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
CROCCL1	84809	broad.mit.edu	37	1	16957414	16957414	+	RNA	SNP	C	T	T	rs2296161	by1000genomes	TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08									Somatic	Phase_I	Capture				Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr1:16957414C>T	uc009vov.1	-	1		c.191G>A			CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA|CROCCL1_uc001azg.1_RNA|CROCCL1_uc001azi.1_RNA	NR_026752				Homo sapiens mRNA for FLJ00313 protein.												0						AAGTGCAGGGCGGAGAGAATC	0.706000													3	7					0	0	0.004672	0	0
ZMYM1	79830	broad.mit.edu	37	1	35579564	35579564	+	Missense_Mutation	SNP	A	G	G			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08									Somatic	Phase_I	Capture				Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr1:35579564A>G	uc001bym.2	+	11	2281	c.2133A>G	c.(2131-2133)ATA>ATG	p.I711M	ZMYM1_uc001byn.2_Missense_Mutation_p.I711M|ZMYM1_uc010ohu.1_Missense_Mutation_p.I692M|ZMYM1_uc001byo.2_Missense_Mutation_p.I351M|ZMYM1_uc009vut.2_Missense_Mutation_p.I636M	NM_024772	NP_079048	Q5SVZ6	ZMYM1_HUMAN	zinc finger, MYM domain containing 1	711						nucleus	nucleic acid binding|protein dimerization activity|zinc ion binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TGGATAAAATACATGGCCAGG	0.353000													3	22					0	0	0.004672	0	0
LOC650368	650368	broad.mit.edu	37	11	3427845	3427845	+	RNA	SNP	C	T	T			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08									Somatic	Phase_I	Capture				Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr11:3427845C>T	uc010qxs.1	+	9		c.838C>T			LOC650368_uc001lxx.2_RNA|LOC650368_uc001lxy.2_RNA	NR_024248				Homo sapiens cDNA FLJ41654 fis, clone FEBRA2025463, weakly  similar to Homo sapiens HMT-1 mRNA for beta-1,4 mannosyltransferase.												0						CTTCAAGTGGCAGGAGCAGAA	0.587000													7	62					0	0	0.001984	0	0
CPSF7	79869	broad.mit.edu	37	11	61183647	61183647	+	Missense_Mutation	SNP	G	T	T			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08									Somatic	Phase_I	Capture				Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr11:61183647G>T	uc001nrq.2	-	6	1029	c.895C>A	c.(895-897)CCA>ACA	p.P299T	CPSF7_uc001nro.2_Missense_Mutation_p.P290T|CPSF7_uc001nrp.2_Missense_Mutation_p.P342T|CPSF7_uc001nrr.2_Missense_Mutation_p.P290T|CPSF7_uc001nrs.1_Missense_Mutation_p.P200T	NM_001136040	NP_001129512	Q8N684	CPSF7_HUMAN	pre-mRNA cleavage factor I, 59 kDa subunit	299	Pro-rich.				mRNA 3'-end processing|nuclear mRNA splicing, via spliceosome|protein tetramerization|termination of RNA polymerase II transcription	mRNA cleavage factor complex	nucleotide binding|protein binding|RNA binding			central_nervous_system(1)	1						GTAGCGTTTGGTGGGGGGAAG	0.557000													6	144					4.096e-09	8.192e-09	0.001168	1	0
PYGM	5837	broad.mit.edu	37	11	64522811	64522811	+	Silent	SNP	G	A	A			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08									Somatic	Phase_I	Capture				Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr11:64522811G>A	uc001oax.3	-	7	1606	c.789C>T	c.(787-789)TAC>TAT	p.Y263Y	PYGM_uc001oay.3_Silent_p.Y175Y	NM_005609	NP_005600	P11217	PYGM_HUMAN	muscle glycogen phosphorylase isoform 1	263					glucose metabolic process|glycogen catabolic process	cytosol	glycogen phosphorylase activity|protein binding			ovary(2)	2					Pyridoxal Phosphate(DB00114)	CAGCCTGGATGTAGCCACCGA	0.617000													10	161					0	0	0.008291	0	0
CRY1	1407	broad.mit.edu	37	12	107399011	107399011	+	Missense_Mutation	SNP	T	C	C			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08									Somatic	Phase_I	Capture				Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr12:107399011T>C	uc001tmi.3	-	3	1142	c.283A>G	c.(283-285)AAA>GAA	p.K95E		NM_004075	NP_004066	Q16526	CRY1_HUMAN	cryptochrome 1 (photolyase-like)	95	DNA photolyase.				DNA repair|protein-chromophore linkage|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	blue light photoreceptor activity|DNA photolyase activity|double-stranded DNA binding|nucleotide binding|protein binding			ovary(3)	3						ATTGAAAGTTTAGTAATGTTC	0.343000													51	86					0	0	0.003610	0	0
Unknown	0	broad.mit.edu	37	16	90161578	90161578	+	Silent	SNP	G	A	A	rs13337896	by1000genomes	TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08									Somatic	Phase_I	Capture				Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr16:90161578G>A	uc002fqp.2	+	3	931	c.453G>A	c.(451-453)ACG>ACA	p.T151T	uc002fqq.2_Silent_p.T168T					Homo sapiens, Similar to tubulin, beta, 2, clone IMAGE:4873024, mRNA.																		GCCAAGGGACGCTACACCGAA	0.587000													5	56					0	0	0.000602	0	0
SYT3	84258	broad.mit.edu	37	19	51135675	51135675	+	Missense_Mutation	SNP	G	A	A			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08									Somatic	Phase_I	Capture				Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr19:51135675G>A	uc002pst.2	-	2	1176	c.542C>T	c.(541-543)CCG>CTG	p.P181L	SYT3_uc002psv.2_Missense_Mutation_p.P181L|SYT3_uc010ycd.1_Missense_Mutation_p.P181L	NM_032298	NP_115674	Q9BQG1	SYT3_HUMAN	synaptotagmin III	181	Cytoplasmic (Potential).					cell junction|endosome|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|breast(1)	3		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		TGTTTGGCTCGGTTTGACCCC	0.657000													20	42					0	0	0.008871	0	0
ZNF304	57343	broad.mit.edu	37	19	57869057	57869057	+	Missense_Mutation	SNP	G	A	A			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08									Somatic	Phase_I	Capture				Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr19:57869057G>A	uc010ygw.1	+	3	2208	c.1820G>A	c.(1819-1821)AGG>AAG	p.R607K	ZNF304_uc010etw.2_Missense_Mutation_p.R654K|ZNF304_uc010etx.2_Missense_Mutation_p.R565K	NM_020657	NP_065708	Q9HCX3	ZN304_HUMAN	zinc finger protein 304	607	C2H2-type 15.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		CTGCACCAGAGGGTTCACACT	0.478000													19	70					0	0	0.008871	0	0
TGFBRAP1	9392	broad.mit.edu	37	2	105886051	105886051	+	Missense_Mutation	SNP	G	A	A			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08									Somatic	Phase_I	Capture				Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr2:105886051G>A	uc002tcq.2	-	11	2168	c.2084C>T	c.(2083-2085)GCG>GTG	p.A695V	TGFBRAP1_uc010fjc.2_Missense_Mutation_p.A464V|TGFBRAP1_uc002tcr.3_Missense_Mutation_p.A695V	NM_004257	NP_004248	Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor	695					regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	cytoplasm|membrane	SMAD binding|small GTPase regulator activity|transforming growth factor beta receptor binding			central_nervous_system(1)|skin(1)	2						GTCCTCGGCCGCTGCAAAGTC	0.657000													5	27					0	0	0.000602	0	0
TTN	7273	broad.mit.edu	37	2	179659659	179659659	+	Missense_Mutation	SNP	C	T	T			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08									Somatic	Phase_I	Capture				Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr2:179659659C>T	uc010zfg.1	-	7	1459	c.1235G>A	c.(1234-1236)GGT>GAT	p.G412D	TTN_uc010zfh.1_Missense_Mutation_p.G412D|TTN_uc010zfi.1_Missense_Mutation_p.G412D|TTN_uc010zfj.1_Missense_Mutation_p.G412D|TTN_uc002unb.2_Missense_Mutation_p.G412D|TTN_uc010frg.1_Missense_Mutation_p.G86D	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	412							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTCTTTAGCACCAGTGGCAAC	0.493000													33	58					0	0	0.004878	0	0
Unknown	0	broad.mit.edu	37	22	18844823	18844823	+	RNA	SNP	C	A	A			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08									Somatic	Phase_I	Capture				Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr22:18844823C>A	uc002zoe.2	+	4		c.2077C>A			uc002zof.2_5'Flank					Homo sapiens cDNA FLJ76361 complete cds.																		CCAGTGCTCACCGATGCCCTC	0.602000													6	15					2.7689e-08	5.27409e-08	0.001984	1	0
LOC96610	96610	broad.mit.edu	37	22	23006960	23006961	+	RNA	DNP	CC	AT	AT			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08									Somatic	Phase_I	Capture				Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr22:23006960_23006961CC>AT	uc011aim.1	+	119		c.7563_7564CC>AT								Parts of antibodies, mostly variable regions.												0						GGGCTCTGCTCCTCCTCACCCT	0.629000													3	12					0	0	0.004672	0	0
Unknown	0	broad.mit.edu	37	5	167979713	167979713	+	RNA	SNP	A	C	C			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08									Somatic	Phase_I	Capture				Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr5:167979713A>C	uc003lzy.3	-	1		c.262T>G								Homo sapiens cDNA clone IMAGE:5299317.																		GACAGAACAAAACGCCATGCC	0.423000													4	1					0	0	0.000248	0	0
DEFB114	245928	broad.mit.edu	37	6	49931770	49931770	+	Silent	SNP	G	A	A			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08									Somatic	Phase_I	Capture				Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr6:49931770G>A	uc011dwp.1	-	1	49	c.49C>T	c.(49-51)CTA>TTA	p.L17L		NM_001037499	NP_001032588	Q30KQ6	DB114_HUMAN	beta-defensin 114 precursor	17					defense response to bacterium	extracellular region				ovary(1)	1	Lung NSC(77;0.042)					TTACCTGGTAGAATGAAGGTC	0.284000													10	38					0	0	0.008291	0	0
MAGEA6	4105	broad.mit.edu	37	X	151870045	151870045	+	Silent	SNP	G	A	A			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08									Somatic	Phase_I	Capture				Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chrX:151870045G>A	uc004ffq.1	+	3	929	c.735G>A	c.(733-735)CTG>CTA	p.L245L	MAGEA6_uc004ffr.1_Silent_p.L245L|MAGEA2_uc010nto.2_Intron	NM_005363	NP_005354	P43360	MAGA6_HUMAN	melanoma antigen family A, 6	245	MAGE.						protein binding				0	Acute lymphoblastic leukemia(192;6.56e-05)					CCAAGAAGCTGCTCACCCAAT	0.562000													7	191					0	0	0.001984	0	0
CCDC71	64925	broad.mit.edu	37	3	49200861	49200862	+	Frame_Shift_Del	DEL	CT	-	-			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08									Somatic	Phase_I	Capture				Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr3:49200861_49200862delCT	uc003cwg.3	-	2	918_919	c.780_781delAG	c.(778-783)AGAGCCfs	p.R260fs		NM_022903	NP_075054	Q8IV32	CCD71_HUMAN	coiled-coil domain containing 71	260_261										ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GACCCAGTGGCTCTGTTGGTTT	0.624													43	109	---	---	---	---					
