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
ABCA4	24	broad.mit.edu	37	1	94463458	94463458	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr1:94463458G>A	uc001dqh.3	-	47	6792	c.6688C>T	c.(6688-6690)Ctc>Ttc	p.L2230F		NM_000350	NP_000341	P78363	ABCA4_HUMAN	Homo sapiens ATP-binding cassette, sub-family A (ABC1), member 4 (ABCA4), mRNA.	2230					phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		TCCTCGATGAGCAGGCTGTCC	0.592												
NBPF10	100132406	broad.mit.edu	37	1	145324371	145324371	+	Missense_Mutation	SNP	T	T	C			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr1:145324371T>C	uc021oul.1	+	27	3601	c.3566T>C	c.(3565-3567)gTa>gCa	p.V1189A	NBPF10_uc021ots.1_Intron|NBPF10_uc010oye.2_Intron|NBPF10_uc010oyi.2_Intron|NBPF10_uc010oyj.2_Intron|NBPF10_uc010oyl.2_Intron|NBPF10_uc001enc.2_Intron|NBPF10_uc021oum.1_Intron|NBPF10_uc021oun.1_Intron|NBPF10_uc021ouo.1_Intron|NBPF10_uc021oup.1_Intron|NBPF10_uc010oyp.1_Non-coding_Transcript	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	Homo sapiens neuroblastoma breakpoint family, member 10 (NBPF10), mRNA.	1189										NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		CTGCTGGAGGTAGTAGCGCCT	0.498												
OPTC	26254	broad.mit.edu	37	1	203472741	203472741	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr1:203472741C>T	uc001gzu.1	+	6	1008	c.892C>T	c.(892-894)Cgc>Tgc	p.R298C		NM_014359	NP_055174	Q9UBM4	OPT_HUMAN	Homo sapiens opticin (OPTC), mRNA.	298						proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding			breast(1)|cervix(1)|kidney(5)|large_intestine(3)|lung(8)|pancreas(1)|stomach(1)	20			BRCA - Breast invasive adenocarcinoma(75;0.109)			CAAACACACCCGCAGGCAGCT	0.587												
PIGR	5284	broad.mit.edu	37	1	207109154	207109154	+	Missense_Mutation	SNP	A	A	T			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr1:207109154A>T	uc001hez.3	-	4	1239	c.1055T>A	c.(1054-1056)aTt>aAt	p.I352N	PIGR_uc009xbz.3_Missense_Mutation_p.I352N	NM_002644	NP_002635	P01833	PIGR_HUMAN	Homo sapiens polymeric immunoglobulin receptor (PIGR), mRNA.	352	Ig-like V-type 3.					extracellular region|integral to plasma membrane	protein binding			central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						GCTGCGGGGAATCGTGGACTC	0.602											OREG0014186	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)
SLC18A2	6571	broad.mit.edu	37	10	119003545	119003545	+	Missense_Mutation	SNP	C	C	T	rs140529367		TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr10:119003545C>T	uc001ldd.2	+	2	348	c.185C>T	c.(184-186)aCg>aTg	p.T62M	SLC18A2_uc009xyy.2_5'UTR	NM_003054	NP_003045	Q05940	VMAT2_HUMAN	Homo sapiens solute carrier family 18 (vesicular monoamine), member 2 (SLC18A2), mRNA.	62					neurotransmitter secretion	clathrin sculpted monoamine transport vesicle membrane|integral to plasma membrane|membrane fraction	monoamine transmembrane transporter activity			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)	29		Colorectal(252;0.19)		all cancers(201;0.029)	Alseroxylon(DB00386)|Reserpine(DB00206)|Tetrabenazine(DB04844)	GAAATCCAGACGGCCAGGCCA	0.493												
CLRN3	119467	broad.mit.edu	37	10	129682096	129682096	+	Silent	SNP	C	C	T			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr10:129682096C>T	uc001lka.1	-	1	436	c.273G>A	c.(271-273)tcG>tcA	p.S91S	CLRN3_uc001ljz.1_Silent_p.S23S	NM_152311	NP_689524	Q8NCR9	CLRN3_HUMAN	Homo sapiens clarin 3 (CLRN3), mRNA.	91						integral to membrane				endometrium(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	6		all_epithelial(44;0.00168)|all_lung(145;0.0586)|Lung NSC(174;0.0765)|all_neural(114;0.201)|Glioma(114;0.222)|Colorectal(57;0.235)				GGATAGTCACCGAATGCAGAG	0.448												
OR51G1	79324	broad.mit.edu	37	11	4945520	4945520	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr11:4945520G>A	uc010qyr.2	-	0	50	c.50C>T	c.(49-51)aCg>aTg	p.T17M		NM_001005237	NP_001005237	Q8NGK1	O51G1_HUMAN	Homo sapiens olfactory receptor, family 51, subfamily G, member 1 (OR51G1), mRNA.	17					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			NS(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(4)|soft_tissue(1)	25		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		TTGGAAGCCCGTCAGGAAGAA	0.458												
OR51A2	401667	broad.mit.edu	37	11	4976936	4976936	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr11:4976936A>G	uc010qyt.2	-	0	8	c.8T>C	c.(7-9)aTt>aCt	p.I3T		NM_001004748	NP_001004748	Q8NGJ7	O51A2_HUMAN	Homo sapiens olfactory receptor, family 51, subfamily A, member 2 (OR51A2), mRNA.	3					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGTGTTGATAATGGACATGAT	0.428												
MS4A7	58475	broad.mit.edu	37	11	60161321	60161321	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr11:60161321G>A	uc001npe.3	+	6	855	c.710G>A	c.(709-711)cGg>cAg	p.R237Q	MS4A7_uc001npf.3_Missense_Mutation_p.R237Q|MS4A7_uc001npg.3_Missense_Mutation_p.R192Q|MS4A7_uc001nph.3_Missense_Mutation_p.R192Q|MS4A14_uc001npi.3_Intron	NM_206939	NP_996822	Q9GZW8	MS4A7_HUMAN	Homo sapiens membrane-spanning 4-domains, subfamily A, member 7 (MS4A7), transcript variant 3, mRNA.	237						integral to membrane	receptor activity			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(2)|lung(8)|ovary(1)|skin(1)	20						AGTTCTTCACGGTCTTGGATA	0.373												
VWCE	220001	broad.mit.edu	37	11	61032003	61032003	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr11:61032003G>A	uc001nra.3	-	18	2465	c.2186C>T	c.(2185-2187)gCc>gTc	p.A729V	VWCE_uc001nrb.3_Non-coding_Transcript	NM_152718	NP_689931	Q96DN2	VWCE_HUMAN	Homo sapiens von Willebrand factor C and EGF domains (VWCE), mRNA.	729	VWFC 6.					extracellular region	calcium ion binding			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						GGCAGGGTCGGCACAGGCCCG	0.592												
HTR3A	3359	broad.mit.edu	37	11	113857684	113857684	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr11:113857684G>A	uc010rxb.2	+	6	1401	c.1168G>A	c.(1168-1170)Gcc>Acc	p.A390T	HTR3A_uc010rxa.2_Missense_Mutation_p.A358T|HTR3A_uc009yyx.3_Non-coding_Transcript|HTR3A_uc010rxc.2_Missense_Mutation_p.A337T	NM_213621	NP_998786	P46098	5HT3A_HUMAN	Homo sapiens 5-hydroxytryptamine (serotonin) receptor 3A (HTR3A), transcript variant 1, mRNA.	352					digestion|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	serotonin binding|serotonin receptor activity|serotonin-activated cation-selective channel activity	p.A384T(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	36		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	Alosetron(DB00969)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Dolasetron(DB00757)|Granisetron(DB00889)|Mirtazapine(DB00370)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Tubocurarine(DB01199)	GGAGAGAATCGCCTGGCTACT	0.587												
C12orf51	283450	broad.mit.edu	37	12	112721040	112721040	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr12:112721040C>T	uc021reb.1	-	7	1366	c.970G>A	c.(970-972)Gaa>Aaa	p.E324K		NM_001109662	NP_001103132			Homo sapiens chromosome 12 open reading frame 51 (C12orf51), mRNA.											breast(1)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(6)|large_intestine(16)|lung(49)|ovary(4)|prostate(1)|urinary_tract(6)	100						TTGGCAGATTCGCCCTCTTTT	0.433												
RB1	5925	broad.mit.edu	37	13	48951144	48951144	+	Nonsense_Mutation	SNP	C	C	T	rs4151534		TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr13:48951144C>T	uc001vcb.3	+	12	1472	c.1306C>T	c.(1306-1308)Cag>Tag	p.Q436*	RB1_uc010act.1_Nonsense_Mutation_p.Q137*	NM_000321	NP_000312	P06400	RB_HUMAN	Homo sapiens retinoblastoma 1 (RB1), mRNA.	436	Domain A.|Pocket; binds T and E1A.		Q -> K (in dbSNP:rs4151534).		androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.0?(15)|p.?(8)|p.G435*(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	AGCTGTGGGACAGGGTTGTGT	0.353		6	"""D, Mis, N, F, S"""		"""retinoblastoma, sarcoma, breast, small cell lung"""	"""retinoblastoma, sarcoma, breast, small cell lung"""			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)		
VRTN	55237	broad.mit.edu	37	14	74825422	74825422	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr14:74825422A>G	uc021rwl.1	+	0	1936	c.1936A>G	c.(1936-1938)Atc>Gtc	p.I646V	VRTN_uc001xpw.4_Missense_Mutation_p.I646V	NM_018228	NP_060698	Q9H8Y1	VRTN_HUMAN	Homo sapiens vertebrae development homolog (pig) (VRTN), mRNA.	646					transposition, DNA-mediated		DNA binding|transposase activity			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(15)|ovary(5)|prostate(2)|skin(1)|urinary_tract(1)	41						GATGGACATGATCGCTACCAC	0.617												
ATP10A	57194	broad.mit.edu	37	15	25925003	25925003	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr15:25925003G>A	uc010ayu.3	-	20	4091	c.3985C>T	c.(3985-3987)Cgc>Tgc	p.R1329C		NM_024490	NP_077816	O60312	AT10A_HUMAN	Homo sapiens ATPase, class V, type 10A (ATP10A), mRNA.	1329					ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		TTCGGGAGGCGTCCCTGAGCA	0.607												
RASGRP1	10125	broad.mit.edu	37	15	38818585	38818585	+	Nonsense_Mutation	SNP	G	G	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr15:38818585G>A	uc001zke.4	-	2	419	c.241C>T	c.(241-243)Cga>Tga	p.R81*	RASGRP1_uc001zkd.4_Nonsense_Mutation_p.R81*	NM_005739	NP_005730	O95267	GRP1_HUMAN	Homo sapiens RAS guanyl releasing protein 1 (calcium and DAG-regulated) (RASGRP1), transcript variant 1, mRNA.	81	N-terminal Ras-GEF.|Ras exchanger motif region; required for transforming activity (By similarity).				cell differentiation|platelet activation|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|lipid binding|protein binding			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)		TGGTTACTTCGACACAGGTTT	0.458												
FAM86A	196483	broad.mit.edu	37	16	5143514	5143514	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr16:5143514G>A	uc002cyo.2	-	2	260	c.211C>T	c.(211-213)Cgg>Tgg	p.R71W	FAM86A_uc002cyp.2_Missense_Mutation_p.R71W	NM_201400	NP_958802	Q96G04	FA86A_HUMAN	Homo sapiens family with sequence similarity 86, member A (FAM86A), transcript variant 1, mRNA.	71								p.A70P(1)		endometrium(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	12						AGAAAGCACCGGGCATATTTG	0.562												
DNAH3	55567	broad.mit.edu	37	16	20976074	20976074	+	Silent	SNP	C	C	T	rs149630157	byFrequency	TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr16:20976074C>T	uc010vbe.2	-	52	9132	c.9132G>A	c.(9130-9132)acG>acA	p.T3044T	DNAH3_uc010vbd.2_Silent_p.T479T	NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	Homo sapiens dynein, axonemal, heavy chain 3 (DNAH3), mRNA.	3044					ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		GATCCCCTAACGTGTGGCTGA	0.498												
KIFC3	3801	broad.mit.edu	37	16	57794781	57794781	+	Missense_Mutation	SNP	T	T	C			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr16:57794781T>C	uc002emq.3	-	15	2286	c.2089A>G	c.(2089-2091)Atc>Gtc	p.I697V	KIFC3_uc010vhw.2_Missense_Mutation_p.I595V|KIFC3_uc002emn.3_Non-coding_Transcript|KIFC3_uc002emm.3_Missense_Mutation_p.I558V|KIFC3_uc010vhx.2_Missense_Mutation_p.I555V|KIFC3_uc010cdf.3_Missense_Mutation_p.I558V|KIFC3_uc002emo.4_Missense_Mutation_p.I558V|KIFC3_uc010vhy.2_Missense_Mutation_p.I639V|KIFC3_uc002emp.3_Missense_Mutation_p.I697V|KIFC3_uc010vhz.2_Missense_Mutation_p.I719V	NM_001130100	NP_001123571	Q9BVG8	KIFC3_HUMAN	Homo sapiens kinesin family member C3 (KIFC3), transcript variant 2, mRNA.	697	Kinesin-motor.				epithelial cell-cell adhesion|microtubule-based movement|visual perception|zonula adherens maintenance	centrosome|cytoplasmic vesicle membrane|kinesin complex|microtubule|zonula adherens	ATP binding|microtubule motor activity			breast(2)|central_nervous_system(3)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(199;0.224)				GACTTGTTGATGTGCTGCGCC	0.682												
CHST6	4166	broad.mit.edu	37	16	75513386	75513386	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr16:75513386C>T	uc021tlj.1	-	0	341	c.341G>A	c.(340-342)cGc>cAc	p.R114H	CHST6_uc002fef.3_Missense_Mutation_p.R114H|CHST6_uc002feg.1_Non-coding_Transcript|CHST6_uc002feh.1_Missense_Mutation_p.R114H	NM_021615	NP_067628	Q9GZX3	CHST6_HUMAN	Homo sapiens carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 6 (CHST6), mRNA.	114					keratan sulfate biosynthetic process|N-acetylglucosamine metabolic process	Golgi membrane|integral to membrane	N-acetylglucosamine 6-O-sulfotransferase activity			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						CAGGTTGCGGCGCCAAGGCAG	0.672												
ADAMTS18	170692	broad.mit.edu	37	16	77355016	77355016	+	Missense_Mutation	SNP	C	C	G			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr16:77355016C>G	uc002ffc.4	-	14	2666	c.2247G>C	c.(2245-2247)aaG>aaC	p.K749N	ADAMTS18_uc010chc.1_Missense_Mutation_p.K337N|ADAMTS18_uc002ffe.1_Missense_Mutation_p.K445N	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	Homo sapiens ADAM metallopeptidase with thrombospondin type 1 motif, 18 (ADAMTS18), mRNA.	749	Cys-rich.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						CTTTATAAAACTTGCAAGTTG	0.383												
KRT16	3868	broad.mit.edu	37	17	39767345	39767345	+	Silent	SNP	G	G	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr17:39767345G>A	uc002hxg.4	-	3	1048	c.909C>T	c.(907-909)gaC>gaT	p.D303D	JUP_uc010wfs.2_Intron	NM_005557	NP_005548	P08779	K1C16_HUMAN	Homo sapiens keratin 16 (KRT16), mRNA.	303	Coil 2.|Rod.				cell proliferation|epidermis development	intermediate filament	protein binding|structural constituent of cytoskeleton			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		Breast(137;0.000307)				AGGTCTCAGCGTCTCTGCGGT	0.607												
CILP2	148113	broad.mit.edu	37	19	19656153	19656153	+	Silent	SNP	G	G	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr19:19656153G>A	uc002nmw.4	+	7	2902	c.2817G>A	c.(2815-2817)ccG>ccA	p.P939P	CILP2_uc002nmv.4_Silent_p.P933P	NM_153221	NP_694953	Q8IUL8	CILP2_HUMAN	Homo sapiens cartilage intermediate layer protein 2 (CILP2), mRNA.	933						proteinaceous extracellular matrix	carbohydrate binding|carboxypeptidase activity			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						GGCCCAACCCGCAGGAGTTCC	0.662												
LMTK3	114783	broad.mit.edu	37	19	49013377	49013377	+	Silent	SNP	C	C	T			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr19:49013377C>T	uc002pjk.3	-	3	351	c.351G>A	c.(349-351)gcG>gcA	p.A117A		NM_001080434	NP_001073903			Homo sapiens lemur tyrosine kinase 3 (LMTK3), mRNA.											breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(9)|prostate(1)	16		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)		AGGTCTCCTCCGCAGGGGGAG	0.622												
ZNF71	58491	broad.mit.edu	37	19	57133286	57133286	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr19:57133286G>A	uc002qnm.4	+	2	869	c.631G>A	c.(631-633)Gag>Aag	p.E211K	ZNF71_uc021vcg.1_Missense_Mutation_p.E211K	NM_021216	NP_067039	Q9NQZ8	ZNF71_HUMAN	Homo sapiens zinc finger protein 71 (ZNF71), mRNA.	211						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			endometrium(3)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	26				GBM - Glioblastoma multiforme(193;0.062)|Lung(386;0.0681)|LUSC - Lung squamous cell carcinoma(496;0.18)		GCACACGGGCGAGAAGCCGTA	0.657												
NBAS	51594	broad.mit.edu	37	2	15493765	15493765	+	Missense_Mutation	SNP	C	C	T	rs140188229		TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr2:15493765C>T	uc002rcc.1	-	33	4027	c.4001G>A	c.(4000-4002)cGt>cAt	p.R1334H	NBAS_uc010exl.1_Missense_Mutation_p.R406H|NBAS_uc002rcd.1_Non-coding_Transcript	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	Homo sapiens neuroblastoma amplified sequence (NBAS), mRNA.	1334										NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						GAGCTCTTGACGAGTGGCCAA	0.453												
CYP26B1	56603	broad.mit.edu	37	2	72360330	72360330	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr2:72360330C>T	uc002sih.1	-	4	968	c.968G>A	c.(967-969)cGg>cAg	p.R323Q	CYP26B1_uc010yra.1_Missense_Mutation_p.R306Q|CYP26B1_uc010yrb.1_Missense_Mutation_p.R248Q	NM_019885	NP_063938	Q9NR63	CP26B_HUMAN	Homo sapiens cytochrome P450, family 26, subfamily B, polypeptide 1 (CYP26B1), mRNA.	323					cell fate determination|embryonic limb morphogenesis|male meiosis|negative regulation of retinoic acid receptor signaling pathway|proximal/distal pattern formation|retinoic acid catabolic process|spermatogenesis|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	electron carrier activity|heme binding|retinoic acid 4-hydroxylase activity|retinoic acid binding			breast(1)|kidney(3)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)	28						CAGCTCATCCCGCAGCTTCTC	0.657												
ST6GAL2	84620	broad.mit.edu	37	2	107460088	107460088	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr2:107460088C>T	uc002tdq.3	-	1	465	c.346G>A	c.(346-348)Gtg>Atg	p.V116M	ST6GAL2_uc002tdr.3_Missense_Mutation_p.V116M|ST6GAL2_uc002tds.3_Missense_Mutation_p.V116M	NM_001142351	NP_115917	Q96JF0	SIAT2_HUMAN	Homo sapiens ST6 beta-galactosamide alpha-2,6-sialyltranferase 2 (ST6GAL2), transcript variant 2, mRNA.	116					growth|multicellular organismal development|oligosaccharide metabolic process|protein glycosylation	Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(30)|ovary(5)|pancreas(6)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	65						TTTCTCCCCACCTGGGATGAA	0.547												
ACTR3	10096	broad.mit.edu	37	2	114691915	114691915	+	Silent	SNP	C	C	T			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr2:114691915C>T	uc002tkx.1	+	5	812	c.492C>T	c.(490-492)acC>acT	p.T164T	ACTR3_uc010yyc.1_Silent_p.T102T|ACTR3_uc010yyd.1_Silent_p.T113T	NM_005721	NP_005712	P61158	ARP3_HUMAN	Homo sapiens ARP3 actin-related protein 3 homolog (yeast) (ACTR3), mRNA.	164					cellular component movement|cilium morphogenesis	Arp2/3 protein complex	actin binding|ATP binding			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(2)	15						GGACGTTGACCGGTACGGTAA	0.418												
PRPF40A	55660	broad.mit.edu	37	2	153515685	153515685	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr2:153515685C>T	uc002tyh.4	-	22	2450	c.2428G>A	c.(2428-2430)Gat>Aat	p.D810N	PRPF40A_uc002tyg.4_Missense_Mutation_p.D266N|PRPF40A_uc010zcd.1_Missense_Mutation_p.D761N	NM_017892	NP_060362	O75400	PR40A_HUMAN	Homo sapiens PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) (PRPF40A), mRNA.	837					mRNA processing|RNA splicing	nuclear matrix|nuclear speck	protein binding			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|prostate(1)|urinary_tract(1)	21						TGGCTATCATCATCATCTGAA	0.343												
STK11IP	114790	broad.mit.edu	37	2	220476376	220476376	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr2:220476376G>A	uc002vml.3	+	17	2231	c.2188G>A	c.(2188-2190)Gct>Act	p.A730T		NM_052902	NP_443134	Q8N1F8	S11IP_HUMAN	Homo sapiens serine/threonine kinase 11 interacting protein (STK11IP), mRNA.	730					protein localization	cytoplasm	protein kinase binding			breast(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	23		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGTTCTCCTCGCTGTGTCTCG	0.627												
SCG2	7857	broad.mit.edu	37	2	224462380	224462380	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr2:224462380C>T	uc021vxk.1	-	0	1621	c.1621G>A	c.(1621-1623)Gaa>Aaa	p.E541K	SCG2_uc002vnm.3_Missense_Mutation_p.E541K	NM_003469	NP_003460	P13521	SCG2_HUMAN	Homo sapiens secretogranin II (SCG2), mRNA.	541					angiogenesis|endothelial cell migration|eosinophil chemotaxis|induction of positive chemotaxis|inflammatory response|MAPKKK cascade|negative regulation of apoptosis|negative regulation of endothelial cell proliferation|positive regulation of endothelial cell proliferation|protein secretion	extracellular space|stored secretory granule	chemoattractant activity|cytokine activity			NS(1)|breast(1)|endometrium(1)|kidney(6)|large_intestine(10)|liver(1)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	44		Renal(207;0.0112)|Lung NSC(271;0.0185)|all_lung(227;0.0271)		Epithelial(121;8.16e-11)|all cancers(144;4.66e-08)|Lung(261;0.00714)|LUSC - Lung squamous cell carcinoma(224;0.008)		TCAATTTGTTCCTCTTCCTGC	0.507												
MLPH	79083	broad.mit.edu	37	2	238449110	238449110	+	Silent	SNP	C	C	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr2:238449110C>A	uc002vwt.3	+	9	1451	c.1224C>A	c.(1222-1224)gcC>gcA	p.A408A	MLPH_uc002vws.3_Silent_p.A265A|MLPH_uc010fyt.1_Silent_p.A380A|MLPH_uc002vwu.3_Silent_p.A380A|MLPH_uc002vwv.3_Silent_p.A340A|MLPH_uc002vww.3_Silent_p.A356A|MLPH_uc002vwx.3_Silent_p.A264A	NM_024101	NP_077006	Q9BV36	MELPH_HUMAN	Homo sapiens melanophilin (MLPH), transcript variant 1, mRNA.	408							metal ion binding	p.E407E(1)		NS(1)|breast(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(11)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)		AGGAGGAAGCCAAGGACGAAA	0.627												
PTPRT	11122	broad.mit.edu	37	20	41101086	41101086	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr20:41101086C>T	uc002xkg.3	-	7	1454	c.1270G>A	c.(1270-1272)Gtg>Atg	p.V424M	PTPRT_uc010ggj.3_Missense_Mutation_p.V424M	NM_007050	NP_008981	O14522	PTPRT_HUMAN	Homo sapiens protein tyrosine phosphatase, receptor type, T (PTPRT), transcript variant 2, mRNA.	424	Fibronectin type-III 2.				homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				TGGTACTGCACGGTGAGGTTG	0.607												
ADM2	79924	broad.mit.edu	37	22	50921222	50921222	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr22:50921222G>A	uc003blj.3	+	1	629	c.337G>A	c.(337-339)Ggc>Agc	p.G113S	ADM2_uc011ary.2_Missense_Mutation_p.G113S	NM_024866	NP_079142	Q7Z4H4	ADM2_HUMAN	Homo sapiens adrenomedullin 2 (ADM2), transcript variant 1, mRNA.	113					positive regulation of angiogenesis	extracellular region	hormone activity			breast(1)|kidney(1)	2		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CTGTGTGCTGGGCACCTGCCA	0.701												
PLA1A	51365	broad.mit.edu	37	3	119316815	119316815	+	Missense_Mutation	SNP	C	C	G			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr3:119316815C>G	uc003ecu.3	+	0	121	c.55C>G	c.(55-57)Ctc>Gtc	p.L19V	PLA1A_uc003ecv.3_Missense_Mutation_p.L19V|PLA1A_uc011bjc.2_5'UTR|PLA1A_uc003ecw.3_Non-coding_Transcript	NM_015900	NP_001193890	Q53H76	PLA1A_HUMAN	Homo sapiens phospholipase A1 member A (PLA1A), transcript variant 1, mRNA.	19					lipid catabolic process|phosphatidylserine metabolic process	extracellular region	phospholipase A1 activity			NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CATTTTGTGGCTCAGCGTTGG	0.507												
MRPL3	11222	broad.mit.edu	37	3	131190114	131190114	+	Silent	SNP	T	T	C			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr3:131190114T>C	uc011blp.2	-	7	915	c.720A>G	c.(718-720)aaA>aaG	p.K240K	MRPL3_uc011blo.2_Silent_p.K108K|MRPL3_uc003eoh.3_Silent_p.K213K	NM_007208	NP_009139	P09001	RM03_HUMAN	Homo sapiens mitochondrial ribosomal protein L3 (MRPL3), nuclear gene encoding mitochondrial protein, mRNA.	213					translation	mitochondrial large ribosomal subunit	RNA binding|structural constituent of ribosome			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	10						CTTGAAAACCTTTACCAATAC	0.408												
RASSF6	166824	broad.mit.edu	37	4	74442417	74442417	+	Silent	SNP	C	C	T	rs147932445	byFrequency	TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr4:74442417C>T	uc003hhd.1	-	8	972	c.849G>A	c.(847-849)ccG>ccA	p.P283P	RASSF6_uc003hhc.1_Silent_p.P251P|RASSF6_uc010iik.1_Silent_p.P217P|RASSF6_uc010iil.1_Silent_p.P239P	NM_201431	NP_803876	Q6ZTQ3	RASF6_HUMAN	Homo sapiens Ras association (RalGDS/AF-6) domain family member 6 (RASSF6), transcript variant 2, mRNA.	283	Ras-associating.				apoptosis|signal transduction		protein binding	p.P283Q(1)|p.I282I(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(4)|pancreas(2)|skin(2)	17	Breast(15;0.00102)		all cancers(17;0.00104)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			TCTGCAGTAGCGGAATGTCTG	0.403												
DSPP	1834	broad.mit.edu	37	4	88534401	88534401	+	Missense_Mutation	SNP	G	G	A	rs61738515	by1000genomes	TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr4:88534401G>A	uc003hqu.3	+	3	1183	c.1063G>A	c.(1063-1065)Gta>Ata	p.V355I		NM_014208	NP_055023	Q9NZW4	DSPP_HUMAN	Homo sapiens dentin sialophosphoprotein (DSPP), mRNA.	355					biomineral tissue development|ossification|skeletal system development	proteinaceous extracellular matrix	calcium ion binding|collagen binding|extracellular matrix structural constituent	p.R354H(1)		breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		AAGCAAACGCGTAGAAAATAG	0.418												
GYPE	2996	broad.mit.edu	37	4	144826671	144826671	+	Translation_Start_Site	SNP	C	C	T			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr4:144826671C>T	uc003ijj.3	-	0					GYPE_uc003ijk.4_5'UTR	NM_198682	NP_941391	P15421	GLPE_HUMAN	Homo sapiens glycophorin E (MNS blood group) (GYPE), transcript variant 2, mRNA.							integral to plasma membrane				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5	all_hematologic(180;0.158)					CCTGAGATCACGAGCTGGCTC	0.398												
TRIM2	23321	broad.mit.edu	37	4	154215581	154215581	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr4:154215581G>A	uc003inh.2	+	4	815	c.730G>A	c.(730-732)Gtg>Atg	p.V244M	TRIM2_uc003ing.2_Missense_Mutation_p.V217M	NM_015271	NP_056086	Q9C040	TRIM2_HUMAN	Homo sapiens tripartite motif containing 2 (TRIM2), transcript variant 1, mRNA.	217						cytoplasm	zinc ion binding			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)	19	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)		GACTTTAAATGTGCGCAAGAG	0.418												
IL7R	3575	broad.mit.edu	37	5	35876389	35876389	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr5:35876389G>A	uc003jjs.3	+	7	1270	c.1181G>A	c.(1180-1182)gGc>gAc	p.G394D	IL7R_uc011cop.2_Non-coding_Transcript	NM_002185	NP_002176	P16871	IL7RA_HUMAN	Homo sapiens interleukin 7 receptor (IL7R), mRNA.	394					immune response|regulation of DNA recombination	extracellular region|integral to membrane	antigen binding|interleukin-7 receptor activity			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(78)|kidney(2)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|skin(5)|stomach(3)	126	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)			AGGGAGAGTGGCAAGAATGGG	0.537			"""Mis, O"""		"""ALL, ETP ALL"""		Severe combined immune deficiency					
UTP15	84135	broad.mit.edu	37	5	72864347	72864347	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr5:72864347G>A	uc003kcw.1	+	3	509	c.286G>A	c.(286-288)Gtg>Atg	p.V96M	UTP15_uc011cso.1_Missense_Mutation_p.V77M|UTP15_uc011csp.1_5'UTR|UTP15_uc010ize.1_Missense_Mutation_p.V96M|ANKRA2_uc003kcu.2_5'Flank	NM_032175	NP_115551	Q8TED0	UTP15_HUMAN	Homo sapiens UTP15, U3 small nucleolar ribonucleoprotein, homolog (S. cerevisiae) (UTP15), mRNA.	96					rRNA processing	cytoplasm|nucleolus				endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	15		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)		TAGATTGCTTGTGGCTGGCAG	0.428												
GRIA1	2890	broad.mit.edu	37	5	153190767	153190767	+	Silent	SNP	G	G	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr5:153190767G>A	uc011dcy.2	+	15	2760	c.2733G>A	c.(2731-2733)ttG>ttA	p.L911L	GRIA1_uc003lva.4_Silent_p.L901L|GRIA1_uc003luy.4_Silent_p.L901L|GRIA1_uc003luz.4_Silent_p.L806L|GRIA1_uc011dcv.2_Non-coding_Transcript|GRIA1_uc011dcw.2_Silent_p.L821L|GRIA1_uc011dcx.2_Silent_p.L832L|GRIA1_uc011dcz.2_Silent_p.L911L	NM_001114183	NP_001107655	P42261	GRIA1_HUMAN	Homo sapiens glutamate receptor, ionotropic, AMPA 1 (GRIA1), transcript variant 2, mRNA.	901					synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			NS(1)|breast(4)|endometrium(7)|kidney(3)|large_intestine(24)|liver(2)|lung(23)|ovary(4)|pancreas(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	81		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	GGATGCCCTTGGGAGCCACGG	0.592												
IRF4	3662	broad.mit.edu	37	6	398928	398928	+	Silent	SNP	G	G	A	rs144395675		TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr6:398928G>A	uc003msz.4	+	5	864	c.738G>A	c.(736-738)gcG>gcA	p.A246A	IRF4_uc010jne.2_Silent_p.A246A|IRF4_uc003mtb.4_Silent_p.A245A|IRF4_uc021ykl.1_Silent_p.A92A|IRF4_uc003mta.4_Non-coding_Transcript|IRF4_uc003mtc.1_Silent_p.A76A	NM_002460	NP_002451	Q15306	IRF4_HUMAN	Homo sapiens interferon regulatory factor 4 (IRF4), transcript variant 1, mRNA.	246					interferon-gamma-mediated signaling pathway|positive regulation of interleukin-10 biosynthetic process|positive regulation of interleukin-13 biosynthetic process|positive regulation of interleukin-2 biosynthetic process|positive regulation of interleukin-4 biosynthetic process|positive regulation of transcription, DNA-dependent|regulation of T-helper cell differentiation|T cell activation|type I interferon-mediated signaling pathway	cytoplasm	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)	5		Breast(5;0.0155)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.03)|BRCA - Breast invasive adenocarcinoma(62;0.0702)		AAGCCTTGGCGTTCTCAGGTG	0.592			T	IGH@	MM							
ECT2L	345930	broad.mit.edu	37	6	139208055	139208055	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr6:139208055G>A	uc003qif.2	+	18	2646	c.2321G>A	c.(2320-2322)tGc>tAc	p.C774Y	ECT2L_uc021zfx.1_Missense_Mutation_p.C774Y|ECT2L_uc011edq.1_Missense_Mutation_p.C628Y	NM_001077706	NP_001181966	Q008S8	ECT2L_HUMAN	Homo sapiens epithelial cell transforming sequence 2 oncogene-like (ECT2L), transcript variant 1, mRNA.	774					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(1)	30						ATCTGGGGATGCCCTGTATGT	0.393			"""N, Splice, Mis"""		ETP ALL							
MAD1L1	8379	broad.mit.edu	37	7	1855850	1855850	+	Silent	SNP	C	C	T			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr7:1855850C>T	uc003slh.1	-	18	2279	c.2013G>A	c.(2011-2013)tcG>tcA	p.S671S	MAD1L1_uc003sle.1_Silent_p.S400S|MAD1L1_uc003slf.1_Silent_p.S671S|MAD1L1_uc003slg.1_Silent_p.S671S|MAD1L1_uc010ksh.1_Silent_p.S671S|MAD1L1_uc003sli.1_Silent_p.S579S|MAD1L1_uc003sld.1_Silent_p.S127S	NM_001013836	NP_003541	Q9Y6D9	MD1L1_HUMAN	Homo sapiens MAD1 mitotic arrest deficient-like 1 (yeast) (MAD1L1), transcript variant 2, mRNA.	671					cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(5)	36		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		TCTTGGAACCCGAGGGGCTGG	0.642												
FKBP9L	360132	broad.mit.edu	37	7	55753014	55753014	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr7:55753014C>T	uc010kzl.3	-	4	536	c.436G>A	c.(436-438)Ggc>Agc	p.G146S	FKBP9L_uc010kzk.3_Missense_Mutation_p.G35S|FKBP9L_uc003tqt.3_Missense_Mutation_p.G35S|FKBP9L_uc011kcs.2_Missense_Mutation_p.G35S|U6_uc022adq.1_5'Flank					Homo sapiens FK506 binding protein 9-like (FKBP9L), transcript variant 4, non-coding RNA.									p.G35R(1)		endometrium(1)|kidney(1)|lung(3)	5						ACGGCACTGCCGGGCACTTCT	0.602												
ELN	2006	broad.mit.edu	37	7	73457353	73457353	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr7:73457353G>A	uc003tzw.3	+	6	456	c.365G>A	c.(364-366)gGa>gAa	p.G122E	ELN_uc003tzm.1_Intron|ELN_uc003tzn.3_Missense_Mutation_p.G122E|ELN_uc003tzy.3_Missense_Mutation_p.G112E|ELN_uc003tzz.3_Missense_Mutation_p.G110E|ELN_uc003tzo.3_Missense_Mutation_p.G122E|ELN_uc003tzp.3_Missense_Mutation_p.G112E|ELN_uc003tzq.3_Intron|ELN_uc003tzr.3_Non-coding_Transcript|ELN_uc003tzs.3_Missense_Mutation_p.G122E|ELN_uc003tzt.3_Missense_Mutation_p.G122E|ELN_uc003tzu.3_Missense_Mutation_p.G122E|ELN_uc003tzv.3_Missense_Mutation_p.G112E|ELN_uc011kfe.2_Non-coding_Transcript|ELN_uc003tzx.3_Missense_Mutation_p.G112E|ELN_uc011kff.2_Missense_Mutation_p.G122E	NM_000501	NP_001075224	P15502	ELN_HUMAN	Homo sapiens elastin (ELN), transcript variant 1, mRNA.	122					blood circulation|cell proliferation|organ morphogenesis|respiratory gaseous exchange	proteinaceous extracellular matrix	extracellular matrix constituent conferring elasticity|protein binding			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)			Rofecoxib(DB00533)	GGTGGCTTAGGAGTGTCTGCA	0.627			T	PAX5	B-ALL		"""Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"""					
GTF2IRD1	9569	broad.mit.edu	37	7	73922465	73922465	+	Missense_Mutation	SNP	C	C	T	rs139144176		TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr7:73922465C>T	uc003uaq.3	+	1	448	c.55C>T	c.(55-57)Cgc>Tgc	p.R19C	GTF2IRD1_uc010lbq.3_Missense_Mutation_p.R19C|GTF2IRD1_uc003uap.3_Missense_Mutation_p.R19C|GTF2IRD1_uc003uar.1_Missense_Mutation_p.R19C	NM_016328	NP_057412	Q9UHL9	GT2D1_HUMAN	Homo sapiens GTF2I repeat domain containing 1 (GTF2IRD1), transcript variant 1, mRNA.	19						nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CGGACCCGACCGCTGGAACTC	0.642												
NPTX2	4885	broad.mit.edu	37	7	98257925	98257925	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr7:98257925G>A	uc003upl.2	+	4	1457	c.1280G>A	c.(1279-1281)cGt>cAt	p.R427H		NM_002523	NP_002514	P47972	NPTX2_HUMAN	Homo sapiens neuronal pentraxin II (NPTX2), mRNA.	427	Pentaxin.			R -> A (in Ref. 1; AAA68980/AAA92296).	synaptic transmission	extracellular region	metal ion binding|sugar binding			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18	all_cancers(62;2.28e-09)|all_epithelial(64;4.86e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0128)|all_lung(186;0.0142)		STAD - Stomach adenocarcinoma(171;0.215)			TGTGAGGAGCGTCTCCTTGAC	0.582												
AZGP1	563	broad.mit.edu	37	7	99564820	99564820	+	Frame_Shift_Del	DEL	T	T	-			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr7:99564820delT	uc003ush.3	-	3	795	c.703delA	c.(703-705)attfs	p.I235fs		NM_001185	NP_001176	P25311	ZA2G_HUMAN	Homo sapiens alpha-2-glycoprotein 1, zinc-binding (AZGP1), mRNA.	235	Ig-like C1-type.				antigen processing and presentation|cell adhesion|immune response|lipid catabolic process|negative regulation of cell proliferation	extracellular region|MHC class I protein complex	fatty acid binding|protein transmembrane transporter activity|ribonuclease activity			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|stomach(1)	16	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					TGCACATCAATTTTCCCTGGG	0.567												
REPIN1	29803	broad.mit.edu	37	7	150068350	150068350	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr7:150068350G>A	uc010lpr.1	+	2	384	c.191G>A	c.(190-192)aGg>aAg	p.R64K	REPIN1_uc003whd.2_5'UTR|REPIN1_uc010lpq.1_Missense_Mutation_p.R7K|REPIN1_uc003whc.2_Missense_Mutation_p.R7K|REPIN1_uc003whe.2_Missense_Mutation_p.R7K	NM_001099695	NP_055189	Q9BWE0	REPI1_HUMAN	Homo sapiens replication initiator 1 (REPIN1), transcript variant 4, mRNA.	7					DNA replication	nuclear origin of replication recognition complex	DNA binding|zinc ion binding			cervix(2)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	14	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.011)			CGTCGTTGCAGGGGCCCCCTG	0.647												
C9orf96	169436	broad.mit.edu	37	9	136260823	136260823	+	Missense_Mutation	SNP	G	G	T			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chr9:136260823G>T	uc004cdk.3	+	8	860	c.799G>T	c.(799-801)Gtg>Ttg	p.V267L	C9orf96_uc004cdl.3_Non-coding_Transcript	NM_153710	NP_714921	Q8NE28	SGK71_HUMAN	Homo sapiens chromosome 9 open reading frame 96 (C9orf96), mRNA.	267	Protein kinase.						ATP binding|protein kinase activity			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|stomach(2)	25				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		GATCCCGGATGTGGAAACCTT	0.552												
BCOR	54880	broad.mit.edu	37	X	39932184	39932185	+	Frame_Shift_Ins	INS	-	-	CAGAC			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chrX:39932184_39932185insCAGAC	uc004den.4	-	3	2706_2707	c.2414_2415insGTCTG	c.(2413-2415)tacfs	p.Y805fs	BCOR_uc004dep.4_Frame_Shift_Ins_p.Y805fs|BCOR_uc004deo.4_Frame_Shift_Ins_p.Y805fs|BCOR_uc004dem.4_Frame_Shift_Ins_p.Y805fs|BCOR_uc004deq.4_Frame_Shift_Ins_p.Y805fs	NM_001123385	NP_001116857	Q6W2J9	BCOR_HUMAN	Homo sapiens BCL6 corepressor (BCOR), transcript variant 5, mRNA.	805					heart development|histone H2A monoubiquitination|negative regulation of bone mineralization|negative regulation of histone H3-K36 methylation|negative regulation of histone H3-K4 methylation|negative regulation of tooth mineralization|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|palate development|specification of axis polarity|transcription, DNA-dependent	nucleus	heat shock protein binding|histone deacetylase binding|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding			breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						GAAGGTCTACGTAGACAAGCTT	0.515			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic					
AKAP4	8852	broad.mit.edu	37	X	49957245	49957245	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0140-01A-01D-1490-08	TCGA-06-0140-10A-01D-1490-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18c94086-d2cc-45cd-9bad-f8968a042d5e	f8eb6b04-153e-4953-8582-c207a5a7cf30	g.chrX:49957245G>A	uc004dow.1	-	4	2243	c.2119C>T	c.(2119-2121)Ctc>Ttc	p.L707F	AKAP4_uc004dou.1_Missense_Mutation_p.L698F|AKAP4_uc004dov.1_Missense_Mutation_p.L324F|AKAP4_uc010njp.1_Missense_Mutation_p.L529F	NM_003886	NP_647450	Q5JQC9	AKAP4_HUMAN	Homo sapiens A kinase (PRKA) anchor protein 4 (AKAP4), transcript variant 1, mRNA.	707					cell projection organization|single fertilization|sperm motility	cAMP-dependent protein kinase complex|cilium|cytoskeleton|microtubule-based flagellum	protein kinase A binding			NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(6)|lung(14)|ovary(1)|skin(4)	41	Ovarian(276;0.236)					ATAAGGCAGAGCTTCATCACA	0.478