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
ATP1A4	480	broad.mit.edu	37	1	160141222	160141222	+	Missense_Mutation	SNP	G	G	A			TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr1:160141222G>A	ENST00000368081.4	+	11	2144	c.1673G>A	c.(1672-1674)cGt>cAt	p.R558H	ATP1A4_ENST00000418334.1_3'UTR	NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	558					ATP biosynthetic process|ATP hydrolysis coupled proton transport|regulation of cellular pH|sperm motility	sodium:potassium-exchanging ATPase complex	ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity	p.R558H(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CTGGGGGAACGTGTGCTAGGT	0.443000													12	20					0	0	1	0	0
AVL9	23080	broad.mit.edu	37	7	32582854	32582854	+	Silent	SNP	C	C	T			TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr7:32582854C>T	ENST00000318709.4	+	2	416	c.195C>T	c.(193-195)ggC>ggT	p.G65G	AVL9_ENST00000404479.1_Silent_p.G65G|AVL9_ENST00000409301.1_Silent_p.G65G	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	65						integral to membrane		p.G65G(2)		endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TACCAGATGGCGCACACAACT	0.423000													5	82					0	0	1	0	0
AC226119.5	0	broad.mit.edu	37	4	3954857	3954857	+	RNA	SNP	C	C	A	rs17410899		TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr4:3954857C>A	ENST00000281228.8	-	0	141				FAM86EP_ENST00000313946.8_RNA																							AATATCCCGCCGCAGCTCAGA	0.488000													3	54					0.00024832	0.00024832	1	1	0
HDLBP	3069	broad.mit.edu	37	2	242187753	242187753	+	Missense_Mutation	SNP	C	C	G			TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr2:242187753C>G	ENST00000391975.1	-	13	1750	c.1523G>C	c.(1522-1524)cGt>cCt	p.R508P	HDLBP_ENST00000427183.2_Missense_Mutation_p.R475P|HDLBP_ENST00000391976.2_Missense_Mutation_p.R508P|HDLBP_ENST00000476807.1_5'UTR|HDLBP_ENST00000310931.4_Missense_Mutation_p.R508P	NM_203346.3	NP_976221.1	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	508	KH 5.				cholesterol metabolic process|lipid transport	cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane	lipid binding|protein binding|RNA binding	p.R508H(1)		breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		ATCCTTGGTACGCTCATTTTC	0.458000													15	29					0	0	1	0	0
FRG1B	0	broad.mit.edu	37	20	29628236	29628236	+	Missense_Mutation	SNP	G	G	C	rs145412486	by1000genomes	TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr20:29628236G>C	ENST00000278882.3	+	6	618	c.238G>C	c.(238-240)Gct>Cct	p.A80P	FRG1B_ENST00000358464.4_Missense_Mutation_p.A80P|FRG1B_ENST00000439954.2_Missense_Mutation_p.A85P														p.A80P(8)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GGGGAAAATGGCTTTGTTGGC	0.363000													3	84					0	0	1	0	0
SLC20A1	6574	broad.mit.edu	37	2	113405018	113405018	+	Missense_Mutation	SNP	A	A	G			TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr2:113405018A>G	ENST00000272542.3	+	3	991	c.452A>G	c.(451-453)aAg>aGg	p.K151R		NM_005415.4	NP_005406.3	Q8WUM9	S20A1_HUMAN	solute carrier family 20 (phosphate transporter), member 1	151					phosphate metabolic process|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to plasma membrane	inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|skin(1)|urinary_tract(3)	28						GAGGGTGTCAAGTGGTCTGAA	0.433000													52	79					0	0	1	0	0
MAP4	4134	broad.mit.edu	37	3	47958222	47958222	+	Silent	SNP	G	G	A			TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr3:47958222G>A	ENST00000426837.2	-	8	1233	c.1146C>T	c.(1144-1146)gcC>gcT	p.A382A	MAP4_ENST00000360240.6_Silent_p.A365A|MAP4_ENST00000383737.4_Intron|MAP4_ENST00000395734.3_Silent_p.A365A			P27816	MAP4_HUMAN	microtubule-associated protein 4	365	17 X 14 AA tandem repeats.				negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)		CCTTGGAAGGGGCTAAGTCCA	0.478000													4	85					0	0	1	0	0
TUBB8P7	0	broad.mit.edu	37	16	90161618	90161618	+	RNA	SNP	C	C	T	rs13338202	by1000genomes	TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr16:90161618C>T	ENST00000567960.1	+	0	354				TUBB8P7_ENST00000564451.1_RNA														p.D118D(2)									CAGTGATGGACGTTGTCAGAA	0.607000													5	27					0	0	1	0	0
MAP4	4134	broad.mit.edu	37	3	47958225	47958225	+	Silent	SNP	T	T	C			TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr3:47958225T>C	ENST00000426837.2	-	8	1230	c.1143A>G	c.(1141-1143)ttA>ttG	p.L381L	MAP4_ENST00000360240.6_Silent_p.L364L|MAP4_ENST00000383737.4_Intron|MAP4_ENST00000395734.3_Silent_p.L364L			P27816	MAP4_HUMAN	microtubule-associated protein 4	364	17 X 14 AA tandem repeats.				negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity	p.L364L(2)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)		TGGAAGGGGCTAAGTCCATTT	0.478000													4	88					0	0	1	0	0
RP11-417J8.6	0	broad.mit.edu	37	1	142713944	142713944	+	RNA	SNP	C	C	T			TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr1:142713944C>T	ENST00000369381.2	-	0	661																											TGATTACCTCCGAAGTTAAAG	0.308000													4	27					0	0	1	0	0
PRRC2B	84726	broad.mit.edu	37	9	134357838	134357838	+	Silent	SNP	G	G	A			TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr9:134357838G>A	ENST00000357304.4	+	20	5119	c.5064G>A	c.(5062-5064)caG>caA	p.Q1688Q	PRRC2B_ENST00000405995.1_Silent_p.Q994Q|PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Silent_p.Q994Q	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1688							protein binding			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						CCTCCTCGCAGCGCAGCTCCC	0.612000													9	87					0	0	1	0	0
NKX6-3	157848	broad.mit.edu	37	8	41504197	41504197	+	Frame_Shift_Del	DEL	C	C	-			TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr8:41504197delC	ENST00000524115.2	-	2	182	c.179delG	c.(178-180)ccfs	p.R61fs		NM_152568.2	NP_689781.1	A6NJ46	NKX63_HUMAN	NK6 homeobox 3	191						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			lung(1)	1	Ovarian(28;0.00541)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Esophageal squamous(32;0.0844)|Hepatocellular(245;0.154)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			CTTGGTCCTGCGGTTCTGGAA	0.677													2	4	---	---	---	---					
RP11-445N18.7	0	broad.mit.edu	37	10	45648292	45648292	+	RNA	DEL	G	G	-			TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr10:45648292delG	ENST00000427229.2	+	0	1681																											TCAGAGAAATGGAATGGTTGC	0.323													2	4	---	---	---	---					
TRAV9-2	0	broad.mit.edu	37	14	22409539	22409540	+	RNA	INS	-	-	T	rs2178778		TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chr14:22409539_22409540insT	ENST00000390441.2	+	0	102																											ctctctctctctTTTTTTTTTT	0.426													3	5	---	---	---	---					
STAG2	10735	broad.mit.edu	37	X	123171406	123171407	+	Frame_Shift_Ins	INS	-	-	A			TCGA-RT-A6Y9-01A-12D-A35D-08	TCGA-RT-A6Y9-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f381cc40-8e51-4922-ac81-66b18cc1cba5	94f22612-3815-4738-9c53-6503f1207146	g.chrX:123171406_123171407insA	ENST00000371160.1	+	6	608_609	c.318_319insA	c.(316-321)taagcafs	p.A107fs	STAG2_ENST00000354548.5_Frame_Shift_Ins_p.A38fs|STAG2_ENST00000371144.3_Frame_Shift_Ins_p.A107fs|STAG2_ENST00000371157.3_Frame_Shift_Ins_p.A107fs|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Frame_Shift_Ins_p.A107fs|STAG2_ENST00000371145.3_Frame_Shift_Ins_p.A107fs			Q8N3U4	STAG2_HUMAN	stromal antigen 2	107					cell division|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|negative regulation of DNA endoreduplication|sister chromatid cohesion	chromatin|chromosome, centromeric region|nucleoplasm	protein binding			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						TAGAATCATACAAGCATGACCG	0.327													47	62	---	---	---	---					
