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
PPFIA4	8497	broad.mit.edu	37	1	203013072	203013072	+	Missense_Mutation	SNP	A	T	T			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr1:203013072A>T	uc009xaj.2	+	8	791	c.791A>T	c.(790-792)CAT>CTT	p.H264L	PPFIA4_uc010pqf.1_5'Flank			O75335	LIPA4_HUMAN	SubName: Full=Liprin alpha4;	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell communication	cell surface|cytoplasm	protein binding			ovary(4)|skin(1)	5						CTTCTGGAACATCTGGAGTGC	0.637000													12	22	---	---	---	---	0	0	0.001855	0	0
ECD	11319	broad.mit.edu	37	10	74896602	74896602	+	Missense_Mutation	SNP	A	T	T			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr10:74896602A>T	uc001jtn.2	-	13	1807	c.1564T>A	c.(1564-1566)TTG>ATG	p.L522M	ECD_uc009xqx.2_Missense_Mutation_p.L555M|ECD_uc009xqy.2_Missense_Mutation_p.L479M|ECD_uc001jto.2_Missense_Mutation_p.L221M	NM_007265	NP_009196	O95905	SGT1_HUMAN	suppressor of S. cerevisiae gcr2 isoform 1	522					regulation of glycolysis|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	transcription coactivator activity			pancreas(1)	1	Prostate(51;0.0119)					TCAAAGTCCAAGTCATCATCA	0.443000													5	165	---	---	---	---	0	0	0.000602	0	0
GALNTL4	374378	broad.mit.edu	37	11	11400737	11400737	+	Missense_Mutation	SNP	G	T	T			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr11:11400737G>T	uc001mjo.2	-	4	1091	c.670C>A	c.(670-672)CGT>AGT	p.R224S		NM_198516	NP_940918	Q6P9A2	GLTL4_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	224	Lumenal (Potential).|Catalytic subdomain A.					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0				all cancers(16;3.67e-05)|Epithelial(150;0.000184)		TTGCTGTGACGCACGACTTTG	0.567000													18	39	---	---	---	---	8.00594e-06	1.14024e-05	0.007413	1	0
SLC22A11	55867	broad.mit.edu	37	11	64326627	64326627	+	Silent	SNP	C	T	T			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr11:64326627C>T	uc001oai.2	+	2	788	c.414C>T	c.(412-414)TCC>TCT	p.S138S	SLC22A11_uc001oah.1_Intron|SLC22A11_uc001oaj.2_Silent_p.S138S|SLC22A11_uc009ypq.2_Silent_p.S138S|SLC22A11_uc001oak.1_5'Flank	NM_018484	NP_060954	Q9NSA0	S22AB_HUMAN	solute carrier family 22 member 11	138	Extracellular (Potential).				urate metabolic process	apical plasma membrane|external side of plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium-independent organic anion transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2					Probenecid(DB01032)	TGTGCAGCTCCCAGGGCTTGA	0.637000													33	60	---	---	---	---	0	0	0.003271	0	0
MALAT1	378938	broad.mit.edu	37	11	65268279	65268279	+	RNA	SNP	A	T	T			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr11:65268279A>T	uc010roh.1	+	1		c.3047A>T			uc001ody.2_RNA|MALAT1_uc001odz.2_5'Flank	NR_002819				Homo sapiens clone alpha1 mRNA sequence.												0						TCTGGAACTTACTTATGGTAA	0.448000													15	21	---	---	---	---	0	0	0.004007	0	0
USP28	57646	broad.mit.edu	37	11	113705033	113705033	+	Nonsense_Mutation	SNP	G	A	A			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr11:113705033G>A	uc001poh.2	-	6	592	c.559C>T	c.(559-561)CGA>TGA	p.R187*	USP28_uc010rwy.1_Nonsense_Mutation_p.R62*|USP28_uc001poi.2_5'UTR|USP28_uc001poj.3_Nonsense_Mutation_p.R187*|USP28_uc010rwz.1_Nonsense_Mutation_p.R187*	NM_020886	NP_065937	Q96RU2	UBP28_HUMAN	ubiquitin specific protease 28	187					cell proliferation|DNA damage checkpoint|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA repair|protein deubiquitination|response to ionizing radiation|ubiquitin-dependent protein catabolic process	nucleolus|nucleoplasm	protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			lung(2)|breast(2)|ovary(1)|large_intestine(1)|kidney(1)	7		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		ACAAGTCTTCGAAATTCAGGC	0.343000													16	35	---	---	---	---	0	0	0.004007	0	0
LOC284232	284232	broad.mit.edu	37	13	19413033	19413033	+	RNA	SNP	G	A	A			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr13:19413033G>A	uc010tcj.1	-	1		c.33077C>T				NR_027995				Homo sapiens ankyrin repeat domain 20 family, member A2 pseudogene (LOC284232), non-coding RNA.												0						GCACATCCATGCACTAAAAAG	0.294000													5	28	---	---	---	---	0	0	0.000602	0	0
CHMP4A	29082	broad.mit.edu	37	14	24685233	24685233	+	5'Flank	SNP	G	C	C			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr14:24685233G>C	uc001wni.2	-						TM9SF1_uc010tob.1_5'Flank|CHMP4A_uc010toc.1_5'Flank|CHMP4A_uc001wnj.2_5'UTR|MDP1_uc001wnk.1_5'UTR|CHMP4A_uc001wnm.1_5'UTR|MDP1_uc001wnl.1_5'UTR	NM_014169	NP_054888	Q9BY43	CHM4A_HUMAN	chromatin modifying protein 4A						cellular membrane organization|endosome transport|protein transport	cytoplasmic vesicle membrane|cytosol|late endosome membrane	lipid binding|protein binding			ovary(2)	2				GBM - Glioblastoma multiforme(265;0.0181)		GGAACCTCCGGCAGCTAAGGC	0.652000											OREG0022620	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	13	9	---	---	---	---	0	0	0.002450	0	0
Unknown	0	broad.mit.edu	37	15	102292785	102292785	+	Missense_Mutation	SNP	C	G	G	rs143389223		TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr15:102292785C>G	uc010usj.1	+	4	432	c.373C>G	c.(373-375)CAG>GAG	p.Q125E	uc002bxp.3_5'Flank|uc002bxt.2_5'Flank|uc002bxz.3_5'Flank|uc002byd.2_5'Flank|uc002bye.2_5'Flank|uc002byf.1_5'Flank|uc002byg.2_5'Flank|uc002byi.2_5'Flank|uc002byk.2_5'Flank|uc002bym.2_5'Flank|uc002byn.2_5'Flank|uc010usm.1_5'Flank					RecName: Full=Uncharacterized protein C15orf51.; Flags: Fragment;																		TGCTGCTTCTCAGAGCTGCTG	0.602000													3	20	---	---	---	---	0	0	0.001984	0	0
HS3ST4	9951	broad.mit.edu	37	16	26147154	26147154	+	Missense_Mutation	SNP	G	A	A			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr16:26147154G>A	uc002dof.2	+	2	1348	c.956G>A	c.(955-957)CGG>CAG	p.R319Q		NM_006040	NP_006031	Q9Y661	HS3S4_HUMAN	heparan sulfate D-glucosaminyl	319	Lumenal (Potential).				heparan sulfate proteoglycan metabolic process	extracellular region|Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity			large_intestine(1)|breast(1)	2				GBM - Glioblastoma multiforme(48;0.0988)		TTCAAAAACCGGACCCTCGGG	0.552000													81	105	---	---	---	---	0	0	0.003610	0	0
KRTAP4-12	83755	broad.mit.edu	37	17	39280071	39280071	+	Missense_Mutation	SNP	G	A	A			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr17:39280071G>A	uc002hwa.2	-	1	349	c.304C>T	c.(304-306)CGC>TGC	p.R102C		NM_031854	NP_114060	Q9BQ66	KR412_HUMAN	keratin associated protein 4-12	102	31 X 5 AA repeats of C-C-[GRQVIL]-[SPTR]- [VSTQPC].|18.					keratin filament					0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			CAGCTGGGGCGGCAGCAGGTG	0.463000													4	117	---	---	---	---	0	0	0.000248	0	0
MUC16	94025	broad.mit.edu	37	19	9070335	9070335	+	Missense_Mutation	SNP	G	A	A			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr19:9070335G>A	uc002mkp.2	-	3	17315	c.17111C>T	c.(17110-17112)ACT>ATT	p.T5704I		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	5706	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						TGTGTGCGCAGTGTCTTTGTA	0.502000													6	70	---	---	---	---	0	0	0.001168	0	0
PYGB	5834	broad.mit.edu	37	20	25257360	25257360	+	Missense_Mutation	SNP	G	A	A			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr20:25257360G>A	uc002wup.2	+	6	848	c.739G>A	c.(739-741)GCC>ACC	p.A247T		NM_002862	NP_002853	P11216	PYGB_HUMAN	brain glycogen phosphorylase	247					glucose metabolic process|glycogen catabolic process	cytoplasm	glycogen phosphorylase activity|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					Pyridoxal Phosphate(DB00114)	GCTGTGGTCCGCCAAGGCTCC	0.617000													3	32	---	---	---	---	0	0	0.000248	0	0
SEMG1	6406	broad.mit.edu	37	20	43836652	43836652	+	Silent	SNP	C	T	T			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr20:43836652C>T	uc002xni.2	+	2	771	c.714C>T	c.(712-714)CTC>CTT	p.L238L	SEMG1_uc002xnj.2_Silent_p.L238L|SEMG2_uc010ggz.2_Intron|SEMG1_uc002xnh.2_Silent_p.L238L	NM_003007	NP_002998	P04279	SEMG1_HUMAN	semenogelin I preproprotein	238	42 AA repeat 2.				insemination|sexual reproduction	extracellular space|stored secretory granule	structural molecule activity			skin(2)	2		Myeloproliferative disorder(115;0.0122)				AAACCTCACTCTGTCCTGCGC	0.378000													6	131	---	---	---	---	0	0	0.001168	0	0
LOC96610	96610	broad.mit.edu	37	22	23040595	23040595	+	RNA	SNP	C	G	G			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr22:23040595C>G	uc011aim.1	+	137		c.8502C>G								Parts of antibodies, mostly variable regions.												0						CTCCCTCTTTCCAGGGTCCTG	0.617000													20	136	---	---	---	---	0	0	0.002780	0	0
POM121L9P	29774	broad.mit.edu	37	22	24659578	24659578	+	RNA	SNP	A	G	G			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr22:24659578A>G	uc002zzs.3	+	7		c.3310A>G			uc011ajp.1_5'Flank	NR_003714				Homo sapiens mRNA; cDNA DKFZp434P211 (from clone DKFZp434P211).												0						TGCGCAGGCCAACACTCACTG	0.617000													5	20	---	---	---	---	0	0	0.000602	0	0
EDEM1	9695	broad.mit.edu	37	3	5255103	5255103	+	Missense_Mutation	SNP	C	T	T			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr3:5255103C>T	uc003bqi.2	+	11	1912	c.1780C>T	c.(1780-1782)CCA>TCA	p.P594S		NM_014674	NP_055489	Q92611	EDEM1_HUMAN	ER degradation enhancer, mannosidase alpha-like	594	Lumenal (Potential).				ER-associated protein catabolic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	integral to endoplasmic reticulum membrane	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding			ovary(2)|breast(1)	3				Epithelial(13;0.0588)|OV - Ovarian serous cystadenocarcinoma(96;0.0682)		TCGGGAATTGCCATGGAAGGA	0.478000													3	33	---	---	---	---	0	0	0.000248	0	0
RAD54L2	23132	broad.mit.edu	37	3	51675796	51675796	+	Missense_Mutation	SNP	G	C	C			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr3:51675796G>C	uc011bdt.1	+	14	2388	c.2263G>C	c.(2263-2265)GAA>CAA	p.E755Q	RAD54L2_uc003dbh.2_Missense_Mutation_p.E346Q|RAD54L2_uc011bdu.1_Missense_Mutation_p.E449Q|RAD54L2_uc003dbj.2_Missense_Mutation_p.E81Q	NM_015106	NP_055921	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2	755	Helicase C-terminal.					nucleus	ATP binding|DNA binding|helicase activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		TCTCATCGAGGAATTCCTTGG	0.483000													2	8	---	---	---	---	0	0	0.004672	0	0
SIDT1	54847	broad.mit.edu	37	3	113300224	113300224	+	Missense_Mutation	SNP	T	G	G			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr3:113300224T>G	uc003eak.2	+	6	1331	c.680T>G	c.(679-681)CTC>CGC	p.L227R	SIDT1_uc011bif.1_RNA|SIDT1_uc003eaj.1_Missense_Mutation_p.L227R|SIDT1_uc011big.1_5'UTR	NM_017699	NP_060169	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1 precursor	227	Extracellular (Potential).					integral to membrane				ovary(3)|pancreas(1)|skin(1)	5						GTGTATGATCTCGACCACAAT	0.458000													30	42	---	---	---	---	0	0	0.002096	0	0
SLITRK3	22865	broad.mit.edu	37	3	164906912	164906912	+	Missense_Mutation	SNP	G	C	C			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr3:164906912G>C	uc003fej.3	-	2	2151	c.1707C>G	c.(1705-1707)GAC>GAG	p.D569E	SLITRK3_uc003fek.2_Missense_Mutation_p.D569E	NM_014926	NP_055741	O94933	SLIK3_HUMAN	slit and trk like 3 protein precursor	569	LRRCT 2.|Extracellular (Potential).					integral to membrane				ovary(6)|skin(3)|pancreas(1)	10						AGGGGACCAGGTCACAGGTGC	0.517000										HNSCC(40;0.11)			19	33	---	---	---	---	0	0	0.001523	0	0
C4orf21	55345	broad.mit.edu	37	4	113508691	113508691	+	Silent	SNP	C	T	T			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr4:113508691C>T	uc003iau.2	-	12	3733	c.3522G>A	c.(3520-3522)GAG>GAA	p.E1174E	C4orf21_uc003iav.2_RNA	NM_018392	NP_060862	Q6ZU11	YD002_HUMAN	prematurely terminated mRNA decay factor-like	Error:Variant_position_missing_in_Q6ZU11_after_alignment						integral to membrane	zinc ion binding				0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		CAGAAACAGCCTCAGCAAAGA	0.413000													77	145	---	---	---	---	0	0	0.003610	0	0
PCDHGC3	5098	broad.mit.edu	37	5	140857072	140857072	+	Silent	SNP	C	T	T			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr5:140857072C>T	uc003lkv.1	+	1	1504	c.1389C>T	c.(1387-1389)GAC>GAT	p.D463D	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc003lkt.1_Intron|PCDHGC3_uc003lku.1_Silent_p.D463D|PCDHGC3_uc003lkw.1_Intron	NM_002588	NP_002579	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3 isoform 1	463	Cadherin 5.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTCCTACGACGTTTACATTG	0.512000													5	158	---	---	---	---	0	0	0.001168	0	0
ATP10B	23120	broad.mit.edu	37	5	160047602	160047602	+	Missense_Mutation	SNP	T	C	C			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr5:160047602T>C	uc003lym.1	-	15	3015	c.2168A>G	c.(2167-2169)GAT>GGT	p.D723G	ATP10B_uc010jit.1_Missense_Mutation_p.D40G|ATP10B_uc003lyn.2_Missense_Mutation_p.D281G	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B	723	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GGCGGCCTCATCAGGGCTCTC	0.642000													6	39	---	---	---	---	0	0	0.003080	0	0
NEIL2	252969	broad.mit.edu	37	8	11637219	11637219	+	Missense_Mutation	SNP	C	T	T			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr8:11637219C>T	uc003wug.2	+	3	926	c.251C>T	c.(250-252)GCG>GTG	p.A84V	NEIL2_uc003wue.2_Missense_Mutation_p.A84V|NEIL2_uc003wuf.2_Missense_Mutation_p.A23V|NEIL2_uc011kxd.1_Intron	NM_145043	NP_659480	Q969S2	NEIL2_HUMAN	nei like 2 isoform a	84					base-excision repair|nucleotide-excision repair	nucleus	damaged DNA binding|DNA-(apurinic or apyrimidinic site) lyase activity|hydrolase activity, hydrolyzing N-glycosyl compounds|zinc ion binding				0	all_epithelial(15;0.103)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.166)		GAAGGGGCTGCGGACCCAAAG	0.557000								BER_DNA_glycosylases					4	132	---	---	---	---	0	0	0.000602	0	0
WRN	7486	broad.mit.edu	37	8	31004953	31004953	+	Missense_Mutation	SNP	T	C	C			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr8:31004953T>C	uc003xio.3	+	30	4321	c.3533T>C	c.(3532-3534)CTG>CCG	p.L1178P	WRN_uc010lvk.2_Missense_Mutation_p.L645P	NM_000553	NP_000544	Q14191	WRN_HUMAN	Werner syndrome protein	1178	HRDC.				base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance	centrosome|nucleolus|nucleoplasm	3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding			ovary(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	7		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		CCAGCTATTCTGGCAACAAAC	0.343000			Mis|N|F|S			osteosarcoma|meningioma|others		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Werner_syndrome				21	32	---	---	---	---	0	0	0.003330	0	0
C9orf72	203228	broad.mit.edu	37	9	27567087	27567087	+	Missense_Mutation	SNP	G	A	A			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr9:27567087G>A	uc003zqq.2	-	2	129	c.32C>T	c.(31-33)GCT>GTT	p.A11V	C9orf72_uc003zqr.1_Missense_Mutation_p.A11V	NM_018325	NP_060795	Q96LT7	CI072_HUMAN	hypothetical protein LOC203228 isoform a	11										ovary(3)|central_nervous_system(1)	4		all_neural(11;7.57e-10)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)		CTTGGCAACAGCTGGAGATGG	0.423000													22	30	---	---	---	---	0	0	0.002780	0	0
TAF1L	138474	broad.mit.edu	37	9	32631455	32631455	+	Missense_Mutation	SNP	G	A	A			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr9:32631455G>A	uc003zrg.1	-	1	4213	c.4123C>T	c.(4123-4125)CGG>TGG	p.R1375W	uc003zrh.1_5'Flank	NM_153809	NP_722516	Q8IZX4	TAF1L_HUMAN	TBP-associated factor RNA polymerase 1-like	1375	Nuclear localization signal (Potential).				male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	transcription factor TFIID complex	DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding			lung(8)|skin(6)|central_nervous_system(4)|large_intestine(3)|ovary(2)|stomach(1)|breast(1)|pancreas(1)	26			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		CCAACTCGCCGTTTCTTCTTT	0.458000													87	141	---	---	---	---	0	0	0.003610	0	0
Unknown	0	broad.mit.edu	37	11	64011615	64011616	+	IGR	DEL	TG	-	-	rs150253900		TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr11:64011615_64011616delTG								FKBP2 (9 upstream) : PPP1R14B (337 downstream)																							GGAGTAAGCCTGTGTGTGTTTG	0.480													5	10	---	---	---	---					
Unknown	0	broad.mit.edu	37	12	9555195	9555196	+	IGR	INS	-	C	C	rs140281398	by1000genomes	TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr12:9555195_9555196insC								LOC642846 (88511 upstream) : DDX12 (15092 downstream)																							AAGCCCCTCTTCCCCCCCTGGC	0.584													9	14	---	---	---	---					
Unknown	0	broad.mit.edu	37	14	34669510	34669513	+	IGR	DEL	GATG	-	-			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr14:34669510_34669513delGATG								EGLN3 (249223 upstream) : C14orf147 (232632 downstream)																							aacagagcaagaTggatggatgga	0.000													3	5	---	---	---	---					
Unknown	0	broad.mit.edu	37	19	52896073	52896074	+	IGR	DEL	TA	-	-			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr19:52896073_52896074delTA								ZNF880 (7029 upstream) : ZNF528 (5047 downstream)																							GTGGAAGCTGTATATATATATA	0.233													2	4	---	---	---	---					
CD93	22918	broad.mit.edu	37	20	23066789	23066791	+	In_Frame_Del	DEL	AGC	-	-			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr20:23066789_23066791delAGC	uc002wsv.2	-	1	187_189	c.39_41delGCT	c.(37-42)CTGCTC>CTC	p.13_14LL>L		NM_012072	NP_036204	Q9NPY3	C1QR1_HUMAN	CD93 antigen precursor	13_14					cell-cell adhesion|interspecies interaction between organisms|macrophage activation|phagocytosis	plasma membrane	calcium ion binding|complement component C1q binding|receptor activity|sugar binding			large_intestine(2)	2	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)					CTGGGTcaggagcagcagcagca	0.621													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	22	20151656	20151657	+	IGR	INS	-	ACC	ACC	rs141600104		TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr22:20151656_20151657insACC								ZDHHC8 (16127 upstream) : LOC150197 (42198 downstream)																							ccaccatcactaccaccaccac	0.000													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	22	50151432	50151432	+	IGR	DEL	C	-	-			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr22:50151432delC								C22orf34 (100242 upstream) : BRD1 (15506 downstream)																							CATGAGCtttctttttttttt	0.184													6	7	---	---	---	---					
Unknown	0	broad.mit.edu	37	4	49512654	49512654	+	IGR	DEL	T	-	-	rs113012804		TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr4:49512654delT								CWH43 (448561 upstream) : None (None downstream)																							ACATTCTGCGTTTTTTTGGGG	0.368													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	5	56615906	56615906	+	IGR	DEL	C	-	-			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr5:56615906delC								GPBP1 (56496 upstream) : ACTBL2 (159938 downstream)																							ATTCTTTAATCtttttttttt	0.224													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	5	156273485	156273486	+	IGR	INS	-	T	T			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr5:156273485_156273486insT								SGCD (78689 upstream) : PPP1R2P3 (4063 downstream)																							aagaaaggaaATTATACCTTTT	0.069													3	5	---	---	---	---					
Unknown	0	broad.mit.edu	37	6	155028499	155028499	+	IGR	DEL	A	-	-	rs147940473		TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr6:155028499delA								CNKSR3 (196746 upstream) : RBM16 (26013 downstream)																							gactccatctaaaaaaaaaaa	0.169													3	5	---	---	---	---					
Unknown	0	broad.mit.edu	37	8	144138674	144138674	+	IGR	DEL	T	-	-			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr8:144138674delT								C8orf31 (2954 upstream) : LY6H (100658 downstream)																							attatttttattttttttttt	0.159													3	3	---	---	---	---					
GALT	2592	broad.mit.edu	37	9	34646573	34646576	+	5'Flank	DEL	CAGT	-	-			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr9:34646573_34646576delCAGT	uc003zve.2	+						GALT_uc003zvf.2_5'Flank|GALT_uc003zvg.2_5'Flank|GALT_uc003zvh.2_5'Flank|GALT_uc011lop.1_5'Flank	NM_000155	NP_000146	P07902	GALT_HUMAN	galactose-1-phosphate uridylyltransferase						galactose catabolic process	cytosol	UDP-glucose:hexose-1-phosphate uridylyltransferase activity|zinc ion binding				0	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.173)		CAGGGCAGCCCAGTCAGTCAGTCA	0.642									Galactosemia		OREG0019158	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	5	---	---	---	---					
