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
ZNF335	63925	broad.mit.edu	37	20	44578157	44578157	+	Silent	SNP	T	T	C			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr20:44578157T>C	ENST00000322927.2	-	25	3820	c.3720A>G	c.(3718-3720)gaA>gaG	p.E1240E	ZNF335_ENST00000426788.1_Silent_p.E1085E	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	1240	Gln-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				CCACAACATATTCCTGGGGGA	0.612000													4	21					0	0	1	0	0
MT-ND1	4535	broad.mit.edu	37	MT	3664	3664	+	Missense_Mutation	SNP	G	G	A			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chrM:3664G>A	ENST00000361390.2	+	1	358	c.358G>A	c.(358-360)Ggg>Agg	p.120_120insR						mitochondrially encoded NADH dehydrogenase 1											breast(1)|endometrium(13)|kidney(17)|lung(2)|prostate(1)	34						TCCTCTGATCAGGGTGAGCAT	0.512000													16	2					0	0	1	0	0
FAM101A	144347	broad.mit.edu	37	12	124798816	124798816	+	Silent	SNP	G	G	A	rs77570261	by1000genomes	TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr12:124798816G>A	ENST00000389727.3	+	3	396	c.396G>A	c.(394-396)acG>acA	p.T132T	FAM101A_ENST00000546355.1_Silent_p.T51T|FAM101A_ENST00000324038.3_Silent_p.T51T|FAM101A_ENST00000338359.4_Silent_p.T51T			Q6ZTI6	F101A_HUMAN	family with sequence similarity 101, member A	132										endometrium(1)|kidney(1)|lung(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;2.38e-05)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-05)|all cancers(50;0.000361)|BRCA - Breast invasive adenocarcinoma(302;0.059)		CCACCGTCACGGCCTACAGCG	0.642000													17	147					0	0	1	0	0
FLG	2312	broad.mit.edu	37	1	152286555	152286555	+	Silent	SNP	A	A	C			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr1:152286555A>C	ENST00000368799.1	-	3	842	c.807T>G	c.(805-807)tcT>tcG	p.S269S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	269	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTTCACTTGAGATGATGATT	0.423000									Ichthyosis				10	125					0	0	1	0	0
RBP3	5949	broad.mit.edu	37	10	48390034	48390034	+	Missense_Mutation	SNP	C	C	T			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr10:48390034C>T	ENST00000224600.4	-	1	957	c.844G>A	c.(844-846)Gtg>Atg	p.V282M		NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	282	4 X approximate tandem repeats.				lipid metabolic process|proteolysis|transport|visual perception	interphotoreceptor matrix	retinal binding|serine-type peptidase activity			central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	GACCTGGACACGGGCACCGTG	0.697000													4	46					0	0	1	0	0
MLLT3	4300	broad.mit.edu	37	9	20414343	20414343	+	Silent	SNP	A	A	G			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr9:20414343A>G	ENST00000380338.4	-	5	787	c.501T>C	c.(499-501)agT>agC	p.S167S	MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S164S|MLLT3_ENST00000355930.6_5'UTR	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	167	Poly-Ser.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding	p.S167S(19)		central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tgctgctgctactgctgctgc	0.532000			T	MLL	ALL								6	54					0	0	1	0	0
RUNX2	860	broad.mit.edu	37	6	45390463	45390463	+	Silent	SNP	G	G	A			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr6:45390463G>A	ENST00000371438.1	+	2	550	c.192G>A	c.(190-192)caG>caA	p.Q64Q	RUNX2_ENST00000465038.2_Silent_p.Q64Q|RUNX2_ENST00000371436.6_Silent_p.Q64Q|RUNX2_ENST00000352853.5_Silent_p.Q132Q|RUNX2_ENST00000359524.5_Silent_p.Q50Q|RUNX2_ENST00000371432.3_Silent_p.Q50Q|RUNX2_ENST00000541979.1_Silent_p.Q132Q|RUNX2_ENST00000576263.1_Silent_p.Q64Q	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	64	Poly-Gln.				negative regulation of transcription, DNA-dependent|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						agcagcagcagcaacagcagc	0.736000													5	57					0	0	1	0	0
CABYR	26256	broad.mit.edu	37	18	21736278	21736278	+	Silent	SNP	T	T	A	rs150107485	byFrequency	TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr18:21736278T>A	ENST00000399481.2	+	2	671	c.519T>A	c.(517-519)ccT>ccA	p.P173P	CABYR_ENST00000399499.1_Intron|CABYR_ENST00000581397.1_Intron|CABYR_ENST00000327201.6_Intron|CABYR_ENST00000415309.2_Intron|CABYR_ENST00000399496.3_Intron			O75952	CABYR_HUMAN	calcium binding tyrosine-(Y)-phosphorylation regulated	271					ciliary or flagellar motility|signal transduction|sperm capacitation	cytoplasm|cytoskeleton|flagellum|motile cilium|nucleus	calcium ion binding|cAMP-dependent protein kinase regulator activity|enzyme binding|protein heterodimerization activity|SH3 domain binding			breast(1)|endometrium(2)|large_intestine(4)|lung(4)	11	all_cancers(21;9.13e-05)|all_epithelial(16;5.49e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0305)|Ovarian(20;0.17)					AAGAACCTCCTGCTTATGATC	0.438000													4	37					0	0	1	0	0
ITGB7	3695	broad.mit.edu	37	12	53586181	53586181	+	Silent	SNP	C	C	T			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr12:53586181C>T	ENST00000267082.5	-	14	2319	c.2088G>A	c.(2086-2088)caG>caA	p.Q696Q	ITGB7_ENST00000338737.4_Silent_p.Q548Q|ITGB7_ENST00000550743.2_Silent_p.Q548Q|ITGB7_ENST00000422257.3_Silent_p.Q696Q	NM_000889.1	NP_000880.1	P26010	ITB7_HUMAN	integrin, beta 7	696					cell-matrix adhesion|integrin-mediated signaling pathway|multicellular organismal development|regulation of immune response	integrin complex	identical protein binding|metal ion binding|receptor activity			NS(2)|breast(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						AGAAGAACAGCTGGTTGTCCA	0.567000													13	81					0	0	1	0	0
ACOT1	641371	broad.mit.edu	37	14	74008372	74008372	+	Silent	SNP	T	T	C			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr14:74008372T>C	ENST00000311148.4	+	2	941	c.633T>C	c.(631-633)gcT>gcC	p.A211A	HEATR4_ENST00000334988.2_Intron|HEATR4_ENST00000560393.1_Intron|HEATR4_ENST00000553558.1_Intron|ACOT1_ENST00000557556.1_Silent_p.A211A	NM_001037161.1	NP_001032238.1			acyl-CoA thioesterase 1											endometrium(1)|large_intestine(1)|lung(2)	4				OV - Ovarian serous cystadenocarcinoma(108;1.37e-45)|BRCA - Breast invasive adenocarcinoma(234;0.0033)		TTGAAGAAGCTGTGAACTACT	0.458000													4	47					0	0	1	0	0
ZNF335	63925	broad.mit.edu	37	20	44578157	44578157	+	Silent	SNP	T	T	C			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr20:44578157T>C	ENST00000322927.2	-	25	3820	c.3720A>G	c.(3718-3720)gaA>gaG	p.E1240E	ZNF335_ENST00000426788.1_Silent_p.E1085E	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	1240	Gln-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				CCACAACATATTCCTGGGGGA	0.612000													4	21					0	0	1	0	0
RUNX2	860	broad.mit.edu	37	6	45390463	45390463	+	Silent	SNP	G	G	A			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr6:45390463G>A	ENST00000371438.1	+	2	550	c.192G>A	c.(190-192)caG>caA	p.Q64Q	RUNX2_ENST00000465038.2_Silent_p.Q64Q|RUNX2_ENST00000541979.1_Silent_p.Q132Q|RUNX2_ENST00000576263.1_Silent_p.Q64Q|RUNX2_ENST00000371432.3_Silent_p.Q50Q|RUNX2_ENST00000352853.5_Silent_p.Q132Q|RUNX2_ENST00000359524.5_Silent_p.Q50Q|RUNX2_ENST00000371436.6_Silent_p.Q64Q	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	64	Poly-Gln.				negative regulation of transcription, DNA-dependent|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						agcagcagcagcaacagcagc	0.736000													5	57					0	0	1	0	0
FAM101A	144347	broad.mit.edu	37	12	124798816	124798816	+	Silent	SNP	G	G	A	rs77570261	by1000genomes	TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr12:124798816G>A	ENST00000389727.3	+	3	396	c.396G>A	c.(394-396)acG>acA	p.T132T	FAM101A_ENST00000338359.4_Silent_p.T51T|FAM101A_ENST00000546355.1_Silent_p.T51T|FAM101A_ENST00000324038.3_Silent_p.T51T			Q6ZTI6	F101A_HUMAN	family with sequence similarity 101, member A	132										endometrium(1)|kidney(1)|lung(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;2.38e-05)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-05)|all cancers(50;0.000361)|BRCA - Breast invasive adenocarcinoma(302;0.059)		CCACCGTCACGGCCTACAGCG	0.642000													17	147					0	0	1	0	0
FLG	2312	broad.mit.edu	37	1	152286555	152286555	+	Silent	SNP	A	A	C			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr1:152286555A>C	ENST00000368799.1	-	3	842	c.807T>G	c.(805-807)tcT>tcG	p.S269S	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	269	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTTCACTTGAGATGATGATT	0.423000									Ichthyosis				10	125					0	0	1	0	0
RBP3	5949	broad.mit.edu	37	10	48390034	48390034	+	Missense_Mutation	SNP	C	C	T			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr10:48390034C>T	ENST00000224600.4	-	1	957	c.844G>A	c.(844-846)Gtg>Atg	p.V282M		NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	282	4 X approximate tandem repeats.				lipid metabolic process|proteolysis|transport|visual perception	interphotoreceptor matrix	retinal binding|serine-type peptidase activity			central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	GACCTGGACACGGGCACCGTG	0.697000													4	46					0	0	1	0	0
SBSN	374897	broad.mit.edu	37	19	36018407	36018407	+	Silent	SNP	T	T	C			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr19:36018407T>C	ENST00000452271.2	-	1	805	c.777A>G	c.(775-777)agA>agG	p.R259R	SBSN_ENST00000518157.1_Intron	NM_001166034.1	NP_001159506.1	Q6UWP8	SBSN_HUMAN	suprabasin	132						extracellular region				large_intestine(5)|lung(6)|ovary(1)|prostate(2)	14	all_lung(56;1.62e-08)|Lung NSC(56;2.47e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			CCTGGCCAAATCTCCCTGCCT	0.627000													4	7					0	0	1	0	0
LL22NC03-80A10.6	0	broad.mit.edu	37	22	22657649	22657649	+	RNA	SNP	G	G	A			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr22:22657649G>A	ENST00000426066.1	+	0	61					NR_027293.1																						GGAAAATCGGGCCCCGATACT	0.512000													4	46					0	0	1	0	0
MT-ND1	4535	broad.mit.edu	37	MT	3664	3664	+	Missense_Mutation	SNP	G	G	A			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chrM:3664G>A	ENST00000361390.2	+	1	358	c.358G>A	c.(358-360)Ggg>Agg	p.120_120insR						mitochondrially encoded NADH dehydrogenase 1											breast(1)|endometrium(13)|kidney(17)|lung(2)|prostate(1)	34						TCCTCTGATCAGGGTGAGCAT	0.512000													16	2					0	0	1	0	0
VCPIP1	80124	broad.mit.edu	37	8	67579177	67579177	+	Missense_Mutation	SNP	G	G	A			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr8:67579177G>A	ENST00000310421.4	-	1	275	c.17C>T	c.(16-18)cCg>cTg	p.P6L		NM_025054.4	NP_079330.2	Q96JH7	VCIP1_HUMAN	valosin containing protein (p97)/p47 complex interacting protein 1	6	Pro-rich.				protein ubiquitination	endoplasmic reticulum|Golgi stack	ubiquitin-specific protease activity			breast(7)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(6)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		Lung NSC(129;0.142)|all_lung(136;0.227)	Epithelial(68;0.000771)|OV - Ovarian serous cystadenocarcinoma(28;0.00248)|all cancers(69;0.00296)|BRCA - Breast invasive adenocarcinoma(89;0.149)			aggcggcggcggcggcggcTG	0.697000													12	17					0	0	1	0	0
CABYR	26256	broad.mit.edu	37	18	21736278	21736278	+	Silent	SNP	T	T	A	rs150107485	byFrequency	TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr18:21736278T>A	ENST00000399481.2	+	2	671	c.519T>A	c.(517-519)ccT>ccA	p.P173P	CABYR_ENST00000415309.2_Intron|CABYR_ENST00000399496.3_Intron|CABYR_ENST00000399499.1_Intron|CABYR_ENST00000327201.6_Intron|CABYR_ENST00000581397.1_Intron			O75952	CABYR_HUMAN	calcium binding tyrosine-(Y)-phosphorylation regulated	271					ciliary or flagellar motility|signal transduction|sperm capacitation	cytoplasm|cytoskeleton|flagellum|motile cilium|nucleus	calcium ion binding|cAMP-dependent protein kinase regulator activity|enzyme binding|protein heterodimerization activity|SH3 domain binding			breast(1)|endometrium(2)|large_intestine(4)|lung(4)	11	all_cancers(21;9.13e-05)|all_epithelial(16;5.49e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0305)|Ovarian(20;0.17)					AAGAACCTCCTGCTTATGATC	0.438000													4	37					0	0	1	0	0
ITGB7	3695	broad.mit.edu	37	12	53586181	53586181	+	Silent	SNP	C	C	T			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr12:53586181C>T	ENST00000267082.5	-	14	2319	c.2088G>A	c.(2086-2088)caG>caA	p.Q696Q	ITGB7_ENST00000422257.3_Silent_p.Q696Q|ITGB7_ENST00000338737.4_Silent_p.Q548Q|ITGB7_ENST00000550743.2_Silent_p.Q548Q	NM_000889.1	NP_000880.1	P26010	ITB7_HUMAN	integrin, beta 7	696					cell-matrix adhesion|integrin-mediated signaling pathway|multicellular organismal development|regulation of immune response	integrin complex	identical protein binding|metal ion binding|receptor activity			NS(2)|breast(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						AGAAGAACAGCTGGTTGTCCA	0.567000													13	81					0	0	1	0	0
ACOT1	641371	broad.mit.edu	37	14	74008372	74008372	+	Silent	SNP	T	T	C			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr14:74008372T>C	ENST00000311148.4	+	2	941	c.633T>C	c.(631-633)gcT>gcC	p.A211A	ACOT1_ENST00000557556.1_Silent_p.A211A|HEATR4_ENST00000553558.1_Intron|HEATR4_ENST00000334988.2_Intron|HEATR4_ENST00000560393.1_Intron	NM_001037161.1	NP_001032238.1			acyl-CoA thioesterase 1											endometrium(1)|large_intestine(1)|lung(2)	4				OV - Ovarian serous cystadenocarcinoma(108;1.37e-45)|BRCA - Breast invasive adenocarcinoma(234;0.0033)		TTGAAGAAGCTGTGAACTACT	0.458000													4	47					0	0	1	0	0
PRG4	10216	broad.mit.edu	37	1	186276143	186276145	+	In_Frame_Del	DEL	CTC	CTC	-			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr1:186276143_186276145delCTC	ENST00000445192.2	+	7	1337_1339	c.1292_1294delCTC	c.(1291-1296)acc>a	p.TP431del	PRG4_ENST00000367485.4_In_Frame_Del_p.TP338del|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367483.4_In_Frame_Del_p.TP390del|PRG4_ENST00000367486.3_In_Frame_Del_p.TP388del	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	431	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						GCACCCACCACTCCCAAGGAGCC	0.655													10	109	---	---	---	---					
TMCC1	23023	broad.mit.edu	37	3	129370576	129370578	+	In_Frame_Del	DEL	CTG	CTG	-			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr3:129370576_129370578delCTG	ENST00000393238.3	-	6	2048_2050	c.1708_1710delCAG	c.(1708-1710)del	p.Q570del	TMCC1_ENST00000329333.5_In_Frame_Del_p.Q391del|TMCC1_ENST00000426664.2_In_Frame_Del_p.Q456del|TMCC1_ENST00000432054.2_In_Frame_Del_p.Q246del	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	570						integral to membrane			PLXND1/TMCC1(4)	breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1)	25						GCTGCACCACCTGCTGCTGCTGC	0.581													7	80	---	---	---	---					
PMS2P4	0	broad.mit.edu	37	7	66762433	66762433	+	RNA	DEL	A	A	-	rs68053451		TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr7:66762433delA	ENST00000414507.1	-	0	184																											tctcaaaaagaaaaaaaaaaa	0.408													7	8	---	---	---	---					
NUFIP2	57532	broad.mit.edu	37	17	27620990	27620992	+	In_Frame_Del	DEL	GCT	GCT	-			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr17:27620990_27620992delGCT	ENST00000225388.4	-	1	144_146	c.86_88delAGC	c.(85-90)ccg>c	p.QP29del	NUFIP2_ENST00000579665.1_In_Frame_Del_p.QP29del	NM_020772.2	NP_065823.1	Q7Z417	NUFP2_HUMAN	nuclear fragile X mental retardation protein interacting protein 2	29	His-rich.					nucleus|polysomal ribosome	protein binding|RNA binding			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	24			BRCA - Breast invasive adenocarcinoma(11;0.000457)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)			tggtggtgcggctgctgctgctg	0.591													7	101	---	---	---	---					
IGLC3	0	broad.mit.edu	37	22	23248852	23248852	+	RNA	DEL	A	A	-	rs71797740		TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	c181d15b-c8ae-4d11-b57f-8de22eb27f81	g.chr22:23248852delA	ENST00000390325.2	+	0	341																											CTCACCCCCCACCACGGGAGA	0.572													9	35	---	---	---	---					
DND1	373863	broad.mit.edu	37	5	140052285	140052285	+	Frame_Shift_Del	DEL	T	T	-			TCGA-BJ-A45E-01A-11D-A23U-08	TCGA-BJ-A45E-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b22bf924-6c87-4ccc-ac51-bcd914c39163	d6d2a21b-6095-4ec9-8254-e5d2564aad50	g.chr5:140052285delT	ENST00000542735.1	-	3	392	c.349delA	c.(349-351)cgfs	p.T117fs		NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	117	RRM 1.				multicellular organismal development|negative regulation of gene silencing by miRNA	cytoplasm|nucleus	AU-rich element binding|nucleotide binding	p.T117fs*24(1)		central_nervous_system(1)|prostate(4)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTGTGCAGCGTGGCGATGGCG	0.682													10	28	---	---	---	---					
