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
GSTA3	2940	broad.mit.edu	37	6	52762673	52762673	+	Missense_Mutation	SNP	A	A	T			TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr6:52762673A>T	ENST00000211122.3	-	6	561	c.496T>A	c.(496-498)Tat>Aat	p.Y166N	GSTA3_ENST00000370968.1_Missense_Mutation_p.Y116N	NM_000847.4	NP_000838.3	Q16772	GSTA3_HUMAN	glutathione S-transferase alpha 3	166	GST C-terminal.				glutathione metabolic process|xenobiotic metabolic process	cytosol	glutathione transferase activity			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(2)	10	Lung NSC(77;0.0912)				Glutathione(DB00143)	TCTTCCACATAGTAGAGAAGT	0.512000													5	88					0	0	1	0	0
NEDD9	4739	broad.mit.edu	37	6	11213930	11213930	+	Missense_Mutation	SNP	C	C	T			TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr6:11213930C>T	ENST00000379446.5	-	2	209	c.43G>A	c.(43-45)Gtc>Atc	p.V15I	NEDD9_ENST00000504387.1_Missense_Mutation_p.V15I|NEDD9_ENST00000379433.5_Missense_Mutation_p.V15I|RP3-510L9.1_ENST00000500636.2_RNA	NM_001271033.1|NM_006403.3	NP_001257962.1|NP_006394.1	Q14511	CASL_HUMAN	neural precursor cell expressed, developmentally down-regulated 9	15	SH3.				actin filament bundle assembly|cell adhesion|cell division|integrin-mediated signaling pathway|mitosis|regulation of growth	cell cortex|focal adhesion|Golgi apparatus|lamellipodium|nucleus	protein binding			endometrium(3)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(50;0.0768)|Ovarian(93;0.152)	all_hematologic(90;0.135)	Epithelial(50;0.0647)|all cancers(50;0.179)			CACTCTGGGACATTGTCATAT	0.517000													20	40					0	0	1	0	0
CTCF	10664	broad.mit.edu	37	16	67645506	67645506	+	Missense_Mutation	SNP	T	T	G			TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr16:67645506T>G	ENST00000264010.4	+	3	1215	c.771T>G	c.(769-771)atT>atG	p.I257M	CTCF_ENST00000401394.1_Intron	NM_006565.3	NP_006556.1	P49711	CTCF_HUMAN	CCCTC-binding factor (zinc finger protein)	257					chromatin modification|chromosome segregation|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|regulation of centromeric sister chromatid cohesion|regulation of molecular function, epigenetic	chromosome, centromeric region|condensed chromosome|nucleolus|nucleoplasm	chromatin insulator sequence binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|transcription regulatory region DNA binding|zinc ion binding			breast(6)|central_nervous_system(2)|cervix(1)|endometrium(34)|haematopoietic_and_lymphoid_tissue(7)|kidney(3)|large_intestine(9)|liver(1)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	79		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)		CAACAAAAATTAAAAAGAAAG	0.373000													20	30					0	0	1	0	0
PRSS3P2	0	broad.mit.edu	37	7	142481789	142481789	+	RNA	SNP	T	T	C	rs140267598	by1000genomes	TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr7:142481789T>C	ENST00000603901.1	+	0	468					NR_001296.3																						ACTACCCAGATGAGCTGCAGT	0.488000													3	41					0	0	1	0	0
ZNF761	388561	broad.mit.edu	37	19	53945909	53945909	+	RNA	SNP	T	T	C	rs28727441	by1000genomes	TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr19:53945909T>C	ENST00000454407.1	+	0	55				TPM3P9_ENST00000424846.3_RNA			Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		ACCCTGACTCTGCCTGAGGCC	0.562000													4	29					0	0	1	0	0
CROCCP2	0	broad.mit.edu	37	1	16946434	16946434	+	RNA	SNP	C	C	T	rs367060		TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr1:16946434C>T	ENST00000412962.1	-	0	1085																											CTCAGCCTTCCGCCGGGCCAG	0.672000													3	23					0	0	1	0	0
RGPD3	653489	broad.mit.edu	37	2	107049681	107049681	+	Missense_Mutation	SNP	T	T	C			TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr2:107049681T>C	ENST00000409886.3	-	16	2353	c.2266A>G	c.(2266-2268)Aac>Gac	p.N756D	RGPD3_ENST00000304514.7_Missense_Mutation_p.N756D	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	756					intracellular transport		binding	p.N756D(6)		breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						TCACTATAGTTTTCGAGTTCC	0.373000													5	292					0	0	1	0	0
AJ271736.10	0	broad.mit.edu	37	X	155255062	155255062	+	RNA	SNP	C	C	G			TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chrX:155255062C>G	ENST00000285718.7	+	0	1367				WASH6P_ENST00000461007.1_RNA																							CACCTTCCCCCCCAGACCCAG	0.627000													3	10					0	0	1	0	0
TRIOBP	11078	broad.mit.edu	37	22	38119859	38119859	+	Silent	SNP	C	C	T	rs66505048		TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr22:38119859C>T	ENST00000406386.3	+	7	1551	c.1296C>T	c.(1294-1296)tgC>tgT	p.C432C	RP1-37E16.12_ENST00000455236.1_RNA	NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	432					actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding	p.C432C(6)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GAACATCCTGCGCCCAGCGGG	0.582000													5	71					0	0	1	0	0
NBPF1	55672	broad.mit.edu	37	1	16918653	16918653	+	Splice_Site	SNP	C	C	T			TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr1:16918653C>T	ENST00000430580.2	-	6	853		c.e6+1			NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1							cytoplasm									UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		TCTTAACTTACTGTTGTGAAA	0.418000													4	62					0	0	1	0	0
RP11-423O2.5	0	broad.mit.edu	37	1	142803543	142803543	+	RNA	SNP	C	C	T			TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr1:142803543C>T	ENST00000423385.1	-	0	1422																											TGTTGGAATTCCTGATGAATC	0.269000													4	114					0	0	1	0	0
AJ271736.10	0	broad.mit.edu	37	X	155255043	155255043	+	RNA	SNP	G	G	A			TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chrX:155255043G>A	ENST00000285718.7	+	0	1348				WASH6P_ENST00000461007.1_RNA																							ATCCTAGGGGGCTCCATGACA	0.642000													3	10					0	0	1	0	0
IDH1	3417	broad.mit.edu	37	2	209113113	209113113	+	Missense_Mutation	SNP	G	G	A	rs121913499		TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr2:209113113G>A	ENST00000415913.1	-	4	775	c.394C>T	c.(394-396)Cgt>Tgt	p.R132C	IDH1_ENST00000345146.2_Missense_Mutation_p.R132C|IDH1_ENST00000446179.1_Missense_Mutation_p.R132C			O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).		2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity	p.R132C(446)|p.R132G(125)|p.R132S(106)|p.G131_R132>VL(1)|p.R132V(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		TAAGCATGACGACCTATGATG	0.398000			Mis		gliobastoma								22	50					0	0	1	0	0
EPHB4	2050	broad.mit.edu	37	7	100411306	100411306	+	Missense_Mutation	SNP	G	G	A	rs60537976		TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr7:100411306G>A	ENST00000358173.3	-	10	2192	c.1724C>T	c.(1723-1725)tCg>tTg	p.S575L	EPHB4_ENST00000360620.3_Missense_Mutation_p.S575L	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	575					cell proliferation|organ morphogenesis|regulation of angiogenesis	cell surface|integral to plasma membrane	ATP binding|ephrin receptor activity	p.S575L(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(3)	47	Lung NSC(181;0.041)|all_lung(186;0.0581)					GTGTTTGTCCGAATATTCTGC	0.493000													5	291					0	0	1	0	0
FUT5	2527	broad.mit.edu	37	19	5867557	5867557	+	Silent	SNP	A	A	G			TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr19:5867557A>G	ENST00000252675.5	-	5	742	c.180T>C	c.(178-180)aaT>aaC	p.N60N	FUT5_ENST00000588525.1_Silent_p.N60N			Q11128	FUT5_HUMAN	fucosyltransferase 5 (alpha (1,3) fucosyltransferase)	60					L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to membrane	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity|alpha(1,3)-fucosyltransferase activity			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12						AGCGGGACCCATTGGGAGCCC	0.632000													12	24					0	0	1	0	0
RNLS	55328	broad.mit.edu	37	10	90122340	90122340	+	Missense_Mutation	SNP	G	G	T			TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr10:90122340G>T	ENST00000371947.3	-	5	2008	c.669C>A	c.(667-669)ttC>ttA	p.F223L	RNLS_ENST00000466945.1_5'UTR|RNLS_ENST00000437752.1_Missense_Mutation_p.F140L|RNLS_ENST00000331772.4_Missense_Mutation_p.F223L	NM_018363.3	NP_060833.1	Q5VYX0	RNLS_HUMAN	renalase, FAD-dependent amine oxidase	223						extracellular region	oxidoreductase activity			breast(1)|kidney(1)|lung(3)|ovary(1)|prostate(1)	7						CAATGGAGACGAAGCGTATGC	0.438000													27	43					2.48779e-11	2.56805e-11	1	1	0
POLR1A	25885	broad.mit.edu	37	2	86276075	86276075	+	Missense_Mutation	SNP	T	T	C			TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr2:86276075T>C	ENST00000263857.6	-	18	2944	c.2566A>G	c.(2566-2568)Agg>Ggg	p.R856G	POLR1A_ENST00000409681.1_Missense_Mutation_p.R856G			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	856					termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	DNA-directed RNA polymerase I complex|nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						TTAAAATCCCTCTGGTCCTTG	0.473000													22	55					0	0	1	0	0
PAQR3	152559	broad.mit.edu	37	4	79860329	79860329	+	Missense_Mutation	SNP	T	T	C			TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr4:79860329T>C	ENST00000512733.1	-	1	263	c.50A>G	c.(49-51)tAc>tGc	p.Y17C	PAQR3_ENST00000295462.3_Missense_Mutation_p.Y17C|PAQR3_ENST00000380645.4_Missense_Mutation_p.Y17C	NM_001040202.1	NP_001035292.1	Q6TCH7	PAQR3_HUMAN	progestin and adipoQ receptor family member III	17						Golgi membrane|integral to membrane	receptor activity			breast(2)|central_nervous_system(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(1)	8						CCAGTACTGGTAGCTGCCCAG	0.672000													25	52					0	0	1	0	0
OAS2	0	broad.mit.edu	37	12	113442843	113442843	+	Silent	SNP	G	G	A			TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr12:113442843G>A	ENST00000392583.2	+	7	1491	c.1284G>A	c.(1282-1284)cgG>cgA	p.R428R	OAS2_ENST00000342315.4_Silent_p.R428R|RP1-71H24.1_ENST00000552784.1_RNA	NM_002535.2	NP_002526.2	P29728	OAS2_HUMAN	2'-5'-oligoadenylate synthetase 2, 69/71kDa	428	OAS domain 2.				interferon-gamma-mediated signaling pathway|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|type I interferon-mediated signaling pathway	endoplasmic reticulum|membrane|microsome|mitochondrion|nucleus	ATP binding|nucleotidyltransferase activity|RNA binding			NS(1)|breast(2)|endometrium(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						AAAACGAGCGGCACAAAATCG	0.502000													3	37					0	0	1	0	0
GMIP	51291	broad.mit.edu	37	19	19747568	19747568	+	Silent	SNP	G	G	A			TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr19:19747568G>A	ENST00000203556.4	-	13	1412	c.1275C>T	c.(1273-1275)agC>agT	p.S425S	GMIP_ENST00000445806.2_Silent_p.S422S|GMIP_ENST00000587238.1_Silent_p.S425S	NM_016573.2	NP_057657.2	Q9P107	GMIP_HUMAN	GEM interacting protein	425					negative regulation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	metal ion binding|protein binding|Rho GTPase activator activity			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						CGCCACCCACGCTGTCCACAT	0.637000													20	35					0	0	1	0	0
ALMS1	7840	broad.mit.edu	37	2	73677492	73677492	+	Missense_Mutation	SNP	G	G	A			TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr2:73677492G>A	ENST00000264448.6	+	8	3946	c.3835G>A	c.(3835-3837)Gct>Act	p.A1279T	ALMS1_ENST00000409009.1_Missense_Mutation_p.A1237T|ALMS1_ENST00000377715.1_Missense_Mutation_p.A1279T	NM_015120.4	NP_055935.4	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	1279	34 X 47 AA approximate tandem repeat.				G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole		p.A1279T(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						TGGCACACCAGCTGTAACCTC	0.433000													4	106					0	0	1	0	0
KRTAP4-8	728224	broad.mit.edu	37	17	39254054	39254054	+	Missense_Mutation	SNP	A	A	T	rs76270529	by1000genomes	TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr17:39254054A>T	ENST00000333822.4	-	1	339	c.283T>A	c.(283-285)Tgc>Agc	p.C95S		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	95	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].					keratin filament		p.C95S(4)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						ctggagatgcagcagcTAGGG	0.677000													4	42					0	0	1	0	0
CC2D2A	57545	broad.mit.edu	37	4	15513007	15513007	+	Missense_Mutation	SNP	A	A	C	rs112367037		TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr4:15513007A>C	ENST00000424120.1	+	8	932	c.678A>C	c.(676-678)gaA>gaC	p.E226D	CC2D2A_ENST00000513811.1_3'UTR|CC2D2A_ENST00000503292.1_Missense_Mutation_p.E226D|CC2D2A_ENST00000389652.5_Missense_Mutation_p.E177D|CC2D2A_ENST00000413206.1_Missense_Mutation_p.E226D			Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	226	Poly-Glu.				cell projection organization	cilium|microtubule basal body				NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						AGGAAGGGGAAGAAGAAGAAC	0.448000													9	8					0	0	1	0	0
RPGR	6103	broad.mit.edu	37	X	38146339	38146339	+	Missense_Mutation	SNP	T	T	G			TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chrX:38146339T>G	ENST00000378505.2	-	15	2089	c.1913A>C	c.(1912-1914)gAa>gCa	p.E638A	RPGR_ENST00000318842.7_Intron|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000339363.3_Intron|RPGR_ENST00000338898.3_Intron|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000309513.3_Intron	NM_001034853.1	NP_001030025.1	Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator	629	Glu-rich.				intracellular protein transport|response to stimulus|visual perception	Golgi apparatus|photoreceptor outer segment	guanyl-nucleotide exchange factor activity|protein binding			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						TGCCTTGCCTTCACTCACCTC	0.483000													48	78					0	0	1	0	0
TFAP2C	7022	broad.mit.edu	37	20	55206271	55206271	+	Missense_Mutation	SNP	A	A	G			TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr20:55206271A>G	ENST00000201031.2	+	2	302	c.59A>G	c.(58-60)gAc>gGc	p.D20G	TFAP2C_ENST00000544508.1_5'UTR	NM_003222.3	NP_003213.1	Q92754	AP2C_HUMAN	transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma)	20					cell-cell signaling|male gonad development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein dimerization activity|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	13			Colorectal(105;0.229)			GATCGCCACGACGGGAGCAGC	0.662000													12	45					0	0	1	0	0
SCN2A	6326	broad.mit.edu	37	2	166172011	166172011	+	Missense_Mutation	SNP	A	A	G			TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr2:166172011A>G	ENST00000357398.3	+	11	1704	c.1414A>G	c.(1414-1416)Aga>Gga	p.R472G	SCN2A_ENST00000283256.6_Missense_Mutation_p.R472G|SCN2A_ENST00000375437.2_Missense_Mutation_p.R472G|SCN2A_ENST00000375427.2_Missense_Mutation_p.R472G			Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	472					myelination	node of Ranvier|voltage-gated sodium channel complex	voltage-gated sodium channel activity			NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)	TGCTGAATCAAGAGACTTCAG	0.413000													22	35					0	0	1	0	0
VARS	7407	broad.mit.edu	37	6	31762953	31762953	+	Frame_Shift_Del	DEL	G	G	-			TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr6:31762953delG	ENST00000375663.3	-	2	482	c.42delC	c.(40-42)ccfs	p.P14fs	VARS_ENST00000444930.2_Intron	NM_006295.2	NP_006286.1	P26640	SYVC_HUMAN	valyl-tRNA synthetase	14					translational elongation|valyl-tRNA aminoacylation	cytosol	ATP binding|protein binding|valine-tRNA ligase activity			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	30					L-Valine(DB00161)	CTCGGAGGCTGGGGAAGGCAT	0.612													2	4	---	---	---	---					
SKIDA1	387640	broad.mit.edu	37	10	21805466	21805467	+	In_Frame_Ins	INS	-	-	CCTCCT	rs138084841	by1000genomes	TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr10:21805466_21805467insCCTCCT	ENST00000449193.2	-	4	3537_3538	c.1285_1286insAGGAGG	c.(1285-1287)ggg>AGGAGGggg	p.428_429insRR	SKIDA1_ENST00000444772.3_In_Frame_Ins_p.349_350insRR	NM_207371.3	NP_997254.3			SKI/DACH domain containing 1									p.E428_G429insEE(2)									CCCGCTGCccccctcctcctcc	0.619													5	1	---	---	---	---					
PNLIPRP2	5408	broad.mit.edu	37	10	118396277	118396278	+	RNA	INS	-	-	T	rs148140777	by1000genomes	TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr10:118396277_118396278insT	ENST00000537242.1	+	0	962				PNLIPRP2_ENST00000433618.4_RNA|PNLIPRP2_ENST00000298771.7_RNA	NM_005396.4	NP_005387.2	P54317	LIPR2_HUMAN	pancreatic lipase-related protein 2						galactolipid catabolic process|lipid digestion|phospholipid catabolic process|triglyceride metabolic process	extracellular space	acylglycerol lipase activity|calcium ion binding|galactolipase activity|phospholipase activity|triglyceride lipase activity			endometrium(1)|large_intestine(1)|lung(11)|prostate(3)	16				all cancers(201;0.015)		GACAAATTATGGTTTTTTTTTT	0.421													2	4	---	---	---	---					
SPON1	10418	broad.mit.edu	37	11	14063263	14063263	+	RNA	DEL	A	A	-	rs113227652		TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr11:14063263delA	ENST00000310358.7	+	0	1017							Q9HCB6	SPON1_HUMAN	spondin 1, extracellular matrix protein						cell adhesion	extracellular space|proteinaceous extracellular matrix	protein binding			NS(1)|endometrium(1)|large_intestine(5)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)	21				Epithelial(150;0.00898)		GATTGCAGGGAAAAAAAAAAA	0.423													4	9	---	---	---	---					
PIGB	9488	broad.mit.edu	37	15	55631503	55631503	+	Frame_Shift_Del	DEL	T	T	-			TCGA-W2-A7HH-01A-11D-A35I-08	TCGA-W2-A7HH-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5814ba13-d1f1-47d0-bfb7-0175d03fbe9e	4f151f1e-f37e-4d90-b9a2-83ec2e1700ec	g.chr15:55631503delT	ENST00000164305.5	+	7	1124	c.833delT	c.(832-834)atfs	p.I278fs	PIGB_ENST00000539642.1_Frame_Shift_Del_p.I83fs	NM_004855.4	NP_004846.4	Q92521	PIGB_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class B	278					C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	integral to membrane|intrinsic to endoplasmic reticulum membrane	glycolipid mannosyltransferase activity			endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	11				all cancers(107;0.0255)		ATTGATCGTATTTTTTTTGGC	0.284													2	4	---	---	---	---					
