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
CHERP	10523	broad.mit.edu	37	19	16640580	16640580	+	Silent	SNP	T	T	C			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr19:16640580T>C	ENST00000546361.2	-	8	1159	c.1008A>G	c.(1006-1008)caA>caG	p.Q336Q	CHERP_ENST00000198939.6_Silent_p.Q347Q|CTD-3222D19.2_ENST00000409035.1_Intron	NM_006387.5	NP_006378.3	Q8IWX8	CHERP_HUMAN	calcium homeostasis endoplasmic reticulum protein	336	Gln-rich.				cellular calcium ion homeostasis|negative regulation of cell proliferation|nervous system development|RNA processing	endoplasmic reticulum|perinuclear region of cytoplasm	RNA binding	p.Q336Q(2)		endometrium(3)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|stomach(1)|urinary_tract(3)	24						gctgctgctgttgctgctgct	0.667000													3	24					0	0	1	0	0
CHERP	10523	broad.mit.edu	37	19	16640583	16640583	+	Silent	SNP	C	C	T			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr19:16640583C>T	ENST00000546361.2	-	8	1156	c.1005G>A	c.(1003-1005)caG>caA	p.Q335Q	CHERP_ENST00000198939.6_Silent_p.Q346Q|CTD-3222D19.2_ENST00000409035.1_Intron	NM_006387.5	NP_006378.3	Q8IWX8	CHERP_HUMAN	calcium homeostasis endoplasmic reticulum protein	335	Gln-rich.				cellular calcium ion homeostasis|negative regulation of cell proliferation|nervous system development|RNA processing	endoplasmic reticulum|perinuclear region of cytoplasm	RNA binding			endometrium(3)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|stomach(1)|urinary_tract(3)	24						gctgctgttgctgctgctgct	0.667000													3	25					0	0	1	0	0
GGT3P	0	broad.mit.edu	37	22	18778612	18778612	+	RNA	SNP	C	C	T	rs1055042	by1000genomes	TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr22:18778612C>T	ENST00000412448.1	-	0	793																											GCGGCCACGGCAGCCCTGGTG	0.637000													4	11					0	0	1	0	0
TUBB8P7	0	broad.mit.edu	37	16	90162298	90162298	+	RNA	SNP	C	C	T			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr16:90162298C>T	ENST00000567960.1	+	0	1034				TUBB8P7_ENST00000564451.1_RNA																							TGCTGACTGGCTCCCCAACAA	0.502000													6	202					0	0	1	0	0
FRG1B	0	broad.mit.edu	37	20	29628251	29628251	+	Missense_Mutation	SNP	A	A	G			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr20:29628251A>G	ENST00000278882.3	+	6	633	c.253A>G	c.(253-255)Aat>Gat	p.N85D	FRG1B_ENST00000439954.2_Missense_Mutation_p.N90D|FRG1B_ENST00000358464.4_Missense_Mutation_p.N85D														p.N85D(2)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GTTGGCCTCAAATAGCTGCTT	0.358000													9	111					0	0	1	0	0
KRTAP4-6	81871	broad.mit.edu	37	17	39296167	39296167	+	Silent	SNP	A	A	G			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr17:39296167A>G	ENST00000345847.4	-	1	572	c.573T>C	c.(571-573)atT>atC	p.I191I		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	187						keratin filament				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						GGCAGGTGGAAATGACACAGG	0.627000													3	10					0	0	1	0	0
CCDC178	374864	broad.mit.edu	37	18	30795529	30795529	+	Missense_Mutation	SNP	G	G	A			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr18:30795529G>A	ENST00000383096.3	-	19	2245	c.2063C>T	c.(2062-2064)aCa>aTa	p.T688I	CCDC178_ENST00000402325.1_Missense_Mutation_p.T688I|CCDC178_ENST00000403303.1_Missense_Mutation_p.T688I|CCDC178_ENST00000583930.1_Missense_Mutation_p.T688I|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000406524.2_Missense_Mutation_p.T688I|CCDC178_ENST00000579947.1_Missense_Mutation_p.T688I|CCDC178_ENST00000300227.8_Missense_Mutation_p.T650I					coiled-coil domain containing 178																		TATTTCAAGTGTCTGATCAAA	0.209000													4	8					0	0	1	0	0
TSSC2	0	broad.mit.edu	37	11	3427845	3427845	+	RNA	SNP	C	C	T			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr11:3427845C>T	ENST00000529482.1	+	0	962																											CTTCAAGTGGCAGGAGCAGAA	0.587000													3	32					0	0	1	0	0
KCNJ4	3761	broad.mit.edu	37	22	38823832	38823832	+	Silent	SNP	A	A	C			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr22:38823832A>C	ENST00000303592.3	-	2	564	c.306T>G	c.(304-306)ggT>ggG	p.G102G		NM_004981.1|NM_152868.2	NP_004972.1|NP_690607.1	P48050	IRK4_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 4	102	Poly-Gly.|Val/Gly/Ala/Pro stretch.				synaptic transmission	basolateral plasma membrane|voltage-gated potassium channel complex	inward rectifier potassium channel activity|PDZ domain binding			endometrium(7)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23	Melanoma(58;0.0286)					CTCCGCCACCAcccgccgccg	0.687000													8	28					0	0	1	0	0
TUBB8P7	0	broad.mit.edu	37	16	90162304	90162304	+	RNA	SNP	A	A	G			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr16:90162304A>G	ENST00000567960.1	+	0	1040				TUBB8P7_ENST00000564451.1_RNA																							CTGGCTCCCCAACAACGTAAA	0.502000													4	199					0	0	1	0	0
RP11-423O2.5	0	broad.mit.edu	37	1	142803493	142803493	+	RNA	SNP	T	T	C	rs80149641	by1000genomes	TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr1:142803493T>C	ENST00000423385.1	-	0	1472																											TGTACATTTATTATTGATTTA	0.323000													8	61					0	0	1	0	0
TVP23C	201158	broad.mit.edu	37	17	15441469	15441469	+	Splice_Site	SNP	C	C	T	rs139351610	by1000genomes	TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr17:15441469C>T	ENST00000584811.1	-	7	1815		c.e7-2		TVP23C_ENST00000225576.3_Intron|TVP23C_ENST00000519970.1_Intron|TVP23C-CDRT4_ENST00000522212.2_Intron|TVP23C_ENST00000438826.3_Splice_Site|TVP23C_ENST00000428082.2_Splice_Site					trans-golgi network vesicle protein 23 homolog C (S. cerevisiae)																		TCCAGTGTTCCGCAAAAGACA	0.393000													4	59					0	0	1	0	0
SPEN	23013	broad.mit.edu	37	1	16255142	16255143	+	Frame_Shift_Del	DEL	GA	GA	-			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr1:16255142_16255143delGA	ENST00000375759.3	+	11	2611_2612	c.2407_2408delGA	c.(2407-2409)gfs	p.E803fs		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	803	Arg-rich.				interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		GGAGAGAGTGGAGAGAGAGAGA	0.431													7	116	---	---	---	---					
MBD4	8930	broad.mit.edu	37	3	129155548	129155548	+	Frame_Shift_Del	DEL	T	T	-			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr3:129155548delT	ENST00000429544.2	-	3	1134	c.939delA	c.(937-939)aafs	p.K313fs	MBD4_ENST00000503197.1_Frame_Shift_Del_p.K313fs|MBD4_ENST00000393278.2_Intron|MBD4_ENST00000249910.1_Frame_Shift_Del_p.K313fs|MBD4_ENST00000507208.1_Frame_Shift_Del_p.K313fs|MBD4_ENST00000509587.1_Intron	NM_001276270.1	NP_001263199.1	O95243	MBD4_HUMAN	methyl-CpG binding domain protein 4	313					depyrimidination	nucleoplasm	DNA N-glycosylase activity|endodeoxyribonuclease activity|protein binding|satellite DNA binding			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)	22						ATGATCTTTCTTTTTTTTTTA	0.373								Base excision repair (BER), DNA glycosylases					10	115	---	---	---	---					
LINC00937	0	broad.mit.edu	37	12	8519552	8519554	+	RNA	DEL	CCA	CCA	-	rs75567061		TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr12:8519552_8519554delCCA	ENST00000544461.1	-	0	1081				RP11-113C12.4_ENST00000537764.1_RNA																							TACCAGCTTCccaccaccaccac	0.473													8	39	---	---	---	---					
TPTE2P1	0	broad.mit.edu	37	13	25525716	25525716	+	RNA	DEL	A	A	-			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr13:25525716delA	ENST00000429698.1	-	0	282																											TGGAAGAAACAAAAAAAAGAA	0.383													5	1	---	---	---	---					
MAP3K9	4293	broad.mit.edu	37	14	71275774	71275776	+	In_Frame_Del	DEL	CCT	CCT	-	rs3832971		TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr14:71275774_71275776delCCT	ENST00000554752.2	-	1	112_114	c.113_115delAGG	c.(112-117)gcg>g	p.EA38del	MAP3K9_ENST00000381250.4_In_Frame_Del_p.EA38del|MAP3K9_ENST00000555993.2_In_Frame_Del_p.EA38del			P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	38	Ala-rich.|Poly-Glu.				activation of JUN kinase activity|protein autophosphorylation		ATP binding|JUN kinase kinase kinase activity|MAP kinase kinase activity|protein homodimerization activity	p.E38delE(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		GCCGCCGCCGcctcctcctcctc	0.773													2	4	---	---	---	---					
KRT10	3858	broad.mit.edu	37	17	38978766	38978768	+	In_Frame_Del	DEL	TCC	TCC	-			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr17:38978766_38978768delTCC	ENST00000269576.5	-	1	79_81	c.70_72delGGA	c.(70-72)del	p.G24del	TMEM99_ENST00000496847.1_Intron|TMEM99_ENST00000301665.3_Intron	NM_000421.3	NP_000412.3	P13645	K1C10_HUMAN	keratin 10	24	Gly-rich.|Head.			Missing (in Ref. 1; AAA60544).	epidermis development		protein binding|structural constituent of epidermis			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				ctcctccacatcctcctcctcct	0.547													7	25	---	---	---	---					
BAGE2	85319	broad.mit.edu	37	21	11085835	11085837	+	RNA	DEL	CAT	CAT	-	rs151194290	by1000genomes	TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr21:11085835_11085837delCAT	ENST00000470054.1	-	0	324									B melanoma antigen family, member 2															Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ccaccatcaccatcaccaccacc	0.586													2	4	---	---	---	---					
BAGE2	85319	broad.mit.edu	37	21	11085940	11085942	+	RNA	DEL	CAC	CAC	-			TCGA-XK-AAJU-01A-11D-A41K-08	TCGA-XK-AAJU-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3e27c976-6830-4deb-9456-5e3615bf7cb0	ccf76f57-aae5-4baf-a1cc-56a0a59c143b	g.chr21:11085940_11085942delCAC	ENST00000470054.1	-	0	324									B melanoma antigen family, member 2															Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ccaccaccatcaccaccaccacc	0.532													2	4	---	---	---	---					
