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	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
RP11-69H14.6	0	broad.mit.edu	37	15	22332570	22332570	+	RNA	SNP	T	T	C			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr15:22332570T>C	ENST00000558896.1	+	0	377																											CCCATGCTCATCTGCTCCAAT	0.398000													4	194					0	0	1	0	0
ATP2B4	493	broad.mit.edu	37	1	203671203	203671203	+	Missense_Mutation	SNP	C	C	G			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr1:203671203C>G	ENST00000357681.5	+	7	2056	c.933C>G	c.(931-933)aaC>aaG	p.N311K	ATP2B4_ENST00000367218.3_Missense_Mutation_p.N311K|ATP2B4_ENST00000367219.3_Intron|ATP2B4_ENST00000341360.2_Missense_Mutation_p.N311K|ATP2B4_ENST00000391954.2_Missense_Mutation_p.N311K	NM_001684.4	NP_001675.3	P23634	AT2B4_HUMAN	ATPase, Ca++ transporting, plasma membrane 4	311					ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(20)|ovary(2)|prostate(6)|skin(1)|stomach(1)|urinary_tract(3)	56	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)			AAAATCGCAACAAAGGTAACC	0.418000											OREG0014124	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	16	29					0	0	1	0	0
UBBP4	0	broad.mit.edu	37	17	21731144	21731144	+	Missense_Mutation	SNP	T	T	G	rs149119138	by1000genomes	TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr17:21731144T>G	ENST00000584755.1	+	2	843	c.446T>G	c.(445-447)cTg>cGg	p.L149R	UBBP4_ENST00000584398.1_3'UTR|UBBP4_ENST00000578713.1_Missense_Mutation_p.L149R|UBBP4_ENST00000583708.1_3'UTR														p.L149R(18)		endometrium(9)|kidney(4)|lung(4)|prostate(3)|urinary_tract(4)	24						GTCCTGCGTCTGAGAGGTGGT	0.542000													4	92					0	0	1	0	0
COPA	1314	broad.mit.edu	37	1	160261696	160261696	+	Silent	SNP	G	G	A			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr1:160261696G>A	ENST00000241704.7	-	30	3400	c.3171C>T	c.(3169-3171)tgC>tgT	p.C1057C	COPA_ENST00000368069.3_Silent_p.C1066C	NM_001098398.1|NM_004371.3	NP_001091868.1|NP_004362.2	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha	1057					COPI coating of Golgi vesicle|intracellular protein transport|pancreatic juice secretion|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol|extracellular space|microsome|soluble fraction	hormone activity|structural molecule activity			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	46	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TGTACTCACGGCAAATGGTGA	0.522000											OREG0013929	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	266					0	0	1	0	0
PLA2G15	23659	broad.mit.edu	37	16	68289778	68289778	+	Silent	SNP	G	G	A			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr16:68289778G>A	ENST00000219345.5	+	5	695	c.612G>A	c.(610-612)acG>acA	p.T204T	PLA2G15_ENST00000566188.1_Intron|PLA2G15_ENST00000444212.2_Intron|PLA2G15_ENST00000413021.2_Intron	NM_012320.3	NP_036452.1	Q8NCC3	PAG15_HUMAN	phospholipase A2, group XV	204					fatty acid catabolic process	extracellular region|lysosome	lysophospholipase activity|phosphatidylcholine-sterol O-acyltransferase activity|phospholipid binding			kidney(2)|large_intestine(2)|lung(2)|ovary(2)|prostate(3)|skin(1)	12						ACATGTACACGCTCTACTTTC	0.637000													30	36					0	0	1	0	0
LRRC19	64922	broad.mit.edu	37	9	26999613	26999613	+	Splice_Site	SNP	C	C	G			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr9:26999613C>G	ENST00000380055.5	-	2	190	c.81_splice	c.e2+1	p.R27_splice	IFT74_ENST00000380062.5_Intron|IFT74_ENST00000433700.1_Intron|IFT74_ENST00000429045.2_Intron|IFT74_ENST00000443698.1_Intron	NM_022901.2	NP_075052.1	Q9H756	LRC19_HUMAN	leucine rich repeat containing 19	27						integral to membrane				breast(1)|endometrium(2)|kidney(1)|lung(2)	6		all_neural(11;1.81e-09)		Lung(218;1.06e-05)|LUSC - Lung squamous cell carcinoma(38;0.0001)		AAAACTTACTCTTTTAGAAGA	0.303000													8	13					0	0	1	0	0
RBP1	5947	broad.mit.edu	37	3	139258330	139258330	+	Silent	SNP	C	C	T			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr3:139258330C>T	ENST00000483943.2	-	1	231	c.231G>A	c.(229-231)gaG>gaA	p.E77E	RBP1_ENST00000492918.1_Silent_p.E77E|RP11-319G6.1_ENST00000515247.1_RNA|RBP1_ENST00000232219.2_Silent_p.E77E	NM_001130993.1	NP_001124465.1	P09455	RET1_HUMAN	retinol binding protein 1, cellular	15						cytoplasm	retinal binding|retinol binding|transporter activity			endometrium(1)|large_intestine(2)|lung(1)|prostate(1)	5					Vitamin A(DB00162)	CCTCGAAATTCTCGTTGACCA	0.667000													10	19					0	0	1	0	0
BRD3	8019	broad.mit.edu	37	9	136901310	136901310	+	Missense_Mutation	SNP	G	G	A			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr9:136901310G>A	ENST00000303407.7	-	10	1965	c.1780C>T	c.(1780-1782)Cgg>Tgg	p.R594W	BRD3_ENST00000473349.1_5'UTR|BRD3_ENST00000371834.2_3'UTR	NM_007371.3	NP_031397.1	Q15059	BRD3_HUMAN	bromodomain containing 3	594						nucleus	protein binding		BRD3/C15orf55(3)	kidney(1)|skin(1)|stomach(4)	6				OV - Ovarian serous cystadenocarcinoma(145;1.43e-08)|Epithelial(140;8.41e-08)|all cancers(34;5.21e-07)		TGCACTACCCGGCCCAGCTTC	0.582000			T	C15orf55	lethal midline carcinoma of young people								6	66					0	0	1	0	0
MEFV	4210	broad.mit.edu	37	16	3293676	3293676	+	Missense_Mutation	SNP	G	G	A			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr16:3293676G>A	ENST00000219596.1	-	10	1850	c.1811C>T	c.(1810-1812)gCa>gTa	p.A604V	MEFV_ENST00000541159.1_3'UTR|MEFV_ENST00000339854.4_Missense_Mutation_p.A424V|MEFV_ENST00000536379.1_Missense_Mutation_p.A393V	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	604	B30.2/SPRY.				inflammatory response	cytoplasm|microtubule|microtubule associated complex|nucleus	actin binding|zinc ion binding			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50					Colchicine(DB01394)	AGCGGTTTCTGCATCCAGAAT	0.488000													10	298					0	0	1	0	0
RNF40	9810	broad.mit.edu	37	16	30780529	30780529	+	Missense_Mutation	SNP	A	A	C			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr16:30780529A>C	ENST00000324685.6	+	16	2705	c.2270A>C	c.(2269-2271)gAg>gCg	p.E757A	RNF40_ENST00000357890.5_Missense_Mutation_p.E657A|RNF40_ENST00000563683.1_Missense_Mutation_p.E717A|RNF40_ENST00000402121.3_Missense_Mutation_p.E449A	NM_001207033.1|NM_014771.3	NP_001193962.1|NP_055586.1	O75150	BRE1B_HUMAN	ring finger protein 40, E3 ubiquitin protein ligase	757					histone H2B ubiquitination|histone monoubiquitination|ubiquitin-dependent protein catabolic process	nucleus|synaptosome|ubiquitin ligase complex	protein homodimerization activity|ubiquitin protein ligase binding|zinc ion binding			central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)	30			Colorectal(24;0.198)			CTGCTCTCAGAGATGGATGTG	0.547000													6	135					0	0	1	0	0
CHEK2	11200	broad.mit.edu	37	22	29091841	29091841	+	Silent	SNP	G	G	A	rs146546850	byFrequency	TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr22:29091841G>A	ENST00000544772.1	-	12	1889	c.453C>T	c.(451-453)tcC>tcT	p.S151S	CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000382580.2_Silent_p.S415S|CHEK2_ENST00000403642.1_Silent_p.S281S|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000404276.1_Silent_p.S372S|CHEK2_ENST00000382578.1_Silent_p.S281S|CHEK2_ENST00000348295.3_Silent_p.S343S|CHEK2_ENST00000405598.1_Silent_p.S372S|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000328354.6_Silent_p.S372S	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN	checkpoint kinase 2	372	FHA.				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	p.S372S(8)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCAAAATCTTGGAGTGCCCAA	0.413000			F			breast		Direct reversal of damage;Other conserved DNA damage response genes					4	69					0	0	1	0	0
FGR	2268	broad.mit.edu	37	1	27943448	27943448	+	Missense_Mutation	SNP	C	C	T			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr1:27943448C>T	ENST00000374005.3	-	7	890	c.602G>A	c.(601-603)cGc>cAc	p.R201H	FGR_ENST00000374004.1_Missense_Mutation_p.R201H|FGR_ENST00000545953.1_Missense_Mutation_p.R135H|FGR_ENST00000399173.1_Missense_Mutation_p.R201H	NM_005248.2	NP_005239.1	P09769	FGR_HUMAN	feline Gardner-Rasheed sarcoma viral oncogene homolog	201	SH2.				platelet activation|response to virus	cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(4)	16		all_lung(284;2.05e-05)|Colorectal(325;3.46e-05)|Lung NSC(340;3.67e-05)|Renal(390;0.00121)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00244)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		GTCCAGTTTGCGGATCTTGTA	0.557000													4	140					0	0	1	0	0
DMXL1	1657	broad.mit.edu	37	5	118533558	118533558	+	Missense_Mutation	SNP	A	A	C			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr5:118533558A>C	ENST00000311085.8	+	32	7732	c.7652A>C	c.(7651-7653)tAt>tCt	p.Y2551S	DMXL1_ENST00000539542.1_Missense_Mutation_p.Y2551S	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	2551										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		CCTCAAAATTATATCGCAAGT	0.443000													4	161					0	0	1	0	0
ANKRD35	148741	broad.mit.edu	37	1	145562072	145562072	+	Missense_Mutation	SNP	G	G	C			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr1:145562072G>C	ENST00000355594.4	+	10	1847	c.1760G>C	c.(1759-1761)aGg>aCg	p.R587T		NM_144698.3	NP_653299.3	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	587										NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					AAGGAGAAAAGGGTTCCTGGG	0.582000													39	50					0	0	1	0	0
MSH5-SAPCD1	0	broad.mit.edu	37	6	31727947	31727947	+	Missense_Mutation	SNP	T	T	A			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr6:31727947T>A	ENST00000493662.2	+	19	1873	c.1817T>A	c.(1816-1818)gTc>gAc	p.V606D	MSH5_ENST00000431848.2_Missense_Mutation_p.V288D|MSH5_ENST00000375755.3_Missense_Mutation_p.V589D|MSH5_ENST00000375703.3_Missense_Mutation_p.V589D|MSH5_ENST00000534153.4_Missense_Mutation_p.V606D|MSH5_ENST00000375740.3_Missense_Mutation_p.V606D|MSH5_ENST00000375742.3_Missense_Mutation_p.V606D|MSH5_ENST00000375750.3_Missense_Mutation_p.V589D|MSH5_ENST00000395853.1_Missense_Mutation_p.V263D																							AGGGTCAAAGTCATCACTGGA	0.567000													51	75					0	0	1	0	0
ADAMTSL1	92949	broad.mit.edu	37	9	18817126	18817126	+	Silent	SNP	G	G	A			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr9:18817126G>A	ENST00000380548.4	+	21	4164	c.3825G>A	c.(3823-3825)acG>acA	p.T1275T		NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	1275						proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		TAGTGAAAACGTCACGAATGA	0.448000													5	8					0	0	1	0	0
KCNH1	3756	broad.mit.edu	37	1	210971076	210971076	+	Missense_Mutation	SNP	C	C	T			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr1:210971076C>T	ENST00000367007.4	-	9	1777	c.1608G>A	c.(1606-1608)atG>atA	p.M536I	KCNH1_ENST00000271751.4_Missense_Mutation_p.M563I	NM_002238.3|NM_172362.2	NP_002229.1|NP_758872.1	O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	563					myoblast fusion|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	calmodulin binding|delayed rectifier potassium channel activity|two-component sensor activity			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		TGTCGGCTCTCATGTCCTTGG	0.597000													17	36					0	0	1	0	0
PLEKHH1	57475	broad.mit.edu	37	14	68053956	68053956	+	Missense_Mutation	SNP	T	T	C			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr14:68053956T>C	ENST00000417684.2	+	12	1511	c.923T>C	c.(922-924)aTt>aCt	p.I308T	PLEKHH1_ENST00000329153.5_3'UTR			Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	0						cytoskeleton	binding			endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		GCTGTGAATATTTCTCCTACC	0.517000													44	50					0	0	1	0	0
TRIM26	7726	broad.mit.edu	37	6	30153814	30153814	+	Missense_Mutation	SNP	G	G	A			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr6:30153814G>A	ENST00000454678.2	-	10	1895	c.1459C>T	c.(1459-1461)Cgg>Tgg	p.R487W	TRIM26_ENST00000453195.1_Missense_Mutation_p.R487W|TRIM26_ENST00000437089.1_Missense_Mutation_p.R487W	NM_003449.4	NP_003440.1	Q12899	TRI26_HUMAN	tripartite motif containing 26	487	B30.2/SPRY.						DNA binding|zinc ion binding			lung(1)|ovary(2)	3						CCCACTCTCCGGGGCCGCAGT	0.642000													11	7					0	0	1	0	0
ALLC	55821	broad.mit.edu	37	2	3749214	3749214	+	Silent	SNP	T	T	A			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr2:3749214T>A	ENST00000252505.3	+	11	1125	c.963T>A	c.(961-963)ctT>ctA	p.L321L	ALLC_ENST00000471711.1_3'UTR	NM_018436.3	NP_060906.3	Q8N6M5	ALLC_HUMAN	allantoicase	340							allantoicase activity			breast(4)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	30	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)		AACCACTGCTTCCAGTGACCA	0.488000										HNSCC(21;0.051)			9	13					0	0	1	0	0
CHEK2	11200	broad.mit.edu	37	22	29091840	29091840	+	Missense_Mutation	SNP	T	T	C	rs142470496	byFrequency	TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr22:29091840T>C	ENST00000544772.1	-	12	1890	c.454A>G	c.(454-456)Aag>Gag	p.K152E	CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E|CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E|CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E|CHEK2_ENST00000405598.1_Missense_Mutation_p.K373E|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN	checkpoint kinase 2	373	FHA.				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	p.K373E(9)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCCAAAATCTTGGAGTGCCCA	0.418000			F			breast		Direct reversal of damage;Other conserved DNA damage response genes					4	70					0	0	1	0	0
VPS53	55275	broad.mit.edu	37	17	556535	556535	+	Missense_Mutation	SNP	C	C	T			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr17:556535C>T	ENST00000437048.2	-	7	750	c.604G>A	c.(604-606)Gaa>Aaa	p.E202K	VPS53_ENST00000401468.3_Intron|VPS53_ENST00000576149.1_Intron|VPS53_ENST00000291074.5_Missense_Mutation_p.E173K|VPS53_ENST00000446250.2_5'UTR|VPS53_ENST00000574029.1_Intron|VPS53_ENST00000571805.1_Missense_Mutation_p.E202K	NM_001128159.2	NP_001121631.1	Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 homolog (S. cerevisiae)	202					protein transport	endosome membrane|Golgi apparatus				breast(1)|endometrium(4)|large_intestine(5)|lung(8)|prostate(1)	19				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		GTTTACCTTTCGGAAAGCTGC	0.483000													5	185					0	0	1	0	0
U2AF1	7307	broad.mit.edu	37	21	44513235	44513235	+	Missense_Mutation	SNP	G	G	A			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr21:44513235G>A	ENST00000459639.1	-	7	1505	c.481C>T	c.(481-483)Cgt>Tgt	p.R161C	U2AF1_ENST00000398137.1_Missense_Mutation_p.R161C|U2AF1_ENST00000291552.4_Missense_Mutation_p.R234C|U2AF1_ENST00000380276.2_Missense_Mutation_p.R234C			Q01081	U2AF1_HUMAN	U2 small nuclear RNA auxiliary factor 1	234					mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	Cajal body|catalytic step 2 spliceosome|nuclear speck	nucleotide binding|RNA binding|zinc ion binding			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(111)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	126						GATCTTTCACGATCTCTCGAC	0.552000			Mis		"""CLL, MDS"""								6	84					0	0	1	0	0
USP9X	8239	broad.mit.edu	37	X	41043349	41043349	+	Missense_Mutation	SNP	C	C	G			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chrX:41043349C>G	ENST00000324545.7	+	22	3880	c.3247C>G	c.(3247-3249)Cct>Gct	p.P1083A	USP9X_ENST00000378308.2_Missense_Mutation_p.P1083A	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1083					BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						TTTCTTTGGTCCTTCAGCCTC	0.353000													9	70					0	0	1	0	0
FBN3	84467	broad.mit.edu	37	19	8168496	8168496	+	Missense_Mutation	SNP	C	C	T			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr19:8168496C>T	ENST00000600128.1	-	39	5303	c.4889G>A	c.(4888-4890)tGt>tAt	p.C1630Y	FBN3_ENST00000601739.1_Missense_Mutation_p.C1630Y|FBN3_ENST00000270509.2_Missense_Mutation_p.C1630Y			Q75N90	FBN3_HUMAN	fibrillin 3	1630	EGF-like 25; calcium-binding.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						AGGGCAGACACAGGTGTAGTT	0.562000													41	45					0	0	1	0	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377		TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	v-raf murine sarcoma viral oncogene homolog B	600	Protein kinase.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).		activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Sorafenib(DB00398)	TCGAGATTTCACTGTAGCTAG	0.368000	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome				33	52					0	0	1	0	0
PLCD1	5333	broad.mit.edu	37	3	38051629	38051629	+	Missense_Mutation	SNP	G	G	C			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr3:38051629G>C	ENST00000463876.1	-	7	1546	c.1193C>G	c.(1192-1194)gCc>gGc	p.A398G	PLCD1_ENST00000334661.4_Missense_Mutation_p.A377G	NM_001130964.1	NP_001124436.1	P51178	PLCD1_HUMAN	phospholipase C, delta 1	377	PI-PLC X-box.				intracellular signal transduction|lipid catabolic process|phospholipid metabolic process	cytoplasm	calcium ion binding|GTPase activating protein binding|phosphatidylinositol phospholipase C activity|signal transducer activity			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		CACCTTGAAGGCATAGTCCCG	0.607000													30	45					0	0	1	0	0
BAGE2	85319	broad.mit.edu	37	21	11058168	11058168	+	RNA	SNP	A	A	T			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr21:11058168A>T	ENST00000470054.1	-	0	479									B melanoma antigen family, member 2															Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TACATCTTTCAGGAGCTTGGT	0.388000													5	88					0	0	1	0	0
TAF1B	9014	broad.mit.edu	37	2	9989571	9989571	+	Frame_Shift_Del	DEL	A	A	-			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr2:9989571delA	ENST00000263663.5	+	3	375	c.187delA	c.(187-189)aafs	p.K65fs	TAF1B_ENST00000396242.3_5'UTR|TAF1B_ENST00000402170.1_3'UTR	NM_005680.2	NP_005671.2	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	65					termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CCGGGGGCTTAAAAAAAAAAA	0.333													2	4	---	---	---	---					
GPR123	84435	broad.mit.edu	37	10	134895345	134895345	+	Frame_Shift_Del	DEL	A	A	-			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr10:134895345delA	ENST00000607359.1	+	5	988	c.988delA	c.(988-990)ccfs	p.T330fs				Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	481						integral to membrane|plasma membrane	G-protein coupled receptor activity			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3)	14		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		CTCTGGCAGGACCCCCTGGAG	0.662													2	4	---	---	---	---					
HNRNPKP3	0	broad.mit.edu	37	11	43283606	43283606	+	RNA	DEL	A	A	-			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr11:43283606delA	ENST00000511537.1	-	0	1329					NR_033868.1																						AAGCAAATGTAAAAAAAAAAA	0.388													4	6	---	---	---	---					
TXLNG2P	0	broad.mit.edu	37	Y	21758004	21758005	+	RNA	DEL	AG	AG	-			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chrY:21758004_21758005delAG	ENST00000253320.4	+	0	3085_3086							Q9BZA5	CY15A_HUMAN												haematopoietic_and_lymphoid_tissue(1)	1						GAAAGACATCAGAGAGAGAGAG	0.347													3	6	---	---	---	---					
