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
SYTL2	54843	broad.mit.edu	37	11	85436918	85436918	+	Silent	SNP	A	A	G			TCGA-ET-A3BN-01A-11D-A19J-08	TCGA-ET-A3BN-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67c66136-9911-40da-a760-b6bc24de8e5e	d652b345-76f2-4f08-bc75-ced94e1c9491	g.chr11:85436918A>G	ENST00000359152.5	-	1	2153	c.2154T>C	c.(2152-2154)ctT>ctC	p.L718L	SYTL2_ENST00000524452.1_Intron|SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000525423.1_Silent_p.L194L|SYTL2_ENST00000389960.4_Intron|SYTL2_ENST00000528231.1_Intron|SYTL2_ENST00000354566.3_Silent_p.L194L	NM_206928.2	NP_996811.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	231	C2 1.			I -> V (in Ref. 4; BAB15030).	intracellular protein transport|vesicle docking involved in exocytosis	exocytic vesicle|extrinsic to plasma membrane|melanosome|membrane fraction	neurexin binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding|Rab GTPase binding			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		CACTTGGTTCAAGCACTTGTT	0.403000													9	84					0	0	1	0	0
SIGLEC16	400709	broad.mit.edu	37	19	50475259	50475259	+	RNA	SNP	G	G	C	rs12463036	by1000genomes	TCGA-ET-A3BN-01A-11D-A19J-08	TCGA-ET-A3BN-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67c66136-9911-40da-a760-b6bc24de8e5e	d652b345-76f2-4f08-bc75-ced94e1c9491	g.chr19:50475259G>C	ENST00000602139.1	+	0	1205									sialic acid binding Ig-like lectin 16 (gene/pseudogene)											endometrium(2)|kidney(2)|lung(6)	10						TGGGGTCCTGGAGCTGCCTCG	0.672000													4	61					0	0	1	0	0
NAPSA	9476	broad.mit.edu	37	19	50864374	50864374	+	Silent	SNP	T	T	G			TCGA-ET-A3BN-01A-11D-A19J-08	TCGA-ET-A3BN-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67c66136-9911-40da-a760-b6bc24de8e5e	d652b345-76f2-4f08-bc75-ced94e1c9491	g.chr19:50864374T>G	ENST00000253719.2	-	5	700	c.492A>C	c.(490-492)tcA>tcC	p.S164S	NR1H2_ENST00000600978.1_Intron|NR1H2_ENST00000542413.1_Intron	NM_004851.1	NP_004842.1	O96009	NAPSA_HUMAN	napsin A aspartic peptidase	164					proteolysis	extracellular region	aspartic-type endopeptidase activity			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(3)	12		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00743)|GBM - Glioblastoma multiforme(134;0.0183)		CGAAAATCACTGATGCACCCT	0.507000													5	90					0	0	1	0	0
OR56A1	120796	broad.mit.edu	37	11	6048549	6048549	+	Missense_Mutation	SNP	C	C	T			TCGA-ET-A3BN-01A-11D-A19J-08	TCGA-ET-A3BN-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67c66136-9911-40da-a760-b6bc24de8e5e	d652b345-76f2-4f08-bc75-ced94e1c9491	g.chr11:6048549C>T	ENST00000316650.5	-	1	422	c.386G>A	c.(385-387)cGt>cAt	p.R129H		NM_001001917.2	NP_001001917.2	Q8NGH5	O56A1_HUMAN	olfactory receptor, family 56, subfamily A, member 1	129					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(22)|ovary(2)	33		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGCCACATAACGGTCATAGGC	0.507000													28	40					0	0	1	0	0
GALNT14	79623	broad.mit.edu	37	2	31147110	31147110	+	Missense_Mutation	SNP	T	T	A			TCGA-ET-A3BN-01A-11D-A19J-08	TCGA-ET-A3BN-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67c66136-9911-40da-a760-b6bc24de8e5e	d652b345-76f2-4f08-bc75-ced94e1c9491	g.chr2:31147110T>A	ENST00000349752.5	-	13	1894	c.1255A>T	c.(1255-1257)Atc>Ttc	p.I419F	GALNT14_ENST00000324589.5_Missense_Mutation_p.I424F|GALNT14_ENST00000406653.1_Missense_Mutation_p.I399F|GALNT14_ENST00000486564.1_Intron|GALNT14_ENST00000356174.3_Missense_Mutation_p.I386F|GALNT14_ENST00000420311.2_Missense_Mutation_p.I384F	NM_024572.3	NP_078848.2	Q96FL9	GLT14_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 14 (GalNAc-T14)	419	Ricin B-type lectin.					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			cervix(1)|endometrium(3)|large_intestine(10)|liver(1)|lung(21)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)	43	Acute lymphoblastic leukemia(172;0.155)					CCCTTCTGGATGGAGGACTCC	0.537000													28	79					0	0	1	0	0
PITPNM2	57605	broad.mit.edu	37	12	123472877	123472877	+	Silent	SNP	G	G	A			TCGA-ET-A3BN-01A-11D-A19J-08	TCGA-ET-A3BN-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67c66136-9911-40da-a760-b6bc24de8e5e	d652b345-76f2-4f08-bc75-ced94e1c9491	g.chr12:123472877G>A	ENST00000280562.5	-	19	3088	c.2883C>T	c.(2881-2883)tcC>tcT	p.S961S	PITPNM2_ENST00000320201.4_Silent_p.S967S|PITPNM2_ENST00000392428.1_Silent_p.S688S|PITPNM2_ENST00000542749.1_Silent_p.S967S			Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein, membrane-associated 2	0	DDHD.				metabolic process|transport	endomembrane system|integral to membrane|intracellular membrane-bounded organelle	calcium ion binding|lipid binding			NS(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	39	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		CCAAGATGCTGGAGTTGTCAT	0.632000													10	146					0	0	1	0	0
ABHD8	79575	broad.mit.edu	37	19	17405126	17405126	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A3BN-01A-11D-A19J-08	TCGA-ET-A3BN-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67c66136-9911-40da-a760-b6bc24de8e5e	d652b345-76f2-4f08-bc75-ced94e1c9491	g.chr19:17405126G>A	ENST00000247706.3	-	4	1359	c.1120C>T	c.(1120-1122)Ccg>Tcg	p.P374S	MRPL34_ENST00000600434.1_Intron|MRPL34_ENST00000595444.1_Intron	NM_024527.4	NP_078803.4	Q96I13	ABHD8_HUMAN	abhydrolase domain containing 8	374							hydrolase activity			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)|urinary_tract(1)	9						TCCTCCACCGGCACAAACTTA	0.672000													3	35					0	0	1	0	0
PIR	8544	broad.mit.edu	37	X	15509287	15509287	+	Missense_Mutation	SNP	C	C	T			TCGA-ET-A3BN-01A-11D-A19J-08	TCGA-ET-A3BN-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67c66136-9911-40da-a760-b6bc24de8e5e	d652b345-76f2-4f08-bc75-ced94e1c9491	g.chrX:15509287C>T	ENST00000380421.3	-	2	554	c.94G>A	c.(94-96)Gag>Aag	p.E32K	BMX_ENST00000357607.2_Intron|PIR_ENST00000476381.1_5'UTR|PIR_ENST00000380420.5_Missense_Mutation_p.E32K	NM_001018109.2|NM_003662.3	NP_001018119.1|NP_003653.1	O00625	PIR_HUMAN	pirin (iron-binding nuclear protein)	32					transcription from RNA polymerase II promoter	cytoplasm|nucleus	metal ion binding|protein binding|quercetin 2,3-dioxygenase activity|transcription cofactor activity			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9	Hepatocellular(33;0.183)					TAGCATACCTCGGGTCTGCCA	0.552000													11	136					0	0	1	0	0
NFATC4	4776	broad.mit.edu	37	14	24839190	24839190	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A3BN-01A-11D-A19J-08	TCGA-ET-A3BN-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67c66136-9911-40da-a760-b6bc24de8e5e	d652b345-76f2-4f08-bc75-ced94e1c9491	g.chr14:24839190G>A	ENST00000413692.2	+	3	919	c.775G>A	c.(775-777)Gac>Aac	p.D259N	NFATC4_ENST00000440487.2_3'UTR|NFATC4_ENST00000556279.1_Missense_Mutation_p.D228N|NFATC4_ENST00000556169.1_Missense_Mutation_p.D184N|NFATC4_ENST00000539237.2_Missense_Mutation_p.D228N|NFATC4_ENST00000553708.1_Missense_Mutation_p.D196N|NFATC4_ENST00000554344.1_Missense_Mutation_p.D126N|NFATC4_ENST00000555590.1_Missense_Mutation_p.D209N|NFATC4_ENST00000553879.1_Missense_Mutation_p.D126N|NFATC4_ENST00000422617.3_Missense_Mutation_p.D184N|NFATC4_ENST00000250373.4_Missense_Mutation_p.D196N|NFATC4_ENST00000555453.1_Missense_Mutation_p.D184N|NFATC4_ENST00000554966.1_Missense_Mutation_p.D209N|NFATC4_ENST00000424781.2_Missense_Mutation_p.D209N|NFATC4_ENST00000557451.1_Missense_Mutation_p.D126N|NFATC4_ENST00000554661.1_Missense_Mutation_p.D126N|NFATC4_ENST00000553469.1_Missense_Mutation_p.D228N|NFATC4_ENST00000554050.1_Missense_Mutation_p.D196N|NFATC4_ENST00000554591.1_Missense_Mutation_p.D259N	NM_001136022.1|NM_001198967.1	NP_001129494.1|NP_001185896.1	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4	196	2 approximate SP repeats.|Pro-rich.				cell differentiation|inflammatory response|transcription from RNA polymerase II promoter	cytoplasm|intermediate filament cytoskeleton|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(7)|liver(4)|lung(12)|ovary(1)|skin(2)	34				GBM - Glioblastoma multiforme(265;0.018)		TGCAGCCTGCGACGAGGTGGA	0.682000													3	32					0	0	1	0	0
BRCA1	672	broad.mit.edu	37	17	41246314	41246314	+	Missense_Mutation	SNP	C	C	T			TCGA-ET-A3BN-01A-11D-A19J-08	TCGA-ET-A3BN-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67c66136-9911-40da-a760-b6bc24de8e5e	d652b345-76f2-4f08-bc75-ced94e1c9491	g.chr17:41246314C>T	ENST00000309486.4	-	9	1373	c.346G>A	c.(346-348)Gta>Ata	p.V116I	BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000354071.3_Missense_Mutation_p.V412I|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000471181.2_Missense_Mutation_p.V412I|BRCA1_ENST00000357654.3_Missense_Mutation_p.V412I|BRCA1_ENST00000493795.1_Missense_Mutation_p.V365I|BRCA1_ENST00000346315.3_Missense_Mutation_p.V412I	NM_007297.3	NP_009228.2	P38398	BRCA1_HUMAN	breast cancer 1, early onset	412					androgen receptor signaling pathway|apoptosis|cellular response to indole-3-methanol|chromosome segregation|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|DNA damage response, signal transduction resulting in induction of apoptosis|double-strand break repair via homologous recombination|fatty acid biosynthetic process|G2/M transition DNA damage checkpoint|negative regulation of centriole replication|negative regulation of fatty acid biosynthetic process|negative regulation of histone H3-K9 methylation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle arrest|positive regulation of DNA repair|positive regulation of histone acetylation|positive regulation of histone H3-K4 methylation|positive regulation of histone H4-K20 methylation|positive regulation of protein ubiquitination|positive regulation of transcription from RNA polymerase II promoter|postreplication repair|protein autoubiquitination|protein K6-linked ubiquitination|regulation of cell motility|regulation of cell proliferation|regulation of transcription from RNA polymerase III promoter|response to estrogen stimulus|response to ionizing radiation|substrate adhesion-dependent cell spreading	BRCA1-A complex|BRCA1-BARD1 complex|gamma-tubulin ring complex|nucleoplasm|plasma membrane|ribonucleoprotein complex|ruffle	androgen receptor binding|identical protein binding|protein binding|RNA binding|transcription coactivator activity|transcription regulatory region DNA binding|tubulin binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding	p.V412L(1)		NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		ACGTCCAATACATCAGCTACT	0.383000			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)			9	114					0	0	1	0	0
USP49	25862	broad.mit.edu	37	6	41773536	41773536	+	Missense_Mutation	SNP	C	C	T			TCGA-ET-A3BN-01A-11D-A19J-08	TCGA-ET-A3BN-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67c66136-9911-40da-a760-b6bc24de8e5e	d652b345-76f2-4f08-bc75-ced94e1c9491	g.chr6:41773536C>T	ENST00000394253.3	-	3	1515	c.1186G>A	c.(1186-1188)Gac>Aac	p.D396N	USP49_ENST00000373006.1_Missense_Mutation_p.D396N|USP49_ENST00000373010.1_Missense_Mutation_p.D396N|USP49_ENST00000297229.2_Missense_Mutation_p.D396N|USP49_ENST00000373009.3_Missense_Mutation_p.D396N			Q70CQ1	UBP49_HUMAN	ubiquitin specific peptidase 49	396					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity|zinc ion binding			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(2)|skin(2)	23	Ovarian(28;0.0919)|Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000309)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TCCTGTTGGTCGTAGCCGCGG	0.622000													6	36					0	0	1	0	0
SF3A3	10946	broad.mit.edu	37	1	38444416	38444416	+	Frame_Shift_Del	DEL	T	T	-			TCGA-ET-A3BN-01A-11D-A19J-08	TCGA-ET-A3BN-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67c66136-9911-40da-a760-b6bc24de8e5e	d652b345-76f2-4f08-bc75-ced94e1c9491	g.chr1:38444416delT	ENST00000373019.4	-	11	1866	c.911delA	c.(910-912)atfs	p.N304fs	SF3A3_ENST00000448721.2_Frame_Shift_Del_p.N251fs|SF3A3_ENST00000489537.1_5'UTR	NM_006802.2	NP_006793.1	Q12874	SF3A3_HUMAN	splicing factor 3a, subunit 3, 60kDa	304					nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|nuclear speck	nucleic acid binding|protein binding|zinc ion binding			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|prostate(2)	12	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				TGACTTGGGATTTTTGGCAAA	0.488													2	4	---	---	---	---					
ATP6V1B2	526	broad.mit.edu	37	8	20077879	20077880	+	In_Frame_Ins	INS	-	-	CGAATTTTA			TCGA-ET-A3BN-01A-11D-A19J-08	TCGA-ET-A3BN-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67c66136-9911-40da-a760-b6bc24de8e5e	d652b345-76f2-4f08-bc75-ced94e1c9491	g.chr8:20077879_20077880insCGAATTTTA	ENST00000276390.2	+	14	1542_1543	c.1502_1503insCGAATTTTA	c.(1501-1503)aga>aCGAATTTTAga	p.500_501insTNF		NM_001693.3	NP_001684.2	P21281	VATB2_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B2	500					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|endomembrane system|Golgi apparatus|melanosome|plasma membrane|proton-transporting V-type ATPase, V1 domain	ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism			endometrium(1)|kidney(2)|lung(5)|prostate(1)	9				Colorectal(74;0.0535)|COAD - Colon adenocarcinoma(73;0.211)		AGCACCCTCAGCGAATTTTACC	0.465													11	90	---	---	---	---					
