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_status	validation_method	validation_tumor_sample	validation_alt_allele	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
RASAL2	9462	broad.mit.edu	37	1	178269183	178269183	+	Silent	SNP	G	A	A			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr1:178269183G>A	uc001glq.2	+	3	1151	c.387G>A	c.(385-387)CTG>CTA	p.L129L	RASAL2_uc009wxb.2_Silent_p.L129L	NM_170692	NP_733793	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2 isoform 2	Error:Variant_position_missing_in_Q9UJF2_after_alignment					negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity			ovary(2)|breast(2)|large_intestine(1)	5						GGCGATGCCTGAGGAGAACTG	0.473000											OREG0014010	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	84	---	---	---	---	0	0	0.014758	0	0
RRP8	23378	broad.mit.edu	37	11	6622217	6622217	+	Missense_Mutation	SNP	G	A	A			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr11:6622217G>A	uc001med.2	-	4	1065	c.986C>T	c.(985-987)CCT>CTT	p.P329L	ILK_uc001mee.2_5'Flank|ILK_uc001mef.2_5'Flank|ILK_uc010rap.1_5'Flank|ILK_uc010raq.1_5'Flank|ILK_uc001meg.2_5'Flank|ILK_uc001meh.2_5'Flank	NM_015324	NP_056139	O43159	RRP8_HUMAN	ribosomal RNA processing 8, methyltransferase,	329					chromatin modification|chromatin silencing at rDNA|rRNA processing|transcription, DNA-dependent	chromatin silencing complex|nucleolus|rDNA heterochromatin	methylated histone residue binding|S-adenosylmethionine-dependent methyltransferase activity				0						GCAATGCACAGGGTTCCGGAT	0.547000													7	75	---	---	---	---	0	0	0.029380	0	0
PRDX5	25824	broad.mit.edu	37	11	64085693	64085693	+	Silent	SNP	A	C	C			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr11:64085693A>C	uc001nzu.2	+	1	125	c.6A>C	c.(4-6)GGA>GGC	p.G2G	TRMT112_uc001nzt.2_5'Flank|PRDX5_uc001nzv.2_Silent_p.G2G|PRDX5_uc001nzw.2_Silent_p.G2G|PRDX5_uc001nzx.2_5'Flank	NM_012094	NP_036226	P30044	PRDX5_HUMAN	peroxiredoxin 5 isoform a precursor	2					cell redox homeostasis|cellular response to reactive oxygen species|inflammatory response|negative regulation of apoptosis	cytosolic part|mitochondrion|peroxisome	caspase inhibitor activity|peroxidase activity|peroxiredoxin activity			breast(1)	1					Auranofin(DB00995)	CGGGTATGGGACTAGCTGGCG	0.697000													11	20	---	---	---	---	0	0	0.105934	0	0
NDUFS8	4728	broad.mit.edu	37	11	67800677	67800677	+	Missense_Mutation	SNP	C	T	T			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr11:67800677C>T	uc001onc.2	+	5	406	c.299C>T	c.(298-300)GCG>GTG	p.A100V	NDUFS8_uc010rpz.1_Missense_Mutation_p.A100V|NDUFS8_uc009ysb.1_Intron|NDUFS8_uc009ysc.1_Missense_Mutation_p.A100V	NM_002496	NP_002487	O00217	NDUS8_HUMAN	NADH dehydrogenase ubiquinone Fe-S 8 precursor	100					mitochondrial electron transport, NADH to ubiquinone|mitochondrial respiratory chain complex I assembly|response to oxidative stress|transport	mitochondrial respiratory chain complex I	4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NADH dehydrogenase (ubiquinone) activity			skin(1)	1					NADH(DB00157)	GGGGAGCATGCGCTGCGCCGG	0.687000													3	24	---	---	---	---	0	0	0.004672	0	0
THSD1P1	374500	broad.mit.edu	37	13	52864028	52864028	+	RNA	SNP	C	T	T	rs138483057	by1000genomes	TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr13:52864028C>T	uc001vgm.1	-	2		c.130G>A								Homo sapiens cDNA FLJ14630 fis, clone NT2RP2000459.												0						TAGAATGATACTCCAAAGGAA	0.308000													3	26	---	---	---	---	0	0	0.014758	0	0
MIPOL1	145282	broad.mit.edu	37	14	37838730	37838730	+	Silent	SNP	G	A	A			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr14:37838730G>A	uc001wuc.2	+	11	1340	c.837G>A	c.(835-837)CGG>CGA	p.R279R	MIPOL1_uc010amr.2_Intron|MIPOL1_uc001wub.3_Silent_p.R248R|MIPOL1_uc001wud.2_Silent_p.R279R|MIPOL1_uc010ams.2_Silent_p.R279R|MIPOL1_uc001wue.2_Silent_p.R248R|MIPOL1_uc010amt.2_Silent_p.R98R	NM_138731	NP_620059	Q8TD10	MIPO1_HUMAN	mirror-image polydactyly 1	279	Potential.									ovary(1)|central_nervous_system(1)	2	Breast(36;0.119)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;6.03e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.047)|all cancers(34;0.0953)|LUSC - Lung squamous cell carcinoma(13;0.0975)|BRCA - Breast invasive adenocarcinoma(188;0.196)	GBM - Glioblastoma multiforme(112;0.0358)		AGTGCAAACGGTTAGAGCAGG	0.393000													3	42	---	---	---	---	0	0	0.009096	0	0
TLN2	83660	broad.mit.edu	37	15	62995030	62995030	+	Missense_Mutation	SNP	G	C	C			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr15:62995030G>C	uc002alb.3	+	16	1971	c.1971G>C	c.(1969-1971)CAG>CAC	p.Q657H		NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	657					cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11						TTCTGAGACAGATTGGAGAGA	0.468000													29	31	---	---	---	---	0	0	0.034045	0	0
GOLGA6L5	374650	broad.mit.edu	37	15	85053142	85053142	+	RNA	SNP	C	T	T			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr15:85053142C>T	uc002bkm.2	-	9		c.1905G>A			uc002bkl.1_5'Flank	NR_003246				Homo sapiens cDNA FLJ33459 fis, clone BRAMY2000585.												0						TTTTTCAATTCCTTGACCCGC	0.393000													6	10	---	---	---	---	0	0	0.047766	0	0
C16orf48	84080	broad.mit.edu	37	16	67697198	67697198	+	Missense_Mutation	SNP	C	T	T	rs138813287	byFrequency	TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr16:67697198C>T	uc002etw.1	-	7	1190	c.907G>A	c.(907-909)GTA>ATA	p.V303I	ACD_uc002etp.3_5'Flank|ACD_uc002etq.3_5'Flank|ACD_uc002etr.3_5'Flank|ACD_uc010vjt.1_5'Flank|C16orf48_uc002etv.1_Missense_Mutation_p.V185I|C16orf48_uc010cem.1_3'UTR	NM_032140	NP_115516	Q9H0I2	CP048_HUMAN	hypothetical protein LOC84080	303						microtubule cytoskeleton	protein binding				0		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.047)|all cancers(182;0.228)		GGCAGCAGTACCAGCTCACGC	0.652000													28	92	---	---	---	---	0	0	0.045705	0	0
ATP2C2	9914	broad.mit.edu	37	16	84456271	84456271	+	Missense_Mutation	SNP	G	A	A			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr16:84456271G>A	uc002fhx.2	+	9	900	c.811G>A	c.(811-813)GGA>AGA	p.G271R	ATP2C2_uc010chj.2_Missense_Mutation_p.G271R|ATP2C2_uc002fhy.2_Missense_Mutation_p.G288R|ATP2C2_uc002fhz.2_Missense_Mutation_p.G120R	NM_014861	NP_055676	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	271	Extracellular (Potential).				ATP biosynthetic process	Golgi membrane|integral to membrane	ATP binding|calcium-transporting ATPase activity|metal ion binding|protein binding			breast(1)|central_nervous_system(1)	2						CTCTCAGTTCGGAGAAGTGTT	0.502000													31	259	---	---	---	---	0	0	0.054565	0	0
QRICH2	84074	broad.mit.edu	37	17	74288474	74288474	+	Silent	SNP	C	T	T			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr17:74288474C>T	uc002jrd.1	-	4	2016	c.1836G>A	c.(1834-1836)CAG>CAA	p.Q612Q	QRICH2_uc010wsz.1_Silent_p.Q538Q|QRICH2_uc010dgw.1_Intron	NM_032134	NP_115510	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	612	Gln-rich.						protein binding			ovary(1)|pancreas(1)|lung(1)|central_nervous_system(1)|skin(1)	5						CCAAACCATGCTGATCCACTC	0.328000													3	57	---	---	---	---	0	0	0.004672	0	0
ABCG8	64241	broad.mit.edu	37	2	44104811	44104811	+	Missense_Mutation	SNP	C	A	A			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr2:44104811C>A	uc002rtq.2	+	12	1958	c.1868C>A	c.(1867-1869)GCG>GAG	p.A623E	ABCG8_uc010yoa.1_Missense_Mutation_p.A622E	NM_022437	NP_071882	Q9H221	ABCG8_HUMAN	ATP-binding cassette sub-family G member 8	623	ABC transmembrane type-2.|Extracellular (Potential).				cholesterol efflux|cholesterol homeostasis|excretion|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			skin(3)|ovary(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				CTCACCATCGCGGTCTCAGGA	0.498000											OREG0014582	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	40	71	---	---	---	---	1.47244e-24	1.75875e-24	0.086207	1	0
COL4A4	1286	broad.mit.edu	37	2	227973945	227973945	+	Missense_Mutation	SNP	A	C	C			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr2:227973945A>C	uc010zlt.1	-	10	1306	c.652T>G	c.(652-654)TTA>GTA	p.L218V		NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor	218	Triple-helical region.				axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|pancreas(1)|breast(1)|skin(1)	11		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		CTTACCACTAACCCTGGCTCT	0.458000													5	97	---	---	---	---	0	0	0.093190	0	0
EIF2S2	8894	broad.mit.edu	37	20	32677564	32677564	+	Missense_Mutation	SNP	C	G	G			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr20:32677564C>G	uc002xaf.2	-	9	1143	c.974G>C	c.(973-975)CGA>CCA	p.R325P	EIF2S2_uc002xag.2_Missense_Mutation_p.R322P|EIF2S2_uc010ges.2_Missense_Mutation_p.R265P	NM_003908	NP_003899	P20042	IF2B_HUMAN	eukaryotic translation initiation factor 2 beta	325						cytosol|eukaryotic translation initiation factor 2 complex	metal ion binding|protein binding|translation initiation factor activity			large_intestine(1)	1						GAGCTGTGCTCGCTTGCCCGT	0.473000													25	42	---	---	---	---	0	0	0.091800	0	0
TSHZ2	128553	broad.mit.edu	37	20	51870661	51870661	+	Missense_Mutation	SNP	G	A	A	rs141167641	by1000genomes	TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr20:51870661G>A	uc002xwo.2	+	2	1620	c.664G>A	c.(664-666)GCG>ACG	p.A222T		NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	222	C2H2-type 1.				multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	p.A222T(1)		ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)			ACAGTGCAGCGCGGCCTATGA	0.562000													10	29	---	---	---	---	0	0	0.058154	0	0
PANX2	56666	broad.mit.edu	37	22	50615510	50615510	+	Silent	SNP	C	T	T			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr22:50615510C>T	uc003bjn.3	+	2	369	c.369C>T	c.(367-369)TTC>TTT	p.F123F	PANX2_uc003bjp.3_5'UTR|PANX2_uc003bjo.3_Silent_p.F123F	NM_052839	NP_443071	Q96RD6	PANX2_HUMAN	pannexin 2 isoform 1	123	Extracellular (Potential).				protein hexamerization|synaptic transmission	gap junction|integral to membrane	gap junction hemi-channel activity|ion channel activity			breast(1)	1		all_cancers(38;1.14e-10)|all_epithelial(38;2.12e-09)|all_lung(38;7.01e-05)|Breast(42;0.000523)|Lung NSC(38;0.0018)|Ovarian(80;0.0365)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.105)		AGCACAAGTTCCTGCCCTACG	0.697000													8	14	---	---	---	---	0	0	0.058154	0	0
SLC9A9	285195	broad.mit.edu	37	3	143513887	143513887	+	Missense_Mutation	SNP	T	G	G			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr3:143513887T>G	uc003evn.2	-	4	671	c.489A>C	c.(487-489)TTA>TTC	p.L163F	SLC9A9_uc011bnk.1_Missense_Mutation_p.L37F	NM_173653	NP_775924	Q8IVB4	SL9A9_HUMAN	solute carrier family 9 (sodium/hydrogen	163					regulation of pH	integral to membrane|late endosome membrane|recycling endosome	sodium:hydrogen antiporter activity			ovary(2)|skin(1)	3						AGGCATACGTTAAAATAGATC	0.388000													4	52	---	---	---	---	0	0	0.014758	0	0
CTBP1	1487	broad.mit.edu	37	4	1206720	1206720	+	Missense_Mutation	SNP	G	A	A			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr4:1206720G>A	uc003gcv.1	-	8	1285	c.1120C>T	c.(1120-1122)CTC>TTC	p.L374F	uc003gcs.1_Intron|CTBP1_uc003gct.1_Missense_Mutation_p.L355F|CTBP1_uc003gcu.1_Missense_Mutation_p.L363F|CTBP1_uc003gcw.2_Missense_Mutation_p.L48F	NM_001328	NP_001319	Q13363	CTBP1_HUMAN	C-terminal binding protein 1 isoform 1	374					interspecies interaction between organisms|negative regulation of cell proliferation|negative regulation of histone H4 acetylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|protein phosphorylation|regulation of cell cycle|regulation of transcription by chromatin organization|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|viral genome replication|white fat cell differentiation	cytoplasm|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein C-terminus binding|protein domain specific binding|transcription factor binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(23;0.00818)	Colorectal(103;0.2)		GCCCCATTGAGCTCAGGGTGC	0.662000													3	63	---	---	---	---	0	0	0.004672	0	0
ADAMTS2	9509	broad.mit.edu	37	5	178555009	178555009	+	Silent	SNP	G	A	A			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr5:178555009G>A	uc003mjw.2	-	17	2568	c.2568C>T	c.(2566-2568)TAC>TAT	p.Y856Y		NM_014244	NP_055059	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1	856	TSP type-1 2.				collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding	p.Y856Y(1)		large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		GGGCCCACTCGTAGACCACAG	0.582000													60	63	---	---	---	---	0	0	0.048971	0	0
POM121C	100101267	broad.mit.edu	37	7	75066953	75066953	+	Missense_Mutation	SNP	A	G	G			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr7:75066953A>G	uc010lde.1	-	5	1046	c.1046T>C	c.(1045-1047)CTG>CCG	p.L349P	POM121C_uc003udk.3_Missense_Mutation_p.L107P			A8CG34	P121C_HUMAN	Homo sapiens POM121-2 mRNA for nuclear pore membrane protein 121-2, partial cds.	349	Required for targeting to the nucleus and nuclear pore complex.|Pore side (Potential).|Ser-rich.				mRNA transport|protein transport|transmembrane transport	endoplasmic reticulum membrane|nuclear membrane|nuclear pore	protein binding				0						GCCTCTCTTCAGAGACCCAGG	0.433000													3	88	---	---	---	---	0	0	0.004672	0	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	T	T			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr7:140453136A>T	uc003vwc.3	-	15	1860	c.1799T>A	c.(1798-1800)GTG>GAG	p.V600E		NM_004333	NP_004324	P15056	BRAF_HUMAN	B-Raf	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(16892)|p.V600?(325)|p.V600K(176)|p.V600R(36)|p.V600M(25)|p.V600A(23)|p.V600D(21)|p.V600G(11)|p.V600_K601>E(8)|p.T599_V600insTT(3)|p.T599_R603>I(2)|p.T599_V600>IAL(2)|p.V600L(2)|p.T599_V600insT(2)|p.V600_W604del(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insV(1)|p.T599_V600insDFGLAT(1)	KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)	TCGAGATTTCACTGTAGCTAG	0.368000	V600E(UACC257_SKIN)|V600D(K029AX_SKIN)|V600E(HS695T_SKIN)|V600E(COLO679_SKIN)|V600E(BT474_BREAST)|V600E(IGR39_SKIN)|V600E(A101D_SKIN)|V600E(COLO783_SKIN)|V600E(IGR37_SKIN)|V600E(A375_SKIN)|V600E(WM793_SKIN)|V600E(COLO818_SKIN)|V600E(HS294T_SKIN)|V600E(SKMEL28_SKIN)|V600E(DU4475_BREAST)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(IGR1_SKIN)|V600E(SKHEP1_LIVER)|V600E(WM983B_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(RVH421_SKIN)|V600D(WM2664_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(SKMEL24_SKIN)|V600D(WM115_SKIN)|V600E(MALME3M_SKIN)|V600E(A673_BONE)|V600E(C32_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(COLO800_SKIN)|V600E(COLO741_SKIN)|V600E(HS939T_SKIN)|V600E(COLO205_LARGE_INTESTINE)|V600E(K029AX_SKIN)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(SH4_SKIN)|V600E(WM88_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(COLO849_SKIN)|V600E(MELHO_SKIN)|V600E(BHT101_THYROID)|V600E(G361_SKIN)|V600E(UACC62_SKIN)|V600E(BCPAP_THYROID)|V600E(8505C_THYROID)|V600E(SW1417_LARGE_INTESTINE)|V600E(COLO829_SKIN)|V600E(RKO_LARGE_INTESTINE)|V600E(A2058_SKIN)|V600E(RPMI7951_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(SKMEL5_SKIN)|V600E(ES2_OVARY)|V600E(LOXIMVI_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				27	35	---	---	---	---	0	0	0.030593	0	0
TRPA1	8989	broad.mit.edu	37	8	72946042	72946042	+	Missense_Mutation	SNP	A	G	G			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr8:72946042A>G	uc003xza.2	-	23	2880	c.2705T>C	c.(2704-2706)TTG>TCG	p.L902S	uc011lff.1_Intron|uc003xyy.2_Intron	NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1	902	Extracellular (Potential).					integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)	TATAGAAAGCAATGGAGAGCT	0.393000													14	26	---	---	---	---	0	0	0.024245	0	0
PCDH11X	27328	broad.mit.edu	37	X	91133972	91133972	+	Silent	SNP	A	G	G			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chrX:91133972A>G	uc004efk.1	+	2	3578	c.2733A>G	c.(2731-2733)CTA>CTG	p.L911L	PCDH11X_uc004efl.1_Silent_p.L911L|PCDH11X_uc004efo.1_Silent_p.L911L|PCDH11X_uc010nmv.1_Silent_p.L911L|PCDH11X_uc004efm.1_Silent_p.L911L|PCDH11X_uc004efn.1_Silent_p.L911L|PCDH11X_uc004efh.1_Silent_p.L911L|PCDH11X_uc004efj.1_Silent_p.L911L	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	911	Cytoplasmic (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						CTATTGATCTAGAAGAGCAAA	0.428000													4	57	---	---	---	---	0	0	0.009096	0	0
NOTCH2	4853	broad.mit.edu	37	1	120612003	120612004	+	Frame_Shift_Del	DEL	GG	-	-			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr1:120612003_120612004delGG	uc001eik.2	-	1	273_274	c.17_18delCC	c.(16-18)CCCfs	p.P6fs	NOTCH2_uc001eil.2_Frame_Shift_Del_p.P6fs|NOTCH2_uc001eim.3_5'UTR	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein	6					anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACAGCAGAGCGGGGCGCAGGGC	0.663			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				6	11	---	---	---	---					
Unknown	0	broad.mit.edu	37	1	121137803	121137805	+	IGR	DEL	CCA	-	-	rs60375635	by1000genomes	TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr1:121137803_121137805delCCA								FCGR1B (201859 upstream) : LOC647121 (123105 downstream)																							ACCGCCGCCGCCACGGCTTTTTG	0.645													3	6	---	---	---	---					
LOC200030	200030	broad.mit.edu	37	1	148349431	148349432	+	5'Flank	INS	-	G	G	rs67020224		TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr1:148349431_148349432insG	uc001eqf.2	-						LOC200030_uc001eqe.2_5'Flank|LOC200030_uc001eqg.2_5'Flank|NBPF14_uc009wkf.1_5'Flank|uc001erd.3_5'Flank|uc001erc.3_5'Flank|uc010paj.1_5'Flank|uc010pav.1_5'Flank|uc010paw.1_5'Flank	NM_017940	NP_060410	Q86T75	NBPFB_HUMAN	hypothetical protein LOC55672							cytoplasm					0						GGGCTGACACTGGGGGGCCAGA	0.559													7	9	---	---	---	---					
KCNN3	3782	broad.mit.edu	37	1	154842199	154842200	+	In_Frame_Ins	INS	-	GCTGCT	GCTGCT	rs3831942		TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr1:154842199_154842200insGCTGCT	uc001ffp.2	-	1	555_556	c.241_242insAGCAGC	c.(241-243)CCA>CAGCAGCCA	p.80_81insQQ	KCNN3_uc009wox.1_In_Frame_Ins_p.80_81insQQ	NM_002249	NP_002240	Q9UGI6	KCNN3_HUMAN	small conductance calcium-activated potassium	80_86						integral to membrane	calmodulin binding			lung(1)	1	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)			GGGATGCGGTGgctgctgctgc	0.347													4	8	---	---	---	---					
GAS5	60674	broad.mit.edu	37	1	173836247	173836248	+	RNA	INS	-	A	A	rs145452199	by1000genomes	TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr1:173836247_173836248insA	uc001gji.2	-	1		c.1_2insT			GAS5_uc001gjj.2_Intron|GAS5_uc001gjk.2_Intron|SNORD81_uc009wwi.1_5'Flank|SNORD47_uc001gjl.2_5'Flank|SNORD80_uc009wwj.1_5'Flank|SNORD79_uc009wwk.1_5'Flank|SNORD78_uc009wwl.2_5'Flank|SNORD44_uc001gjn.1_5'Flank|SNORD77_uc009wwm.1_5'Flank|SNORD76_uc009wwn.1_5'Flank|SNORD75_uc009wwo.1_5'Flank|ZBTB37_uc001gjp.1_5'Flank|ZBTB37_uc001gjq.3_5'Flank|ZBTB37_uc009wwp.1_5'Flank|ZBTB37_uc001gjr.2_5'Flank					Homo sapiens mRNA; cDNA DKFZp564D0164 (from clone DKFZp564D0164).												0						GAGTGTTCTTTAAAAAAACGGT	0.381													6	12	---	---	---	---					
Unknown	0	broad.mit.edu	37	12	130683677	130683679	+	IGR	DEL	TCC	-	-	rs147037687	by1000genomes	TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr12:130683677_130683679delTCC								FZD10 (33393 upstream) : PIWIL1 (138935 downstream)																							TAGTTTCTCTTCCTCCTCCTCCT	0.517													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	19	19944259	19944260	+	IGR	DEL	GT	-	-			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr19:19944259_19944260delGT								ZNF506 (11699 upstream) : ZNF253 (32454 downstream)																							TGGTAAAAACGTGTGTGTGTGT	0.426													7	137	---	---	---	---					
MIR1283-1	100302265	broad.mit.edu	37	19	54191516	54191536	+	5'Flank	DEL	GTTTGAGAACAAAACTCGGGA	-	-	rs11274495		TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr19:54191516_54191536delGTTTGAGAACAAAACTCGGGA	hsa-mir-1283-1|MI0003832	+						MIR520A_hsa-mir-520a|MI0003149_5'Flank																	0						TGCTTTTTCTGTTTGAGAACAAAACTCGGGAGGATTGTCCC	0.416													3	3	---	---	---	---					
ING5	84289	broad.mit.edu	37	2	242662663	242662664	+	Frame_Shift_Ins	INS	-	AG	AG			TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr2:242662663_242662664insAG	uc002wcd.2	+	7	682_683	c.657_658insAG	c.(655-660)CTTACCfs	p.L219fs		NM_032329	NP_115705	Q8WYH8	ING5_HUMAN	inhibitor of growth family, member 5	219_220	PHD-type.				DNA replication|histone H3 acetylation|negative regulation of cell proliferation|negative regulation of growth|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex	protein binding|zinc ion binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.16e-33)|all cancers(36;4.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.6e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839)		GCGTGGACCTTACCACGAAACC	0.525													25	314	---	---	---	---					
CCT5	22948	broad.mit.edu	37	5	10250047	10250047	+	5'Flank	DEL	C	-	-	rs2607301		TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr5:10250047delC	uc003jeq.2	+						FAM173B_uc003jeo.2_5'Flank|FAM173B_uc003jep.2_5'Flank|FAM173B_uc010itr.2_5'Flank|CCT5_uc011cmq.1_5'Flank|CCT5_uc003jer.2_5'Flank|CCT5_uc010its.2_5'Flank|CCT5_uc011cmr.1_5'Flank|CCT5_uc011cms.1_5'Flank|CCT5_uc011cmt.1_5'Flank	NM_012073	NP_036205	P48643	TCPE_HUMAN	chaperonin containing TCP1, subunit 5 (epsilon)						'de novo' posttranslational protein folding|response to virus	microtubule organizing center|nucleolus	ATP binding|unfolded protein binding			ovary(2)	2						aaaaaaaaaaCCGGAAATGGG	0.423													5	2	---	---	---	---					
Unknown	0	broad.mit.edu	37	9	98910245	98910246	+	IGR	INS	-	A	A	rs139074595		TCGA-FE-A231-01A-11D-A14W-08	TCGA-FE-A231-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	be4d3229-23af-4a01-a8b3-264c22703ea4	f97453ea-688f-4bb3-959d-cc42cf32e2b7	g.chr9:98910245_98910246insA								NCRNA00092 (126208 upstream) : HSD17B3 (87343 downstream)																							ACCATCTCCTGAAAAAAAAAAA	0.312													2	4	---	---	---	---					
