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
EBI3	10148	broad.mit.edu	37	19	4234672	4234672	+	Missense_Mutation	SNP	G	G	T			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr19:4234672G>T	uc002lzu.3	+	3	396	c.388G>T	c.(388-390)Gac>Tac	p.D130Y		NM_005755	NP_005746	Q14213	IL27B_HUMAN	Homo sapiens Epstein-Barr virus induced 3 (EBI3), mRNA.	130	Fibronectin type-III 2.				T-helper 1 type immune response|humoral immune response|positive regulation of alpha-beta T cell proliferation|positive regulation of interferon-gamma biosynthetic process	extracellular space|plasma membrane	cytokine activity|cytokine receptor activity			large_intestine(1)|lung(2)|ovary(1)|urinary_tract(1)	5		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0336)|STAD - Stomach adenocarcinoma(1328;0.18)		AGTCAAGCCCGACCCTCCAGA	0.547000													8	274					0	0	1	0	0
CDH13	1012	broad.mit.edu	37	16	83520201	83520201	+	Missense_Mutation	SNP	A	A	G			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr16:83520201A>G	uc010vns.2	+	7	1306	c.1042A>G	c.(1042-1044)Atc>Gtc	p.I348V	CDH13_uc002fgx.3_Missense_Mutation_p.I301V|CDH13_uc010vnt.2_Missense_Mutation_p.I47V|CDH13_uc010vnu.2_Missense_Mutation_p.I262V	NM_001220488	NP_001207417	P55290	CAD13_HUMAN	Homo sapiens cadherin 13, H-cadherin (heart) (CDH13), transcript variant 2, mRNA.	301	Cadherin 2.				Rac protein signal transduction|Rho protein signal transduction|adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		CATGTTCTACATCGATCCTGA	0.493000													4	135					0	0	1	0	0
TMEM89	440955	broad.mit.edu	37	3	48658391	48658391	+	Missense_Mutation	SNP	G	G	A			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr3:48658391G>A	uc011bbo.2	-	1	364	c.364C>T	c.(364-366)Ctc>Ttc	p.L122F		NM_001008269	NP_001008270	A2RUT3	TMM89_HUMAN	Homo sapiens transmembrane protein 89 (TMEM89), mRNA.	122						integral to membrane				breast(1)|lung(1)|stomach(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000286)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		ACCCCACGGAGCAGGGTGTGG	0.612000													3	118					0	0	1	0	0
MUC2	4583	broad.mit.edu	37	11	1094843	1094843	+	Silent	SNP	C	C	T	rs41417150	by1000genomes	TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr11:1094843C>T	uc001lsx.1	+	32	5946	c.5919C>T	c.(5917-5919)aaC>aaT	p.N1973N		NM_002457	NP_002448	Q02817	MUC2_HUMAN	Homo sapiens mucin 2, oligomeric mucus/gel-forming (MUC2), mRNA.	2029						inner mucus layer|outer mucus layer	protein binding			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GTGTCCTGAACGACACCTACT	0.617000													6	352					0	0	1	0	0
STUB1	10273	broad.mit.edu	37	16	732365	732365	+	Splice_Site	SNP	G	G	A			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr16:732365G>A	uc002cit.3	+	7	1198	c.787_splice	c.e7-1	p.R263_splice	STUB1_uc002ciu.3_Splice_Site_p.R191_splice|JMJD8_uc002ciw.1_3'UTR|JMJD8_uc002ciy.1_3'UTR	NM_005861	NP_005852	Q9UNE7	CHIP_HUMAN	Homo sapiens STIP1 homology and U-box containing protein 1, E3 ubiquitin protein ligase (STUB1), mRNA.	263	U-box.				DNA repair|cellular response to misfolded protein|misfolded or incompletely synthesized protein catabolic process|positive regulation of cellular chaperone-mediated protein complex assembly|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process|protein K63-linked ubiquitination|protein autoubiquitination|protein maturation|regulation of glucocorticoid metabolic process|ubiquitin-dependent SMAD protein catabolic process	cytoplasm|nuclear inclusion body|ubiquitin conjugating enzyme complex|ubiquitin ligase complex	Hsp70 protein binding|Hsp90 protein binding|SMAD binding|TPR domain binding|kinase binding|misfolded protein binding|protein binding, bridging|protein homodimerization activity|ubiquitin-ubiquitin ligase activity			endometrium(2)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	6		Hepatocellular(780;0.00335)				TCACTGCAGCGTGTGGGTCAT	0.617000													5	156					0	0	1	0	0
ADAMTS2	9509	broad.mit.edu	37	5	178541107	178541107	+	Missense_Mutation	SNP	G	G	A			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr5:178541107G>A	uc003mjw.3	-	21	3499	c.3397C>T	c.(3397-3399)Cgg>Tgg	p.R1133W		NM_014244	NP_055059	O95450	ATS2_HUMAN	Homo sapiens ADAM metallopeptidase with thrombospondin type 1 motif, 2 (ADAMTS2), transcript variant 1, mRNA.	1133					collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding	p.R1133Q(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	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)		GGTGATGGCCGCACCTCCATG	0.587000													4	183					0	0	1	0	0
CTNND1	1500	broad.mit.edu	37	11	57573460	57573460	+	Missense_Mutation	SNP	A	A	C			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr11:57573460A>C	uc001nmc.4	+	9	2400	c.1829A>C	c.(1828-1830)aAt>aCt	p.N610T	CTNND1_uc001nlf.2_Missense_Mutation_p.N610T|CTNND1_uc021qjk.1_Missense_Mutation_p.N610T|CTNND1_uc001nlh.1_Missense_Mutation_p.N610T|CTNND1_uc001nlj.4_Missense_Mutation_p.N556T|CTNND1_uc001nlq.4_Missense_Mutation_p.N509T|CTNND1_uc001nlr.4_Missense_Mutation_p.N556T|CTNND1_uc001nln.4_Missense_Mutation_p.N610T|CTNND1_uc001nli.4_Missense_Mutation_p.N610T|CTNND1_uc001nlo.4_Missense_Mutation_p.N509T|CTNND1_uc001nlp.4_Missense_Mutation_p.N556T|CTNND1_uc001nlu.4_Missense_Mutation_p.N509T|CTNND1_uc001nlt.4_Missense_Mutation_p.N509T|CTNND1_uc001nlv.4_Missense_Mutation_p.N509T|CTNND1_uc001nls.4_Missense_Mutation_p.N509T|CTNND1_uc001nlw.4_Missense_Mutation_p.N509T|CTNND1_uc001nmf.4_Missense_Mutation_p.N610T|CTNND1_uc001nlx.4_Missense_Mutation_p.N287T|CTNND1_uc001nlz.4_Missense_Mutation_p.N287T|CTNND1_uc009ymn.3_Missense_Mutation_p.N287T|CTNND1_uc001nly.4_Missense_Mutation_p.N287T|CTNND1_uc001nmb.4_Missense_Mutation_p.N287T|CTNND1_uc001nma.4_Missense_Mutation_p.N287T|CTNND1_uc001nmd.4_Missense_Mutation_p.N556T|CTNND1_uc001nlk.4_Missense_Mutation_p.N556T|CTNND1_uc001nme.4_Missense_Mutation_p.N610T|CTNND1_uc001nll.4_Missense_Mutation_p.N556T|CTNND1_uc001nlm.4_Missense_Mutation_p.N610T|CTNND1_uc001nmi.4_Missense_Mutation_p.N509T|CTNND1_uc001nmg.4_Missense_Mutation_p.N556T|CTNND1_uc001nmh.4_Missense_Mutation_p.N610T	NM_001085458	NP_001078932	O60716	CTND1_HUMAN	Homo sapiens catenin (cadherin-associated protein), delta 1 (CTNND1), transcript variant 1, mRNA.	610					Wnt receptor signaling pathway|adherens junction organization|cell junction assembly|negative regulation of canonical Wnt receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|midbody|nucleus	cadherin binding|protein binding|receptor binding			breast(5)|endometrium(8)|kidney(4)|large_intestine(7)|liver(2)|lung(16)|ovary(1)|upper_aerodigestive_tract(2)	45		all_epithelial(135;0.155)				GTTGCCAACAATACTGGGCCA	0.498000													3	29					0	0	1	0	0
DGCR8	54487	broad.mit.edu	37	22	20079439	20079439	+	Missense_Mutation	SNP	G	G	A			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr22:20079439G>A	uc002zri.3	+	6	1981	c.1552G>A	c.(1552-1554)Gag>Aag	p.E518K	DGCR8_uc010grz.3_Missense_Mutation_p.E518K|DGCR8_uc002zrj.3_Missense_Mutation_p.E161K	NM_022720	NP_073557	Q8WYQ5	DGCR8_HUMAN	Homo sapiens DiGeorge syndrome critical region gene 8 (DGCR8), transcript variant 1, mRNA.	518	DRBM 1.|Necessary for heme-binding and pri-miRNA processing.|Necessary for interaction with DROSHA.				primary miRNA processing	cytoplasm|microtubule cytoskeleton|nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding			NS(2)|breast(1)|endometrium(5)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	22	Colorectal(54;0.0993)					CATCCTGCACGAGTACATGCA	0.463000													32	31					0	0	1	0	0
MUC16	94025	broad.mit.edu	37	19	9090831	9090831	+	Silent	SNP	A	A	G			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr19:9090831A>G	uc002mkp.3	-	0	1188	c.984T>C	c.(982-984)ccT>ccC	p.P328P		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	Homo sapiens mucin 16, cell surface associated (MUC16), mRNA.	328	Thr-rich.				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TCATGGAAAAAGGGATAGCTG	0.522000													3	98					0	0	1	0	0
RTN2	6253	broad.mit.edu	37	19	45996575	45996575	+	Missense_Mutation	SNP	A	A	C			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr19:45996575A>C	uc002pcb.3	-	4	1106	c.876T>G	c.(874-876)atT>atG	p.I292M	RTN2_uc002pcc.3_Intron|RTN2_uc002pcd.3_Intron	NM_005619	NP_005610	O75298	RTN2_HUMAN	Homo sapiens reticulon 2 (RTN2), transcript variant 1, mRNA.	292						integral to endoplasmic reticulum membrane	signal transducer activity			cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(4)|skin(1)|urinary_tract(1)	20		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00829)|Epithelial(262;0.184)|GBM - Glioblastoma multiforme(486;0.246)		ACAATTCCAAAATTGGAACCG	0.502000													3	155					0	0	1	0	0
GPR116	221395	broad.mit.edu	37	6	46849818	46849818	+	Silent	SNP	T	T	C			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr6:46849818T>C	uc003oyo.3	-	6	928	c.639A>G	c.(637-639)ccA>ccG	p.P213P	GPR116_uc003oyp.3_Silent_p.P213P|GPR116_uc003oyq.3_Silent_p.P213P|GPR116_uc010jzi.1_5'Flank|GPR116_uc003oyr.2_Silent_p.P213P	NM_001098518	NP_056049	Q8IZF2	GP116_HUMAN	Homo sapiens G protein-coupled receptor 116 (GPR116), transcript variant 2, mRNA.	213	SEA.				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			CCTTGAAGCCTGGTAAAATTC	0.378000													4	346					0	0	1	0	0
CYB5R2	51700	broad.mit.edu	37	11	7687683	7687683	+	Splice_Site	SNP	A	A	C			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr11:7687683A>C	uc001mfm.3	-	8	896	c.658_splice	c.e8+1	p.G220_splice	CYB5R2_uc001mfn.3_Splice_Site|CYB5R2_uc009yfk.3_Splice_Site_p.G220_splice	NM_016229	NP_057313	Q6BCY4	NB5R2_HUMAN	Homo sapiens cytochrome b5 reductase 2 (CYB5R2), mRNA.	220					sterol biosynthetic process	membrane|soluble fraction	cytochrome-b5 reductase activity			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)	11				Epithelial(150;5.48e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		ATGTCGTACCAATGGGAGGCC	0.493000											OREG0020724	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	14	77					0	0	1	0	0
TRDV3	28516	broad.mit.edu	37	14	22938320	22938320	+	Silent	SNP	A	A	G			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr14:22938320A>G	uc001web.1	-	1	106	c.54T>C	c.(52-54)tgT>tgC	p.C18C	TCRA_uc001wbw.2_Intron|T-Cell_Receptor_V-alpha_region_uc021rpl.1_Intron|TCRA_uc010tmo.2_Intron|TCRA_uc001wco.3_Intron|TCRA_uc010aje.1_Intron|TCRA_uc001wcp.2_Intron|TCRA_uc001wcr.1_Intron|TCRA_uc001wcs.1_Intron|TCRA_uc010ajf.1_Intron|TCRA_uc001wcu.4_Intron|TCRA_uc021rpn.1_Intron|TCRA_uc001wcx.4_Intron|TCRA_uc021rpr.1_Intron|TCRA_uc001wdd.2_Intron|TCRA_uc010ajj.1_Intron|TCRA_uc001wde.1_Intron|TCRA_uc010ajk.2_Intron|TCRA_uc001wdg.1_Intron|TCRA_uc021rpt.1_Intron|TCRA_uc010ajl.1_Intron|AV4S1_uc021rpv.1_Intron|TCRA_uc010ajo.1_Intron|TCRA_uc010ajp.1_Intron|TCRA_uc021rpw.1_Intron|TRAV38-2DV8_uc010tmr.2_Intron|AK093552_uc001wds.1_Intron|TCRA_uc001wdv.4_Intron					SubName: Full=HDV103S1; Flags: Fragment;																		TTACTTTGTCACACAGCGTGC	0.502000													20	17					0	0	1	0	0
COL20A1	57642	broad.mit.edu	37	20	61956821	61956821	+	Missense_Mutation	SNP	G	G	A			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr20:61956821G>A	uc011aau.2	+	27	3423	c.3323G>A	c.(3322-3324)gGa>gAa	p.G1108E	COL20A1_uc011aav.2_Missense_Mutation_p.G929E	NM_020882	NP_065933	Q9P218	COKA1_HUMAN	Homo sapiens collagen, type XX, alpha 1 (COL20A1), mRNA.	1108	Collagen-like 1.				cell adhesion	collagen|extracellular space	structural molecule activity			NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					GGAGAGAAGGGAGACCATGGG	0.667000													5	122					0	0	1	0	0
ZIC3	7547	broad.mit.edu	37	X	136649433	136649433	+	Missense_Mutation	SNP	C	C	T			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chrX:136649433C>T	uc004fak.3	+	0	1088	c.583C>T	c.(583-585)Cgt>Tgt	p.R195C		NM_003413	NP_003404	O60481	ZIC3_HUMAN	Homo sapiens Zic family member 3 (ZIC3), mRNA.	195					cell differentiation|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(3)|liver(1)|lung(18)|ovary(3)|soft_tissue(2)|urinary_tract(1)	37	Acute lymphoblastic leukemia(192;0.000127)					GCTGTTCGGCCGTGCTGACCC	0.672000													4	112					0	0	1	0	0
OR2M2	391194	broad.mit.edu	37	1	248344320	248344320	+	Missense_Mutation	SNP	T	T	C			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr1:248344320T>C	uc010pzf.2	+	0	1033	c.1033T>C	c.(1033-1035)Tac>Cac	p.Y345H		NM_001004688	NP_001004688	Q96R28	OR2M2_HUMAN	Homo sapiens olfactory receptor, family 2, subfamily M, member 2 (OR2M2), mRNA.	345					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(45)|ovary(3)|prostate(1)|skin(3)	70	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			ATTGATTATGTACATTGCCTA	0.264000													4	146					0	0	1	0	0
KIF14	9928	broad.mit.edu	37	1	200539119	200539119	+	Missense_Mutation	SNP	A	A	T			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr1:200539119A>T	uc010ppk.1	-	22	4020	c.3581T>A	c.(3580-3582)aTg>aAg	p.M1194K	KIF14_uc010ppj.1_Missense_Mutation_p.M703K	NM_014875	NP_055690	Q15058	KIF14_HUMAN	Homo sapiens kinesin family member 14 (KIF14), mRNA.	1194	Required for CIT-binding.				microtubule-based movement	cytoplasm|microtubule|nucleus|spindle	ATP binding|microtubule motor activity|protein binding			NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						TCTGTTCTTCATCAAACTCCT	0.289000													41	84					0	0	1	0	0
STS	412	broad.mit.edu	37	X	7177465	7177465	+	Missense_Mutation	SNP	A	A	G			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chrX:7177465A>G	uc004cry.4	+	4	718	c.473A>G	c.(472-474)tAt>tGt	p.Y158C		NM_000351	NP_000342	P08842	STS_HUMAN	Homo sapiens steroid sulfatase (microsomal), isozyme S (STS), mRNA.	158					female pregnancy|steroid catabolic process	Golgi apparatus|endoplasmic reticulum membrane|endosome|integral to membrane|lysosome|microsome|plasma membrane	metal ion binding|steryl-sulfatase activity			NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|prostate(2)|skin(1)	27		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)			Estrone(DB00655)	GGCTTCAATTATTTCTATGGG	0.522000									Ichthyosis				3	138					0	0	1	0	0
TDRD1	56165	broad.mit.edu	37	10	115978234	115978234	+	Silent	SNP	A	A	G			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr10:115978234A>G	uc001lbg.1	+	17	2538	c.2385A>G	c.(2383-2385)gtA>gtG	p.V795V	TDRD1_uc001lbf.3_Intron|TDRD1_uc001lbh.1_Silent_p.V786V|TDRD1_uc001lbi.1_Silent_p.V786V|TDRD1_uc010qsc.2_Silent_p.V399V|TDRD1_uc001lbj.3_Silent_p.V504V	NM_198795	NP_942090	Q9BXT4	TDRD1_HUMAN	Homo sapiens tudor domain containing 1 (TDRD1), mRNA.	795	Tudor 3.				DNA methylation involved in gamete generation|gene silencing by RNA|germ cell development|meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	pi-body	nucleic acid binding|protein binding|zinc ion binding			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5)	48		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		ATGTTAAAGTACATTTTGTGG	0.383000													6	199					0	0	1	0	0
IK	3550	broad.mit.edu	37	5	140032663	140032663	+	Missense_Mutation	SNP	A	A	T			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr5:140032663A>T	uc003lgq.3	+	4	448	c.338A>T	c.(337-339)gAt>gTt	p.D113V	IK_uc011czk.1_Missense_Mutation_p.D113V|IK_uc021yen.1_Missense_Mutation_p.D54V	NM_006083	NP_006074	Q13123	RED_HUMAN	Homo sapiens IK cytokine, down-regulator of HLA II (IK), mRNA.	113					cell-cell signaling|immune response	extracellular space|nucleus|soluble fraction				large_intestine(1)	1		all_hematologic(541;4.8e-07)|all_lung(500;0.000434)|Lung NSC(810;0.00161)|Breast(839;0.128)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGAACAAAGATTATGAAGAA	0.502000													34	80					0	0	1	0	0
OR2L1P	26247	broad.mit.edu	37	1	248154046	248154046	+	Silent	SNP	G	G	T			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr1:248154046G>T	uc001idv.1	+	0	478	c.234G>T	c.(232-234)acG>acT	p.T78T	OR2L13_uc001ids.3_Intron					Homo sapiens olfactory receptor, family 2, subfamily L, member 1 pseudogene (OR2L1P), non-coding RNA.											lung(11)	11						GTGCTCACACGGTATATGCAC	0.468000													4	135					0	0	1	0	0
COL22A1	169044	broad.mit.edu	37	8	139890069	139890069	+	Silent	SNP	G	G	A			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr8:139890069G>A	uc003yvd.3	-	2	1029	c.582C>T	c.(580-582)tcC>tcT	p.S194S		NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	Homo sapiens collagen, type XXII, alpha 1 (COL22A1), mRNA.	194	VWFA.				cell adhesion	collagen|cytoplasm	structural molecule activity			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			AGACGTGGGCGGACTTGGGCT	0.672000										HNSCC(7;0.00092)			3	85					0	0	1	0	0
PDPR	55066	broad.mit.edu	37	16	70187304	70187304	+	Missense_Mutation	SNP	A	A	T			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr16:70187304A>T	uc002eyf.1	+	17	3020	c.2063A>T	c.(2062-2064)cAt>cTt	p.H688L	CLEC18A_uc002exy.3_Intron|PDPR_uc010vlr.1_Missense_Mutation_p.H588L|PDPR_uc002eyg.1_Intron|PDPR_uc002eyh.2_Missense_Mutation_p.H33L|PDPR_uc010vls.1_Missense_Mutation_p.H33L	NM_017990	NP_060460	Q8NCN5	PDPR_HUMAN	Homo sapiens pyruvate dehydrogenase phosphatase regulatory subunit (PDPR), mRNA.	688					glycine catabolic process|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	aminomethyltransferase activity|oxidoreductase activity			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		TACGCCCTGCATGTATACAAT	0.448000													10	47					0	0	1	0	0
CPE	1363	broad.mit.edu	37	4	166416761	166416761	+	Missense_Mutation	SNP	A	A	G			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr4:166416761A>G	uc003irg.4	+	7	1541	c.1264A>G	c.(1264-1266)Aca>Gca	p.T422A		NM_001873	NP_001864	P16870	CBPE_HUMAN	Homo sapiens carboxypeptidase E (CPE), mRNA.	422					cardiac left ventricle morphogenesis|neuropeptide signaling pathway|protein modification process	extracellular region|nucleus|plasma membrane	metallocarboxypeptidase activity|protein binding|zinc ion binding			endometrium(2)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	26	all_hematologic(180;0.221)	Prostate(90;0.0962)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.137)	Glucagon recombinant(DB00040)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	CTATAAACTTACAGCCTCAGC	0.408000													10	181					0	0	1	0	0
NRAS	4893	broad.mit.edu	37	1	115256530	115256530	+	Missense_Mutation	SNP	G	G	T	rs121913254		TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr1:115256530G>T	uc009wgu.3	-	2	435	c.181C>A	c.(181-183)Caa>Aaa	p.Q61K		NM_002524	NP_002515	P01111	RASN_HUMAN	Homo sapiens neuroblastoma RAS viral (v-ras) oncogene homolog (NRAS), mRNA.	61			Q -> K (in neuroblastoma cell).|Q -> R (in lung carcinoma cell and melanoma; dbSNP:rs11554290).		Ras protein signal transduction|activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway	Golgi membrane|plasma membrane	GTP binding|GTPase activity	p.Q61K(1229)|p.Q61R(898)|p.Q61L(198)|p.Q61H(123)|p.Q61P(23)|p.Q61E(18)|p.G60E(6)|p.Q61?(5)|p.Q61Q(3)|p.G60>?(2)|p.G60R(1)|p.Q61*(1)|p.Q61_E62>HK(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TACTCTTCTTGTCCAGCTGTA	0.458000	Q61K(CHP212_AUTONOMIC_GANGLIA)|Q61K(HCC15_LUNG)|Q61K(HS936T_SKIN)|Q61K(HS944T_SKIN)|Q61K(HT1080_SOFT_TISSUE)|Q61K(HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(NCIH1299_LUNG)|Q61K(NCIH2087_LUNG)|Q61K(OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(SKNAS_AUTONOMIC_GANGLIA)|Q61K(SKNSH_AUTONOMIC_GANGLIA)|Q61K(TYKNU_OVARY)	50	Mis		"""melanoma, MM, AML, thyroid"""				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)			90	204					0	0	1	0	0