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
KRTAP10-12	386685	broad.mit.edu	37	21	46117516	46117516	+	Nonsense_Mutation	SNP	C	C	T			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr21:46117516C>T	ENST00000400365.3	+	1	430	c.400C>T	c.(400-402)Cag>Tag	p.Q134*	TSPEAR_ENST00000323084.4_Intron	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN	keratin associated protein 10-12	134	19 X 5 AA repeats of C-C-X(3).					keratin filament				large_intestine(1)|lung(8)	9						ATGCTGCCAGCAGTCTAGCTG	0.617000													6	122					0	0	1	0	0
IGFBP7	3490	broad.mit.edu	37	4	57898634	57898634	+	Missense_Mutation	SNP	T	T	C			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr4:57898634T>C	ENST00000295666.4	-	4	820	c.787A>G	c.(787-789)Att>Gtt	p.I263V	IGFBP7_ENST00000537922.1_Missense_Mutation_p.I263V|IGFBP7_ENST00000512512.1_5'UTR	NM_001553.2	NP_001544.1	Q16270	IBP7_HUMAN	insulin-like growth factor binding protein 7	263	Ig-like C2-type.				cell adhesion|negative regulation of cell proliferation|regulation of cell growth	extracellular space	insulin-like growth factor binding			central_nervous_system(1)|endometrium(1)|lung(3)	5	Glioma(25;0.08)|all_neural(26;0.181)				Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	ACCACTGTAATTTTTGCTGAT	0.368000													6	35					0	0	1	0	0
TRMT1	55621	broad.mit.edu	37	19	13220604	13220604	+	Silent	SNP	T	T	C			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr19:13220604T>C	ENST00000592062.1	-	11	1725	c.1155A>G	c.(1153-1155)gaA>gaG	p.E385E	TRMT1_ENST00000357720.4_Silent_p.E385E|TRMT1_ENST00000437766.1_Silent_p.E385E|TRMT1_ENST00000221504.8_Silent_p.E356E			Q9NXH9	TRM1_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)	385							RNA binding|tRNA (guanine-N2-)-methyltransferase activity|zinc ion binding			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(19;6.08e-22)	GBM - Glioblastoma multiforme(1328;0.0356)		GCCCACAGTGTTCACACTCGG	0.627000													10	26					0	0	1	0	0
B3GNT3	10331	broad.mit.edu	37	19	17922809	17922809	+	Missense_Mutation	SNP	G	G	T			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr19:17922809G>T	ENST00000318683.6	+	3	1144	c.997G>T	c.(997-999)Gac>Tac	p.D333Y	B3GNT3_ENST00000595387.1_Missense_Mutation_p.D333Y	NM_014256.3	NP_055071.2	Q9Y2A9	B3GN3_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3	333					protein glycosylation	Golgi membrane|integral to plasma membrane	galactosyltransferase activity			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	21						GTCCTCCTTTGACCCCTGCTT	0.622000													13	114					2.32078e-09	2.32078e-09	1	1	0
NPR1	4881	broad.mit.edu	37	1	153660685	153660685	+	Missense_Mutation	SNP	G	G	A	rs148747309		TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr1:153660685G>A	ENST00000368680.3	+	15	2877	c.2405G>A	c.(2404-2406)cGc>cAc	p.R802H		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor A/guanylate cyclase A (atrionatriuretic peptide receptor A)	802	Protein kinase.				body fluid secretion|intracellular signal transduction|negative regulation of angiogenesis|negative regulation of cell growth|positive regulation of renal sodium excretion|positive regulation of urine volume|receptor guanylyl cyclase signaling pathway|regulation of blood pressure|regulation of blood vessel size|regulation of vascular permeability|regulation of vasodilation		ATP binding|GTP binding|guanylate cyclase activity|natriuretic peptide receptor activity|peptide receptor activity, G-protein coupled|protein kinase activity			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Nesiritide(DB04899)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	CTGACGTTGCGCAAATTTAAC	0.582000													5	36					0	0	1	0	0
FOXP4	116113	broad.mit.edu	37	6	41555115	41555115	+	Missense_Mutation	SNP	A	A	T			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr6:41555115A>T	ENST00000373060.1	+	7	1195	c.737A>T	c.(736-738)aAg>aTg	p.K246M	FOXP4_ENST00000307972.4_Missense_Mutation_p.K246M|FOXP4_ENST00000373063.3_Missense_Mutation_p.K245M|FOXP4_ENST00000409208.1_Missense_Mutation_p.K246M|FOXP4_ENST00000373057.3_Missense_Mutation_p.K244M	NM_001012426.1|NM_001012427.1	NP_001012426.1|NP_001012427.1	Q8IVH2	FOXP4_HUMAN	forkhead box P4	246					embryonic foregut morphogenesis|heart development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					GACAGCGTCAAGCAGGAGGGG	0.692000											OREG0004065	type=REGULATORY REGION|Gene=FOXP4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	4	71					0	0	1	0	0
FAM111A	63901	broad.mit.edu	37	11	58920619	58920619	+	Missense_Mutation	SNP	G	G	A			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr11:58920619G>A	ENST00000528737.1	+	5	4296	c.1478G>A	c.(1477-1479)cGa>cAa	p.R493Q	FAM111A_ENST00000420244.1_Missense_Mutation_p.R493Q|FAM111A_ENST00000533703.1_Missense_Mutation_p.R493Q|FAM111A_ENST00000361723.3_Missense_Mutation_p.R493Q|FAM111A_ENST00000531147.1_Missense_Mutation_p.R493Q			Q96PZ2	F111A_HUMAN	family with sequence similarity 111, member A	493					proteolysis		serine-type endopeptidase activity			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22		all_epithelial(135;0.139)				CAGGGTCAGCGAGCAAAGAAA	0.403000													7	89					0	0	1	0	0
ANO8	57719	broad.mit.edu	37	19	17435806	17435806	+	Silent	SNP	G	G	A			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr19:17435806G>A	ENST00000159087.4	-	17	3209	c.3051C>T	c.(3049-3051)agC>agT	p.S1017S		NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN	anoctamin 8	1017						chloride channel complex	chloride channel activity			autonomic_ganglia(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(3)	27						GGCGGGTGTCGCTGCCTGTGG	0.667000													6	104					0	0	1	0	0
NRAS	4893	broad.mit.edu	37	1	115256529	115256529	+	Missense_Mutation	SNP	T	T	C	rs11554290		TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr1:115256529T>C	ENST00000369535.4	-	3	435	c.182A>G	c.(181-183)cAa>cGa	p.Q61R		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61			Q -> K (in neuroblastoma cell).|Q -> R (in lung carcinoma cell and melanoma; dbSNP:rs11554290).		activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	Golgi membrane|plasma membrane	GTP binding|GTPase activity	p.Q61R(817)|p.Q61L(175)|p.Q61P(23)|p.Q61K(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTACTCTTCTTGTCCAGCTGT	0.458000	Q61L(C3A_LIVER)|Q61L(HEPG2_LIVER)|Q61L(HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(IPC298_SKIN)|Q61L(KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(MELJUSO_SKIN)|Q61L(MHHES1_BONE)|Q61L(MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61P(TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(HT1197_URINARY_TRACT)|Q61R(KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(KU1919_URINARY_TRACT)|Q61R(NCIH2347_LUNG)|Q61R(ONS76_CENTRAL_NERVOUS_SYSTEM)|Q61R(SKMEL2_SKIN)|Q61R(SW1271_LUNG)|Q61R(TT2609C02_THYROID)	50	Mis		"""melanoma, MM, AML, thyroid"""				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)			52	62					0	0	1	0	0
NODAL	4838	broad.mit.edu	37	10	72195326	72195326	+	Missense_Mutation	SNP	C	C	T	rs10999334		TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr10:72195326C>T	ENST00000287139.3	-	2	606	c.607G>A	c.(607-609)Gag>Aag	p.E203K	AC022532.1_ENST00000420338.2_Silent_p.L91L	NM_018055.4	NP_060525.3	Q96S42	NODAL_HUMAN	nodal growth differentiation factor	203			E -> K (in HTX5; decrease in signal transduction; dbSNP:rs10999334).		growth	extracellular space	cytokine activity|growth factor activity			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(2)	15						TGCCTCTGCTCCTGCGAGAGG	0.662000													3	32					0	0	1	0	0
NPAS4	266743	broad.mit.edu	37	11	66189993	66189993	+	Silent	SNP	G	G	A			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr11:66189993G>A	ENST00000311034.2	+	3	575	c.399G>A	c.(397-399)caG>caA	p.Q133Q		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	133	PAS 1.				transcription, DNA-dependent		DNA binding|signal transducer activity			breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						CTGTGCGCCAGCAACTCACCC	0.582000													3	45					0	0	1	0	0
ACAN	176	broad.mit.edu	37	15	89391161	89391161	+	Missense_Mutation	SNP	C	C	T	rs143697605	by1000genomes	TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr15:89391161C>T	ENST00000439576.2	+	9	1998	c.1624C>T	c.(1624-1626)Cgg>Tgg	p.R542W	ACAN_ENST00000352105.7_Missense_Mutation_p.R542W|ACAN_ENST00000559004.1_Missense_Mutation_p.R542W|ACAN_ENST00000561243.1_Missense_Mutation_p.R542W|ACAN_ENST00000558207.1_Missense_Mutation_p.R542W	NM_013227.3	NP_037359.3	E7EX88	E7EX88_HUMAN	aggrecan	542					cell adhesion		hyaluronic acid binding|sugar binding	p.R542W(1)		NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			TGTGAGCCCCCGGACCCCATG	0.607000													4	56					0	0	1	0	0
MT1JP	0	broad.mit.edu	37	16	56670827	56670827	+	RNA	SNP	C	C	T	rs11076159	by1000genomes	TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr16:56670827C>T	ENST00000564564.1	+	0	806																											TGCAAAGGGACGTCGGAGAAG	0.537000													3	47					0	0	1	0	0
COG7	91949	broad.mit.edu	37	16	23428325	23428325	+	Missense_Mutation	SNP	A	A	G			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr16:23428325A>G	ENST00000307149.5	-	9	1440	c.1255T>C	c.(1255-1257)Tgc>Cgc	p.C419R		NM_153603.3	NP_705831.1	P83436	COG7_HUMAN	component of oligomeric golgi complex 7	419					intracellular protein transport|protein glycosylation|protein localization in Golgi apparatus|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|Golgi transport complex	protein binding			breast(1)|central_nervous_system(1)|endometrium(7)|large_intestine(9)|liver(1)|lung(7)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.0401)		AACAGGCCGCAGGTCCCCAGG	0.567000													3	37					0	0	1	0	0
OR4M1	441670	broad.mit.edu	37	14	20248797	20248797	+	Missense_Mutation	SNP	T	T	A			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr14:20248797T>A	ENST00000315957.4	+	1	397	c.316T>A	c.(316-318)Ttt>Att	p.F106I		NM_001005500.1	NP_001005500.1	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M, member 1	106					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(32)|prostate(1)|skin(2)	42	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CTTCTTACACTTTGTTGGGGC	0.473000													9	261					0	0	1	0	0
RNASE1	6035	broad.mit.edu	37	14	21270003	21270003	+	Silent	SNP	C	C	T			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr14:21270003C>T	ENST00000397967.4	-	2	731	c.225G>A	c.(223-225)gtG>gtA	p.V75V	RNASE1_ENST00000397970.4_Silent_p.V75V|RNASE1_ENST00000340900.3_Silent_p.V75V|RNASE1_ENST00000555698.1_Silent_p.V35V|RNASE1_ENST00000412779.2_Silent_p.V75V	NM_002933.4	NP_002924.1	P07998	RNAS1_HUMAN	ribonuclease, RNase A family, 1 (pancreatic)	75						extracellular region	nucleic acid binding|pancreatic ribonuclease activity|protein binding			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	5	all_cancers(95;0.00671)	all_lung(585;0.235)	Epithelial(56;9.21e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0126)		GGGGCTCGTGCACAAAGGTGT	0.542000													5	73					0	0	1	0	0
SIRPA	140885	broad.mit.edu	37	20	1902292	1902292	+	Missense_Mutation	SNP	G	G	A			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr20:1902292G>A	ENST00000358771.4	+	3	840	c.688G>A	c.(688-690)Gtg>Atg	p.V230M	SIRPA_ENST00000356025.3_Missense_Mutation_p.V230M|SIRPA_ENST00000400068.3_Missense_Mutation_p.V230M	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	230	Ig-like C1-type 1.				blood coagulation|cell adhesion|cell junction assembly|leukocyte migration	integral to membrane|plasma membrane	SH3 domain binding	p.V230M(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CATCTGCGAGGTGGCCCACGT	0.612000													3	39					0	0	1	0	0
MMAA	166785	broad.mit.edu	37	4	146560393	146560393	+	Silent	SNP	C	C	T	rs146372922	byFrequency	TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr4:146560393C>T	ENST00000281317.5	+	2	1312	c.102C>T	c.(100-102)ctC>ctT	p.L34L	MMAA_ENST00000541599.1_5'UTR	NM_172250.2	NP_758454.1	Q8IVH4	MMAA_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblA type	34						mitochondrion	GTP binding|nucleoside-triphosphatase activity			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)	17	all_hematologic(180;0.151)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GTACTCATCTCGGATCAGGAA	0.443000													46	78					0	0	1	0	0
KRTAP10-12	386685	broad.mit.edu	37	21	46117516	46117516	+	Nonsense_Mutation	SNP	C	C	T			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr21:46117516C>T	ENST00000400365.3	+	1	430	c.400C>T	c.(400-402)Cag>Tag	p.Q134*	TSPEAR_ENST00000323084.4_Intron	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN	keratin associated protein 10-12	134	19 X 5 AA repeats of C-C-X(3).					keratin filament				large_intestine(1)|lung(8)	9						ATGCTGCCAGCAGTCTAGCTG	0.617000													6	122					0	0	1	0	0
IGFBP7	3490	broad.mit.edu	37	4	57898634	57898634	+	Missense_Mutation	SNP	T	T	C			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr4:57898634T>C	ENST00000295666.4	-	4	820	c.787A>G	c.(787-789)Att>Gtt	p.I263V	IGFBP7_ENST00000512512.1_5'UTR|IGFBP7_ENST00000537922.1_Missense_Mutation_p.I263V	NM_001553.2	NP_001544.1	Q16270	IBP7_HUMAN	insulin-like growth factor binding protein 7	263	Ig-like C2-type.				cell adhesion|negative regulation of cell proliferation|regulation of cell growth	extracellular space	insulin-like growth factor binding			central_nervous_system(1)|endometrium(1)|lung(3)	5	Glioma(25;0.08)|all_neural(26;0.181)				Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	ACCACTGTAATTTTTGCTGAT	0.368000													6	35					0	0	1	0	0
TRMT1	55621	broad.mit.edu	37	19	13220604	13220604	+	Silent	SNP	T	T	C			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr19:13220604T>C	ENST00000592062.1	-	11	1725	c.1155A>G	c.(1153-1155)gaA>gaG	p.E385E	TRMT1_ENST00000357720.4_Silent_p.E385E|TRMT1_ENST00000437766.1_Silent_p.E385E|TRMT1_ENST00000221504.8_Silent_p.E356E			Q9NXH9	TRM1_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)	385							RNA binding|tRNA (guanine-N2-)-methyltransferase activity|zinc ion binding			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(19;6.08e-22)	GBM - Glioblastoma multiforme(1328;0.0356)		GCCCACAGTGTTCACACTCGG	0.627000													10	26					0	0	1	0	0
B3GNT3	10331	broad.mit.edu	37	19	17922809	17922809	+	Missense_Mutation	SNP	G	G	T			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr19:17922809G>T	ENST00000318683.6	+	3	1144	c.997G>T	c.(997-999)Gac>Tac	p.D333Y	B3GNT3_ENST00000595387.1_Missense_Mutation_p.D333Y	NM_014256.3	NP_055071.2	Q9Y2A9	B3GN3_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3	333					protein glycosylation	Golgi membrane|integral to plasma membrane	galactosyltransferase activity			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	21						GTCCTCCTTTGACCCCTGCTT	0.622000													13	114					2.32078e-09	2.40674e-09	1	1	0
NPR1	4881	broad.mit.edu	37	1	153660685	153660685	+	Missense_Mutation	SNP	G	G	A	rs148747309		TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr1:153660685G>A	ENST00000368680.3	+	15	2877	c.2405G>A	c.(2404-2406)cGc>cAc	p.R802H		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor A/guanylate cyclase A (atrionatriuretic peptide receptor A)	802	Protein kinase.				body fluid secretion|intracellular signal transduction|negative regulation of angiogenesis|negative regulation of cell growth|positive regulation of renal sodium excretion|positive regulation of urine volume|receptor guanylyl cyclase signaling pathway|regulation of blood pressure|regulation of blood vessel size|regulation of vascular permeability|regulation of vasodilation		ATP binding|GTP binding|guanylate cyclase activity|natriuretic peptide receptor activity|peptide receptor activity, G-protein coupled|protein kinase activity			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Nesiritide(DB04899)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	CTGACGTTGCGCAAATTTAAC	0.582000													5	36					0	0	1	0	0
EP400	57634	broad.mit.edu	37	12	132547087	132547087	+	Silent	SNP	G	G	A	rs12366766		TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr12:132547087G>A	ENST00000333577.4	+	48	8392	c.8283G>A	c.(8281-8283)caG>caA	p.Q2761Q	EP400_ENST00000389562.2_Silent_p.Q2724Q|EP400_ENST00000332482.4_Silent_p.Q2688Q|EP400_ENST00000389561.2_Silent_p.Q2725Q|EP400_ENST00000330386.6_Silent_p.Q2644Q			Q96L91	EP400_HUMAN	E1A binding protein p400	2761	Interaction with ZNF42 (By similarity).|Poly-Gln.				histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity	p.Q2724Q(16)|p.Q2725Q(1)		NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		agcagcagcagcaacaacagc	0.562000													3	29					0	0	1	0	0
FOXP4	116113	broad.mit.edu	37	6	41555115	41555115	+	Missense_Mutation	SNP	A	A	T			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr6:41555115A>T	ENST00000373060.1	+	7	1195	c.737A>T	c.(736-738)aAg>aTg	p.K246M	FOXP4_ENST00000373063.3_Missense_Mutation_p.K245M|FOXP4_ENST00000373057.3_Missense_Mutation_p.K244M|FOXP4_ENST00000409208.1_Missense_Mutation_p.K246M|FOXP4_ENST00000307972.4_Missense_Mutation_p.K246M	NM_001012426.1|NM_001012427.1	NP_001012426.1|NP_001012427.1	Q8IVH2	FOXP4_HUMAN	forkhead box P4	246					embryonic foregut morphogenesis|heart development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					GACAGCGTCAAGCAGGAGGGG	0.692000											OREG0004065	type=REGULATORY REGION|Gene=FOXP4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	4	71					0	0	1	0	0
FAM111A	63901	broad.mit.edu	37	11	58920619	58920619	+	Missense_Mutation	SNP	G	G	A			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr11:58920619G>A	ENST00000528737.1	+	5	4296	c.1478G>A	c.(1477-1479)cGa>cAa	p.R493Q	FAM111A_ENST00000361723.3_Missense_Mutation_p.R493Q|FAM111A_ENST00000533703.1_Missense_Mutation_p.R493Q|FAM111A_ENST00000420244.1_Missense_Mutation_p.R493Q|FAM111A_ENST00000531147.1_Missense_Mutation_p.R493Q			Q96PZ2	F111A_HUMAN	family with sequence similarity 111, member A	493					proteolysis		serine-type endopeptidase activity			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22		all_epithelial(135;0.139)				CAGGGTCAGCGAGCAAAGAAA	0.403000													7	89					0	0	1	0	0
ANO8	57719	broad.mit.edu	37	19	17435806	17435806	+	Silent	SNP	G	G	A			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr19:17435806G>A	ENST00000159087.4	-	17	3209	c.3051C>T	c.(3049-3051)agC>agT	p.S1017S		NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN	anoctamin 8	1017						chloride channel complex	chloride channel activity			autonomic_ganglia(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(3)	27						GGCGGGTGTCGCTGCCTGTGG	0.667000													6	104					0	0	1	0	0
NRAS	4893	broad.mit.edu	37	1	115256529	115256529	+	Missense_Mutation	SNP	T	T	C	rs11554290		TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr1:115256529T>C	ENST00000369535.4	-	3	435	c.182A>G	c.(181-183)cAa>cGa	p.Q61R		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61			Q -> K (in neuroblastoma cell).|Q -> R (in lung carcinoma cell and melanoma; dbSNP:rs11554290).		activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	Golgi membrane|plasma membrane	GTP binding|GTPase activity	p.Q61R(817)|p.Q61L(175)|p.Q61P(23)|p.Q61K(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTACTCTTCTTGTCCAGCTGT	0.458000	Q61L(C3A_LIVER)|Q61L(HEPG2_LIVER)|Q61L(HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(IPC298_SKIN)|Q61L(KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(MELJUSO_SKIN)|Q61L(MHHES1_BONE)|Q61L(MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61P(TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(HT1197_URINARY_TRACT)|Q61R(KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(KU1919_URINARY_TRACT)|Q61R(NCIH2347_LUNG)|Q61R(ONS76_CENTRAL_NERVOUS_SYSTEM)|Q61R(SKMEL2_SKIN)|Q61R(SW1271_LUNG)|Q61R(TT2609C02_THYROID)	50	Mis		"""melanoma, MM, AML, thyroid"""				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)			52	62					0	0	1	0	0
NODAL	4838	broad.mit.edu	37	10	72195326	72195326	+	Missense_Mutation	SNP	C	C	T	rs10999334		TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr10:72195326C>T	ENST00000287139.3	-	2	606	c.607G>A	c.(607-609)Gag>Aag	p.E203K	AC022532.1_ENST00000420338.2_Silent_p.L91L	NM_018055.4	NP_060525.3	Q96S42	NODAL_HUMAN	nodal growth differentiation factor	203			E -> K (in HTX5; decrease in signal transduction; dbSNP:rs10999334).		growth	extracellular space	cytokine activity|growth factor activity			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(2)	15						TGCCTCTGCTCCTGCGAGAGG	0.662000													3	32					0	0	1	0	0
NPAS4	266743	broad.mit.edu	37	11	66189993	66189993	+	Silent	SNP	G	G	A			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr11:66189993G>A	ENST00000311034.2	+	3	575	c.399G>A	c.(397-399)caG>caA	p.Q133Q		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	133	PAS 1.				transcription, DNA-dependent		DNA binding|signal transducer activity			breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						CTGTGCGCCAGCAACTCACCC	0.582000													3	45					0	0	1	0	0
ACAN	176	broad.mit.edu	37	15	89391161	89391161	+	Missense_Mutation	SNP	C	C	T	rs143697605	by1000genomes	TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr15:89391161C>T	ENST00000439576.2	+	9	1998	c.1624C>T	c.(1624-1626)Cgg>Tgg	p.R542W	ACAN_ENST00000559004.1_Missense_Mutation_p.R542W|ACAN_ENST00000352105.7_Missense_Mutation_p.R542W|ACAN_ENST00000558207.1_Missense_Mutation_p.R542W|ACAN_ENST00000561243.1_Missense_Mutation_p.R542W	NM_013227.3	NP_037359.3	E7EX88	E7EX88_HUMAN	aggrecan	542					cell adhesion		hyaluronic acid binding|sugar binding	p.R542W(1)		NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			TGTGAGCCCCCGGACCCCATG	0.607000													4	56					0	0	1	0	0
MT1JP	0	broad.mit.edu	37	16	56670827	56670827	+	RNA	SNP	C	C	T	rs11076159	by1000genomes	TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr16:56670827C>T	ENST00000564564.1	+	0	806																											TGCAAAGGGACGTCGGAGAAG	0.537000													3	47					0	0	1	0	0
RNASE1	6035	broad.mit.edu	37	14	21270003	21270003	+	Silent	SNP	C	C	T			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr14:21270003C>T	ENST00000397967.4	-	2	731	c.225G>A	c.(223-225)gtG>gtA	p.V75V	RNASE1_ENST00000412779.2_Silent_p.V75V|RNASE1_ENST00000340900.3_Silent_p.V75V|RNASE1_ENST00000397970.4_Silent_p.V75V|RNASE1_ENST00000555698.1_Silent_p.V35V	NM_002933.4	NP_002924.1	P07998	RNAS1_HUMAN	ribonuclease, RNase A family, 1 (pancreatic)	75						extracellular region	nucleic acid binding|pancreatic ribonuclease activity|protein binding			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	5	all_cancers(95;0.00671)	all_lung(585;0.235)	Epithelial(56;9.21e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0126)		GGGGCTCGTGCACAAAGGTGT	0.542000													5	73					0	0	1	0	0
OR4M1	441670	broad.mit.edu	37	14	20248797	20248797	+	Missense_Mutation	SNP	T	T	A			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr14:20248797T>A	ENST00000315957.4	+	1	397	c.316T>A	c.(316-318)Ttt>Att	p.F106I		NM_001005500.1	NP_001005500.1	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M, member 1	106					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(32)|prostate(1)|skin(2)	42	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CTTCTTACACTTTGTTGGGGC	0.473000													9	261					0	0	1	0	0
COG7	91949	broad.mit.edu	37	16	23428325	23428325	+	Missense_Mutation	SNP	A	A	G			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr16:23428325A>G	ENST00000307149.5	-	9	1440	c.1255T>C	c.(1255-1257)Tgc>Cgc	p.C419R		NM_153603.3	NP_705831.1	P83436	COG7_HUMAN	component of oligomeric golgi complex 7	419					intracellular protein transport|protein glycosylation|protein localization in Golgi apparatus|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|Golgi transport complex	protein binding			breast(1)|central_nervous_system(1)|endometrium(7)|large_intestine(9)|liver(1)|lung(7)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.0401)		AACAGGCCGCAGGTCCCCAGG	0.567000													3	37					0	0	1	0	0
SIRPA	140885	broad.mit.edu	37	20	1902292	1902292	+	Missense_Mutation	SNP	G	G	A			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr20:1902292G>A	ENST00000358771.4	+	3	840	c.688G>A	c.(688-690)Gtg>Atg	p.V230M	SIRPA_ENST00000356025.3_Missense_Mutation_p.V230M|SIRPA_ENST00000400068.3_Missense_Mutation_p.V230M	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	230	Ig-like C1-type 1.				blood coagulation|cell adhesion|cell junction assembly|leukocyte migration	integral to membrane|plasma membrane	SH3 domain binding	p.V230M(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CATCTGCGAGGTGGCCCACGT	0.612000													3	39					0	0	1	0	0
MMAA	166785	broad.mit.edu	37	4	146560393	146560393	+	Silent	SNP	C	C	T	rs146372922	byFrequency	TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr4:146560393C>T	ENST00000281317.5	+	2	1312	c.102C>T	c.(100-102)ctC>ctT	p.L34L	MMAA_ENST00000541599.1_5'UTR	NM_172250.2	NP_758454.1	Q8IVH4	MMAA_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblA type	34						mitochondrion	GTP binding|nucleoside-triphosphatase activity			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)	17	all_hematologic(180;0.151)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GTACTCATCTCGGATCAGGAA	0.443000													46	78					0	0	1	0	0
SIRPA	140885	broad.mit.edu	37	20	1902301	1902301	+	Missense_Mutation	SNP	G	G	A			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr20:1902301G>A	ENST00000358771.4	+	3	849	c.697G>A	c.(697-699)Gtc>Atc	p.V233I	SIRPA_ENST00000356025.3_Missense_Mutation_p.V233I|SIRPA_ENST00000400068.3_Missense_Mutation_p.V233I	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	233	Ig-like C1-type 1.				blood coagulation|cell adhesion|cell junction assembly|leukocyte migration	integral to membrane|plasma membrane	SH3 domain binding	p.V233I(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		GGTGGCCCACGTCACCTTGCA	0.617000													3	37					0	0	1	0	0
FAM46A	55603	broad.mit.edu	37	6	82461727	82461727	+	Silent	SNP	A	A	G	rs150380746	byFrequency	TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr6:82461727A>G	ENST00000369754.3	-	2	501	c.189T>C	c.(187-189)ggT>ggC	p.G63G	FAM46A_ENST00000369756.3_Silent_p.G125G|FAM46A_ENST00000320172.6_Silent_p.G44G			Q96IP4	FA46A_HUMAN	family with sequence similarity 46, member A	44										endometrium(2)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	12		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)		BRCA - Breast invasive adenocarcinoma(397;0.0428)		Agctgccgccaccgccgaagt	0.682000													3	16					0	0	1	0	0
GPX1	2876	broad.mit.edu	37	3	49395674	49395676	+	In_Frame_Del	DEL	GCC	GCC	-	rs56041243		TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr3:49395674_49395676delGCC	ENST00000419783.1	-	1	357_359	c.36_38delGGC	c.(34-39)gcc>gc	p.AA12del	GPX1_ENST00000496791.1_5'UTR|GPX1_ENST00000419349.1_In_Frame_Del_p.AA12del	NM_000581.2	NP_000572.2	P07203	GPX1_HUMAN	glutathione peroxidase 1	12					anti-apoptosis|cell redox homeostasis|glutathione metabolic process|heart contraction|hydrogen peroxide catabolic process|negative regulation of caspase activity|purine base metabolic process|purine nucleotide catabolic process|regulation of gene expression, epigenetic|regulation of mammary gland epithelial cell proliferation|regulation of proteasomal protein catabolic process|release of cytochrome c from mitochondria|response to selenium ion|UV protection	cytosol|mitochondrion	endopeptidase inhibitor activity|glutathione peroxidase activity|SH3 domain binding	p.A12_A13delAA(1)		breast(1)|large_intestine(2)|lung(1)	4				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)	Glutathione(DB00143)	CACCGACTGGgccgccgccgccg	0.690													2	4	---	---	---	---					
NKD2	85409	broad.mit.edu	37	5	1038447	1038449	+	In_Frame_Del	DEL	CAC	CAC	-	rs3840989		TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr5:1038447_1038449delCAC	ENST00000296849.5	+	10	1544_1546	c.1315_1317delCAC	c.(1315-1317)del	p.H447del	NKD2_ENST00000382730.2_In_Frame_Del_p.AP78del|NKD2_ENST00000274150.4_3'UTR	NM_033120.2	NP_149111.1	Q969F2	NKD2_HUMAN	naked cuticle homolog 2 (Drosophila)	447	His-rich.				exocytosis|Wnt receptor signaling pathway	cytoplasmic membrane-bounded vesicle|plasma membrane	calcium ion binding|ubiquitin protein ligase binding			breast(1)|central_nervous_system(3)|large_intestine(1)|lung(8)|pancreas(1)	14	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)			ccaccacgagcaccaccaccacc	0.690													2	4	---	---	---	---					
MED13	9969	broad.mit.edu	37	17	60142516	60142516	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr17:60142516delA	ENST00000397786.2	-	1	127	c.51delT	c.(49-51)tgfs	p.C17fs		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	17					androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						AGAAGAGGTTACAGTGACAAT	0.716													2	4	---	---	---	---					
AC016995.3	0	broad.mit.edu	37	2	38710019	38710019	+	RNA	DEL	T	T	-	rs2005502	by1000genomes	TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr2:38710019delT	ENST00000417039.1	-	0	696																											CTTtaaaaaataaataaataa	0.244													5	4	---	---	---	---					
NKD2	85409	broad.mit.edu	37	5	1038447	1038449	+	In_Frame_Del	DEL	CAC	CAC	-	rs3840989		TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr5:1038447_1038449delCAC	ENST00000296849.5	+	10	1544_1546	c.1315_1317delCAC	c.(1315-1317)del	p.H447del	NKD2_ENST00000274150.4_3'UTR|NKD2_ENST00000382730.2_In_Frame_Del_p.AP78del	NM_033120.2	NP_149111.1	Q969F2	NKD2_HUMAN	naked cuticle homolog 2 (Drosophila)	447	His-rich.				exocytosis|Wnt receptor signaling pathway	cytoplasmic membrane-bounded vesicle|plasma membrane	calcium ion binding|ubiquitin protein ligase binding			breast(1)|central_nervous_system(3)|large_intestine(1)|lung(8)|pancreas(1)	14	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)			ccaccacgagcaccaccaccacc	0.690													2	4	---	---	---	---					
THSD7A	221981	broad.mit.edu	37	7	11871470	11871481	+	In_Frame_Del	DEL	GCAGCGGCAGCG	GCAGCGGCAGCG	-			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr7:11871470_11871481delGCAGCGGCAGCG	ENST00000423059.3	-	1	343_354	c.92_103delCGCTGCCGCTGC	c.(91-105)ctc>c	p.PLPLL31del		NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	31						integral to membrane				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		agcagcaggagcagcggcagcggcagcggcag	0.774										HNSCC(18;0.044)			4	6	---	---	---	---					
MED13	9969	broad.mit.edu	37	17	60142516	60142516	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr17:60142516delA	ENST00000397786.2	-	1	127	c.51delT	c.(49-51)tgfs	p.C17fs		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	17					androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						AGAAGAGGTTACAGTGACAAT	0.716													2	4	---	---	---	---					
LRCH2	57631	broad.mit.edu	37	X	114414309	114414309	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chrX:114414309delA	ENST00000317135.8	-	4	657	c.627delT	c.(625-627)atfs	p.I209fs	LRCH2_ENST00000538422.1_Frame_Shift_Del_p.I209fs	NM_020871.3	NP_065922.3	Q5VUJ6	LRCH2_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 2	209										breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	19						CATTGCAGCTAATATCCTAAG	0.279													2	4	---	---	---	---					
