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
ZSWIM2	151112	broad.mit.edu	37	2	187693177	187693177	+	Missense_Mutation	SNP	T	A	A			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr2:187693177T>A	uc002upu.1	-	8	1476	c.1436A>T	c.(1435-1437)aAt>aTt	p.N479I		NM_182521	NP_872327	Q8NEG5	ZSWM2_HUMAN	Homo sapiens zinc finger, SWIM-type containing 2 (ZSWIM2), mRNA.	479					apoptosis		zinc ion binding			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			TTTTTTTGAATTTGAATTATC	0.299000														34			6		0	0	0.021553	0	0
ARID2	196528	broad.mit.edu	37	12	46244916	46244916	+	Missense_Mutation	SNP	A	T	T			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr12:46244916A>T	uc001ros.1	+	14	3010	c.3010A>T	c.(3010-3012)Agt>Tgt	p.S1004C	ARID2_uc001ror.3_Missense_Mutation_p.S1004C|ARID2_uc009zkg.1_Missense_Mutation_p.S460C|ARID2_uc009zkh.1_Missense_Mutation_p.S631C|ARID2_uc001rou.1_Missense_Mutation_p.S338C	NM_152641	NP_689854	Q68CP9	ARID2_HUMAN	Homo sapiens AT rich interactive domain 2 (ARID, RFX-like) (ARID2), mRNA.	1004	Gln-rich.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TCCTACTGTCAGTCAAATGTT	0.502000			"""N, S, F"""		hepatocellular carcinoma									107			21		0	0	0.008871	0	0
RYR3	6263	broad.mit.edu	37	15	33954438	33954438	+	Silent	SNP	C	T	T			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr15:33954438C>T	uc001zhi.3	+	34	4777	c.4707C>T	c.(4705-4707)tgC>tgT	p.C1569C	RYR3_uc010bar.3_Silent_p.C1569C	NM_001036	NP_001027	Q15413	RYR3_HUMAN	Homo sapiens ryanodine receptor 3 (RYR3), transcript variant 1, mRNA.	1569	4 X approximate repeats.				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		GCGCGGTGTGCGCCCTGGGAA	0.612000														20			3		0	0	0.004672	0	0
NLRP7	199713	broad.mit.edu	37	19	55452315	55452315	+	Silent	SNP	C	T	T			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr19:55452315C>T	uc002qih.4	-	2	412	c.336G>A	c.(334-336)tcG>tcA	p.S112S	NLRP7_uc010esk.3_Silent_p.S112S|NLRP7_uc002qig.4_Silent_p.S112S|NLRP7_uc002qii.4_Silent_p.S112S|NLRP7_uc010esl.3_Silent_p.S140S	NM_206828	NP_996611	Q8WX94	NALP7_HUMAN	Homo sapiens NLR family, pyrin domain containing 7 (NLRP7), transcript variant 2, mRNA.	112							ATP binding			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		TTGCTAACTCCGAGTCTTCTT	0.433000														154			46		0	0	0.014410	0	0
CCT4	10575	broad.mit.edu	37	2	62115531	62115531	+	Missense_Mutation	SNP	T	C	C			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr2:62115531T>C	uc002sbo.3	-	0	261	c.112A>G	c.(112-114)Att>Gtt	p.I38V	CCT4_uc010ypr.2_5'UTR|CCT4_uc010yps.2_Missense_Mutation_p.I38V|CCT4_uc010ypq.2_5'UTR	NM_006430	NP_006421	P50991	TCPD_HUMAN	Homo sapiens chaperonin containing TCP1, subunit 4 (delta) (CCT4), mRNA.	38					'de novo' posttranslational protein folding	melanosome|microtubule organizing center|nucleus	ATP binding|unfolded protein binding			breast(1)|large_intestine(2)|lung(6)|ovary(2)	11	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;6.5e-06)|Epithelial(17;0.0647)|all cancers(80;0.221)			GCGGCGGAAATGTTGCTGAAG	0.677000														22			16		0	0	0.012319	0	0
PRIC285	85441	broad.mit.edu	37	20	62198513	62198513	+	Missense_Mutation	SNP	C	T	T			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr20:62198513C>T	uc002yfm.2	-	6	3090	c.2198G>A	c.(2197-2199)cGg>cAg	p.R733Q	PRIC285_uc002yfl.1_Missense_Mutation_p.R164Q	NM_001037335	NP_001032412	Q9BYK8	PR285_HUMAN	Homo sapiens peroxisomal proliferator-activated receptor A interacting complex 285 (PRIC285), transcript variant 1, mRNA.	733					cellular lipid metabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|RNA binding|helicase activity|ribonuclease activity|transcription coactivator activity|zinc ion binding			NS(1)|breast(1)|central_nervous_system(4)|cervix(3)|endometrium(6)|kidney(3)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(4)|urinary_tract(2)	47	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;1.27e-08)|all cancers(9;7.32e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)			GCGGCTCTGCCGCGCCACCTC	0.662000														123			9		0	0	0.004482	0	0
HERC2	8924	broad.mit.edu	37	15	28370205	28370205	+	Missense_Mutation	SNP	T	G	G			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr15:28370205T>G	uc001zbj.3	-	83	13043	c.12937A>C	c.(12937-12939)Acc>Ccc	p.T4313P		NM_004667	NP_004658	O95714	HERC2_HUMAN	Homo sapiens hect domain and RLD 2 (HERC2), mRNA.	4313					DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CAGGCGAGGGTATGTGCTGAG	0.622000														148			10		0	0	0.018920	0	0
AKAP3	10566	broad.mit.edu	37	12	4736579	4736579	+	Missense_Mutation	SNP	G	C	C			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr12:4736579G>C	uc001qnb.4	-	3	1733	c.1489C>G	c.(1489-1491)Cct>Gct	p.P497A		NM_006422	NP_006413	O75969	AKAP3_HUMAN	Homo sapiens A kinase (PRKA) anchor protein 3 (AKAP3), mRNA.	497					acrosome reaction|cellular component movement	acrosomal vesicle	protein kinase A binding			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						ATATCTTCAGGGTACTCAAAG	0.463000														33			9		0	0	0.004482	0	0
COL28A1	340267	broad.mit.edu	37	7	7412963	7412963	+	Silent	SNP	C	T	T			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr7:7412963C>T	uc003src.1	-	31	2691	c.2574G>A	c.(2572-2574)aaG>aaA	p.K858K	COL28A1_uc011jxe.1_Silent_p.K541K	NM_001037763	NP_001032852	Q2UY09	COSA1_HUMAN	Homo sapiens collagen, type XXVIII, alpha 1 (COL28A1), mRNA.	858	VWFA 2.				cell adhesion	basement membrane|collagen	serine-type endopeptidase inhibitor activity			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		TGAAGTCATCCTTGCTGGAGA	0.512000														83			22		0	0	0.012319	0	0
FLJ43315	644316	broad.mit.edu	37	GL000211.1	107044	107044	+	RNA	SNP	T	C	C			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chrGL000211.1:107044T>C	uc003boa.3	+	3		c.743T>C								Homo sapiens asparagine synthetase pseudogene (FLJ43315), non-coding RNA.																		ACAAAGAAAATAGAACGCCTT	0.358000														247			11		0	0	0.010729	0	0
WASH6P	653440	broad.mit.edu	37	X	155252783	155252783	+	Missense_Mutation	SNP	G	T	T			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chrX:155252783G>T	uc004fnw.1	+	5	1486	c.827G>T	c.(826-828)aGt>aTt	p.S276I	WASH6P_uc022cip.1_Missense_Mutation_p.S62I	NM_182905	NP_878908			Homo sapiens WAS protein family homolog 1 (WASH1), mRNA.																		CTCATGTACAGTGCCGACCTG	0.607000														9			3		0.004672	0.0061904	0.004672	1	0
BAGE1	0	broad.mit.edu	37	GL000237.1	2525	2525	+	RNA	SNP	C	T	T			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chrGL000237.1:2525C>T	uc011mgu.1	-	0		c.162G>A								Homo sapiens B melanoma antigen variant f (BAGE1) mRNA, complete cds, alternatively spliced.																		ctcaggccaccctcctaacac	0.637000														26			4		0	0	0.009096	0	0
FDXR	2232	broad.mit.edu	37	17	72860612	72860612	+	Missense_Mutation	SNP	G	C	C			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr17:72860612G>C	uc010wrl.2	-	7	1008	c.921C>G	c.(919-921)gaC>gaG	p.D307E	FDXR_uc010wri.2_Missense_Mutation_p.D212E|FDXR_uc010wrj.2_Missense_Mutation_p.D262E|FDXR_uc002jlw.3_Missense_Mutation_p.D21E|FDXR_uc002jlx.3_Missense_Mutation_p.D270E|FDXR_uc002jly.3_Missense_Mutation_p.D264E|FDXR_uc010wrk.2_Missense_Mutation_p.D295E|FDXR_uc010wrm.2_Missense_Mutation_p.D224E|FDXR_uc002jlz.3_Missense_Mutation_p.D256E|FDXR_uc002jmb.3_Intron	NM_024417	NP_077728	P22570	ADRO_HUMAN	Homo sapiens ferredoxin reductase (FDXR), nuclear gene encoding mitochondrial protein, transcript variant 1, mRNA.	264					cholesterol metabolic process|electron transport chain|steroid biosynthetic process|transport	mitochondrial matrix	ferredoxin-NADP+ reductase activity|protein binding			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16	all_lung(278;0.172)|Lung NSC(278;0.207)					CCTTGATCTTGTCCTGGAGAC	0.612000											OREG0024720	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		67			6		0	0	0.001984	0	0
INPP5J	27124	broad.mit.edu	37	22	31529986	31529986	+	Missense_Mutation	SNP	C	T	T			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr22:31529986C>T	uc003aju.4	+	12	2694	c.2602C>T	c.(2602-2604)Ctc>Ttc	p.L868F	INPP5J_uc003ajw.3_3'UTR|INPP5J_uc003ajt.4_Missense_Mutation_p.L500F|INPP5J_uc003ajv.4_Missense_Mutation_p.L501F|INPP5J_uc003ajs.4_Missense_Mutation_p.L501F|INPP5J_uc011alk.2_Missense_Mutation_p.L801F|INPP5J_uc010gwg.3_Missense_Mutation_p.L433F	NM_001002837	NP_001002837	Q15735	PI5PA_HUMAN	Homo sapiens inositol polyphosphate-5-phosphatase J (INPP5J), mRNA.	868	Ser-rich.					cytoplasm|ruffle	SH3 domain binding|inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(1)	12						CACACTGGAGCTCCTTGCACC	0.657000														26			7		0	0	0.001984	0	0
LRRC16B	90668	broad.mit.edu	37	14	24523942	24523942	+	Missense_Mutation	SNP	G	A	A	rs141263195	byFrequency	TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr14:24523942G>A	uc001wlj.2	+	5	542	c.385G>A	c.(385-387)Gca>Aca	p.A129T		NM_138360	NP_612369	Q8ND23	LR16B_HUMAN	Homo sapiens leucine rich repeat containing 16B (LRRC16B), mRNA.	129										breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		GCGTGGAAACGCAGACACCCC	0.552000														46			7		0	0	0.001984	0	0
CHD6	84181	broad.mit.edu	37	20	40033696	40033696	+	Missense_Mutation	SNP	G	A	A			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr20:40033696G>A	uc002xka.1	-	36	7863	c.7685C>T	c.(7684-7686)aCg>aTg	p.T2562M	CHD6_uc002xjz.1_Missense_Mutation_p.T99M	NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	Homo sapiens chromodomain helicase DNA binding protein 6 (CHD6), mRNA.	2562					chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding|chromatin binding			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				AGTCACTGCCGTACCACTTTT	0.527000														214			5		0	0	0.014758	0	0
RCHY1	25898	broad.mit.edu	37	4	76439476	76439476	+	Silent	SNP	T	C	C			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr4:76439476T>C	uc003hik.3	-	0	165	c.21A>G	c.(19-21)gaA>gaG	p.E7E	RCHY1_uc003hij.3_Silent_p.E7E|RCHY1_uc021xpe.1_Non-coding_Transcript|RCHY1_uc010iiq.3_Non-coding_Transcript|RCHY1_uc003hil.3_Silent_p.E7E|RCHY1_uc010iip.3_Silent_p.E7E|RCHY1_uc010iir.3_Silent_p.E7E|THAP6_uc010iis.1_5'Flank|THAP6_uc003him.3_5'Flank|THAP6_uc003hin.3_5'Flank|THAP6_uc011cbm.2_5'Flank|THAP6_uc010iiu.1_5'Flank|THAP6_uc003hio.1_5'Flank|THAP6_uc010iiv.3_5'Flank	NM_015436	NP_056251	Q96PM5	ZN363_HUMAN	Homo sapiens ring finger and CHY zinc finger domain containing 1 (RCHY1), transcript variant 1, mRNA.	7					positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein autoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nuclear speck|ubiquitin ligase complex	electron carrier activity|p53 binding|protein homodimerization activity|ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|pancreas(1)	3			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			TGGCGCCATCTTCCCGGGCCG	0.602000														53			10		0	0	0.008291	0	0
CDKN2A	1029	broad.mit.edu	37	9	21974720	21974720	+	Missense_Mutation	SNP	G	C	C			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr9:21974720G>C	uc003zpk.3	-	0	413	c.107C>G	c.(106-108)gCg>gGg	p.A36G	MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.3_Missense_Mutation_p.A36G|CDKN2A_uc010miu.3_Missense_Mutation_p.A36G|CDKN2A_uc003zpl.3_Intron	NM_000077	NP_000068	P42771	CD2A1_HUMAN	Homo sapiens cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) (CDKN2A), transcript variant 1, mRNA.	36					G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|Ras protein signal transduction|cell cycle arrest|cell cycle checkpoint|induction of apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|replicative senescence	cytosol|nucleus	NF-kappaB binding|cyclin-dependent protein kinase inhibitor activity|protein binding|protein kinase binding	p.0?(1315)|p.?(23)|p.L32_L37del(11)|p.A36T(3)|p.G35E(3)|p.G35fs*13(2)|p.V28_V51del(2)|p.G35R(2)|p.0(1)|p.A36fs*8(1)|p.G35V(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		GTTGGGCAGCGCCCCCGCCTC	0.726000		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)				64			6		0	0	0.023175	0	0
KDM3B	51780	broad.mit.edu	37	5	137766032	137766032	+	Missense_Mutation	SNP	A	G	G			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr5:137766032A>G	uc003lcy.1	+	21	5188	c.4988A>G	c.(4987-4989)tAt>tGt	p.Y1663C	KDM3B_uc010jew.1_Missense_Mutation_p.Y1319C|KDM3B_uc011cys.1_Missense_Mutation_p.Y695C	NM_016604	NP_057688	Q7LBC6	KDM3B_HUMAN	Homo sapiens lysine (K)-specific demethylase 3B (KDM3B), mRNA.	1663	JmjC.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						AAGCGACTCTATGAGGAGTAT	0.542000														131			24		0	0	0.021523	0	0
SULT1E1	6783	broad.mit.edu	37	4	70713465	70713465	+	Missense_Mutation	SNP	T	C	C			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr4:70713465T>C	uc003heo.3	-	5	655	c.542A>G	c.(541-543)aAg>aGg	p.K181R		NM_005420	NP_005411	P49888	ST1E1_HUMAN	Homo sapiens sulfotransferase family 1E, estrogen-preferring, member 1 (SULT1E1), mRNA.	181					3'-phosphoadenosine 5'-phosphosulfate metabolic process|sulfation|xenobiotic metabolic process	cytosol|nuclear membrane	estrone sulfotransferase activity|flavonol 3-sulfotransferase activity|steroid binding|steroid sulfotransferase activity			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	10						ACTCTTTCCCTTTTCCCACCA	0.373000														100			3		0	0	0.004672	0	0
TMC2	117532	broad.mit.edu	37	20	2621849	2621849	+	Missense_Mutation	SNP	A	G	G			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr20:2621849A>G	uc002wgf.1	+	19	2588	c.2573A>G	c.(2572-2574)aAt>aGt	p.N858S	TMC2_uc002wgg.1_Missense_Mutation_p.N842S	NM_080751	NP_542789	Q8TDI7	TMC2_HUMAN	Homo sapiens transmembrane channel-like 2 (TMC2), mRNA.	858						integral to membrane				NS(1)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						GGGACCTCCAATTCTGCCAGC	0.582000														180			5		0	0	0.021553	0	0
FLJ43315	644316	broad.mit.edu	37	GL000211.1	107007	107007	+	RNA	SNP	G	A	A			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chrGL000211.1:107007G>A	uc003boa.3	+	3		c.706G>A								Homo sapiens asparagine synthetase pseudogene (FLJ43315), non-coding RNA.																		CTCCTGGTTAGCAGAAAATGC	0.408000														287			10		0	0	0.008291	0	0
OR2G2	81470	broad.mit.edu	37	1	247751788	247751788	+	Silent	SNP	T	C	C			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr1:247751788T>C	uc010pyy.2	+	0	127	c.127T>C	c.(127-129)Ttg>Ctg	p.L43L		NM_001001915	NP_001001915	Q8NGZ5	OR2G2_HUMAN	Homo sapiens olfactory receptor, family 2, subfamily G, member 2 (OR2G2), mRNA.	43					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			endometrium(4)|kidney(4)|large_intestine(3)|lung(30)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			ACTAACTATTTTGGGGAATAC	0.408000														192			70		0	0	0.014410	0	0
COL28A1	340267	broad.mit.edu	37	7	7412962	7412962	+	Missense_Mutation	SNP	C	A	A			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr7:7412962C>A	uc003src.1	-	31	2692	c.2575G>T	c.(2575-2577)Gat>Tat	p.D859Y	COL28A1_uc011jxe.1_Missense_Mutation_p.D542Y	NM_001037763	NP_001032852	Q2UY09	COSA1_HUMAN	Homo sapiens collagen, type XXVIII, alpha 1 (COL28A1), mRNA.	859	VWFA 2.				cell adhesion	basement membrane|collagen	serine-type endopeptidase inhibitor activity			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		TTGAAGTCATCCTTGCTGGAG	0.512000														82			21		3.51602e-12	5.03646e-12	0.008871	1	0
MST1P9	11223	broad.mit.edu	37	1	17085791	17085791	+	Missense_Mutation	SNP	G	A	A	rs2297532	by1000genomes	TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr1:17085791G>A	uc010ock.2	-	7	1030	c.1030C>T	c.(1030-1032)Cgt>Tgt	p.R344C	CROCC_uc009voy.1_Intron|MST1P9_uc001azp.4_5'UTR					Homo sapiens macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9 (MST1P9), non-coding RNA.											breast(1)|endometrium(11)|kidney(9)|large_intestine(1)|lung(5)|pancreas(1)|prostate(4)|stomach(1)|urinary_tract(1)	34						TCTGTACAACGCCGGATCTGG	0.692000														30			4		0	0	0.009096	0	0
C6orf211	79624	broad.mit.edu	37	6	151789725	151789725	+	Missense_Mutation	SNP	T	G	G			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr6:151789725T>G	uc003qok.1	+	4	1065	c.806T>G	c.(805-807)tTg>tGg	p.L269W	C6orf211_uc011ees.1_Missense_Mutation_p.L150W	NM_024573	NP_078849	Q9H993	CF211_HUMAN	Homo sapiens chromosome 6 open reading frame 211 (C6orf211), mRNA.	269							protein binding			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(7)	15			BRCA - Breast invasive adenocarcinoma(37;0.183)	OV - Ovarian serous cystadenocarcinoma(155;5.27e-11)		GCCGACTTCTTGTTGTCCTCT	0.328000														102			11		0	0	0.010729	0	0
X97876	0	broad.mit.edu	37	9	66499891	66499891	+	Missense_Mutation	SNP	T	C	C			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr9:66499891T>C	uc004aee.1	+	0	701	c.701T>C	c.(700-702)aTg>aCg	p.M234T	X97876_uc004aed.1_Non-coding_Transcript					Homo sapiens hypothetical LOC442421, mRNA (cDNA clone IMAGE:40031134).																		ACCATCGCCATGTACATGAAG	0.572000														23			4		0	0	0.010729	0	0
BAGE1	0	broad.mit.edu	37	GL000237.1	830	830	+	RNA	SNP	G	T	T			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chrGL000237.1:830G>T	uc011mgu.1	-	1		c.388C>A								Homo sapiens B melanoma antigen variant f (BAGE1) mRNA, complete cds, alternatively spliced.																		GCCTCCATGGGTAccctccta	0.587000														25			7		0.00621372	0.00803236	0.006214	1	0
CTSL3	392360	broad.mit.edu	37	9	90401711	90401711	+	Missense_Mutation	SNP	A	C	C			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr9:90401711A>C	uc004apm.1	+	4	569	c.563A>C	c.(562-564)cAg>cCg	p.Q188P						Homo sapiens cathepsin L family member 3 (CTSL3), non-coding RNA.											endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(1)	15						GAGGCTCTGCAGATGCTAAGT	0.478000														101			5		0	0	0.021553	0	0
NANOS3	342977	broad.mit.edu	37	19	13988494	13988494	+	Silent	SNP	A	G	G			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr19:13988494A>G	uc002mxj.4	+	0	432	c.432A>G	c.(430-432)cgA>cgG	p.R144R		NM_001098622	NP_001092092	P60323	NANO3_HUMAN	Homo sapiens nanos homolog 3 (Drosophila) (NANOS3), mRNA.	125					anti-apoptosis|germ cell development|multicellular organismal development|oogenesis|regulation of cell cycle|regulation of translation|spermatogenesis	cytoplasmic mRNA processing body|nucleus|stress granule	RNA binding|zinc ion binding			breast(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	7			OV - Ovarian serous cystadenocarcinoma(19;2e-21)			ACACCACCCGAAACTCGGCAG	0.662000														23			7		0	0	0.003080	0	0
FLII	2314	broad.mit.edu	37	17	18149935	18149935	+	Silent	SNP	G	A	A			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr17:18149935G>A	uc002gsr.1	-	22	3075	c.3024C>T	c.(3022-3024)ttC>ttT	p.F1008F	FLII_uc002gsq.1_Silent_p.F879F|FLII_uc010vxn.1_Silent_p.F977F|FLII_uc010vxo.1_Silent_p.F953F|FLII_uc002gss.1_Silent_p.F1007F	NM_002018	NP_002009	Q13045	FLII_HUMAN	Homo sapiens flightless I homolog (Drosophila) (FLII), transcript variant 1, mRNA.	1008					multicellular organismal development|muscle contraction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|nucleus	actin binding			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32	all_neural(463;0.228)					AGAGGCTCTCGAACTTCTTTT	0.627000														37			13		0	0	0.013537	0	0
SCAF11	9169	broad.mit.edu	37	12	46320707	46320708	+	Frame_Shift_Del	DEL	TC	-	-			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr12:46320707_46320708delTC	uc001rox.3	-	10	3063_3064	c.2776_2777delGA	c.(2776-2778)gaafs	p.E926fs	SCAF11_uc001row.3_Frame_Shift_Del_p.E611fs|SCAF11_uc001roy.1_Frame_Shift_Del_p.E1000fs	NM_004719	NP_004710	Q99590	SCAFB_HUMAN	Homo sapiens SR-related CTD-associated factor 11 (SCAF11), mRNA.	926	Arg-rich.				spliceosome assembly	nucleus	protein binding|zinc ion binding			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						GGTTCTCCTTTCTCTCTCTCTC	0.446													---	267	---	---	8	---					
RXFP2	122042	broad.mit.edu	37	13	32376429	32376429	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr13:32376429delA	uc001utt.3	+	17	2223	c.2152delA	c.(2152-2154)aaafs	p.K718fs	RXFP2_uc010aba.3_Frame_Shift_Del_p.K694fs	NM_130806	NP_570718	Q8WXD0	RXFP2_HUMAN	Homo sapiens relaxin/insulin-like family peptide receptor 2 (RXFP2), transcript variant 1, mRNA.	718						integral to membrane|plasma membrane				cervix(1)|endometrium(2)|large_intestine(15)|lung(13)|prostate(1)|stomach(1)	33		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)		TTTCAAAATTAAAAAAAAAAG	0.348													---	183	---	---	7	---					
RNMT	8731	broad.mit.edu	37	18	13731629	13731630	+	Frame_Shift_Ins	INS	-	T	T			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr18:13731629_13731630insT	uc002ksk.1	+	1	180_181	c.113_114insT	c.(112-114)gctfs	p.A38fs	RNMT_uc002ksl.1_Frame_Shift_Ins_p.A38fs|RNMT_uc002ksm.1_Frame_Shift_Ins_p.A38fs|RNMT_uc010dlk.2_Frame_Shift_Ins_p.A38fs|RNMT_uc010xae.1_Intron	NM_003799	NP_003790	O43148	MCES_HUMAN	Homo sapiens RNA (guanine-7-) methyltransferase (RNMT), mRNA.	38					mRNA capping|transcription from RNA polymerase II promoter|viral reproduction	nucleoplasm	RNA binding|mRNA (guanine-N7-)-methyltransferase activity			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|skin(2)	18						AACACAACAGCTTCTGGGACTG	0.371													---	111	---	---	31	---					
