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
MYT1	4661	broad.mit.edu	37	20	62854521	62854521	+	Silent	SNP	C	C	T			TCGA-RT-A6YC-01A-12D-A35D-08	TCGA-RT-A6YC-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	583d10a7-9d12-45d1-861b-5c2231935b2e	7a23bba7-57b3-4705-aeb3-f0fbdd7b3f19	g.chr20:62854521C>T	ENST00000536311.1	+	15	2899	c.2535C>T	c.(2533-2535)caC>caT	p.H845H	MYT1_ENST00000360149.4_Silent_p.H520H|MYT1_ENST00000328439.1_Silent_p.H818H			Q01538	MYT1_HUMAN	myelin transcription factor 1	818					cell differentiation|nervous system development	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					ACGCCTCCCACCGCAGGTTTG	0.612000													4	122					0	0	1	0	0
NFYB	4801	broad.mit.edu	37	12	104517193	104517193	+	Silent	SNP	T	T	C			TCGA-RT-A6YC-01A-12D-A35D-08	TCGA-RT-A6YC-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	583d10a7-9d12-45d1-861b-5c2231935b2e	7a23bba7-57b3-4705-aeb3-f0fbdd7b3f19	g.chr12:104517193T>C	ENST00000240055.3	-	5	467	c.240A>G	c.(238-240)aaA>aaG	p.K80K	NFYB_ENST00000551727.1_Silent_p.K80K	NM_006166.3	NP_006157.1	P25208	NFYB_HUMAN	nuclear transcription factor Y, beta	80	B domain.					CCAAT-binding factor complex	repressing transcription factor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|lung(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	6						CTTTGGCATCTTTTGCAATCT	0.348000													3	27					0	0	1	0	0
RP11-435B5.4	0	broad.mit.edu	37	1	143403563	143403563	+	RNA	SNP	C	C	A			TCGA-RT-A6YC-01A-12D-A35D-08	TCGA-RT-A6YC-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	583d10a7-9d12-45d1-861b-5c2231935b2e	7a23bba7-57b3-4705-aeb3-f0fbdd7b3f19	g.chr1:143403563C>A	ENST00000423249.1	-	0	59																											TTTCTTTGGCCACTTTGGCTG	0.453000													3	9					0.00909568	0.00909568	1	1	0
KRTAP4-9	100132386	broad.mit.edu	37	17	39261693	39261693	+	Missense_Mutation	SNP	A	A	T	rs113059833	by1000genomes	TCGA-RT-A6YC-01A-12D-A35D-08	TCGA-RT-A6YC-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	583d10a7-9d12-45d1-861b-5c2231935b2e	7a23bba7-57b3-4705-aeb3-f0fbdd7b3f19	g.chr17:39261693A>T	ENST00000391415.1	+	1	110	c.53A>T	c.(52-54)gAc>gTc	p.D18V		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	18						keratin filament		p.D18V(1)		central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						TGCGGCCAAGACCTCTGTCAG	0.627000													6	17					0	0	1	0	0
EVPL	2125	broad.mit.edu	37	17	74005061	74005061	+	Missense_Mutation	SNP	C	C	T			TCGA-RT-A6YC-01A-12D-A35D-08	TCGA-RT-A6YC-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	583d10a7-9d12-45d1-861b-5c2231935b2e	7a23bba7-57b3-4705-aeb3-f0fbdd7b3f19	g.chr17:74005061C>T	ENST00000301607.3	-	22	4478	c.4225G>A	c.(4225-4227)Gtg>Atg	p.V1409M	EVPL_ENST00000586740.1_Missense_Mutation_p.V1431M	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1409	Central fibrous rod domain.				keratinization|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural molecule activity			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						AGCTGCTGCACCTCAAGCTCT	0.701000													18	36					0	0	1	0	0
SACM1L	22908	broad.mit.edu	37	3	45748365	45748365	+	Missense_Mutation	SNP	A	A	G			TCGA-RT-A6YC-01A-12D-A35D-08	TCGA-RT-A6YC-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	583d10a7-9d12-45d1-861b-5c2231935b2e	7a23bba7-57b3-4705-aeb3-f0fbdd7b3f19	g.chr3:45748365A>G	ENST00000389061.5	+	4	503	c.299A>G	c.(298-300)tAt>tGt	p.Y100C	SACM1L_ENST00000541314.1_Intron|SACM1L_ENST00000418611.1_5'UTR|SACM1L_ENST00000464524.1_3'UTR	NM_014016.3	NP_054735.3	Q9NTJ5	SAC1_HUMAN	SAC1 suppressor of actin mutations 1-like (yeast)	100						Golgi apparatus				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)		GTCCTTTCTTATAAGAAGACA	0.373000													24	40					0	0	1	0	0
GYPE	2996	broad.mit.edu	37	4	144826671	144826671	+	Translation_Start_Site	SNP	C	C	T			TCGA-RT-A6YC-01A-12D-A35D-08	TCGA-RT-A6YC-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	583d10a7-9d12-45d1-861b-5c2231935b2e	7a23bba7-57b3-4705-aeb3-f0fbdd7b3f19	g.chr4:144826671C>T	ENST00000358615.4	-	0	41				GYPE_ENST00000437468.2_De_novo_Start_OutOfFrame	NM_198682.2	NP_941391.2	P15421	GLPE_HUMAN	glycophorin E (MNS blood group)							integral to plasma membrane				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5	all_hematologic(180;0.158)					CCTGAGATCACGAGCTGGCTC	0.398000													5	53					0	0	1	0	0
MIR548A1	0	broad.mit.edu	37	6	18572094	18572094	+	RNA	SNP	T	T	A			TCGA-RT-A6YC-01A-12D-A35D-08	TCGA-RT-A6YC-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	583d10a7-9d12-45d1-861b-5c2231935b2e	7a23bba7-57b3-4705-aeb3-f0fbdd7b3f19	g.chr6:18572094T>A	ENST00000385041.1	+	0	80					NR_030312.1																						caattacttttgcaccaaACC	0.353000													9	23					0	0	1	0	0
OR7G3	390883	broad.mit.edu	37	19	9237506	9237506	+	Missense_Mutation	SNP	C	C	T			TCGA-RT-A6YC-01A-12D-A35D-08	TCGA-RT-A6YC-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	583d10a7-9d12-45d1-861b-5c2231935b2e	7a23bba7-57b3-4705-aeb3-f0fbdd7b3f19	g.chr19:9237506C>T	ENST00000305444.2	-	1	120	c.121G>A	c.(121-123)Ggg>Agg	p.G41R		NM_001001958.1	NP_001001958.1	Q8NG95	OR7G3_HUMAN	olfactory receptor, family 7, subfamily G, member 3	41					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			NS(2)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						AGCAGGTTCCCCAGCATTGTG	0.542000													3	52					0	0	1	0	0
AHR	196	broad.mit.edu	37	7	17382667	17382667	+	Silent	SNP	G	G	A			TCGA-RT-A6YC-01A-12D-A35D-08	TCGA-RT-A6YC-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	583d10a7-9d12-45d1-861b-5c2231935b2e	7a23bba7-57b3-4705-aeb3-f0fbdd7b3f19	g.chr7:17382667G>A	ENST00000242057.4	+	11	3169	c.2526G>A	c.(2524-2526)ttG>ttA	p.L842L		NM_001621.4	NP_001612.1	P35869	AHR_HUMAN	aryl hydrocarbon receptor	842				LNETYPAELNNINNTQTTTHLQPLHHPSEARPFPDLTSSGF L -> FK (in Ref. 1; BAA03857).	apoptosis|blood vessel development|cell cycle|regulation of B cell proliferation|response to stress|transcription from RNA polymerase II promoter|xenobiotic metabolic process	cytosolic aryl hydrocarbon receptor complex|transcription factor complex	Hsp90 protein binding|ligand-dependent nuclear receptor activity|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|urinary_tract(3)	33	Lung NSC(10;0.0392)|all_lung(11;0.0754)					TTCCTGATTTGACATCCAGTG	0.368000													7	280					0	0	1	0	0
HIST1H2AA	221613	broad.mit.edu	37	6	25726526	25726527	+	Frame_Shift_Ins	INS	-	-	T			TCGA-RT-A6YC-01A-12D-A35D-08	TCGA-RT-A6YC-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	583d10a7-9d12-45d1-861b-5c2231935b2e	7a23bba7-57b3-4705-aeb3-f0fbdd7b3f19	g.chr6:25726526_25726527insT	ENST00000297012.3	-	1	263_264	c.229_230insA	c.(229-231)tcgfs	p.S77fs		NM_170745.3	NP_734466.1	Q96QV6	H2A1A_HUMAN	histone cluster 1, H2aa	77					nucleosome assembly	nucleosome|nucleus	DNA binding			breast(1)|endometrium(2)|large_intestine(2)|lung(8)	13						AATAATGCGAGTTTTTTTGTTA	0.545													31	73	---	---	---	---					
RP11-178C3.2	0	broad.mit.edu	37	17	58050841	58050841	+	RNA	DEL	T	T	-	rs74362551		TCGA-RT-A6YC-01A-12D-A35D-08	TCGA-RT-A6YC-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	583d10a7-9d12-45d1-861b-5c2231935b2e	7a23bba7-57b3-4705-aeb3-f0fbdd7b3f19	g.chr17:58050841delT	ENST00000586209.1	+	0	158																											acagggtttcTTTTTTTTTTT	0.413													3	4	---	---	---	---					
AC008103.5	0	broad.mit.edu	37	22	18842473	18842473	+	RNA	DEL	G	G	-	rs66618606		TCGA-RT-A6YC-01A-12D-A35D-08	TCGA-RT-A6YC-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	583d10a7-9d12-45d1-861b-5c2231935b2e	7a23bba7-57b3-4705-aeb3-f0fbdd7b3f19	g.chr22:18842473delG	ENST00000412938.1	+	0	2208																											AGCTGCTGGTGGGGAGGTCTT	0.647													5	5	---	---	---	---					
