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
LPPR5	163404	broad.mit.edu	37	1	99380467	99380467	+	Missense_Mutation	SNP	C	C	T			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr1:99380467C>T	ENST00000370188.3	-	5	1168	c.808G>A	c.(808-810)Gtg>Atg	p.V270M	LPPR5_ENST00000263177.4_Missense_Mutation_p.V270M	NM_001010861.2	NP_001010861.1	Q32ZL2	LPPR5_HUMAN		270						integral to membrane	hydrolase activity										TTATTCACCACGCACACAACC	0.393													4	99	---	---	---	---
USH2A	7399	broad.mit.edu	37	1	216246603	216246603	+	Missense_Mutation	SNP	C	C	T	rs140895792	byFrequency	TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr1:216246603C>T	ENST00000366943.2	-	28	5998	c.5612G>A	c.(5611-5613)gGt>gAt	p.G1871D	USH2A_ENST00000307340.3_Missense_Mutation_p.G1871D|RP11-22M7.2_ENST00000446411.1_RNA|RP11-22M7.2_ENST00000430890.1_RNA|RP11-22M7.2_ENST00000445619.1_RNA			O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1871	Fibronectin type-III 5.|Laminin G-like 2.				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		AACGACAGCACCCCGTGTAAA	0.443										HNSCC(13;0.011)			10	6	---	---	---	---
ALMS1	7840	broad.mit.edu	37	2	73717897	73717897	+	Nonsense_Mutation	SNP	T	T	G			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr2:73717897T>G	ENST00000264448.6	+	10	8919	c.8808T>G	c.(8806-8808)taT>taG	p.Y2936*	ALMS1_ENST00000409009.1_Nonsense_Mutation_p.Y2894*	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2936					G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						AAGCCCCATATGTAGATCATC	0.428													5	136	---	---	---	---
IGKV1-6	28943	broad.mit.edu	37	2	89265896	89265896	+	RNA	SNP	C	C	T			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr2:89265896C>T	ENST00000464162.1	-	0	264																											TGATGGGACCCCACTTTGTAA	0.488													37	120	---	---	---	---
POTEE	445582	broad.mit.edu	37	2	131976101	131976101	+	Silent	SNP	C	C	T			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr2:131976101C>T	ENST00000356920.5	+	1	220	c.126C>T	c.(124-126)aaC>aaT	p.N42N	POTEE_ENST00000358087.5_Silent_p.N42N|PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000404460.1_Intron	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	42							ATP binding										GCAAGAGCAACGTGGGCACTT	0.592													4	160	---	---	---	---
ITGA2	3673	broad.mit.edu	37	5	52344214	52344214	+	Missense_Mutation	SNP	C	C	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr5:52344214C>A	ENST00000296585.5	+	5	552	c.409C>A	c.(409-411)Cag>Aag	p.Q137K		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	137					axon guidance|blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|organ morphogenesis	integrin complex	collagen binding|identical protein binding|receptor activity			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				TCTGTGGGCACAGCAATGTGG	0.438													13	6	---	---	---	---
NRG2	9542	broad.mit.edu	37	5	139232068	139232068	+	Missense_Mutation	SNP	G	G	C			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr5:139232068G>C	ENST00000541337.1	-	6	1524	c.1295C>G	c.(1294-1296)tCc>tGc	p.S432C	NRG2_ENST00000289409.4_Missense_Mutation_p.S492C|CTB-35F21.4_ENST00000504413.1_RNA|NRG2_ENST00000340391.3_Missense_Mutation_p.S295C|NRG2_ENST00000289422.7_Missense_Mutation_p.S506C|NRG2_ENST00000545385.1_Missense_Mutation_p.S500C|NRG2_ENST00000361474.1_Missense_Mutation_p.S498C|NRG2_ENST00000358522.3_Missense_Mutation_p.S500C|NRG2_ENST00000394770.1_3'UTR	NM_001184935.1	NP_001171864.1	O14511	NRG2_HUMAN	neuregulin 2	498					embryo development	extracellular region|integral to membrane|plasma membrane	growth factor activity			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	25			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGAGAACAGGAGTGGCTCCC	0.537													11	26	---	---	---	---
PCDHGA8	9708	broad.mit.edu	37	5	140772818	140772818	+	Silent	SNP	G	G	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr5:140772818G>A	ENST00000398604.2	+	1	438	c.438G>A	c.(436-438)gcG>gcA	p.A146A	PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron	NM_032088.1	NP_114477.1														endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGAAATCGCGGTTCCTGGAG	0.453													26	39	---	---	---	---
C6orf89	221477	broad.mit.edu	37	6	36891198	36891198	+	Missense_Mutation	SNP	C	C	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr6:36891198C>A	ENST00000480824.2	+	9	1319	c.1025C>A	c.(1024-1026)aCc>aAc	p.T342N	C6orf89_ENST00000510325.2_Missense_Mutation_p.T236N|C6orf89_ENST00000359359.2_Missense_Mutation_p.T236N|C6orf89_ENST00000355190.3_Missense_Mutation_p.T349N|C6orf89_ENST00000373685.1_Missense_Mutation_p.T342N			Q6UWU4	CF089_HUMAN	chromosome 6 open reading frame 89	342						integral to membrane				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(2)	15						TGCGATGGAACCGCTTTCTCA	0.473													12	40	---	---	---	---
HGF	3082	broad.mit.edu	37	7	81359092	81359092	+	Missense_Mutation	SNP	T	T	C			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr7:81359092T>C	ENST00000222390.5	-	8	1095	c.869A>G	c.(868-870)gAc>gGc	p.D290G	HGF_ENST00000457544.2_Missense_Mutation_p.D285G	NM_000601.4	NP_000592.3	P14210	HGF_HUMAN	hepatocyte growth factor (hepapoietin A; scatter factor)	290					epithelial to mesenchymal transition|mitosis|platelet activation|platelet degranulation|proteolysis|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling	platelet alpha granule lumen	growth factor activity|serine-type endopeptidase activity			NS(2)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(41)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	75						CATAGTATTGTCAGCTATTGG	0.358													21	42	---	---	---	---
LAMB1	3912	broad.mit.edu	37	7	107626753	107626753	+	Missense_Mutation	SNP	C	C	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr7:107626753C>A	ENST00000393561.1	-	4	735	c.551G>T	c.(550-552)tGg>tTg	p.W184L	LAMB1_ENST00000393560.1_Missense_Mutation_p.W160L|LAMB1_ENST00000222399.6_Missense_Mutation_p.W160L			P07942	LAMB1_HUMAN	laminin, beta 1	160	Laminin N-terminal.				axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm	extracellular matrix structural constituent			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	ATACACACCCCAGGTTTTCCC	0.438													15	40	---	---	---	---
GOT1L1	137362	broad.mit.edu	37	8	37794525	37794525	+	Missense_Mutation	SNP	C	C	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr8:37794525C>A	ENST00000307599.4	-	5	669	c.570G>T	c.(568-570)aaG>aaT	p.K190N		NM_152413.2	NP_689626.2	Q8NHS2	AATC2_HUMAN	glutamic-oxaloacetic transaminase 1-like 1	190					biosynthetic process|cellular amino acid metabolic process	cytoplasm	pyridoxal phosphate binding|transaminase activity			central_nervous_system(1)|endometrium(3)|lung(8)|ovary(1)|prostate(1)	14	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;1.37e-11)			TTGGTGTCAACTTGCAGTCGA	0.537													14	29	---	---	---	---
LRP12	29967	broad.mit.edu	37	8	105509398	105509398	+	Missense_Mutation	SNP	T	T	C			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr8:105509398T>C	ENST00000276654.5	-	5	1490	c.1382A>G	c.(1381-1383)aAt>aGt	p.N461S	LRP12_ENST00000424843.2_Missense_Mutation_p.N442S	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	461	LDL-receptor class A 5.				endocytosis|regulation of growth	coated pit|integral to plasma membrane	low-density lipoprotein receptor activity|protein binding			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			CACACAACGATTGTTTTTACA	0.423													13	44	---	---	---	---
A1CF	29974	broad.mit.edu	37	10	52573721	52573721	+	Missense_Mutation	SNP	C	C	G			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr10:52573721C>G	ENST00000374001.2	-	9	1358	c.1219G>C	c.(1219-1221)Gga>Cga	p.G407R	A1CF_ENST00000373995.3_Missense_Mutation_p.G415R|A1CF_ENST00000493415.1_5'UTR|ASAH2B_ENST00000483649.1_Intron|A1CF_ENST00000395495.1_Missense_Mutation_p.G360R|A1CF_ENST00000373997.3_Missense_Mutation_p.G407R|A1CF_ENST00000395489.2_Missense_Mutation_p.G408R|A1CF_ENST00000282641.2_Missense_Mutation_p.G415R|A1CF_ENST00000373993.1_Missense_Mutation_p.G415R			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor		Required for nuclear localization.				cytidine to uridine editing|mRNA modification|mRNA processing|protein stabilization	apolipoprotein B mRNA editing enzyme complex|endoplasmic reticulum|nucleoplasm	nucleotide binding|protein binding|single-stranded RNA binding			NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3)	29						CTTTTGTCTCCTTTGACCTGG	0.493													17	39	---	---	---	---
LRRTM3	347731	broad.mit.edu	37	10	68687766	68687766	+	Missense_Mutation	SNP	T	T	G			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr10:68687766T>G	ENST00000361320.4	+	2	1670	c.1092T>G	c.(1090-1092)agT>agG	p.S364R	CTNNA3_ENST00000433211.2_Intron|CTNNA3_ENST00000373744.4_Intron	NM_178011.3	NP_821079.3	Q86VH5	LRRT3_HUMAN	leucine rich repeat transmembrane neuronal 3	364						integral to membrane				breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	41						GTGGCAAAAGTACTACAGAGA	0.512													4	36	---	---	---	---
PNLIPRP1	5407	broad.mit.edu	37	10	118352048	118352048	+	Missense_Mutation	SNP	T	T	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr10:118352048T>A	ENST00000528052.1	+	4	396	c.325T>A	c.(325-327)Tgc>Agc	p.C109S	PNLIPRP1_ENST00000480870.2_3'UTR|PNLIPRP1_ENST00000358834.4_Missense_Mutation_p.C109S|PNLIPRP1_ENST00000534537.1_Missense_Mutation_p.C109S|PNLIPRP1_ENST00000442761.1_Missense_Mutation_p.C109S			P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1	109					lipid metabolic process		calcium ion binding|triglyceride lipase activity			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	38				all cancers(201;0.0161)		GACAGACATGTGCAAGGTAGG	0.448													12	28	---	---	---	---
LRP4	4038	broad.mit.edu	37	11	46924428	46924428	+	Silent	SNP	T	T	G			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr11:46924428T>G	ENST00000378623.1	-	2	347	c.105A>C	c.(103-105)gcA>gcC	p.A35A		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	35	LDL-receptor class A 1.				endocytosis|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane	calcium ion binding|receptor activity			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		GAGCACTCACTGCACATGTGA	0.587													11	22	---	---	---	---
OR5L2	26338	broad.mit.edu	37	11	55594965	55594965	+	Missense_Mutation	SNP	G	G	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr11:55594965G>A	ENST00000378397.1	+	1	271	c.271G>A	c.(271-273)Gcc>Acc	p.A91T		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	91					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	p.A91T(1)		breast(2)|kidney(1)|large_intestine(1)|lung(42)|ovary(1)|prostate(3)|skin(1)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	59		all_epithelial(135;0.208)				CAAGGACAAAGCCATCTCCTT	0.463										HNSCC(27;0.073)			5	132	---	---	---	---
TBX3	6926	broad.mit.edu	37	12	115118775	115118775	+	Missense_Mutation	SNP	T	T	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr12:115118775T>A	ENST00000349155.2	-	2	1529	c.566A>T	c.(565-567)gAc>gTc	p.D189V	TBX3_ENST00000257566.3_Missense_Mutation_p.D189V	NM_005996.3	NP_005987.3	O15119	TBX3_HUMAN	T-box 3	189					anterior/posterior axis specification, embryo|anti-apoptosis|cell aging|embryonic arm morphogenesis|embryonic digit morphogenesis|female genitalia development|follicle-stimulating hormone secretion|luteinizing hormone secretion|male genitalia development|mesoderm morphogenesis|negative regulation of myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle|positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter|skeletal system development	nucleus	sequence-specific DNA binding			breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		AGCGGGGCTGTCCGGGTGAAT	0.468													5	58	---	---	---	---
THTPA	79178	broad.mit.edu	37	14	24026130	24026130	+	Missense_Mutation	SNP	G	G	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr14:24026130G>A	ENST00000288014.6	+	1	900	c.164G>A	c.(163-165)cGa>cAa	p.R55Q	RP11-66N24.4_ENST00000555446.1_RNA|THTPA_ENST00000554789.1_Missense_Mutation_p.R55Q|THTPA_ENST00000556015.1_Missense_Mutation_p.R55Q|RP11-66N24.4_ENST00000553985.1_RNA|THTPA_ENST00000404535.3_Missense_Mutation_p.R55Q|THTPA_ENST00000554970.1_Missense_Mutation_p.R55Q|RP11-66N24.4_ENST00000556354.1_RNA			Q9BU02	THTPA_HUMAN	thiamine triphosphatase	55					dephosphorylation|generation of precursor metabolites and energy|thiamine metabolic process	cytosol|nucleolus|soluble fraction	thiamin-triphosphatase activity			large_intestine(1)|prostate(2)	3	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00643)	Thiamine(DB00152)	CACTGGCTGCGACGACGAGAG	0.577													4	10	---	---	---	---
DDX24	57062	broad.mit.edu	37	14	94526642	94526642	+	Missense_Mutation	SNP	G	G	C			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr14:94526642G>C	ENST00000330836.5	-	5	1846	c.1715C>G	c.(1714-1716)aCt>aGt	p.T572S	DDX24_ENST00000555054.1_Missense_Mutation_p.T529S|DDX24_ENST00000544005.1_Missense_Mutation_p.T322S	NM_020414.3	NP_065147.1	Q9GZR7	DDX24_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 24	572					RNA metabolic process	cytoplasm|nucleolus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			cervix(3)|endometrium(4)|kidney(4)|large_intestine(5)|lung(3)|ovary(2)|skin(1)|urinary_tract(1)	23		all_cancers(154;0.12)		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)		TTTCTCATCAGTCTCACAATG	0.498													28	46	---	---	---	---
AHNAK2	113146	broad.mit.edu	37	14	105414154	105414154	+	Missense_Mutation	SNP	C	C	T			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr14:105414154C>T	ENST00000333244.5	-	7	7753	c.7634G>A	c.(7633-7635)gGc>gAc	p.G2545D	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2545						nucleus				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GTCCACTTGGCCAGCCTGGAC	0.642													4	157	---	---	---	---
TCF12	6938	broad.mit.edu	37	15	57484403	57484403	+	Silent	SNP	A	A	G			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr15:57484403A>G	ENST00000267811.5	+	7	742	c.438A>G	c.(436-438)ctA>ctG	p.L146L	TCF12_ENST00000452095.2_Silent_p.L142L|TCF12_ENST00000557843.1_Silent_p.L146L|TCF12_ENST00000333725.5_Silent_p.L146L|TCF12_ENST00000438423.2_Silent_p.L146L	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12	146					immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity		TCF12/NR4A3(2)	breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		CAGCACAGCTATCTTCTTCAG	0.468			T	TEC	extraskeletal myxoid chondrosarcoma								16	42	---	---	---	---
SPOP	8405	broad.mit.edu	37	17	47696644	47696644	+	Missense_Mutation	SNP	A	A	C			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr17:47696644A>C	ENST00000393331.3	-	6	774	c.304T>G	c.(304-306)Ttc>Gtc	p.F102V	SPOP_ENST00000503676.1_Missense_Mutation_p.F102V|SPOP_ENST00000347630.2_Missense_Mutation_p.F102V|SPOP_ENST00000393328.2_Missense_Mutation_p.F102V|SPOP_ENST00000504102.1_Missense_Mutation_p.F102V	NM_001007226.1|NM_001007227.1	NP_001007227.1|NP_001007228.1	O43791	SPOP_HUMAN	speckle-type POZ protein	102	MATH.|Required for nuclear localization.				mRNA processing	nucleus	protein binding			endometrium(18)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(3)|prostate(33)	63						GAGAATTTGAATTTTGCCCGA	0.408										Prostate(2;0.17)			23	62	---	---	---	---
GYS1	2997	broad.mit.edu	37	19	49490530	49490530	+	Missense_Mutation	SNP	T	T	C			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr19:49490530T>C	ENST00000323798.3	-	3	609	c.413A>G	c.(412-414)aAc>aGc	p.N138S	GYS1_ENST00000263276.6_Intron|GYS1_ENST00000541188.1_Missense_Mutation_p.N58S|GYS1_ENST00000544287.1_Intron|GYS1_ENST00000540532.1_Missense_Mutation_p.N58S|GYS1_ENST00000457974.1_5'UTR	NM_002103.4	NP_002094.2	P13807	GYS1_HUMAN	glycogen synthase 1 (muscle)	138					glucose metabolic process|glycogen biosynthetic process	cytosol	glycogen (starch) synthase activity|protein binding			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000164)|all cancers(93;0.000226)|GBM - Glioblastoma multiforme(486;0.00561)|Epithelial(262;0.0286)		CACTCCGATGTTGCAGGTATC	0.637													3	5	---	---	---	---
NCOA3	8202	broad.mit.edu	37	20	46267838	46267838	+	Missense_Mutation	SNP	A	A	G			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr20:46267838A>G	ENST00000372004.3	+	14	2815	c.2599A>G	c.(2599-2601)Agt>Ggt	p.S867G	NCOA3_ENST00000371998.3_Missense_Mutation_p.S867G|NCOA3_ENST00000371997.3_Missense_Mutation_p.S877G|NCOA3_ENST00000341724.6_Intron	NM_001174087.1|NM_001174088.1|NM_006534.3|NM_181659.2	NP_001167558.1|NP_001167559.1|NP_006525.2|NP_858045.1	Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	867					androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleoplasm	androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						TGTTGGCTCAAGTCCTCCAGT	0.438													25	56	---	---	---	---
THOC5	8563	broad.mit.edu	37	22	29904508	29904508	+	Splice_Site	SNP	C	C	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr22:29904508C>A	ENST00000490103.1	-	20	2112	c.1990G>T	c.(1990-1992)Ggt>Tgt	p.G664C	THOC5_ENST00000397873.2_Splice_Site_p.G664C|THOC5_ENST00000397871.1_Splice_Site_p.G664C|THOC5_ENST00000397872.1_Splice_Site_p.G664C	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN	THO complex 5	664					intronless viral mRNA export from host nucleus|monocyte differentiation|mRNA processing|primitive hemopoiesis|RNA splicing	cytoplasm|intermediate filament cytoskeleton|THO complex part of transcription export complex	protein binding|RNA binding			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CTGCTAGGACCCCTAGAGAAA	0.458													3	14	---	---	---	---
ATM	472	broad.mit.edu	37	11	108180935	108180935	+	Frame_Shift_Del	DEL	T	T	-			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr11:108180935delT	ENST00000278616.4	+	39	6196	c.5811delT	c.(5809-5811)aatfs	p.N1937fs	ATM_ENST00000452508.2_Frame_Shift_Del_p.N1937fs|C11orf65_ENST00000525729.1_Intron	NM_000051.3	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated	1937					cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		TGGATTTAAATTATCTAGAAG	0.328			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)			12	34	---	---	---	---
