00000376016.3_Intron|YME1L1_ENST00000375972.3_Intron			Q96TA2	YMEL1_HUMAN	YME1-like 1 ATPase	0					protein catabolic process|proteolysis	membrane|mitochondrion	ATP binding|metal ion binding|metalloendopeptidase activity|nucleoside-triphosphatase activity			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23						TTTGGAGAAACCCGCAGTGTA	0.468													3	69	---	---	---	---
CNGA4	1262	broad.mit.edu	37	11	6261464	6261464	+	Missense_Mutation	SNP	C	C	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr11:6261464C>T	ENST00000379936.2	+	4	555	c.440C>T	c.(439-441)gCg>gTg	p.A147V	CNGA4_ENST00000533426.1_Intron	NM_001037329.3	NP_001032406.1	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	147					response to stimulus|sensory perception of smell		cAMP binding	p.A147V(1)		endometrium(2)|kidney(1)|large_intestine(9)|lung(24)|prostate(3)|skin(1)	40		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTTCTCCGCGCGCCCCGCCTC	0.587													5	205	---	---	---	---
SLC2A14	144195	broad.mit.edu	37	12	7982567	7982567	+	Missense_Mutation	SNP	G	G	A	rs145793375	byFrequency	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr12:7982567G>A	ENST00000543909.1	-	10	1136	c.377C>T	c.(376-378)gCc>gTc	p.A126V	SLC2A14_ENST00000539924.1_Missense_Mutation_p.A141V|SLC2A14_ENST00000542505.1_Intron|SLC2A14_ENST00000431042.2_Missense_Mutation_p.A103V|SLC2A14_ENST00000340749.5_Missense_Mutation_p.A103V|SLC2A14_ENST00000535295.1_Missense_Mutation_p.A17V|SLC2A14_ENST00000542546.1_Missense_Mutation_p.A17V|SLC2A14_ENST00000396589.2_Missense_Mutation_p.A126V			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	126					cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane	glucose transmembrane transporter activity	p.A126V(1)		central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	38				Kidney(36;0.0883)		GCCACCAGTGGCAGCCAACAG	0.478													3	69	---	---	---	---
POC1B-GALNT4	100528030	broad.mit.edu	37	12	89917323	89917323	+	Missense_Mutation	SNP	C	C	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr12:89917323C>G	ENST00000548729.1	-	3	1297	c.995G>C	c.(994-996)gGa>gCa	p.G332A	POC1B_ENST00000313546.3_Intron|POC1B_ENST00000393179.4_Intron|POC1B_ENST00000549504.1_Intron|POC1B_ENST00000541909.1_Intron|GALNT4_ENST00000529983.2_Missense_Mutation_p.G335A|GALNT4_ENST00000413530.1_Missense_Mutation_p.G163A|POC1B_ENST00000549035.1_Intron|POC1B-GALNT4_ENST00000547474.1_3'UTR	NM_001199781.1|NM_001199782.1	NP_001186710.1|NP_001186711.1												p.G335A(1)									GTTTTCACCTCCCCACACTTC	0.522													42	257	---	---	---	---
NOX5	79400	broad.mit.edu	37	15	69348910	69348910	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr15:69348910C>A	ENST00000260364.5	+	17	2419	c.2118C>A	c.(2116-2118)ttC>ttA	p.F706L	NOX5_ENST00000530406.2_Missense_Mutation_p.F696L|NOX5_ENST00000388866.3_Missense_Mutation_p.F724L|NOX5_ENST00000455873.3_Missense_Mutation_p.F689L|NOX5_ENST00000448182.3_Missense_Mutation_p.F678L			Q96PH1	NOX5_HUMAN	NADPH oxidase, EF-hand calcium binding domain 5	724					angiogenesis|cytokine secretion|cytokinesis|electron transport chain|endothelial cell proliferation|induction of apoptosis|positive regulation of reactive oxygen species metabolic process|regulation of fusion of sperm to egg plasma membrane|regulation of proton transport|superoxide anion generation	endoplasmic reticulum|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|hydrogen ion channel activity|NADP binding|superoxide-generating NADPH oxidase activity	p.F706L(1)		breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35						TCCAGGTGTTCCAGAAAGTGG	0.557													26	145	---	---	---	---
HRC	3270	broad.mit.edu	37	19	49656664	49656664	+	Splice_Site	SNP	C	C	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr19:49656664C>A	ENST00000252825.4	-	1	2017	c.1831G>T	c.(1831-1833)Ggt>Tgt	p.G611C	HRC_ENST00000595625.1_Splice_Site_p.G611C	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	611					muscle contraction	sarcoplasmic reticulum lumen	calcium ion binding	p.G611C(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		GGCCACTTACCTGTGTCCTCA	0.632													3	72	---	---	---	---
NCAM2	4685	broad.mit.edu	37	21	22849736	22849736	+	Missense_Mutation	SNP	A	A	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96a30919-cafe-43b9-9f46-226a8a38d246	040ca048-b608-4268-968c-2d436e9293cd	g.chr21:22849736A>G	ENST00000400546.1	+	15	2270	c.2021A>G	c.(2020-2022)tAt>tGt	p.Y674C	NCAM2_ENST00000284894.7_Missense_Mutation_p.Y532C	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	674	Fibronectin type-III 2.				neuron cell-cell adhesion	integral to membrane|plasma membrane		p.Y674C(1)		breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		AGATTGGGATATTCTGAACCG	0.368													21	129	---	---	---	---
