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
MECP2	4204	broad.mit.edu	37	X	153296900	153296900	+	Splice_Site	SNP	G	G	A	rs61748382		TCGA-FY-A2QD-01A-11D-A19J-08	TCGA-FY-A2QD-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e7335a24-e5fc-4558-9eba-511c5a802320	7aeb39cd-79b5-4b8b-b801-9ea170d402c5	g.chrX:153296900G>A	ENST00000303391.6	-	4	628	c.377_splice	c.e4-1	p.P127_splice	MECP2_ENST00000453960.2_Splice_Site_p.P139_splice|MECP2_ENST00000407218.1_Splice_Site_p.P127_splice	NM_004992.3	NP_004983.1	P51608	MECP2_HUMAN	methyl CpG binding protein 2 (Rett syndrome)	127	MBD.				negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	heterochromatin|nucleus	double-stranded methylated DNA binding|protein domain specific binding|protein N-terminus binding|transcription corepressor activity			breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(8)|prostate(2)|urinary_tract(1)	23	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TTTCCCTGGGGACTGTGGGGA	0.488000													8	73					0	0	0.038147	0	0
SLC23A2	9962	broad.mit.edu	37	20	4839991	4839991	+	Missense_Mutation	SNP	G	G	T			TCGA-FY-A2QD-01A-11D-A19J-08	TCGA-FY-A2QD-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e7335a24-e5fc-4558-9eba-511c5a802320	7aeb39cd-79b5-4b8b-b801-9ea170d402c5	g.chr20:4839991G>T	ENST00000379333.1	-	16	2056	c.1664C>A	c.(1663-1665)aCa>aAa	p.T555K	SLC23A2_ENST00000424750.2_Missense_Mutation_p.T441K|SLC23A2_ENST00000338244.1_Missense_Mutation_p.T555K	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	555					L-ascorbic acid metabolic process|molecular hydrogen transport|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|transepithelial L-ascorbic acid transport	apical plasma membrane|integral to plasma membrane|membrane fraction	nucleobase transmembrane transporter activity|sodium-dependent L-ascorbate transmembrane transporter activity|sodium-dependent multivitamin transmembrane transporter activity			endometrium(1)|kidney(3)|large_intestine(9)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						CATAGCAGTTGTGAGAAGGAC	0.433000													36	85					1.57019e-19	4.31803e-19	0.098360	1	0
PLEKHA7	144100	broad.mit.edu	37	11	16810715	16810715	+	Silent	SNP	C	C	T			TCGA-FY-A2QD-01A-11D-A19J-08	TCGA-FY-A2QD-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e7335a24-e5fc-4558-9eba-511c5a802320	7aeb39cd-79b5-4b8b-b801-9ea170d402c5	g.chr11:16810715C>T	ENST00000355661.3	-	23	3295	c.3285G>A	c.(3283-3285)ctG>ctA	p.L1095L	PLEKHA7_ENST00000532079.1_3'UTR|PLEKHA7_ENST00000448080.2_Silent_p.L1096L|PLEKHA7_ENST00000531066.1_Silent_p.L1095L|PLEKHA7_ENST00000332954.4_5'UTR			Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A member 7	1095					epithelial cell-cell adhesion|zonula adherens maintenance	centrosome|zonula adherens	delta-catenin binding			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	37						CCCCTTGGCCCAGTGTCCTCT	0.647000													3	47					0	0	0.115264	0	0
ESX1	80712	broad.mit.edu	37	X	103498972	103498972	+	Silent	SNP	C	C	T			TCGA-FY-A2QD-01A-11D-A19J-08	TCGA-FY-A2QD-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e7335a24-e5fc-4558-9eba-511c5a802320	7aeb39cd-79b5-4b8b-b801-9ea170d402c5	g.chrX:103498972C>T	ENST00000372588.4	-	2	452	c.369G>A	c.(367-369)ccG>ccA	p.P123P		NM_153448.3	NP_703149.1	Q8N693	ESX1_HUMAN	ESX homeobox 1	123					negative regulation of transcription, DNA-dependent|regulation of cell cycle	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			endometrium(2)|large_intestine(10)|lung(12)|ovary(1)|skin(2)	27						GCCCCTCCGCCGGCTGTGGCC	0.682000													8	50					0	0	0.038147	0	0
CCDC88B	283234	broad.mit.edu	37	11	64124622	64124622	+	Missense_Mutation	SNP	G	G	A	rs61886888	by1000genomes	TCGA-FY-A2QD-01A-11D-A19J-08	TCGA-FY-A2QD-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e7335a24-e5fc-4558-9eba-511c5a802320	7aeb39cd-79b5-4b8b-b801-9ea170d402c5	g.chr11:64124622G>A	ENST00000359902.2	+	14	1951	c.1801G>A	c.(1801-1803)Gga>Aga	p.G601R	CCDC88B_ENST00000356786.5_3'UTR|CCDC88B_ENST00000301897.4_3'UTR|CCDC88B_ENST00000463837.1_3'UTR			A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	1424					microtubule cytoskeleton organization	cytoplasm	microtubule binding			endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GAGTGTCAGCGGAGGCCCCAG	0.667000													3	10					0	0	0.115264	0	0
HPS1	3257	broad.mit.edu	37	10	100189586	100189586	+	Missense_Mutation	SNP	G	G	A			TCGA-FY-A2QD-01A-11D-A19J-08	TCGA-FY-A2QD-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e7335a24-e5fc-4558-9eba-511c5a802320	7aeb39cd-79b5-4b8b-b801-9ea170d402c5	g.chr10:100189586G>A	ENST00000325103.6	-	9	1062	c.829C>T	c.(829-831)Cac>Tac	p.H277Y	HPS1_ENST00000338546.5_Missense_Mutation_p.H277Y|HPS1_ENST00000467246.1_Intron|HPS1_ENST00000361490.4_Missense_Mutation_p.H277Y	NM_000195.3	NP_000186.2	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1	277					lysosome organization|response to stimulus|visual perception	cytoplasmic membrane-bounded vesicle|integral to plasma membrane|lysosome|membrane fraction|soluble fraction	protein dimerization activity			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)		CCCGTGGAGTGAGGGCTCCAG	0.677000									Hermansky-Pudlak syndrome				7	90					0	0	0.047766	0	0
DLGAP2	9228	broad.mit.edu	37	8	1649537	1649537	+	Missense_Mutation	SNP	G	G	A			TCGA-FY-A2QD-01A-11D-A19J-08	TCGA-FY-A2QD-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e7335a24-e5fc-4558-9eba-511c5a802320	7aeb39cd-79b5-4b8b-b801-9ea170d402c5	g.chr8:1649537G>A	ENST00000421627.2	+	12	3027	c.2893G>A	c.(2893-2895)Gag>Aag	p.E965K		NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	1044					neuron-neuron synaptic transmission	cell junction|neurofilament|postsynaptic density|postsynaptic membrane	protein binding	p.E973K(1)		breast(1)|endometrium(6)|lung(31)|prostate(3)	41		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		GGACAGCATCGAGATCTACAT	0.716000													4	4					0	0	0.014758	0	0
STK38	11329	broad.mit.edu	37	6	36475299	36475299	+	Silent	SNP	G	G	A			TCGA-FY-A2QD-01A-11D-A19J-08	TCGA-FY-A2QD-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e7335a24-e5fc-4558-9eba-511c5a802320	7aeb39cd-79b5-4b8b-b801-9ea170d402c5	g.chr6:36475299G>A	ENST00000229812.7	-	8	1035	c.750C>T	c.(748-750)aaC>aaT	p.N250N		NM_007271.2	NP_009202.1	Q15208	STK38_HUMAN	serine/threonine kinase 38	250	Protein kinase.				intracellular protein kinase cascade|negative regulation of MAP kinase activity	cytoplasm|MLL5-L complex	ATP binding|magnesium ion binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine kinase activity			NS(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GGAGGCTGTGGTTCAGATTCC	0.418000													114	171					0	0	0.139131	0	0
RP11-50E11.3	0	broad.mit.edu	37	10	52390506	52390506	+	RNA	SNP	A	A	T	rs11006369	by1000genomes	TCGA-FY-A2QD-01A-11D-A19J-08	TCGA-FY-A2QD-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e7335a24-e5fc-4558-9eba-511c5a802320	7aeb39cd-79b5-4b8b-b801-9ea170d402c5	g.chr10:52390506A>T	ENST00000443374.1	+	0	1199																											CCTTAATAACATCACTCAATT	0.438000													3	34					0	0	0.115264	0	0
SLCO1B3	28234	broad.mit.edu	37	12	21028307	21028307	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FY-A2QD-01A-11D-A19J-08	TCGA-FY-A2QD-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e7335a24-e5fc-4558-9eba-511c5a802320	7aeb39cd-79b5-4b8b-b801-9ea170d402c5	g.chr12:21028307delA	ENST00000381545.3	+	9	1085	c.866delA	c.(865-867)gafs	p.E289fs	LST3_ENST00000540229.1_Frame_Shift_Del_p.E289fs|SLCO1B3_ENST00000553473.1_Frame_Shift_Del_p.E289fs|SLCO1B3_ENST00000261196.2_Frame_Shift_Del_p.E289fs|SLCO1B7_ENST00000554957.1_Intron|LST3_ENST00000381541.3_Intron	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	289					bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)					CCACAAAAAGAAAGAAAAATT	0.333													19	46	---	---	---	---					
TRAV9-2	0	broad.mit.edu	37	14	22409537	22409537	+	RNA	DEL	C	C	-	rs57759840		TCGA-FY-A2QD-01A-11D-A19J-08	TCGA-FY-A2QD-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e7335a24-e5fc-4558-9eba-511c5a802320	7aeb39cd-79b5-4b8b-b801-9ea170d402c5	g.chr14:22409537delC	ENST00000390441.2	+	0	102																											ctctctctctctctTTTTTTT	0.418													2	4	---	---	---	---					
RP11-178C3.2	0	broad.mit.edu	37	17	58066608	58066608	+	RNA	DEL	T	T	-			TCGA-FY-A2QD-01A-11D-A19J-08	TCGA-FY-A2QD-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e7335a24-e5fc-4558-9eba-511c5a802320	7aeb39cd-79b5-4b8b-b801-9ea170d402c5	g.chr17:58066608delT	ENST00000586209.1	+	0	158																											TTGATTGTGATTTTTTTTTTT	0.313													4	5	---	---	---	---