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
ALX3	257	broad.mit.edu	37	1	110604148	110604148	+	Missense_Mutation	SNP	C	C	T			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr1:110604148C>T	uc001dzb.3	-	2	720	c.632G>A	c.(631-633)cGc>cAc	p.R211H		NM_006492	NP_006483	O95076	ALX3_HUMAN	Homo sapiens ALX homeobox 3 (ALX3), mRNA.	211						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6		all_cancers(81;2.35e-05)|all_epithelial(167;7.69e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.015)|all cancers(265;0.0706)|Epithelial(280;0.0758)|Colorectal(144;0.113)|LUSC - Lung squamous cell carcinoma(189;0.135)		ATAACGCTCGCGCTTCCGCCA	0.622000													23	42					0	0	1	0	0
CCT8L2	150160	broad.mit.edu	37	22	17071981	17071981	+	Missense_Mutation	SNP	T	T	A			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr22:17071981T>A	uc002zlp.1	-	0	1720	c.1460A>T	c.(1459-1461)aAt>aTt	p.N487I		NM_014406	NP_055221	Q96SF2	TCPQM_HUMAN	Homo sapiens chaperonin containing TCP1, subunit 8 (theta)-like 2 (CCT8L2), mRNA.	487					cellular protein metabolic process	cytoplasm	ATP binding|anion channel activity|calcium-activated potassium channel activity			breast(3)|endometrium(7)|kidney(1)|large_intestine(8)|liver(2)|lung(37)|ovary(3)|prostate(3)|skin(2)|stomach(1)	67	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				CTGGGCCACATTTATTATCCC	0.517000													64	92					0	0	1	0	0
GLI1	2735	broad.mit.edu	37	12	57865272	57865272	+	Missense_Mutation	SNP	G	G	T			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr12:57865272G>T	uc001snx.3	+	11	2843	c.2749G>T	c.(2749-2751)Gat>Tat	p.D917Y	GLI1_uc021qzi.1_Missense_Mutation_p.D876Y|GLI1_uc009zpq.3_Missense_Mutation_p.D789Y	NM_005269	NP_001153517	P08151	GLI1_HUMAN	Homo sapiens GLI family zinc finger 1 (GLI1), transcript variant 1, mRNA.	917					epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	transcription regulatory region DNA binding|zinc ion binding			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			GGGCAGGGAAGATGCCCCCGC	0.562000													5	64					0	0	1	0	0
HSP90AB4P	664618	broad.mit.edu	37	15	58983569	58983569	+	Silent	SNP	C	C	T			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr15:58983569C>T	uc002afh.1	-	2	1251	c.1251G>A	c.(1249-1251)gaG>gaA	p.E417E	ADAM10_uc002afd.1_Intron|ADAM10_uc010bgc.1_Intron|ADAM10_uc010ugz.1_Intron|ADAM10_uc002afe.1_Intron					Homo sapiens heat shock protein 90kDa alpha (cytosolic), class B member 4, pseudogene (HSP90AB4P), non-coding RNA.																		TATATATTACCTCGAAGCCCT	0.493000													3	9					0	0	1	0	0
PDE1B	5153	broad.mit.edu	37	12	54966490	54966490	+	Missense_Mutation	SNP	A	A	G			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr12:54966490A>G	uc001sgd.2	+	6	1093	c.700A>G	c.(700-702)Aca>Gca	p.T234A	PDE1B_uc010soz.2_Missense_Mutation_p.T97A|PDE1B_uc010spa.1_Missense_Mutation_p.T193A|PDE1B_uc001sge.3_Missense_Mutation_p.T214A|PDE1B_uc001sgf.3_Missense_Mutation_p.T97A|PDE1B_uc009znq.3_Missense_Mutation_p.T30A	NM_000924	NP_000915	Q01064	PDE1B_HUMAN	Homo sapiens phosphodiesterase 1B, calmodulin-dependent (PDE1B), transcript variant 1, mRNA.	234	Catalytic (By similarity).				activation of phospholipase C activity|apoptosis|nerve growth factor receptor signaling pathway|platelet activation	cytosol|nucleus	3',5'-cyclic-AMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			endometrium(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(4)	31						TGTTACCCAGACAGTCCATTG	0.512000													32	301					0	0	1	0	0
PTPRC	5788	broad.mit.edu	37	1	198721481	198721481	+	Missense_Mutation	SNP	T	T	C			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr1:198721481T>C	uc001gur.1	+	29	3485	c.3305T>C	c.(3304-3306)tTt>tCt	p.F1102S	PTPRC_uc001gut.1_Missense_Mutation_p.F941S	NM_002838	NP_002829	P08575	PTPRC_HUMAN	Homo sapiens protein tyrosine phosphatase, receptor type, C (PTPRC), transcript variant 1, mRNA.	1102	Tyrosine-protein phosphatase 2.				B cell proliferation|B cell receptor signaling pathway|T cell differentiation|T cell receptor signaling pathway|axon guidance|defense response to virus|immunoglobulin biosynthetic process|negative regulation of T cell mediated cytotoxicity|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|positive regulation of B cell proliferation|positive regulation of T cell proliferation|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of protein kinase activity|regulation of S phase|release of sequestered calcium ion into cytosol	focal adhesion|integral to plasma membrane|membrane raft	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						CTTCGTGTCTTTGAACTGAGA	0.373000													16	26					0	0	1	0	0
RYR3	6263	broad.mit.edu	37	15	33795933	33795933	+	Silent	SNP	C	C	T			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr15:33795933C>T	uc001zhi.3	+	2	343	c.273C>T	c.(271-273)ggC>ggT	p.G91G	RYR3_uc010bar.3_Silent_p.G91G	NM_001036	NP_001027	Q15413	RYR3_HUMAN	Homo sapiens ryanodine receptor 3 (RYR3), transcript variant 1, mRNA.	91					cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		AAAATGGCGGCGAAGGGGTGA	0.478000													6	15					0	0	1	0	0
PNPLA4	8228	broad.mit.edu	37	X	7880088	7880088	+	Missense_Mutation	SNP	A	A	G			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chrX:7880088A>G	uc011mhq.1	-	4	620	c.458T>C	c.(457-459)cTa>cCa	p.L153P	PNPLA4_uc011mhr.1_Missense_Mutation_p.L153P|PNPLA4_uc011mhs.1_Missense_Mutation_p.L66P	NM_004650	NP_001166143	P41247	PLPL4_HUMAN	Homo sapiens patatin-like phospholipase domain containing 4 (PNPLA4), transcript variant 1, mRNA.	153	Patatin.				lipid catabolic process		triglyceride lipase activity			kidney(1)|large_intestine(3)|lung(2)|prostate(1)	7		Colorectal(8;0.0329)|Medulloblastoma(8;0.232)				GTATTCCACTAGCTTCAGTCC	0.378000													34	5					0	0	1	0	0
TBX5	6910	broad.mit.edu	37	12	114841632	114841632	+	Silent	SNP	G	G	A			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr12:114841632G>A	uc001tvo.3	-	1	567	c.72C>T	c.(70-72)tgC>tgT	p.C24C	TBX5_uc001tvp.3_Silent_p.C24C|TBX5_uc001tvq.3_Intron|TBX5_uc010syv.2_Silent_p.C24C	NM_181486	NP_542448	Q99593	TBX5_HUMAN	Homo sapiens T-box 5 (TBX5), transcript variant 4, mRNA.	24				GFGLAHTPLEPDAKDLPCDSKPESALGAPSKSPSSPQAAFT QQ -> ALAGAHLWSLTQKTCLRFEPRARSGPPASPPGRPR SRLHPA (in Ref. 1; CAA70592).	cardiac left ventricle formation|cell migration involved in coronary vasculogenesis|cell-cell signaling|embryonic arm morphogenesis|induction of apoptosis|negative regulation of cardiac muscle cell proliferation|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|pericardium development|positive regulation of cardioblast differentiation|positive regulation of transcription from RNA polymerase II promoter|ventricular septum development	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(29)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)		GTTTCGAATCGCAGGGCAGGT	0.701000													25	41					0	0	1	0	0
AMZ1	155185	broad.mit.edu	37	7	2752278	2752278	+	Missense_Mutation	SNP	A	A	C	rs148314719	byFrequency	TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr7:2752278A>C	uc003smr.1	+	6	1624	c.1263A>C	c.(1261-1263)gaA>gaC	p.E421D	AMZ1_uc003sms.1_3'UTR|AMZ1_uc011jwa.1_Missense_Mutation_p.E170D	NM_133463	NP_597720	Q400G9	AMZ1_HUMAN	Homo sapiens archaelysin family metallopeptidase 1 (AMZ1), mRNA.	421							metallopeptidase activity|zinc ion binding			breast(2)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	16		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)		TGCAGCGGGAAGTGGCAGAGG	0.692000													16	25					0	0	1	0	0
SLC18A1	6570	broad.mit.edu	37	8	20004825	20004825	+	Missense_Mutation	SNP	C	C	T			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr8:20004825C>T	uc011kyq.2	-	15	1879	c.1408G>A	c.(1408-1410)Gtc>Atc	p.V470I	SLC18A1_uc003wzm.3_Missense_Mutation_p.V470I|SLC18A1_uc011kyr.2_Intron|SLC18A1_uc003wzn.3_Missense_Mutation_p.V438I|SLC18A1_uc010ltf.3_Non-coding_Transcript	NM_001135691	NP_003044	P54219	VMAT1_HUMAN	Homo sapiens solute carrier family 18 (vesicular monoamine), member 1 (SLC18A1), transcript variant 1, mRNA.	470					neurotransmitter transport	clathrin sculpted monoamine transport vesicle membrane|integral to membrane|membrane fraction	drug transmembrane transporter activity|monoamine transmembrane transporter activity			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	29				Colorectal(74;0.0747)		GGAGCATAGACGATGTTGATG	0.512000													13	51					0	0	1	0	0
MC3R	4159	broad.mit.edu	37	20	54823920	54823920	+	Silent	SNP	G	G	T			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr20:54823920G>T	uc002xxb.2	+	0	133	c.21G>T	c.(19-21)ctG>ctT	p.L7L		NM_019888	NP_063941	P41968	MC3R_HUMAN	Homo sapiens melanocortin 3 receptor (MC3R), mRNA.	44					activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|positive regulation of cAMP biosynthetic process	integral to plasma membrane	melanocyte-stimulating hormone receptor activity|neuropeptide binding|protein binding			breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(3)|skin(1)	26			Colorectal(105;0.202)			CGTGCTGCCTGCCCTCTGTTC	0.567000													66	117					0	0	1	0	0
CLPSL1	340204	broad.mit.edu	37	6	35754858	35754858	+	Silent	SNP	C	C	T			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr6:35754858C>T	uc003old.4	+	1	240	c.183C>T	c.(181-183)tgC>tgT	p.C61C		NM_001010886	NP_001010886	A2RUU4	CF127_HUMAN	Homo sapiens chromosome 6 open reading frame 127 (C6orf127), mRNA.	61					digestion|lipid catabolic process	extracellular region	enzyme activator activity										AGTCGCACTGCGCGGAGAAGG	0.662000													6	32					0	0	1	0	0
NCOA6	23054	broad.mit.edu	37	20	33345744	33345744	+	Silent	SNP	C	C	T			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr20:33345744C>T	uc002xav.3	-	7	3378	c.807G>A	c.(805-807)caG>caA	p.Q269Q	NCOA6_uc002xaw.3_Silent_p.Q269Q|NCOA6_uc021wcd.1_Silent_p.Q269Q|NCOA6_uc021wce.1_Silent_p.Q269Q|NCOA6_uc021wcf.1_Silent_p.Q269Q|NCOA6_uc010gew.1_Silent_p.Q226Q	NM_014071	NP_054790	Q14686	NCOA6_HUMAN	Homo sapiens nuclear receptor coactivator 6 (NCOA6), transcript variant 1, mRNA.	269	CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.				DNA recombination|DNA repair|DNA replication|brain development|cellular lipid metabolic process|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter	transcription factor complex	chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding	p.Q269Q(29)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						gctgctgctgctgttgttgtt	0.537000													6	37					0	0	1	0	0
PDZD2	23037	broad.mit.edu	37	5	32089674	32089674	+	Silent	SNP	G	G	A	rs150986745		TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr5:32089674G>A	uc003jhl.3	+	19	6508	c.6120G>A	c.(6118-6120)gcG>gcA	p.A2040A	PDZD2_uc003jhm.3_Silent_p.A2040A	NM_178140	NP_835260	O15018	PDZD2_HUMAN	Homo sapiens PDZ domain containing 2 (PDZD2), mRNA.	2040					cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						GTCCGGCAGCGTCTAGGAACG	0.647000													12	248					0	0	1	0	0
GRID2	2895	broad.mit.edu	37	4	94138039	94138039	+	Missense_Mutation	SNP	G	G	T			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr4:94138039G>T	uc011cdt.2	+	5	1198	c.940G>T	c.(940-942)Gat>Tat	p.D314Y	GRID2_uc010ikx.3_Missense_Mutation_p.D314Y|GRID2_uc011cdu.2_Missense_Mutation_p.D219Y|GRID2_uc010ikz.1_5'UTR	NM_001510	NP_001501	O43424	GRID2_HUMAN	Homo sapiens glutamate receptor, ionotropic, delta 2 (GRID2), mRNA.	314					glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity	p.K313Q(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)	TGATCCAAAGGATCCATTTGC	0.413000													50	66					0	0	1	0	0
CNTNAP1	8506	broad.mit.edu	37	17	40843294	40843294	+	Silent	SNP	C	C	T	rs144310425		TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr17:40843294C>T	uc002iay.3	+	13	2415	c.2199C>T	c.(2197-2199)gaC>gaT	p.D733D	CNTNAP1_uc010wgs.2_Non-coding_Transcript	NM_003632	NP_003623	P78357	CNTP1_HUMAN	Homo sapiens contactin associated protein 1 (CNTNAP1), mRNA.	733	Fibrinogen C-terminal.				axon guidance|cell adhesion	paranode region of axon	SH3 domain binding|SH3/SH2 adaptor activity|receptor activity|receptor binding			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|lung(15)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.143)		GCAACTGTGACGCTGACCAGC	0.632000													65	109					0	0	1	0	0
AL117485	0	broad.mit.edu	37	22	18844763	18844763	+	RNA	SNP	T	T	C			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr22:18844763T>C	uc002zoe.3	+	3		c.2017T>C			AL117485_uc002zof.3_5'Flank					Homo sapiens cDNA FLJ76361 complete cds.																		TCACAGCCTCTGAGGGCAGCA	0.562000													3	13					0	0	1	0	0
TAB2	23118	broad.mit.edu	37	6	149700269	149700269	+	Silent	SNP	A	A	G			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr6:149700269A>G	uc003qmj.3	+	2	1396	c.1218A>G	c.(1216-1218)acA>acG	p.T406T	TAB2_uc011eec.2_Silent_p.T374T|TAB2_uc010kia.1_Silent_p.T406T|TAB2_uc010kib.2_Silent_p.T406T|TAB2_uc003qmk.4_Non-coding_Transcript	NM_015093	NP_055908	Q9NYJ8	TAB2_HUMAN	Homo sapiens TGF-beta activated kinase 1/MAP3K7 binding protein 2 (TAB2), mRNA.	406					I-kappaB kinase/NF-kappaB cascade|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|T cell receptor signaling pathway|Toll signaling pathway|activation of MAPK activity|heart development|innate immune response|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|stress-activated MAPK cascade|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	K63-linked polyubiquitin binding|zinc ion binding			breast(2)|endometrium(6)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	22						ATCAGCCCACACTCTTCATAT	0.502000													13	25					0	0	1	0	0
CACNB2	783	broad.mit.edu	37	10	18429692	18429692	+	Silent	SNP	G	G	T			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr10:18429692G>T	uc001ipr.2	+	0	87	c.27G>T	c.(25-27)tcG>tcT	p.S9S	CACNB2_uc001ipt.2_Silent_p.S9S|CACNB2_uc009xjz.1_Silent_p.S9S|CACNB2_uc001ips.2_Silent_p.S9S|CACNB2_uc010qcl.2_5'Flank|CACNB2_uc001ipu.3_5'Flank|CACNB2_uc001ipv.3_5'Flank|CACNB2_uc009xka.2_5'Flank	NM_201596	NP_963890	Q08289	CACB2_HUMAN	Homo sapiens calcium channel, voltage-dependent, beta 2 subunit (CACNB2), transcript variant 2, mRNA.	9					axon guidance|neuromuscular junction development	integral to plasma membrane|sarcolemma|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|stomach(2)	31					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	TGTCCAAGTCGCCTCCCACAG	0.711000													9	2					0	0	1	0	0
OTOF	9381	broad.mit.edu	37	2	26696866	26696866	+	Missense_Mutation	SNP	C	C	T			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr2:26696866C>T	uc002rhk.3	-	26	3528	c.3401G>A	c.(3400-3402)cGa>cAa	p.R1134Q	OTOF_uc010yla.2_5'Flank|OTOF_uc002rhh.3_Missense_Mutation_p.R387Q|OTOF_uc002rhi.3_Missense_Mutation_p.R444Q|OTOF_uc002rhj.3_Missense_Mutation_p.R387Q	NM_194248	NP_919224	Q9HC10	OTOF_HUMAN	Homo sapiens otoferlin (OTOF), transcript variant 1, mRNA.	1134					cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis	basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane	calcium ion binding			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CACCTCCACTCGGTACTTGCT	0.647000													30	43					0	0	1	0	0
VAV2	7410	broad.mit.edu	37	9	136857224	136857224	+	Missense_Mutation	SNP	G	G	T			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr9:136857224G>T	uc004ces.3	-	0	223	c.177C>A	c.(175-177)gaC>gaA	p.D59E	VAV2_uc004cer.3_Missense_Mutation_p.D59E	NM_001134398	NP_001127870	P52735	VAV2_HUMAN	Homo sapiens vav 2 guanine nucleotide exchange factor (VAV2), transcript variant 1, mRNA.	59	CH.				angiogenesis|apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity|metal ion binding			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(1)	35				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)		GGAAGTTGATGTCCTTGAGGT	0.726000													8	17					0	0	1	0	0
BCLAF1	9774	broad.mit.edu	37	6	136599814	136599814	+	Nonsense_Mutation	SNP	G	G	A			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr6:136599814G>A	uc003qgx.1	-	3	458	c.205C>T	c.(205-207)Cga>Tga	p.R69*	BCLAF1_uc003qgy.1_Nonsense_Mutation_p.R67*|BCLAF1_uc011edc.1_Non-coding_Transcript|BCLAF1_uc011edd.1_Non-coding_Transcript|BCLAF1_uc011ede.1_Nonsense_Mutation_p.R67*|BCLAF1_uc003qgw.1_Nonsense_Mutation_p.R69*	NM_014739	NP_055554	Q9NYF8	BCLF1_HUMAN	Homo sapiens BCL2-associated transcription factor 1 (BCLAF1), transcript variant 1, mRNA.	69					induction of apoptosis|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		CCATAAGGTCGTCTCATTCCT	0.433000													9	79					0	0	1	0	0
LRIG2	9860	broad.mit.edu	37	1	113658960	113658960	+	Missense_Mutation	SNP	C	C	T			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr1:113658960C>T	uc001edf.1	+	15	2780	c.2582C>T	c.(2581-2583)aCg>aTg	p.T861M	LRIG2_uc009wgn.1_Missense_Mutation_p.T758M	NM_014813	NP_055628	O94898	LRIG2_HUMAN	Homo sapiens leucine-rich repeats and immunoglobulin-like domains 2 (LRIG2), mRNA.	861						cytoplasm|integral to membrane|plasma membrane				breast(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(10)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	31	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)		TCCCAAGGAACGCTGTCTGAG	0.488000													14	18					0	0	1	0	0
KCNJ4	3761	broad.mit.edu	37	22	38823055	38823055	+	Silent	SNP	C	C	G			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr22:38823055C>G	uc003avs.1	-	1	1180	c.1083G>C	c.(1081-1083)ctG>ctC	p.L361L	KCNJ4_uc003avt.1_Silent_p.L361L|KCNJ4_uc021wpp.1_Silent_p.L361L	NM_004981	NP_690607	P48050	IRK4_HUMAN	Homo sapiens potassium inwardly-rectifying channel, subfamily J, member 4 (KCNJ4), transcript variant 2, mRNA.	361					synaptic transmission	basolateral plasma membrane|voltage-gated potassium channel complex	PDZ domain binding|inward rectifier potassium channel activity			endometrium(7)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23	Melanoma(58;0.0286)					GTGGGGCGGGCAGCACGGTGA	0.642000													4	59					0	0	1	0	0
SRSF4	6429	broad.mit.edu	37	1	29475219	29475221	+	In_Frame_Del	DEL	CTT	CTT	-	rs138237342	by1000genomes	TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr1:29475219_29475221delCTT	uc001bro.3	-	5	1559_1561	c.1186_1188delAAG	c.(1186-1188)aagdel	p.K396del	SRSF4_uc010ofy.2_3'UTR	NM_005626	NP_005617	Q08170	SRSF4_HUMAN	Homo sapiens serine/arginine-rich splicing factor 4 (SRSF4), mRNA.	396	Arg/Ser-rich (RS domain).				mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nuclear speck	RNA binding|nucleotide binding			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(1)	27						CAGTGTCTTCCTTCTTCTTCTTC	0.601													7	151	---	---	---	---					
KIAA0907	22889	broad.mit.edu	37	1	155886422	155886423	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr1:155886422_155886423delCT	uc001fmi.1	-	11	1570_1571	c.1546_1547delAG	c.(1546-1548)aggfs	p.R516fs	KIAA0907_uc001fmj.1_Frame_Shift_Del_p.R516fs|KIAA0907_uc009wrl.1_Non-coding_Transcript	NM_014949	NP_055764	Q7Z7F0	K0907_HUMAN	Homo sapiens KIAA0907 (KIAA0907), mRNA.	516								p.R516fs*21(2)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|urinary_tract(1)	21	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)			TTACCTGTCCCTCTCTCTCTCT	0.396													7	151	---	---	---	---					
GRB14	2888	broad.mit.edu	37	2	165365287	165365288	+	Frame_Shift_Ins	INS	-	-	T			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr2:165365287_165365288insT	uc002ucl.3	-	6	1432_1433	c.891_892insA	c.(889-894)aaacatfs	p.K297fs	GRB14_uc010zcv.2_Frame_Shift_Ins_p.K210fs	NM_004490	NP_004481	Q14449	GRB14_HUMAN	Homo sapiens growth factor receptor-bound protein 14 (GRB14), mRNA.	297	PH.				blood coagulation|leukocyte migration	Golgi membrane|cytosol|endosome membrane|microsome|plasma membrane	SH3/SH2 adaptor activity	p.K297fs*23(4)		breast(3)|endometrium(2)|large_intestine(6)|lung(10)|ovary(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32						GGTGCTCCATGTTTTTTTTTGC	0.371													7	126	---	---	---	---					
OR52D1	390066	broad.mit.edu	37	11	5510687	5510688	+	Frame_Shift_Ins	INS	-	-	C	rs7101919	byFrequency	TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr11:5510687_5510688insC	uc010qzg.2	+	0	773_774	c.751_752insC	c.(751-753)atcfs	p.I251fs	HBG1_uc001mak.1_Intron|HBE1_uc001mam.1_Intron|OR51B5_uc021qcv.1_Intron|OR51B5_uc001maq.2_Intron	NM_001005163	NP_001005163	Q9H346	O52D1_HUMAN	Homo sapiens olfactory receptor, family 52, subfamily D, member 1 (OR52D1), mRNA.	251			I -> T (in dbSNP:rs7101919).		sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	22		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.46e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CATTGGCATCATCCTGGTTTTC	0.495													13	111	---	---	---	---					
CD3EAP	10849	broad.mit.edu	37	19	45911859	45911861	+	In_Frame_Del	DEL	GAA	GAA	-			TCGA-J4-A6M7-01A-11D-A31L-08	TCGA-J4-A6M7-10A-01D-A31J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68eadfba-d2ec-47a5-9ae8-cbbf066962e8	a8d17ab3-05e9-4f09-a76b-c5740ee14f41	g.chr19:45911859_45911861delGAA	uc002pbr.1	+	2	645_647	c.639_641delGAA	c.(637-642)cggaag>cgg	p.K219del	PPP1R13L_uc002pbo.3_5'Flank|PPP1R13L_uc002pbp.2_5'Flank|CD3EAP_uc002pbq.1_In_Frame_Del_p.K217del|ERCC1_uc002pbt.2_3'UTR|ERCC1_uc002pbs.2_3'UTR|ERCC1_uc002pbu.2_3'UTR	NM_012099	NP_036231	O15446	RPA34_HUMAN	Homo sapiens CD3e molecule, epsilon associated protein (CD3EAP), mRNA.	217					rRNA transcription|transmembrane receptor protein tyrosine kinase signaling pathway	RNA polymerase I transcription factor complex|chromosome	DNA-directed RNA polymerase activity	p.N218fs*58(2)		breast(2)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	11		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0251)		TGGATGTGCGGAAGAAGAAGAAG	0.581													7	151	---	---	---	---					
