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
TIA1	7072	broad.mit.edu	37	2	70439917	70439917	+	Silent	SNP	C	C	T			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr2:70439917C>T	ENST00000433529.2	-	13	1305	c.1095G>A	c.(1093-1095)ggG>ggA	p.G365G	TIA1_ENST00000282574.4_Silent_p.G364G|TIA1_ENST00000415783.2_Silent_p.G354G|C2orf42_ENST00000470096.1_Intron|TIA1_ENST00000445587.1_Silent_p.G264G	NM_022173.2	NP_071505.2	P31483	TIA1_HUMAN	TIA1 cytotoxic granule-associated RNA binding protein	365					apoptosis|induction of apoptosis|regulation of nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|poly(A) RNA binding|protein binding			endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|skin(1)|urinary_tract(1)	17						TGCCATTTTGCCCTTGAGGCG	0.502000													4	130					0	0	0.009096	0	0
NPR1	4881	broad.mit.edu	37	1	153660571	153660571	+	Missense_Mutation	SNP	G	G	A			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr1:153660571G>A	ENST00000368680.3	+	15	2763	c.2291G>A	c.(2290-2292)cGg>cAg	p.R764Q		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor A/guanylate cyclase A (atrionatriuretic peptide receptor A)	764	Protein kinase.				body fluid secretion|intracellular signal transduction|negative regulation of angiogenesis|negative regulation of cell growth|positive regulation of renal sodium excretion|positive regulation of urine volume|receptor guanylyl cyclase signaling pathway|regulation of blood pressure|regulation of blood vessel size|regulation of vascular permeability|regulation of vasodilation		ATP binding|GTP binding|guanylate cyclase activity|natriuretic peptide receptor activity|peptide receptor activity, G-protein coupled|protein kinase activity			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Nesiritide(DB04899)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	CCCCCCTTCCGGCCCTCCCTG	0.657000													26	44					0	0	0.027356	0	0
AC008103.5	0	broad.mit.edu	37	22	18845995	18845995	+	RNA	SNP	T	T	C			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr22:18845995T>C	ENST00000412938.1	+	0	3353																											CATCCCGTCCTGCGCAGGCCG	0.592000													8	54					0	0	0.008291	0	0
NBPF10	100132406	broad.mit.edu	37	1	145367739	145367739	+	Silent	SNP	A	A	G	rs146714035	by1000genomes	TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr1:145367739A>G	ENST00000342960.5	+	83	10370	c.10335A>G	c.(10333-10335)aaA>aaG	p.K3445K	NBPF10_ENST00000369339.2_Intron|NBPF10_ENST00000369338.1_Intron	NM_001039703.4	NP_001034792.4	A6NDV3	A6NDV3_HUMAN	neuroblastoma breakpoint family, member 10	3445								p.K3445K(4)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ggaaggggaaaaaaagaaggg	0.413000													3	112					0	0	0.004672	0	0
FRG1B	0	broad.mit.edu	37	20	29628278	29628278	+	Missense_Mutation	SNP	G	G	A			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr20:29628278G>A	ENST00000278882.3	+	6	660	c.280G>A	c.(280-282)Gca>Aca	p.A94T	FRG1B_ENST00000439954.2_Missense_Mutation_p.A99T|FRG1B_ENST00000358464.4_Missense_Mutation_p.A94T																endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						ATGCAATGAAGCAGGGGACAT	0.373000													5	96					0	0	0.004482	0	0
ANKEF1	63926	broad.mit.edu	37	20	10025188	10025188	+	Silent	SNP	C	C	T			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr20:10025188C>T	ENST00000378380.3	+	4	1022	c.693C>T	c.(691-693)ttC>ttT	p.F231F	SNAP25-AS1_ENST00000421143.2_RNA|ANKEF1_ENST00000488991.1_3'UTR|ANKEF1_ENST00000378392.1_Silent_p.F231F|SNAP25-AS1_ENST00000603542.1_RNA	NM_198798.1	NP_942093.1			ankyrin repeat and EF-hand domain containing 1																		GAGGCTTTTTCGATGTAATAA	0.358000													4	101					0	0	0.014758	0	0
SLC2A9	56606	broad.mit.edu	37	4	9982230	9982230	+	Missense_Mutation	SNP	C	C	T	rs147289616	byFrequency	TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr4:9982230C>T	ENST00000506583.1	-	7	797	c.580G>A	c.(580-582)Gag>Aag	p.E194K	SLC2A9_ENST00000264784.3_Missense_Mutation_p.E223K|SLC2A9_ENST00000309065.3_Missense_Mutation_p.E194K			Q9NRM0	GTR9_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 9	223					glucose transport|urate metabolic process	integral to membrane|plasma membrane	sugar:hydrogen symporter activity			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(1)	35						CCCAGCAGCTCGGGCAGGCCC	0.567000													5	49					0	0	0.021553	0	0
PHF6	84295	broad.mit.edu	37	X	133527567	133527567	+	Missense_Mutation	SNP	G	G	T			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chrX:133527567G>T	ENST00000332070.3	+	4	479	c.277G>T	c.(277-279)Ggt>Tgt	p.G93C	PHF6_ENST00000370799.1_Missense_Mutation_p.G93C|PHF6_ENST00000416404.2_Missense_Mutation_p.G59C|PHF6_ENST00000370803.3_Missense_Mutation_p.G93C|PHF6_ENST00000370800.4_Missense_Mutation_p.G93C|PHF6_ENST00000394292.1_Missense_Mutation_p.G93C	NM_032458.2	NP_115834.1	Q8IWS0	PHF6_HUMAN	PHD finger protein 6	93					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	zinc ion binding			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(88)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|ovary(1)|skin(1)|urinary_tract(1)	103	Acute lymphoblastic leukemia(192;0.000127)					AGCAACAATTGGTTGTGATGT	0.368000			"""F, N, Splice, Mis"""		ETP ALL								15	167					6.72482e-11	1.15945e-10	0.024245	1	0
PMS2	5395	broad.mit.edu	37	7	6018249	6018249	+	Silent	SNP	A	A	G	rs140779135	by1000genomes	TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr7:6018249A>G	ENST00000265849.7	-	13	2358	c.2253T>C	c.(2251-2253)ttT>ttC	p.F751F	PMS2_ENST00000382321.4_Silent_p.F350F|PMS2_ENST00000406569.3_Intron|PMS2_ENST00000441476.2_Silent_p.F645F	NM_000535.5	NP_000526.1	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	751					mismatch repair|reciprocal meiotic recombination|somatic hypermutation of immunoglobulin genes	MutLalpha complex	ATP binding|ATPase activity|endonuclease activity|protein binding|single base insertion or deletion binding			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		TAACAAAATCAAAGCCATTCT	0.393000			"""Mis, N, F"""			"""colorectal, endometrial, ovarian, medulloblastoma, glioma"""		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				4	26					0	0	0.009096	0	0
KCNN3	3782	broad.mit.edu	37	1	154841828	154841828	+	Missense_Mutation	SNP	C	C	T			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr1:154841828C>T	ENST00000271915.3	-	1	928	c.613G>A	c.(613-615)Ggc>Agc	p.G205S		NM_002249.5	NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	210						integral to membrane	calmodulin binding			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)			AGGGGTTGGCCCTCAGTCTCG	0.632000													32	33					0	0	0.013726	0	0
CGB1	114335	broad.mit.edu	37	19	49539494	49539494	+	Missense_Mutation	SNP	G	G	A			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr19:49539494G>A	ENST00000301407.7	-	2	180	c.76C>T	c.(76-78)Cgg>Tgg	p.R26W	CTB-60B18.6_ENST00000591656.1_Intron|CGB1_ENST00000391869.3_Missense_Mutation_p.R26W	NM_033377.1	NP_203695.2	A6NKQ9	CGB1_HUMAN	chorionic gonadotropin, beta polypeptide 1	58						extracellular region	hormone activity			liver(1)|lung(1)	2		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)		GGGCGGCACCGTGGCCGAAGC	0.652000													6	89					0	0	0.003080	0	0
TRO	7216	broad.mit.edu	37	X	54954164	54954164	+	Missense_Mutation	SNP	C	C	T			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chrX:54954164C>T	ENST00000173898.7	+	11	1940	c.1828C>T	c.(1828-1830)Cgc>Tgc	p.R610C	TRO_ENST00000319167.8_Missense_Mutation_p.R610C|TRO_ENST00000420798.2_Missense_Mutation_p.R141C|TRO_ENST00000375022.4_Missense_Mutation_p.R610C|TRO_ENST00000399736.1_Missense_Mutation_p.R213C|TRO_ENST00000375041.2_Missense_Mutation_p.R213C	NM_001039705.1	NP_001034794.1	Q12816	TROP_HUMAN	trophinin	610	MAGE.				embryo implantation|homophilic cell adhesion	integral to plasma membrane		p.R610C(2)		breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						CTGGGGCTTGCGCTCCTACCA	0.483000													4	93					0	0	0.009096	0	0
DCAF12L2	340578	broad.mit.edu	37	X	125298907	125298907	+	Missense_Mutation	SNP	G	G	A			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chrX:125298907G>A	ENST00000538699.1	-	2	1081	c.1001C>T	c.(1000-1002)cCg>cTg	p.P334L	DCAF12L2_ENST00000360028.2_Missense_Mutation_p.P334L	NM_001013628.2	NP_001013650.1	Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	334										NS(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(36)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(3)	64						GCGCTGGCGCGGATCCAGGAA	0.617000													49	81					0	0	0.014410	0	0
STC2	8614	broad.mit.edu	37	5	172752921	172752921	+	Missense_Mutation	SNP	G	G	A			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr5:172752921G>A	ENST00000265087.4	-	2	1553	c.244C>T	c.(244-246)Cat>Tat	p.H82Y		NM_003714.2	NP_003705.1	O76061	STC2_HUMAN	stanniocalcin 2	82					cell surface receptor linked signaling pathway|cell-cell signaling	extracellular region	hormone activity			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(3)	25	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.223)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CAAATCCCATGTAAGCCCCGA	0.468000													12	373					0	0	0.013537	0	0
LL22NC03-80A10.6	0	broad.mit.edu	37	22	22664606	22664606	+	RNA	SNP	A	A	G			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr22:22664606A>G	ENST00000426066.1	+	0	787					NR_027293.1																						GTCTTCATGCAAACTTGGTAT	0.398000													3	18					0	0	0.004672	0	0
FIP1L1	81608	broad.mit.edu	37	4	54310242	54310242	+	Silent	SNP	T	T	C			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr4:54310242T>C	ENST00000337488.6	+	15	1451	c.1257T>C	c.(1255-1257)cgT>cgC	p.R419R	FIP1L1_ENST00000507166.1_Intron|FIP1L1_ENST00000306932.6_Silent_p.R345R|FIP1L1_ENST00000358575.5_Silent_p.R413R	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	419					mRNA processing	nucleus	RNA binding			large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			ATGATAGTCGTTCTGCACGTG	0.303000			T	PDGFRA	idiopathic hypereosinophilic syndrome								3	82					0	0	0.014758	0	0
TMPRSS11F	389208	broad.mit.edu	37	4	68939712	68939712	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr4:68939712G>A	ENST00000356291.2	-	4	357	c.298C>T	c.(298-300)Cga>Tga	p.R100*	RP11-453E17.1_ENST00000511571.1_RNA|RP11-453E17.1_ENST00000500538.2_RNA|RP11-453E17.1_ENST00000499180.2_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	100	SEA.				proteolysis	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						GAAGAATGTCGAAATATCCTA	0.244000													10	16					0	0	0.008291	0	0
PRDM9	56979	broad.mit.edu	37	5	23526762	23526762	+	Missense_Mutation	SNP	C	C	T			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr5:23526762C>T	ENST00000296682.3	+	11	1747	c.1565C>T	c.(1564-1566)gCa>gTa	p.A522V		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	522					meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleoplasm	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						TCAAGAATTGCAAAAGTCAAG	0.433000										HNSCC(3;0.000094)			5	71					0	0	0.014758	0	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377		TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	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				31	59					0	0	0.010818	0	0
MGAM	8972	broad.mit.edu	37	7	141767225	141767225	+	Splice_Site	SNP	C	C	T	rs7778384	by1000genomes	TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr7:141767225C>T	ENST00000475668.2	+	42	5058	c.5004_splice	c.e42+1	p.R1668_splice	MGAM_ENST00000549489.2_Intron			O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1668	Glucoamylase.				polysaccharide digestion|starch catabolic process	apical plasma membrane|integral to membrane	carbohydrate binding|glucan 1,4-alpha-glucosidase activity|maltose alpha-glucosidase activity			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TCCTGGAGCGCGTGAGTATGG	0.592000													5	26					0	0	0.021553	0	0
CACNA1G	8913	broad.mit.edu	37	17	48680555	48680555	+	Silent	SNP	G	G	A			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr17:48680555G>A	ENST00000352832.5	+	20	4467	c.4095G>A	c.(4093-4095)ccG>ccA	p.P1365P	CACNA1G_ENST00000503485.1_Silent_p.P1388P|CACNA1G_ENST00000515765.1_Silent_p.P1388P|CACNA1G_ENST00000515165.1_Silent_p.P1388P|CACNA1G_ENST00000442258.2_Silent_p.P1365P|CACNA1G_ENST00000514717.1_Silent_p.P1365P|CACNA1G_ENST00000507609.1_Silent_p.P1388P|CACNA1G_ENST00000514181.1_Silent_p.P1388P|CACNA1G_ENST00000514079.1_Silent_p.P1388P|CACNA1G_ENST00000513964.1_Silent_p.P1388P|CACNA1G_ENST00000513689.2_Silent_p.P1388P|CACNA1G_ENST00000416767.4_Silent_p.P1388P|CACNA1G_ENST00000429973.2_Silent_p.P1388P|CACNA1G_ENST00000360761.4_Silent_p.P1365P|CACNA1G_ENST00000507896.1_Silent_p.P1388P|CACNA1G_ENST00000512389.1_Silent_p.P1388P|CACNA1G_ENST00000510366.1_Silent_p.P1388P|CACNA1G_ENST00000505165.1_Silent_p.P1388P|CACNA1G_ENST00000507510.2_Silent_p.P1388P|CACNA1G_ENST00000358244.5_Silent_p.P1365P|CACNA1G_ENST00000507336.1_Silent_p.P1388P|CACNA1G_ENST00000510115.1_Silent_p.P1365P|CACNA1G_ENST00000515411.1_Silent_p.P1388P|CACNA1G_ENST00000502264.1_Silent_p.P1365P|CACNA1G_ENST00000354983.4_Silent_p.P1365P|CACNA1G_ENST00000359106.5_Silent_p.P1388P	NM_001256334.1|NM_198376.2|NM_198379.2|NM_198387.2|NM_198388.2	NP_001243263.1|NP_938190.1|NP_938193.1|NP_938201.1|NP_938202.1	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	1388					axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	CCCTGCGCCCGCTCAGGTGAC	0.637000													10	17					0	0	0.008291	0	0
PLEKHA4	0	broad.mit.edu	37	19	49351244	49351244	+	Silent	SNP	A	A	C			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr19:49351244A>C	ENST00000263265.6	-	14	2034	c.1479T>G	c.(1477-1479)ggT>ggG	p.G493G	PLEKHA4_ENST00000355496.5_Silent_p.G468G	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	493						cytoplasm|membrane	1-phosphatidylinositol binding			NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		GGCCACCCAGACCTGCCAGCG	0.592000													4	23					0	0	0.014758	0	0
GTF2IRD2P1	0	broad.mit.edu	37	7	72658179	72658179	+	RNA	SNP	T	T	C	rs147293416	by1000genomes	TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr7:72658179T>C	ENST00000425256.1	-	0	1732					NR_002164.1																						cagagtgatttcggatgaatt	0.507000													5	55					0	0	0.021553	0	0
IARS	3376	broad.mit.edu	37	9	95030578	95030578	+	Missense_Mutation	SNP	G	G	C			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr9:95030578G>C	ENST00000375643.3	-	14	1575	c.1309C>G	c.(1309-1311)Cca>Gca	p.P437A	IARS_ENST00000375629.3_5'UTR|IARS_ENST00000447699.2_Missense_Mutation_p.P327A|IARS_ENST00000443024.2_Missense_Mutation_p.P437A	NM_013417.2	NP_038203.2	P41252	SYIC_HUMAN	isoleucyl-tRNA synthetase	437					isoleucyl-tRNA aminoacylation	cytosol|nucleus|soluble fraction	ATP binding|isoleucine-tRNA ligase activity|protein binding			breast(3)|endometrium(2)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	35					L-Isoleucine(DB00167)	ACCAACTCTGGGACCCTGCAA	0.418000													15	139					0	0	0.024245	0	0
GBA3	57733	broad.mit.edu	37	4	22749784	22749785	+	RNA	DEL	TA	TA	-	rs73803318		TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr4:22749784_22749785delTA	ENST00000503442.1	+	0	377				GBA3_ENST00000511446.1_RNA|GBA3_ENST00000508166.1_RNA	NM_001128432.2	NP_001121904.1	Q9H227	GBA3_HUMAN	glucosidase, beta, acid 3 (gene/pseudogene)						glycoside catabolic process|glycosylceramide catabolic process	cytosol	beta-galactosidase activity|beta-glucosidase activity|cation binding|glycosylceramidase activity			breast(1)|kidney(2)|large_intestine(4)|lung(20)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						CAGGCatatgtatatatatata	0.342													4	3	---	---	---	---					
SLC22A2	6582	broad.mit.edu	37	6	160664756	160664757	+	Frame_Shift_Del	DEL	AT	AT	-			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr6:160664756_160664757delAT	ENST00000366953.3	-	7	1384_1385	c.1126_1127delAT	c.(1126-1128)cfs	p.I376fs	SLC22A2_ENST00000491092.1_5'UTR	NM_003058.3	NP_003049.2	O15244	S22A2_HUMAN	solute carrier family 22 (organic cation transporter), member 2	376					body fluid secretion|neurotransmitter biosynthetic process|neurotransmitter secretion	integral to plasma membrane|membrane fraction	neurotransmitter transporter activity|organic cation transmembrane transporter activity			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(16)|prostate(2)|skin(1)	27		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.28e-17)|BRCA - Breast invasive adenocarcinoma(81;6.29e-06)		ATCCAGGTAGATATTGTCACCT	0.535													41	56	---	---	---	---					
APOA4	337	broad.mit.edu	37	11	116693873	116693873	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr11:116693873delA	ENST00000357780.3	-	1	149	c.35delT	c.(34-36)cgfs	p.L12fs		NM_000482.3	NP_000473.2			apolipoprotein A-IV											cervix(1)|endometrium(2)|lung(10)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		GACAGCCACCAGGGCCAGGGT	0.592													107	140	---	---	---	---					
RP11-273B20.3	0	broad.mit.edu	37	12	7338794	7338794	+	RNA	DEL	G	G	-	rs34548221		TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr12:7338794delG	ENST00000545794.1	-	0	279				RP11-273B20.3_ENST00000543061.1_RNA																							cctgttgagaggggggactga	0.502													3	5	---	---	---	---					
RP11-33N16.3	0	broad.mit.edu	37	14	90203668	90203668	+	RNA	DEL	C	C	-	rs67505159		TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr14:90203668delC	ENST00000555070.1	-	0	170																											CTCTTTCTTTCtttttttttt	0.368													5	8	---	---	---	---					
RP11-439I14.2	0	broad.mit.edu	37	16	64770704	64770705	+	RNA	INS	-	-	CCAGTGATGGTCACCT	rs140029302	by1000genomes	TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr16:64770704_64770705insCCAGTGATGGTCACCT	ENST00000564293.1	+	0	453_454																											TGTCACCACTGCCACCTTGTTC	0.371													3	4	---	---	---	---