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
NLRC4	58484	broad.mit.edu	37	2	32475161	32475161	+	Missense_Mutation	SNP	A	A	T			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr2:32475161A>T	ENST00000404025.2	-	5	2260	c.1772T>A	c.(1771-1773)aTc>aAc	p.I591N	NLRC4_ENST00000402280.1_Missense_Mutation_p.I591N|NLRC4_ENST00000360906.5_Missense_Mutation_p.I591N|NLRC4_ENST00000342905.6_Intron			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	591					activation of caspase activity|defense response to bacterium|detection of bacterium|interleukin-1 beta secretion|positive regulation of apoptosis	cytoplasm	ATP binding|magnesium ion binding|protein homodimerization activity	p.I591N(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					GTAATCGGGGATGTTCCCTGA	0.408													6	245	---	---	---	---
THNSL2	55258	broad.mit.edu	37	2	88478453	88478453	+	Silent	SNP	G	G	A			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr2:88478453G>A	ENST00000324166.5	+	4	2414	c.723G>A	c.(721-723)caG>caA	p.Q241Q	THNSL2_ENST00000496844.1_3'UTR|THNSL2_ENST00000343544.4_Silent_p.Q241Q|THNSL2_ENST00000449349.1_Silent_p.Q209Q|THNSL2_ENST00000358591.2_Silent_p.Q241Q|THNSL2_ENST00000402102.1_Silent_p.Q241Q|THNSL2_ENST00000377254.3_Silent_p.Q241Q	NM_018271.4	NP_060741.3	Q86YJ6	THNS2_HUMAN	threonine synthase-like 2 (S. cerevisiae)	241					threonine biosynthetic process		threonine synthase activity	p.Q241Q(1)		breast(4)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	27						CTTACTTCCAGTGTACGCCAT	0.552													10	447	---	---	---	---
CP	1356	broad.mit.edu	37	3	148905905	148905905	+	Missense_Mutation	SNP	A	A	C			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr3:148905905A>C	ENST00000264613.6	-	10	2060	c.1798T>G	c.(1798-1800)Ttt>Gtt	p.F600V	CP_ENST00000462336.1_5'UTR	NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	600	F5/8 type A 2.|Plastocyanin-like 4.				cellular iron ion homeostasis|copper ion transport|transmembrane transport	extracellular space	chaperone binding|ferroxidase activity	p.F600V(1)		breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	GCAGTTGTAAACATTCTAATA	0.343													6	261	---	---	---	---
ADCY1	107	broad.mit.edu	37	7	45744119	45744119	+	Silent	SNP	C	C	A			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr7:45744119C>A	ENST00000297323.7	+	17	2743	c.2721C>A	c.(2719-2721)ctC>ctA	p.L907L		NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	907					activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|calmodulin binding|metal ion binding	p.L907L(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Adenosine(DB00640)	AAACAAAGCTCATGGAAAAAG	0.498													6	134	---	---	---	---
SPATA31C1	441452	broad.mit.edu	37	9	90535290	90535290	+	RNA	SNP	T	T	C	rs55701842	by1000genomes	TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr9:90535290T>C	ENST00000602681.1	+	0	1194																											CTATGGAAGATGCTGCTCCCA	0.592													5	302	---	---	---	---
CPSF2	53981	broad.mit.edu	37	14	92608697	92608697	+	Splice_Site	SNP	T	T	C			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr14:92608697T>C	ENST00000298875.4	+	8	1134		c.e8+2			NM_017437.2	NP_059133.1	Q9P2I0	CPSF2_HUMAN	cleavage and polyadenylation specific factor 2, 100kDa						histone mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	hydrolase activity|protein binding|RNA binding	p.?(1)		breast(2)|cervix(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	24		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)		AAGTCCCAGGTTTGTTCTCAT	0.383													5	286	---	---	---	---
CDAN1	146059	broad.mit.edu	37	15	43022880	43022880	+	Missense_Mutation	SNP	A	A	C			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr15:43022880A>C	ENST00000356231.3	-	14	2113	c.2090T>G	c.(2089-2091)gTg>gGg	p.V697G		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	697						integral to membrane	protein binding	p.V697G(1)		endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		GAGAAACTCCACCAGCCAGGG	0.637													6	41	---	---	---	---
CSPG4	1464	broad.mit.edu	37	15	75980335	75980335	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr15:75980335C>A	ENST00000308508.5	-	3	3163	c.3071G>T	c.(3070-3072)aGc>aTc	p.S1024I		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1024	Gly/Ser-rich (glycosaminoglycan attachment domain).|Interaction with COL5A1 (By similarity).|Interaction with COL6A2 (By similarity).				angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling	apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane	protein kinase binding|signal transducer activity	p.S1024I(1)		breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						GAAGATCCGGCTGATGGTCTG	0.657													4	118	---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9075833	9075833	+	Silent	SNP	C	C	T			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr19:9075833C>T	ENST00000397910.4	-	3	11816	c.11613G>A	c.(11611-11613)gaG>gaA	p.E3871E		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3872	Thr-rich.				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding	p.E3871E(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ATTTTTCTTTCTCATTCCAGG	0.448													8	100	---	---	---	---
PBX4	80714	broad.mit.edu	37	19	19675795	19675795	+	Missense_Mutation	SNP	G	G	A	rs139542458		TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr19:19675795G>A	ENST00000251203.9	-	6	1158	c.872C>T	c.(871-873)aCg>aTg	p.T291M		NM_025245.2	NP_079521.1	Q9BYU1	PBX4_HUMAN	pre-B-cell leukemia homeobox 4								sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	p.T291M(1)		large_intestine(1)|lung(4)|ovary(1)|prostate(3)	9						CCCAACTTCCGTGGTATCCAC	0.527													9	377	---	---	---	---
NSFL1C	55968	broad.mit.edu	37	20	1433675	1433675	+	Splice_Site	SNP	C	C	T			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr20:1433675C>T	ENST00000216879.4	-	6	1515		c.e6+1		NSFL1C_ENST00000476071.1_Splice_Site|NSFL1C_ENST00000381658.4_Splice_Site|NSFL1C_ENST00000353088.2_Splice_Site|NSFL1C_ENST00000461211.1_Splice_Site|NSFL1C_ENST00000350991.4_Splice_Site	NM_016143.4	NP_057227.2	Q9UNZ2	NSF1C_HUMAN	NSFL1 (p97) cofactor (p47)							chromosome|Golgi stack|nucleus	lipid binding|protein binding	p.?(1)		breast(1)|large_intestine(5)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	16						TTTTCACTCACCCTCTGCGGA	0.453													7	354	---	---	---	---
SLC4A11	83959	broad.mit.edu	37	20	3209652	3209652	+	Missense_Mutation	SNP	A	A	C			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr20:3209652A>C	ENST00000380059.3	-	17	2254	c.2153T>G	c.(2152-2154)gTg>gGg	p.V718G	SLC4A11_ENST00000380056.3_Missense_Mutation_p.V691G|SLC4A11_ENST00000488544.1_5'UTR|SLC4A11_ENST00000539553.2_Missense_Mutation_p.V675G	NM_001174090.1	NP_001167561.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11	691	Membrane (bicarbonate transporter).				cellular cation homeostasis|fluid transport|phosphoenolpyruvate-dependent sugar phosphotransferase system	basolateral plasma membrane|integral to membrane	bicarbonate transmembrane transporter activity|borate transmembrane transporter activity|hydrogen ion channel activity|inorganic anion exchanger activity|sodium channel activity|sugar:hydrogen symporter activity	p.V718G(1)|p.V691G(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(4)|soft_tissue(1)|urinary_tract(1)	40						AGTGCCCTTCACCAGCCTGCA	0.667													8	25	---	---	---	---
XRCC6	2547	broad.mit.edu	37	22	42057337	42057337	+	Missense_Mutation	SNP	C	C	T			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr22:42057337C>T	ENST00000359308.4	+	11	2180	c.1525C>T	c.(1525-1527)Ccc>Tcc	p.P509S	XRCC6_ENST00000428575.2_Missense_Mutation_p.P376S|XRCC6_ENST00000405506.1_Missense_Mutation_p.P459S|XRCC6_ENST00000360079.3_Missense_Mutation_p.P509S|XRCC6_ENST00000402580.3_Missense_Mutation_p.P468S|XRCC6_ENST00000405878.1_Missense_Mutation_p.P509S			P12956	XRCC6_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 6	509					DNA ligation|double-strand break repair via nonhomologous end joining|initiation of viral infection|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|provirus integration|telomere maintenance|transcription, DNA-dependent	DNA-dependent protein kinase-DNA ligase 4 complex|Ku70:Ku80 complex|membrane fraction|nuclear telomere cap complex|transcription factor complex	5'-deoxyribose-5-phosphate lyase activity|ATP binding|ATP-dependent DNA helicase activity|double-stranded DNA binding|protein C-terminus binding|transcription regulatory region DNA binding	p.P509S(2)		central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	31						TTTTCTAGTGCCCAAGGTTGA	0.473								Non-homologous end-joining					7	250	---	---	---	---
XIST	7503	broad.mit.edu	37	X	73066367	73066367	+	RNA	SNP	T	T	C			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chrX:73066367T>C	ENST00000429829.1	-	0	6221					NR_001564.2																						AGTAGGACCTTATTCACATGG	0.448													6	127	---	---	---	---
PPP1R3A	5506	broad.mit.edu	37	7	113519968	113519968	+	Frame_Shift_Del	DEL	T	T	-			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr7:113519968delT	ENST00000284601.3	-	4	1247	c.1179delA	c.(1177-1179)aaafs	p.K393fs		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	393					glycogen metabolic process	integral to membrane				NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						CTGAGGAATATTTTTCATTGC	0.393													8	413	---	---	---	---
